Publications COMI

2022
Bigott, Y. ; Gallego, S. ; Montemurro, N. ; Breuil, M.C. ; Pérez, S. ; Michas, A. ; Martin-Laurent, F. ; Schröder, P.
Sci. Total Environ. 831:154674 (2022)
The reuse of water for agricultural practices becomes progressively more important due to increasing demands for a transition to a circular economy. Treated wastewater can be an alternative option of blue water used for the irrigation of crops but its risks need to be evaluated. This study assesses the uptake and metabolization of pharmaceuticals and personal care products (PPCPs) derived from treated wastewater into lettuce as well as the impact on root-associated bacteria under a realistic and worst-case scenario. Lettuce was grown in a controlled greenhouse and irrigated with water or treated wastewater spiked with and without a mixture of fourteen different PPCPs at 10 μg/L or 100 μg/L. After harvesting the plants, the same soil was reused for a consecutive cultivation campaign to test for the accumulation of PPCPs. Twelve out of fourteen spiked PPCPs were detected in lettuce roots, and thirteen in leaves. In roots, highest concentrations were measured for sucralose, sulfamethoxazole and citalopram, while sucralose, acesulfame and carbamazepine were the highest in leaves. Higher PPCP concentrations were found in lettuce roots irrigated with spiked treated wastewater than in those irrigated with spiked water. The absolute bacterial abundance remained stable over both cultivation campaigns and was not affected by any of the treatments (type of irrigation water (water vs. wastewater) nor concentration of PPCPs). However, the irrigation of lettuce with treated wastewater had a significant effect on the microbial α-diversity indices at the end of the second cultivation campaign, and modified the structure and community composition of root-associated bacteria at the end of both campaigns. Five and fourteen bacterial families were shown to be responsible for the observed changes at the end of the first and second cultivation campaign, respectively. Relative abundance of Haliangium and the clade Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium was significantly affected in response to PCPPs exposure. Caulobacter, Cellvibrio, Hydrogenophaga and Rhizobacter were significantly affected in microcosms irrigated with wastewater.
Wissenschaftlicher Artikel
Scientific Article
Hallama, M. ; Pekrun, C. ; Mayer-Gruner, P. ; Uksa, M. ; Abdullaeva, Y. ; Pilz, S. ; Schloter, M. ; Lambers, H. ; Kandeler, E.
Plant Soil, DOI: 10.1007/s11104-022-05340-5 (2022)
Background and aims: The characterisation of plant-available phosphorus (P) pools and the assessment of the microbial community in the rhizosheath of cover crops can improve our understanding of plant–microbe interactions and P availability. Methods: Mustard (Sinapis alba), phacelia (Phacelia tanacetifolia) and buckwheat (Fagopyrum esculentum) were grown as cover crops before soybean (Glycine max) in an on-farm experiment on a soil low in available P in southwest Germany. The cycling of P through the cover crop biomass and the enzyme-availability of organic P (Porg) pools in the cover crop rhizosheath were characterised. The soil microbial community (PLFA), activity (acid and alkaline phosphomonoesterase, as well as phosphodiesterase), and microbial P were assessed. The abundance of 16S-rRNA and phoD, coding for alkaline phosphomonoesterase in bacteria, were quantified using real-time qPCR. Results: Mustard contained the greatest amount of P in its large biomass. In the rhizosheath of all cover crops, the concentration of enzyme-labile Porg was higher than that in the control bulk soil, along with substantial increases of microbial abundance and activity. There were little differences among cover crop species, few changes in the bulk soil and only a limited carryover effect to soybean, except for fungi. Conclusions: Turnover of microbial biomass, especially saprotrophic fungi, increased by rhizodeposition of cover crop roots; this was likely responsible for the observed increases in enzyme-available Porg. Microbial function was correlated linearly with microbial biomass, and the data of enzyme activity and phoD did not suggest a difference of their specific activity between bulk and rhizosheath soil.
Wissenschaftlicher Artikel
Scientific Article
Muster, C. ; Leiva, D. ; Morales, C. ; Grafe, M. ; Schloter, M. ; Carú, M. ; Orlando, J.
Front. Microbiol. 13:843490 (2022)
Phosphorus (P) is one of the most critical macronutrients in forest ecosystems. More than 70 years ago, some Chilean Patagonian temperate forests suffered wildfires and the subsequent afforestation with foreign tree species such as pines. Since soil P turnover is interlinked with the tree cover, this could influence soil P content and bioavailability. Next to soil microorganisms, which are key players in P transformation processes, a vital component of Patagonian temperate forest are lichens, which represent microbial hotspots for bacterial diversity. In the present study, we explored the impact of forest cover on the abundance of phosphate solubilizing bacteria (PSB) from three microenvironments of the forest floor: Peltigera frigida lichen thallus, their underlying substrates, and the forest soil without lichen cover. We expected that the abundance of PSB in the forest soil would be strongly affected by the tree cover composition since the aboveground vegetation influences the edaphic properties; but, as P. frigida has a specific bacterial community, lichens would mitigate this impact. Our study includes five sites representing a gradient in tree cover types, from a mature forest dominated by the native species Nothofagus pumilio, to native second-growth forests with a gradual increase in the presence of Pinus contorta in the last sites. In each site, we measured edaphic parameters, P fractions, and the bacterial potential to solubilize phosphate by quantifying five specific marker genes by qPCR. The results show higher soluble P, labile mineral P, and organic matter in the soils of the sites with a higher abundance of P. contorta, while most of the molecular markers were less abundant in the soils of these sites. Contrarily, the abundance of the molecular markers in lichens and substrates was less affected by the tree cover type. Therefore, the bacterial potential to solubilize phosphate is more affected by the edaphic factors and tree cover type in soils than in substrates and thalli of P. frigida lichens. Altogether, these results indicate that the microenvironments of lichens and their substrates could act as an environmental buffer reducing the influence of forest cover composition on bacteria involved in P turnover.
Wissenschaftlicher Artikel
Scientific Article
Ramm, E. ; Liu, C. ; Mueller, C.W. ; Gschwendtner, S. ; Yue, H. ; Wang, X. ; Bachmann, J. ; Bohnhoff, J.A. ; Ostler, U. ; Schloter, M. ; Rennenberg, H. ; Dannenmann, M.
Soil Biol. Biochem. 172:108757 (2022)
For the prediction of permafrost nitrogen (N) climate feedbacks, a better process-based understanding of the N cycle in permafrost ecosystems is urgently needed. Therefore, we characterized and quantified soil organic matter, gross soil microbial ammonification and nitrification and soil-atmosphere exchange of nitrous oxide (N2O) of boreal permafrost ecosystems on the southern edge of the Eurasian permafrost area in situ. Soil organic carbon (SOC) and total nitrogen (TN) stocks (top 0.5 m) of tree-free lowland peatland (LP) soils exceeded those of gravel-rich upland forest (UF) soils by an order of magnitude. Nuclear magnetic resonance spectroscopy revealed more recalcitrant organic matter at greater depth and more bioavailable organic matter substrates in upper peat horizons. In line with this result, gross ammonification and nitrification generally decreased with increasing sampling depth. Gross rates of mineral N turnover in active layers were comparable to those of temperate ecosystems. Despite substantial gross ammonification, the low nitrification:ammonification ratios and negligible soil N2O emissions depicted however a closed N cycle at UF and LP characterized by N limitation. In strong contrast, the lowland peat soils underneath alder trees (LA), being associated with diazotrophic bacteria in root nodules, showed an accelerated N turnover with very high gross rates of ammonification (3.1 g N m−2 d−1) and nitrification (0.5 g N m−2 d−1), exceeding those of UF and LP soils by an order of magnitude. This was accompanied by substantial N2O emissions comparable to temperate agricultural systems or tropical forests. The increase in gross soil microbial ammonification and nitrification was most pronounced in the rooted soil layer, where N inputs from biological N fixation almost doubled TN concentrations and halved SOC:TN ratios. The frozen ground of LA contained strongly increased ammonium concentrations that might be prone to release upon thaw via subsequent nitrification. This study shows that alder forests that further expand on permafrost-affected peatlands with global change create hot spots of soil mineral N turnover, thereby potentially enhancing permafrost N climate feedbacks via N2O emissions.
Wissenschaftlicher Artikel
Scientific Article
Wang, Z. ; Hulpusch, C. ; Schwierzeck, V. ; Alharbi, S.A. ; Reiger, M. ; Traidl-Hoffmann, C. ; Schloter, M. ; Fösel, B.
Microbio. Res. Ann. 11:e0007222 (2022)
Staphylococcus aureus is a widely distributed, opportunistic pathogen and has been linked to the human skin disease atopic dermatitis (AD). Here, we present 44 complete and 4 draft genome sequences of S. aureus strains isolated from the nose and skin of AD patients and healthy controls from a German study cohort.
Wissenschaftlicher Artikel
Scientific Article
Chen, F. ; Wang, C. ; Yue, L. ; Tang, J. ; Du, H. ; Wu, Y. ; Schröder, P. ; Wang, Z. ; Xing, B.
Environ. Sci.-Nano, DOI: 10.1039/d1en01126j (2022)
The potential toxicity of nano-TiO2 (nTiO2) in the next generation of organisms is important for the environmental toxicological profile of nTiO2. nTiO 2 has been shown to disrupt maternal thyroid hormone metabolism, whereas the effects of prenatal exposure to nTiO2 on the transplacental transfer of thyroid hormones (THs) to the fetus have not been clarified. In this study, pregnant SD rats at gestation days (GDs) 0–17 were daily orally administered with 6.17, 12.34, 61.70, and 308.50 mg kg−1 of nTiO2 (29.6 ± 8.1 nm). Results showed that nTiO2 exposure could inhibit the development of rat placenta and fetus at GD 18. Notably, THs (T3 and T4) were highly accumulated (increased by 19–90%) in the placenta. The retention of placental THs may be related to the down-regulation of TH transporters. nTiO2 could induce oxidative stress on the maternal liver where TH transporters are produced. Genes encoding for TH transporters were mostly down-regulated by 29–65% and a decreased abundance of these transporters in the placenta was observed. An increased concentration of titanium can be observed in the placenta and fetus and subsequently the vascularization of labyrinth tissue was impaired. These findings imply that prenatal exposure to nTiO2 in rats at levels converted from the human daily dietary level might restrict the transplacental transfer of THs and compromise placental function, thus inhibiting fetal growth and development, which could have implications for human health and safety.
Wissenschaftlicher Artikel
Scientific Article
Reichel, R. ; Kamau, C.W. ; Kumar, A. ; Li, Z. ; Radl, V. ; Temperton, V.M. ; Schloter, M. ; Brüggemann, N.
Biol. Fertil. Soils 58, 375–388 (2022)
Plant residues with larger carbon (C) to nitrogen (N) ratios can stimulate microbial growth and thereby protect soil nutrients from leaching. In poorly fertilized soil, excessive immobilization may limit nutrient availability and thus plant growth. Little is known about the impact of a shallow straw incorporation on soil microbial regulation of top-dressing fertilizer nutrients and spring crop establishment. We aimed to evaluate if wheat straw in combination with mineral fertilizer has more positive effects on plant performance than mineral fertilization alone and if this relates to changes of the extractable C:N:P ratio and microbial activity close to the roots. In order to conduct small-scale sampling with minimal disturbance during growth of spring barley (Hordeum vulgare L.), we developed rhizotrons with resealable ports. Rhizotrons were filled with loamy-sandy soil and fertilized with an equivalent of 150 kg N and 80 kg P ha−1. Half of the rhizotrons received the top dressing together with 4500 kg wheat straw-C ha−1. Throughout a 90-day greenhouse experiment, we analyzed soil C:N:P dynamics, and carbon dioxide (CO2) and nitrous oxide (N2O) emission, together with microbial biomass, selected bacterial genes (abundance), and transcripts (activity) in bulk and root-affected soil at multiple times. We focused on nitrifiers and denitrifiers and linked our data to barley growth. Interactions between straw and roots caused shifts towards larger C:P and C:N ratios in root-affected soil. These shifts were associated with increased 16S rRNA transcripts and denitrifier activities. Straw increased microbial biomass by 124% in the topsoil and at the same time increased root biomass by 125% and number of tillers by 80%. We concluded that microbial activation at the root-straw interface may positively feed back on soil nutrient regulation and plant performance. Further research has to evaluate if plant roots actively prime mining of previously immobilized nutrients in the straw detritusphere or if effects of pathogen suppression and growth promotion are dominating.
Wissenschaftlicher Artikel
Scientific Article
Duffner, C. ; Kublik, S. ; Fösel, B. ; Frostegård, ; Schloter, M. ; Bakken, L. ; Schulz, S.
Environ. Microbiol. 24, 1887-1901 (2022)
Stimulating litho-autotrophic denitrification in aquifers with hydrogen is a promising strategy to remove excess NO3 - , but it often entails accumulation of the cytotoxic intermediate NO2 - and the greenhouse gas N2 O. To explore if these high NO2 - and N2 O concentrations are caused by differences in the genomic composition, the regulation of gene transcription or the kinetics of the reductases involved, we isolated hydrogenotrophic denitrifiers from a polluted aquifer, performed whole-genome sequencing and investigated their phenotypes. We therefore assessed the kinetics of NO2 - , NO, N2 O, N2 and O2 as they depleted O2 and transitioned to denitrification with NO3 - as the only electron acceptor and hydrogen as the electron donor. Isolates with a complete denitrification pathway, although differing intermediate accumulation, were closely related to Dechloromonas denitrificans, Ferribacterium limneticum or Hydrogenophaga taeniospiralis. High NO2 - accumulation was associated with the reductases' kinetics. While available, electrons only flowed towards NO3 - in the narG-containing H. taeniospiralis but flowed concurrently to all denitrification intermediates in the napA-containing D. denitrificans and F. limneticum. The denitrification regulator RegAB, present in the napA strains, may further secure low intermediate accumulation. High N2 O accumulation only occurred during the transition to denitrification and is thus likely caused by delayed N2 O reductase expression.
Wissenschaftlicher Artikel
Scientific Article
Ramm, E. ; Liu, C. ; Ambus, P. ; Butterbach-Bahl, K. ; Hu, B. ; Martikainen, P.J. ; Marushchak, M.E. ; Mueller, C.W. ; Rennenberg, H. ; Schloter, M. ; Siljanen, H.M.P. ; Voigt, C. ; Werner, C. ; Biasi, C. ; Dannenmann, M.
Environ. Res. Lett. 17:013004 (2022)
The paradigm that permafrost-affected soils show restricted mineral nitrogen (N) cycling in favor of organic N compounds is based on the observation that net N mineralization rates in these cold climates are negligible. However, we find here that this perception is wrong. By synthesizing published data on N cycling in the plant-soil-microbe system of permafrost ecosystems we show that gross ammonification and nitrification rates in active layers were of similar magnitude and showed a similar dependence on soil organic carbon (C) and total N concentrations as observed in temperate and tropical systems. Moreover, high protein depolymerization rates and only marginal effects of C:N stoichiometry on gross N turnover provided little evidence for N limitation. Instead, the rather short period when soils are not frozen is the single main factor limiting N turnover. High gross rates of mineral N cycling are thus facilitated by released protection of organic matter in active layers with nitrification gaining particular importance in N-rich soils, such as organic soils without vegetation. Our finding that permafrost-affected soils show vigorous N cycling activity is confirmed by the rich functional microbial community which can be found both in active and permafrost layers. The high rates of N cycling and soil N availability are supported by biological N fixation, while atmospheric N deposition in the Arctic still is marginal except for fire-affected areas. In line with high soil mineral N production, recent plant physiological research indicates a higher importance of mineral plant N nutrition than previously thought. Our synthesis shows that mineral N production and turnover rates in active layers of permafrost-affected soils do not generally differ from those observed in temperate or tropical soils. We therefore suggest to adjust the permafrost N cycle paradigm, assigning a generally important role to mineral N cycling. This new paradigm suggests larger permafrost N climate feedbacks than assumed previously.
Review
Review
Peña Sanchez, A. ; Duffner, C. ; Wunderlich, A. ; Mayer, B. ; Schulz, S. ; Schloter, M. ; Einsiedl, F.
Limnol. Oceanogr. 67, 1194-1210 (2022)
In aquatic ecosystems, nitrogen (N) loading is mitigated in redox transition zones principally through the processes of denitrification and anaerobic oxidation of ammonium (anammox). Here, we investigate the N cycling processes in the water column of a seasonal stratified lake influenced by benthic processes in Southern Germany (Fohnsee) during the development of the vertical redox stratification between April and September. Concentration profiles and stable isotope compositions of NO3− and NH4+ together with numerical modeling and quantification of the hydrazine synthase gene (hzsB) and nitrite reductase (nirK and nirS) genes were used to identify the predominant nitrogen-transformation processes at lake Fohnsee throughout the spring and summer periods. Water chemistry data, quantitative polymerase chain reaction analysis and increases of δ15N and δ18O values of nitrate from 7.0‰ to 41.0‰ and 2.0‰ to 28.0‰, respectively, showed that nitrate reduction to nitrite and NO occurs in an upward moving zone of the water column from June to September following the displacement of the oxycline caused by thermal stratification. We also observed an increase in δ15N of ammonium from 15‰ to 28‰ in the anoxic water column. Modeling results suggest that this shift in δ15N-NH4+ is predominantly controlled by mixing between ammonium stemming from the oxic water column with δ15N values of 25‰ and ammonium that is likely formed in the lake sediments by oxidation of organic matter with δ15N values of 11‰. Observed gene abundances (hzsB, nirK, and nirS) in lake water samples collected in June and July indicated the co-occurrence of nitrate reduction and low rates of anammox, while the presence of sulfide in August and September may have inhibited the activity of anammox bacteria near the sulfate-reduction zone at the lake bottom. This study revealed temporal and spatial (e.g., depth dependent) variations in the dominant N-transformation processes in the investigated lake.
Wissenschaftlicher Artikel
Scientific Article
Duffner, C. ; Kublik, S. ; Fösel, B. ; Schloter, M. ; Schulz, S.
Microbio. Res. Ann. 11:e0102021 (2022)
Hydrogenotrophic denitrifiers are important bacteria for nitrate removal in wastewater and aquifers. Here, we report the complete genome sequences of three hydrogenotrophic denitrifiers, namely, Dechloromonas denitrificans strain D110, Ferribacterium limneticum strain F76, and Hydrogenophaga taeniospiralis strain H3, all of which were isolated from a nitrate-polluted aquifer in Bavaria (Germany).
Wissenschaftlicher Artikel
Scientific Article
Wang, Z. ; Jimenez-Fernandez, O. ; Osenbrück, K. ; Schwientek, M. ; Schloter, M. ; Fleckenstein, J.H. ; Lueders, T.
Water Res. 217:118334 (2022)
The input of nitrate and other agricultural pollutants in higher-order streams largely derives from first-order streams. The streambed as the transition zone between groundwater and stream water has a decisive impact on the attenuation of such pollutants. This reactivity is not yet well understood for lower-order agricultural streams, which are often anthropogenically altered and lack the streambed complexity allowing for extensive hyporheic exchange. Reactive hot spots in such streambeds have been hypothesized as a function of hydrology, which controls the local gaining (groundwater exfiltration) or losing (infiltration) of stream water. However, streambed microbial communities and activities associated with such reactive zones remain mostly uncharted. In this study, sediments of a first-order agriculturally impacted stream in southern Germany were investigated. Along with a hydraulic dissection of distinct gaining and losing reaches of the stream, community composition and the abundance of bacterial communities in the streambed were investigated using PacBio long-read sequencing of bacterial 16S rRNA gene amplicons, and qPCR of bacterial 16S rRNA and denitrification genes (nirK and nirS). We show that bidirectional water exchange between groundwater and the stream represents an important control for sediment microbiota, especially for nitrate-reducing populations. Typical heterotrophic denitrifiers were most abundant in a midstream net losing section, while up- and downstream net gaining sections were associated with an enrichment of sulfur-oxidizing potential nitrate reducers affiliated with Sulfuricurvum and Thiobacillus spp. Dispersal-based community assembly was found to dominate such spots of groundwater exfiltration. Our results indicate a coupling of N- and S-cycling processes in the streambed of an agricultural first-order stream, and a prominent control of microbiology by hydrology and hydrochemistry in situ. Such detailed local heterogeneities in exchange fluxes and streambed microbiomes have not been reported to date, but seem relevant for understanding the reactivity of lower-order streams.
Wissenschaftlicher Artikel
Scientific Article
Weber, U. ; Attinger, S. ; Baschek, B. ; Boike, J. ; Borchardt, D. ; Brix, H. ; Brüggemann, N. ; Bussmann, I. ; Dietrich, P. ; Fischer, P. ; Greinert, I. ; Hajnsek, I. ; Kamjunke, N. ; Kerschke, D. ; Kiendler-Scharr, A. ; Körtzinger, A. ; Kottmeier, C. ; Merz, B. ; Merz, R. ; Riese, M. ; Schloter, M. ; Schmid, H. ; Schnitzler, J.-P. ; Sachs, T. ; Schütze, C. ; Tillmann, R. ; Vereecken, H. ; Wieser, A. ; Teutsch, G.
Bull. Amer. Meteorol. Soc. 103, E339–E348 (2022)
MOSES (Modular Observation Solutions for Earth Systems) is a novel observation system that is specifically designed to unravel the impact of distinct, dynamic events on the long-term development of environmental systems. Hydro-meteorological extremes such as the recent European droughts or the floods of 2013 caused severe and lasting environmental damage. Modelling studies suggest that abrupt permafrost thaw events accelerate Arctic greenhouse gas emissions. Short-lived ocean eddies seem to comprise a significant share of the marine carbon uptake or release. Although there is increasing evidence that such dynamic events bear the potential for major environmental impacts, our knowledge on the processes they trigger is still very limited. MOSES aims at capturing such events, from their formation to their end, with high spatial and temporal resolution. As such, the observation system extends and complements existing national and international observation networks, which are mostly designed for long-term monitoring.Several German Helmholtz Association centers have developed this research facility as a mobile and modular “system of systems” to record energy, water, greenhouse gas and nutrient cycles on the land surface, in coastal regions, in the ocean, in polar regions, and in the atmosphere – but especially the interactions between the Earth compartments. During the implementation period (2017-2021), the measuring systems were put into operation and test campaigns were performed to establish event-driven campaign routines. With MOSES’ regular operation starting in 2022, the observation system will then be ready for cross-compartment and cross-discipline research on the environmental impacts of dynamic events.
Wissenschaftlicher Artikel
Scientific Article
Guigue, J. ; Just, C. ; Luo, S. ; Fogt, M. ; Schloter, M. ; Kögel-Knabner, I. ; Hobley, E.
Eur. J. Soil Sci. 73:e13207 (2022)
Soil organic matter (SOM) is composed of fractions with different functionsand reactivity. Among these, particulate organic matter (POM) is the maineduct of new inputs of organic matter in soils and its chemical fate correspondsto the first stages of the SOM decomposition cascade ultimately leading to theassociation of organic and mineral phases. We aimed at investigating themolecular changes of POM during decomposition at a sub-millimetre scale bycombining direct measurements of POM elemental and molecular compositionwith laboratory imaging visible–near-infrared (VNIR) spectroscopy. For this,we set up an incubation experiment to compare the molecular composition ofstraw and composted green manure, materials greatly differing in their C/Nratio, during their decomposition in reconstituted topsoil or subsoil of a Luvisol,and recorded hyperspectral images at high spatial and spectral resolutions ofcomplete soil cores at the start and end of the incubation. Hyperspectral imagingwas successfully combined with machine learning ensembles to produce a pre-cise mapping of POM alkyl/O-N alkyl ratio and C/N, revealing the spatial het-erogeneity in the composition of both straw and green manure. We found thatboth types of organic amendment were more degraded in the reconstituted top-soil than in subsoil after the incubation. We also measured consistent trends inmolecular changes undergone by straw, with the alkyl/O-N alkyl ratio slightlyincreasing from 0.06 to 0.07, and C/N dropping by about 40 units. The greenmanure material was very heterogeneous, with no clear molecular changesdetected as a result of incubation. The imaging VNIR spectroscopy approachpresented here enables high-resolution mapping of the spatial distribution of themolecular characteristics of organic particles in soil cores, and offers opportuni-ties to disentangle the roles of POM chemistry and morphology during the firststeps of the decomposition cascade of organic matter in soils.
Wissenschaftlicher Artikel
Scientific Article
Crosbie, D.B. ; Mahmoudi, M. ; Radl, V. ; Brachmann, A. ; Schloter, M. ; Kemen, E. ; Marín, M.
New Phytol. 234, 242-255 (2022)
Nodule microbiota is dominated by symbiotic nitrogen-fixing rhizobia, however, other non-rhizobial bacteria also colonise this niche. Although many of these bacteria harbour plant-growth-promoting functions, it is not clear whether these less abundant nodule colonisers impact root-nodule symbiosis. We assessed the relationship between the nodule microbiome and nodulation as influenced by the soil microbiome, by using a metabarcoding approach to characterise the communities inside nodules of healthy and starved Lotus species. A machine learning algorithm and network analyses were used to identify nodule bacteria of interest, which were re-inoculated onto plants in controlled conditions to observe their potential functionality. The nodule microbiome of all tested species differed according to inoculum, but only that of Lotus burttii varied with plant health. Amplicon sequence variants representative of Pseudomonas species were the most indicative non-rhizobial signatures inside healthy L. burttii nodules and negatively correlated with Rhizobium sequences. A representative Pseudomonas isolate co-colonised nodules infected with a beneficial Mesorhizobium, but not with an ineffective Rhizobium isolate and another even reduced the number of ineffective nodules induced on Lotus japonicus. Our results show that nodule endophytes influence the overall outcome of the root-nodule symbiosis, albeit in a plant host-specific manner.
Wissenschaftlicher Artikel
Scientific Article
Karlina, R. ; Flexeder, C. ; Musiol, S. ; Bhattacharyya, M. ; Schneider, E. ; Altun, I. ; Gschwendtner, S. ; Neumann, A.U. ; Nano, J. ; Schloter, M. ; Peters, A. ; Schulz, H. ; Schulz, H. ; Schmidt-Weber, C.B. ; Standl, M. ; Traidl-Hoffmann, C. ; Alessandrini, F. ; Ussar, S.
Allergy, DOI: 10.1111/all.15226 (2022)
BACKGROUND: The rates of obesity, its associated diseases, and allergies are raising at alarming rates in most countries. House dust mites (HDM) are highly allergenic and exposure often associates with an urban sedentary indoor lifestyle, also resulting in obesity. The aim of this study was to investigate the epidemiological association and physiological impact of lung inflammation on obesity and glucose homeostasis. METHODS: Epidemiological data from 2207 adults of the population-based KORA FF4 cohort were used to test associations between asthma and rhinitis with metrics of body weight and insulin sensitivity. To obtain functional insights, C57BL/6J mice were intranasally sensitized and challenged with HDM and simultaneously fed with either low-fat or high-fat diet for 12 weeks followed by a detailed metabolic and biochemical phenotyping of the lung, liver, and adipose tissues. RESULTS: We found a direct association of asthma with insulin resistance but not body weight in humans. In mice, co-development of obesity and HDM-induced lung inflammation attenuated inflammation in lung and perigonadal fat, with little impact on body weight, but small shifts in the composition of gut microbiota. Exposure to HDM improved glucose tolerance, reduced hepatosteatosis, and increased energy expenditure and basal metabolic rate. These effects associate with increased activity of thermogenic adipose tissues independent of uncoupling protein 1. CONCLUSIONS: Asthma associates with insulin resistance in humans, but HDM challenge results in opposing effects on glucose homeostasis in mice due to increased energy expenditure, reduced adipose inflammation, and hepatosteatosis.
Wissenschaftlicher Artikel
Scientific Article
Khalaf, D.M. ; Cruzeiro, C. ; Schröder, P.
Sci. Total Environ. 809:151164 (2022)
Tramadol (TRD) is widely detected in aquatic ecosystems as a result of massive abuse and insufficient removal from wastewater facilities. As a result, TRD can contaminate groundwater sources and/or agricultural soils. While TRD toxicity has been reported from aquatic biota, data about TRD detection in plants are scarce. Moreover, information regarding plant capability for TRD removal is lacking. To understand the fate of this opioid, we have investigated the uptake, translocation and removal capacity of TRD by plants, addressing short-term and long-term uptake. The uptake rates of TRD, in excised barley and cattail roots, were 5.18 and 5.79 μg g−1 root fresh weight day−1, respectively. However, TRD uptake was strongly inhibited after co-exposing these roots either with the drug venlafaxine (similar molecular structure as TRD) or with quinidine (an inhibitor of cellular organic cation transporters). When barley seedlings were exposed to TRD in a hydroponic experiment a removal efficiency up to 90% (within 15 days) was obtained, with bioconcentration and translocation factors close to 9 and 1, respectively. The combination of results from both plants and the inhibition observed after treatment with quinidine revealed that organic cation transporters may be involved in the uptake of TRD by plants.
Wissenschaftlicher Artikel
Scientific Article
Wahman, R. ; Cruzeiro, C. ; Graßmann, J. ; Schröder, P. ; Letzel, T.
Chemosphere 287:132078 (2022)
Metabolomics is an emerging approach that investigates the changes in the metabolome profile. In the present study, Lemna minor —considered as an experimental aquatic plant model— was incubated with 10 and 100 μM diclofenac (DCF) for 96 h, respectively. Knowing that DCF is internationally often problematic in wastewater effluents and that it might affect particularly the metabolic profiles in aquatic plants, mainly the oxidoreductase, dehydrogenase, peroxidase, and glutathione reductase activities, here it was hypothesized (H) that in the common duckweed, DCF might increase the phenolic and flavonoids pathways, as an antioxidant response to this stress (H1). Also, it was expected DCF to alternate the physiological characteristics, especially the molecular interaction and biochemical properties, of Lemna (H2). Metabolic changes were investigated with target and untargeted screening analysis using RPLC-HILIC-ESI-TOF-MS. Twelve amino acids were identified in all treatments, together with three organic acids (p-coumaric, cinnamic, and sinapic acids). In untargeted screening, the important metabolites to discriminate between different treatments were assigned to Lemna such as organic acids, lignin, sugars, amino acids, dipeptides, flavonoids, biflavonoids, fatty acids, among others. In resume, Lemna responded to both DCF concentrations, showing different stress patterns. A similar metabolic response had already been identified in other studies in exposing Lemna to other anthropogenic stressors (like pesticides).
Wissenschaftlicher Artikel
Scientific Article
Schröder, P. ; Mench, M. ; Povilaitis, V. ; Rineau, F. ; Rutkowska, B. ; Schloter, M. ; Szulc, W. ; Žydelis, R. ; Loit, E.
Sci. Total Environ. 803:149844 (2022)
In the EU and world-wide, agriculture is in transition. Whilst we just converted conventional farming imprinted by the post-war food demand and heavy agrochemical usage into integrated and sustainable farming with optimized production, we now have to focus on even smarter agricultural management. Enhanced nutrient efficiency and resistance to pests/pathogens combined with a greener footprint will be crucial for future sustainable farming and its wider environment. Future land use must embrace efficient production and utilization of biomass for improved economic, environmental, and social outcomes, as subsumed under the EU Green Deal, including also sites that have so far been considered as marginal and excluded from production. Another frontier is to supply high-quality food and feed to increase the nutrient density of staple crops. In diets of over two-thirds of the world's population, more than one micronutrient (Fe, Zn, I or Se) is lacking. To improve nutritious values of crops, it will be necessary to combine integrated, systems-based approaches of land management with sustainable redevelopment of agriculture, including central ecosystem services, on so far neglected sites: neglected grassland, set aside land, and marginal lands, paying attention to their connectivity with natural areas. Here we need new integrative approaches which allow the application of different instruments to provide us not only with biomass of sufficient quality and quantity in a site specific manner, but also to improve soil ecological services, e.g. soil C sequestration, water quality, habitat and soil resistance to erosion, while keeping fertilization as low as possible. Such instruments may include the application of different forms of high carbon amendments, the application of macro- and microelements to improve crop performance and quality as well as a targeted manipulation of the soil microbiome. Under certain caveats, the potential of such sites can be unlocked by innovative production systems, ready for the sustainable production of crops enriched in micronutrients and providing services within a circular economy.
Review
Review
2021
Wahman, R. ; Moser, S. ; Bieber, S. ; Cruzeiro, C. ; Schröder, P. ; Gilg, A. ; Lesske, F. ; Letzel, T.
Metabolites 11:832 (2021)
Metabolomics approaches provide a vast array of analytical datasets, which require a comprehensive analytical, statistical, and biochemical workflow to reveal changes in metabolic profiles. The biological interpretation of mass spectrometric metabolomics results is still obstructed by the reliable identification of the metabolites as well as annotation and/or classification. In this work, the whole Lemna minor (common duckweed) was extracted using various solvents and analyzed utilizing polarity-extended liquid chromatography (reversed-phase liquid chromatography (RPLC)-hydrophilic interaction liquid chromatography (HILIC)) connected to two time-of-flight (TOF) mass spectrometer types, individually. This study (introduces and) discusses three relevant topics for the untargeted workflow: (1) A comparison study of metabolome samples was performed with an untargeted data handling workflow in two different labs with two different mass spectrometers using the same plant material type. (2) A statistical procedure was observed prioritizing significant detected features (dependent and independent of the mass spectrometer using the predictive methodology Orthogonal Partial Least Squares-Discriminant Analysis (OPLS-DA). (3) Relevant features were transferred to a prioritization tool (the FOR-IDENT platform (FI)) and were compared with the implemented compound database PLANT-IDENT (PI). This compound database is filled with relevant compounds of the Lemnaceae, Poaceae, Brassicaceae, and Nymphaceae families according to analytical criteria such as retention time (polarity and LogD (pH 7)) and accurate mass (empirical formula). Thus, an untargeted analysis was performed using the new tool as a prioritization and identification source for a hidden-target screening strategy. Consequently, forty-two compounds (amino acids, vitamins, flavonoids) could be recognized and subsequently validated in Lemna metabolic profile using reference standards. The class of flavonoids includes free aglycons and their glycosides. Further, according to our knowledge, the validated flavonoids robinetin and norwogonin were for the first time identified in the Lemna minor extracts.
Wissenschaftlicher Artikel
Scientific Article
Siani, R. ; Stabl, G. ; Gutjahr, C. ; Schloter, M. ; Radl, V.
Microb. Genomics 7:000666 (2021)
Beta-proteobacteria belonging to the genus Acidovorax have been described from various environments. Many strains can interact with a range of hosts, including humans and plants, forming neutral, beneficial or detrimental associations. In the frame of this study, we investigated the genomic properties of 52 bacterial strains of the genus Acidovorax, isolated from healthy roots of Lotus japonicus, with the intent of identifying traits important for effective plant-growth promotion. Based on single-strain inoculation bioassays with L. japonicus, performed in a gnotobiotic system, we distinguished seven robust plant-growth promoting strains from strains with no significant effects on plant-growth. We showed that the genomes of the two groups differed prominently in protein families linked to sensing and transport of organic acids, production of phytohormones, as well as resistance and production of compounds with antimicrobial properties. In a second step, we compared the genomes of the tested isolates with those of plant pathogens and free-living strains of the genus Acidovorax sourced from public repositories. Our pan-genomics comparison revealed features correlated with commensal and pathogenic lifestyle. We showed that commensals and pathogens differ mostly in their ability to use plant-derived lipids and in the type of secretion-systems being present. Most free-living Acidovorax strains did not harbour any secretion-systems. Overall, our data indicate that Acidovorax strains undergo extensive adaptations to their particular lifestyle by horizontal uptake of novel genetic information and loss of unnecessary genes.
Wissenschaftlicher Artikel
Scientific Article
Vitow, N. ; Zicker, T. ; Chiba, A. ; Zacher, A. ; Eichler-Loebermann, B. ; Schulz, S. ; Schloter, M. ; Baum, C. ; Leinweber, P.
Agronomy 11:2437 (2021)
Legume catch crops can enhance soil fertility and promote the N and P supply of the subsequent main crop, especially with low mineral fertilizer use. However, the specific impact of catch crops on arbuscular mycorrhiza formation of the following main crop is unknown. Therefore, the impact of serradella (Ornithopus sativus) vs. bare fallow was tested on mycorrhiza formation, potential soil enzyme activities and plant-available P under subsequently grown barley (Hordeum vulgare) and different fertilization treatments (P-unfertilized-P0; triple superphosphate-TSP; compost-COM; combined-COM + TSP) in a long-term field experiment in northeastern Germany. Catch cropping significantly increased mycorrhiza formation of barley up to 14% compared to bare fallow. The impact of serradella on mycorrhiza formation exceeded that of the fertilization treatment. Serradella led to increased phosphodiesterase activities and decreased ss-glucosidase activities in soil. Plant availability of P was not significantly affected by serradella. These findings provide initial evidence that even serradella as a non-host crop of mycorrhizal fungi can promote the mycorrhiza formation of the subsequent crop and P mobilization in soil. We conclude that the prolonged vegetation cover of arable soils by the use of catch crops can promote P mobilization and transfer from P pools to the following main crops.
Wissenschaftlicher Artikel
Scientific Article
Hwang, Y. ; Schulze-Makuch, D. ; Arens, F.L. ; Saenz Medina, J.S. ; Adam, P.S. ; Sager, C. ; Bornemann, T.L.V. ; Zhao, W. ; Zhang, Y. ; Airo, A. ; Schloter, M. ; Probst, A.J.
Microbiome 9:234 (2021)
BACKGROUND: The hyperarid core of the Atacama Desert is an extremely harsh environment thought to be colonized by only a few heterotrophic bacterial species. Current concepts for understanding this extreme ecosystem are mainly based on the diversity of these few species, yet a substantial area of the Atacama Desert hyperarid topsoil is covered by expansive boulder accumulations, whose underlying microbiomes have not been investigated so far. With the hypothesis that these sheltered soils harbor uniquely adapted microbiomes, we compared metagenomes and geochemistry between soils below and beside boulders across three distantly located boulder accumulations in the Atacama Desert hyperarid core. RESULTS: Genome-resolved metagenomics of eleven samples revealed substantially different microbial communities in soils below and beside boulders, despite the presence of shared species. Archaea were found in significantly higher relative abundance below the boulders across all samples within distances of up to 205 km. These key taxa belong to a novel genus of ammonia-oxidizing Thaumarchaeota, Candidatus Nitrosodeserticola. We resolved eight mid-to-high quality genomes of this genus and used comparative genomics to analyze its pangenome and site-specific adaptations. Ca. Nitrosodeserticola genomes contain genes for ammonia oxidation, the 3-hydroxypropionate/4-hydroxybutyrate carbon fixation pathway, and acetate utilization indicating a chemolithoautotrophic and mixotrophic lifestyle. They also possess the capacity for tolerating extreme environmental conditions as highlighted by the presence of genes against oxidative stress and DNA damage. Site-specific adaptations of the genomes included the presence of additional genes for heavy metal transporters, multiple types of ATP synthases, and divergent genes for aquaporins. CONCLUSION: We provide the first genomic characterization of hyperarid soil microbiomes below the boulders in the Atacama Desert, and report abundant and highly adapted Thaumarchaeaota with ammonia oxidation and carbon fixation potential. Ca. Nitrosodeserticola genomes provide the first metabolic and physiological insight into a thaumarchaeal lineage found in globally distributed terrestrial habitats characterized by various environmental stresses. We consequently expand not only the known genetic repertoire of Thaumarchaeota but also the diversity and microbiome functioning in hyperarid ecosystems. Video Abstract.
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Scientific Article
Malique, F. ; Wangari, E. ; Andrade Linares, D.R. ; Schloter, M. ; Wolf, B. ; Dannenmann, M. ; Schulz, S. ; Butterbach-Bahl, K.
J. Plant Nutr. Soil Sci. 184, 696-708 (2021)
Background: Reductions of ammonia volatilization resulting from slurry applications to intensively managed grassland may be achieved via slurry acidification. However, it remains uncertain if this may result in pollution swapping, that is, due to reduced ammonia volatilization and increased soil N availability, emission of nitrous oxide from soils may increase. Aims: In this study, we compared control (no fertilizer) and slurry fertilized grassland treatments [not acidified (S) and acidified (AS)] to assess whether slurry acidification results in changes of soil N availability, denitrification potential and activity as well as soil fluxes of nitrous oxide. Methods: The study was carried out in a montane grassland system in southern Germany, and parameters were followed over a 43-days period with continuous measurements of soil GHG fluxes and biweekly measurements of microbial and soil parameters preceding and following two fertilizing events. Results: Over the entire observation period cumulative N2O emissions were significantly elevated for treatments receiving slurry applications, with differences between acidified and non-acidified slurry treatments being overall insignificant. Transcripts of the nirK type nitrite reductase showed significantly higher numbers in soils of the AS treatment. While soil potential denitrification rates (PDR) did not differ between treatments, there was a strong tendency of increased PDRs for the AS treatment. Conclusions: Against expectation, we did not find that application of AS affects PDR or soil N2O emissions significantly, though in tendency higher rates of soil N2O emissions as well as higher potential denitrification rates were found in treatments receiving acidified slurry as compared to the slurry only treatment. Our results indicate that longer observation periods and given the significant spatial variability, higher numbers of replicates are needed, to finally assess if slurry application indeed results in increased soil denitrification activity, soil N2O production and soil-atmosphere N2O emissions.
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Scientific Article
Ohigashi, T. ; Schloter, M. ; Schulz, S. ; Munthali, K. ; Uchida, Y.
Soil Syst. 5:62 (2021)
Sub‐Saharan Africa is one of the most severely affected regions regarding soil degradation, a global issue with the loss of nutrients caused by inappropriate management, leading to low agricultural productivity. Here we asked the question of how soil prokaryotic communities are affected by shifts in land use management and subsequent losses in soil organic carbon. We sampled soils from three sites in Zambia which have neighboring natural and managed sites. After the measurement of soil properties, soil DNA was sequenced, targeting the 16S rRNA gene. As expected, total carbon in soil was decreased in the managed sites, with significant reductions of bacterial biomass. However, the diversity indices in the managed soils were higher than in natural soils. Particularly, the relative abundance of nitrifiers was increased in the managed soils, most likely as a result of fertilization. However also other bacteria, e.g., those which formed tight interactions with the cultivated crops including the genera Balneimonas, and Bacillus, were increased in the managed soils. In contrast bacteria belonging to the family Chloroflexi, which were high in abundance in the natural soil were outcompeted by other prokaryotes in the managed soils most likely as a result of changes in the amount of soil organic carbon. Overall, our results suggest that we need to discuss the trends of prokaryotic diversity separately from those for prokaryotic abundance. Even when bacterial abundances were decreased in the managed soils, nitrifiers’ relative abundance and diversity increased in our experiment, suggesting the possible alteration of the nitrogen cycle in managed soils in sub‐Saharan Africa.
Wissenschaftlicher Artikel
Scientific Article
Broadbent, A.A.D. ; Bahn, M. ; Pritchard, W.J. ; Newbold, L.K. ; Goodall, T. ; Guinta, A. ; Snell, H.S.K. ; Cordero, I. ; Michas, A. ; Grant, H.K. ; Soto, D.X. ; Kaufmann, R. ; Schloter, M. ; Griffiths, R.I. ; Bardgett, R.D.
Ecol. Lett., DOI: 10.1111/ele.13903 (2021)
Climate change is disproportionately impacting mountain ecosystems, leading to large reductions in winter snow cover, earlier spring snowmelt and widespread shrub expansion into alpine grasslands. Yet, the combined effects of shrub expansion and changing snow conditions on abiotic and biotic soil properties remains poorly understood. We used complementary field experiments to show that reduced snow cover and earlier snowmelt have effects on soil microbial communities and functioning that persist into summer. However, ericaceous shrub expansion modulates a number of these impacts and has stronger belowground effects than changing snow conditions. Ericaceous shrub expansion did not alter snow depth or snowmelt timing but did increase the abundance of ericoid mycorrhizal fungi and oligotrophic bacteria, which was linked to decreased soil respiration and nitrogen availability. Our findings suggest that changing winter snow conditions have cross-seasonal impacts on soil properties, but shifts in vegetation can modulate belowground effects of future alpine climate change.
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Scientific Article
Pinart, M. ; Nimptsch, K. ; Schlicht, K. ; Gueimonde, M. ; Brigidi, P. ; Turroni, S. ; Ahrens, W. ; Hebestreit, A. ; Wolters, M. ; Dötsch, A. ; Nöthlings, U. ; Oluwagbemigun, K. ; Cuadrat, R.R.C. ; Schulze, M.B. ; Standl, M. ; Schloter, M. ; de Angelis, M. ; Iozzo, P. ; Guzzardi, M.A. ; Vlaemynck, G. ; Penders, J. ; Jonkers, D.M.A.E. ; Stemmer, M. ; Chiesa, G. ; Cavalieri, D. ; De Filippo, C. ; Ercolini, D. ; De Filippis, F. ; Ribet, D. ; Achamrah, N. ; Tavolacci, M.P. ; Déchelotte, P. ; Bouwman, J. ; Laudes, M.
Nutrients 13:3292 (2021)
In any research field, data access and data integration are major challenges that even large, well-established consortia face. Although data sharing initiatives are increasing, joint data analyses on nutrition and microbiomics in health and disease are still scarce. We aimed to identify observational studies with data on nutrition and gut microbiome composition from the Intestinal Microbiomics (INTIMIC) Knowledge Platform following the findable, accessible, interoperable, and reusable (FAIR) principles. An adapted template from the European Nutritional Phenotype Assessment and Data Sharing Initiative (ENPADASI) consortium was used to collect microbiome-specific information and other related factors. In total, 23 studies (17 longitudinal and 6 cross-sectional) were identified from Italy (7), Germany (6), Netherlands (3), Spain (2), Belgium (1), and France (1) or multiple countries (3). Of these, 21 studies collected information on both dietary intake (24 h dietary recall, food frequency questionnaire (FFQ), or Food Records) and gut microbiome. All studies collected stool samples. The most often used sequencing platform was Illumina MiSeq, and the preferred hypervariable regions of the 16S rRNA gene were V3–V4 or V4. The combination of datasets will allow for sufficiently powered investigations to increase the knowledge and understanding of the relationship between food and gut microbiome in health and disease.
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Scientific Article
Pfeiffer, S. ; Herzmann, C. ; Gaede, K.I. ; Kovacevic, D. ; Krauss-Etschmann, S. ; Schloter, M.
Thorax 8, DOI: 10.1136/thoraxjnl-2020-216153 (2021)
To examine the role of smoking on the bacterial community composition of the upper and the lower respiratory tract, a monocentric, controlled prospective study was performed, including healthy smokers, ex-smokers and never-smokers. Smokers were further grouped according to their smoking history. Bacterial diversity was analysed using a molecular barcoding approach based on directly extracted DNA. Our study shows for the first time distinct bacterial response patterns in the upper and lower respiratory tract to cigarette smoking leading to a higher abundance of opportunistic pathogens. The clinical significance of these dysbioses for health needs to be further explored.
Wissenschaftlicher Artikel
Scientific Article
Chen, F. ; Wang, C. ; Yue, L. ; Zhu, L. ; Tang, J. ; Yu, X. ; Cao, X. ; Schröder, P. ; Wang, Z.
ACS Nano 15, 13166–13177 (2021)
Yttrium oxide nanoparticles (nY2O3), one of the broadly used rare earth nanoparticles, can interact with plants and possibly cause plant health and environmental impacts, but the plant defense response particularly at the nanoparticle-cell interface is largely unknown. To elucidate this, Bright Yellow 2 (BY-2) tobacco (Nicotiana tabacum L.) suspension-cultured cells were exposed to 50 mg L-1 nY2O3 (30 nm) for 12 h. Although 42.2% of the nY2O3 remained outside of protoplasts, nY2O3 could still traverse the cell wall and was partially deposited inside the vacuole. In addition to growth inhibition, morphological and compositional changes in cell walls occurred. Together with a locally thickened (7-13-fold) cell wall, increased content (up to 58%) of pectin and reduction in (up to 29%) hemicellulose were observed. Transcriptome analysis revealed that genes involved in cell wall metabolism and remodeling were highly regulated in response to nY2O3 stress. Expression of genes for pectin synthesis and degradation was up- and down-regulated by 31-78% and 13-42%, respectively, and genes for xyloglucan and pectin modifications were up- and down-regulated by 82% and 81-92%, respectively. Interestingly, vesicle trafficking seemed to be activated, enabling the repair and defense against nY2O3 disturbance. Our findings indicate that, although nY2O3 generated toxicity on BY-2 cells, it is very likely that during the recovery process cell wall remodeling was initiated to gain resistance to nY2O3 stress, demonstrating the plant's cellular regulatory machinery regarding repair and adaptation to nanoparticles like nY2O3.
Wissenschaftlicher Artikel
Scientific Article
Michas, A. ; Pastore, G. ; Chiba, A. ; Grafe, M. ; Clausing, S. ; Polle, A. ; Schloter, M. ; Spohn, M. ; Schulz, S.
Front. For. Glob. Change 4:696983 (2021)
Phosphorus (P) solubilization is an important process for P acquisition by plants and soil microbes in most temperate forests. The abundance of inorganic P solubilizing bacteria (PSB) is affected by the P concentration in the soil and the carbon input by plants. We used a girdling approach to investigate the interplay of root-derived C and initial P content on the community composition of gcd-harboring bacteria as an example of PSB, which produce gluconic acid. We hypothesized that gcd-harboring PSB communities from P-poor sites are more vulnerable to girdling, because of their lower diversity, and that a shift in gcd-harboring PSB communities by girdling is caused by a response of few, mostly oligotrophic, taxa. We used a high-throughput metabarcoding approach targeting the gcd gene, which codes for the quinoprotein glucose dehydrogenase, an enzyme involved in the solubilization of inorganic P. We compared the diversity of gcd-harboring PSB in the mineral topsoil from two temperate beech forests with contrasting P stocks, where girdling was applied and compared our data to the respective control plots with untreated young beech trees. At both sites, gcd-harboring PSB were dominated by Proteobacteria and Acidobacteria, however, with differences in relative abundance pattern on the higher phylogenetic levels. The P-poor site was characterized by a high relative abundance of Kaistia, whereas at the P-rich site, Dongia dominated the gcd-harboring bacterial communities. Girdling induced an increase in the relative abundance of Kaistia at the P-poor site, whereas other bacterial groups of the family Rhizobiaceae were reduced. At the P-rich site, major microbial responders differed between treatments and mostly Bradyrhizobium and Burkholderia were positively affected by girdling in contrast to uncultured Acidobacteria, where reduced relative abundance was found. Overall, these effects were consistent at different time points analyzed after the introduction of girdling. Our data demonstrate that plant-derived carbon influences community structure of gcd-harboring bacteria in temperate beech forest soils.
Wissenschaftlicher Artikel
Scientific Article
Benning, S. ; Brugnone, N. ; Siani, R. ; Kublik, S. ; Schloter, M. ; Radl, V.
Microbio. Res. Ann. 10:e0015921 (2021)
Members of the genus Rhodococcus are usually able to catalyze a number of processes, which are of great interest for ecosystem performance as well as biotechnology. Here, we report the complete genome sequences of two Rhodococcus strains that were isolated from rhizosphere soil from an apple orchard in northern Germany.
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Scientific Article
Amar, Y. ; Lagkouvardos, I. ; Silva, R.L. ; Ishola, O.A. ; Fösel, B. ; Kublik, S. ; Schöler, A. ; Niedermeier, S. ; Bleuel, R. ; Zink, A. ; Neuhaus, K. ; Schloter, M. ; Biedermann, T. ; Köberle, M.
Microbiome 9:123 (2021)
Background: The identification of microbiota based on next-generation sequencing (NGS) of extracted DNA has drastically improved our understanding of the role of microbial communities in health and disease. However, DNA-based microbiome analysis cannot per se differentiate between living and dead microorganisms. In environments such as the skin, host defense mechanisms including antimicrobial peptides and low cutaneous pH result in a high microbial turnover, likely resulting in high numbers of dead cells present and releasing substantial amounts of microbial DNA. NGS analyses may thus lead to inaccurate estimations of microbiome structures and consequently functional capacities. Results: We investigated in this study the feasibility of a Benzonase-based approach (BDA) to pre-digest unprotected DNA, i.e., of dead microbial cells, as a method to overcome these limitations, thus offering a more accurate assessment of the living microbiome. A skin mock community as well as skin microbiome samples were analyzed using 16S rRNA gene sequencing and metagenomics sequencing after DNA extraction with and without a Benzonase digest to assess bacterial diversity patterns. The BDA method resulted in less reads from dead bacteria both in the skin mock community and skin swabs spiked with either heat-inactivated bacteria or bacterial-free DNA. This approach also efficiently depleted host DNA reads in samples with high human-to-microbial DNA ratios, with no obvious impact on the microbiome profile. We further observed that low biomass samples generate an α-diversity bias when the bacterial load is lower than 10 CFU and that Benzonase digest is not sufficient to overcome this bias. Conclusions: The BDA approach enables both a better assessment of the living microbiota and depletion of host DNA reads. [MediaObject not available: see fulltext.] Graphical abstract: [Figure not available: see fulltext.]
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Scientific Article
Hwang, Y. ; Rahlff, J. ; Schulze-Makuch, D. ; Schloter, M. ; Probst, A.J.
mSystems 6:e00385-21 (2021)
Viruses play an essential role in shaping microbial community structures and serve as reservoirs for genetic diversity in many ecosystems. In hyperarid desert environments, where life itself becomes scarce and loses diversity, the interactions between viruses and host populations have remained elusive. Here, we resolved host-virus interactions in the soil metagenomes of the Atacama Desert hyperarid core, one of the harshest terrestrial environments on Earth. We show evidence of diverse viruses infecting a wide range of hosts found in sites up to 205 km apart. Viral genomes carried putative extremotolerance features (i.e., spore formation proteins) and auxiliary metabolic genes, indicating that viruses could mediate the spread of microbial resilience against environmental stress across the desert. We propose a mutualistic model of host-virus interactions in the hyperarid core where viruses seek protection in microbial cells as lysogens or pseudolysogens, while viral extremotolerance genes aid survival of their hosts. Our results suggest that the host-virus interactions in the Atacama Desert soils are dynamic and complex, shaping uniquely adapted microbiomes in this highly selective and hostile environment.IMPORTANCE Deserts are one of the largest and rapidly expanding terrestrial ecosystems characterized by low biodiversity and biomass. The hyperarid core of the Atacama Desert, previously thought to be devoid of life, is one of the harshest environments, supporting only scant biomass of highly adapted microbes. While there is growing evidence that viruses play essential roles in shaping the diversity and structure of nearly every ecosystem, very little is known about the role of viruses in desert soils, especially where viral contact with viable hosts is significantly reduced. Our results demonstrate that diverse viruses are widely dispersed across the desert, potentially spreading key stress resilience and metabolic genes to ensure host survival. The desertification accelerated by climate change expands both the ecosystem cover and the ecological significance of the desert virome. This study sheds light on the complex virus-host interplay that shapes the unique microbiome in desert soils.
Wissenschaftlicher Artikel
Scientific Article
Schulze-Makuch, D. ; Lipus, D. ; Arens, F.L. ; Baqué, M. ; Bornemann, T.L.V. ; Devere, J.P. ; Flury, M. ; Frösler, J. ; Heinz, J. ; Hwang, Y. ; Kounaves, S.P. ; Mangelsdorf, K. ; Meckenstock, R.U. ; Pannekens, M. ; Probst, A.J. ; Sáenz, J.S. ; Schirmack, J. ; Schloter, M. ; Schmitt-Kopplin, P. ; Schneider, B. ; Uhl, J. ; Vestergaard, G. ; Valenzuela, B. ; Zamorano, P. ; Wagner, D.
Microorganisms 9:1038 (2021)
The existence of microbial activity hotspots in temperate regions of Earth is driven by soil heterogeneities, especially the temporal and spatial availability of nutrients. Here we investigate whether microbial activity hotspots also exist in lithic microhabitats in one of the most arid regions of the world, the Atacama Desert in Chile. While previous studies evaluated the total DNA fraction to elucidate the microbial communities, we here for the first time use a DNA separation approach on lithic microhabitats, together with metagenomics and other analysis methods (i.e., ATP, PLFA, and metabolite analysis) to specifically gain insights on the living and potentially active microbial community. Our results show that hypolith colonized rocks are microbial hotspots in the desert environment. In contrast, our data do not support such a conclusion for gypsum crust and salt rock environments, because only limited microbial activity could be observed. The hypolith community is dominated by phototrophs, mostly Cyanobacteria and Chloroflexi, at both study sites. The gypsum crusts are dominated by methylotrophs and heterotrophic phototrophs, mostly Chloroflexi, and the salt rocks (halite nodules) by phototrophic and halotolerant endoliths, mostly Cyanobacteria and Archaea. The major environmental constraints in the organic-poor arid and hyperarid Atacama Desert are water availability and UV irradiation, allowing phototrophs and other extremophiles to play a key role in desert ecology.
Wissenschaftlicher Artikel
Scientific Article
Timsy, T. ; Spanner, T. ; Ulrich, A. ; Kublik, S. ; Fösel, B. ; Kolb, S. ; Horn, M.A. ; Behrendt, U.
Int. J. Syst. Evol. Microbiol. 71, DOI: 10.1099/ijsem.0.004799 (2021)
A novel strain was isolated from grassland soil that has the potential to assimilate ammonium by the reduction of nitrate in the presence of oxygen. Whole genome sequence analysis revealed the presence of an assimilatory cytoplasmic nitrate reductase gene nasA and the assimilatory nitrite reductase genes nirBD which are involved in the sequential reduction of nitrate to nitrite and further to ammonium, respectively. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolate represents a member of the genus Pseudomonas. The closest phylogenetic neighbours based on 16S rRNA gene sequence analysis are the type strains of Pseudomonas peli (98.17%) and Pseudomonas guineae (98.03%). In contrast, phylogenomic analysis revealed a close relationship to Pseudomonas alcaligenes. Computation of the average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) with the closest phylogenetic neighbours of S1-A32-2 revealed genetic differences at the species level, which were further substantiated by differences in several physiological characteristics. On the basis of these results, it was concluded that the soil isolate represents a novel species of the genus Pseudomonas, for which the name Pseu-domonas campi sp. nov. (type strain S1-A32-2 =LMG 31521 =DSM 110222 ) is proposed. T T T T
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Scientific Article
Baumert, V.L. ; Forstner, S.J. ; Zethof, J.H.T. ; Vogel, C. ; Heitkötter, J. ; Schulz, S. ; Kögel-Knabner, I. ; Mueller, C.W.
Soil Biol. Biochem. 157:108244 (2021)
Subsoils are characterized by low concentrations of organic carbon (OC). Nevertheless, they contain more than half of the global soil OC because of their large volume. This discrepancy suggests that subsoils might further sequester carbon (C), thus acting as potential sinks for atmospheric C. Plant roots and associated rhizodeposits are a major OC input source to subsoils. However, whether and how increased OC inputs via plant roots to subsoils affect soil C sequestration mechanisms remains unclear. Here we set up a pot experiment with European Beech (Fagus sylvatica L.) seedlings to investigate the effect of tree roots and associated rhizosphere development on soil aggregation and C allocation in topsoil vs. subsoil material collected from three forest sites of different parent materials. Over a 5-month growth period, the seedlings developed a dense root system transforming the whole soil volume into root-affected (i.e., rhizosphere) soil. We found that roots and the associated rhizosphere development increased the amount of macroaggregates in the two finest-textured subsoils. The most C-poor and fine-textured subsoil had a 15% increase in bulk OC concentration, indicating a potential for C sequestration in subsoils by enhanced macroaggregation. Across subsoils, rooting strongly enhanced microbial abundance and was especially correlated with fungal abundance and a shift in the fungal-to-bacterial- ratio. The strong fungal growth was likely the cause for the enhanced macroaggregation in these subsoils. In topsoils, however, rooting treatment decreased macroaggregate abundance, potentially through the disruption of preexisting aggregates, as indicated by the concomitant increase in microaggregates. Our study supports the growing awareness that OC dynamics may be governed by different mechanisms in top- and subsoils, respectively. It demonstrates that the enhanced addition of OM via plant roots to subsoils boosts fungal growth and thereby increases macroaggregate formation, potentially facilitating C sequestration by occlusion.
Wissenschaftlicher Artikel
Scientific Article
Andrade Linares, D.R. ; Zistl-Schlingmann, M. ; Fösel, B. ; Dannenmann, M. ; Schulz, S. ; Schloter, M.
Sci. Total Environ. 780:146672 (2021)
Montane grasslands in Europe are exposed to increasing temperatures twice as fast as the global average. Changes in climatic conditions are possibly accompanied by an increase in land use intensity, caused by a prolongation of the vegetation period and the need to improve productivity. Therefore, the investigation of combined effects of climate change and land use intensity is needed to further implement agricultural management strategies. Here we present results from a study performed in the pre-alpine region of southern Germany, where intact plant-soil mesocosms from grasslands, were translocated along an altitudinal gradient, resulting in an increase in soil temperature (moderate treatment: +0.5 K; strong treatment: +1.9 K warming) during the experimental period. Additionally, we applied an extensive or intensive agricultural management (two vs. five times of mowing and slurry application) on the transplanted mesocosms. After an exposure of one year, we measured plant growth and soil properties and quantified abundances of soil microorganisms catalyzing key steps in the nitrogen (N) cycle. Our data indicate, significant interactions between climate change and management. For example, microbial biomass was significantly reduced (−47.7% and −49.8% for C and N respectively), which was further accompanied by lower abundances of N -fixing bacteria (up to −89,3%), as well as ammonia oxidizing bacteria (−81.4%) under intensive management, whereas N-mineralizing bacteria increased in abundance (up to +139.8%) under extensive management. Surprisingly, the abundances of denitrifying bacteria as well as mean N O emissions were not affected by the treatments. Overall, our data suggest pronounced shifts in the abundance of microbes driving the N cycle in soil as a result of combined climate change and land use intensification already after a short simulation period of one year. mic mic 2 2
Wissenschaftlicher Artikel
Scientific Article
Duffner, C. ; Wunderlich, A. ; Schloter, M. ; Schulz, S. ; Einsiedl, F.
Front. Microbiol. 12:610437 (2021)
Bioremediation of polluted groundwater is one of the most difficult actions in environmental science. Nonetheless, the clean-up of nitrate polluted groundwater may become increasingly important as nitrate concentrations frequently exceed the EU drinking water limit of 50 mg L , largely due to intensification of agriculture and food production. Denitrifiers are natural catalysts that can reduce increasing nitrogen loading of aquatic ecosystems. Porous aquifers with high nitrate loading are largely electron donor limited and additionally, high dissolved oxygen concentrations are known to reduce the efficiency of denitrification. Therefore, denitrification lag times (time prior to commencement of microbial nitrate reduction) up to decades were determined for such groundwater systems. The stimulation of autotrophic denitrifiers by the injection of hydrogen into nitrate polluted regional groundwater systems may represent a promising remediation strategy for such environments. However, besides high costs other drawbacks, such as the transient or lasting accumulation of the cytotoxic intermediate nitrite or the formation of the potent greenhouse gas nitrous oxide, have been described. In this article, we detect causes of incomplete denitrification, which include environmental factors and physiological characteristics of the underlying bacteria and provide possible mitigation approaches. –1
Review
Review
Grafe, M. ; Kurth, J. ; Panten, K. ; Raj, A.D. ; Baum, C. ; Zimmer, D. ; Leinweber, P. ; Schloter, M. ; Schulz, S.
Agric. Ecosyst. Environ. 314:107419 (2021)
Phosphorous (P) is one of the most critical macronutrient elements for plant growth, yield and quality. However, natural P sources are finite and an improved P recycling is necessary. Therefore, we investigated the effect of bone char (BC) and bone char plus (BC ) as recycling products and alternative P fertilizers, on the abundance of microorganisms, which catalyze major steps in P turnover in a field experiment in Central Germany. The effects were compared to conventional triple super phosphate (TSP) and no P fertilization. Samples were analyzed from soils with three different initial soil P concentrations (very low, low, optimal) and three times during winter wheat cultivation (stem elongation, heading, ripening) to reveal interactions of fertilizers and soil properties. Abundances of microorganisms involved in P uptake, solubilization and mineralization were assessed by quantitative real time PCR (qPCR). Additionally, potential acidic- and alkaline phosphatase activity, water extractable P and plant available P were measured. Bacterial strategies to maintain P pools differed among the treatments. While the addition of BC increased the solubilization potential, the low P concentration in control plots and slow release of P from BC favor P recycling from biomass and P inducible uptake systems, which is displayed by either high abundance bacteria harboring the phoD or pstS gene, respectively. All effects were most pronounced at the time of heading and in soils with optimal initial P concentration. It can be assumed that sulfurization of bone char (BC ) influences bacterial P turnover by promoting solubilization of the fertilizer thereby increasing P availability for plants. Additionally, plant development stage and initial soil P concentrations hamper the effect of BC and BC on bacterial P turnover. plus plus plus plus
Wissenschaftlicher Artikel
Scientific Article
Chiba, A. ; Uchida, Y. ; Kublik, S. ; Vestergaard, G. ; Buegger, F. ; Schloter, M. ; Schulz, S.
Microorganisms 9:357 (2021)
This study aimed to investigate the effects of different levels of soil‐ and plant‐associated bacterial diversity on the rates of litter decomposition, and bacterial community dynamics during its early phases. We performed an incubation experiment where soil bacterial diversity (but not abundance) was manipulated by autoclaving and reinoculation. Natural or autoclaved maize leaves were applied to the soils and incubated for 6 weeks. Bacterial diversity was assessed before and during litter decomposition using 16S rRNA gene metabarcoding. We found a positive correlation between litter decomposition rates and soil bacterial diversity. The soil with the highest bacterial diversity was dominated by oligotrophic bacteria including Acidobacteria, Nitrospiraceae, and Gai-ellaceae, and its community composition did not change during the incubation. In the less diverse soils, those taxa were absent but were replaced by copiotrophic bacteria, such as Caulobacteraceae and Beijerinckiaceae, until the end of the incubation period. SourceTracker analysis revealed that lit-ter‐associated bacteria, such as Beijerinckiaceae, only became part of the bacterial communities in the less diverse soils. This suggests a pivotal role of oligotrophic bacteria during the early phases of litter decomposition and the predominance of copiotrophic bacteria at low diversity.
Wissenschaftlicher Artikel
Scientific Article
Bigott, Y. ; Khalaf, D.M. ; Schröder, P. ; Schröder, P.M. ; Cruzeiro, C.
In: Interaction and Fate of Pharmaceuticals in Soil-Crop Systems. 2021. 103-140 (Handb. Environ. Chem. ; 103)
Pharmaceuticals originating from reclaimed wastewater or biosolid-, livestock manure- or sewage sludge-amended soils can enter crops by irrigation and fertilization. Generally, the putative uptake occurs through the plants’ roots and can lead to the bioaccumulation in different plant parts. The uptake and translocation therefore is dependent on multiple parameters, i.e. physicochemical properties of compounds, plant physiology and environmental factors. This book chapter combines a theoretical background on the main principles of uptake and translocation of pharmaceuticals by plants and a critical evaluation of current available literature, by analysing studies for the bioconcentration and translocation factors of different pharmaceutical groups in several plant species. Thereby, interesting results were obtained by looking at the translocation of various pharmaceuticals in radish and at cationic compounds in soil studies. Comparing the different studies, the relevance of testing not only high but also real environmental concentrations became obvious, since for some pharmaceuticals, higher uptake and translocation ratios were achieved with lower applied concentrations. Basic guidelines could provide a possibility to make scientific data more comparable and reliable and to avoid the exclusion of potential reasons for the missing uptake or translocation of pharmaceuticals. This book chapter provides recommendations for future research studies to generate more valid conclusions within the scientific community.
Harris, E. ; Díaz-Pinés, E. ; Stoll, E. ; Schloter, M. ; Schulz, S. ; Duffner, C. ; Li, K. ; Moore, K.L. ; Ingrisch, J. ; Reinthaler, D. ; Zechmeister-Boltenstern, S. ; Glatzel, S. ; Brüggemann, N. ; Bahn, M.
Sci. Adv. 7:eabb7118 (2021)
Nitrous oxide is a powerful greenhouse gas whose atmospheric growth rate has accelerated over the past decade. Most anthropogenic N2O emissions result from soil N fertilization, which is converted to N2O via oxic nitrification and anoxic denitrification pathways. Drought-affected soils are expected to be well oxygenated; however, using high-resolution isotopic measurements, we found that denitrifying pathways dominated N2O emissions during a severe drought applied to managed grassland. This was due to a reversible, drought-induced enrichment in nitrogen-bearing organic matter on soil microaggregates and suggested a strong role for chemo- or codenitrification. Throughout rewetting, denitrification dominated emissions, despite high variability in fluxes. Total N2O flux and denitrification contribution were significantly higher during rewetting than for control plots at the same soil moisture range. The observed feedbacks between precipitation changes induced by climate change and N2O emission pathways are sufficient to account for the accelerating N2O growth rate observed over the past decade.
Wissenschaftlicher Artikel
Scientific Article
Broadbent, A.A.D. ; Snell, H.S.K. ; Michas, A. ; Pritchard, W.J. ; Newbold, L. ; Cordero, I. ; Goodall, T. ; Schallhart, N. ; Kaufmann, R. ; Griffiths, R.I. ; Schloter, M. ; Bahn, M. ; Bardgett, R.D.
ISME J. 15, 2264–2275 (2021)
Soil microbial communities regulate global biogeochemical cycles and respond rapidly to changing environmental conditions. However, understanding how soil microbial communities respond to climate change, and how this influences biogeochemical cycles, remains a major challenge. This is especially pertinent in alpine regions where climate change is taking place at double the rate of the global average, with large reductions in snow cover and earlier spring snowmelt expected as a consequence. Here, we show that spring snowmelt triggers an abrupt transition in the composition of soil microbial communities of alpine grassland that is closely linked to shifts in soil microbial functioning and biogeochemical pools and fluxes. Further, by experimentally manipulating snow cover we show that this abrupt seasonal transition in wide-ranging microbial and biogeochemical soil properties is advanced by earlier snowmelt. Preceding winter conditions did not change the processes that take place during snowmelt. Our findings emphasise the importance of seasonal dynamics for soil microbial communities and the biogeochemical cycles that they regulate. Moreover, our findings suggest that earlier spring snowmelt due to climate change will have far reaching consequences for microbial communities and nutrient cycling in these globally widespread alpine ecosystems.
Wissenschaftlicher Artikel
Scientific Article
Balazs, H.-E. ; Schmid, C. ; Cruzeiro, C. ; Podar, D. ; Szatmari, P.M. ; Buegger, F. ; Hufnagel, G. ; Radl, V. ; Schröder, P.
Sci. Total Environ. 767:144653 (2021)
The toxicity, volatility and persistence of the obsolete organochlorine pesticide hexachlorocyclohexane (HCH), makes reclamation of contaminated areas a priority for the health and welfare of neighboring human communities. Microbial diversity and functions and their relation to spontaneous vegetation in post-excavation situations, are essential indicators to consider in bioaugmentation or microbe-assisted phytoremediation strategies at field scale. Our study aimed to evaluate the effects of long-term HCH contamination on soil and plant-associated microbial communities, and whether contaminated soil has the potential to act as a bacterial inoculum in post-excavation bioremediation strategies. To scrutinize the role of vegetation, the potential nitrogen fixation of free-living and symbiotic diazotrophs of the legume Lotus tenuis was assessed as a measure of nutrient cycling functions in soil under HCH contamination. Potential nitrogen fixation was generally not affected by HCH, with the exception of lower nifH gene counts in excavated contaminated rhizospheres, most probably a short-term HCH effect on early bacterial succession in this compartment. HCH shaped microbial communities in long-term contaminated bulk soil, where we identified possible HCH tolerants such as Sphingomonas and Altererythrobacter. In L. tenuis rhizosphere, microbial community composition was additionally influenced by plant growth stage. Sphingobium and Massilia were the bacterial genera characteristic for HCH contaminated rhizospheres. Long-term HCH contamination negatively affected L. tenuis growth and development. However, root-associated bacterial community composition was driven solely by plant age, with negligible HCH effect. Results showed that L. tenuis acquired possible HCH tolerant bacteria such as the Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium clade, Sphingomonas, Massilia or Pantoea which could simultaneously offer plant growth promoting (PGP) benefits for the host. Finally, we identified an inoculum with possibly HCH tolerant, PGP bacteria transferred from the contaminated bulk soil to L. tenuis roots through the rhizosphere compartment, consisting of Mesorhizobium loti, Neorhizobium galegae, Novosphingobium lindaniclasticum, Pantoea agglomerans and Lysobacter bugurensis.
Wissenschaftlicher Artikel
Scientific Article
Simons, N.K. ; Felipe-Lucia, M.R. ; Schall, P. ; Ammer, C. ; Bauhus, J. ; Blüthgen, N. ; Boch, S. ; Buscot, F. ; Fischer, M. ; Goldmann, K. ; Gossner, M.M. ; Hänsel, F. ; Jung, K. ; Manning, P. ; Nauss, T. ; Oelmann, Y. ; Pena, R. ; Polle, A. ; Renner, S.C. ; Schloter, M. ; Schöning, I. ; Schulze, E.D. ; Solly, E.F. ; Sorkau, E. ; Stempfhuber, B. ; Wubet, T. ; Müller, J. ; Seibold, S. ; Weisser, W.W.
For. Ecosyst. 8:5 (2021)
Background: Forests perform various important ecosystem functions that contribute to ecosystem services. In many parts of the world, forest management has shifted from a focus on timber production to multi-purpose forestry, combining timber production with the supply of other forest ecosystem services. However, it is unclear which forest types provide which ecosystem services and to what extent forests primarily managed for timber already supply multiple ecosystem services. Based on a comprehensive dataset collected across 150 forest plots in three regions differing in management intensity and species composition, we develop models to predict the potential supply of 13 ecosystem services. We use those models to assess the level of multifunctionality of managed forests at the national level using national forest inventory data. Results: Looking at the potential supply of ecosystem services, we found trade-offs (e.g. between both bark beetle control or dung decomposition and both productivity or soil carbon stocks) as well as synergies (e.g. for temperature regulation, carbon storage and culturally interesting plants) across the 53 most dominant forest types in Germany. No single forest type provided all ecosystem services equally. Some ecosystem services showed comparable levels across forest types (e.g. decomposition or richness of saprotrophs), while others varied strongly, depending on forest structural attributes (e.g. phosphorous availability or cover of edible plants) or tree species composition (e.g. potential nitrification activity). Variability in potential supply of ecosystem services was only to a lesser extent driven by environmental conditions. However, the geographic variation in ecosystem function supply across Germany was closely linked with the distribution of main tree species. Conclusions: Our results show that forest multifunctionality is limited to subsets of ecosystem services. The importance of tree species composition highlights that a lack of multifunctionality at the stand level can be compensated by managing forests at the landscape level, when stands of complementary forest types are combined. These results imply that multi-purpose forestry should be based on a variety of forest types requiring coordinated planning across larger spatial scales.
Wissenschaftlicher Artikel
Scientific Article
Duffner, C. ; Holzapfel, S. ; Wunderlich, A. ; Einsiedl, F. ; Schloter, M. ; Schulz, S.
FEMS Microbiol. Ecol. 97:fiab004 (2021)
Globally occurring nitrate pollution in groundwater is harming the environment and human health. In situ hydrogen addition to stimulate denitrification has been proposed as a remediation strategy. However, observed nitrite accumulation and incomplete denitrification are severe drawbacks that possibly stem from the specific microbial community composition. We set up a microcosm experiment comprising sediment and groundwater from a nitrate polluted oxic oligotrophic aquifer. After the microcosms were sparged with hydrogen gas, samples were taken regularly within 122 h for nitrate and nitrite measurements, community composition analysis via 16S rRNA gene amplicon sequencing, and gene and transcript quantification via qPCR of reductase genes essential for complete denitrification. The highest nitrate reduction rates and greatest increase in bacterial abundance coincided with the 15.3-fold increase in Rhodocyclaceae, specifically six ASVs that are closely related to the genus Dechloromonas. The denitrification reductase genes napA, nirS, and clade I nosZ also increased significantly over the observation period. We conclude that taxa of the genus Dechloromonas are the prevailing hydrogenotrophic denitrifiers in this nitrate polluted aquifer and the ability of hydrogenotrophic denitrification under the given conditions is species-specific.
Wissenschaftlicher Artikel
Scientific Article
Ryan, M.J. ; Schloter, M. ; Berg, G. ; Kinkel, L.L. ; Eversole, K. ; Macklin, J.A. ; Rybakova, D. ; Sessitsch, A.
Environ. Microbiol. 23, 372-375 (2021)
High-quality microbiome research relies on the integrity, management and quality of supporting data. Currently biobanks and culture collections have different formats and approaches to data management. This necessitates a standard data format to underpin research, particularly in line with the FAIR data standards of findability, accessibility, interoperability and reusability. We address the importance of a unified, coordinated approach that ensures compatibility of data between that needed by biobanks and culture collections, but also to ensure linkage between bioinformatic databases and the wider research community.
Wissenschaftlicher Artikel
Scientific Article
Wahman, R. ; Sauvetre, A. ; Schröder, P. ; Moser, S. ; Letzel, T.
Metabolites 11:2 (2021)
Plants produce a huge number of functionally and chemically different natural products that play an important role in linking the plant with the adjacent environment. Plants can also absorb and transform external organic compounds (xenobiotics). Currently there are only a few studies concerning the effects of xenobiotics and their transformation products on plant metabolites using a mass spectrometric untargeted screening strategy. This study was designed to investigate the changes of the Phragmites australis metabolome following/after diclofenac or carbamazepine incubation, using a serial coupling of reversed-phase liquid chromatography (RPLC) and hydrophilic interaction liquid chromatography (HILIC) combined with accurate high-resolution time-of-flight mass spectrometer (TOF-MS). An untargeted screening strategy of metabolic fingerprints was developed to purposefully compare samples from differently treated P. australis plants, revealing that P. australis responded to each drug differently. When solvents with significantly different polarities were used, the metabolic profiles of P. australis were found to change significantly. For instance, the production of polyphenols (such as quercetin) in the plant increased after diclofenac incubation. Moreover, the pathway of unsaturated organic acids became more prominent, eventually as a reaction to protect the cells against reactive oxygen species (ROS). Hence, P. australis exhibited an adaptive mechanism to cope with each drug. Consequently, the untargeted screening approach is essential for understanding the complex response of plants to xenobiotics.
Wissenschaftlicher Artikel
Scientific Article
Kamau, C.W. ; van Duijnen, R. ; Schmid, C. ; Balazs, H.-E. ; Roy, J. ; Rillig, M. ; Schröder, P. ; Radl, V. ; Temperton, V.M. ; Schloter, M.
Biol. Fertil. Soils 57, 305-317 (2021)
A 2-year outdoor mesocosm experiment was carried out to determine the effects of high C amendments (HCAs; wheat straw and sawdust) compared to a control with no addition of HCAs (no-HCA) and 2 different crop rotation systems (spring barley/winter barley and faba bean/winter barley) on soil bacterial communities using a molecular barcoding approach. Samples were analyzed after pre-crop harvest (T1) and harvest of winter barley (T2). Our data demonstrate a clear drop in bacterial diversity after winter barley harvest in the no-HCA and wheat straw treatment compared to the pre-crops. Sawdust application had a stabilizing effect on bacterial diversity compared to the pre-crops and induced an increase in carbon (C) stocks in soil which were however negatively correlated with yields. Main responders in the no-HCA and wheat straw treatment compared to the pre-crops were bacteria of the phyla Actinobacteria and Bacteroidetes which were enriched and bacteria belonging to Firmicutes, Gemmatimonadetes, Proteobacteria, and Gemmatimonadaceae which were depleted. Overall differences between wheat straw–amended and no-HCA control samples were small and included single ASVs from various phyla. In sawdust-amended samples, only a shift of some Proteobacteria families was observed compared to the no-HCA control. Overall, pre-crop plant species had small influence on the observed response pattern of the soil microbiome towards the amendments and was only visible for wheat straw.
Wissenschaftlicher Artikel
Scientific Article
Clausing, S. ; Pena, R. ; Song, B. ; Müller, K. ; Mayer-Gruner, P. ; Marhan, S. ; Grafe, M. ; Schulz, S. ; Krüger, J. ; Lang, F. ; Schloter, M. ; Kandeler, E. ; Polle, A.
New Phytol. 229, 2611-2624 (2021)
Nutrient imbalances cause the deterioration of tree health in European forests, but the underlying physiological mechanisms are unknown. Here, we investigated the consequences of decreasing root carbohydrate reserves for phosphorus (P) mobilization and uptake by forest trees. In P-rich and P-poor beech (Fagus sylvatica) forests, naturally grown, young trees were girdled and used to determine root, ectomycorrhizal and microbial activities related to P mobilization in the organic layer and mineral topsoil in comparison with those in non-girdled trees. After girdling, root carbohydrate reserves decreased. Root phosphoenolpyruvate carboxylase activities linking carbon and P metabolism increased. Root and ectomycorrhizal phosphatase activities and the abundances of bacterial genes catalysing major steps in P turnover increased, but soil enzymes involved in P mobilization were unaffected. The physiological responses to girdling were stronger in P-poor than in P-rich forests. P uptake was decreased after girdling. The soluble and total P concentrations in roots were stable, but fine root biomass declined after girdling. Our results support that carbohydrate depletion results in reduced P uptake, enhanced internal P remobilization and root biomass trade-off to compensate for the P shortage. Since reductions in root biomass render trees more susceptible to drought, our results link tree deterioration with disturbances in the P supply as a consequence of decreased belowground carbohydrate allocation.
Wissenschaftlicher Artikel
Scientific Article
Tanuwidjaja, I. ; Vogel, C. ; Pronk, G.J. ; Schöler, A. ; Kublik, S. ; Vestergaard, G. ; Kögel-Knabner, I. ; Mrkonjic Fuka, M. ; Schloter, M. ; Schulz, S.
Microb. Ecol. 81, 897–907 (2021)
Nutrient turnover in soils is strongly driven by soil properties, including clay mineral composition. One main nutrient is phosphorus (P), which is known to be easily immobilized in soil. Therefore, the specific surface characteristics of clay minerals might substantially influence P availability in soil and thus the microbial strategies for accessing P pools. We used a metagenomic approach to analyze the microbial potential to access P after 842 days of incubation in artificial soils with a clay mineral composition of either non-expandable illite (IL) or expandable montmorillonite (MT), which differ in their surface characteristics like soil surface area and surface charge. Our data indicate that microorganisms of the two soils developed different strategies to overcome P depletion, resulting in similar total P concentrations. Genes predicted to encode inorganic pyrophosphatase (ppa), exopolyphosphatase (ppx), and the pstSCAB transport system were higher in MT, suggesting effective P uptake and the use of internal poly-P stores. Genes predicted to encode enzymes involved in organic P turnover like alkaline phosphatases (phoA, phoD) and glycerophosphoryl diester phosphodiesterase were detected in both soils in comparable numbers. In addition, P-o concentrations did not differ significantly. Most identified genes were assigned to microbial lineages generally abundant in agricultural fields, but some were assigned to lineages known to include oligotrophic specialists, such as Bacillaceae and Microchaetaceae.
Wissenschaftlicher Artikel
Scientific Article
Ryan, M.J. ; Schloter, M. ; Berg, G. ; Kostic, T. ; Kinkel, L.L. ; Eversole, K. ; Macklin, J.A. ; Schelkle, B. ; Kazou, M. ; Sarand, I. ; Singh, B.K. ; Fischer, D. ; Maguin, E. ; Ferrocino, I. ; Lima, N. ; McClure, R.S. ; Charles, T.C. ; de Souza, R.S.C. ; Kiran, G.S. ; Krug, H.L. ; Taffner, J. ; Roume, H. ; Selvin, J. ; Smith, D. ; Rybakova, D. ; Sessitsch, A.
Trends Microbiol. 29, 89-92 (2021)
The microbiome research field is rapidly evolving, but the required biobanking infrastructure is currently fragmented and not prepared for the biobanking of microbiomes. The rapid advancement of technologies requires an urgent assessment of how biobanks can underpin research by preserving microbiome samples and their functional potential.
Letter to the Editor
Letter to the Editor
Bigott, Y. ; Chowdhury, S.P. ; Pérez, S. ; Montemurro, N. ; Manasfi, R. ; Schröder, P.
J. Hazard. Mater. 403:123881 (2021)
Vegetable crops irrigated with treated wastewater can take up the environmentally persistent pharmaceuticals diclofenac and lamotrigine. This study aimed at quantifying the uptake and translocation of the two pharmaceuticals in lettuce (Lactuca sativa) as well as on the elucidation of the molecular and physiological changes triggered by them. Therefore, plants were cultivated in a phytochamber in hydroponic systems under controlled conditions and treated independently with diclofenac (20 μg L−1) and lamotrigine (60 μg L−1) for 48 h. A low translocation of lamotrigine but not of diclofenac or its metabolite 4’-hydroxydiclofenac to leaves was observed, which corresponded with the expression of stress related genes only in roots of diclofenac treated plants. We observed an oxidative burst in roots and leaves occurring around the same time point when lamotrigine was detected in leaves. This could be responsible for the significantly changed gene expression pattern in both tissues. Our results showed for the first time that pharmaceuticals like lamotrigine or diclofenac might act as signals or zeitgebers, affecting the circadian expression of stress related genes in lettuce possibly causing a repressed physiological status of the plant.
Wissenschaftlicher Artikel
Scientific Article
2020
Berg, G. ; Rybakova, D. ; Fischer, D. ; Cernava, T. ; Vergès, M.C.C. ; Charles, T. ; Chen, X. ; Cocolin, L. ; Eversole, K. ; Corral, G.H. ; Kazou, M. ; Kinkel, L. ; Lange, L. ; Lima, N. ; Loy, A. ; Macklin, J.A. ; Maguin, E. ; Mauchline, T. ; McClure, R. ; Mitter, B. ; Ryan, M. ; Sarand, I. ; Smidt, H. ; Schelkle, B. ; Roume, H. ; Kiran, G.S. ; Selvin, J. ; de Souza, R.S.C. ; van Overbeek, L. ; Singh, B.K. ; Wagner, M. ; Walsh, A. ; Sessitsch, A. ; Schloter, M.
Microbiome 8:119 (2020)
An amendment to this paper has been published and can be accessed via the original article.
Mahnkopp-Dirks, F. ; Radl, V. ; Kublik, S. ; Gschwendtner, S. ; Schloter, M. ; Winkelmann, T.
Phytobio. J. 5, 177-189 (2020)
Apple replant disease (ARD) occurs when apple is repeatedly planted at the same site, leading to growth reductions and losses in fruit yield and quality. Up to now the etiology is poorly understood, but soil (micro)biota are known to be involved. Since endophytes often colonize plants via the rhizosphere this study aimed at comparing the bacterial endophytic root microbiome in plants growing in ARD affected and unaffected soils from three different sites based on greenhouse biotests using a molecular barcoding approach. The initial endophytic microbiome of the starting material (in vitro propagated plants of the apple rootstock M26) did not significantly affect the overall richness and diversity of the endophytic community in plants after 8 weeks of growth in the respective soils, but some genera of the initial microbiome managed to establish in apple roots. Proteobacteria were the dominant phylum in all samples. No differences in diversity or number of amplicon sequence variants (ASVs) between plants grown in ARD soil and unaffected soil was observed. However, several ASVs of high abundance uniquely found in plants grown in ARD affected soils were Streptomyces. In soil from all three sites these Streptomyces were negatively correlated to plant growth parameters. Future inoculation experiments using selected Streptomyces isolates have to prove if bacteria from this genus are opportunists or part of the ARD complex. For the first time, the bacterial endophytic community of apple roots grown in ARD affected soils was characterized which will help to understand the etiology of ARD and develop countermeasures.
Wissenschaftlicher Artikel
Scientific Article
Felipe-Lucia, M.R. ; Soliveres, S. ; Penone, C. ; Fischer, M. ; Ammer, C. ; Boch, S. ; Boeddinghaus, R.S. ; Bonkowski, M. ; Buscot, F. ; Fiore-Donno, A.M. ; Frank, K. ; Goldmann, K. ; Gossner, M.M. ; Hölzel, N. ; Jochum, M. ; Kandeler, E. ; Klaus, V.H. ; Kleinebecker, T. ; Leimer, S. ; Manning, P. ; Oelmann, Y. ; Saiz, H. ; Schall, P. ; Schloter, M. ; Schöning, I. ; Schrumpf, M. ; Solly, E.F. ; Stempfhuber, B. ; Weisser, W.W. ; Wilcke, W. ; Wubet, T. ; Allan, E.
Proc. Natl. Acad. Sci. U.S.A. 117, 28140-28149 (2020)
Land-use intensification can increase provisioning ecosystem services, such as food and timber production, but it also drives changes in ecosystem functioning and biodiversity loss, which may ultimately compromise human wellbeing. To understand how changes in land-use intensity affect the relationships between biodiversity, ecosystem functions, and services, we built networks from correlations between the species richness of 16 trophic groups, 10 ecosystem functions, and 15 ecosystem services. We evaluated how the properties of these networks varied across land-use intensity gradients for 150 forests and 150 grasslands. Land-use intensity significantly affected network structure in both habitats. Changes in connectance were larger in forests, while changes in modularity and evenness were more evident in grasslands. Our results show that increasing land-use intensity leads to more homogeneous networks with less integration within modules in both habitats, driven by the belowground compartment in grasslands, while forest responses to land management were more complex. Land-use intensity strongly altered hub identity and module composition in both habitats, showing that the positive correlations of provisioning services with biodiversity and ecosystem functions found at low land-use intensity levels, decline at higher intensity levels. Our approach provides a comprehensive view of the relationships between multiple components of biodiversity, ecosystem functions, and ecosystem services and how they respond to land use. This can be used to identify overall changes in the ecosystem, to derive mechanistic hypotheses, and it can be readily applied to further global change drivers.
Wissenschaftlicher Artikel
Scientific Article
Schloter, M. ; Meyer, F. ; Berg, G.
BioSpektrum 26, 714-717 (2020)
Microbiomes are complex microbial communities, with manifold interactions in a given ecosystem. They are characterized by defined functional properties and pattern of activities. Microbiomes play an important role as parts of “holobionts” and strongly drive the health of their particular hosts. The article describes challenges and chances of recent microbiome research and future strategies how to make use of findings from basic research in environmental sciences as well as in medicine.
Review
Review
Wang, Z. ; Minarsch, E.-M.L. ; Kublik, S. ; Heine, H. ; Schloter, M. ; Fösel, B.
Microbio. Res. Ann. 9:e00777-20 (2020)
Early childhood exposure to a farming environment has been found to be protective against asthma and other atopic disorders. Here, we report the complete genome sequence of Lactococcus lactis subsp. lactis G121, which was isolated from the kitchen of a farm in Bavaria (Germany) and is recognized for its allergy-protective properties. It could be assembled into one circular chromosome, three circular plasmids, and one linear plasmid.
Wissenschaftlicher Artikel
Scientific Article
Lund, J.V. ; Kovacevic, D. ; Schloter, M. ; Krauss-Etschmann, S.
Padiat. Praxis 93, 444-452 (2020)
The human microbiome is represented by a variety of microorganisms including bacteria, archaea, viruses and fungi that live on and inside our body. Most of them do not cause disease. In fact, microbes provide many important functions that humans did not develop themselves. They can digest food and supply host cells with nutrients, metabolize drugs, and activate and support the host's immune system. Knowledge about the microbiome has expanded with the development of novel culture-independent techniques, which revealed that healthy lungs also harbor diverse microbial communities and that variations in their composition can correlate with severity of lung diseases. Limited experimental evidence suggests an influence of the gut microbiome on respiratory health, involving different communication pathways, such as through the release of gut microbial metabolites, or via induced host metabolites or gut-lung immune cell trade. This implies that nutrition, by shaping the gut microbiome, could have an impact on respiratory diseases. However, this requires a precise mechanistic understanding how the gut microbiome affects microbial communities in the lungs and vice versa. Once better understood, this mechanism could be of particular interest in the future for the application of nutritive strategies in critical time window during the early childhood to improve lung health.
Review
Review
Kurth, J. ; Albrecht, M. ; Karsten, U. ; Gläser, K. ; Schloter, M. ; Schulz, S.
Biol. Fertil. Soils 57, 179-192 (2020)
Soil P pools are strongly driven by microbial activities, and vice versa, P pools shape bacterial communities and their functional potential. Biological soil crusts (biocrusts) represent a microbial hotspot for nutrient turnover. We compared biocrusts and bulk soil samples from different temperate beech (Fagus sylvaticaL.) forests representing a gradient in soil texture, nutrient concentrations, and pH values at biocrust peak biomass. We measured the total and plant-available P and N concentrations and assessed the bacterial potential to mineralize (phoD,phnX), solubilize (gcd), and take up P (pstSandpitA) and mineralize (chiA,apr) and fix N (nifH) by quantifying the respective marker genes (qPCR). We found an increase of absolute and relative bacterial abundance involved in P turnover in biocrusts, but the strategy to acquire P differed between the regions as bacteria harboring the starvation-inducedpstSgene were most abundant where labile P was lowest. In contrast, the region with lowest total P concentrations has a higher potential to utilize more stable phosphonates. N mineralization was strongly correlated to P turnover at regions with increased labile N and P concentrations. Interestingly, the potential to fix N was highest in the bulk soil where total P concentrations were highest. Even though the correlation of N and P turnover is strongest if their ratio is low, the acquisition strategy strongly depends on soil properties.
Wissenschaftlicher Artikel
Scientific Article
Michas, A. ; Harir, M. ; Lucio, M. ; Vestergaard, G. ; Himmelberg, A.M. ; Schmitt-Kopplin, P. ; Lueders, T. ; Hatzinikolaou, D.G. ; Schöler, A. ; Rabus, R. ; Schloter, M.
Front. Microbiol. 11:556793 (2020)
Sulfate-reducing microorganisms (SRMs) often compete with methanogens for common substrates. Due to thermodynamic reasons, SRMs should outcompete methanogens in the presence of sulfate. However, many studies have documented coexistence of these microbial groups in natural environments, suggesting that thermodynamics alone cannot explain the interactions among them. In this study, we investigated how SRMs compete with the established methanogenic communities in sediment from a long-term, electron acceptor-depleted, asphalt-exposed ecosystem and how they affect the composition of the organic material. We hypothesized that, upon addition of sulfate, SRMs (i) outcompete the methanogenic communities and (ii) markedly contribute to transformations of the organic material. We sampled sediments from the test and proximate control sites under anoxic conditions and incubated them in seawater medium with or without sulfate. Abundance and activity pattern of SRMs and methanogens, as well as the total prokaryotic community, were followed for 6 weeks by using qPCR targeting selected marker genes. Some of these genes were also subjected to amplicon sequencing to assess potential shifts in diversity patterns. Alterations of the organic material in the microcosms were determined by mass spectrometry. Our results indicate that the competition of SRMs with methanogens upon sulfate addition strongly depends on the environment studied and the starting microbiome composition. In the asphalt-free sediments (control), the availability of easily degradable organic material (mainly plant-derived) allows SRMs to use a larger variety of substrates, reducing interspecies competition with methanogens. In contrast, the abundant presence of recalcitrant compounds in the asphalt-exposed sediment was associated with a strong competition between SRMs and methanogens, ultimately detrimental for the latter. Our data underpin the importance of the quality of bioavailable organic materials in anoxic environments as a driver for microbial community structure and function.
Wissenschaftlicher Artikel
Scientific Article
Estendorfer, J. ; Stempfhuber, B. ; Vestergaard, G. ; Schulz, S. ; Rillig, M.C. ; Joshi, J. ; Schröder, P. ; Schloter, M.
Diversity 12:392 (2020)
Plant-associated bacterial assemblages are critical for plant fitness. Thus, identifying a consistent plant-associated core microbiome is important for predicting community responses to environmental changes. Our target was to identify the core bacterial microbiome of orchard grass Dactylis glomerata L. and to assess the part that is most sensitive to land management. Dactylis glomerata L. samples were collected from grassland sites with contrasting land use intensities but comparable soil properties at three different timepoints. To assess the plant-associated bacterial community structure in the compartments rhizosphere, bulk soil and endosphere, a molecular barcoding approach based on high throughput 16S rRNA amplicon sequencing was used. A distinct composition of plant-associated core bacterial communities independent of land use intensity was identified. Pseudomonas, Rhizobium and Bradyrhizobium were ubiquitously found in the root bacterial core microbiome. In the rhizosphere, the majority of assigned genera were Rhodoplanes, Methylibium, Kaistobacter and Bradyrhizobium. Due to the frequent occurrence of plant-promoting abilities in the genera found in the plant-associated core bacterial communities, our study helps to identify "healthy" plant-associated bacterial core communities. The variable part of the plant-associated microbiome, represented by the fluctuation of taxa at the different sampling timepoints, was increased under low land use intensity. This higher compositional variation in samples from plots with low land use intensity indicates a more selective recruitment of bacteria with traits required at different timepoints of plant development compared to samples from plots with high land use intensity.
Wissenschaftlicher Artikel
Scientific Article
Yang, L. ; Schröder, P. ; Vestergaard, G. ; Schloter, M. ; Radl, V.
Microorganisms 8:1414 (2020)
Mechanisms used by plants to respond to water limitation have been extensively studied. However, even though the inoculation of beneficial microbes has been shown to improve plant performance under drought stress, the inherent role of soil microbes on plant response has been less considered. In the present work, we assessed the importance of the soil microbiome for the growth of barley plants under drought stress. Plant growth was not significantly affected by the disturbance of the soil microbiome under regular watering. However, after drought stress, we observed a significant reduction in plant biomass, particularly of the root system. Plants grown in the soil with disturbed microbiome were significantly more affected by drought and did not recover two weeks after re-watering. These effects were accompanied by changes in the composition of endophytic fungal and bacterial communities. Under natural conditions, soil-derived plant endophytes were major colonizers of plant roots, such as Glycomyces and Fusarium, whereas, for plants grown in the soil with disturbed microbiome seed-born bacterial endophytes, e.g., Pantoea, Erwinia, and unclassified Pseudomonaceae and fungal genera normally associated with pathogenesis, such as Gibberella and Gaeumannomyces were observed. Therefore, the role of the composition of the indigenous soil microbiota should be considered in future approaches to develop management strategies to make plants more resistant towards abiotic stress, such as drought.
Wissenschaftlicher Artikel
Scientific Article
Metwaly, A. ; Dunkel, A. ; Waldschmitt, N. ; Durai Raj, A.C. ; Lagkouvardos, I. ; Corraliza, A.M. ; Mayorgas, A. ; Martinez-Medina, M. ; Reiter, S. ; Schloter, M. ; Hofmann, T. ; Allez, M. ; Panes, J. ; Salas, A. ; Haller, D.
Nat. Commun. 11:4322 (2020)
Gut microbial and metabolite alterations have been linked to the pathogenesis of inflammatory bowel diseases. Here we perform a multi-omics microbiome and metabolite analysis of a longitudinal cohort of Crohn’s disease patients undergoing autologous hematopoietic stem cell transplantation, and investigational therapy that induces drug free remission in a subset of patients. Via comparison of patients who responded and maintained remission, responded but experienced disease relapse and patients who did not respond to therapy, we identify shared functional signatures that correlate with disease activity despite the variability of gut microbiota profiles at taxonomic level. These signatures reflect the disease state when transferred to gnotobiotic mice. Taken together, the integration of microbiome and metabolite profiles from human cohort and mice improves the predictive modelling of disease outcome, and allows the identification of a network of bacteria-metabolite interactions involving sulfur metabolism as a key mechanism linked to disease activity in Crohn’s disease.
Wissenschaftlicher Artikel
Scientific Article
Lauer, T. ; Behnke, J. ; Oehmke, F. ; Baecker, J. ; Gentil, K. ; Chakraborty, T. ; Schloter, M. ; Gertheiss, J. ; Ehrhardt, H.
J. Clin. Med. 9:2240 (2020)
Bronchopulmonary dysplasia (BPD) is a multifactorial disease mainly provoked by pre- and postnatal infections, mechanical ventilation, and oxygen toxicity. In severely affected premature infants requiring mechanical ventilation, association of bacterial colonization of the lung and BPD was recently disclosed. To analyze the impact of bacterial colonization of the upper airway and gastrointestinal tract on moderate/severe BPD, we retrospectively analyzed nasopharyngeal and anal swabs taken weekly during the first 6 weeks of life at a single center inn= 102 preterm infants <1000 g. Colonization mostly occurred between weeks 2 and 6 and displayed a high diversity requiring categorization. Analyses of deviance considering all relevant confounders revealed statistical significance solely for upper airway colonization with bacteria with pathogenic potential and moderate/severe BPD (p= 0.0043) while no link could be established to the Gram response or the gastrointestinal tract. Our data highlight that specific colonization of the upper airway poses a risk to the immature lung. These data are not surprising taking into account the tremendous impact of microbial axes on health and disease across ages. We suggest that studies on upper airway colonization using predefined categories represent a feasible approach to investigate the impact on the pulmonary outcome in ventilated and non-ventilated preterm infants.
Wissenschaftlicher Artikel
Scientific Article
Obermeier, M. ; Minarsch, E.-M.L. ; Durai Raj, A.C. ; Rineau, F. ; Schröder, P.
Plant Soil 455, 489–506 (2020)
Aims In order to counteract the enduring decreases in the quality of agricultural land, mechanistic studies for a more sustainable agricultural crop production were performed. They aimed to assess the effects of organic amendments in combination with mineral fertilizer on soil-rhizosphere microbiota and their influence on soil health and plant performance. Methods In a short-term greenhouse experiment, the effects of pelletized spent mushroom substrate, with different combinations of biochar and mineral fertilizer, on agricultural soil and performance ofHordeum vulgareL were scrutinized. To evaluate improved soil quality, different soil biological and chemical properties, microbial activity, bacterial diversity and plant performance were assessed. Results Plant performance increased across all fertilizer combinations. Bacterial beta-diversity changed from the initial to the final sampling, pointing at a strong influence of plant development on the rhizosphere with increasing abundances ofAcidobacteriaand decreasing abundances ofActinobacteria, Chloroflexi, andBacteroidetes. Microbial activity (FDA), potential enzyme activity and metabolic diversity of the microbial community (BIOLOG) were not affected by the amendments, whereas bacterial community structure changed on family level, indicating functional redundancy. Treatments containing biochar and the highest amount of mineral fertilizer (B_MF140) caused the strongest changes, which were most pronounced for the familiesXanthobacteraceae, Mycobacteriaceae,andHaliangiaceae. Conclusion Applying organic amendments improved plant performance and maintained soil health, contributing to more sustainable crop production. Nevertheless, long-term field studies are recommended to verify the findings of this short-term experiment.
Wissenschaftlicher Artikel
Scientific Article
Schmid, C. ; Reichel, R. ; Schröder, P. ; Brüggemann, N. ; Schloter, M.
Sci. Total Environ. 745:140955 (2020)
Opencast mining for lignite continuously creates areas of land that require restoration. Here we applied a chronosequence approach to investigate the development of soil bacterial communities during 52 years as influenced by the restoration process and subsequent changes in soil physico-chemical conditions starting from the initial reclamation of the sites. By comparison with the unaffected soils near the mine, we were able to address the question if soil bacterial communities have reached a steady state within 52 years, which is comparable to the original soil. Our study revealed three distinct phases of the restoration process, each with a specific bacterial community composition. The effect size of these changes was similar to the one observed for seasonal dynamics at our sites. At the beginning of the restoration process Flavobacteriaceae, Cytophagaceae and Sphingobacteriaceae were found as typical members of the bacterial community as well as Rhizobiales as a result of the cultivation of alfalfa on the restored plots. At later stage the families Peptostreptococcaceae, Desulfurellaceae as well as Streptomycetaceae increased in relative abundance and became dominant members of the bacterial community. Even though overall bacterial abundance and richness exhibited values comparable to the original soil already 5 years after the start of the restoration process, main responder analyses reveal differences in the bacterial community structure even 52 years after the start of the restoration process. Mostly Nitrospirae were reduced in abundance in the soils restored for 52 years compared to the original soils. To broaden the significance of our study, we compared our data bioinformatically with published results from other restored areas, which were previously affected by opencast mining. Despite different durations of the different restoration phase, we could observe a large degree of conformity when bacterial patterns of succession were compared indicating common modes of action of ecological restoration tools for bacterial communities.
Wissenschaftlicher Artikel
Scientific Article
Berg, G. ; Rybakova, D. ; Fischer, D. ; Cernava, T. ; Vergès, M.C.C. ; Charles, T. ; Chen, X. ; Cocolin, L. ; Eversole, K. ; Corral, G.H. ; Kazou, M. ; Kinkel, L. ; Lange, L. ; Lima, N. ; Loy, A. ; Macklin, J.A. ; Maguin, E. ; Mauchline, T. ; McClure, R. ; Mitter, B. ; Ryan, M. ; Sarand, I. ; Smidt, H. ; Schelkle, B. ; Roume, H. ; Kiran, G.S. ; Selvin, J. ; Souza, R.S.C.d. ; van Overbeek, L. ; Singh, B.K. ; Wagner, M. ; Walsh, A. ; Sessitsch, A. ; Schloter, M.
Microbiome 8:103 (2020)
The field of microbiome research has evolved rapidly over the past few decades and has become a topic of great scientific and public interest. As a result of this rapid growth in interest covering different fields, we are lacking a clear commonly agreed definition of the term "microbiome." Moreover, a consensus on best practices in microbiome research is missing. Recently, a panel of international experts discussed the current gaps in the frame of the European-funded MicrobiomeSupport project. The meeting brought together about 40 leaders from diverse microbiome areas, while more than a hundred experts from all over the world took part in an online survey accompanying the workshop. This article excerpts the outcomes of the workshop and the corresponding online survey embedded in a short historical introduction and future outlook. We propose a definition of microbiome based on the compact, clear, and comprehensive description of the term provided by Whipps et al. in 1988, amended with a set of novel recommendations considering the latest technological developments and research findings. We clearly separate the terms microbiome and microbiota and provide a comprehensive discussion considering the composition of microbiota, the heterogeneity and dynamics of microbiomes in time and space, the stability and resilience of microbial networks, the definition of core microbiomes, and functionally relevant keystone species as well as co-evolutionary principles of microbe-host and inter-species interactions within the microbiome. These broad definitions together with the suggested unifying concepts will help to improve standardization of microbiome studies in the future, and could be the starting point for an integrated assessment of data resulting in a more rapid transfer of knowledge from basic science into practice. Furthermore, microbiome standards are important for solving new challenges associated with anthropogenic-driven changes in the field of planetary health, for which the understanding of microbiomes might play a key role.
Review
Review
Wahman, R. ; Graßmann, J. ; Sauvetre, A. ; Schröder, P. ; Letzel, T.
J. Pharm. Biomed. Anal. 188:113362 (2020)
Plant metabolomic studies cover a broad band of compounds, including various functional groups with different polarities and other physiochemical properties. For this reason, specific optimized methods are needed in order to enable efficient and non-destructive extraction of molecules over a large range of LogD values. This study presents a simple and efficient extraction procedure for Lemna minor samples demonstrating polarity extension of the molecular range. The Lemna samples chosen were kept under the following storage conditions: 1) fresh, 2) stored for a few days at -80 degrees C, and 3) stored for 6 months at -80 degrees C. The samples were extracted using five specifically chosen solvents: 100 % ethanol, 100 % methanol (MeOH), acidic 90 % MeOH (MeOH-water-formic acid (FAC) (90:9.5:0.5, v/v/v), MeOH-water (50:50, v/v), and 100 % water. The final extraction procedure was conducted subject to three solvent conditions, and the subsequent polarity-extended analysis was applied for Lemna minor samples using RPLC-HILIC-ESI-TOF-MS. The extraction yield is in descending order (acidic 90 % MeOH), 50 % MeOH, 100 % water and 100 % MeOH. The results displayed significant molecular differences, both in the extracts investigated and in the fresh Lemna samples, compared to stored samples, in terms of the extraction yield and reducing contents as well as the number of features. The storage of Lemna minor resulted in changes to the fingerprint of its metabolites as the reducing contents increased. The comparisons enable a direct view of molecule characterizations, in terms of their polarity, molecular mass, and signal intensity. This parametric information would appear ideal for further statistical data analysis. Consequently, the extraction procedure and the analysis/data evaluation are highly suitable for the so-called extended-polarity non-target screening procedure.
Wissenschaftlicher Artikel
Scientific Article
Vidal, A. ; Schucknecht, A. ; Toechterle, P. ; Andrade Linares, D.R. ; Garcia-Franco, N. ; Von Heßberg, A. ; Krämer, A. ; Sierts, A. ; Fischer, A. ; Willibald, G. ; Fuetterer, S. ; Ewald, J. ; Baumert, V. ; Weiss, M. ; Schulz, S. ; Schloter, M. ; Bogacki, W. ; Wiesmeier, M. ; Mueller, C.W. ; Dannenmann, M.
Agric. Ecosyst. Environ. 300:107008 (2020)
Grazed alpine pastures have shaped landscapes of the European Alps for millennia, but have partially been abandoned since the 1950s. Re-grazing of abandoned pastures could preserve this cultural landscape with its high species diversity, but also alter soil carbon and nitrogen cycles, as well as microbial communities, potentially affecting ecosystem services (e.g., water purification, carbon and nitrogen storage). However, there is a lack of information on the resistance of soil characteristics to re-grazing effects. After characterising the distribution of vegetation types of an abandoned pasture in the German Alps, we investigated short-term effects of re-grazing on soil organic carbon and nitrogen biochemistry, soil microbial communities, and water quality along a gradient of grazing intensity. The abandoned grassland studied presented a remarkably high diversity of species and habitats even 60 years after abandonment. It was also found to be particularly rich in terms of microbial biomass, as well as in soil carbon and nitrogen. A few months after re-grazing started, extractable organic carbon, gross nitrogen mineralisation rates and inorganic nitrogen concentrations were increased only in intensively grazing-affected areas with bare soil (i.e. concentration of cows with excreta inputs), which insignificantly contributed to the overall area. Re-grazing did not affect the microbial abundance, whatever the grazing intensity, but induced a community shift towards a smaller proportion of fungi compared to bacteria and an increase of ammonia oxidizers (archaea/bacteria) under bare soil conditions. Concentrations of dissolved organic carbon and nitrate in the draining creek remained very low. Overall, re-grazing of pastures in the first season had very limited effects on microbial communities and associated carbon and nitrogen turnover and concentrations, highlighting the resistance of the studied alpine soils to extensive re-grazing. Our results indicate how to develop sustainable management strategies that preserve alpine pastures from degradation.
Wissenschaftlicher Artikel
Scientific Article
Ramm, E. ; Liu, C. ; Wang, X. ; Yue, H. ; Zhang, W. ; Pan, Y. ; Schloter, M. ; Gschwendtner, S. ; Mueller, C.W. ; Hu, B. ; Rennenberg, H. ; Dannenmann, M.
Adv. Atmos. Sci. 37, DOI: 10.1007/s00376-020-0027-5 (2020)
Sonstiges: Meinungsartikel
Other: Opinion
Wu, X. ; Chen, Z. ; Kiese, R. ; Fu, J. ; Gschwendtner, S. ; Schloter, M. ; Liu, C. ; Butterbach-Bahl, K. ; Wolf, B. ; Dannenmann, M.
Biol. Fertil. Soils 56, 959–972 (2020)
Short-lived pulses of soil nitrous oxide (N2O) emissions during freeze-thaw periods can dominate annual cumulative N2O fluxes from temperate managed and natural soils. However, the effects of freeze thaw cycles (FTCs) on dinitrogen (N-2) emissions, i.e., the dominant terminal product of the denitrification process, and ratios of N-2/N2O emissions have remained largely unknown because methodological difficulties were so far hampering detailed studies. Here, we quantified both N-2 and N2O emissions of montane grassland soils exposed to three subsequent FTCs under two different soil moisture levels (40 and 80% WFPS) and under manure addition at 80% WFPS. In addition, we also quantified abundance and expression of functional genes involved in nitrification and denitrification to better understand microbial drivers of gaseous N losses. Our study shows that each freeze thaw cycle was associated with pulse emissions of both N2O and N-2, with soil N-2 emissions exceeding N2O emissions by a factor of 5-30. Increasing soil moisture from 40 to 80% WFPS and addition of cow slurry increased the cumulative FTC N-2 emissions by 102% and 77%, respectively. For N2O, increasing soil moisture from 40 to 80% WFPS and addition of slurry increased the cumulative emissions by 147% and 42%, respectively. Denitrification gene cnorB and nosZ clade I transcript levels showed high explanatory power for N2O and N-2 emissions, thereby reflecting both N gas flux dynamics due to FTC and effects of different water availability and fertilizer addition. In agreement with several other studies for various ecosystems, we show here for mountainous grassland soils that pulse emissions of N2O were observed during freeze-thaw. More importantly, this study shows that the freeze-thaw N-2 pulse emissions strongly exceeded those of N2O in magnitude, which indicates that N-2 emissions during FTCs could represent an important N loss pathway within the grassland N mass balances. However, their actual significance needs to be assessed under field conditions using intact plant-soil systems.
Wissenschaftlicher Artikel
Scientific Article
Herpell, J.B. ; Schindler, F. ; Bejtović, M. ; Fragner, L. ; Diallo, B. ; Bellaire, A. ; Kublik, S. ; Fösel, B. ; Gschwendtner, S. ; Kerou, M. ; Schloter, M. ; Weckwerth, W.
Front. Microbiol. 11:581 (2020)
The genus Paraburkholderia includes a variety of species with promising features for sustainable biotechnological solutions in agriculture through increasing crop productivity. Here, we present a novel Paraburkholderia isolate, a permanent and predominant member of the Dioscoreae bulbifera (yam family, Dioscoreaceae) phyllosphere, making up to 25% of the microbial community on leaf acumens. The 8.5 Mbp genome of isolate Msb3 encodes an unprecedented combination of features mediating a beneficial plant-associated lifestyle, including biological nitrogen fixation (BNF), plant hormone regulation, detoxification of various xenobiotics, degradation of aromatic compounds and multiple protein secretion systems including both T3SS and T6SS. The isolate exhibits significant growth promotion when applied to agriculturally important plants such as tomato, by increasing the total dry biomass by up to 40%. The open question about the "beneficial" nature of this strain led us to investigate ecological and generic boundaries in Burkholderia sensu lato. In a refined phylogeny including 279 Burkholderia sensu lato isolates strain Msb3 clusters within Clade I Paraburkholderia, which also includes few opportunistic strains that can potentially act as pathogens, as revealed by our ecological meta-data analysis. In fact, we demonstrate that all genera originating from the "plant beneficial and environmental" (PBE) Burkholderia species cluster include opportunists. This indicates that further functional examinations are needed before safe application of these strains in sustainable agricultural settings can be assured.
Wissenschaftlicher Artikel
Scientific Article
Cania, B. ; Vestergaard, G. ; Suhadolc, M. ; Mihelič, R. ; Krauss, M. ; Fliessbach, A. ; Mäder, P. ; Szumełda, A. ; Schloter, M. ; Schulz, S.
Front. Microbiol. 11:568 (2020)
Agro-ecosystems experience huge losses of land every year due to soil erosion induced by poor agricultural practices such as intensive tillage. Erosion can be minimized by the presence of stable soil aggregates, the formation of which can be promoted by bacteria. Some of these microorganisms have the ability to produce exopolysaccharides and lipopolysaccharides that "glue" soil particles together. However, little is known about the influence of tillage intensity on the bacterial potential to produce these polysaccharides, even though more stable soil aggregates are usually observed under less intense tillage. As the effects of tillage intensity on soil aggregate stability may vary between sites, we hypothesized that the response of polysaccharide-producing bacteria to tillage intensity is also determined by site-specific conditions. To investigate this, we performed a high-throughput shotgun sequencing of DNA extracted from conventionally and reduced tilled soils from three tillage system field trials characterized by different soil parameters. While we confirmed that the impact of tillage intensity on soil aggregates is site-specific, we could connect improved aggregate stability with increased absolute abundance of genes involved in the production of exopolysaccharides and lipopolysaccharides. The potential to produce polysaccharides was generally promoted under reduced tillage due to the increased microbial biomass. We also found that the response of most potential producers of polysaccharides to tillage was site-specific, e.g., Oxalobacteraceae had higher potential to produce polysaccharides under reduced tillage at one site, and showed the opposite response at another site. However, the response of some potential producers of polysaccharides to tillage did not depend on site characteristics, but rather on their taxonomic affiliation, i.e., all members of Actinobacteria that responded to tillage intensity had higher potential for exopolysaccharide and lipopolysaccharide production specifically under reduced tillage. This could be especially crucial for aggregate stability, as polysaccharides produced by different taxa have different "gluing" efficiency. Overall, our data indicate that tillage intensity could affect aggregate stability by both influencing the absolute abundance of genes involved in the production of exopolysaccharides and lipopolysaccharides, as well as by inducing shifts in the community of potential polysaccharide producers. The effects of tillage intensity depend mostly on site-specific conditions.
Wissenschaftlicher Artikel
Scientific Article
Thiele-Bruhn, S. ; Schloter, M. ; Wilke, B.-M. ; Beaudette, L.A. ; Martin-Laurent, F. ; Cheviron, N. ; Mougin, C. ; Roembke, J.
Soil 6, 17-34 (2020)
The activity of microorganisms in soil is important for a robust functioning of soil and related ecosystem services. Hence, there is a necessity to identify the composition, diversity, and function of the soil microbiome in order to determine its natural properties, functioning, and operating range as well as to assess eco-toxicological effects due to anthropogenic activities. Numerous microbiological methods currently exist in the literature and new, more advanced methods continue to be developed; however, only a limited number of these methods are standardised. Consequently, there is a need to identify the most promising non-standardised methods for assessing soil quality and to transform them into standards. In agreement with the "Ecosystem Service Approach", new methods should focus more on soil microbial functions, including nutrient cycling and greenhouse gas emission, pest control and plant growth promotion, carbon cycling and sequestration, as well as soil structure development and filter function. The few existing standardised methods available that focus on the function of the soil microbiome mostly include measurements, like basal respiration, enzyme activities, and biodegradation of organic matter, under well-defined conditions in the lab. This paper sets out to summarise and expand on recent discussions within the International Organization for Standardization (ISO), Soil Quality - Biological Characterization sub-committee (ISO TC 190/SC 4), where a need was identified to develop scientifically sound methods which would best fulfil the practical needs of future users for assessing soil quality, going beyond the existing test systems. Of particular note is the current evolution of molecular methods in microbial ecology that use quantitative real-time PCR (qPCR) to produce a large number of new functional endpoints which are more sensitive as compared to "classical" methods. Quantitative PCR assesses the abundance of microbes that catalyse major transformation steps in nitrogen and phosphorus cycling, greenhouse gas emissions, chemical transformations including pesticide degradation, and plant growth promotion pathways based on the assessment of marker gene sequences that drive the related processes. In the assessment of soil quality methods, it was found that most methods focus on bacteria and related endpoints. Techniques to describe fungal communities as well as their functional traits are far less represented. As such, techniques to analyse fungal enzyme activities are proposed. Additionally, methods for the determination of microbial growth rates and efficiencies, including the use of glomalin as a biochemical marker for soil aggregation, are discussed. Furthermore, field methods indicative of carbon turnover, including the litter bag test and a modification to the tea bag test, are presented. However, it is obvious that with increasing developments in high throughput sequencing technologies and big data analyses, including metagenomics analysis, it will be possible to implement these technologies into the standardisation process for assessing the functions of the soil microbiome. Overall, it is suggested that endpoints should represent a potential function of soil microorganisms rather than actual activity levels, as the latter can largely be dependent on short-term variable soil properties such as pedoclimatic conditions, nutrient availability, and anthropogenic soil cultivation activities.
Review
Review
Ghirardo, A. ; Lindstein, F. ; Koch, K. ; Buegger, F. ; Schloter, M. ; Albert, A. ; Michelsen, A. ; Winkler, J.B. ; Schnitzler, J.-P. ; Rinnan, R.
Glob. Change Biol. 26, 1908-1925 (2020)
Warming occurs in the Arctic twice as fast as the global average, which in turn leads to a large enhancement in terpenoid emissions from vegetation. Volatile terpenoids are the main class of biogenic volatile organic compounds (VOCs) that play crucial roles in atmospheric chemistry and climate. However, the biochemical mechanisms behind the temperature-dependent increase in VOC emissions from subarctic ecosystems are largely unexplored. Using 13 CO2 -labeling, we studied the origin of VOCs and the carbon (C) allocation under global warming in the soil-plant-atmosphere system of contrasting subarctic heath tundra vegetation communities characterized by dwarf shrubs of the genera Salix or Betula. The projected temperature rise of the subarctic summer by 5°C was realistically simulated in sophisticated climate chambers. VOC emissions strongly depended on the plant species composition of the heath tundra. Warming caused increased VOC emissions and significant changes in the pattern of volatiles toward more reactive hydrocarbons. The 13 C was incorporated to varying degrees in different monoterpene and sesquiterpene isomers. We found that de novo monoterpene biosynthesis contributed to 40%-44% (Salix) and 60%-68% (Betula) of total monoterpene emissions under the current climate, and that warming increased the contribution to 50%-58% (Salix) and 87%-95% (Betula). Analyses of above- and belowground 12/13 C showed shifts of C allocation in the plant-soil systems and negative effects of warming on C sequestration by lowering net ecosystem exchange of CO2 and increasing C loss as VOCs. This comprehensive analysis provides the scientific basis for mechanistically understanding the processes controlling terpenoid emissions, required for modeling VOC emissions from terrestrial ecosystems and predicting the future chemistry of the arctic atmosphere. By changing the chemical composition and loads of VOCs into the atmosphere, the current data indicate that global warming in the Arctic may have implications for regional and global climate and for the delicate tundra ecosystems.
Wissenschaftlicher Artikel
Scientific Article
Zhu, B. ; Wang, Z. ; Kublik, S. ; Ge, T. ; Casper, P. ; Schloter, M. ; Lueders, T.
Microb. Ecol. 80, 243-247 (2020)
Microorganisms play an essential role in nitrogen cycling and greenhouse gas emissions in soils and sediments. The recently discovered oxygenic denitrifiers are proposed to reduce nitrate and nitrite via nitric oxide dismutation directly to N-2 and O-2. So far, the ecological role of these microbes is not well understood. The only available tool for a targeted study of oxygenic denitrifiers is their respective maker gene, nitric oxide dismutase (nod). Here, we established the use of PacBio long-read sequencing of nod gene amplicons to study the diversity and community structure of oxygenic denitrifiers. Two distinct sets of environmental samples, agricultural soil and lake sediment, were investigated as examples. The circular consensus sequences (ca 1.0 kb) obtained covered most substitution characteristic of NO dismutase and allowed for reliable classification of oxygenic denitrifiers. Distinct nod gene pools and community structure were revealed for the different habitats, with most sequence types affiliated to yet unidentified environmental nod lineages. The abundance of nod genes ranged 2.2 x 10(6)-3.2 x 10(7) gene copies g(-1) soil or sediment, accounting for up to 3% of total bacterial 16S rRNA gene counts. This study indicates that nod-gene-targeted long-read sequencing can be a powerful tool for studying the ecology of these novel microbes, and the results also suggest that oxygenic denitrifiers are prevalent and abundant in different terrestrial samples, where they could play an important, but yet overlooked role in nitrogen transformations.
Wissenschaftlicher Artikel
Scientific Article
Santos, S.S. ; Schöler, A. ; Nielsen, T.K. ; Hansen, L.H. ; Schloter, M. ; Winding, A.
Sci. Total Environ. 717:137228 (2020)
Soil biodiversity is threatened by intensification of land use. The consequences of different land use on belowground biodiversity remain insufficiently explored for soil protists. Alongside being abundant and extremely diverse in soil, protists provide many ecosystem services: key players in the microbial loop, turnover of organic matter and stimulation of plant growth-promoting rhizobacteria. However, we lack knowledge of effects of site, land use intensity and management on diversity of soil profists. Here we assessed protist communities in four European arable sites with contrasting land use intensities at each site: Lusignan, France; Moskanjci, Slovenia; Castro Verde, Portugal and Scheyem, Germany as well as two grassland sites: Hainich, Germany and Lancaster, UK. Each site has consistent agricultural management history of low and high land use intensities quantified in terms of land use index (LUI). We employed high-throughput sequencing of environmental DNA, targeting the V4 region of the 18S rRNA gene. By assigning the protist composition to trophic groups, we inspected for effects of management, and other biotic and abiotic variables. While overall protist richness was unaffected by LUI within sites, specific trophic groups such as plant pathogens and saprotrophs were affected. Effects on protist biome across land uses and sites were also observed. LUI sensitive taxa were taxonomically diverse in each plot, and their trophic groups responded in specific patterns to specific practices. The most abundant trophic group was phagotrophs (73%), followed by photoautotrophs (16%), plant pathogens (4%), animal parasites (2%) and saprotrophs (1%). Community compositions and factors affecting the structure of individual trophic groups differed between land uses and management systems. The agricultural management selected for distinct protist populations as well as specific functional traits, and the protist community and diversity were indeed affected by site, LUI and management, which indicates the ecological significance of protists in the soil food web. (C) 2020 Elsevier B.V. All rights reserved.
Wissenschaftlicher Artikel
Scientific Article
Techen, A.K. ; Helming, K. ; Brüggemann, N. ; Veldkamp, E. ; Reinhold-Hurek, B. ; Lorenz, M. ; Bartke, S. ; Heinrich, U. ; Amelung, W. ; Augustin, K. ; Boy, J. ; Corre, M. ; Duttman, R. ; Gebbers, R. ; Gentsch, N. ; Grosch, R. ; Guggenberger, G. ; Kern, J. ; Kiese, R. ; Kuhwald, M. ; Leinweber, P. ; Schloter, M. ; Wiesmeier, M. ; Winkelmann, T. ; Vogel, H.J.
In:. 125 London Wall, London Ec2y 5as, England: Academic Press Ltd-elsevier Science Ltd, 2020. 179-240 (Adv. Agron. ; 161)
Agricultural management is a key force affecting soil processes and functions. Triggered by biophysical constraints as well as rapid structural and technological developments, new management practices are emerging with largely unknown impacts on soil processes and functions. This impedes assessments of the potential of such emerging practices for sustainable intensification, a paradigm coined to address the growing demand for food and nonfood products. In terms of soil management, sustainable intensification means that soil productivity is increased while other soil functions and services, such as carbon storage and habitat for organisms, are simultaneously maintained or even improved. In this paper we provide an overview of research challenges to better understand how emerging soil management practices affect soil processes and functions. We distinguish four categories of soil management practices: spatial arrangements of cropping systems, crops and rotations, mechanical pressures, and inputs into the soil. Key research needs identified for each include nutrient efficiency in agroforestry versus conventional cropping systems, soil-rhizosphere microbiome elucidation to understand the interacting roles of crops and rotations, the effects of soil compaction on soil–plant–atmosphere interactions, and the ecotoxicity of plastics, pharmaceuticals and other pollutants that are introduced into the soil. We establish an interdisciplinary, systemic approach to soil science and include cross-cutting research activities related to process modeling, data management, stakeholder interaction, sustainability assessment and governance. The identification of soil research challenges from the perspective of agricultural management facilitates cooperation between different scientific disciplines in the field of sustainable agricultural production.
Vuko, M. ; Cania, B. ; Vogel, C. ; Kublik, S. ; Schloter, M. ; Schulz, S.
Microb. Biotechnol. 13, 584-598 (2020)
Polymeric substances produced by microbes play a key role for the development of soil aggregates. Here, we investigated the dynamics of bacterial families contributing to the formation of exopolysaccharides and lipopolysaccharides, major constituents of polymeric substances, at a managed land reclamation site of a post-mining area. We collected soil samples from the initial and the agricultural management phase and expected a peak in the abundance of bacteria capable for exopolysaccharide and lipopolysaccharide production at the points of the biggest disturbances. We used shotgun metagenomic sequencing in combination with measurements of exopolysaccharide concentrations. Our results underline the importance of exopolysaccharide and lipopolysaccharide-producing bacteria after nutrient input combined with structural disturbance events, caused here by the initial planting of alfalfa and the introduction of a tillage regime together with organic fertilization in the agricultural management phase. Moreover, the changes in management caused a shift in the exopolysaccharide/lipopolysaccharide-producing community. The initial phase was dominated by typical colonizers of oligotrophic environments, specifically nitrogen fixers (Rhizobiaceae, Comamonadaceae, Hyphomicrobiaceae), while bacteria common in agricultural soils, such as Sphingomonadaceae, Oxalobacteraceae and Nitrospiraceae, prevailed in the agricultural management phase.
Wissenschaftlicher Artikel
Scientific Article
Sauvetre, A. ; Wegrzyn, A. ; Yang, L. ; Vestergaard, G. ; Miksch, K. ; Schröder, P. ; Radl, V.
Environ. Sci. Pollut. Res. 27, 11892–11904 (2020)
This study investigates how wastewater containing 2 mg l(-1) of sulfamethoxazole (SMX) and 2 mg l(-1) of diclofenac (DCF) affects the composition of bacterial communities present in the roots and rhizomes of Miscanthus x giganteus plants grown in laboratory-scale constructed wetlands. Bacterial communities in plant roots and rhizomes were identified in treated and control samples by 16S rRNA amplicon sequencing. Moreover, bacterial endophytes were isolated in R2A and 1/10 869 media and screened for their ability to metabolize SMX and DCF in liquid medium by HPLC. Our results show significant changes in the abundance of main genera, namely Sphingobium and Streptomyces between control and treated plants. Around 70% of the strains isolated from exposed plants belonged to the phylum Actinobacteria and were classified as Streptomyces, Microbacterium, and Glycomyces. In non-exposed plants, Proteobacteria represented 43.5% to 63.6% of the total. We identified 17 strains able to remove SMX and DCF in vitro. From those, 76% were isolated from exposed plants. Classified mainly as Streptomyces, they showed the highest SMX (33%) and DCF (41%) removal efficiency. These isolates, alone or in combination, might be used as bio-inoculants in constructed wetlands to enhance the phytoremediation of SMX and DCF during wastewater treatment.
Wissenschaftlicher Artikel
Scientific Article
Laffite, A. ; Florio, A. ; Andrianarisoa, K.S. ; des Chatelliers, C.C. ; Schloter-Hai, B. ; Ndaw, S.M. ; Periot, C. ; Schloter, M. ; Zeller, B. ; Poly, F. ; Le Roux, X.
Environ. Microbiol., DOI: 10.1111/1462-2920.14905 (2020)
Some temperate tree species are associated with very low soil nitrification rates, with important implications for forest N dynamics, presumably due to their potential for biological nitrification inhibition (BNI). However, evidence for BNI in forest ecosystems is scarce so far and the nitrifier groups controlled by BNI-tree species have not been identified. Here, we evaluated how some tree species can control soil nitrification by providing direct evidence of BNI and identifying the nitrifier group(s) affected. First, by comparing 28 year-old monocultures of several tree species, we showed that nitrification rates correlated strongly with the abundance of the nitrite oxidizers Nitrobacter (50- to 1000-fold changes between tree monocultures) and only weakly with the abundance of ammonia oxidizing archaea (AOA). Second, using reciprocal transplantation of soil cores between low and high nitrification stands, we demonstrated that nitrification changed 16 months after transplantation and was correlated with changes in the abundance of Nitrobacter, not AOA. Third, extracts of litter or soil collected from the low nitrification stands of Picea abies and Abies nordmanniana inhibited the growth of Nitrobacter hamburgensis X14. Our results provide for the first time direct evidence of BNI by tree species directly affecting the abundance of Nitrobacter.
Wissenschaftlicher Artikel
Scientific Article
Balazs, H.-E. ; Schmid, C. ; Podar, D. ; Hufnagel, G. ; Radl, V. ; Schröder, P.
Appl. Soil Ecol. 150:103467 (2020)
In order to meet constantly increasing demands for land without damaging pristine environments like forests or grasslands, reclamation and re-purposing of historically contaminated areas should become a priority. Successful reclamation goes hand in hand with the soil functional recovery potential and with resilient microbial communities capable of performing the necessary ecosystem services. In this context, we designed a greenhouse pot experiment as a mock reclamation situation, where traces of lindane at hazard threshold and twice the concentration accepted for waste deposits are left in the soil after conventional clean-up by excavation and land filling. We assessed the effects of lindane at 50 and 100 mg kg(-1) regarding crop growth and nutrient turnover (with focus on the nitrogen cycle) as two key parameters for soil functions. The bulk and rhizosphere soil bacterial community composition were chosen as parameters for soil resilience in lindane contamination conditions. Lindane severely affected plant growth and development. The potential nitrogen fixation, quantified as nifH gene copy number, suffered direct negative effects of lindane contamination in bulk soil, which could represent an additional obstacle for phytoremediation. Changes in rhizosphere bacterial community composition were related to lindane toxic effects towards the plants, which might have supported the growth of opportunists and saprophytes. In bulk soil, the bacterial community shifted towards lindane tolerant taxa like Sphingomonas and Porphyrobacter that are interesting with regard to their applications in bioremediation. We concluded that lindane at hazard threshold concentration left in soil after clean-up has negative effects both soil functionality, and the recovery of the bacterial communities to their original composition when lindane resistant plant crops are not involved.
Wissenschaftlicher Artikel
Scientific Article
Nannipieri, P. ; Ascher-Jenull, J. ; Ceccerini, M.T. ; Pietramellara, G. ; Renella, G. ; Schloter, M.
Pedosphere 30, 5-17 (2020)
Since the advent of sequencing technologies, the determination of microbial diversity to predict microbial functions, which are the major determinants of soil functions, has become a major topic of interest, as evidenced by the 900 publications dealing with soil metagenome published up to 2017. However, the detection of a gene in soil does not mean that the relative function is expressed, and the presence of a particular taxon does not mean that the relative functions determined in pure culture also occur in the studied soil. Another critical step is to link microbial community composition or function to the product analyzed to determine flux rates. Indeed, flux rates might not only be highly dynamic, but several metabolites can depend on different reactions, which makes the link to one process of interest difficult or even impossible. This review also discusses biases caused by sampling, storage of samples, DNA extraction and purification, sequencing (amplicon- vs. metagenome sequencing), and bioinformatic data analysis. Insights and the limits of predicting microbial interactions by network inference methods are critically discussed, and finally, future directions for a better understanding of soil functions by using measurements of microbial diversity are presented.
Review
Review
Zadel, U. ; Nesme, J. ; Michalke, B. ; Vestergaard, G. ; Płaza, G.A. ; Schröder, P. ; Radl, V. ; Schloter, M.
Sci. Total Environ. 711:134433 (2020)
Miscanthus x giganteus is a high biomass producing plant with tolerance to heavy metals. This makes Miscanthus interesting to be used for phytoremediation of heavy metal contaminated areas coupled with energy production. Since plant performance in metal polluted areas is impaired, their growth and phytoremediation effect can be improved with bacterial assistance. To identify positive and negative responders of M. x giganteus associated microbiome influenced by Cd, Pb and Zn stress compared to noncontaminated controls, we designed a greenhouse experiment. Structure of the bacterial community in three rhizocompartments, namely rhizosphere, rhizoplane and root endosphere was analysed using an isolation independent molecular approach based on 16S rRNA gene barcoding. Furthermore, quantitative PCR (qPCR) was used for bacterial biomass estimation. Our results indicated that biomass and total bacterial diversity in rhizosphere, rhizoplane and root endosphere did not significantly change despite of substantial root uptake of heavy metals. Overall, we detected 6621 OTUs, from which 171 were affected by metal addition. Whereas Streptomyces and Amycolatopsis taxa were negatively affected by the heavy metal treatment in endosphere, taxa assigned to Luteolibacter in rhizosphere and rhizoplane (log(2) fold change 1.9-4.1) and Micromonospora in endosphere (log2 fold change 10.2) were found to be significantly enriched and highly abundant (0.1-3.7% relative abundance) under heavy metal stress. Those taxa might be of key importance for M. x giganteus performance under heavy metal pollution and might be interesting candidates for the development of new bioinocula in the future to promote plant growth and phytoremediation in heavy metal contaminated soils. (C) 2019 Elsevier B.V. All rights reserved.
Wissenschaftlicher Artikel
Scientific Article
Milaković, M. ; Vestergaard, G. ; González-Plaza, J.J. ; Petrić, I. ; Kosić-Vukšić, J. ; Senta, I. ; Kublik, S. ; Schloter, M. ; Udiković-Kolić, N.
Sci. Total Environ. 706:136001 (2020)
Environmental discharges of very high (mg/L) antibiotic levels from pharmaceutical production contributed to the selection, spread and persistence of antibiotic resistance. However, the effects of less antibiotic-polluted effluents (mu g/L) from drug-formulation on exposed aquatic microbial communities are still scarce. Here we analyzed formulation effluents and sediments from the receiving creek collected at the discharge site (DW0), upstream (UP) and 3000 m downstream of discharge (DW3000) during winter and summer season. Chemical analyses indicated the largest amounts of trimethoprim (up to 5.08 mg/kg) and azithromycin (up to 039 mg/kg) at DW0, but sulfonamides accumulated at DW3000 (total up to 1.17 mg/kg). Quantitative PCR revealed significantly increased relative abundance of various antibiotic resistance genes (ARGs) against beta-lactams, macrolides, sulfonamides, trimethoprim and tetracyclines in sediments from DW0, despite relatively high background levels of some ARGs already at UP site. However, only sulfonamide (sul2) and macrolide ARG subtypes (mphG and msrE) were still elevated at DW3000 compared to UP. Sequencing of 165 rRNA genes revealed pronounced changes in the sediment bacterial community composition from both DW sites compared to UP site, regardless of the season. Numerous taxa with increased relative abundance at DW0 decreased to background levels at DW3000, suggesting die-off or lack of transport of effluent-originating bacteria. In contrast, various taxa that were more abundant in sediments than in effluents increased in relative abundance at DW3000 but not at DWO, possibly due to selection imposed by high sulfonamide levels. Network analysis revealed strong correlation between some clinically relevant ARGs (e.g. bla(GEs), bki(OXA), ennB, tet39,sul2) and taxa with elevated abundance at DW sites, and known to harbour opportunistic pathogens, such as Acinetobacter, Arcobacter,Aeromonas and Slietvanella. Our results demonstrate the necessity for improved management of pharmaceutical and rural waste disposal for mitigating the increasing problems with antibiotic resistance.
Wissenschaftlicher Artikel
Scientific Article
Bagnoud, A. ; Guye-Humbert, S. ; Schloter-Hai, B. ; Schloter, M. ; Zopfi, J.
FEMS Microbiol. Ecol. 96:fiz191 (2020)
In contrast to the pervasive occurrence of denitrification in soils, anammox (anaerobic ammonium oxidation) is a spatially restricted process that depends on specific ecological conditions. To identify the factors that constrain the distribution and activity of anammox bacteria in terrestrial environments, we investigated four different soil types along a catena with opposing ecological gradients of nitrogen and water content, from an amended pasture to an ombrotrophic bog. Anammox was detected by polymerase chain reaction (PCR) and quantitative PCR (qPCR) only in the nitrophilic wet meadow and the minerotrophic fen, in soil sections remaining water-saturated for most of the year and whose interstitial water contained inorganic nitrogen. Contrastingly, aerobic ammonia oxidizing microorganisms were present in all examined samples and outnumbered anammox bacteria usually by at least one order of magnitude. 16S rRNA gene sequencing revealed a relatively high diversity of anammox bacteria with one Ca. Brocadia cluster. Three additional clusters could not be affiliated to known anammox genera, but have been previously detected in other soil systems. Soil incubations using N-15-labeled substrates revealed that anammox processes contributed about <2% to total N-2 formation, leaving nitrification and denitrification as the dominant N-removal mechanism in these soils that represent important buffer zones between agricultural land and ombrotrophic peat bogs.
Wissenschaftlicher Artikel
Scientific Article
Obermeier, M. ; Durai Raj, A.C. ; Obermeier, W.A. ; Schmid, C. ; Balazs, H.-E. ; Schröder, P. ; Gnädinger, F.
Sci. Total Environ. 703:135494 (2020)
Projected population growth and climate change will make it inevitable to convert neglected and marginal land into productive arable land. We investigate the influence of agricultural management practices on nutrient stocks and soil functions during the conversion of former extensively used grassland to arable land. Effects of grassland removal, tillage, intercropping with faba bean (Vicia faba) and its later incorporation were studied with respect to soil properties and bacterial community structure. Therefore, composite samples were collected with a core sampler from the topsoil (0-20 cm) in (a) the initial grassland, (b) the transitional phase during the vegetation period of V. faba, (c) after ploughing the legume in, and (d) untreated controls. In all samples, nitrate-N, ammonium-N, dissolved organic carbon (DOC) and total nitrogen bound (TNb) were analyzed and comparisons of the bacterial community structure after 16S-amplicon sequencing were performed to assess soil functions. Mineralization after grassland conversion followed by the biological nitrogen fixation of broad beans enhanced the nitrate-N content in bulk soil from 4 to almost 50 mu g N g(-1) dw. Bacterial community structure on phylum level in bulk soil was dominated by Proteobacteria, Actinobacteria, Acidobacteria, Chloroflexi, and Bacteroidetes and remained almost stable. However, alpha and beta-diversity analysis revealed a change of the bacterial composition at the final state of the conversion. This change was primarily driven by increasing abundances of the genera Massilia and Lysobacter, both members of the Proteobacteria, after the decay of the leguminous plant residues. Furthermore, increasing abundances of the family Gaiellaceae and its genus Gaiella fostered this change and were related to the decreasing carbon to nitrogen ratio. In short, gentle management strategies could replace the input of mineral fertilizer with the aim to contribute to future sustainable and intensified production even on converted grassland.
Wissenschaftlicher Artikel
Scientific Article
Mrkonjic Fuka, M. ; Tanuwidjaja, I. ; Zgomba Maksimovic, A. ; Zunabovic-Pichler, M. ; Kublik, S. ; Hulak, N. ; Domig, K.J. ; Schloter, M.
LWT 118, DOI: 10.1016/j.lwt.2019.108782 (2020)
Bacterial communities associated with the ripening process in artisanal wild boar and deer meat sausages were investigated by molecular barcoding using the 16S rRNA gene as a marker. A core microbiota shared by 83.54% of the samples indicated remarkable level of Lactobacillus sake/and Lactobacillus curvatus, accounting for 20.55% in initial and 70.48% in final products as well as spoilage-associated bacteria including Stenotrophomonas, Bacillus, Pseudomonas, Carnobacterium and Brochothrbc, with an average abundance 44.15% at the beginning and 13.98% at the end of the production. Of selected LAB isolates (n = 555), 43.83% were not suitable for food application due to the antibiotic resistance or the presence of the tric gene. Most of the strains designated as safe were able to grow at 25 degrees C even in the presence of 3.0 and 6.0% of NaCl or pH 4.5, but exposure to the same stressors resulted in growth reduction at 12 degrees C. Acidification and antimicrobial activity were found in 65.62% and 37.50% of strains, respectively. Most of the strains showed lipolytic and proteolytic activity, but only 9.37% were able to degrade sarcoplasmic proteins. These results give important information for the development of new starter formulation for the production of high quality game meat sausages.
Wissenschaftlicher Artikel
Scientific Article
Cania, B. ; Vestergaard, G. ; Kublik, S. ; Köhne, J.M. ; Fischer, T. ; Albert, A. ; Winkler, J.B. ; Schloter, M. ; Schulz, S.
Microb. Ecol. 79, 326-341 (2020)
Biological soil crusts (biocrusts) play an important role in improving soil stability and resistance to erosion by promoting aggregation of soil particles. During initial development, biocrusts are dominated by bacteria. Some bacterial members of the biocrusts can contribute to the formation of soil aggregates by producing exopolysaccharides and lipopolysaccharides that act as "glue" for soil particles. However, little is known about the dynamics of "soil glue" producers during the initial development of biocrusts. We hypothesized that different types of initial biocrusts harbor distinct producers of adhesive polysaccharides. To investigate this, we performed a microcosm experiment, cultivating biocrusts on two soil substrates. High-throughput shotgun sequencing was used to obtain metagenomic information on microbiomes of bulk soils from the beginning of the experiment, and biocrusts sampled after 4 and 10 months of incubation. We discovered that the relative abundance of genes involved in the biosynthesis of exopolysaccharides and lipopolysaccharides increased in biocrusts compared with bulk soils. At the same time, communities of potential "soil glue" producers that were highly similar in bulk soils underwent differentiation once biocrusts started to develop. In the bulk soils, the investigated genes were harbored mainly by Betaproteobacteria, whereas in the biocrusts, the major potential producers of adhesive polysaccharides were, aside from Alphaproteobacteria, either Cyanobacteria or Chloroflexi and Acidobacteria. Overall, our results indicate that the potential to form exopolysaccharides and lipopolysaccharides is an important bacterial trait for initial biocrusts and is maintained despite the shifts in bacterial community composition during biocrust development.
Wissenschaftlicher Artikel
Scientific Article
2019
Kovacevic, D. ; Bartel, S. ; Pfeiffer, S. ; Schloter, M. ; Krauss-Etschmann, S.
Eur. Respir. J. 54 (2019)
Meeting abstract
Meeting abstract
Wahman, R. ; Grassmann, J. ; Schröder, P. ; Letzel, T.
LC GC N. Am. 37, 8-15 (2019)
In the field of metabolomics, researchers seek to acquire almost complete information about the metabolic composition of a sample to provide fundamental information about the cellular state of organisms. In metabolomics analysis today, typically reversed-phase (RP) liquid chromatography (LC) is coupled with specific, sensitive, and robust mass spectrometry (MS). That approach, however, misses many moderately polar, and all very polar, compounds; this situation is a problem in plant metabolomics, because plant metabolites are mainly water-soluble species and thus very polar. Here, we describe new developments in polarity-extended separations using the serial coupling of reversed-phase LC and hydrophilic-interaction chromatography (HILIC) separation steps, in combination with electrospray ionization-time-of-flight-mass spectrometry (ESI-TOF-MS), and the application of this approach to plant metabolomics. The resulting retention time versus mass plots are molecular fingerprints, as well as sources of further molecular descriptors. Extraction methods, molecular analysis, and data evaluation have to be adapted to the matrix under consideration. Representative strategies using this polarity extending approach, following so-called suspects and nontargeted screening approaches, are presented.
Wissenschaftlicher Artikel
Scientific Article
Radl, V. ; Winkler, J.B. ; Kublik, S. ; Yang, L. ; Winkelmann, T. ; Vestergaard, G. ; Schröder, P. ; Schloter, M.
Environ. Microbiome 14:9 (2019)
Following publication of the original article [1], the authors advised that their article had published with an error in the title. The title read "Reduced microbial potential for the degradation of phenolic compounds in the rhizosphere of apples seedlings grown in soils affected by replant disease". While the correct title is "Reduced microbial potential for the degradation of phenolic compounds in the rhizosphere of apple plantlets grown in soils affected by replant disease". That is, the title referred to 'seedlings' in place of 'plant lets', which was the incorrect term because clonal plantlets (from the apple rootstock M26) were used, not seedlings. The title has since been corrected in the original article. The authors apologize for any inconvenience caused.
Eisenhauer, N. ; Bonkowski, M. ; Brose, U. ; Buscot, F. ; Durka, W. ; Ebeling, A. ; Fischer, M. ; Gleixner, G. ; Heintz-Buschart, A. ; Hines, J. ; Jesch, A. ; Lange, M. ; Meyer, S. ; Roscher, C. ; Scheu, S. ; Schielzeth, H. ; Schloter, M. ; Schulz, S. ; Unsicker, S. ; van Dam, N.M. ; Weigelt, A. ; Weisser, W.W. ; Wirth, C. ; Wolf, J. ; Schmid, B.
RIO 5:e47042 (2019)
The functioning and service provisioning of ecosystems in the face of anthropogenic environmental and biodiversity change is a cornerstone of ecological research. The last three decades of biodiversity–ecosystem functioning (BEF) research have provided compelling evidence for the significant positive role of biodiversity in the functioning of many ecosystems. Despite broad consensus of this relationship, the underlying ecological and evolutionary mechanisms have not been well understood. This complicates the transition from a description of patterns to a predictive science. The proposed Research Unit aims at filling this gap of knowledge by applying novel experimental and analytical approaches in one of the longest-running biodiversity experiments in the world: the Jena Experiment. The central aim of the Research Unit is to uncover the mechanisms that determine BEF relationships in the short- and in the long-term. Increasing BEF relationships with time in long-term experiments do not only call for a paradigm shift in the appreciation of the relevance of biodiversity change, they likely are key to understanding the mechanisms of BEF relationships in general. The subprojects of the proposed Research Unit fall into two tightly linked main categories with two research areas each that aim at exploring variation in community assembly processes and resulting differences in biotic interactions as determinants of the long-term BEF relationship. Subprojects under “Microbial community assembly” and “Assembly and functions of animal communities” mostly focus on plant diversity effects on the assembly of communities and their feedback effects on biotic interactions and ecosystem functions. Subprojects under “Mediators of plant-biotic interactions” and “Intraspecific diversity and micro-evolutionary changes” mostly focus on plant diversity effects on plant trait expression and micro-evolutionary adaptation, and subsequent feedback effects on biotic interactions and ecosystem functions. This unification of evolutionary and ecosystem processes requires collaboration across the proposed subprojects in targeted plant and soil history experiments using cutting-edge technology and will produce significant synergies and novel mechanistic insights into BEF relationships. The Research Unit of the Jena Experiment is uniquely positioned in this context by taking an interdisciplinary and integrative approach to capture whole-ecosystem responses to changes in biodiversity and to advance a vibrant research field.
Wissenschaftlicher Artikel
Scientific Article
Herzog, C. ; Honegger, A. ; Hegglin, D. ; Wittwer, R. ; de Ferron, A. ; Verbruggen, E. ; Jeanneret, P. ; Schloter, M. ; Banerjee, S. ; van der Heijden, M.G.A.
Agric. Ecosyst. Environ. 284:106596 (2019)
Organic farming is gaining importance in view of its beneficial effects on soil quality, environmental performance and biodiversity. However, it is still unclear how organic management performs over time and whether the duration of organic management influences crop yield and ecosystem functioning. Here we compared 34 fields in Swiss farms assigned to four groups: 1) conventionally managed farms; 2) farms in transition to organic farming (in the 1st - 3rd year); 3) farms converted moderately long ago (9-13 years); and 4) farms subjected to long-term organic farming (15-32 years). We selected one field per farm and examined in two subsequent years whether management practices (conventional vs. organic farming) and the duration of organic management affected crop yield, weed cover, soil fertility and biodiversity as well as the overall system performance, assessed as ecosystem multifunctionality. Maize yield (-6.0%) and wheat yield (-22.2%) decreased in organic compared to conventional fields. However, the duration of organic management did not affect crop yield. There was also no effect of the duration of organic management on weed cover but it was much higher under organic management, with mean values of 33.0% in organic compared to 2.0% in conventional fields in maize, and 13.4% compared to 1.2% in wheat, respectively. Soil fertility and microbial activities were not significantly different between management practices, which might be due to the large variation among fields. Root colonization of arbuscular mycorrhizal fungi increased (+19.7%) under organic management in wheat. Overall, this study demonstrates a rapid shift of agro-ecological functions after conversion to organic farming and that the duration of organic management has no impact on crop yield, weed cover and soil fertility.
Wissenschaftlicher Artikel
Scientific Article
Berauer, B.J. ; Wilfahrt, P.A. ; Arfin-Khan, M.A.S. ; Eibes, P. ; Von Heßberg, A. ; Ingrisch, J. ; Schloter, M. ; Schuchardt, M.A. ; Jentsch, A.
Arctic Antarc. Alpine Res. 51, 215-231 (2019)
High-elevation ecosystems will experience increasing periods of above-average warmth and altered precipitation changes because of climate change. This causes uncertainties for community properties such as productivity and biodiversity. Increasing temperature may increase productivity by increasing growing season length and metabolic rate or decrease productivity by causing drought stress. Competitive outcomes between species may change with altered climatic conditions, causing shifts in community composition. This study investigates the resistance of aboveground biomass and plant community composition of montane and alpine grassland ecosystems to abruptly altered temperature and precipitation conditions. Intact plant-soil communities were translocated downslope spanning an elevational gradient of 2,090 m in the European Alps. We hypothesize that increasing temperature leads to (1) increased aboveground biomass in the absence of precipitation deficits, (2) decreased species richness, and (3) shifts in plant community composition. After one year of exposure to their new environment, aboveground biomass changes appeared to be dependent on precipitation regimes, whereas species richness declined consistently with changed climatic conditions. No deterministic shift in community composition was found. Abrupt changes in climatic conditions can lead to rapid responses of community properties, indicating that these high-elevation communities may have low initial resistance to future heat waves and droughts.
Wissenschaftlicher Artikel
Scientific Article
Frank, U. ; Kublik, S. ; Mayer, D. ; Engel, M. ; Schloter, M. ; Durner, J. ; Gaupels, F.
BMC Plant Biol. 19:539 (2019)
Background: Nitrogen dioxide (NO2) triggers hypersensitive response (HR)-like cell death in Arabidopsis thaliana. A high-throughput mutant screen was established to identify genes involved in this type of programmed cell death.Results: Altogether 14,282 lines of SALK T-DNA insertion mutants were screened. Growing 1000 pooled mutant lines per tray and simultaneous NO2 fumigation of 4 trays in parallel facilitated high-throughput screening. Candidate mutants were selected based on visible symptoms. Sensitive mutants showed lesions already after fumigation for 1 h with 10 ppm (ppm) NO2 whereas tolerant mutants were hardly damaged even after treatment with 30 ppm NO2. Identification of T-DNA insertion sites by adapter ligation-mediated PCR turned out to be successful but rather time consuming. Therefore, next generation sequencing after T-DNA-specific target enrichment was tested as an alternative screening method. The targeted genome sequencing was highly efficient due to (1.) combination of the pooled DNA from 124 candidate mutants in only two libraries, (2.) successful target enrichment using T-DNA border-specific 70mer probes, and (3.) stringent filtering of the sequencing reads. Seventy mutated genes were identified by at least 3 sequencing reads. Ten corresponding mutants were re-screened of which 8 mutants exhibited NO2-sensitivity or -tolerance confirming that the screen yielded reliable results. Identified candidate genes had published functions in HR, pathogen resistance, and stomata regulation.Conclusions: The presented NO2 dead-or-alive screen combined with next-generation sequencing after T-DNAspecific target enrichment was highly efficient. Two researchers finished the screen within 3 months. Moreover, the target enrichment approach was cost-saving because of the limited number of DNA libraries and sequencing runs required. The experimental design can be easily adapted to other screening approaches e.g. involving high-throughput treatments with abiotic stressors or phytohormones.
Wissenschaftlicher Artikel
Scientific Article
Radl, V. ; Winkler, J.B. ; Kublik, S. ; Yang, L. ; Winkelmann, T. ; Vestergaard, G. ; Schröder, P. ; Schloter, M.
Environ. Microbiome 14:8 (2019)
Background: Apple replant disease (ARD) is a syndrome that occurs in areas where apple plants or closely related species have been previously cultivated. Even though ARD is a well-known phenomenon, which has been observed in different regions worldwide and occurs independent of the soil type, its causes still remain unclear.Results: As expected, the biomass of plants grown in replant soil was significantly lower compared to those grown in control (virgin) soil. A shotgun metagenome analysis showed a clear differentiation between the rhizosphere and bulk soil compartments independent from the soil used. However, significant differences associated with apple replant disease were only observed in the rhizosphere compartment, for which we detected changes in the abundance of major bacterial genera. Interestingly, reads assigned to Actinobacteria were significantly reduced in relative abundance in rhizosphere samples of the soil affected by replant disease. Even though reads assigned to pathogenic fungi were detected, their relative abundance was low and did not differ significantly between the two different soils. Differences in microbiome structure also resulted in shifts in functional pattern. We observed an increase in genes related to stress sensing in the rhizosphere of soils affected by replant disease, whereas genes linked to nutrient sensing and uptake dominated in control soils. Moreover, we observed a lower abundance of genes coding for enzymes which trigger the degradation of aromatic compounds in rhizosphere of soils affected by replant disease, which is probably connected with higher concentration of phenolic compounds, generally associated with disease progression.Conclusions: Our study shows, for the first time, how apple replanting affects soil functioning by altering the soil microbiome. Particularly, the decrease in the abundance of genes which code for enzymes catalyzing the degradation of aromatic compounds, observed in the rhizosphere of plants grown in soil affected by apple replant disease, is of interest. Apple rootstocks are known to synthetize many phenolic compounds, including defense related phytoalexins, which have been considered for long to be connected with the emergence of replant disease. The knowledge gained in this study might help to develop targeted strategies to overcome or at least reduce the effects of ARD symptoms.
Wissenschaftlicher Artikel
Scientific Article
Saenz Medina, J.S. ; Airo, A. ; Schulze-Makuch, D. ; Schloter, M. ; Vestergaard, G.
Diversity 11:205 (2019)
Mobile genetic elements (MGEs) play an essential role in bacterial adaptation and evolution. These elements are enriched within bacterial communities from extreme environments. However, very little is known if specific genes co-occur with MGEs in extreme environments and, if so, what their function is. We used shotgun-sequencing to analyse the metagenomes of 12 soil samples and characterized the composition of MGEs and the genes co-occurring with them. The samples ranged from less arid coastal sites to the inland hyperarid core of the Atacama Desert, as well as from sediments below boulders, protected from UV-irradiation. MGEs were enriched at the hyperarid sites compared with sediments from below boulders and less arid sites. MGEs were mostly co-occurring with genes belonging to the Cluster Orthologous Group (COG) categories "replication, recombination and repair," "transcription" and "signal transduction mechanisms." In general, genes coding for transcriptional regulators and histidine kinases were the most abundant genes proximal to MGEs. Genes involved in energy production were significantly enriched close to MGEs at the hyperarid sites. For example, dehydrogenases, reductases, hydrolases and chlorite dismutase and other enzymes linked to nitrogen metabolism such as nitrite- and nitro-reductase. Stress response genes, including genes involved in antimicrobial and heavy metal resistance genes, were rarely found near MGEs. The present study suggests that MGEs could play an essential role in the adaptation of the soil microbiome in hyperarid desert soils by the modulation of housekeeping genes such as those involved in energy production.
Wissenschaftlicher Artikel
Scientific Article
Kuhl, T. ; Felder, M. ; Nussbaumer, T. ; Fischer, D. ; Kublik, S. ; Chowdhury, S.P. ; Schloter, M. ; Rothballer, M.
Microbio. Res. Ann. 8, e01106-19 (2019)
Rhodococcus qingshengii RL1 was isolated from surface-sterilized leaves of Eruca sativa Mill. and shows plant growth-promoting (PGP) properties. The de novo genome assembly consists of one chromosome with 6,253,838 bp and two plasmids with 144,038 bp and 448,745 bp. Many genes could be identified reflecting its PGP potential.
Wissenschaftlicher Artikel
Scientific Article
Nannipieri, P. ; Penton, C.R. ; Purahong, W. ; Schloter, M. ; van Elsas, J.D.
Biol. Fertil. Soils 55, 765-766 (2019)
Editorial
Editorial
Csiszár, J. ; Hecker, A. ; Labrou, N.E. ; Schröder, P. ; Riechers, D.E.
Front. Plant Sci. 10:1304 (2019)
Editorial
Editorial
Stabl, G. ; Schalk, S. ; Siani, R. ; Schloter, M. ; Dawid, C. ; Gutjahr, C.
Mol. Plant Microbe Interact. 32, 54-54 (2019)
Meeting abstract
Meeting abstract
Turan, V. ; Schröder, P. ; Bilen, S. ; Insam, H. ; Fernández-Delgado Juárez, M.
Sci. Rep. 9:15178 (2019)
Essential oils (EO) of several plant species have the potential to combat plant and fungal diseases. However, the effects of Achillea millefolium EO on the development of common bean (Phaseolus vulgaris L.), is still unknown. Moreover, its effect on N-2-fixing bacteria, and in general on soil properties has not been studied yet. A greenhouse trial was set up to evaluate both the influence that Achillea millefolium EO and the inoculation with three different Rhizobium strains have on the bean plant and on the chemical and microbiological properties of an agriculturally used Cambisol. Non-inoculated pots were used as control. Our findings showed a decrease in bacterial colony forming units due to EO application and an increase following the Rhizobium inoculation compared to the control. The EO application decreased soil basal respiration and activities of dehydrogenase, urease, beta-glucosidase and acid phosphatase. Such effects were stronger with higher oil concentrations. Moreover, the treatments combining Rhizobium inoculation with EO showed a positive effect on nodulation and plant height. Overall, the combined application of Achillea millefolium EO and rhizobia works as an efficient biocide that could be applied in organic agriculture without hampering the activity of nodule-forming N-fixing bacteria and the development of common bean.
Wissenschaftlicher Artikel
Scientific Article
Kreyling, J. ; Grant, K. ; Hammerl, V. ; Arfin-Khan, M.A.S. ; Malyshev, A.V. ; Peñuelas, J. ; Pritsch, K. ; Sardans, J. ; Schloter, M. ; Schuerings, J. ; Jentsch, A. ; Beierkuhnlein, C.
Sci. Rep. 9:14632 (2019)
Climate change affects all seasons, but warming is more pronounced in winter than summer at mid-and high latitudes. Winter warming can have profound ecological effects, which are rarely compared to the effects of summer warming, and causal explanations are not well established. We compared mild aboveground infrared warming in winter to warming in summer in a semi-natural, cool-temperate grassland in Germany for four years. Aboveground plant biomass increased following winter warming (+18%) and was unaffected by summer warming. Winter warming affected the composition of the plant community more than summer warming, favoring productive species. Winter warming increased soil respiration more than summer warming. Prolonged growing seasons and changes in plant-community composition accounted for the increased aboveground biomass production. Winter warming stimulated ecological processes, despite causing frost damage to plant roots and microorganisms during an extremely cold period when warming reduced the thermal insulation provided by snow. Future warming beyond such intermittent frosts may therefore further increase the accelerating effects of winter warming on ecological processes.
Wissenschaftlicher Artikel
Scientific Article
Bernat, P. ; Nesme, J. ; Paraszkiewicz, K. ; Schloter, M. ; Plaza, G.
Curr. Microbiol. 76, 1320-1329 (2019)
Pseudomonas putida E41 isolated from root interior of Sida hermaphrodita (grown on a field contaminated with heavy metals) showed high biosurfactant activity. In this paper, we describe data from mass spectrometry and genome analysis, to improve our understanding on the phenotypic properties of the strain. Supernatant derived from P. putida E41 liquid culture exhibited a strong decrease in the surface tension accompanied by the ability for emulsion stabilization. We identified extracellular lipopeptides, putisolvin I and II expression but did not detect rhamnolipids. Their presence was confirmed by matrix-assisted laser desorption and ionization (MALDI) TOF/TOF technique. Moreover, ten phospholipids (mainly phosphatidylethanolamines PE 33:1 and PE 32:1) which were excreted by vesicles were also detected. In contrast the bacterial cell pellet was dominated by phosphatidylglycerols (PGs), which were almost absent in the supernatant. It seems that the composition of extracellular (secreted to the environment) and cellular lipids in this strain differs. Long-read sequencing and complete genome reconstruction allowed the identification of a complete putisolvin biosynthesis pathway. In the genome of P. putida E41 were also found all genes involved in glycerophospholipid biosynthesis, and they are likely responsible for the production of detected phospholipids. Overall this is the first report describing the expression of extracellular lipopeptides (identified as putisolvins) and phospholipids by a P. putida strain, which might be explained by the need to adapt to the highly contaminated environment.
Wissenschaftlicher Artikel
Scientific Article
Kovacevic, D. ; Bartel, S. ; Pfeiffer, S. ; Schloter, M. ; Krauss-Etschmann, S.
Allergy 74, 262-262 (2019)
Meeting abstract
Meeting abstract
Gschwendtner, S. ; Kang, H. ; Thiering, E. ; Kublik, S. ; Fösel, B. ; Schulz, H. ; Krauss-Etschmann, S. ; Heinrich, J. ; Schöler, A. ; Schloter, M. ; Standl, M.
Sci. Rep. 9:12675 (2019)
While the association between early life determinants and the development of the gut microbiome composition in infancy has been widely investigated, a potential persistent influence of early life determinants on the gut microbial community after its stabilization at later childhood remains largely unknown. Therefore, we aimed to identify the association between several early life determinants and the gut microbiome composition in six-year-old children from the LISA birth cohort. A total number of 166 fecal samples were analyzed using 16S rRNA gene-based barcoding to assess bacterial diversity pattern. The bacterial profiles were investigated for their association with maternal smoking during pregnancy, mode of delivery, breastfeeding, antibiotic treatment between one and two years of age, gender and socioeconomic status (SES). While alpha and beta diversity of the infants' gut microbiome remained unaffected, amplicon sequence variants (ASVs) annotated to Firmicutes and Actinobacteria responded to early life determinants, mostly to feeding practice and antibiotics use. ASVs associated to Bacteriodetes remained unaffected. Our findings indicate that early life determinants could have a long-term sustainable effect on the gut microflora of six-year-old children, however, associations with early life determinates are weaker than reported for infants.
Wissenschaftlicher Artikel
Scientific Article
Schröder, P. ; Sauvetre, A. ; Gnädinger, F. ; Pesaresi, P. ; Chmeliková, L. ; Doğan, N. ; Gerl, G. ; Gökçe, A. ; Hamel, C. ; Millan, R. ; Persson, T. ; Ravnskov, S. ; Rutkowska, B. ; Schmid, T. ; Szulc, W. ; Teodosiu, C. ; Terzi, V.
Sci. Total Environ. 678, 146-161 (2019)
During the next decade it will be necessary to develop novel combinations of management strategies to sustainably increase crop production and soil resilience. Improving agricultural productivity, while conserving and enhancing biotic and abiotic resources, is an essential requirement to increase global food production on a sustainable basis. The role of farmers in increasing agricultural productivity growth sustainably will be crucial. Farmers are at the center of any process of change involving natural resources and for this reason they need to be encouraged and guided, through appropriate incentives and governance practices, to conserve natural ecosystems and their biodiversity, and minimize the negative impact agriculture can have on the environment. Farmers and stakeholders need to revise traditional approaches not as productive as the modern approaches but more friendly with natural and environmental ecosystems values as well as emerging novel tools and approaches addressing precise farming, organic amendments, lowered water consumption, integrated pest control and beneficial plant-microbe interactions. While practical solutions are developing, science based recommendations for crop rotations, breeding and harvest/postharvest strategies leading to environmentally sound and pollinator friendly production and better life in rural areas have to be provided. (C) 2019 Elsevier B.V. All rights reserved.
Review
Review
Liu, S. ; Schloter, M. ; Hu, R. ; Vereecken, H. ; Brüggemann, N.
Front. Env. Sci. 7:47 (2019)
Nitrite (NO2-) and hydroxylamine (NH 2 OH) are important intermediates of the nitrogen (N) cycle in soils. They play a crucial role in the loss of nitrous oxide (N2O) and nitric oxide (NO) from soil due to their high reactivity. In this study, we collected soil samples from three ecosystems (grassland, arable land, and forest with a riparian zone) and explored the contribution of NO2- and NH 2 OH to N 2 O formation in the different soils after exposure to oxic or anoxic pre-treatment. In addition, the importance of abiotic processes on the N 2 O formation from the two intermediates was studied by irradiating the soil samples with γ-irradiation. Our results demonstrate that NO2- addition induced the largest N 2 O production in the grassland soil, followed by the forest and arable soils. Only 9-39% of the produced N 2 O after NO2- addition came from abiotic processes. NH 2 OH addition increased N 2 O emissions the most from the arable soil, followed by the grassland and forest soils. The conversion of NH 2 OH to N 2 O was mostly (73-93%) abiotic. Anoxic pre-treatment decreased N 2 O production from NH 2 OH remarkably, especially for the grassland soil, while it increased N 2 O production from NO2- for most of the soils. Correlation analysis showed that NO2- effects on N 2 O production were strongly correlated to NH4+ content in soils with anoxic pre-treatment, while NH 2 OH effects on N 2 O production were strongly correlated to soil Mn and C content in soils with oxic pre-treatment. Our results indicate that NH 2 OH plays an important role for abiotic N 2 O formation in soils with low C and high Mn content, while the effect of NO2- was important mainly during biotic N 2 O production. Anoxic periods prior to N addition may increase the contribution of NO2-, but reduce the contribution of NH 2 OH, to soil N 2 O formation.
Wissenschaftlicher Artikel
Scientific Article
Pihlap, E. ; Vuko, M. ; Lucas, M. ; Steffens, M. ; Schloter, M. ; Vetterlein, D. ; Endenich, M. ; Kögel-Knabner, I.
Soil Tillage Res. 191, 224-237 (2019)
After reclamation of open-cast mining pits, soil formation starts from the deposited calcareous loess characterised by its basic physical and chemical properties whereas soil biology and structure need to develop to achieve a fully functional soil. In this study we used a chronosequence approach to elucidate soil formation on agriculturally reclaimed loess soils in an open-cast lignite mining area in Garzweiler (Germany). We selected six fields aged 0, 1, 3, 6, 12, and 24 years after the first seeding in order to observe the initial stage of development of soil properties and assess the role of management with conventional crop rotation in soil structure formation and soil organic carbon (SOC) accumulation. Loess parent material had a strong impact on aggregation, as CaCO3 acted as a strong cementing agent. Alfalfa cultivation in the pioneering phase was of high importance in the development of microbial biomass, as it protects microbes from N limitation. Soil macroporosity and pore connectivity increased only after compost application and ploughing during agricultural crop rotation. Soil organic matter (SOM) build-up was strongly dependent on the addition of compost, as crop residues from conventional crop rotation are not sufficient to maintain high SOC contents.
Wissenschaftlicher Artikel
Scientific Article
Cania, B. ; Vestergaard, G. ; Krauss, M. ; Fliessbach, A. ; Schloter, M. ; Schulz, S.
Environ. Microbiome 14:1 (2019)
Background: Stable soil aggregates are essential for optimal crop growth and preventing soil erosion. However, tillage is often used in agriculture to loosen the soil, which disrupts the integrity of these aggregates. Soil aggregation can be enhanced by bacteria through their ability to produce exopolysaccharides and lipopolysaccharides. These compounds stabilize soil aggregates by "gluing" soil particles together. However, it has yet to be shown how tillage influences the bacterial potential to produce aggregate-stabilizing agents. Therefore, we sampled conventional and reduced tillage treatments at 0-10 cm, 10-20 cm and 20-50 cm from a long-term field trial in Frick, Switzerland. We compared the stable aggregate fraction of the soil and the bacterial potential to produce exopolysaccharides (EPS) and lipopolysaccharides (LPS) under different tillage regimes by employing a shotgun metagenomic approach. We established a method which combines hidden Markov model searches with blasts against sequences derived from the Kyoto Encyclopedia of Genes and Genomes database to analyze genes specific for the biosynthesis of these compounds.Results: Our data revealed that the stable aggregate fraction as well as the bacterial potential to produce EPS and LPS were comparable under both tillage regimes. The highest potential to produce these compounds was found in the upper soil layer, which was disturbed by tillage, but had higher content of organic carbon compared to the layer below the tillage horizon. Additionally, key players of EPS and LPS production differed at different sampling depths. Some families with high potential to produce EPS and LPS, such as Chitinophagaceae and Bradyrhizobiaceae, were more abundant in the upper soil layers, while others, e.g. Nitrospiraceae and Planctomycetaceae, preferred the lowest sampled soil depth. Each family had the potential to form a limited number of different aggregate-stabilizing agents.Conclusions: Our results indicate that conventional tillage and reduced tillage equally promote the bacterial potential to produce EPS and LPS in the tillage horizon. However, as major bacterial groups triggering EPS and LPS formation were not the same, it is likely that gene expression pattern differ in the different treatments due to various pathways of gene induction and transcription in different bacterial species.
Wissenschaftlicher Artikel
Scientific Article
Kölbl, A. ; Bucka, F. ; Marschner, P. ; Mosley, L. ; Fitzpatrick, R. ; Schulz, S. ; Lueders, T. ; Kögel-Knabner, I.
Geoderma 347, 220-232 (2019)
Saturated acid sulfate soils with hypersulfidic material are productive wetland soils, but when they dry, they generate large amounts of sulfuric acid due to oxidation of pyrite to form sulfuric material (pH <4) and consequently sulfuric soils. After re-saturation of sulfuric soils and thus the re-establishment of reduced conditions, activity of sulfate reducing bacteria (SRB) can lead to a renewed formation of Fe sulfides and pH increase. Many SRB are heterotrophic and require sufficient available organic matter; however, little is known about OC consumption and changes of the composition of organic substrates during the amelioration process. To investigate remediation of a sandy, OC-poor sulfuric soil (initial pH = 2.5), short-term anoxic incubation experiments over a period of approx. 10 weeks were conducted after re-submerging under controlled laboratory conditions. We tested different organic matter quantities between 10% up to 200% of the native soil OC content. Besides wheat straw, we used lactate additions to test if this selectively promotes the activity of SRB, and thus, accelerates sulfate reduction and pH neutralization. The results showed that OC additions of ≥50% of native soil OC content and pre-adjustment of pH to values ≥5.0 were necessary to subsequently enable microbial reduction reactions to occur, which increased the pH to values ≥5.5. OC additions of ≥100% instead of 50% of native soil OC as wheat straw led to quicker changes of redox and pH values, to slightly higher microbial activity as indicated by CO 2 release, and to higher proportions of newly-formed mineral-associated OC. The addition of OC as lactate solution to promote specifically SRB was only successful in combination with wheat straw addition. Here, the presence of lactate led to the quickest changes of pH and redox values and resulted in pH ≥7 and redox values ≤ −300 mV due to an active microbial population. Our results indicate that a diverse microbial community is more important for successful remediation than a selective promotion of SRB.
Wissenschaftlicher Artikel
Scientific Article
Millan, R. ; Schröder, P. ; Saebo, A.
Front. Plant Sci. 10:346 (2019)
Editorial
Editorial
Amar, Y. ; Bleuel, R. ; Silva, R.I. ; Fösel, B. ; Schöler, A. ; Schloter, M. ; Graf, E. ; Strom, T.M. ; Lagkouvardos, I. ; Neuhaus, K. ; Biedermann, T. ; Köberle, M.
Exp. Dermatol. 28, E8-E9 (2019)
Meeting abstract
Meeting abstract
Degrune, F. ; Dumack, K. ; Fiore-Donno, A.M. ; Bonkowski, M. ; Sosa-Hernández, M.A. ; Schloter, M. ; Kautz, T. ; Fischer, D. ; Rillig, M.C.
FEMS Microbiol. Ecol. 95:fiz041 (2019)
Protists are the most important predators of soil microbes like bacteria and fungi and are highly diverse in terrestrial ecosystems. However, the structure of protistan communities throughout the soil profile is still poorly explored. Here, we used Illumina sequencing to track differences in the relative abundance and diversity of Cercozoa, a major group of protists, at two depths; 10-30 cm (topsoil) and 60-75 cm (subsoil) in an agricultural field in Germany. At the two depths, we also distinguished among three soil compartments: rhizosphere, drilosphere (earthworm burrows) and bulk soil. With increasing depth, we found an overall decline in richness, but we were able to detect subsoil specific phylotypes and contrasting relative abundance patterns between topsoil and subsoil for different clades. We also found that the compartment effect disappeared in the subsoil when compared to the topsoil. More studies are now needed to describe and isolate these possibly subsoil specific phylotypes and better understand their ecology and function.
Wissenschaftlicher Artikel
Scientific Article
Fösel, B. ; Pfeiffer, S. ; Raj, A.C.D. ; Krauss-Etschmann, S. ; Schloter, M.
In: The Lung Microbiome. 2019. 50-66 (ERS Monograph)
Pedrazzani, R. ; Bertanza, G. ; Brnardić, I. ; Cetecioglu, Z. ; Dries, J. ; Dvarionienė, J. ; García-Fernández, A.J. ; Langenhoff, A. ; Libralato, G. ; Lofrano, G. ; Škrbić, B. ; Martínez-López, E. ; Meriç, S. ; Mutavdžić Pavlović, D. ; Papa, M. ; Schröder, P. ; Tsagarakis, K.P. ; Vogelsang, C.
Sci. Total Environ. 669, 1062-1062 (2019)
The authors regret that, despite thoroughly reviewing the manuscript, the content of a paragraph has been duplicated and has to be ignored .
Hammerl, V. ; Kastl, E.-M. ; Schloter, M. ; Kublik, S. ; Schmidt, H. ; Welzl, G. ; Jentsch, A. ; Beierkuhnlein, C. ; Gschwendtner, S.
Sci. Rep. 9:2280 (2019)
The frequency of extreme drought and heavy rain events during the vegetation period will increase in Central Europe according to future climate change scenarios, which will affect the functioning of terrestrial ecosystems in multiple ways. In this study, we simulated an extreme drought event (40 days) at two different vegetation periods (spring and summer) to investigate season-related effects of drought and subsequent rewetting on nitrifiers and denitrifiers in a grassland soil. Abundance of the microbial groups of interest was assessed by quantification of functional genes (amoA, nirS/nirK and nosZ) via quantitative real-time PCR. Additionally, the diversity of ammonia-oxidizing archaea was determined based on fingerprinting of the archaeal amoA gene. Overall, the different time points of simulated drought and rewetting strongly influenced the obtained response pattern of microbial communities involved in N turnover as well as soil ammonium and nitrate dynamics. In spring, gene abundance of nirS was irreversible reduced after drought whereas nirK and nosZ remained unaffected. Furthermore, community composition of ammonia-oxidizing archaea was altered by subsequent rewetting although amoA gene abundance remained constant. In contrast, no drought/rewetting effects on functional gene abundance or diversity pattern of nitrifying archaea were observed in summer. Our results showed (I) high seasonal dependency of microbial community responses to extreme events, indicating a strong influence of plant-derived factors like vegetation stage and plant community composition and consequently close plant-microbe interactions and (II) remarkable resistance and/or resilience of functional microbial groups involved in nitrogen cycling to extreme weather events what might indicate that microbes in a silty soil are better adapted to stress situations as expected.
Wissenschaftlicher Artikel
Scientific Article
Saenz Medina, J.S. ; Marques, T.V. ; Barone, R.S.C. ; Cyrino, J.E.P. ; Kublik, S. ; Nesme, J. ; Schloter, M. ; Rath, S. ; Vestergaard, G.
Microbiome 7:24 (2019)
BackgroundAquaculture is on the rise worldwide, and the use of antibiotics is fostering higher production intensity. However, recent findings suggest that the use of antibiotics comes at the price of increased antibiotic resistance. Yet, the effect of the oral administration of antibiotics on the mobility of microbial resistance genes in the fish gut is not well understood. In the present study, Piaractus mesopotamicus was used as a model to evaluate the effect of the antimicrobial florfenicol on the diversity of the gut microbiome as well as antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) using a metagenomic approach.ResultsThe total relative abundance of ARGs and MGEs significantly increased during the antibiotic exposure. Additionally, phage integrases, transposases, and transposons flanking ARGs accumulated in the gut microbiome of P. mesopotamicus because of the antibiotic exposure. MGEs co-occurring with ARGs showed a significant positive correlation with the total ARGs found. Furthermore, shifts in the gut microbiome towards well-known putative pathogens such as Salmonella, Plesiomonas, and Citrobacter were observed following florfenicol treatment. Mainly Plesiomonas and Citrobacter harbored genes that code for multidrug and phenicol efflux pumps. Moreover, several genes related to RNA processing and modification, cell motility, SOS response, and extracellular structure were enriched due to the antibiotic application. The observed effects were visible during the complete application phase and disappeared at the post-exposure phase.ConclusionsOur findings suggest that the oral administration of antibiotics increases the potential for MGE-mediated exchange of ARGs in the gut of fish and could contribute to the enrichment and dispersion of ARGs in aquaculture systems. Importantly, this increase in the potential for ARGs exchange could be an effect of changes in community structure and/or ARG mobilization.
Wissenschaftlicher Artikel
Scientific Article
Winkler, P. ; Kaiser, K. ; Jahn, R. ; Mikutta, R. ; Fiedler, S. ; Cerli, C. ; Kölbl, A. ; Schulz, S. ; Jankowska, M. ; Schloter, M. ; Müller-Niggemann, C. ; Schwark, L. ; Woche, S.K. ; Kümmel, S. ; Utami, S.R. ; Kalbitz, K.
Biogeochemistry 143, 31-54 (2019)
Submerged rice cultivation is characterized by redox fluctuations and results in the formation of paddy soils, often accompanied by soil organic carbon (SOC) accumulation. The impact of redox fluctuations and the underlying soil type on the fate of organic carbon (OC) in paddy soils are unknown. Hence, we mimicked paddy soil development in the laboratory by exposing two soil types with contrasting mineral assemblages (Alisol and Andosol) to eight anoxic-oxic cycles over 1year. Soils regularly received C-13-labeled rice straw. As control we used a second set of samples without straw addition as well as samples under static oxic conditions with and without straw. Headspaces were analyzed for carbon dioxide and methane as well as their C-13 signatures, whereas soil solutions were analyzed for redox potential, pH, dissolved iron, and dissolved organic carbon (DOC and (DOC)-C-13). At the end of the experiment, when eight redox cycles were completed, mineral-associated organic matter (MOM) was isolated by density fractionation and characterized for C-13, non-cellulosic carbohydrates, and lignin-derived phenols. Moreover, changes in the soil's microbial community structure were measured. For both soil types, headspace data confirmed less respiration in straw-amended soils with redox fluctuation than in those under static oxic conditions. The C-13 data revealed that, irrespective of soil type, straw carbon allocation into MOM was larger in soils with redox fluctuation than in those with static oxic conditions. A net increase in MOM after the one-year incubation, however, was only observed in the respective Andosol, probably due to abundant reactive minerals capable of OC uptake. In the Alisol, straw OC most likely exchanged initial MOM. A potential for lignin accumulation in the MOM of soils incubated with straw and redox fluctuation was observed for both soil types. Lignin and carbohydrates suggest a plant origin of MOM formed under redox fluctuation. The initially similar bacterial community composition of the Alisol and Andosol changed differently under redox fluctuation. The stronger change in the Alisol indicates less protective microbial habitats. In summary, the overall turnover of straw OC in soils under redox fluctuation seems to be independent of soil type, while net accumulation of SOC as well as the evolution of the bacterial community structure may in part depend on soil type, suggesting an impact of the soil's mineral composition.
Wissenschaftlicher Artikel
Scientific Article
Treichel, N. ; Prevoršek, Z. ; Mrak, V. ; Kostric, M. ; Vestergaard, G. ; Fösel, B. ; Pfeiffer, S. ; Stres, B. ; Schöler, A. ; Schloter, M.
Microb. Ecol. 78, 517–527 (2019)
The development of the gut microbiome is influenced by several factors. It is acquired during and after birth and involves both maternal and environmental factors as well as the genetic disposition of the offspring. However, it is unclear if the microbiome development is directly triggered by the mode of delivery and very early contact with the mother or mostly at later stages of initial development mainly by breast milk provided by the mother. To investigate to what extent the gut microbiome composition of the offspring is determined by the nursing mother, providing breast milk, compared to the birth mother during early development, a cross-fostering experiment involving two genetically different mouse lines was developed, being prone to be obese or lean, respectively. The microbiome of the colon was analyzed by high-throughput 16S rRNA gene sequencing, when the mice were 3 weeks old. The nursing mother affected both α- and β-diversity of the offspring’s gut microbiome and shaped its composition. Especially bacterial families directly transferred by breast milk, like Streptococcaceae, or families which are strongly influenced by the quality of the breast milk like Rikenellaceae, showed a strong response. The core microbiome transferred from the obese nursing mother showed a higher robustness in comparison to the microbiome transferred from the lean nursing mother. Overall, the nursing mother impacts the gut microbial composition of the offspring during early development and might play an important role for health and disease of the animals at later stages of life.
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Scientific Article
Hammerl, V. ; Grant, K. ; Pritsch, K. ; Jentsch, A. ; Schloter, M. ; Beierkuhnlein, C. ; Gschwendtner, S.
Front. Env. Sci. 6:157 (2019)
Magnitude and timing of precipitation events within the growing season might be decisive for alterations in potential extracellular enzyme activity (PEEA), with consequences for nutrient cycle, and carbon storage in grassland ecosystems. Pattern of PEEA catalyzing major steps of the carbon cycle (β-glucosidase (β-gls), cellobiohydrolase (cel), glucuronidase (glr), and xylosidase (xyl), soil respiration rates and extractable organic carbon were analyzed in response to increased intra-annual precipitation variability in a European, mesic temperate grassland. The field experiment was carried out in three subsequent years by simulating recurrent drought events combined with heavy rainfall either early or late in the growing season (spring or summer) by rainout shelters and irrigation systems. Our data indicated comparable effects of the drought settings independent from the timing of the drought. Both for the simulated spring- and summer drought a decrease of enzymatic activities was observed compared to the control plots, with ß-gls activity after the summer drought being the only exception. However, response pattern toward rewetting differed depending on the seasonal timing of the drought being introduced. After spring drought, a fast recovery to control level was observed for PEEA of ß-gls and xyl, whereas cel and glr activity remained constantly lower. Rewetting after summer drought induced an increase of all enzymatic activities to values even higher compared to the controls. Overall, our data indicate a high resilience of PEEA toward drought and rewetting events in grassland soils, which is modulated by the seasonal timing of the extreme weather events.
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Scientific Article
Schloter, M.
In: Die unbekannte Welt der Mikrobiome. 2019. 57-68 (Rundgespräche Forum Ökologie ; 47)
Das Mikrobiom von Böden spielt als Katalysator bedeutender Ökosystemdienstleistungen eine wichtige Rolle. Neben der direkten Unterstützung des Pflanzenwachstums sind das vor allem die Strukturbildung von Böden, die Kohlenstoffsequestrierung und der Abbau von Schadstoffen. Eine weitere Motivation, das Bodenmikrobiom besser zu verstehen, liegt darin begründet, dass in Böden auch eine Reihe humanpathogener Mikroorganis-men überleben und sich ggf. vermehren können. Das genetische Potenzial von Böden erscheint durch die enorme Diversität des Bodenmikrobioms und die damit verbundene funktionelle Redundanz oftmals relativ stabil. Landwirtschaftliches Management beeinflusst daher selten das im Boden vorhandene Potenzial für einen bestimmten Prozess, jedoch die Expression einzelner Enzyme, wie anhand des Phosphorzyklus, der Bildung von Exo- und Lipopolysacchariden und des anaeroben Alkanabbaus gezeigt wird. Um die Regulierung der Genaktivierung im Boden besser zu verstehen und damit gezielte Managementstrategien für die Zukunft ableiten zu können, müssen allerdings räumlich wie zeitlich viel kleinere Skalen betrachtet werden, als dies bisher der Fall ist. Wir müssen lernen zu verstehen, wie sich räumliche Heterogenitäten auf der μm- bis mm-Skala bilden und mit welcher zeitlichen Dynamik sich diese wieder ändern.
Milaković, M. ; Vestergaard, G. ; González-Plaza, J.J. ; Petrić, I. ; Šimatović, A. ; Senta, I. ; Kublik, S. ; Schloter, M. ; Smalla, K. ; Udiković-Kolić, N.
Environ. Int. 123, 501-511 (2019)
Effluents from antibiotic manufacturing may contain high concentrations of antibiotics, which are the main driving force behind the selection and spread of antibiotic resistance genes in the environment. However, our knowledge about the impact of such effluent discharges on the antibiotic resistome and bacterial communities is still limited. To gain insight into this impact, we collected effluents from an azithromycin-manufacturing industry discharge site as well as upstream and downstream sediments from the receiving Sava river during both winter and summer season. Chemical analyses of sediment and effluent samples indicated that the effluent discharge significantly increased the amount of macrolide antibiotics, heavy metals and nutrients in the receiving river sediments. Quantitative PCR revealed a significant increase of relative abundances of macrolide-resistance genes and class 1 integrons in effluent-impacted sediments. Amplicon sequencing of 16S rRNA genes showed spatial and seasonal bacterial community shifts in the receiving sediments. Redundancy analysis and Mantel test indicated that macrolides and copper together with nutrients significantly correlated with community shift close to the effluent discharge site. The number of taxa that were significantly increased in relative abundance at the discharge site decreased rapidly at the downstream sites, showing the resilience of the indigenous sediment bacterial community. Seasonal changes in the chemical properties of the sediment along with changes in effluent community composition could be responsible for sediment community shifts between winter and summer. Altogether, this study showed that the discharge of pharmaceutical effluents altered physicochemical characteristics and bacterial community of receiving river sediments, which contributed to the enrichment of macrolide-resistance genes and integrons.
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Scientific Article
Pérez Brandan, C. ; Merlies, J.M. ; Meyer, A. ; Huidobro, J. ; Schloter, M. ; Vargas-Gil, S.
Soil water res. 14, 1-9 (2019)
The aim of this study was to evaluate the response pattern of diazotrophic microbes, denitrifiers and nitrifiers to different types of land use management, such as soybean monoculture (M) during 5 and 24 years (M5 and M24) and soybean-maize rotation (R) during 4 and 15 years (R4 and R15) in two subsequent years at the time point of flowering. Soil samples from a site recently introduced into agriculture (RUA) and a pristine soil under native vegetation (NV) were used as controls. Abundances of different functional groups of microbes were assessed using the direct quantification of marker genes by quantitative real-time PCR using extracted DNA from rhizosphere samples. In addition, soil chemical and physical properties were analysed and correlated with the abundance data from the functional microbial groups under investigation. Overall, the results indicate that the abundance of nifH genes was higher under R treatments compared to M treatments. The abundance of ammonium monooxygenase genes amoA (AOA) was generally higher under rotation systems and decreased under M24. RUA evidenced a negative effect on the establishment and development of AOA communities. The influence of land use on nirS abundance was inconsistent. However, R treatments showed a high abundance of nirK genes compared to M treatments. In both growing seasons, the abundance of nosZ genes was higher under NV compared with the other treatments. Furthermore, M24 treatment was related to strongly changed chemical and physical soil properties compared with the other sites. As expected, soil samples from RUA showed the strong dynamics of measured parameters indicating the high sensitivity of soils under transition to environmental parameters. Our results also indicated that the long-term crop rotation modified the abundance of the investigated microbial groups compared to the monoculture and increased soil chemical and physical quality. Therefore, our results provide evidence for a stimulatory effect of the long-term crop rotation on the abundance of microbes involved in N transformation.
Wissenschaftlicher Artikel
Scientific Article
Pedrazzani, R. ; Bertanza, G. ; Brnardić, I. ; Cetecioglu, Z. ; Dries, J. ; Dvarionienė, J. ; García-Fernández, A.J. ; Langenhoff, A. ; Libralato, G. ; Lofrano, G. ; Škrbić, B. ; Martínez-López, E. ; Meriç, S. ; Pavlović, D.M. ; Papa, M. ; Schröder, P. ; Tsagarakis, K.P. ; Vogelsang, C.
Sci. Total Environ. 651, 3202-3221 (2019)
This opinion paper focuses on the role of eco-toxicological tools in the assessment of possible impacts of emerging contaminants on the aquatic ecosystem, hence, on human health. Indeed, organic trace pollutants present in raw and treated wastewater are the pivot targets: a multidisciplinary approach allows defining the basic principles for managing this issue, from setting a proper monitoring campaign up to evaluating the optimal process treatment. Giving hints on trace pollutants fate and behaviour, attention is focused on the choice of the bioassay(s), by analysing the meaning of possible biological answers. Data interpretation and exploitation are detailed with the final goal of providing criteria in order to be able to select the best targeted treatment options.The manuscript dealswith conventional and innovative analytical approaches for assessing toxicity, by reviewing laboratory and field assays; illustrative real scale and laboratory applications integrate and exemplify the proposed approach. (C) 2018 Elsevier B.V. All rights reserved.
Review
Review
van der Plas, F. ; Allan, E. ; Fischer, M. ; Alt, F. ; Arndt, H. ; Binkenstein, J. ; Blaser, S. ; Blüthgen, N. ; Böhm, S. ; Hölzel, N. ; Klaus, V.H. ; Kleinebecker, T. ; Morris, K.J. ; Oelmann, Y. ; Prati, D. ; Renner, S.C. ; Rillig, M.C. ; Schaefer, H.M. ; Schloter, M. ; Schmitt, B. ; Schöning, I. ; Schrumpf, M. ; Solly, E.F. ; Sorkau, E. ; Steckel, J. ; Steffan-Dewenter, I. ; Stempfhuber, B. ; Tschapka, M. ; Weiner, C.N. ; Weisser, W.W. ; Werner, M. ; Westphal, C. ; Wilcke, W. ; Manning, P.
J. Appl. Ecol. 56, 168-179 (2019)
Rapid growth of the world's human population has increased pressure on landscapes to deliver high levels of multiple ecosystem services, including food and fibre production, carbon storage, biodiversity conservation, and recreation. However, we currently lack general principles describing how to achieve this landscape multifunctionality. We combine theoretical simulations and empirical data on 14 ecosystem services measured across 150 grasslands in three German regions. In doing so, we investigate the circumstances under which spatial heterogeneity in a driver of ecosystem functioning (an "ecosystem-driver," e.g., the presence of keystone species, land-use intensification, or habitat types) increases landscape-level ecosystem multifunctionality. Simulations based on theoretical data demonstrated that relationships between heterogeneity and landscape multifunctionality are highly variable and can range from nonsignificant to strongly positive. Despite this variability, we could identify criteria under which heterogeneity-landscape multifunctionality relationships were most strongly positive: this happened when multiple ecosystem services responded contrastingly (both positively and negatively) to an ecosystem-driver. These findings were confirmed using empirical data, which showed that heterogeneity in land-use intensity (LUI) promoted landscape multifunctionality in cases where functions with both positive (e.g., plant biomass) and negative (e.g., flower cover) responses to land use intensification were included. For example, the simultaneous provisioning of ecosystem functions related to forage production (generally profiting from land-use intensification), biodiversity conservation and recreation (generally decreasing with land-use intensification) was highest in landscapes consisting of sites varying in LUI. Synthesis and applications. Our findings show that there are general principles governing landscape multifunctionality. A knowledge of these principles may support land management decisions. For example, knowledge of relationships between ecosystem services and their drivers, such as land use type, can help estimate the consequences of increasing or decreasing heterogeneity for landscape-level ecosystem service supply, although interactions between landscape units (e.g., the movement of pollinators) must also be considered.
Wissenschaftlicher Artikel
Scientific Article
Szukics, U. ; Grigulis, K. ; Legay, N. ; Kastl, E.-M. ; Baxendale, C. ; Bardgett, R.D. ; Clément, J.C. ; Lavorel, S. ; Schloter, M. ; Bahn, M.
Sci. Total Environ. 648, 745-753 (2019)
It is well established that the abundances of nitrogen (N) transforming microbes are strongly influenced by land-use intensity in lowland grasslands. However, their responses to management change in less productive and less fertilized mountain grasslands are largely unknown. We studied eight mountain grasslands, positioned along gradients of management intensity in Austria, the UK, and France, which differed in their historical management trajectories. We measured the abundance of ammonia-oxidizing bacteria (AOB) and archaea (AOA) as well as nitrite-reducing bacteria using specific marker genes. We found that management affected the abundance of these microbial groups along each transect, though the specific responses differed between sites, due to different management histories and resulting variations in environmental parameters. In Austria, cessation of management caused an increase in nirK and nirS gene abundances. In the UK, intensification of grassland management led to 10-fold increases in the abundances of AOA and AOB and doubling of nirK gene abundance. In France, ploughing of previously mown grassland caused a 20-fold increase in AOA abundance. Across sites the abundance of AOB was most strongly related to soil NO3--N availability, and AOA were favored by higher soil pH. Among the nitrite reducers, nirS abundance correlatedwas most strongly with N parameters, such as soil NO3--N, microbial N. leachate NH4+-N, while the abundance of nirK-denitrifiers was affected by soil total N, organic matter (SOM) and water content. We conclude that alteration of soil environmental conditions is the dominant mechanism by which land management practices influence the abundance of each group of ammonia oxidizers and nitrite reducers. (C) 2018 Elsevier B.V. All rights reserved.
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Scientific Article
Winkelmann, T. ; Smalla, K. ; Amelung, W. ; Baab, G. ; Grunewaldt-Stöcker, G. ; Kanfra, X. ; Meyhöfer, R. ; Reim, S. ; Schmitz, M. ; Vetterlein, D. ; Wrede, A. ; Zühlke, S. ; Grunewaldt, J. ; Weiß, S. ; Schloter, M.
Current Issues Molec. Biol. 30, 89-106 (2019)
After replanting apple (Malus domestica Borkh.) on the same site severe growth suppressions, and a decline in yield and fruit quality are observed in all apple producing areas worldwide. The causes of this complex phenomenon, called apple replant disease (ARD), are only poorly understood up to now which is in part due to inconsistencies in terms and methodologies. Therefore we suggest the following definition for ARD: ARD describes a harmfully disturbed physiological and morphological reaction of apple plants to soils that faced alterations in their (micro-) biome due to the previous apple cultures. The underlying interactions likely have multiple causes that extend beyond common analytical tools in microbial ecology. They are influenced by soil properties, faunal vectors, and trophic cascades, with genotype-specific effects on plant secondary metabolism, particularly phytoalexin biosynthesis. Yet, emerging tools allow to unravel the soil and rhizosphere (micro-) biome, to characterize alterations of habitat quality, and to decipher the plant reactions. Thereby, deep insights into the reactions taking place at the root rhizosphere interface will be gained. Counteractions are suggested, taking into account that culture management should emphasize on improving soil microbial and faunal diversity as well as habitat quality rather than focus on soil disinfection.
Wissenschaftlicher Artikel
Scientific Article
2018
Peine, M. ; Vitow, N. ; Grafe, M. ; Baum, C. ; Zicker, T. ; Eichler-Löbermann, B. ; Schulz, S. ; Schloter, M. ; Leinweber, P.
J. Plant Nutr. Soil Sci. 182, 167-174 (2018)
Phosphorus (P) fertilizers and mycorrhiza formation can both significantly improve the P supply of plants, but P fertilizers might inhibit mycorrhiza formation and change the microbial P cycling. To test the dimension and consequences of P fertilizer impacts under maize (Zea mays L.), three fertilizer treatments (1) triple superphosphate (TSP, 21-30 kg P ha(-1) annually), biowaste compost (ORG, 30 Mg ha(-1) wet weight every third year) and a combination of both (OMI) were compared to a non-P-fertilized control (C) in 2015 and 2016. The test site was a long-term field experiment on a Stagnic Cambisol in Rostock (NE Germany). Soil microbial biomass P (P-mic) and soil enzyme activities involved in P mobilization (phosphatases and ss-glucosidase), plant-available P content (double lactate-extract; P-DL), mycorrhizal colonization, shoot biomass, and shoot P concentrations were determined. P deficiency led to decreased P immobilization in microbial biomass, but the maize growth was not affected. TSP application alone promoted the P uptake by the microbial biomass but reduced the mycorrhizal colonization of maize compared to the control by more than one third. Biowaste compost increased soil enzyme activities in the P cycling, increased P-mic and slightly decreased the mycorrhizal colonization of maize. Addition of TSP to biowaste compost increased the content of P-DL in soil to the level of optimal plant supply. Single TSP supply decreased the ratio of P-DL:P-mic to 1:1 from about 4:1 in the control. Decreased plant-benefits from mycorrhizal symbiosis were assumed from decreased mycorrhizal colonization of maize with TSP supply. The undesirable side effects of TSP supply on the microbial P cycling can be alleviated by the use of compost. Thus, it can be concluded that the plant-availability of P from soil amendments is controlled by the amendment-specific microbial P cycling and, likely, P transfer to plants.
Wissenschaftlicher Artikel
Scientific Article
Gullner, G. ; Komives, T. ; Király, L. ; Schröder, P.
Front. Plant Sci. 871, 1836:1836 (2018)
Plant glutathione S-transferases (GSTs) are ubiquitous and multifunctional enzymes encoded by large gene families. A characteristic feature of genes is their high inducibility by a wide range of stress conditions including biotic stress. Early studies on the role of GSTs in plant biotic stress showed that certain genes are specifically up-regulated by microbial infections. Later numerous transcriptome-wide investigations proved that distinct groups of s are markedly induced in the early phase of bacterial, fungal and viral infections. Proteomic investigations also confirmed the accumulation of multiple GST proteins in infected plants. Furthermore, functional studies revealed that overexpression or silencing of specific can markedly modify disease symptoms and also pathogen multiplication rates. However, very limited information is available about the exact metabolic functions of disease-induced GST isoenzymes and about their endogenous substrates. The already recognized roles of GSTs are the detoxification of toxic substances by their conjugation with glutathione, the attenuation of oxidative stress and the participation in hormone transport. Some GSTs display glutathione peroxidase activity and these GSTs can detoxify toxic lipid hydroperoxides that accumulate during infections. GSTs can also possess ligandin functions and participate in the intracellular transport of auxins. Notably, the expression of multiple is massively activated by salicylic acid and some GST enzymes were demonstrated to be receptor proteins of salicylic acid. Furthermore, induction of genes or elevated GST activities have often been observed in plants treated with beneficial microbes (bacteria and fungi) that induce a systemic resistance response (ISR) to subsequent pathogen infections. Further research is needed to reveal the exact metabolic functions of GST isoenzymes in infected plants and to understand their contribution to disease resistance.
Review
Review
Zanardo, M. ; Rosselli, R. ; Meneghesso, A. ; Sablok, G. ; Stevanato, P. ; Engel, M. ; Altissimo, A. ; Peserico, L. ; Dezuani, V. ; Concheri, G. ; Schloter, M. ; Squartini, A.
Soil Syst. 2:52 (2018)
Assessing the response of microbial communities to nutrient inputs in man-managed soils is of primary importance to understand the impact on ecosystem services provided by the soil microbiome. In this study, a low-nutrient soil was supplemented with seven different innovative fertilizers including matrixes of plant, animal, fungal or synthetic origin, and dosed to deliver the same amount of nitrogen. Growth of a potted grass crop (Cynodon dactylon) was recorded and the fertilizers were scored by the plant yield obtained in a greenhouse study. Soil was sampled at 9 and 58 days after the addition and bacterial community composition was analyzed after soil DNA extraction through pyrosequencing of 16S rDNA gene amplicons. Over 900 bacterial genera were detected, belonging to 21 described and 19 candidate phyla. In spite of the equal dose of nitrogen delivered, specific groups were fostered by given fertilizers; in particular marked effects on some phyla were displayed by a yeast-based fertilizer, which was also most effective in plant productivity. The main shifts were observed shortly after the fertilizer application, followed by a gradual stabilization of the equilibrium and by a rise in community evenness.
Wissenschaftlicher Artikel
Scientific Article
Bradford, L. ; Vestergaard, G. ; Táncsics, A. ; Zhu, B. ; Schloter, M. ; Lueders, T.
Front. Microbiol. 9:2696 (2018)
While most studies using RNA-stable isotope probing (SIP) to date have focused on ribosomal RNA, the detection of C-labeled mRNA has rarely been demonstrated. This approach could alleviate some of the major caveats of current non-target environmental "omics." Here, we demonstrate the feasibility of total RNA-SIP in an experiment where hydrocarbon-degrading microbes from a BTEX-contaminated aquifer were studied in microcosms with C-labeled toluene under microoxic conditions. From the total sequencing reads (∼30 mio. reads per density-resolved RNA fraction), an average of 1.2% of reads per sample were identified as non-rRNA, including mRNA. Members of the (including those related to spp.) were most abundant and enriched in C-rRNA, while well-known aerobic degraders such as spp. remained unlabeled. Transcripts related to cell motility, secondary metabolite formation and xenobiotics degradation were highly labeled with C. mRNA of phenol hydroxylase genes were highly labeled and abundant, while other transcripts of toluene-activation were not detected. Clear labeling of catechol 2,3-dioxygenase transcripts supported previous findings that some of these extradiol dioxygenases were adapted to low oxygen concentrations. We introduce a novel combination of total RNA-SIP with calculation of transcript-specific enrichment factors (EFs) in C-RNA, enabling a targeted approach to process-relevant gene expression in complex microbiomes.
Wissenschaftlicher Artikel
Scientific Article
Felipe-Lucia, M.R. ; Soliveres, S. ; Penone, C. ; Manning, P. ; van der Plas, F. ; Boch, S. ; Prati, D. ; Ammer, C. ; Schall, P. ; Gossner, M.M. ; Bauhus, J. ; Buscot, F. ; Blaser, S. ; Blüthgen, N. ; de Frutos, A. ; Ehbrecht, M. ; Frank, K. ; Goldmann, K. ; Hänsel, F. ; Jung, K. ; Kahl, T. ; Nauss, T. ; Oelmann, Y. ; Pena, R. ; Polle, A. ; Renner, S. ; Schloter, M. ; Schöning, I. ; Schrumpf, M. ; Schulze, E.D. ; Solly, E. ; Sorkau, E. ; Stempfhuber, B. ; Tschapka, M. ; Weisser, W.W. ; Wubet, T. ; Fischer, M. ; Allan, E.
Nat. Commun. 9:4839 (2018)
Trade-offs and synergies in the supply of forest ecosystem services are common but the drivers of these relationships are poorly understood. To guide management that seeks to promote multiple services, we investigated the relationships between 12 stand-level forest attributes, including structure, composition, heterogeneity and plant diversity, plus 4 environmental factors, and proxies for 14 ecosystem services in 150 temperate forest plots. Our results show that forest attributes are the best predictors of most ecosystem services and are also good predictors of several synergies and trade-offs between services. Environmental factors also play an important role, mostly in combination with forest attributes. Our study suggests that managing forests to increase structural heterogeneity, maintain large trees, and canopy gaps would promote the supply of multiple ecosystem services. These results highlight the potential for forest management to encourage multifunctional forests and suggest that a coordinated landscape-scale strategy could help to mitigate trade-offs in human-dominated landscapes.
Wissenschaftlicher Artikel
Scientific Article
Chen, F. ; Schröder, P.
Desalin. Water Treat. 127, 111-120 (2018)
Oxybenzone (OBZ) present in the environment as an emerging contaminant may occur jointly with the nanoparticle TiO2 due to the typical composition of many sunscreens. Thus, potential effects caused by TiO2 must be considered when investigating the environmental fate of sunscreens and also when plant performance with regard to remediation of OBZ is scrutinized. Toxicity effects of OBZ and TiO2 on plant development were evaluated by recording germination rates and root lengths of tomato and barley. Results showed that OBZ significantly inhibited germination rate of tomato seeds, while no effect was observed for germination of barley seeds. Interestingly, co-exposure with TiO2 lowered the toxicity of OBZ on the tomato seedlings as there were no differences on germination rate and root length between co-exposure and control treatments. Moreover, growth inhibition tests with Lemna minor showed that addition of TiO2 even enhanced plant growth by increasing the frond area. Furthermore, influence of TiO2 (3 mg/L) on removal of OBZ (5 mu M) by plants was examined with respect to the variations in uptake and metabolism of OBZ in a hairy root culture system. Co-exposure to TiO2 amplified the accumulation of OBZ in plants, while transient slower transformation to OBZ metabolites was recognized when TiO2 had been added. Therefore, it can be concluded that Ti nanoparticles may generally reduce the phytotoxicity of OBZ and increase the uptake of this compound in phytoremediation, while the interaction with the transformation capacity should be considered when applying phytoremediation for UV-filter contaminated water.
Wissenschaftlicher Artikel
Scientific Article
Staude, B. ; Oehmke, F. ; Lauer, T. ; Behnke, J. ; Göpel, W. ; Schloter, M. ; Schulz, H. ; Krauss-Etschmann, S. ; Ehrhardt, H.
Biomed Res. Int. 2018:7218187 (2018)
Preterm birth poses a global challenge with a continuously increasing disease burden during the last decades. Advances in understanding the etiopathogenesis did not lead to a reduction of prematurely born infants so far. A balanced development of the host microbiome in early life is key for the maturation of the immune system and many other physiological functions. With the tremendous progress in new diagnostic possibilities, the contribution of microbiota changes to preterm birth and the acute and long-term sequelae of prematurity have come into the research focus. This review summarizes the latest advances in the understanding of microbiomes in the amniotic cavity and the female lower genital tract and how changes in microbiota structures contribute to preterm delivery. The exhibition of these highly vulnerable infants to the hostile environment in the neonatal intensive care unit necessarily entails the rapid colonization with a nonbalanced microbiome in a situation where the organism is still very prone and at an early stage of development. The global research efforts to decipher pathologic changes will pave the way to new pre- and postnatal therapeutic concepts.
Review
Review
Liu, S. ; Schloter, M. ; Brüggemann, N.
Eur. J. Soil Sci. 69, 936-946 (2018)
Rewetting of soil might contribute considerably to the annual production of nitrous oxide (N2O) in ecosystems subjected to long dry periods. Therefore, it is crucial to elucidate the most important factors responsible for large pulses of N2O with rewetting. In this study, we carried out a series of rewetting experiments with soil samples collected from upland and riparian forest, grassland and arable land. We analysed the dynamics of ammonium (NH4+), nitrite (NO2-), nitrate (NO3-) and dissolved organic matter (DOM) of air-dried soil samples after rewetting. We also analysed the effects of sterilization of soil samples by -irradiation on N2O production with rewetting. Furthermore, we explored the effects of rewetting and sterilization on the isotopic composition of N2O in the different soil samples. The grassland soil produced the largest amount of N2O (64.1gNkg(-1)) in 1hour on rewetting, followed by upland forest soil, whereas it was least for soils from riparian forest and arable land. Gamma irradiation, however, decreased soil N2O production from forest soil samples by 30-90% after rewetting, but increased N2O production in grassland and arable land soils three-fold and two-fold, respectively. Correlation analysis revealed that NO2- concentration in the soil samples at the time of rewetting was the most relevant factor that explained soil N2O production after rewetting. Furthermore, the addition of NO2- before rewetting increased N2O production during rewetting more than with additions of NO3- and NH4+ in all soil samples. The N-15 site preference values of N2O produced after rewetting were close to 0, indicating a denitrification-related production process according to the classical view. However, additional abiotic processes responsible for soil N2O production during rewetting cannot be excluded.Highlights Mechanisms responsible for large N2O production during rewetting of soil are not well understood. Nitrite content in dry soil was strongly correlated with N2O production after rewetting. The 15N site preference of the N2O produced was close to 0% after rewetting. Additional abiotic processes could have contributed to N2O formation from NO2 -.
Wissenschaftlicher Artikel
Scientific Article
Jatzlauk, G. ; Bartel, S. ; Pfeiffer, S. ; Schloter, M. ; Krauss-Etschmann, S.
Allergy 73, 302-302 (2018)
Meeting abstract
Meeting abstract
Reichel, R. ; Wei, J. ; Islam, M.S. ; Schmid, C. ; Wissel, H. ; Schröder, P. ; Schloter, M. ; Brüggemann, N.
Front. Plant Sci. 9:900 (2018)
Plants like winter wheat are known for their insufficient N uptake between sowing and the following growing season. Especially after N-rich crops like oilseed rape or field bean, nitrogen retention of the available soil N can be poor, and the risk of contamination of the hydrosphere with nitrate (NO3-) and the atmosphere with nitrous oxide (N2O) is high. Therefore, novel strategies are needed to preserve these unused N resources for subsequent agricultural production. High organic carbon soil amendments (HCA) like wheat straw promote microbial N immobilization by stimulating microbes to take up N from soil. In order to test the suitability of different HCA for immobilization of excess N, we conducted a laboratory incubation experiment with soil columns, each containing 8 kg of sandy loam of an agricultural Ap horizon. We created a scenario with high soil mineral N content by adding 150 kg NH4+-N ha-1 to soil that received either wheat straw, spruce sawdust or lignin at a rate of 4.5 t C ha-1, or no HCA as control. Wheat straw turned out to be suitable for fast immobilization of excess N in the form of microbial biomass N (up to 42 kg N ha-1), followed by sawdust. However, under the experimental conditions this effect weakened over a few weeks, finally ranging between 8 and 15 kg N ha-1 immobilized in microbial biomass in the spruce sawdust and wheat straw treatment, respectively. Pure lignin did not stimulate microbial N immobilization. We also revealed that N immobilization by the remaining straw and sawdust HCA material in the soil had a greater importance for storage of excess N (on average 24 kg N ha-1) than microbial N immobilization over the 4 months. N fertilization and HCA influenced the abundance of ammonia oxidizing bacteria and archaea as the key players for nitrification, as well as the abundance of denitrifiers. Soil with spruce sawdust emitted more N2O compared to soil with wheat straw, which in relation released more CO2, resulting in a comparable overall global warming potential. However, this was counterbalanced by advantages like N immobilization and mitigation of potential NO3- losses.
Wissenschaftlicher Artikel
Scientific Article
Grün, A.L. ; Straskraba, S. ; Schulz, S. ; Schloter, M. ; Emmerling, C.
J. Environ. Sci. 69, 12-22 (2018)
The increasing production and use of engineered silver nanoparticles (AgNP) in industry and private households are leading to increased concentrations of AgNP in the environment. An ecological risk assessment of AgNP is needed, but it requires understanding the long term effects of environmentally relevant concentrations of AgNP on the soil microbiome. Hence, the aim of this study was to reveal the long-term effects of AgNP on soil microorganisms. The study was conducted as a laboratory incubation experiment over a period of one year using a loamy soil and AgNP concentrations ranging from 0.01 to 1 mg AgNP/kg soil. The short term effects of AgNP were, in general, limited. However, after one year of exposure to 0.01 mg AgNP/kg, there were significant negative effects on soil microbial biomass (quantified by extractable DNA; p = 0.000) and bacterial ammonia oxidizers (quantified by amoA gene copy numbers; p = 0.009). Furthermore, the tested AgNP concentrations significantly decreased the soil microbial biomass, the leucine aminopeptidase activity (quantified by substrate turnover; p = 0.014), and the abundance of nitrogen fixing microorganisms (quantified by nifH gene copy numbers; p = 0.001). The results of the positive control with AgNO3 revealed predominantly stronger effects due to Ag+ ion release. Thus, the increasing toxicity of AgNP during the test period may reflect the long-term release of Ag+ ions. Nevertheless, even very low concentrations of AgNP caused disadvantages for the microbial soil community, especially for nitrogen cycling, and our results confirmed the risks of releasing AgNP into the environment.
Wissenschaftlicher Artikel
Scientific Article
Balazs, H.-E. ; Schmid, C. ; Feher, I. ; Podar, D. ; Szatmari, P.M. ; Marincaş, O. ; Balázs, Z.R. ; Schröder, P.
J. Environ. Manage. 223, 286-296 (2018)
Current physical or chemical methods used for remediation of soils contaminated with hexachlocyclohexane (HCH), leave behind significant levels of pollutants. Given the compounds volatility and persistence in the environment, sites contaminated with HCH remain a concern for the population living in nearby areas. By making use of both the recovery capacity and the pollutant uptake ability of spontaneously growing vegetation, our study aimed to identify native plant species able to cover and moreover take up the HCH left at a former lindane production unit in Turda, Romania. The results showed that dominant species across the study site like Lotus tenuis, Artemisia vulgaris or Tanacetum vulgare, were capable of taking up HCH in their tissues, according to different patterns that combined at the scale of the plant community. Regardless of the proximity of the HCH contamination hotspots, the development of the plant cover was characteristic for vegetation succession on disturbed soils of the Central European region. Finally, we conclude that plant species which grow spontaneously at the HCH contaminated site in Turda and are capable of taking up the pollutant, represent a self-sustainable and low maintenance phytomanagement approach that would allow for the reintegration of the site in the urban or industrial circuit and nevertheless would reduce the toxicity risk to the neighboring human inhabitants.
Wissenschaftlicher Artikel
Scientific Article
Pierattini, E.C. ; Francini, A. ; Huber, C. ; Sebastiani, L. ; Schröder, P.
Sci. Total Environ. 636, 944-952 (2018)
Poplar plants may have an important role in the removal of pharmaceuticals from contaminated waters. In this context, plant uptake of the non-steroidal anti-inflammatory drug diclofenac, as well as physiological response in terms of growth traits and stress enzymes activity was assessed in Populus alba Villafranca clone, in order to establish the effectiveness of this species against pharmaceutical active compounds pollution.This evaluation was conducted in mesocosms with 1 mg L-1 of this pharmaceutical for a maximum period of 28 days. Root appears to be the organ with clear uptake of diclofenac (14.76 +/- 2.42 ng g(-1) fresh weight after 1 day of treatment), and presence of products derived from its metabolism. Indeed, 4-OH-diclofenac metabolite was detected in root tissues, indicating diclofenac uptake and metabolism inside the plants, already after 1 day of treatment.Regarding enzyme activities, glutathione-S-transferases increased in roots after long-term exposure to diclofenac, while an increase in activity of ascorbate peroxidase and glutathione reductase was detected in short and medium-term exposure, as a result of abiotic stress caused by diclofenac. Results suggest the ability of poplar to actively participate in the removal of diclofenac from water when used for phytoremediation purpose. (C) 2018 Elsevier B.V. All rights reserved.
Wissenschaftlicher Artikel
Scientific Article
Chen, F. ; Schnick, S. ; Schröder, P.
Environ. Sci. Pollut. Res. 25, 16080-16090 (2018)
Phytoremediation has been proposed to reduce the load of the sunscreen oxybenzone (OBZ) in the aquatic environment. Despite the proven removal efficiency of this compound, little is known about its influence, particularly oxidative stress on plants. In this study, a short-term incubation of macrophytic Cyperus alternifolius was performed to prove the plant's ability to withstand the stress. Detached shoots were immersed in medium spiked with different concentrations of OBZ (50, 100, and 500 mu M) for 2, 4, and 7 days, respectively. Increased formation of O-2 and H2O2 in Cyperus treated with OBZ was characterized by intense colorization following histochemical staining. Alterations of enzyme activities involved in the antioxidative defense system indicate an adaptive response of C. alternifolius to this xenobiotic stress. Quantification of lipid peroxidation reveals that no significant membrane damage occurred during incubation with OBZ. Overall, 50 mu M OBZ (tenfold higher than the amount frequently detected in the environment) exhibited low toxic effects. Accordingly, this pilot study provides information on the potential use of Cyperus to remove emerging sunscreen contaminants from water bodies.
Wissenschaftlicher Artikel
Scientific Article
Grafe, M. ; Goers, M. ; Tucher, S.V. ; Baum, C. ; Zimmer, D. ; Leinweber, P. ; Vestergaard, G. ; Kublik, S. ; Schloter, M. ; Schulz, S.
Environ. Microbiol. Rep. 10, 320-327 (2018)
Phosphorus is one of the most important macronutrient for plants. In agriculture, amending fertilizer with phosphorus (P) is common practice. However, natural phosphorus sources are finite, making research for more sustainable management practices necessary. We postulated that the addition of carbon (C) and nitrogen (N) would stimulate phosphorus mobilization by bacteria because of their desire to maintain a stable intracellular C:N:P stoichiometry. Therefore, we chose a metagenomic approach to investigate two agricultural soils, which only received mineral N fertilizer or mineral N and organic fertilizer for more than 20 years. The most abundant genes involved in the acquisition of external P sources in our study were those involved in solubilization and subsequent uptake of inorganic phosphorus. Independent of site and season, the relative abundance of genes involved in P turnover was not significantly affected by the addition of fertilizers. However, the type of fertilization had a significant impact on the diversity pattern of bacterial families harbouring genes coding for the different P transformation processes. This gives rise to the possibility that fertilizers can substantially change phosphorus turnover efficiency by favouring different families. Additionally, none of the families involved in phosphorus turnover covered all investigated processes. Therefore, promoting bacteria which play an essential role specifically in mobilization of hardly accessible phosphorus could help to secure the phosphorus supply of plants in soils with low P input.
Wissenschaftlicher Artikel
Scientific Article
Chen, Z. ; Lin, S. ; Yao, Z. ; Zheng, X. ; Gschwendtner, S. ; Schloter, M. ; Liu, M. ; Zhang, Y. ; Butterbach-Bahl, K. ; Dannenmann, M.
Soil Biol. Biochem. 121, 77-86 (2018)
An alternative to conventional cultivation of rice on submerged paddy soil is the ground cover rice production system (GCRPS), in which soil is covered with a plastic film to reduce the use of irrigation water. However, reduced soil water, increased aeration and temperature under GCRPS could promote soil nitrogen (N) mineralizing, nitrifying and denitrifying microbes and thus enhance soil N turnover and environmental losses e.g., through emission of the potent greenhouse gas nitrous oxide (N 2 O). At two sites with paired GCRPS and conventional paddy fields in Central China, we followed the abundance and activity of N-mineralizers, nitrifiers, denitrifiers and N 2 -fixing microbes based on qPCR from DNA and RNA directly extracted from soil. With decreasing soil water during the growing season, GCRPS strongly increased N mineralization as illustrated by several fold increased transcript levels of chiA. Furthermore, GCRPS reduced the nifH transcripts (encoding for nitrogenase) by 38% to 70% but increased the qnorB transcripts by 160% and archaeal amoA (AOA) transcripts by one order of magnitude (encoding for nitric oxide reductase and ammonia monooxygenase). This indicated a higher potential for N losses due to decreased biological N 2 fixation, increased N leaching and increased N 2 O emission in GCRPS. The latter was confirmed by increased in situ N 2 O emissions. In addition, the N 2 -fixing and denitrifying microbial community composition as measured by a community fingerprinting approach was strongly influenced by GCRPS cultivation. Hence, our study reveals the microbial mechanisms underlying the risks for increased N mineralization, nitrification and N 2 O emissions and decreased biological N fixation in GCRPS. However, analysis of topsoil N stocks provided evidence that at least under N fertilizer application, GCRPS might overall maintain soil N stocks. This might result from a GCRPS-induced increase in fertilizer N use efficiency, root development and C and N return via residues, which appear to outbalance the observed effects on nitrification, gaseous N losses and biological N fixation, thereby preventing a net loss of total soil N.
Wissenschaftlicher Artikel
Scientific Article
Šket, R. ; Debevec, T. ; Kublik, S. ; Schloter, M. ; Schöler, A. ; Murovec, B. ; Mikuš, K.V. ; Makuc, D. ; Pečnik, K. ; Plavec, J. ; Mekjavić, I.B. ; Eiken, O. ; Prevoršek, Z. ; Stres, B.
Front. Physiol. 9:198 (2018)
We explored the metagenomic, metabolomic and trace metal makeup of intestinal microbiota and environment in healthy male participants during the run-in (5 day) and the following three 21-day interventions: normoxic bedrest (NBR), hypoxic bedrest (HBR) and hypoxic ambulation (HAmb) which were carried out within a controlled laboratory environment (circadian rhythm, fluid and dietary intakes, microbial bioburden, oxygen level, exercise). The fraction of inspired O(FO) and partial pressure of inspired O(PO) were 0.209 and 133.1 ± 0.3 mmHg for the NBR and 0.141 ± 0.004 and 90.0 ± 0.4 mmHg (~4,000 m simulated altitude) for HBR and HAmb interventions, respectively. Shotgun metagenomes were analyzed at various taxonomic and functional levels,H- andC -metabolomes were processed using standard quantitative and human expert approaches, whereas metals were assessed using X-ray fluorescence spectrometry. Inactivity and hypoxia resulted in a significant increase in the genusin HBR, in genes coding for proteins involved in iron acquisition and metabolism, cell wall, capsule, virulence, defense and mucin degradation, such as beta-galactosidase (EC3.2.1.23), α-L-fucosidase (EC3.2.1.51), Sialidase (EC3.2.1.18), and α-N-acetylglucosaminidase (EC3.2.1.50). In contrast, the microbial metabolomes, intestinal element and metal profiles, the diversity of bacterial, archaeal and fungal microbial communities were not significantly affected. The observed progressive decrease in defecation frequency and concomitant increase in the electrical conductivity (EC) preceded or took place in absence of significant changes at the taxonomic, functional gene, metabolome and intestinal metal profile levels. The fact that the genusand proteins involved in iron acquisition and metabolism, cell wall, capsule, virulence and mucin degradation were enriched at the end of HBR suggest that both constipation and EC decreased intestinal metal availability leading to modified expression of co-regulated genes ingenomes. Bayesian network analysis was used to derive the first hierarchical model of initial inactivity mediated deconditioning steps over time. The PlanHab wash-out period corresponded to a profound life-style change (i.e., reintroduction of exercise) that resulted in stepwise amelioration of the negative physiological symptoms, indicating that exercise apparently prevented the crosstalk between the microbial physiology, mucin degradation and proinflammatory immune activities in the host.
Wissenschaftlicher Artikel
Scientific Article
Jia, J. ; Conlon, T.M. ; Sarker, R.S. ; Taşdemir, D. ; Smirnova, N.F. ; Srivastava, B. ; Verleden, S.E. ; Güneş, G. ; Wu, X. ; Prehn, C. ; Gao, J. ; Heinzelmann, K. ; Lintelmann, J. ; Irmler, M. ; Pfeiffer, S. ; Schloter, M. ; Zimmermann, R. ; Hrabě de Angelis, M. ; Beckers, J. ; Adamski, J. ; Bayram, H. ; Eickelberg, O. ; Yildirim, A.Ö.
EMBO Mol. Med. 10:e8349 (2018)
The development of chronic obstructive pulmonary disease (COPD) pathogenesis remains unclear, but emerging evidence supports a crucial role for inducible bronchus-associated lymphoid tissue (iBALT) in disease progression. Mechanisms underlying iBALT generation, particularly during chronic CS exposure, remain to be defined. Oxysterol metabolism of cholesterol is crucial to immune cell localization in secondary lymphoid tissue. Here, we demonstrate that oxysterols also critically regulate iBALT generation and the immune pathogenesis of COPD. In both COPD patients and cigarette smoke (CS)-exposed mice, we identified significantly upregulated CH25H and CYP7B1 expression in airway epithelial cells, regulating CS-induced B-cell migration and iBALT formation. Mice deficient in CH25H or the oxysterol receptor EBI2 exhibited decreased iBALT and subsequent CS-induced emphysema. Further, inhibition of the oxysterol pathway using clotrimazole resolved iBALT formation and attenuated CS-induced emphysema in vivo therapeutically. Collectively, our studies are the first to mechanistically interrogate oxysterol-dependent iBALT formation in the pathogenesis of COPD, and identify a novel therapeutic target for the treatment of COPD and potentially other diseases driven by the generation of tertiary lymphoid organs.
Wissenschaftlicher Artikel
Scientific Article
Schulze-Makuch, D. ; Wagner, D. ; Kounaves, S.P. ; Mangelsdorf, K. ; Devine, K.G. ; de Vera, J.P. ; Schmitt-Kopplin, P. ; Grossart, H.P. ; Parro, V. ; Kaupenjohann, M. ; Galy, A. ; Schneider, B. ; Airo, A. ; Frösler, J. ; Davila, A.F. ; Arens, F.L. ; Cáceres, L. ; Cornejo, F.S. ; Carrizo, D. ; Dartnell, L. ; DiRuggiero, J. ; Flury, M. ; Ganzert, L. ; Gessner, M.O. ; Grathwohl, P. ; Guan, L. ; Heinz, J. ; Hess, M. ; Keppler, F. ; Maus, D. ; McKay, C.P. ; Meckenstock, R.U. ; Montgomery, W. ; Oberlin, E.A. ; Probst, A.J. ; Sáenz, J.S. ; Sattler, T. ; Schirmack, J. ; Sephton, M.A. ; Schloter, M. ; Uhl, J. ; Valenzuela, B. ; Vestergaard, G. ; Wörmer, L. ; Zamorano, P.
Proc. Natl. Acad. Sci. U.S.A. 115, 2670-2675 (2018)
Traces of life are nearly ubiquitous on Earth. However, a central unresolved question is whether these traces always indicate an active microbial community or whether, in extreme environments, such as hyperarid deserts, they instead reflect just dormant or dead cells. Although microbial biomass and diversity decrease with increasing aridity in the Atacama Desert, we provide multiple lines of evidence for the presence of an at times metabolically active, microbial community in one of the driest places on Earth. We base this observation on four major lines of evidence: (i) a physico-chemical characterization of the soil habitability after an exceptional rain event, (ii) identified biomolecules indicative of potentially active cells [e.g., presence of ATP, phospholipid fatty acids (PLFAs), metabolites, and enzymatic activity], (iii) measurements of in situ replication rates of genomes of uncultivated bacteria reconstructed from selected samples, and (iv) microbial community patterns specific to soil parameters and depths. We infer that the microbial populations have undergone selection and adaptation in response to their specific soil microenvironment and in particular to the degree of aridity. Collectively, our results highlight that even the hyperarid Atacama Desert can provide a habitable environment for microorganisms that allows them to become metabolically active following an episodic increase in moisture and that once it decreases, so does the activity of the microbiota. These results have implications for the prospect of life on other planets such as Mars, which has transitioned from an earlier wetter environment to today's extreme hyperaridity.
Wissenschaftlicher Artikel
Scientific Article
Sosa-Hernández, M.A. ; Roy, J. ; Hempel, S. ; Kautz, T. ; Köpke, U. ; Uksa, M. ; Schloter, M. ; Caruso, T. ; Rillig, M.C.
Soil Biol. Biochem. 117, 83-86 (2018)
Arbuscular mycorrhizal fungi are recognized as important drivers of plant health and productivity in agriculture but very often existing knowledge is limited to the topsoil. With growing interest in the role of subsoil in sustainable agriculture, we used high-throughput Illumina sequencing on a set of samples encompassing drilosphere, rhizosphere and bulk soil, in both top- and subsoil. Our results show subsoil AMF communities harbor unique Operational Taxonomic Units (OTUs) and that both soil depths differ in community structure both at the OTU and family level. Our results emphasize the distinctness of subsoil AMF communities and the potential role of subsoil as a biodiversity reservoir.
Wissenschaftlicher Artikel
Scientific Article
Spohn, M. ; Zavišić, A. ; Nassal, P. ; Bergkemper, F. ; Schulz, S. ; Marhan, S. ; Schloter, M. ; Kandeler, E. ; Polle, A.
Soil Biol. Biochem. 117, 191-202 (2018)
The objective of this study was to determine temporal variations of phosphorus (P) uptake by young beech trees (Fagus sylvatica L.) and soil microorganisms in two forests with contrasting P stocks with the aim to better understand P dynamics in forest ecosystems. For this purpose, we conducted a mesocosm experiment and determined P uptake by F. sylvatica, total soil microbial biomass (SMB) and ectomycorrhizal fungi (EMF) at the root tip based on P-33 labeling at five times during the year. Furthermore, we measured EMF community composition, potential acid phosphatase activity (APA), and abundance of bacterial acid phosphatase (phoN) genes. The results showed that plant P uptake was elevated in summer and autumn in the mesocosms from the P-poor site, while it was elevated only in autumn in the mesocosms from the P-rich site. P uptake by SMB was higher in the organic layer at the P-poor site than in the organic layer at the P-rich site throughout the year, underlining the importance of the microbial P pool in the organic layer of P-poor forests. The finding shows that the SMB was able to compensate for the lower P availability in the soil of the P-poor site. The EMF community composition was very variable over the year, and plant P uptake seemed to be independent of EMF community composition. Despite the high species turnover in the EMF community, the potential APA was high throughout the year, indicating functional redundancy of the microbial community with respect to P mineralization. Taken together, our results show important differences in temporal patterns of P uptake by F. sylvatica and the SMB as well as in the total partitioning of P between the SMB and F. sylvatica across the sites. Moreover, decreasing P availability in forests would not only change the size of P stocks and of P cycling rates, but would also affect temporal dynamics of P uptake and the overall partitioning of P between different biotic compartments.
Wissenschaftlicher Artikel
Scientific Article
Sauvetre, A. ; May, R.G. ; Harpaintner, R. ; Poschenrieder, C. ; Schröder, P.
J. Hazard. Mater. 342, 85-95 (2018)
Carbamazepine (CBZ) is a pharmaceutical frequently categorized as a recalcitrant pollutant in the aquatic environment. Endophytic bacteria previously isolated from reed plants have shown the ability to promote growth of their host and to contribute to CBZ metabolism. In this work, a horseradish (Armoracia rusticana) hairy root (HR) culture has been used as a plant model to study the interactions between roots and endophytic bacteria in response to CBZ exposure. HRs could remove up to 5% of the initial CBZ concentration when they were grown in spiked Murashige and Skoog (MS) medium. Higher removal rates were observed when HRs were inoculated with the endophytic bacteria Rhizobium radiobacter (21%) and Diaphorobacter nitroreducens (10%). Transformation products resulting from CBZ degradation were identified using liquid chromatography-ultra high-resolution quadrupole time of flight mass spectrometry (LC-UHR-QTOF-MS). CBZ metabolism could be divided in four pathways. Metabolites involving GSH conjugation and 2,3-dihydroxylation, as well as acridine related compounds are described in plants for the first time. This study presents strong evidence that xenobiotic metabolism and degradation pathways in plants can be modulated by the interaction with their endophytic community. Hence it points to plausible applications for the elimination of recalcitrant compounds such as CBZ from wastewater in CWs.
Wissenschaftlicher Artikel
Scientific Article
Schmid, C. ; Schröder, P. ; Armbruster, M. ; Schloter, M.
Microb. Ecol. 76, 226–239 (2018)
This study intended to elucidate the long-term effects of organic soil amendments on bacterial co-occurrence in bulk soil with and without addition of mineral fertiliser. Previous research mostly neglected the bacterial co-occurrence structure and focussed mainly on the parameters species diversity and abundance changes of species. Here we present a systematic comparison of two frequently used soil amendments, manure and straw, with regard to their impact on bacterial co-occurrence in a long-term field trial in Speyer, Germany. The approach involved 16S amplicon sequencing in combination with a bacterial network analysis, comparing the different fertiliser regimes. The results show an increase of bacterial diversity as well as an accumulation of bacteria of the order Bacillales in plots fertilised with manure compared to a control treatment. In the straw-amended plots neither an increase in diversity was found nor were indicative species detectable. Furthermore, network analysis revealed a clear impact of mineral fertiliser addition on bacterial co-occurrence structure. Most importantly, both organic amendments increased network complexity irrespective of mineral fertilisation regime. At the same time, the effects of manure and straw exhibited differences that might be explained by differences in their nutritional/chemical contents. It is concluded that bacterial interactions are a crucial parameter for the assessment of amendment effects regarding soil health and sustainability.
Wissenschaftlicher Artikel
Scientific Article
Varanini, Z. ; Cesco, S. ; Tomasi, N. ; Pinton, R. ; Guzzo, F. ; Zamboni, A. ; Schloter-Hai, B. ; Schloter, M. ; Giagnoni, L. ; Arenella, M. ; Nannipieri, P. ; Renella, G.
Plant Soil 422, 331–347 (2018)
The rate of nitrate (NO3 (-)) uptake and changes in rhizosphere properties were studied growing seedlings of two maize inbred lines differing in nitrogen use efficiency (NUE) in rhizoboxes. Changes in NO3 (-) uptake rates occurred in response to anion addition (induction) in seedlings grown both in hydroponic culture and in soil in rhizoboxes. The characterization of root exudate composition showed a line-specific metabolite profile, which was also affected by NO3 (-) availability. The induction affected respiration, nitrification, ammonification and enzyme activities of the rhizosphere. Furthermore, the composition of rhizosphere bacterial communities of the two maize lines differed suggesting the selective capacity of plants. Overall, results showed a strong and fast modification of rhizospheric soil properties in response to physiological changes in plants caused by fluctuating NO3 (-) availability.
Wissenschaftlicher Artikel
Scientific Article
Baraniya, D. ; Nannipieri, P. ; Kublik, S. ; Vestergaard, G. ; Schloter, M. ; Schöler, A.
Microb. Ecol. 75, 830–833 (2018)
While root exudation follows diurnal rhythms, little is known about the consequences for the microbiome of the rhizosphere. In this study, we used a metatranscriptomic approach to analyze the active microbial communities, before and after sunrise, in the rhizosphere of barley. We detected increased activities of many prokaryotic microbial taxa and functions at the pre-dawn stage, compared to post-dawn. Actinomycetales, Planctomycetales, Rhizobiales, and Burkholderiales were the most abundant and therefore the most active orders in the barley rhizosphere. The latter two, as well as Xanthomonadales, Sphingomonadales, and Caulobacterales showed a significantly higher abundance in pre-dawn samples compared to post-dawn samples. These changes in taxonomy coincide with functional changes as genes involved in both carbohydrate and amino acid metabolism were more abundant in pre-dawn samples compared to post-dawn samples. This study significantly enhances our present knowledge on how rhizospheric microbiota perceives and responds to changes in the soil during dark and light periods.
Wissenschaftlicher Artikel
Scientific Article
Kostric, M. ; Milger, K. ; Krauss-Etschmann, S. ; Engel, M. ; Vestergaard, G. ; Schloter, M. ; Schöler, A.
Microb. Ecol. 75, 529-542 (2018)
The lower respiratory tract has been previously considered sterile in a healthy state, but advances in culture-independent techniques for microbial identification and characterization have revealed that the lung harbors a diverse microbiome. Although research on the lung microbiome is increasing and important questions were already addressed, longitudinal studies aiming to describe developmental stages of the microbial communities from the early neonatal period to adulthood are lacking. Thus, little is known about the early-life development of the lung microbiome and the impact of external factors during these stages. In this study, we applied a barcoding approach based on high-throughput sequencing of 16S ribosomal RNA gene amplicon libraries to determine age-dependent differences in the bacterial fraction of the murine lung microbiome and to assess potential influences of differing "environmental microbiomes" (simulated by the application of used litter material to the cages). We could clearly show that the diversity of the bacterial community harbored in the murine lung increases with age. Interestingly, bacteria belonging to the genera Delftia and Rhodococcus formed an age-independent core microbiome. The addition of the used litter material influenced the lung microbiota of young mice but did not significantly alter the community composition of adult animals. Our findings elucidate the dynamic nature of the early-life lung microbiota and its stabilization with age. Further, this study indicates that even slight environmental changes modulate the bacterial community composition of the lung microbiome in early life, whereas the lung microbes of adults demonstrate higher resilience towards environmental variations.
Wissenschaftlicher Artikel
Scientific Article
2017
Nesme, J. ; Cania, B. ; Zadel, U. ; Schöler, A. ; Płaza, G.A. ; Schloter, M.
Genome Announc. 5:e01330-17 (2017)
We report here the complete genome sequences of two Pseudomonas putida isolates recovered from surface-sterilized roots of Sida hermaphrodita The two isolates were characterized by an increased tolerance to zinc, cadmium, and lead. Furthermore, the strains showed typical plant growth-promoting properties, such as the production of indole acetic acid, cellulolytic enzymes, and siderophores.
Wissenschaftlicher Artikel
Scientific Article
Marin, C. ; Godoy, R. ; Valenzuela, E. ; Schloter, M. ; Wubet, T. ; Boy, J. ; Gschwendtner, S.
J. Soil Sci. Plant Nutr. 17, 985-1002 (2017)
By reducing soil organic matter and litter input, land-use changes are predicted to decrease total soil fungal diversity, but at functional levels this have been poorly studied. It is expected, though, that increasing disturbance decreases saprotrophic and mycorrhizal fungi biodiversity. This study aimed to determine the effects of land-use changes on the phylogenetic and functional diversity of soil fungi in the Southern Andes. We assessed the fungal communities of Andosol topsoil at 1 cm and 10 cm soil depth. The soil samples were obtained from a gradient of anthropogenic disturbance; specifically, plots were located within pristine forest, overstory-managed, and clear-cut conditions. We used a cultivation-independent molecular barcoding approach to assess fungal diversity and identify 1,173 OTUs from which 401 were assigned to a functional guild. While we found higher phylogenetic richness in clear-cut conditions, these soils had higher relative abundances of plant pathogen fungi and lower relative abundances of saprotrophic and ectomycorrhizal fungi compared to the other treatments. The opposite pattern was found in pristine forest. Thus, fungal species richness itself does not seem to reflect ecosystem health. Interestingly though, the lower phylogenetic diversity found in pristine forest was compensated by a higher diversity of fungi involved in nutrient cycling.
Wissenschaftlicher Artikel
Scientific Article
Šket, R. ; Treichel, N. ; Kublik, S. ; Debevec, T. ; Eiken, O. ; Mekjavić, I. ; Schloter, M. ; Vital, M. ; Chandler, J. ; Tiedje, J.M. ; Murovec, B. ; Prevoršek, Z. ; Likar, M. ; Stres, B.
PLoS ONE 12:e0188556 (2017)
We explored the assembly of intestinal microbiota in healthy male participants during the randomized crossover design of run-in (5 day) and experimental phases (21-day normoxic bed rest (NBR), hypoxic bed rest (HBR) and hypoxic ambulation (HAmb) in a strictly controlled laboratory environment, with balanced fluid and dietary intakes, controlled circadian rhythm, microbial ambiental burden and 24/7 medical surveillance. The fraction of inspired O2 (FiO2) and partial pressure of inspired O2 (PiO2) were 0.209 and 133.1 ± 0.3 mmHg for NBR and 0.141 ± 0.004 and 90.0 ± 0.4 mmHg for both hypoxic variants (HBR and HAmb; ~4000 m simulated altitude), respectively. A number of parameters linked to intestinal environment such as defecation frequency, intestinal electrical conductivity (IEC), sterol and polyphenol content and diversity, indole, aromaticity and spectral characteristics of dissolved organic matter (DOM) were measured (64 variables). The structure and diversity of bacterial microbial community was assessed using 16S rRNA amplicon sequencing. Inactivity negatively affected frequency of defecation and in combination with hypoxia increased IEC (p < 0.05). In contrast, sterol and polyphenol diversity and content, various characteristics of DOM and aromatic compounds, the structure and diversity of bacterial microbial community were not significantly affected over time. A new in-house PlanHab database was established to integrate all measured variables on host physiology, diet, experiment, immune and metabolic markers (n = 231). The observed progressive decrease in defecation frequency and concomitant increase in IEC suggested that the transition from healthy physiological state towards the developed symptoms of low magnitude obesity-related syndromes was dose dependent on the extent of time spent in inactivity and preceded or took place in absence of significant rearrangements in bacterial microbial community. Species B. thetaiotamicron, B. fragilis, B. dorei and other Bacteroides with reported relevance for dysbiotic medical conditions were significantly enriched in HBR, characterized with most severe inflammation symptoms, indicating a shift towards host mucin degradation and proinflammatory immune crosstalk.
Wissenschaftlicher Artikel
Scientific Article
Schröder, P. ; Beckers, B. ; Daniels, S. ; Gnädinger, F. ; Maestri, E. ; Marmiroli, N. ; Mench, M. ; Millan, R. ; Obermeier, M. ; Oustriere, N. ; Persson, T. ; Poschenrieder, C. ; Rineau, F. ; Rutkowska, B. ; Schmid, T.E. ; Szulc, W. ; Witters, N. ; Sæbø, A.
Sci. Total Environ. 616, 1101-1123 (2017)
The rapid increase of the world population constantly demands more food production fromagricultural soils. This causes conflicts, since at the same time strong interest arises on novel bio-based products from agriculture, and newperspectives for rural landscapes with their valuable ecosystemservices. Agriculture is in transition to fulfill these demands. In many countries, conventional farming, influenced by post-war food requirements, has largely been transformed into integrated and sustainable farming. However, since it is estimated that agricultural production systems will have to produce food for a global population that might amount to 9.1 billion by 2050 and over 10 billion by the end of the century, we will require an even smarter use of the available land, including fallow and derelict sites. One of the biggest challenges is to reverse non-sustainable management and land degradation. Innovative technologies and principles have to be applied to characterize marginal lands, explore options for remediation and re-establish productivity. With view to the heterogeneity of agricultural lands, it is more than logical to apply specific crop management and production practices according to soil conditions. Cross-fertilizing with conservation agriculture, such a novel approach will provide (1) increased resource use efficiency by producing more with less (ensuring food security), (2) improved product quality, (3) ameliorated nutritional status in food and feed products, (4) increased sustainability, (5) product traceability and (6) minimized negative environmental impacts notably on biodiversity and ecological functions. A sustainable strategy for future agriculture should concentrate on production of food and fodder, before utilizing bulk fractions for emerging bio-based products and convert residual stage products to compost, biochar and bioenergy. The present position paper discusses recent developments to indicate how to unlock the potentials of marginal land. (C) 2017 The Authors. Published by Elsevier B.V.
Wissenschaftlicher Artikel
Scientific Article
Schloter, M. ; Nannipieri, P. ; Sørensen, S.J. ; van Elsas, J.D.
Biol. Fertil. Soils 54, DOI: 10.1007/s00374-017-1248-3 (2017)
The living soil is instrumental to key life support functions (LSF) that safeguard life on Earth. The soil microbiome has a main role as a driver of these LSF. Current global developments, like anthropogenic threats to soil (e.g., via intensive agriculture) and climate change, pose a burden on soil functioning. Therefore, it is important to dispose of robust indicators that report on the nature of deleterious changes and thus soil quality. There has been a long debate on the best selection of biological indicators (bioindicators) that report on soil quality. Such indicators should ideally describe organisms with key functions in the system, or with key regulatory/connecting roles (so-called keystone species). However, in the light of the huge functional redundancy in most soil microbiomes, finding specific keystone markers is not a trivial task. The current rapid development of molecular (DNA-based) methods that facilitate deciphering microbiomes with respect to key functions will enable the development of improved criteria by which molecular information can be tuned to yield molecular markers of soil LSF. This review critically examines the current state-of-the-art in molecular marker development and recommends avenues to come to improved future marker systems.
Wissenschaftlicher Artikel
Scientific Article
Fuka, M.M. ; Maksimovic, A.Z. ; Tanuwidjaja, I. ; Hulak, N. ; Schloter, M.
Food Technol. Biotechnol. 55, 368-380 (2017)
In this study, prevalence, biotechnological and safety profi les of 588 Enterococcus isolates isolated from raw milk and Istrian cheese during diff erent stages of ripening were analyzed. Despite the low and variable presence of enterococci in milk ((3.65 +/- 2.93) log CFU/mL), highly comparable enterococcal populations were established aft er 30 days of cheese ripening ((7.96 +/- 0.80) log CFU/g), confirming Enterococcus spp. as a major part of the core microbiota of Istrian cheese. The dominant species were E. faecium (53.8 %) and E. faecalis (42.4 %), while minor groups, consisting of E. durans (2.84 %) and E. casselifl avus (0.95 %), also occurred. A pronounced intraspecies variability was noticed based on molecular fi ngerprinting, with 35 strains (genotypes) detected. Most of the genotypes were farm- specifi c with one third being shared between the farms. This genotype variability refl ected particular diff erences of Istrian cheese production, mainly variable salt concentration, ripening temperature and air humidity as well as microclimatic or vegetation conditions. There was considerable variation between the strains of the same species regarding wide range of biotechnologically important traits as well as their ability to survive in simulated gastrointestinal conditions. A considerable number of strains were resistant to critically important antibiotics such as tetracycline (43.56 %), erythromycin (35.79 %) and vancomycin (23.48 %). Polymerase chain reaction- based detection did not identify any of the common genetic determinants for vancomycin and erythromycin resistance; for tetracycline tetM gene was detected. The presence of virulence genes including agg, efaAfs, gelE, cylM, cylB, cylA, esp, efaAfm, cob and cpd was frequently recorded, especially among E. faecalis strains.
Wissenschaftlicher Artikel
Scientific Article
Michas, A. ; Vestergaard, G. ; Trautwein, K. ; Hatzinikolaou, D.G. ; Vorgias, C.E. ; Wilkes, H. ; Rabus, R. ; Schloter, M. ; Schöler, A.
Microbiome 5:136 (2017)
Alessandrini, F. ; Vennemann, A. ; Gschwendtner, S. ; Neumann, A.U. ; Rothballer, M. ; Seher, T. ; Wimmer, M. ; Kublik, S. ; Traidl-Hoffmann, C. ; Schloter, M. ; Wiemann, M. ; Schmidt-Weber, C.B.
Nanomaterials 7:300 (2017)
The growing use of silver nanoparticles (Ag-NPs) in consumer products raises concerns about their toxicological potential. The purpose of the study was to investigate the size- and coating-dependent pulmonary toxicity of Ag-NPs in vitro and in vivo, using an ovalbumin (OVA)-mouse allergy model. Supernatants from (5.6-45 µg/mL) Ag50-PVP, Ag200-PVP or Ag50-citrate-treated NR8383 alveolar macrophages were tested for lactate dehydrogenase and glucuronidase activity, tumor necrosis factor (TNF)-α release and reactive oxygen species (ROS) production. For the in vivo study, NPs were intratracheally instilled in non-sensitized (NS) and OVA-sensitized (S) mice (1-50 µg/mouse) prior to OVA-challenge and bronchoalveolar lavage fluid (BALF) inflammatory infiltrate was evaluated five days after challenge. In vitro results showed a dose-dependent cytotoxicity of Ag-NPs, which was highest for Ag50-polyvinilpyrrolidone (PVP), followed by Ag50-citrate, and lowest for Ag200-PVP. In vivo 10-50 µg Ag50-PVP triggered a dose-dependent pulmonary inflammatory milieu in NS and S mice, which was significantly higher in S mice and was dampened upon instillation of Ag200-PVP. Surprisingly, instillation of 1 µg Ag50-PVP significantly reduced OVA-induced inflammatory infiltrate in S mice and had no adverse effect in NS mice. Ag50-citrate showed similar beneficial effects at low concentrations and attenuated pro-inflammatory effects at high concentrations. The lung microbiome was altered by NPs instillation dependent on coating and/or mouse batch, showing the most pronounced effects upon instillation of 50 µg Ag50-citrate, which caused an increased abundance of operational taxonomic units assigned to Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria. However, no correlation with the biphasic effect of low and high Ag-NPs dose was found. Altogether, both in vitro and in vivo data on the pulmonary effects of Ag-NPs suggest the critical role of the size, dose and surface functionalization of Ag-NPs, especially in susceptible allergic individuals. From the perspective of occupational health, care should be taken by the production of Ag-NPs-containing consumer products.
Wissenschaftlicher Artikel
Scientific Article
Lang, F. ; Krüger, J. ; Amelung, W. ; Willbold, S. ; Frossard, E. ; Bünemann, E.K. ; Bauhus, J. ; Nitschke, R. ; Kandeler, E. ; Marhan, S. ; Schulz, S. ; Bergkemper, F. ; Schloter, M. ; Luster, J. ; Guggisberg, F. ; Kaiser, K. ; Mikutta, R. ; Guggenberger, G. ; Polle, A. ; Pena, R. ; Prietzel, J. ; Rodionov, A.V. ; Talkner, U. ; Meesenburg, H. ; von Wilpert, K. ; Hölscher, A. ; Dietrich, H.P. ; Chmara, I.
Biogeochemistry 136, 5–29 (2017)
Phosphorus availability may shape plant–microorganism–soil interactions in forest ecosystems. Our aim was to quantify the interactions between soil P availability and P nutrition strategies of European beech (Fagus sylvatica) forests. We assumed that plants and microorganisms of P-rich forests carry over mineral-bound P into the biogeochemical P cycle (acquiring strategy). In contrast, P-poor ecosystems establish tight P cycles to sustain their P demand (recycling strategy). We tested if this conceptual model on supply-controlled P nutrition strategies was consistent with data from five European beech forest ecosystems with different parent materials (geosequence), covering a wide range of total soil P stocks (160–900 g P m −2 ; < 1 m depth). We analyzed numerous soil chemical and biological properties. Especially P-rich beech ecosystems accumulated P in topsoil horizons in moderately labile forms. Forest floor turnover rates decreased with decreasing total P stocks (from 1/5 to 1/40 per year) while ratios between organic carbon and organic phosphorus (C:P org ) increased from 110 to 984 (A horizons). High proportions of fine-root biomass in forest floors seemed to favor tight P recycling. Phosphorus in fine-root biomass increased relative to microbial P with decreasing P stocks. Concomitantly, phosphodiesterase activity decreased, which might explain increasing proportions of diester-P remaining in the soil organic matter. With decreasing P supply indicator values for P acquisition decreased and those for recycling increased, implying adjustment of plant–microorganism–soil feedbacks to soil P availability. Intense recycling improves the P use efficiency of beech forests.
Wissenschaftlicher Artikel
Scientific Article
Bartel, S. ; Jatzlauk, G. ; Kepert, I. ; Fonseca, J. ; Müller, C. ; Milger, K. ; Hochwind, K. ; Kostric, M. ; Eickelberg, O. ; Schloter, M. ; Hartmann, A. ; Schmitt-Kopplin, P. ; Krauss-Etschmann, S.
Allergy 72, 59-59 (2017)
Meeting abstract
Meeting abstract
Hücker, S.M. ; Ardern, Z. ; Goldberg, T. ; Schafferhans, A. ; Bernhofer, M. ; Vestergaard, G. ; Nelson, C.W. ; Schloter, M. ; Rost, B. ; Scherer, S. ; Neuhaus, K.
PLoS ONE 12:e0184119 (2017)
In the past, short protein-coding genes were often disregarded by genome annotation pipelines. Transcriptome sequencing (RNAseq) signals outside of annotated genes have usually been interpreted to indicate either ncRNA or pervasive transcription. Therefore, in addition to the transcriptome, the translatome (RIBOseq) of the enteric pathogen Escherichia coli O157:H7 strain Sakai was determined at two optimal growth conditions and a severe stress condition combining low temperature and high osmotic pressure. All intergenic open reading frames potentially encoding a protein of ≥ 30 amino acids were investigated with regard to coverage by transcription and translation signals and their translatability expressed by the ribosomal coverage value. This led to discovery of 465 unique, putative novel genes not yet annotated in this E. coli strain, which are evenly distributed over both DNA strands of the genome. For 255 of the novel genes, annotated homologs in other bacteria were found, and a machine-learning algorithm, trained on small protein-coding E. coli genes, predicted that 89% of these translated open reading frames represent bona fide genes. The remaining 210 putative novel genes without annotated homologs were compared to the 255 novel genes with homologs and to 250 short annotated genes of this E. coli strain. All three groups turned out to be similar with respect to their translatability distribution, fractions of differentially regulated genes, secondary structure composition, and the distribution of evolutionary constraint, suggesting that both novel groups represent legitimate genes. However, the machine-learning algorithm only recognized a small fraction of the 210 genes without annotated homologs. It is possible that these genes represent a novel group of genes, which have unusual features dissimilar to the genes of the machine-learning algorithm training set.
Wissenschaftlicher Artikel
Scientific Article
Michas, A. ; Vestergaard, G. ; Trautwein, K. ; Avramidis, P. ; Hatzinikolaou, D.G. ; Vorgias, C.E. ; Wilkes, H. ; Rabus, R. ; Schloter, M. ; Schöler, A.
Microbiome 5, 118:118 (2017)
BACKGROUND: Natural oil seeps offer the opportunity to study the adaptation of ecosystems and the associated microbiota to long-term oil exposure. In the current study, we investigated a land-to-sea transition ecosystem called "Keri Lake" in Zakynthos Island, Greece. This ecosystem is unique due to asphalt oil springs found at several sites, a phenomenon already reported 2500 years ago. Sediment microbiomes at Keri Lake were studied, and their structure and functional potential were compared to other ecosystems with oil exposure histories of various time periods.RESULTS: Replicate sediment cores (up to 3-m depth) were retrieved from one site exposed to oil as well as a non-exposed control site. Samples from three different depths were subjected to chemical analysis and metagenomic shotgun sequencing. At the oil-exposed site, we observed high amounts of asphalt oil compounds and a depletion of sulfate compared to the non-exposed control site. The numbers of reads assigned to genes involved in the anaerobic degradation of hydrocarbons were similar between the two sites. The numbers of denitrifiers and sulfate reducers were clearly lower in the samples from the oil-exposed site, while a higher abundance of methanogens was detected compared to the non-exposed site. Higher abundances of the genes of methanogenesis were also observed in the metagenomes from other ecosystems with a long history of oil exposure, compared to short-term exposed environments.CONCLUSIONS: The analysis of Keri Lake metagenomes revealed that microbiomes in the oil-exposed sediment have a higher potential for methanogenesis over denitrification/sulfate reduction, compared to those in the non-exposed site. Comparison with metagenomes from various oil-impacted environments suggests that syntrophic interactions of hydrocarbon degraders with methanogens are favored in the ecosystems with a long-term presence of oil.
Wissenschaftlicher Artikel
Scientific Article
Schöler, A. ; Jacquiod, S. ; Vestergaard, G. ; Schulz, S. ; Schloter, M.
Biol. Fertil. Soils 53, 485–489 (2017)
The use of cultivation independent methods has revolutionized soil biology in the last decades. Most popular approaches are based on directly extracted DNA from soil and subsequent analysis of PCR-amplified marker genes by next-generation sequencing. While these high-throughput methods offer novel possibilities over cultivation-based approaches, several key points need to be considered to minimize potential biases during library preparation and downstream bioinformatic analysis. This opinion paper highlights crucial steps that should be considered for accurate analysis and data interpretation.
Review
Review
Uksa, M. ; Buegger, F. ; Gschwendtner, S. ; Lueders, T. ; Kublik, S. ; Kautz, T. ; Athmann, M. ; Köpke, U. ; Charles Munch, J. ; Schloter, M. ; Fischer, D.
Environ. Microbiol. Rep. 9, 729-741 (2017)
Root exudates shape microbial communities at the plant soil interface. Here we compared bacterial communities that utilise plant-derived carbon in the rhizosphere of wheat in different soil depths, including topsoil, as well as two subsoil layers up to 1 m depth. The experiment was performed in a green house using soil monoliths with intact soil structure taken from an agricultural field. To identify bacteria utilizing plant derived carbon, (13) C-CO2 labelling of plants was performed for two weeks at the EC50 stage, followed by stable isotope probing of extracted DNA from the rhizosphere combined with 16S rRNA gene-based amplicon sequencing. Our findings suggest substantially different bacterial key players and interaction mechanisms between plants and bacteria utilising plant-derived carbon in the rhizosphere of subsoils and topsoil. Among the three soil depths, clear differences were found in (13) C enrichment pattern across abundant operational taxonomic units (OTUs). Whereas OTUs linked to Proteobacteria were enriched in (13) C mainly in the topsoil, in both subsoil layers OTUs related to Cohnella, Paenibacillus, Flavobacterium showed a clear (13) C signal, indicating an important, so far overseen role of Firmicutes and Bacteriodetes in the subsoil rhizosphere.
Wissenschaftlicher Artikel
Scientific Article
Christou, A. ; Agüera, A. ; Bayona, J.M. ; Cytryn, E. ; Fotopoulos, V. ; Lambropoulou, D. ; Manaia, C.M. ; Michael, C. ; Revitt, M. ; Schröder, P. ; Fatta-Kassinos, D.
Water Res. 123, 448-467 (2017)
The use of reclaimed wastewater (RWW) for the irrigation of crops may result in the continuous exposure of the agricultural environment to antibiotics, antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs). In recent years, certain evidence indicate that antibiotics and resistance genes may become disseminated in agricultural soils as a result of the amendment with manure and biosolids and irrigation with RWW. Antibiotic residues and other contaminants may undergo sorption/desorption and transformation processes (both biotic and abiotic), and have the potential to affect the soil microbiota. Antibiotics found in the soil pore water (bioavailable fraction) as a result of RWW irrigation may be taken up by crop plants, bioaccumulate within plant tissues and subsequently enter the food webs; potentially resulting in detrimental public health implications. It can be also hypothesized that ARGs can spread among soil and plant-associated bacteria, a fact that may have serious human health implications. The majority of studies dealing with these environmental and social challenges related with the use of RWW for irrigation were conducted under laboratory or using, somehow, controlled conditions. This critical review discusses the state of the art on the fate of antibiotics, ARB and ARGs in agricultural environment where RWW is applied for irrigation. The implications associated with the uptake of antibiotics by plants (uptake mechanisms) and the potential risks to public health are highlighted. Additionally, knowledge gaps as well as challenges and opportunities are addressed, with the aim of boosting future research towards an enhanced understanding of the fate and implications of these contaminants of emerging concern in the agricultural environment. These are key issues in a world where the increasing water scarcity and the continuous appeal of circular economy demand answers for a long-term safe use of RWW for irrigation.
Wissenschaftlicher Artikel
Scientific Article
Engel, M. ; Endesfelder, D. ; Schloter-Hai, B. ; Kublik, S. ; Granitsiotis, M.S. ; Boschetto, P. ; Stendardo, M. ; Barta, I. ; Döme, B. ; Deleuze, J.F. ; Boland, A. ; Müller-Quernheim, J. ; Prasse, A. ; Welte, T. ; Hohlfeld, J. ; Subramanian, D. ; Parr, D. ; Gut, I.G. ; Greulich, T. ; Koczulla, A.R. ; Nowinski, A. ; Gorecka, D. ; Singh, D. ; Gupta, S. ; Brightling, C.E. ; Hoffmann, H. ; Frankenberger, M. ; Hofer, T.P. ; Burggraf, D. ; Heiss-Neumann, M.S. ; Ziegler-Heitbrock, L. ; Schloter, M. ; zu Castell, W.
PLoS ONE 12:e0180859 (2017)
BACKGROUND: Changes in microbial community composition in the lung of patients suffering from moderate to severe COPD have been well documented. However, knowledge about specific microbiome structures in the human lung associated with CT defined abnormalities is limited. METHODS: Bacterial community composition derived from brush samples from lungs of 16 patients suffering from different CT defined subtypes of COPD and 9 healthy subjects was analyzed using a cultivation independent barcoding approach applying 454-pyrosequencing of 16S rRNA gene fragment amplicons. RESULTS: We could show that bacterial community composition in patients with changes in CT (either airway or emphysema type changes, designated as severe subtypes) was different from community composition in lungs of patients without visible changes in CT as well as from healthy subjects (designated as mild COPD subtype and control group) (PC1, Padj = 0.002). Higher abundance of Prevotella in samples from patients with mild COPD subtype and from controls and of Streptococcus in the severe subtype cases mainly contributed to the separation of bacterial communities of subjects. No significant effects of treatment with inhaled glucocorticoids on bacterial community composition were detected within COPD cases with and without abnormalities in CT in PCoA. Co-occurrence analysis suggests the presence of networks of co-occurring bacteria. Four communities of positively correlated bacteria were revealed. The microbial communities can clearly be distinguished by their associations with the CT defined disease phenotype. CONCLUSION: Our findings indicate that CT detectable structural changes in the lung of COPD patients, which we termed severe subtypes, are associated with alterations in bacterial communities, which may induce further changes in the interaction between microbes and host cells. This might result in a changed interplay with the host immune system.
Wissenschaftlicher Artikel
Scientific Article
Estendorfer, J. ; Stempfhuber, B. ; Haury, P. ; Vestergaard, G. ; Rillig, M.C. ; Joshi, J. ; Schröder, P. ; Schloter, M.
Front. Plant Sci. 8:930 (2017)
In this study, we investigated the impact of different land use intensities (LUI) on the root-associated microbiome of Dactylis glomerata (orchardgrass). For this purpose, eight sampling sites with different land use intensity levels but comparable soil properties were selected in the southwest of Germany. Experimental plots covered land use levels from natural grassland up to intensively managed meadows. We used 16S rRNA gene based barcoding to assess the plant-associated community structure in the endosphere, rhizosphere and bulk soil of D. glomerata. Samples were taken at the reproductive stage of the plant in early summer. Our data indicated that roots harbor a distinct bacterial community, which clearly differed from the microbiome of the rhizosphere and bulk soil. Our results revealed Pseudomonadaceae, Enterobacteriaceae and Comamonadaceae as the most abundant endophytes independently of land use intensity. Rhizosphere and bulk soil were dominated also by Proteobacteria, but the most abundant families differed from those obtained from root samples. In the soil, the effect of land use intensity was more pronounced compared to root endophytes leading to a clearly distinct pattern of bacterial communities under different LUI from rhizosphere and bulk soil vs. endophytes. Overall, a change of community structure on the plant–soil interface was observed, as the number of shared OTUs between all three compartments investigated increased with decreasing land use intensity. Thus, our findings suggest a stronger interaction of the plant with its surrounding soil under low land use intensity. Furthermore, the amount and quality of available nitrogen was identified as a major driver for shifts in the microbiome structure in all compartments.
Wissenschaftlicher Artikel
Scientific Article
Proença, D.N. ; Francisco, R. ; Kublik, S. ; Schöler, A. ; Vestergaard, G. ; Schloter, M. ; Morais, P.V.
Sci. Rep. 7:4205 (2017)
Pine wilt disease (PWD) is a devastating forest disease present worldwide. In this study we analyzed the effects of the invasion of the pinewood nematode Bursaphelenchus xylophilus, the major pathogen causing PWD, on the endophytic microbiome of adult P. pinaster trees. Wood samples from trees with different degrees of PWD disease were collected at two sites (A and M) in Portugal. Endophytic bacteria were characterized based on directly extracted DNA by fingerprinting and barcoding using the 16S rRNA gene as marker. Furthermore, cultivation-based approaches were used to obtain isolates of the major taxa to study their ecophysiology. The endophytic microbiome from P. pinaster trees differed significantly between the two sampling sites. Main bacterial OTUs belonged to the Proteobacteria (39% (site M) - 97% (site A)), and Firmicutes (0.70% (site A) - 44% (site M)). However, consequences of the invasion with the pathogen were comparable. Interestingly diversity of wood endophytic bacteria increased with the severity of the diseases, with highest diversity levels observed in in the most affected trees. Our results suggest that in the first stages of the disease, the defence mechanisms of plants are repressed by the pathogen, resulting in a colonization of the wood interior by soil microorganisms.
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Scientific Article
Cui, H. ; Hrabě de Angelis, M. ; Schröder, P.
Water Res. 122, 290-298 (2017)
Iopromide is frequently detected in water bodies due to its widespread use as an X-ray contrast agent in medicine. Due to its rapid clearance from the human body and its incomplete removal by wastewater treatment, an elevation of its concentration in the environment is observed that might lead to a serious impact on human and environmental health. Alternative or additional removal technologies may be more effective to remove iopromide from the effluents of wastewater treatment facilities, like phytoremediation with aquatic macrophytes. To test this, a hydroponic experiment was carried out to assess the fate of iopromide in Typha latifolia. The transformation products (TPs) in the plant were investigated to predict possible transformation mechanisms. The removal process followed first order kinetics with a linear regression R(2) value of 0.983. The iopromide concentration in roots and rhizomes reached a maximum value of 20.70 ± 0.81 and 16.82 ± 1.78 nmol g(-1) on the 7th day, respectively, thereafter decreased until the end of experiment. A different result was found in leaves, where iopromide concentration decreased over the whole experimental period. A total of eight transformation products were detected in T. latifolia, including 23 isomers. The relative content of aldehyde and ketone TPs decreased in roots and rhizomes while the relative content of carboxylic TPs increased. However, the relative content of aldehyde and ketone TPs only showed a slight decrease in leaves while the relative content of carboxylic TPs remained stable during the experimental period. In addition, a significant increase of decarboxylated TPs was found in leaves, but not in roots and rhizomes. These results indicate that a difference in transformation mechanisms exists among plant tissues. The findings of this study are important to better understand the transformation mechanisms of iopromide in plants and to improve phytoremediation technologies for such kind of compounds.
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Scientific Article
Jatzlauk, G. ; Bartel, S. ; Heine, H. ; Schloter, M. ; Krauss-Etschmann, S.
Allergy 72, 1859-1867 (2017)
The prevalence of allergic diseases and asthma has dramatically increased over the last decades, resulting in a high burden for patients and health care systems. Thus, there is an unmet need to develop preventative strategies for these diseases. Epidemiological studies show that reduced exposure to environmental bacteria in early life (e.g birth by cesarian section, being formula-fed, growing up in an urban environment or with less contact to various persons) is associated with an increased risk to develop allergies and asthma later in life. Conversely, a reduced risk for asthma is consistently found in children growing up on traditional farms, thereby being exposed to a wide spectrum of microbes. However, clinical studies are still rare and to some extent contradicting. A detailed mechanistic understanding how environmental microbes influence the development of the human microbiome and the immune system is important to enable the development of novel preventative approaches that are based on the early modulation of the host microbiota and immunity. In this mini-review we summarize current knowledge and experimental evidence for the potential of bacteria and their metabolites to be used for the prevention of asthma and allergic diseases.
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Scientific Article
Yang, L. ; Danzberger, J. ; Schöler, A. ; Schröder, P. ; Schloter, M. ; Radl, V.
Front. Plant Sci. 8:1005 (2017)
Endophytes are microorganisms colonizing plant internal tissues. They are ubiquitously associated with plants and play an important role in plant growth and health. In this work, we grew five modern cultivars of barley in axenic systems using sterile sand mixture as well as in greenhouse with natural soil. We characterized the potentially active microbial communities associated with seeds and roots using rRNA based amplicon sequencing. The seeds of the different cultivars share a great part of their microbiome, as we observed a predominance of a few bacterial OTUs assigned to Phyllobacterium, Paenibacillus, and Trabusiella. Seed endophytes, particularly members of the Enterobacteriacea and Paenibacillaceae, were important members of root endophytes in axenic systems, where there were no external microbes. However, when plants were grown in soil, seed endophytes became less abundant in root associated microbiome. We observed a clear enrichment of Actinobacteriacea and Rhizobiaceae, indicating a strong influence of the soil bacterial communities on the composition of the root microbiome. Two OTUs assigned to Phyllobacteriaceae were found in all seeds and root samples growing in soil, indicating a relationship between seed-borne and root associated microbiome in barley. Even though the role of endophytic bacteria remains to be clarified, it is known that many members of the genera detected in our study produce phytohormones, shape seedling exudate profile and may play an important role in germination and establishment of the seedlings.
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Scientific Article
Vestergaard, G. ; Schulz, S. ; Schöler, A. ; Schloter, M.
Biol. Fertil. Soils 53, 479-484 (2017)
Editorial
Editorial
Schulz, S. ; Kölbl, A. ; Ebli, M. ; Buegger, F. ; Schloter, M. ; Fiedler, S.
Microb. Ecol. 74, 765-770 (2017)
More than 50% of all anthropogenic N2O emissions come from the soil. Drained Histosols that are used for agricultural purposes are particularly potent sources of denitrification due to higher stocks of organic matter and fertiliser application. However, conditions that favour denitrification can vary considerably across a field and change significantly throughout the year. Spatial and temporal denitrifier dynamics were assessed in a drained, intensely managed Histosol by focusing on the genetic nitrite and N2O reduction potential derived from the abundance of nirK, nirS and nosZ genes. These data were correlated with soil properties at two different points in time in 2013. N2O emissions were measured every 2 weeks over three vegetation periods (2012-2014). Very low N2O emission rates were measured throughout the entire period of investigation in accordance with the geostatistical data that revealed an abundance of microbes carrying the N2O reductase gene nosZ. This, along with neutral soil pH values, is indicative of high microbial denitrification potential. While the distribution of the microbial communities was strongly influenced by total organic carbon and nitrogen pools in March, the spatial distribution pattern was not related to the distribution of soil properties in October, when higher nutrient availability was observed. Different nitrite reducer groups prevailed in spring and autumn. While nirS, followed by nosZ and nirK, was most abundant in March, the latter was the dominant nitrite reductase in October.
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Scientific Article
Šket, R. ; Treichel, N. ; Debevec, T. ; Eiken, O. ; Mekjavic, I. ; Schloter, M. ; Vital, M. ; Chandler, J. ; Tiedje, J.M. ; Murovec, B. ; Prevoršek, Z. ; Stres, B.
Front. Physiol. 8:250 (2017)
We explored the assembly of intestinal microbiota in healthy male participants during the run-in (5 day) and experimental phases [21-day normoxic bed rest (NBR), hypoxic bedrest (HBR)], and hypoxic ambulation (HAmb) in a strictly controlled laboratory environment, balanced fluid, and dietary intakes, controlled circadian rhythm, microbial ambiental burden, and 24/7 medical surveillance. The fraction of inspired O2 (FiO2) and partial pressure of inspired O2 (PiO2) were 0.209 and 133.1 ± 0.3 mmHg for NBR and 0.141 ± 0.004 and 90.0 ± 0.4 mmHg for both hypoxic variants (HBR and HAmb; ~4,000 m simulated altitude), respectively. A number of parameters linked to intestinal transit spanning Bristol Stool Scale, defecation rates, zonulin, α1-antitrypsin, eosinophil derived neurotoxin, bile acids, reducing sugars, short chain fatty acids, total soluble organic carbon, water content, diet composition, and food intake were measured (167 variables). The abundance, structure, and diversity of butyrate producing microbial community were assessed using the two primary bacterial butyrate synthesis pathways, butyryl-CoA: acetate CoA-transferase (but) and butyrate kinase (buk) genes. Inactivity negatively affected fecal consistency and in combination with hypoxia aggravated the state of gut inflammation (p < 0.05). In contrast, gut permeability, various metabolic markers, the structure, diversity, and abundance of butyrate producing microbial community were not significantly affected. Rearrangements in the butyrate producing microbial community structure were explained by experimental setup (13.4%), experimentally structured metabolites (12.8%), and gut metabolite-immunological markers (11.9%), with 61.9% remaining unexplained. Many of the measured parameters were found to be correlated and were hence omitted from further analyses. The observed progressive increase in two immunological intestinal markers suggested that the transition from healthy physiological state toward the developed symptoms of low magnitude obesity-related syndromes was primarily driven by the onset of inactivity (lack of exercise in NBR) that were exacerbated by systemic hypoxia (HBR) and significantly alleviated by exercise, despite hypoxia (HAmb). Butyrate producing community in colon exhibited apparent resilience toward short-term modifications in host exercise or hypoxia. Progressive constipation (decreased intestinal motility) and increased local inflammation marker suggest that changes in microbial colonization and metabolism were taking place at the location of small intestine.
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Scientific Article
Chen, F. ; Huber, C. ; Schröder, P.
Chemosphere 182, 638-646 (2017)
Oxybenzone (OBZ), a common ingredient in sunscreens and personal care products, has been frequently detected in effluents from municipal wastewater treatment plants and also in surface waters. OBZ is an emerging contaminant due to its adverse impacts on marine/aquatic ecosystems. To investigate the removal and degradation capacity of phytotreatment for OBZ, the common wetland plant species Cyperus alternifolius L. was exposed to this compound at 5, 25 and 50 μM for 120 h, respectively. Continuous uptake by roots and accumulation in plant tissues was observed over the exposure time, and depletion of spiked OBZ from the aqueous medium exceeded 73.9 ± 9.1% after 120 h. Similar to its fate in mammalian cells, OBZ is activated in a phase I reaction resulting in the hydroxylated metabolite 2,4-dihydroxybenzophenone (DHB). Independently, two phase II metabolites were identified as oxybenzone-glucoside (OBZ-Glu) and oxybenzone-(6-O-malonyl)-glucoside (OBZ-Mal-Glu) by LC-MS/MS. Formation of these metabolites increased over the experimental period. To our knowledge this is the first time that DHB, OBZ-Glu and OBZ-Mal-Glu are shown to be formed in higher plant tissues. Furthermore, plant defense systems-antioxidative enzymes (SOD, CAT, APOX and POX) were found to be elevated to counteract stress caused by exposure to OBZ. This study presents the huge potential of aquatic plants to cope with benzophenone type UV filters in contaminated water bodies.
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Scientific Article
He, Y. ; Langenhoff, A.A.M. ; Sutton, N.B. ; Rijnaarts, H.H.M. ; Blokland, M.H. ; Chen, F. ; Huber, C. ; Schröder, P.
Environ. Sci. Technol. 51, 4576-4584 (2017)
This study explores ibuprofen (IBP) uptake and transformation in the wetland plant species Phragmites australis and the underlying mechanisms. We grew P. australis in perlite under greenhouse conditions and treated plants with 60 μg/L of IBP. Roots and rhizomes (RR), stems and leaves (SL), and liquid samples were collected during 21 days of exposure. Results show that P. australis can take up, translocate, and degrade IBP. IBP was completely removed from the liquid medium after 21 days with a half-life of 2.1 days. IBP accumulated in RR and was partly translocated to SL. Meanwhile, four intermediates were detected in the plant tissues: hydroxy-IBP, 1,2-dihydroxy-IBP, carboxy-IBP and glucopyranosyloxy-hydroxy-IBP. Cytochrome P450 monooxygenase was involved in the production of the two hydroxy intermediates. We hypothesize that transformation of IBP was first catalyzed by P450, and then by glycosyltransferase, followed by further storage or metabolism in vacuoles or cell walls. No significant phytotoxicity was observed based on relative growth of plants and stress enzyme activities. In conclusion, we demonstrated for the first time that P. australis degrades IBP from water and is therefore a suitable species for application in constructed wetlands to clean wastewater effluents containing IBP and possibly also other micropollutants.
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Stempfhuber, B. ; Richter-Heitmann, T. ; Bienek, L. ; Schöning, I. ; Schrumpf, M. ; Friedrich, M. ; Schulz, S. ; Schloter, M.
Biol. Fertil. Soils 53, 691–700 (2017)
In this study, we investigated how co-occurrence patters of ammonia and nitrite oxidizers, which drive autotrophic nitrification, are influenced by tree species composition as well as soil pH in different forest soils. We expected that a decline of ammonia oxidizers in coniferous forests, as a result of excreted nitrification inhibitors and at acidic sites with low availability of ammonia, would reduce the abundance of nitrite-oxidizing bacteria (NOB). To detect shifts in co-occurrence patterns, the abundance of key players was measured at 50 forest plots with coniferous respectively deciduous vegetation and different soil pH levels in the region Schwäbische Alb (Germany). We found ammonia-oxidizing archaea (AOA) and Nitrospira-like NOB (NS) to be dominating in numbers over their counterparts across all forest types. AOA co-occurred mostly with NS, while bacterial ammonia oxidizers (AOB) were correlated with Nitrobacter-like NOB (NB). Co-occurrence patterns changed from tight significant relationships of all ammonia and nitrite oxidizers in deciduous forests to a significant relationship of AOB and NB in coniferous forests, where AOA abundance was reduced. Surprisingly, no co-occurrence structures between ammonia and nitrite oxidizers could be determined at acidic sites, although abundances were correlated to the respective nitrogen pools. This raises the question whether interactions with heterotrophic nitrifiers may occur, which needs to be addressed in future studies.
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de Matos, G.F. ; Zilli, J.E. ; de Araújo, J.L.S. ; Parma, M.M. ; Melo, I.S. ; Radl, V. ; Baldani, J.I. ; Rouws, L.F.M.
Arch. Microbiol. 199, 1251–1258 (2017)
Members of the genus Bradyrhizobium are well-known as nitrogen-fixing microsymbionts of a wide variety of leguminous species, but they have also been found in different environments, notably as endophytes in non-legumes such as sugarcane. This study presents a detailed polyphasic characterization of four Bradyrhizobium strains (type strain BR 10280(T)), previously isolated from roots of sugarcane in Brazil. 16S rRNA sequence analysis, multilocus sequence analysis (MLSA) and analysis of the 16S-23S rRNA internal transcribed spacer showed that these strains form a novel clade close to, but different from B. huanghuaihaiense strain CCBAU 23303(T). Average nucleotide identity (ANI) analyses confirmed that BR 10280(T) represents a novel species. Phylogenetic analysis based on nodC gene sequences also placed the strains close to CCBAU 23303(T), but different from this latter strain, the sugarcane strains did not nodulate soybean, although they effectively nodulated Vigna unguiculata, Cajanus cajan and Macroptilium atropurpureum. Physiological traits are in agreement with the placement of the strains in the genus Bradyrhizobium as a novel species for which the name Bradyrhizobium sacchari sp. nov. is proposed.
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Scientific Article
Yang, S. ; Liebner, S. ; Winkel, M. ; Alawi, M. ; Horn, F. ; Dörfer, C. ; Ollivier, J. ; He, J.s. ; Jin, H. ; Kühn, P. ; Schloter, M. ; Scholten, T. ; Wagner, D.
Soil Biol. Biochem. 111, 66-77 (2017)
The organic carbon of permafrost affected soils is receiving particular attention with respect to its fate and potential feedback to global warming. The structural and activity changes of methanogenic communities in the degrading permafrost-affected wetlands on the Tibetan Plateau can serve as fundamental elements for modelling feedback interaction of ecosystems to climate change. Hence, we aimed at anticipating if and how the rapid environmental changes occurring especially on the high altitude Tibetan platform will affect methanogenic communities. We identified methanogenic community composition, activity and abundance in wetland soils with different hydrological settings, permafrost extent and soil properties and pinpoint the environmental controls. We show that despite a pronounced natural gradient, the Tibetan high elevation wetland soils host a large methanogenic core microbiome. Hydrogenotrophic methanogens, in particular Methanoregula, and H2-dependent methanogenesis were overall dominant although acetoclastic methanogens in addition to hydrogenotrophs were among the dominating taxa in a minerotrophic fen. Tracing the Methanoregula community of the Tibetan Plateau using public databases revealed its global relevance in natural terrestrial habitats. Unlike the composition, the activity and abundance of methanogens varied strongly in the studied soils with higher values in alpine swamps than in alpine meadows. This study indicates that in the course of current wetland and permafrost degradation and the loss in soil moisture, a decrease in the methane production potential is expected on the high Tibetan Plateau but it will not lead to pronounced changes within the methanogenic community structure.
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Scientific Article
Chen, F. ; Schröder, P.
In: (15th International Conference on Environmental Science and Technology, 27 August 2017, Rhodos). 2017. 5
Oxybenzone (OBZ), also commonly known as Benzophenone-3, is a frequently detected UV filter in sun tans and skin protectants, which enters aquatic systems mostly directly due to recreational activities or indirectly through wastewater treatment plants dis­charges. OBZ is an emerging contaminant due to its adverse impacts on marine/aquatic ecosystems. To study the degradation capacity of OBZ in phyto­treatment, a well-established system of a horseradish hairy root culture (Armoracia rusticana) as well as the wetland species Cyperus alternifolius were treated with OBZ. Depletion of spiked OBZ from the aqueous medium exceeded 70% after 120 h of incubation, and continuous uptake by roots and accumulation in plant tissues was observed. Similar to its fate in mammalian cells OBZ could be shown to be activated in a phase I reaction resulting in the hydroxylated metabolite 2,4-dihydroxybenzophenone (DHB). Two subsequently appearing metabolites were identi­fied as oxybenzone-glucoside (OBZ-Glu) and oxy­ben­zone-(6-O-malonyl)-glucoside (OBZ-Mal-Glu) by LC-MS/MS. Formation of these metabolites increased over the experimental period. The identity of the meta­bolites was further confirmed by enzymatic syn­thesis, enzy­matic and alkaline hydrolysis. Incubation with O-glucosyltransferase (O-GT) extracted from roots formed OBZ-Glu; β-D-Glucosidase hydrolyzed OBZ-Glu; Alkaline hydrolysis led to a cleavage of OBZ-Mal-Glu and yielded OBZ-Glu. To our know­ledge this is the first time that DHB, OBZ-Glu and OBZ-Mal-Glu are shown to occur in higher plant tissues, and that plant defense systems were elevated to counteract stress caused by exposure to OBZ. This study presents the huge potential of aquatic plants to cope with benzophenone type UV filters in contami­nated water bodies. The significance of phyto­reme­dia­tion to cope with emerging pollutants like these envi­ronmentally critical UV-filters is discussed.
Hendrix, S. ; Schröder, P. ; Keunen, E. ; Huber, C. ; Cuypers, A.
Adv. Bot. Res. 83, 223-276 (2017)
Environmental contamination with metals and organic compounds poses a serious threat to human health. Investigating plant responses to these contaminants at the molecular and cellular level is crucial to optimize phytoremediation strategies to clean up contaminated soils. Two key players in plant stress responses are the sulphur-containing amino acids cysteine and methionine. Cysteine is an important constituent of the metal-chelating metallothioneins and is also the precursor for glutathione and subsequent phytochelatin synthesis. During stress conditions, glutathione is involved in (1) metal chelation, (2) xenobiotic detoxification and (3) antioxidative defence. The activated form of methionine, S-adenosylmethionine, is involved in the synthesis of ethylene and polyamines, both playing important roles in signal transduction. This review provides an overview of sulphur uptake and assimilation and its conversion into basic metabolites essential for detoxification and signal transduction during metal and organic contaminant exposure in plants. Furthermore, the cross talk between these pathways and their relation to the contaminant-induced oxidative challenge are discussed.
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Scientific Article
Wei, J. ; Amelung, W. ; Lehndorff, E. ; Schloter, M. ; Vereecken, H. ; Brüggemann, N.
Biogeochemistry 132, 325-342 (2017)
Abstract: Nitrite (NO2−) as an important intermediate of the biological nitrogen cycle is particularly reactive in acidic soils and acts as a source of N2O and NOx (NO and NO2). However, abiotic and biotic pathways of NO2−-driven N2O and NOx production in forest soil and the role of soil organic matter (SOM) in these processes are still unclear. In this study, NO2− was applied to both unsterile and sterilized soil samples as well as to different SOM fractions from a Norway spruce forest. Biotic and abiotic N2O emission was measured with an infrared absorption analyzer and gas chromatography, while NOx emission was quantified with a chemiluminescence analyzer. Isotopic signatures of N2O (δ15Nbulk, δ18O, and 15N-N2O site preference) were analyzed with an isotope ratio mass spectrometer. After NO2− addition, a large amount of NOx was emitted immediately, while N2O emission occurred 15–60 min later and was much lower compared to NOx. Sterilization of soil decreased N2O emission significantly, but not NOx emission. The 15N site preference of N2O ranged from 7.98 to 11.58‰ for abiotic and 4.69–7.42‰ for biotic sources. The fulvic acid fraction contributed the most to abiotic N2O emission, while the fastest NO and N2O emission occurred after NO2−application to the humin fraction, followed by the humic acid fraction. These results are important for the future understanding of NOx and N2O sources, as well as the use of isotopic signatures for source-partitioning N2O emission from soil. Graphical Abstract: [Figure not available: see fulltext.]
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Scientific Article
Wasserstrom, H. ; Kublik, S. ; Wasserstrom, R. ; Schulz, S. ; Schloter, M. ; Steinberger, Y.
Sci. Rep. 7:40266 (2017)
Sand dunes are unique ecosystems with distinct features which limited the accumulation of biomass. The distance from seashore affects both the physical properties of the sand dunes and the biota living above-and below ground. The goal of the present study was to determine the effects of the distance from shore to inland on soil bacterial community composition during wet and dry season. We studied a chronosequence of sites close to the eastern Mediterranean coast. Bacterial diversity was assessed using directly extracted DNA from soil samples and 16 S ribosomal RNA gene fingerprinting. Our data indicates a significant influence of season and site on bacterial community structure. We showed that during the wet season soil organic matter, pH and salinity strongly influence bacterial community composition, whereas during the dry period bacterial diversity was mainly driven by the shortage of water at all sites. Consequently diversity was lowest during dry season at dunes close to the shore, whereas during the wet season the higher water content and the reduced salinity at the dunes which are more at the inland induced an increase in diversity, which illustrates the pronounced dynamics of microbial communities in soil over a season mainly at inland dunes.
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Scientific Article
Leite, J. ; Fischer, D. ; Rouws, L.F.M. ; Fernandes-Junior, P. ; Hofmann, A. ; Kublik, S. ; Schloter, M. ; Xavier, G.R. ; Radl, V.
Front. Plant Sci. 7:2064 (2017)
Many studies have been pointing to a high diversity of bacteria associated to legume root nodules. Even though most of these bacteria do not form nodules with legumes themselves, it was shown that they might enter infection threads when co-inoculated with rhizobial strains. The aim of this work was to describe the diversity of bacterial communities associated with cowpea (Vigna unguiculata L. Walp) root nodules using 16S rRNA gene amplicon sequencing, regarding the factors plant genotype and soil type. As expected, Bradyrhizobium was the most abundant genus of the detected genera. Furthermore, we found a high bacterial diversity associated to cowpea nodules; OTUs related to the genera Enterobacter, Chryseobacterium, Sphingobacterium, and unclassified Enterobacterfacea were the most abundant. The presence of these groups was significantly influenced by the soil type and, to a lesser extent, plant genotype. Interestingly, OTUs assigned to Chryseobacterium were highly abundant, particularly in samples obtained from an Ultisol soil. We confirmed their presence in root nodules and assessed their diversity using a target isolation approach. Though their functional role still needs to be addressed, we postulate that Chryseobacterium strains might help cowpea plant to cope with salt stress in semi-arid regions.
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Pronk, G.J. ; Heister, K. ; Vogel, C. ; Babin, D. ; Bachmann, J. ; Ding, G.C. ; Ditterich, F. ; Gerzabek, M.H. ; Giebler, J. ; Hemkemeyer, M. ; Kandeler, E. ; Kunhi Mouvenchery, Y. ; Miltner, A. ; Poll, C. ; Schaumann, G.E. ; Smalla, K. ; Steinbach, A. ; Tanuwidjaja, I. ; Tebbe, C.C. ; Wick, L.Y. ; Woche, S.K. ; Totsche, K.U. ; Schloter, M. ; Kögel-Knabner, I.
Biol. Fertil. Soils 53, 9-22 (2017)
Our understanding of the interactions between minerals, organic matter, and microorganisms at so-called biogeochemical interfaces in soil is still hampered by the inherent complexity of these systems. Artificial soil maturation experiments can help to bridge a gap in complexity between simple abiotic sorption experiments and larger-scale field experiments. By controlling other soil-forming factors, the effect of a particular variable can be identified in a simplified system. Here, we review the findings of a series of artificial soil incubation experiments with the aim of revealing general trends and conclusions. The artificial soils were designed to determine the effect of mineral composition and charcoal presence on the development of abiotic and biotic soil properties during maturation. In particular, the development of soil aggregates, organic matter (OM) composition and turnover, sorption properties, and the establishment of microbial community composition and function were considered. The main objectives of the research were to determine (1) how surface properties and sorption of chemicals modify biogeochemical interfaces; (2) how much time is required to form aggregates from mixtures of pure minerals, OM, and a microbial inoculum; and (3) how the presence of different mineral and charcoal surfaces affects aggregation, OM turnover, and the development of microbial community composition.
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Scientific Article
Regan, K. ; Stempfhuber, B. ; Schloter, M. ; Rasche, F. ; Prati, D. ; Philippot, L. ; Boeddinghaus, R.S. ; Kandeler, E. ; Marhan, S.
Soil Biol. Biochem. 109, 214-226 (2017)
The microbial groups of nitrogen fixers, ammonia oxidizers, and denitrifiers largely drive the inorganic nitrogen cycle in temperate terrestrial ecosystems. Their spatial and temporal dynamics, however, vary depending on the studied scale. The present study aimed to fill a knowledge gap by providing an explicit picture of spatial and temporal dynamics of a subset of these soil microorganisms at the plot scale. We selected an unfertilized perennial grassland, where nitrogen cycling is considered to be efficient and tightly coupled to plant growth. At six times over one growing season 60 soil samples were taken from a 10 m × 10 m area and abundances of marker genes for total archaea and bacteria (16S rRNA), nitrogen fixing bacteria (nifH), ammonia oxidizing archaea (amoA AOA) and bacteria (amoA AOB), and denitrifying bacteria (nirS, . nirK and . nosZ) were determined by qPCR. Potential nitrification activity (PNA) and denitrifying enzyme activity (DEA) were determined. Seasonal changes in abundance patterns of marker genes were detected, and were associated with changes in substrate availability associated with plant growth stages. Potential nitrification and denitrification enzyme activities were strongly spatially structured at the studied scale, corresponding to periods of rapid plant growth, June and October, and their spatial distributions were similar, providing visual evidence of highly localized spatial and temporal conditions at this scale. Temporal variability in the N-cycling communities versus the stability of their respective potential activities provided evidence of both short-lived temporal niche partitioning and a degree of microbial functional redundancy. Our results indicate that in an unfertilized grassland, at the meter scale, abundances of microbial N-cycling organisms can exhibit transient changes, while nitrogen cycling processes remain stable.
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Scientific Article
Pfeiffer, S. ; Mitter, B. ; Oswald, A. ; Schloter-Hai, B. ; Schloter, M. ; Declerck, S. ; Sessitsch, A.
FEMS Microbiol. Ecol. 93:fiw242 (2017)
The rhizosphere hosts a rich microflora supporting plant nutrition and health. We examined bacterial rhizosphere microbiota of Solanum tuberosum grown in its center of origin, the Central Andean Highlands, at different vegetation stages and sites at altitudes ranging from 3245 to 4070 m.a.s.l., differing in soil characteristics, climate and the agricultural practices by 454 sequence analysis of 16S rRNA genes. We observed that the taxonomic composition of bacteria repeatedly occurring at particular stages of plant development was almost unaffected by highly diverse environmental conditions. A detailed statistical analysis on the operational taxonomic unit (OTU) level, representing bacterial species, revealed a complex community structure of the rhizosphere. We identified an opportunistic microbiome which comprises OTUs that occur randomly or under specific environmental conditions. In contrast, core microbiome members were found at all sites. The ‘stable’ component of the core microbiome consisted of few ubiquitous OTUs that were continuously abundant in all samples and vegetation stages, whereas the ‘dynamic’ component comprised OTUs that were enriched at specific vegetation stages.
Wissenschaftlicher Artikel
Scientific Article
Kepert, I. ; Fonseca, J. ; Müller, C. ; Milger, K. ; Hochwind, K. ; Kostric, M. ; Fedoseeva, M. ; Ohnmacht, C. ; Dehmel, S. ; Nathan, P. ; Bartel, S. ; Eickelberg, O. ; Schloter, M. ; Hartmann, A. ; Schmitt-Kopplin, P. ; Krauss-Etschmann, S.
J. Allergy Clin. Immunol. 139, 1525-1535 (2017)
BACKGROUND: Chronic immune diseases (CIDs), such as asthma, are highly prevalent. Currently available pharmaceuticals improve symptoms, but cannot cure the disease. This prompted demands for alternatives to pharmaceuticals such as probiotics for prevention of allergic disease. However, clinical trials have given inconsistent results. This is at least partly explained by the highly complex crosstalk among probiotic bacteria, the host´s microbiota, and immune cells. The identification of a bioactive substance from probiotic bacteria could circumvent this difficulty. OBJECTIVE: To identify and characterize a bioactive, probiotic metabolite for potential prevention of allergic airway disease. METHODS: Probiotic supernatants were screened for their ability to concordantly lower the constitutive CCL17 secretion of a human Hodgkin lymphoma cell line and prevent upregulation of costimulatory molecules of LPS-stimulated human dendritic cells. RESULTS: Supernatants from 13 of 37 tested probiotic strains showed immunoactivity. Bioassay-guided chromatographic fractionation of two supernatants according to polarity, followed by total ion chromatograms and mass spectrometry, yielded C11H12N2O2 as molecular formula of a bioactive substance. Proton nuclear magnetic resonance and enantiomeric separation identified D-Tryptophan. In contrast, L-Tryptophan and eleven other D-amino acids were inactive. Feeding D-Tryptophan to mice prior to experimental asthma induction, increased numbers of lung and gut regulatory T cells, lowered lung Th2 responses, and ameliorated allergic airway inflammation and hyperresponsiveness. Allergic airway inflammation reduced the gut microbial diversity, which was increased by D-Tryptophan. CONCLUSIONS: D-Tryptophan is a newly identified product from probiotic bacteria. Our findings support the concept that defined bacterial products might be exploited in novel preventative strategies for CIDs.
Wissenschaftlicher Artikel
Scientific Article
Birzele, L.T. ; Depner, M. ; Ege, M.J. ; Engel, M. ; Kublik, S. ; Bernau, C. ; Loss, G.J. ; Genuneit, J. ; Horak, E. ; Schloter, M. ; Braun-Fahrländer, C. ; Danielewicz, H. ; Heederik, D. ; von Mutius, E. ; Legatzki, A.
Allergy 72, 109-119 (2017)
BACKGROUND: High microbial diversity in the environment has been associated with lower asthma risk, particularly in children exposed to farming. It remains unclear whether this effect operates through an altered microbiome of the mucosal surfaces of the airways. METHODS: DNA from mattress dust and nasal samples of 86 school-age children was analyzed by 454-pyrosequencing of the 16S rRNA gene fragments. Based on operational taxonomic units bacterial diversity and composition was related to farm exposure and asthma status. RESULTS: Farm exposure was positively associated with bacterial diversity in mattress dust samples as determined by richness (p=8.1 * 10(-6) ) and Shannon index (p=1.3 * 10(-5) ). Despite considerable agreement of richness between mattress and nasal samples, the association of richness with farming in nasal samples was restricted to a high gradient of farm exposure, i.e. exposure to cows and straw versus no exposure at all. In mattress dust the genera Clostridium, Facklamia, an unclassified genus within the family of Ruminococcaceae and six OTUs were positively associated with farming. Asthma was inversely associated with richness (aOR= 0.48 [0.22-1.02]) and Shannon Index (aOR=0.41 [0.21-0.83]) in mattress dust and to a lower extent in nasal samples (richness aOR 0.63[0.38-1.06], Shannon Index aOR= 0.66 [0.39-1.12]). CONCLUSION: The stronger inverse association of asthma and bacterial diversity in mattress dust as compared to nasal samples suggests microbial involvement beyond mere colonization of the upper airways. Whether inhalation of metabolites of environmental bacteria contributes to this phenomenon should be the focus of future research.
Wissenschaftlicher Artikel
Scientific Article
2016
Legay, N. ; Lavore, S. ; Baxendale, C. ; Krainer, U. ; Binet, M.N. ; Cantare, A.A.M. ; Colace, M.P. ; Foulquier, A. ; Kastl, E.-M. ; Grigulis, K. ; Mouhamadou, B. ; Poly, F. ; Pommier, T. ; Schloter, M. ; Clément, J.C. ; Bardgett, R.D.
Ecosphere 7:e01448 (2016)
Although it is known that multiple interactions among plant functional traits, microbial properties, and abiotic soil parameters influence the nutrient turnover, the relative contribution of each of these groups of variables is poorly understood. We manipulated grassland plant functional composition and soil nitrogen (N) availability in a multisite mesocosm experiment to quantify their relative effects on soil N turnover. Overall, root traits, arbuscular mycorrhizal colonization, denitrification potential, as well as N availability and water availability, best explained the variation in measured ecosystem properties, especially the trade-off between nutrient sequestration and plant biomass production. Their relative contributions varied with soil N availability. In relatively N-poor soils (10-20 μgNg-1 soil), N turnover was mainly controlled by microbial properties and abiotic soil parameters, whereas in the relatively N-rich soils (110-120 μgNg-1 soil), N turnover was mainly controlled by plant traits and microbial properties. This experiment is a strong demonstration of the importance of functional characteristics of both plants and soil microbes, and their interplay with soil N availability, for N turnover in grassland soils.
Wissenschaftlicher Artikel
Scientific Article
Komives, T. ; Schröder, P.
Ecocycles 2, 1-8 (2016)
This Editorial briefly discusses the current issues surrounding glyphosate - the most controversial pesticide active ingredient of our time . The paper pays special attention to the effects of glyphosate on plant - pathogen interactions.
Editorial
Editorial
Rankl, S. ; Gunse, B. ; Sieper, T. ; Schmid, C. ; Poschenrieder, C. ; Schröder, P.
Plant Sci. 253, 130-140 (2016)
While colonizing the rhizosphere, bacterial intra- and inter-specific communication is accomplished by N-Acyl-homoserine-lactones (AHLs) in a density-dependent manner. Moreover, plants are naturally exposed to AHLs and respond with tissue-specificity. In the present study, we investigated the influence of N-hexanoyl- (C6-HSL), N-octanoyl- (C8-HSL) and N-dodecanoyl-D/L-homoserine lactone (C12-HSL) on growth and root development in barley (Hordeum vulgare L.), and identified initial reactions in root cells after AHL exposures using physiological, staining, and electrophysiological methods. Treatment with short- and long-chain AHLs modulated plant growth and branched root architecture and induced nitric oxide (NO) accumulation in the calyptra and root elongation zone of excised roots in an AHL derivative-independent way. Additionally, C6- and C8-HSL treatments stimulated K+ uptake in root cells only at certain concentrations, whereas all tested concentrations of C12-HSL induced K+ uptake. In further experiments, C8-HSL promoted membrane hyperpolarization in epidermal root cells. Thus, we conclude AHLs promote plant growth and lateral root formation, and cause NO accumulation as an early response to AHLs. Furthermore, the AHL-mediated membrane hyperpolarization is leading to increased K+ uptake of the root tissue.
Wissenschaftlicher Artikel
Scientific Article
Bergkemper, F. ; Welzl, G. ; Lang, F. ; Krüger, J. ; Schloter, M. ; Schulz, S.
J. Plant Nutr. Soil Sci. 179, 472-480 (2016)
Among several environmental factors shaping soil microbial communities the impact of soil nutrients is of special interest. While continuous application mainly of N and P dramatically shifts community composition during fertilization, it remains unclear whether this effect is consistent in generic, unfertilized beech forest ecosystems of Germany, where differences in nutrient contents are mostly a result of the parental material and climatic conditions. We postulate that in such ecosystems nutrient effects are less pronounced due to the possibility of the soil microbiome to adapt to the corresponding conditions over decades and the vegetation acts as the major driver. To test this hypothesis, we investigated the bacterial community composition in five different German beech dominated forest soils, representing a natural gradient of total- and easily available mineral-P. A community fingerprinting approach was performed using terminal-Restriction Fragment Length Polymorphism analysis of the 16S rRNA gene, while abundance of bacteria was measured applying quantitative real-time PCR. Bacterial communities at the five forest sites were distinctly separated, with strongest differences between the end-members of the P-gradient. However the majority of identified microbial groups (43%) were present at all sites, forming a core microbiome independent from the differences in soil chemical properties. Especially in the P-deficient soil the abundance of unique bacterial groups was highly increased, indicating a special adaption of the community to P limitation at this site. In this regard Correspondence Analysis elucidated that exclusively soil pH significantly affected community composition at the investigated sites. In contrast soil C, N and P contents did mainly affect the overall abundance of bacteria.
Wissenschaftlicher Artikel
Scientific Article
Zanardo, M. ; Rosselli, R. ; Meneghesso, A. ; Sablok, G. ; Stevanato, P. ; Altissimo, A. ; Perserico, L. ; Dezuani, V. ; Concheri, G. ; Schloter, M. ; Squartini, A.
Eur. J. Soil Biol. 76, 83-91 (2016)
Organic fertilizers are of high interest in agriculture as they promise a retarded release of the nitrogen to soil, which improves uptake efficiency by plants and reduces negative impacts like the formation of nitrate by nitrifiers or N2O by denitrifying microorganisms. In this study we tested the effects of seven different commercially available organic fertilizers of plant-, animal-, or microbial origin in a two-month greenhouse trial, using the perennial grass Cynodon dactylon in pots and monitoring effects on plant growth as well as on the abundance of prokaryotic nitrifiers and denitrifiers by realtime PCR. In most cases a single application of the fertilizers induced plant growth but did not increase the abundance of nitrifiers and denitrifiers. In contrast a repeated application stimulated, in addition to plant growth, also the increase of the two functional groups studied and a faster mobilization of nitrogen from the different fertilizers. Upon analyzing total bacterial DNA extracted from soil nirK abundance was found responsive to plant presence. Bacterial amoA and nosZ gene copies were significantly positively correlated with plant growth and cumulative dry weight at harvest. The latter was responsive as early as 9 days after fertilizer supplementation.
Wissenschaftlicher Artikel
Scientific Article
Soliveres, S. ; van der Plas, F. ; Manning, P. ; Prati, D. ; Gossner, M.M. ; Renner, S.C. ; Alt, F. ; Arndt, H. ; Baumgartner, V. ; Binkenstein, J. ; Birkhofer, K. ; Blaser, S. ; Blüthgen, N. ; Boch, S. ; Böhm, S. ; Börschig, C. ; Buscot, F. ; Diekötter, T. ; Heinze, J. ; Hölzel, N. ; Jung, K. ; Klaus, V.H. ; Kleinebecker, T. ; Klemmer, S. ; Krauss, J. ; Lange, M. ; Morris, E.K. ; Müller, J. ; Oelmann, Y. ; Overmann, J. ; Pašalić, E. ; Rillig, M.C. ; Schaefer, H.M. ; Schloter, M. ; Schmitt, B. ; Schöning, I. ; Schrumpf, M. ; Sikorski, J. ; Socher, S.A. ; Solly, E.F. ; Sonnemann, I. ; Sorkau, E. ; Steckel, J. ; Steffan-Dewenter, I. ; Stempfhuber, B. ; Tschapka, M. ; Türke, M. ; Venter, P.C. ; Weiner, C.N. ; Weisser, W.W. ; Werner, M. ; Westphal, C. ; Wilcke, W. ; Wolters, V. ; Wubet, T. ; Wurst, S. ; Fischer, M. ; Allan, E.
Nature 536, 456-459 (2016)
Many experiments have shown that loss of biodiversity reduces the capacity of ecosystems to provide the multiple services on which humans depend. However, experiments necessarily simplify the complexity of natural ecosystems and will normally control for other important drivers of ecosystem functioning, such as the environment or land use. In addition, existing studies typically focus on the diversity of single trophic groups, neglecting the fact that biodiversity loss occurs across many taxa and that the functional effects of any trophic group may depend on the abundance and diversity of others. Here we report analysis of the relationships between the species richness and abundance of nine trophic groups, including 4,600 above- and below-ground taxa, and 14 ecosystem services and functions and with their simultaneous provision (or multifunctionality) in 150 grasslands. We show that high species richness in multiple trophic groups (multitrophic richness) had stronger positive effects on ecosystem services than richness in any individual trophic group; this includes plant species richness, the most widely used measure of biodiversity. On average, three trophic groups influenced each ecosystem service, with each trophic group influencing at least one service. Multitrophic richness was particularly beneficial for 'regulating' and 'cultural' services, and for multifunctionality, whereas a change in the total abundance of species or biomass in multiple trophic groups (the multitrophic abundance) positively affected supporting services. Multitrophic richness and abundance drove ecosystem functioning as strongly as abiotic conditions and land-use intensity, extending previous experimental results to real-world ecosystems. Primary producers, herbivorous insects and microbial decomposers seem to be particularly important drivers of ecosystem functioning, as shown by the strong and frequent positive associations of their richness or abundance with multiple ecosystem services. Our results show that multitrophic richness and abundance support ecosystem functioning, and demonstrate that a focus on single groups has led to researchers to greatly underestimate the functional importance of biodiversity.
Wissenschaftlicher Artikel
Scientific Article
Bergkemper, F. ; Bünemann, E.K. ; Hauenstein, S. ; Heuck, C. ; Kandeler, E. ; Krüger, J. ; Marhan, S. ; Mészáros, E. ; Nassal, D. ; Nassal, P. ; Oelmann, Y. ; Pistocchi, C. ; Schloter, M. ; Spohn, M. ; Talkner, U. ; Zederer, D.P. ; Schulz, S.
J. Microbiol. Methods 128, 66-68 (2016)
In an inter-laboratory trial, gaseous ("CFE") and liquid fumigation ("Resin") based methods for measuring microbial phosphorus (Pmic) were compared, based on the analysis of soil samples from five forests, which differ in their P stocks. Both methods reliably detected the same Pmic gradient in the different soils. However, when the individual recovery rates of spiked P were taken into account, the "CFE" based methods consistently generated higher Pmic values (factor 2) compared to the "Resin" based approaches.
Wissenschaftlicher Artikel
Scientific Article
Dannenmann, M. ; Bimüller, C. ; Gschwendtner, S. ; Leberecht, M. ; Tejedor, J. ; Bilela, S. ; Gasche, R. ; Hanewinkel, M. ; Baltensweiler, A. ; Kögel-Knabner, I. ; Polle, A. ; Schloter, M. ; Simon, J. ; Rennenberg, H.
PLoS ONE 11:e0158823 (2016)
European beech forests growing on marginal calcareous soils have been proposed to be vulnerable to decreased soil water availability. This could result in a large-scale loss of ecological services and economical value in a changing climate. In order to evaluate the potential consequences of this drought-sensitivity, we investigated potential species range shifts for European beech forests on calcareous soil in the 21st century by statistical species range distribution modelling for present day and projected future climate conditions. We found a dramatic decline by 78% until 2080. Still the physiological or biogeochemical mechanisms underlying the drought sensitivity of European beech are largely unknown. Drought sensitivity of beech is commonly attributed to plant physiological constraints. Furthermore, it has also been proposed that reduced soil water availability could promote nitrogen (N) limitation of European beech due to impaired microbial N cycling in soil, but this hypothesis has not yet been tested. Hence we investigated the influence of simulated climate change (increased temperatures, reduced soil water availability) on soil gross microbial N turnover and plant N uptake in the beech-soil interface of a typical mountainous beech forest stocking on calcareous soil in SW Germany. For this purpose, triple 15N isotope labelling of intact beech seedling-soil-microbe systems was combined with a space-for-time climate change experiment. We found that nitrate was the dominant N source for beech natural regeneration. Reduced soil water content caused a persistent decline of ammonia oxidizing bacteria and therefore, a massive attenuation of gross nitrification rates and nitrate availability in the soil. Consequently, nitrate and total N uptake of beech seedlings were strongly reduced so that impaired growth of beech seedlings was observed already after one year of exposure to simulated climatic change. We conclude that the N cycle in this ecosystem and here specifically nitrification is vulnerable to reduced water availability, which can directly lead to nutritional limitations of beech seedlings. This tight link between reduced water availability, drought stress for nitrifiers, decreased gross nitrification rates and nitrate availability and finally nitrate uptake by beech seedlings could represent the Achilles' heel for beech under climate change stresses.
Wissenschaftlicher Artikel
Scientific Article
Schaeffer, A. ; Amelung, W. ; Hollert, H. ; Kästner, M. ; Kandeler, E. ; Kruse, J. ; Miltner, A. ; Ottermanns, R. ; Pagel, H. ; Peth, S. ; Poll, C. ; Rambold, G. ; Schloter, M. ; Schulz, S. ; Streck,T. ; Roß-Nickoll, M.
Sci. Total Environ. 568, 1076-1085 (2016)
Soils are faced with man-made chemical stress factors, such as the input of organic or metal-containing pesticides, in combination with non-chemical stressors like soil compaction and natural disturbance like drought. Although multiple stress factors are typically co-occurring in soil ecosystems, research in soil sciences on this aspect is limited and focuses mostly on single structural or functional endpoints. A mechanistic understanding of the reaction of soils to multiple stressors is currently lacking. Based on a review of resilience theory, we introduce a new concept for research on the ability of polluted soil (xenobiotics or other chemical pollutants as one stressor) to resist further natural or anthropogenic stress and to retain its functions and structure. There is strong indication that pollution as a primary stressor will change the system reaction of soil, i.e., its resilience, stability and resistance. It can be expected that pollution affects the physiological adaption of organisms and the functional redundancy of the soil to further stress. We hypothesize that the recovery of organisms and chemical-physical properties after impact of a follow-up stressor is faster in polluted soil than in non-polluted soil, i.e., polluted soil has a higher dynamical stability (dynamical stability=1/recovery time), whereas resilience of the contaminated soil is lower compared to that of not or less contaminated soil. Thus, a polluted soil might be more prone to change into another system regime after occurrence of further stress. We highlight this issue by compiling the literature exemplarily for the effects of Cu contamination and compaction on soil functions and structure. We propose to intensify research on effects of combined stresses involving a multidisciplinary team of experts and provide suggestions for corresponding experiments. Our concept offers thus a framework for system level analysis of soils paving the way to enhance ecological theory.
Wissenschaftlicher Artikel
Scientific Article
Purahong, W. ; Wubet, T. ; Lentendu, G. ; Schloter, M. ; Pecyna, M.J. ; Kapturska, D. ; Hofrichter, M. ; Krüger, D. ; Buscot, F.
Mol. Ecol. 25, 4059-4074 (2016)
Microorganisms play a crucial role in the biological decomposition of plant litter in terrestrial ecosystems. Due to the permanently changing litter quality during decomposition, studies of both fungi and bacteria at a fine taxonomic resolution are required during the whole process. Here we investigated microbial community succession in decomposing leaf litter of temperate beech forest using pyrotag sequencing of the bacterial 16S and the fungal internal transcribed spacer (ITS) rRNA genes. Our results reveal that both communities underwent rapid changes. Proteobacteria, Actinobacteria and Bacteroidetes dominated over the entire study period, but their taxonomic composition and abundances changed markedly among sampling dates. The fungal community also changed dynamically as decomposition progressed, with ascomycete fungi being increasingly replaced by basidiomycetes. We found a consistent and highly significant correlation between bacterial and fungal richness (R = 0.76, P < 0.001) and community structure (RM antel = 0.85, P < 0.001), providing evidence of coupled dynamics in the fungal and bacterial communities. A network analysis highlighted non-random co-occurrences among bacterial and fungal taxa as well as a shift in the cross-kingdom co-occurrence pattern of their communities from the early to the later stages of decomposition. During this process, macronutrients, micronutrients, C:N ratio and pH were significantly correlated with the fungal and bacterial communities, while bacterial richness positively correlated with three hydrolytic enzymes important for C, N and P acquisition. Overall, we provide evidence that the complex litter decay is the result of a dynamic cross-kingdom functional succession.
Wissenschaftlicher Artikel
Scientific Article
Gunse, B. ; Poschenrieder, C. ; Rankl, S. ; Schröder, P. ; Rodrigo-Moreno, A. ; Barcelo, J.
MethodsX 3, 436-451 (2016)
In this study we present a highly versatile and easily configurable system for measuring plant electrophysiological parameters and ionic flow rates, connected to a computer-controlled highly accurate positioning device. The modular software used allows easy customizable configurations for the measurement of electrophysiological parameters. Both the operational tests and the experiments already performed have been fully successful and rendered a low noise and highly stable signal. Assembly, programming and configuration examples are discussed. The system is a powerful technique that not only gives precise measuring of plant electrophysiological status, but also allows easy development of ad hoc configurations that are not constrained to plant studies. We developed a highly modular system for electrophysiology measurements that can be used either in organs or cells and performs either steady or dynamic intra- and extracellular measurements that takes advantage of the easiness of visual object-oriented programming High precision accuracy in data acquisition under electrical noisy environments that allows it to run even in a laboratory close to electrical equipment that produce electrical noise. The system makes an improvement of the currently used systems for monitoring and controlling high precision measurements and micromanipulation systems providing an open and customizable environment for multiple experimental needs.
Wissenschaftlicher Artikel
Scientific Article
Gschwendtner, S. ; Mansfeldt, T. ; Kublik, S. ; Touliari, E. ; Buegger, F. ; Schloter, M.
Microb. Biotechnol. 9, 502-513 (2016)
Cyanides are highly toxic and produced by various microorganisms as defence strategy or to increase their competitiveness. As degradation is the most efficient way of detoxification, some microbes developed the capability to use cyanides as carbon and nitrogen source. However, it is not clear if this potential also helps to lower cyanide concentrations in roadside soils where deicing salt application leads to significant inputs of ferrocyanide. The question remains if biodegradation in soils can occur without previous photolysis. By conducting a microcosm experiment using soils with/without pre-exposition to road salts spiked with (13) C-labelled ferrocyanide, we were able to confirm biodegradation and in parallel to identify bacteria using ferrocyanide as C source via DNA stable isotope probing (DNA-SIP), TRFLP fingerprinting and pyrosequencing. Bacteria assimilating (13) C were highly similar in the pre-exposed soils, belonging mostly to Actinomycetales (Kineosporia, Mycobacterium, Micromonosporaceae). In the soil without pre-exposition, bacteria belonging to Acidobacteria (Gp3, Gp4, Gp6), Gemmatimonadetes (Gemmatimonas) and Gammaproteobacteria (Thermomonas, Xanthomonadaceae) used ferrocyanide as C source but not the present Actinomycetales. This indicated that (i) various bacteria are able to assimilate ferrocyanide-derived C and (ii) long-term exposition to ferrocyanide applied with deicing salts leads to Actinomycetales outcompeting other microorganisms for the use of ferrocyanide as C source.
Wissenschaftlicher Artikel
Scientific Article
Wang, C. ; Chen, Z. ; Unteregelsbacher, S. ; Lu, H. ; Gschwendtner, S. ; Gasche, R. ; Kolar, A. ; Schloter, M. ; Kiese, R. ; Butterbach-Bahl, K. ; Dannenmann, M.
Glob. Change Biol. 22, 2963-2978 (2016)
The carbon and nitrogen rich soils of montane grasslands are exposed to above average warming and to altered precipitation patterns as a result of global change. In order to investigate the consequences of climatic change for soil nitrogen turnover, we translocated intact plant-soil mesocosms along an elevational gradient, resulting in an increase of the mean annual temperature by approx. 2°C while decreasing precipitation from approx. 1500 to 1000 mm. Following three years of equilibration, we monitored the dynamics of gross nitrogen turnover and ammonia oxidizing bacteria (AOB) and archaea (AOA) in soils over an entire year. Gross nitrogen turnover and gene levels of AOB and AOA showed pronounced seasonal dynamics. Both summer and winter periods equally contributed to cumulative annual N turnover. However, highest gross N turnover and abundance of ammonia oxidizers were observed in frozen soil of the climate change site, likely due to physical liberation of organic substrates and their rapid turnover in the unfrozen soil water film. This effect was not observed at the control site, where as soil freezing did not occur due to a significant insulating snowpack. Climate change conditions accelerated gross nitrogen mineralization by 250% on average. Increased N mineralization significantly stimulated gross nitrification by AOB rather than by AOA. However, climate change impacts were restricted to the 2-6 cm topsoil and rarely occurred at 12-16 cm depth, where generally much lower N turnover was observed. Our study shows that significant mineralization pulses occur under changing climate, which is likely to result in soil organic matter losses with their associated negative impacts on key soil functions. We also show that N cycling processes in frozen soil can be hot moments for N turnover and thus are of paramount importance for understanding seasonal patterns, annual sum of N turnover and possible climate change feedbacks.
Wissenschaftlicher Artikel
Scientific Article
Schulz, S. ; Bergkemper, F. ; de Vries, M.C. ; Schöler, A. ; Schloter, M.
BioSpektrum 22, 265-269 (2016)
Microorganisms are essential to maintain ecosystem functions and health as they catalyze most keystone processes. Formerly the quantification of key functions was performed by broad ranged primers, which were mainly based on genomes of cultivated microbes. To take advantage of the enormous development of next generation sequencing technologies, we propose to use metagenomic data for the design of new primer systems. Here we describe a two-phasic approach for a targeted and site specific primer design for qPCR.
Wissenschaftlicher Artikel
Scientific Article
Bergkemper, F. ; Kublik, S. ; Lang, F. ; Krüger, J. ; Vestergaard, G. ; Schloter, M. ; Schulz, S.
J. Microbiol. Methods 125, 91-97 (2016)
Phosphorus (P) is of central importance for cellular life but likewise a limiting macronutrient in numerous environments. Certainly microorganisms have proven their ability to increase the phosphorus bioavailability by mineralization of organic-P and solubilization of inorganic-P. On the other hand they efficiently take up P and compete with other biotas for phosphorus. However the actual microbial community that is associated to the turnover of this crucial macronutrient in different ecosystems remains largely anonymous especially in taking effects of seasonality and spatial heterogeneity into account. In this study seven oligonucleotide primers are presented which target genes coding for microbial acid and alkaline phosphatases (phoN, phoD), phytases (appA), phosphonatases (phnX) as well as the quinoprotein glucose dehydrogenase (gcd) and different P transporters (pitA, pstS). Illumina amplicon sequencing of soil genomic DNA underlined the high rate of primer specificity towards the respective target gene which usually ranged between 98% and 100% (phoN: 87%). As expected the primers amplified genes from a broad diversity of distinct microorganisms. Using DNA from a beech dominated forest soil, the highest microbial diversity was detected for the alkaline phosphatase (phoD) gene which was amplified from 15 distinct phyla respectively 81 families. Noteworthy the primers also allowed amplification of phoD from 6 fungal orders. The genes coding for acid phosphatase (phoN) and the quinoprotein glucose dehydrogenase (gcd) were amplified from 20 respectively 17 different microbial orders. In comparison the phytase and phosphonatase (appA, phnX) primers covered 13 bacterial orders from 2 different phyla respectively. Although the amplified microbial diversity was apparently limited to both primers that reliably detected all orders that contributed to the P turnover in the investigated soil as revealed by a previous metagenomic approach. Genes that code for microbial P transporter (pitA, pstS) were amplified from 13 respectively 9 distinct microbial orders. Accordingly the introduced primers represent a valuable tool for further analysis of the microbial community involved in the turnover of phosphorus in soils but most likely also in other environments.
Wissenschaftlicher Artikel
Scientific Article
Talk, A. ; Kublik, S. ; Uksa, M. ; Engel, M. ; Berghahn, R. ; Welzl, G. ; Schloter, M. ; Mohr, S.
J. Environ. Sci. 46, 116-25 (2016)
In the first tier risk assessment (RA) of pesticides, risk for aquatic communities is estimated by using results from standard laboratory tests with algae, daphnids and fish for single pesticides such as herbicides, fungicides, and insecticides. However, fungi as key organisms for nutrient cycling in ecosystems as well as multiple pesticide applications are not considered in the RA. In this study, the effects of multiple low pesticide pulses using regulatory acceptable concentrations (RACs) on the dynamics of non-target aquatic fungi were investigated in a study using pond mesocosm. For that, fungi colonizing black alder (Alnus glutinosa) leaves were exposed to multiple, low pulses of 11 different pesticides over a period of 60. days using a real farmer's pesticide application protocol for apple cropping. Four pond mesocosms served as treatments and 4 as controls. The composition of fungal communities colonizing the litter material was analyzed using a molecular fingerprinting approach based on the terminal Restriction Fragment Length Polymorphism (t-RFLP) of the fungal Internal Transcribed Spacer (ITS) region of the ribonucleic acid (RNA) gene(s). Our data indicated a clear fluctuation of fungal communities based on the degree of leaf litter degradation. However significant effects of the applied spraying sequence were not observed. Consequently also degradation rates of the litter material were not affected by the treatments. Our results indicate that the nutrient rich environment of the leaf litter material gave fungal communities the possibility to express genes that induce tolerance against the applied pesticides. Thus our data may not be transferred to other fresh water habitats with lower nutrient availability.
Wissenschaftlicher Artikel
Scientific Article
Gschwendtner, S. ; Engel, M. ; Lueders, T. ; Buegger, F. ; Schloter, M.
Plant Soil 407, 203-215 (2016)
Background and aims: Forest ecosystems may act as sinks for or source of atmospheric CO2. While inorganic nitrogen (N) fertilization increases aboveground tree biomass, the effects on soil and rhizosphere microorganisms are less clear, indicating potentially unpredictable changes in nutrient cycling processes maintaining ecosystem functioning. Although plant-derived carbon (C) is the main C source in soils during the vegetation period, information on the response of rhizosphere bacteria assimilating rhizodeposits to increased soil N availability mainly for trees is missing. Methods: We performed a greenhouse experiment with 13C-CO2 labelled young beech seedlings grown under different N fertilization levels. DNA Stable Isotope Probing (DNA-SIP) in combination with TRFLP and pyrosequencing enabled us to identify bacteria assimilating plant-derived C and to assess the main responders phylogenetically. Results: Although above- and belowground allocation of recently fixed photosynthates remained unchanged, microbial rhizosphere community composition was clearly affected by fertilization. Besides, we found lower 13C incorporation into microbial biomass in fertilized soil. Moreover, it could be shown that only a small subset of the rhizosphere microbiome incorporated recently fixed C into its DNA, dominated by Proteobacteria (Alpha- and Betaproteobacteria) and Actinobacteria (Actinomycetales). Conclusions: Our results suggest that N fertilization may change both the diversity of bacterial communities using rhizodeposits and assimilation rates of recently fixed photosynthates. Given the close interaction of beneficial and/or deleterious microbes and plants in the rhizosphere, this could potentially have positive or negative implications for plant performance on long-term.
Wissenschaftlicher Artikel
Scientific Article
Soliveres, S. ; Manning, P. ; Prati, D. ; Gossner, M.M. ; Alt, F. ; Arndt, H. ; Baumgartner, V. ; Binkenstein, J. ; Birkhofer, K. ; Blaser, S. ; Blüthgen, N. ; Boch, S. ; Böhm, S. ; Börschig, C. ; Buscot, F. ; Diekötter, T. ; Heinze, J. ; Hölzel, N. ; Jung, K. ; Klaus, V.H. ; Klein, A.M. ; Kleinebecker, T. ; Klemmer, S. ; Krauss, J. ; Lange, M. ; Morris, E.K. ; Müller, J. ; Oelmann, Y. ; Overmann, J. ; Pašalić, E. ; Renner, S.C. ; Rillig, M.C. ; Schaefer, H.M. ; Schloter, M. ; Schmitt, B. ; Schöning, I. ; Schrumpf, M. ; Sikorski, J. ; Socher, S.A. ; Solly, E.F. ; Sonnemann, I. ; Sorkau, E. ; Steckel, J. ; Steffan-Dewenter, I. ; Stempfhuber, B. ; Tschapka, M. ; Türke, M. ; Venter, P. ; Weiner, C.N. ; Weisser, W.W. ; Werner, M. ; Westphal, C. ; Wilcke, W. ; Wolters, V. ; Wubet, T. ; Wurst, S.H. ; Fischer, M. ; Allan, E.
Philos. Trans. R. Soc. B - Biol. Sci. 371:20150269 (2016)
Species diversity promotes the delivery of multiple ecosystem functions (multifunctionality). However, the relative functional importance of rare and common species in driving the biodiversity-multifunctionality relationship remains unknown. We studied the relationship between the diversity of rare and common species (according to their local abundances and across nine different trophic groups), and multifunctionality indices derived from 14 ecosystem functions on 150 grasslands across a land-use intensity (LUI) gradient. The diversity of above- and below-ground rare species had opposite effects, with rare above-ground species being associated with high levels of multifunctionality, probably because their effects on different functions did not trade off against each other. Conversely, common species were only related to average, not high, levels of multifunctionality, and their functional effects declined with LUI. Apart from the community-level effects of diversity, we found significant positive associations between the abundance of individual species and multifunctionality in 6% of the species tested. Species-specific functional effects were best predicted by their response to LUI: species that declined in abundance with land use intensification were those associated with higher levels of multifunctionality. Our results highlight the importance of rare species for ecosystem multifunctionality and help guiding future conservation priorities.
Wissenschaftlicher Artikel
Scientific Article
Orlofsky, E.M. ; Kozhoridze, G. ; Lyubenova, L. ; Ostrozhenkova, E. ; Winkler, J.B. ; Schröder, P. ; Bacher, A. ; Eisenreich, W. ; Guy, M. ; Golan-Goldhirsh, A.
Metabolites 6, DOI: 10.3390/metabo6020013 (2016)
The research presented stemmed from the observations that female plants of the annual dioecious Mercurialis annua outlive male plants. This led to the hypothesis that female plants of M. annua would be more tolerant to stress than male plants. This hypothesis was addressed in a comprehensive way, by comparing morphological, biochemical and metabolomics changes in female and male plants during their development and under salinity. There were practically no differences between the genders in vegetative development and physiological parameters. However, under salinity conditions, female plants produced significantly more new reproductive nodes. Gender-linked differences in peroxidase (POD) and glutathione transferases (GSTs) were involved in anti-oxidation, detoxification and developmental processes in M. annua. ¹H NMR metabolite profiling of female and male M. annua plants showed that under salinity the activity of the TCA cycle increased. There was also an increase in betaine in both genders, which may be explainable by its osmo-compatible function under salinity. The concentration of ten metabolites changed in both genders, while 'Female-only-response' to salinity was detected for five metabolites. In conclusion, dimorphic responses of M. annua plant genders to stress may be attributed to female plants' capacity to survive and complete the reproductive life cycle.
Wissenschaftlicher Artikel
Scientific Article
Papadimitriou, K. ; Baharidis, P.K. ; Georgoulis, A. ; Engel, M. ; Louka, M. ; Karamolegkou, G. ; Tsoka, A. ; Blom, J. ; Pot, B. ; Malecki, P. ; Rypniewski, W. ; Huber, H. ; Schloter, M. ; Vorgias, C.
Extremophiles 20, 351-361 (2016)
Here we analyze the first complete genome sequence of Pyrococcus chitonophagus. The archaeon was previously suggested to belong to the Thermococcus rather than the Pyrococcus genus. Whole genome phylogeny as well as whole proteome comparisons using all available complete genomes in Thermococcales clearly showed that the species belongs to the Pyrococcus genus. P. chitonophagus was originally isolated from a hydrothermal vent site and it has been described to effectively degrade chitin debris, and therefore is considered to play a major role in the sea water ecology and metabolic activity of microbial consortia within hot sea water ecosystems. Indeed, an obvious feature of the P. chitonophagus genome is that it carries proteins showing complementary activities for chitin degradation, i.e. endo- and exo-chitinase, diacetylchitobiose deacetylase and exo-β-D glucosaminidase activities. This finding supports the hypothesis that compared to other Thermococcales species P. chitonophagus is adapted to chitin degradation.
Wissenschaftlicher Artikel
Scientific Article
Schröder, P. ; Helmreich, B. ; Škrbić, B. ; Carballa, M. ; Papa, M. ; Pastore, C. ; Emre, Z. ; Oehmen, A. ; Langenhoff, A. ; Molinos, M. ; Dvarioniene, J. ; Huber, C. ; Tsagarakis, K.P. ; Martinez-Lopez, E. ; Pagano, S.M. ; Vogelsang, C. ; Mascolo, G.
Environ. Sci. Pollut. Res. 23, 12835-12866 (2016)
Present technologies for wastewater treatment do not sufficiently address the increasing pollution situation of receiving water bodies, especially with the growing use of personal care products and pharmaceuticals (PPCP) in the private household and health sector. The relevance of addressing this problem of organic pollutants was taken into account by the Directive 2013/39/EU that introduced (i) the quality evaluation of aquatic compartments, (ii) the polluter pays principle, (iii) the need for innovative and affordable wastewater treatment technologies, and (iv) the identification of pollution causes including a list of principal compounds to be monitored. In addition, a watch list of 10 other substances was recently defined by Decision 2015/495 on March 20, 2015. This list contains, among several recalcitrant chemicals, the painkiller diclofenac and the hormones 17β-estradiol and 17α-ethinylestradiol. Although some modern approaches for their removal exist, such as advanced oxidation processes (AOPs), retrofitting most wastewater treatment plants with AOPs will not be acceptable as consistent investment at reasonable operational cost. Additionally, by-product and transformation product formation has to be considered. The same is true for membrane-based technologies (nanofiltration, reversed osmosis) despite of the incredible progress that has been made during recent years, because these systems lead to higher operation costs (mainly due to higher energy consumption) so that the majority of communities will not easily accept them. Advanced technologies in wastewater treatment like membrane bioreactors (MBR) that integrate biological degradation of organic matter with membrane filtration have proven a more complete elimination of emerging pollutants in a rather cost- and labor-intensive technology. Still, most of the presently applied methods are incapable of removing critical compounds completely. In this opinion paper, the state of the art of European WWTPs is reflected, and capacities of single methods are described. Furthermore, the need for analytical standards, risk assessment, and economic planning is stressed. The survey results in the conclusion that combinations of different conventional and advanced technologies including biological and plant-based strategies seem to be most promising to solve the burning problem of polluting our environment with hazardous emerging xenobiotics.
Review
Review
Jechalke, S. ; Radl, V. ; Schloter, M. ; Heuer, H. ; Smalla, K.
FEMS Microbiol. Ecol. 92:fiw066 (2016)
Naturally occurring drying-rewetting events in soil have been shown to affect the dissipation of veterinary antibiotics entering soil by manure fertilization. However, knowledge of effects on the soil microbial community structure and resistome is scarce.Here, consequences of drying-rewetting cycles on effects of sulfadiazine (SDZ) in soil planted withDactylis glomerataL. were investigated in microcosms. Manure containing SDZ or not was applied to the pregrown grass and incubated for 56 days in a climate chamber. Water was added either daily or was reduced during two drying events of seven days, each followed by a recovery phase. Total community DNA was analyzed to reveal effects on the bacterial community structure and on the abundance ofsul1,sul2,intI1,intI2,qacE+qacEΔ1,traNandkorBgenes relative to 16S rRNA genes.16S rRNA gene based DGGE fingerprints indicated that drying-rewetting cycles modulated effects of SDZ on the bacterial community structure in the soil. Furthermore, the SDZ treatment increased the relative abundance of sulfonamide resistance and integrase genes compared to the control. However, this increase was not different between moisture regimes, indicating that drying-rewetting had only a negligible effect on the selection of the resistome by SDZ in the manured soil.
Wissenschaftlicher Artikel
Scientific Article
Cooper, J. ; Baranski, M. ; Stewart, G. ; Nobel-de Lange, M. ; Bàrberi, P. ; Fließbach, A. ; Peigné, J. ; Berner, A. ; Brock, C. ; Casagrande, M. ; Crowley, O. ; David, C. ; de Vliegher, A. ; Döring, T.F. ; Dupont, A. ; Entz, M. ; Grosse, M. ; Haase, T. ; Halde, C. ; Hammerl, V. ; Huiting, H. ; Leithold, G. ; Messmer, M. ; Schloter, M. ; Sukkel, W. ; van der Heijden, M.G.A. ; Willekens, K. ; Wittwer, R. ; Mäder, P.
Agron. Sustain. Dev. 36:22 (2016)
Reduced tillage is increasingly promoted to improve sustainability and productivity of agricultural systems. Nonetheless, adoption of reduced tillage by organic farmers has been slow due to concerns about nutrient supply, soil structure, and weeds that may limit yields. Here, we compiled the results from both published and unpublished research comparing deep or shallow inversion tillage, with various categories of reduced tillage under organic management. Shallow refers to less than 25 cm. We found that (1) division of reduced tillage practices into different classes with varying degrees of intensity allowed us to assess the trade-offs between reductions in tillage intensity, crop yields, weed incidence, and soil C stocks. (2) Reducing tillage intensity in organic systems reduced crop yields by an average of 7.6 % relative to deep inversion tillage with no significant reduction in yield relative to shallow inversion tillage. (3) Among the different classes of reduced tillage practice, shallow non-inversion tillage resulted in non-significant reductions in yield relative to deep inversion; whereas deep non-inversion tillage resulted in the largest yield reduction, of 11.6 %. (4) Using inversion tillage to only a shallow depth resulted in minimal reductions in yield, of 5.5 %, but significantly higher soil C stocks and better weed control. This finding suggests that this is a good option for organic farmers wanting to improve soil quality while minimizing impacts on yields. (5) Weeds were consistently higher, by about 50 %, when tillage intensity was reduced, although this did not always result in reduced yields.
Review
Review
Nesme, J. ; Achouak, W. ; Agathos, S.N. ; Bailey, M. ; Baldrian, P. ; Brunel, D. ; Frostegård, ; Heulin, T. ; Jansson, J.K. ; Jurkevitch, E. ; Kruus, K.L. ; Kowalchuk, G.A. ; Lagares, A. ; Lappin-Scott, H.M. ; Lemanceau, P. ; Le Paslier, D. ; Mandic-Mulec, I. ; Murrell, J.C. ; Myrold, D.D. ; Nalin, R. ; Nannipieri, P. ; Neufeld, J.D. ; O'Gara, F. ; Parnell, J.J. ; Pühler, A. ; Pylro, V. ; Ramos, J.L. ; Roesch, L.F. ; Schloter, M. ; Schleper, C. ; Sczyrba, A. ; Sessitsch, A. ; Sjöling, S. ; Sørensen, J. ; Sørensen, S.J. ; Tebbe, C.C. ; Topp, E.M. ; Tsiamis, G. ; van Elsas, J.D. ; van Keulen, G. ; Widmer, F. ; Wagner, M. ; Zhang, T. ; Zhang, X. ; Zhao, L. ; Zhu, Y.G. ; Vogel, T.M. ; Simonet, P.
Front. Microbiol. 7:73 (2016)
Wissenschaftlicher Artikel
Scientific Article
Cui, H. ; Schröder, P.
J. Hazard. Mater. 308, 355-361 (2016)
The increasing load of pharmaceutical compounds has raised concerns about their potential residues in aquatic environments and ecotoxicity. Metformin (MET), a widely prescribed antidiabetic II medicine, has been detected in high concentration in sewage and in wastewater treatment effluents. An uptake and translocation study was carried out to assess the ultimate fate of MET in phytoremediation. MET was removed from media by Typha latifolia, and the removal processes followed first order kinetics. After 28 days, the removal efficiencies were in a range of 74.0±4.1-81.1±3.3%. In roots, MET concentration was increasing during the first two weeks of the experiment but thereafter decreasing. In contrast, MET concentration was continuously increasing in rhizomes and leaves. Bioaccumulation of MET in roots was much higher than in leaves and rhizomes. As degradation product of metformin in the plant, methylbiguanide (MBG) was detected whereas guanylurea was undetectable. Moreover, MBG concentration in roots was increasing with exposure time. An enzymatic degradation experiment showed the degradation rate followed the order of MET
Wissenschaftlicher Artikel
Scientific Article
Schöler, A. ; de Vries, M.C. ; Vestergaard, G. ; Schloter, M.
Methods Mol. Biol. 1399, 197-206 (2016)
Microorganisms are central players in the turnover of nutrients in soil and drive the decomposition of complex organic materials into simpler forms that can be utilized by other biota. Therefore microbes strongly drive soil quality and ecosystem services provided by soils, including plant yield and quality. Thus it is one of the major goals of soil sciences to describe the most relevant enzymes that are involved in nutrient mobilization and to understand the regulation of gene expression of the corresponding genes. This task is however impeded by the enormous microbial diversity in soils. Indeed, we are far to appreciate the number of species present in 1 g of soil, as well as the major functional traits they carry. Here, also most next-generation sequencing (NGS) approaches fail as immense sequencing efforts are needed to fully uncover the functional diversity of soils. Thus even if a gene of interest can be identified by BLAST similarity analysis, the obtained number of reads by NGS is too low for a quantitative assessment of the gene or for a description of its taxonomic diversity. Here we present an integrated approach, which we termed the second-generation full cycle approach, to quantify the abundance and diversity of key enzymes involved in nutrient mobilization. This approach involves the functional annotation of metagenomic data with a relative low coverage (5 Gbases or less) and the design of highly targeted primer systems to assess the abundance or diversity of enzyme-coding genes that are drivers for a particular transformation step in nutrient turnover.
Wissenschaftlicher Artikel
Scientific Article
Bergkemper, F. ; Schöler, A. ; Engel, M. ; Lang, F. ; Krüger, J. ; Schloter, M. ; Schulz, S.
Environ. Microbiol. 18, 1988-2000 (2016)
Phosphorus (P) is an important macronutrient for all biota on earth but similarly a finite resource. Microorganisms play on both sides of the fence as they effectively mineralize organic and solubilize precipitated forms of soil phosphorus, but conversely also take up and immobilize P. Therefore, we analyzed the role of microbes in two beech forest soils with high and low P content by direct sequencing of metagenomic DNA. For inorganic P solubilization, a significantly higher microbial potential was detected in the P-rich soil. This trait especially referred to Candidatus Solibacter usiatus, likewise one of the dominating species in the datasets. A higher microbial potential for efficient phosphate uptake systems (pstSCAB) was detected in the P-depleted soil. Genes involved in P starvation response regulation (phoB, phoR) were prevalent in both soils. This underlines the importance of effective phosphate (Pho) regulon control for microorganisms to use alternative P sources during phosphate limitation. Predicted genes were primarily harbored by Rhizobiales, Actinomycetales and Acidobacteriales.
Wissenschaftlicher Artikel
Scientific Article
Huber, C. ; Preis, M. ; Harvey, P.J. ; Grosse, S.D. ; Letzel, T. ; Schröder, P.
Chemosphere 146, 435-441 (2016)
Human pharmaceuticals and their residues are constantly detected in our waterbodies, due to poor elimination rates, even in the most advanced waste water treatment plants. Their impact on the environment and human health still remains unclear. When phytoremediation is applied to aid water treatment, plants may transform and degrade xenobiotic contaminants through phase I and phase II metabolism to more water soluble and less toxic intermediates. In this context, peroxidases play a major role in activating compounds during phase I via oxidation. In the present work, the ability of a plant peroxidase to oxidize the human painkiller diclofenac was confirmed using stopped flow spectroscopy in combination with LC-MS analysis. Analysis of an orange colored product revealed the structure of the highly reactive Diclofenac-2,5-Iminoquinone, which may be the precursor of several biological conjugates and breakdown products in planta.
Wissenschaftlicher Artikel
Scientific Article
Chen, F. ; Huber, C. ; May, R. ; Schröder, P.
J. Hazard. Mater. 306, 230-236 (2016)
Oxybenzone (OBZ), known as Benzophenone-3, is a commonly used UV filter in sun tans and skin protectants, entering aquatic systems either directly during recreational activities or indirectly through wastewater treatment plants discharge. To study the potential degradation capacity of plants for OBZ in phytotreatment, a well-established hairy root culture (Armoracia rusticana) was treated with OBZ. More than 20% of spiked OBZ (100μM) was eliminated from the medium by hairy roots after 3h of exposure. Two metabolites were identified as oxybenzone-glucoside (OBZ-Glu) and oxybenzone-(6-O-malonyl)-glucoside (OBZ-Mal-Glu) by LC-MS/MS and TOF-MS. Formation of these metabolites was confirmed by enzymatic synthesis, as well as enzymatic and alkaline hydrolysis. Incubation with O-glucosyltransferase (O-GT) extracted from roots formed OBZ-Glu; whereas β-d-Glucosidase hydrolyzed OBZ-Glu. However, alkaline hydrolysis led to cleavage of OBZ-Mal-Glu and yielded OBZ-Glu. In the hairy root culture, an excretion of OBZ-Glu into the growth medium was observed while the corresponding OBZ-Mal-Glu remained stored in root cells over the incubation time. We propose that metabolism of oxybenzone in plants involves initial conjugation with glucose to form OBZ-Glu followed by malonylation to yield OBZ-Mal-Glu. To our best knowledge this first finding presenting the potential of plants to degrade benzophenone type UV filters by phytoremediation.
Wissenschaftlicher Artikel
Scientific Article
Gschwendtner, S. ; Alatossava, T. ; Kublik, S. ; Fuka, M.M. ; Schloter, M. ; Munsch-Alatossava, P.
PLoS ONE 11:e0146015 (2016)
The quality and safety of raw milk still remains a worldwide challenge. Culture-dependent methods indicated that the continuous N2 gas-flushing of raw milk reduced the bacterial growth during cold storage by up to four orders of magnitude, compared to cold storage alone. This study investigated the influence of N2 gas-flushing on bacterial diversity in bovine raw-milk samples, that were either cold stored at 6°C or additionally flushed with pure N2 for up to one week. Next-generation sequencing (NGS) of the V1-V2 hypervariable regions of 16S rRNA genes, derived from amplified cDNA, which was obtained from RNA directly isolated from raw-milk samples, was performed. The reads, which were clustered into 2448 operational taxonomic units (OTUs), were phylogenetically classified. Our data revealed a drastic reduction in the diversity of OTUs in raw milk during cold storage at 6°C at 97% similarity level; but, the N2-flushing treatment alleviated this reduction and substantially limited the loss of bacterial diversity during the same cold-storage period. Compared to cold-stored milk, the initial raw-milk samples contained less Proteobacteria (mainly Pseudomonadaceae, Moraxellaceae and Enterobacteriaceae) but more Firmicutes (mainly Ruminococcaceaea, Lachnospiraceae and Oscillospiraceaea) and Bacteroidetes (mainly Bacteroidales). Significant differences between cold-stored and additionally N2-flushed milk were mainly related to higher levels of Pseudomononadaceae (including the genera Pseudomonas and Acinetobacter) in cold-stored milk samples; furthermore, rare taxa were better preserved by the N2 gas flushing compared to the cold storage alone. No major changes in bacterial composition with time were found regarding the distribution of the major 9 OTUs, that dominated the Pseudomonas genus in N2-flushed or non-flushed milk samples, other than an intriguing predominance of bacteria related to P. veronii. Overall, this study established that neither bacteria causing milk spoilage nor any well-known human pathogen or anaerobe benefited from the N2 gas flushing even though the N2-flushed and non-flushed cold-stored milk differed in bacterial counts by up to 104-fold.
Wissenschaftlicher Artikel
Scientific Article
Stempfhuber, B. ; Richter-Heitmann, T. ; Regan, K.M. ; Kölbl, A. ; Kaul, P. ; Marhan, S. ; Sikorski, J. ; Overmann, J. ; Friedrich, M.W. ; Kandeler, E. ; Schloter, M.
Front. Microbiol. 6:1567 (2016)
Interrelated successive transformation steps of nitrification are performed by distinct microbial groups – the ammonia-oxidizers, comprising ammonia-oxidizing archaea (AOA) and bacteria (AOB), and nitrite-oxidizers such as Nitrobacter and Nitrospira, which are the dominant genera in the investigated soils. Hence, not only their presence and activity in the investigated habitat is required for nitrification, but also their temporal and spatial interactions. To demonstrate the interdependence of both groups and to address factors promoting putative niche differentiation within each group, temporal and spatial changes in nitrifying organisms were monitored in an unfertilized grassland site over an entire vegetation period at the plot scale of 10 m2. Nitrifying organisms were assessed by measuring the abundance of marker genes (amoA for AOA and AOB, nxrA for Nitrobacter, 16S rRNA gene for Nitrospira) selected for the respective sub-processes. A positive correlation between numerically dominant AOA and Nitrospira, and their co-occurrence at the same spatial scale in August and October, suggests that the nitrification process is predominantly performed by these groups and is restricted to a limited timeframe. Amongst nitrite-oxidizers, niche differentiation was evident in observed seasonally varying patterns of co-occurrence and spatial separation. While their distributions were most likely driven by substrate concentrations, oxygen availability may also have played a role under substrate-limited conditions. Phylogenetic analysis revealed temporal shifts in Nitrospira community composition with an increasing relative abundance of OTU03 assigned to sublineage V from August onward, indicating its important role in nitrite oxidation.
Wissenschaftlicher Artikel
Scientific Article
Lehotai, N. ; Lyubenova, L. ; Schröder, P. ; Feigl, G. ; Ördög, A. ; Szilágyi, K. ; Erdei, L. ; Kolbert, Z.
Plant Soil 400, 107-122 (2016)
Background and aims: Selenium (Se) phytotoxicity at the cellular level disturbs the synthesis and functions of proteins, together with the generation of an oxidative stress condition. This study reveals the nitro-oxidative stress events, supplemented by a broad spectrumed characterisation of the Se-induced symptoms. Methods: Applying several, carefully selected methods, we investigated the selenite treatment-induced changes in the Se and sulphur contents, pigment composition, hydrogen peroxide level, activity of the most important antioxidative enzymes, glutathione, nitric oxide and peroxynitrite, lipid peroxidation and protein tyrosine nitration. Results: The Se content increased intensively and concentration-dependently in the organs of the treated plants, which led to altered vegetative and reproductive development. The level of the investigated reactive oxygen species and antioxidants supported the presence of the Se-induced oxidative stress, but also pointed out nitrosative changes, in parallel. Conclusions: The presented results aim to map the altered vegetative and reproductive development of Se-treated pea plants. Mild dose of Se has supportive effect, while high concentrations inhibit growth. Behind Se toxicity, we discovered both oxidative and nitrosative stress-induced modifications. Moreover, the presented data first reveals selenite-induced concentration- and organ-dependent tyrosine nitration in pea.
Wissenschaftlicher Artikel
Scientific Article
2015
Fuka, M.M. ; Blažinkov, M. ; Radl, V. ; Jug, D. ; Hulak, N. ; Redzepovic, S. ; Schloter, M.
Agric. Conspec. Sci. 80, 147-151 (2015)
Several studies have indicated that intensive tillage has notable effect on properties of the soil microbiota that may influence numerous important soils functions, e.g. mobilization of nutrients or change of the overall emission rates of greenhouse gases. Therefore, the aim of our study was to investigate dynamic of microbial communities in soil planted with soybean under different tillage systems. Moreover, abundance of populations harboring the nitrous- oxide reductase gene (nosZ) as an indicator for potential shift s in N2O emission rates was studied. The study was established at chernozem soil of Northern Baranja region in Republic of Croatia as completely randomized block design of four replicate plots for each tillage system in three years experiment. The soil was managed as followed: CT - conventional tillage (moldboard ploughing at 25-30 cm depth), DH - multiple discs harrowing (10-15 cm depth), and NT – no-tillage system. Soil samples were collected in summer and autumn in year 2003. Our results suggested that the reduction of tillage had no effects on the bacterial community structure. This might be a result of the very dry climatic conditions at the investigated site and /or a result of plant species effect (soybean). Slight effects of the tillage management became visible at least when samples were taken in autumn for microbes harboring the N2O reductase gene, indicating that there might be shift s in denitrification pattern in response to changes in tillage practice.
Wissenschaftlicher Artikel
Scientific Article
Uksa, M. ; Schloter, M. ; Endesfelder, D. ; Kublik, S. ; Engel, M. ; Kautz, T. ; Köpke, U. ; Fischer, D.
Front. Microbiol. 6:1269 (2015)
Microbial communities in soil provide a wide range of ecosystem services. On the small scale, nutrient rich hotspots in soil developed from the activities of animals or plants are important drivers for the composition of microbial communities and their functional patterns. However, in subsoil, the spatial heterogeneity of microbes with differing lifestyles has been rarely considered so far. In this study, the phylogenetic composition of the bacterial and archaeal microbiome based on 16S rRNA gene pyrosequencing was investigated in the soil compartments bulk soil, drilosphere, and rhizosphere in top- and in the subsoil of an agricultural field. With co-occurrence network analysis, the spatial separation of typically oligotrophic and copiotrophic microbes was assessed. Four bacterial clusters were identified and attributed to bulk topsoil, bulk subsoil, drilosphere, and rhizosphere. The bacterial phyla Proteobacteria and Bacteroidetes, representing mostly copiotrophic bacteria, were affiliated mainly to the rhizosphere and drilosphere—both in topsoil and subsoil. Acidobacteria, Actinobacteria, Gemmatimonadetes, Planctomycetes, and Verrucomicrobia, bacterial phyla which harbor many oligotrophic bacteria, were the most abundant groups in bulk subsoil. The bacterial core microbiome in this soil was estimated to cover 7.6% of the bacterial sequencing reads including both oligotrophic and copiotrophic bacteria. In contrast the archaeal core microbiome includes 56% of the overall archaeal diversity. Thus, the spatial variability of nutrient quality and quantity strongly shapes the bacterial community composition and their interaction in subsoil, whereas archaea build a stable backbone of the soil prokaryotes due to their low variability in the different soil compartments.
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Scientific Article
Kaurin, A. ; Mihelic, R. ; Kastelec, D. ; Schloter, M. ; Suhaldoc, M. ; Grčman, H.
Biol. Fertil. Soils 51, 923-933 (2015)
A long-term field experiment was run for 12 years to evaluate the impact of minimum tillage (MT) compared to conventional mouldboard ploughing (CT) on soil chemical, physical and microbial properties in a shallow Cambisol formed over fluvioglacial deposits of Drava river in Slovenia. Significant differences between MT and CT were found in vertical distribution of soil organic C (SOC) and nutrients (total N and plant available potassium); under MT, concentrations decreased from the soil surface to the lower layers, as opposed to CT which maintained rather uniform distribution down to the ploughing depth. MT in comparison with CT also increased the proportion of water-stable 2–4-mm-sized aggregates (80.9 and 61.3 %, respectively), water holding capacity (24.8 and 22.2 %, respectively) and plant available water (13.4 and 10.3 %, respectively) in the upper 0–10-cm soil layer. Bulk density, porosity, the proportion of water-stable 1–2-mm-sized aggregates and infiltration rate showed no significant differences between the tillage treatments. SOC content in the upper 0–10-cm soil layer was not significantly different between MT and CT (1.60 ± 0.07 and 1.45 ± 0.05 %, respectively), as well as the overall stock in the investigated soil profile (0–60 cm) remained unaffected (57.4 ± 0.8 and 59.1 ± 2.2 t ha−1, respectively). Microbial biomass, estimated by the total soil DNA, was higher in MT than CT in the 0–10-cm layer. Furthermore, a positive linear dependence of microbial biomass on SOC content was observed. Fingerprinting of bacterial, fungal and archaeal communities indicated that microbial community composition changed by long-term MT, whereas changes in microbial diversity were not detected for any domain. The most pronounced shifts in the composition were found for bacterial communities in the 10–20-cm layer, while the composition of fungal communities slightly changed in the upper 0–10 cm of MT soil. The composition of archaeal communities was not affected by the tillage or by the soil depth. Our results indicate that MT generates modest changes in soil structure and soil water retention properties and could support measures against erosion, drought and nutrient leaching. Considering increased microbial biomass in the topsoil of MT and shifts in microbial diversity, the impacts of MT on soil microbiome are also evident and need to be further investigated to identify the affected functional traits.
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Braun, P. ; Grass, G. ; Aceti, A. ; Serrecchia, L. ; Affuso, A. ; Marino, L. ; Grimaldi, S. ; Pagano, S. ; Hanczaruk, M. ; Georgi, E. ; Northoff, B. ; Schöler, A. ; Schloter, M. ; Antwerpen, M. ; Fasanella, A.
PLoS ONE 10:e0135346 (2015)
During an anthrax outbreak at the Pollino National Park (Basilicata, Italy) in 2004, diseased cattle were buried and from these anthrax-foci Bacillus anthracis endospores still diffuse to the surface resulting in local accumulations. Recent data suggest that B. anthracis multiplies in soil outside the animal-host body. This notion is supported by the frequent isolation of B. anthracis from soil lacking one or both virulence plasmids. Such strains represent an evolutionary dead end, as they are likely no longer able to successfully infect new hosts. This loss of virulence plasmids is explained most simply by postulating a soil-borne life cycle of the pathogen. To test this hypothesis we investigated possible microevolution at two natural anthrax foci from the 2004 outbreak. If valid, then genotypes of strains isolated from near the surface at these foci should be on a different evolutionary trajectory from those below residing in deeper-laying horizons close to the carcass. Thus, the genetic diversity of B. anthracis isolates was compared conducting Progressive Hierarchical Resolving Assays using Nucleic Acids (PHRANA) and next generation Whole Genome Sequencing (WGS). PHRANA was not discriminatory enough to resolve the fine genetic relationships between the isolates. Conversely, WGS of nine isolates from near-surface and nine from near-carcass revealed five isolate specific SNPs, four of which were found only in different near-surface isolates. In support of our hypothesis, one surface-isolate lacked plasmid pXO1 and also harbored one of the unique SNPs. Taken together, our results suggest a limited soil-borne life cycle of B. anthracis.
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Obermeier, M. ; Schröder, C.A. ; Helmreich, B. ; Schröder, P.
Environ. Sci. Pollut. Res. 22, 18495-18507 (2015)
Lemna minor L., a widely used model plant for toxicity tests has raised interest for its application to phytoremediation due to its rapid growth and ubiquitous occurrence. In rural areas, the pollution of water bodies with heavy metals and agrochemicals poses a problem to surface water quality. Among problematic compounds, heavy metals (copper) and pesticides are frequently found in water bodies. To establish duckweed as a potential plant for phytoremediation, enzymatic and antioxidative stress responses of Lemna minor during exposure to copper and a chloroacetamide herbicide were investigated in laboratory studies. The present study aimed at evaluating growth and the antioxidative and glutathione-dependent enzyme activity of Lemna plants and its performance in a scenario for phytoremediation of copper and a chloroacetamide herbicide. Lemna minor was grown in Steinberg medium under controlled conditions. Plants were treated with CuSO4 (ion conc. 50 and 100 μg/L) and pethoxamide (1.25 and 2.5 μg/L). Measurements following published methods focused on plant growth, oxidative stress, and basic detoxification enzymes. Duckweed proved to survive treatment with the respective concentrations of both pollutants very well. Its growth was inhibited scarcely, and no visible symptoms occurred. On the cellular basis, accumulation of O2− and H2O2 were detected, as well as stress reactions of antioxidative enzymes. Duckweed detoxification potential for organic pollutants was high and increased significantly with incubation. Pethoxamide was found to be conjugated with glutathione. Copper was accumulated in the fronds at high levels, and transient oxidative defense reactions were triggered. This work confirms the significance of L. minor for the removal of copper from water and the conjugation of the selective herbicide pethoxamide. Both organic and inorganic xenobiotics induced different trends of enzymatic and antioxidative stress response. The strong increase of stress responses following copper exposure is well known as oxidative burst, which is probably different from the much more long-lasting responses found in plants exposed to pethoxamide. Lemna sp. might be used as a tool for phytoremediation of low-level contamination with metals and organic xenobiotics, however the authors recommend a more detailed analysis of the development of the oxidative burst following copper exposure and of the enzymatic metabolism of pethoxamide in order to elucidate the extent of its removal from water.
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Chronakova, A. ; Schloter-Hai, B. ; Radl, V. ; Endesfelder, D. ; Quince, C. ; Elhottova, D. ; Simek, M. ; Schloter, M.
PLoS ONE 10:e0135627 (2015)
Archaea and bacteria are important drivers for nutrient transformations in soils and catalyse the production and consumption of important greenhouse gases. In this study, we investigate changes in archaeal and bacterial communities of four Czech grassland soils affected by outdoor cattle husbandry. Two show short-term (3 years; STI) and long-term impact (17 years; LTI), one is regenerating from cattle impact (REG) and a control is unaffected by cattle (CON). Cattle manure (CMN), the source of allochthonous microbes, was collected from the same area. We used pyrosequencing of 16S rRNA genes to assess the composition of archaeal and bacterial communities in each soil type and CMN. Both short- and long- term cattle impact negatively altered archaeal and bacterial diversity, leading to increase of homogenization of microbial communities in overwintering soils over time. Moreover, strong shifts in the prokaryotic communities were observed in response to cattle overwintering, with the greatest impact on archaea. Oligotrophic and acidophilic microorganisms (e.g. Thaumarchaeota, Acidobacteria, and α-Proteobacteria) dominated in CON and expressed strong negative response to increased pH, total C and N. Whereas copiotrophic and alkalophilic microbes (e.g. methanogenic Euryarchaeota, Firmicutes, Chloroflexi, Actinobacteria, and Bacteroidetes) were common in LTI showing opposite trends. Crenarchaeota were also found in LTI, though their trophic interactions remain cryptic. Firmicutes, Bacteroidetes, Methanobacteriaceae, and Methanomicrobiaceae indicated the introduction and establishment of faecal microbes into the impacted soils, while Chloroflexi and Methanosarcinaceae suggested increased abundance of soil-borne microbes under altered environmental conditions. The observed changes in prokaryotic community composition may have driven corresponding changes in soil functioning.
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Radl, V. ; Kindler, R. ; Welzl, G. ; Albert, A. ; Wilke, B.M. ; Amelung, W. ; Schloter, M.
Appl. Soil Ecol. 95, 99-106 (2015)
Application of manure for soil fertilization is a common practice in arable and pasture soils. As antibiotics are regularly used in animal husbandry, these compounds often enter the soil via manure application. The effects of antibiotics on microbial communities, however, might depend on soil moisture, as water availability may influence both the fate of the compound and the activity of the microbes. To test this hypothesis, we investigated the effects of the application of manure containing the antibiotic sulfadiazine (SDZ) on the abundance and activity of nitrifies and denitrifies in soil, based on the copy number of marker genes and their related potential activities, as affected by different moisture regimes. We observed significant effects of SDZ on potential denitrification activity, but those were not influenced by the soil moisture regime. Nevertheless, neither SDZ nor changes on moisture significantly affected the abundance of denitrifies. In contrast, both potential nitrification activity and abundance of ammonia oxidizing bacteria were significantly affected by the application of manure containing SDZ and moisture regime. Interestingly, no effects were observed for ammonia oxidizing archaea. Overall, our data show that soil moisture modulates the effects of antibiotics in soil microbial communities, and we recommend to include this parameter in the risk assessment of new chemicals.
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Spohn, M. ; Treichel, N. ; Cormann, M. ; Schloter, M. ; Fischer, D.
Soil Biol. Biochem. 89, 44-51 (2015)
Despite the importance of the rhizosphere for nutrient turnover, little is known about the spatial patterns of organic phosphorus mineralization by plants and by microorganisms in the rhizosphere. Therefore, the distribution of acid and alkaline phosphatase activity and the abundance of bacteria belonging to various bacterial phyla were investigated in the rhizosphere of barley (Hordeum vulgare L.) as dependent on the availability of inorganic P. For this purpose, we conducted a greenhouse experiment with barley growing in inclined boxes that can be opened to the bottom side (rhizoboxes), and applied soil zymography and fluorescence-in situ-hybridization (FISH). Acid phosphatase activity was strongly associated with the root and was highest at the root tips. Due to P fertilization, acid phosphatase activity decreased in the bulk soil, and less strongly in the rhizosphere. Alkaline phosphatase activity, i.e., microbial phosphatase activity was high throughout the soil in the control treatment and was reduced due to inorganic P fertilization especially in the rhizosphere and less strongly in the bulk soil. P-fertilization slightly increased the total number of bacteria in the rhizosphere. Moreover, P-fertilization decreased the abundance of Firmicutes and increased the abundances of Beta- and Gamma-Proteobacteria. The total number of bacterial cells was significantly higher at the root surface than at the root tip and at a distance of 30 μm from the root surface. Our results show that alkaline phosphatase activity decreased more strongly in the rhizosphere than in the bulk soil due to P fertilization, which might be because of greater C deficiency in the bulk soil compared to the rhizosphere. Furthermore, the results indicate a spatial separation between hotspots of acid phosphatase activity and hotspots of bacteria in the rhizosphere of H. vulgare. Taken together, our study shows that bacteria and phosphatase activity were very heterogeneously distributed in soil, and that the effects of P fertilization on phosphatase activity differed strongly between bulk soil and rhizosphere as well as between various zones of the rhizosphere.
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Lyubenova, L. ; Sabodash, X. ; Schröder, P. ; Michalke, B.
Environ. Sci. Pollut. Res. 22, 16978-16986 (2015)
The trace element selenium has an essential role for human health. It is involved in redox center functions, and it is related to the immune system response. Legumes are among the main suppliers of selenium into the human food chain. Not only Se concentration as such but also more the chemical species of Se is of higher importance for successful Se supply to the human diet and its bioavailability. The current study was focused on the investigation of the Se species present in chickpea plants exposed to 0, 10, 25, 50, and 100 μM selenite in short- and long-term treatment studies. The linear increase of total Se concentration could be linked to the increased concentrations of Se exposure. The selenium species (SeMet, SeCys, selenite, selenate, GPx) detected in varying concentrations in shoots and roots depend on the exposure's concentration and duration. The investigation showed that chickpea can accumulate Se in favorable concentrations and its transformation to bioavailable Se species may have positive impacts on human health and aid to implement Se into the diet.
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de Vries, M.C. ; Schöler, A. ; Ertl, J. ; Xu, Z. ; Schloter, M.
FEMS Microbiol. Ecol. 91:fiv069 (2015)
Incorporation of plant litter is a frequent agricultural practice to increase nutrient availability in soil and heavily relies on the activity of cellulose degrading microorganisms. Here we address the question how different tillage treatments affect soil microbial communities and their cellulose degrading potential in a long-term agricultural experiment. To identify potential differences in microbial taxonomy and functionality, we generated six soil metagenomes of conventional (CT) and reduced (RT) tillage-treated topsoil samples, which differed in their potential extracellular cellulolytic activity as well as microbial biomass. Taxonomic analysis of metagenomic data revealed few differences between RT and CT and a dominance of Proteobacteria and Actinobacteria, whereas eukaryotic phyla were not prevalent. Prediction of cellulolytic enzymes revealed glycoside hydrolase families 1, 3, 5, 94, auxiliary activity family 8 and carbohydrate binding module 2 as the most abundant in soil. These were annotated mainly to the phyla of Proteobacteria, Actinobacteria and Bacteroidetes. These results suggest that the observed higher cellulolytic activity in RT soils can be explained by a higher microbial biomass or changed expression levels but not by shifts in the soil microbiome. Overall this study reveals stability of soil microbial communities and cellulolytic gene composition under the investigated tillage treatments.
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Allan, E. ; Manning, P. ; Alt, F. ; Binkenstein, J. ; Blaser, S. ; Blüthgen, N. ; Böhm, S. ; Grassein, F. ; Hölzel, N. ; Klaus, V.H. ; Kleinebecker, T. ; Morris, E.K. ; Oelmann, Y. ; Prati, D. ; Renner, S.C. ; Rillig, M.C. ; Schaefer, M. ; Schloter, M. ; Schmitt, B. ; Schöning, I. ; Schrumpf, M. ; Solly, E. ; Sorkau, E. ; Steckel, J. ; Steffen-Dewenter, I. ; Stempfhuber, B. ; Tschapka, M. ; Weiner, C.N. ; Weisser, W.W. ; Werner, M. ; Westphal, C. ; Wilcke, W. ; Fischer, M.
Ecol. Lett. 18, 834-843 (2015)
Global change, especially land-use intensification, affects human well-being by impacting the delivery of multiple ecosystem services (multifunctionality). However, whether biodiversity loss is a major component of global change effects on multifunctionality in real-world ecosystems, as in experimental ones, remains unclear. Therefore, we assessed biodiversity, functional composition and 14 ecosystem services on 150 agricultural grasslands differing in land-use intensity. We also introduce five multifunctionality measures in which ecosystem services were weighted according to realistic land-use objectives. We found that indirect land-use effects, i.e. those mediated by biodiversity loss and by changes to functional composition, were as strong as direct effects on average. Their strength varied with land-use objectives and regional context. Biodiversity loss explained indirect effects in a region of intermediate productivity and was most damaging when land-use objectives favoured supporting and cultural services. In contrast, functional composition shifts, towards fast-growing plant species, strongly increased provisioning services in more inherently unproductive grasslands.
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Leberecht, M. ; Dannenmann, M. ; Gschwendtner, S. ; Bilela, S. ; Meier, R. ; Simon, J. ; Rennenberg, H. ; Schloter, M. ; Polle, A.
Appl. Environ. Microbiol. 81, 5957-5967 (2015)
Beech (Fagus sylvatica), a dominant forest species in Central Europe, competes for nitrogen with soil microbes and suffers from N limitation under dry conditions. We hypothesized that ectomycorrhizal communities and the free living rhizosphere microbes from beech trees of two contrasting climatic conditions exhibit differences in N acquisition that contribute to differences in host N uptake and are related to differences in host below-ground carbon allocation. To test these hypotheses young trees from the natural regeneration of two genetically similar populations, one from dryer conditions (SW) and the other from cooler, moist climate (NE) were transplanted into a homogeneous substrate in the same environment and labelled with (13)CO2 and (15)NH4 (+). Free living rhizosphere microbes were characterized by marker genes for the N cycle, but no differences between the rhizosphere of SW or NE trees were found. Lower (15)N enrichment was found in the ectomycorrhizal communities of NE compared with the SW communities, whereas no significant differences were observed for non-mycorrhizal root tips of SW and NE trees. Neither ectomycorrhizal communities nor non-mycorhizal root tips showed differences in (13)C signatures between the NE and SW origins. Because (15)N accumulation in fine roots and transfer to leaves were lower in NE compared to SW trees, our data support that ectomycorrhizal community influence N transfer to their host and demonstrate that the fungal community from the dry condition was more efficient in N acquisition when environmental constraints were relieved. These findings highlight the importance of adapted ectomycorrhizal communities for forest nutrition in a changing climate.
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Weikl, F. ; Radl, V. ; Munch, J.-C. ; Pritsch, K.
Sci. Total Environ. 529, 223-230 (2015)
Fungi are, after pollen, the second most important producers of outdoor airborne allergens. To identify sources of airborne fungal allergens, a workflow for qPCR quantification from environmental samples was developed, thoroughly tested, and finally applied. We concentrated on determining the levels of allergenic fungi belonging to Alternaria, Cladosporium, Fusarium, and Trichoderma in plant and soil samples from agricultural fields in which cereals were grown. Our aims were to identify the major sources of allergenic fungi and factors potentially influencing their occurrence. Plant materials were the main source of the tested fungi at and after harvest. Amounts of A. alternata and C. cladosporioides varied significantly in fields under different management conditions, but absolute levels were very high in all cases. This finding suggests that high numbers of allergenic fungi may be an inevitable side effect of farming in several crops. Applied in large-scale studies, the concept described here may help to explain the high number of sensitization to airborne fungal allergens.
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Chen, Z. ; Wang, C. ; Gschwendtner, S. ; Willibald, G. ; Unteregelsbacher, S. ; Lu, H. ; Kolar, A. ; Schloter, M. ; Butterbach-Bahl, K. ; Dannenmann, M.
Soil Biol. Biochem. 87, 67-77 (2015)
The montane grassland soils of Europe store significant amounts of nitrogen (N), and climate change might drive their volatilization due to the stimulation of gaseous nitrous oxide (N2O) and dinitrogen (N2) losses. Hence, a thorough, mechanistic understanding of the processes responsible for N loss and retention such as denitrification and dissimilatory nitrate reduction to ammonium (DNRA) in these soils is urgently needed. Here we aimed to explore the relationships between denitrifier gene abundance and expression with N2 and N2O production and the importance of DNRA versus denitrification in nitrate consumption and N2O production for typical montane grassland soils of Southern Germany. In a laboratory incubation experiment with glucose and nitrate addition, we combined direct measurements of N2O and N2 production with a molecular analysis of the denitrifier communities involved in nitrite, nitric oxide (NO) and N2O reduction and with the quantification of DNRA. The soils originated from a space-for-time climate change experiment, where intact plant-soil mesocosms were exposed for three years either to ambient conditions at a high elevation site ("HE" control treatment) or to predicted climate change conditions (warming, reduced summer precipitation and reduced winter snow cover) by translocation to lower elevation ("LE" climate change treatment).The abundance (DNA) of cnorB genes was significantly reduced in LE soils, whereas the abundance of nosZ genes did not differ between the HE and LE soils. However, the decreased abundance of cnorB genes unexpectedly resulted in slightly increased rather than decreased potential N2O emissions. This effect could be explained by the increased levels of cnorB mRNA and, therefore, the higher physiological activity of the NO reducers in the LE soils. In contrast with the DNA levels, the dynamics of the cnorB mRNA levels followed N2O emission patterns, whereas the nosZ expression was strongly correlated with the N2 emission (R2=0.83). The potential rates of DNRA were approximately one-third of the rates of denitrification, and DNRA was not a source for N2O.We conclude that DNRA significantly competes with denitrification in these soils, thus contributing to N conservation. This work demonstrates that the molecular analysis of nosZ gene expression has great potential to contribute to solving the enigmatic problem of understanding N2 loss from soil.
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Cui, H. ; Hense, B.A. ; Müller, J. ; Schröder, P.
Chemosphere 134, 307-312 (2015)
Metformin (MET) as an emerging contaminant has been detected in surface water and wastewater in numerous countries, due to insufficient retention in classical waste water treatment plants. In order to characterize the uptake of the compound during phytotreatment of waste water, a short term Pitman chamber experiment was carried out to assess the characteristics of MET uptake and transport by roots. Three different concentrations (0.5, 1.0 and 2.0mmolL(-)(1)) were applied to cattail (Typha latifolia) and reed (Phragmites australis) roots which were used to investigate the uptake mechanism because they are frequently utilized in phytoremediation. In addition, quinidine was used as an inhibitor to assess the role of organic cation transporters (OCTs) in the uptake of MET by T. latifolia. The transport process of MET is different from carbamazepine (CBZ) and caffeine (CFN). In both T. latifolia and P. australis, the uptake processes were independent of initial concentrations. Quinidine, a known inhibitor of organic cation transporters, can significantly affect MET uptake by T. latifolia roots with inhibition ratios of 70-74%. Uptake into the root could be characterized by a linear model with R(2) values in the range of 0.881-0.999. Overall, the present study provides evidence that MET is taken up by plant roots and has the potential for subsequent translocation. OCTs could be one of the important pathways for MET uptake into the plant.
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Regan, K.M. ; Nunan, N. ; Boeddinghaus, R.S. ; Baumgartner, V. ; Berner, D. ; Boch, S. ; Oelmann, Y. ; Overmann, J. ; Prati, D. ; Schloter, M. ; Schmitt, B. ; Sorkau, E. ; Steffens, M. ; Kandeler, E. ; Marhan, S.
Soil Biol. Biochem. 86, 212-214 (2015)
Götz-Rösch, C. ; Sieper, T. ; Fekete, A. ; Schmitt-Kopplin, P. ; Hartmann, A. ; Schröder, P.
Front. Plant Sci. 6:205 (2015)
Bacteria are able to communicate with each other and sense their environment in a population density dependent mechanism known as quorum sensing (QS). N-acyl- homoserine lactones (AHLs) are the QS signaling compounds of Gram-negative bacteria which are frequent colonizers of rhizospheres. While cross-kingdom signaling and AHL- dependent gene expression in plants has been confirmed, the responses of enzyme activities in the eukaryotic host upon AHLs are unknown. Since AHL are thought to be used as so-called plant boosters or strengthening agents, which might change their resistance toward radiation and/or xenobiotic stress, we have examined the plants pigment status and their antioxidative and detoxifying capacities upon AHL treatment. Because the yield of a crop plant should not be negatively influenced, we have also checked for growth and root parameters. We investigated the influence of three different AHLs, namely N-hexanoyl- (C6-HSL), N-octanoyl- (C8-HSL), and N-decanoyl- homoserine lactone (C10-HSL) on two agricultural crop plants. The AHL-effects on Hordeum vulgare (L.) as an example of a monocotyledonous crop and on the tropical leguminous crop plant Pachyrhizus erosus (L.) were compared. While plant growth and pigment contents in both plants showed only small responses to the applied AHLs, AHL treatment triggered tissue- and compound-specific changes in the activity of important detoxification enzymes. The activity of dehydroascorbate reductase in barley shoots after C10-HSL treatment for instance increased up to 384% of control plant levels, whereas superoxide dismutase activity in barley roots was decreased down to 23% of control levels upon C6-HSL treatment. Other detoxification enzymes reacted similarly within this range, with interesting clusters of positive or negative answers toward AHL treatment.In general the changes on the enzyme level were more severe in barley than in yam bean which might be due to the differentabilities of the plants to degrade AHLs to metabolites such as thehy droxy-or keto-form of the original compound.
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Scientific Article
Cantarel, A.A. ; Pommier, T. ; Desclos-Theveniau, M. ; Diquelou, S. ; Dumont, M. ; Grassein, F. ; Kastl, E.-M. ; Grigulis, K. ; Laine, P. ; Lavorel, S. ; Lemauviel-Lavenant, S. ; Personeni, E. ; Schloter, M. ; Poly, F.
Ecology 96, 788-799 (2015)
© 2015 by the Ecological Society of America. It has long been recognized that plant species and soil microorganisms are tightly linked, but understanding how different species vary in their effects on soil is currently limited. In this study, we identified those plant characteristics (identity, specific functional traits, or resource acquisition strategy) that were the best predictors of nitrification and denitrification processes. Ten plant populations representing eight species collected from three European grassland sites were chosen for their contrasting plant trait values and resource acquisition strategies. For each individual plant, leaf and root traits and the associated potential microbial activities (i.e., potential denitrification rate [DEA], maximal nitrification rate [NEA], and NH4+affinity of the microbial community [NHScom]) were measured at two fertilization levels under controlled growth conditions. Plant traits were powerful predictors of plant-microbe interactions, but relevant plant traits differed in relation to the microbial function studied. Whereas denitrification was linked to the relative growth rate of plants, nitrification was strongly correlated to root trait characteristics (specific root length, root nitrogen concentration, and plant affinity for NH4+) linked to plant N cycling. The leaf economics spectrum (LES) that commonly serves as an indicator of resource acquisition strategies was not correlated to microbial activity. These results suggest that the LES alone is not a good predictor of microbial activity, whereas root traits appeared critical in understanding plant-microbe interactions.
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Purahong, W. ; Kapturska, D. ; Pecyna, M.J. ; Jariyavidyanont, K. ; Kaunzner, J. ; Juncheed, K. ; Uengwetwanit, T. ; Rudloff, R. ; Schulz, E. ; Hofrichter, M. ; Schloter, M. ; Kruger, D. ; Buscot, F.
Microb. Ecol. 69, 905-913 (2015)
Forest management practices (FMPs) significantly influence important ecological processes and services in Central European forests, such as leaf litter decomposition and nutrient cycling. Changes in leaf litter diversity, and thus, its quality as well as microbial community structure and function induced by different FMPs were hypothesized to be the main drivers causing shifts in decomposition rates and nutrient release in managed forests. In a litterbag experiment lasting 473 days, we aimed to investigate the effects of FMPs (even-aged timber management, selective logging and unmanaged) on bacterial and fungal communities involved in leaf litter degradation over time. Our results showed that microbial communities in leaf litter were strongly influenced by both FMPs and sampling date. The results from nonmetric multidimensional scaling (NMDS) ordination revealed distinct patterns of bacterial and fungal successions over time in leaf litter. We demonstrated that FMPs and sampling dates can influence a range of factors, including leaf litter quality, microbial macronutrients, and pH, which significantly correlate with microbial community successions.
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Purahong, W. ; Stempfhuber, B. ; Lentendu, G. ; Francioli, D. ; Reitz, T. ; Buscot, F. ; Schloter, M. ; Krüger, D.
PLoS ONE 10:e0118967 (2015)
Due to the high diversity of bacteria in many ecosystems, their slow generation times, specific but mostly unknown nutrient requirements and syntrophic interactions, isolation based approaches in microbial ecology mostly fail to describe microbial community structure. Thus, cultivation independent techniques, which rely on directly extracted nucleic acids from the environment, are a well-used alternative. For example, bacterial automated ribosomal intergenic spacer analysis (B-ARISA) is one of the widely used methods for fingerprinting bacterial communities after PCR-based amplification of selected regions of the operon coding for rRNA genes using community DNA. However, B-ARISA alone does not provide any taxonomic information and the results may be severely biased in relation to the primer set selection. Furthermore, amplified DNA stemming from mitochondrial or chloroplast templates might strongly bias the obtained fingerprints. In this study, we determined the applicability of three different B-ARISA primer sets to the study of bacterial communities. The results from in silico analysis harnessing publicly available sequence databases showed that all three primer sets tested are specific to bacteria but only two primers sets assure high bacterial taxa coverage (1406f/23Sr and ITSF/ITSReub). Considering the study of bacteria in a plant interface, the primer set ITSF/ITSReub was found to amplify (in silico) sequences of some important crop species such as Sorghum bicolor and Zea mays. Bacterial genera and plant species potentially amplified by different primer sets are given. These data were confirmed when DNA extracted from soil and plant samples were analyzed. The presented information could be useful when interpreting existing B-ARISA results and planning B-ARISA experiments, especially when plant DNA can be expected.
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Scientific Article
Sauvetre, A. ; Schröder, P.
Front. Plant Sci. 6:83 (2015)
Carbamazepine is an antiepileptic and mood-stabilizing drug which is used widely in Europe and North America. In the environment, it is found as a persistent and recalcitrant contaminant, being one of the most prominent hazardous pharmaceuticals and personal care products in effluents of wastewater treatment plants. Phragmites australis is one of the species with both, the highest potential of detoxification and phytoremediation. It has been used successfully in the treatment of industrial and municipal wastewater. Recently, the identification of endophytic microorganisms from different plant species growing in contaminated sites has provided a list of candidates which could be used as bio-inoculants for bioremediation of difficult compounds. In this study, Phragmites australis plants were exposed to 5 mg/L of carbamazepine. After 9 days the plants had removed 90% of the initial concentration. Endophytic bacteria were isolated from these plants and further characterized. Phylogenetic analysis based on 16S rDNA sequencing revealed that the majority of these isolates belong to three groups: Proteobacteria, Actinobacteria, and Bacteroidetes. Carbamazepine uptake and plant growth promoting (PGP) traits were analyzed among the isolates. Ninety percent of the isolates produce indole acetic acid (IAA) and all of them possess at least one of the PGP traits tested. One isolate identified as Chryseobacterium taeanense combines good carbamazepine uptake and all of the PGP traits. Rhizobium daejeonense can remove carbamazepine and produces 23 μg/mL of IAA. Diaphorobacter nitroreducens and Achromobacter mucicolens are suitable for carbamazepine removal while both, Pseudomonas veronii and Pseudomonas lini show high siderophore production and phosphate solubilization. Alone or in combination, these isolates might be applied as inoculates in constructed wetlands in order to enhance the phytoremediation of carbamazepine during wastewater treatment.
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Scientific Article
Schloter, M. ; Kostric, M. ; Schöler, A. ; Treichel, N. ; Krauss-Etschmann, S. ; Berg, G.
BioSpektrum 21, 39-40 (2015)
The human microbiome drives important functional traits like transformation of food, generation of vitamins, stimulation of the immune system and defense from pathogens, which can be considered as the key for human health and disease. In this short note we present a brief overview on recent developments, perspectives for human health and emerging challenges in the field of human health research.
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Scientific Article
Ehrlich, R. ; Schulz, S. ; Schloter, M. ; Steinberger, Y.
Biol. Fertil. Soils 51, 507-510 (2015)
The topography significantly affects microclimatic conditions and the physical properties of soil along and between slopes of different orientations in desert ecosystems. The goal of the present study was to determine the relationship between slope orientation and bacterial, as well as fungal, community composition both in bulk soil and soil particle-size fractions at different time points throughout the seasons (very dry autumn and moister winter). The soil bacterial and fungal community composition was assessed by 16S ribosomal RNA (rRNA) gene respectively ITS fingerprinting after PCR amplification of extracted DNA from soil. Our results indicate that bacterial community composition was mainly affected by the different sampling time points, whereas fungal community composition was affected by both slope orientation and sampling time point. Soil fractionation revealed that these differences are mainly due to shifts of fungal communities in the clay fractions.
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Vogel, C. ; Heister, K. ; Buegger, F. ; Tanuwidjaja, I. ; Haug, S. ; Schloter, M. ; Kögel-Knabner, I.
Biol. Fertil. Soils 51, 427-442 (2015)
The interaction between minerals and organic matter (OM) is a key to the turnover of OM in soils. In particular, clay minerals, iron oxides and charcoal are considered as important constituents affecting the sequestration of carbon (C) and nitrogen (N). Here, we incubated pre-produced artificial soils (842 days) and a natural soil (Ap, Luvisol) with 13C- and 15N-labelled plant litter over 63 days to follow OM turnover and the formation of organo-mineral associations regarding different compositions (montmorillonite (MT), illite (IL), montmorillonite + charcoal (MT+CH), illite + ferrihydrite (IL+FH)). The microbial biomass, salt extractable organic C, the isotopic C and N composition in the bulk soil and the soil fractions (combined density and particle size fractionation) were determined. By comparison of the artificial soils with the natural soil, we were able to show that the produced soil-like systems have OM dynamics comparable to the natural soil. We found out that the decomposition of the added plant litter was affected by the type of clay mineral that formed the artificial soils, as the soil MT exhibited a slower mineralisation compared to IL, which was in line with a lower microbial biomass. Although a high specific surface area (SSA) provides a high sequestration capacity for C and N, smaller amounts were sequestered in the MT soil with a higher SSA compared to the soil IL. We suppose that a more intensive decomposition is associated with a higher microbial biomass and thus leads to higher amounts of microbial products sequestered in the clay-sized fraction. Charcoal and ferrihydrite had no additional effect in this experiment.
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Uksa, M. ; Schloter, M. ; Kautz, T. ; Athmann, M. ; Köpke, U. ; Fischer, D.
Biol. Fertil. Soils 51, 517-521 (2015)
© 2015 Springer-Verlag Berlin Heidelberg The spatial heterogeneity of nutrient turnover in subsoils has been rarely studied in the past, although drilosphere and rhizosphere are found to be important microbial hotspots in this oligotrophic environment. In this study, we measured different potential enzyme activities in different soil compartments of subsoil and topsoil. It could be shown that the activities of hydrolases, which cleave readily available organic substrates, are significantly higher in samples from the drilosphere and rhizosphere both in topsoil and subsoil. In bulk soil, hydrolase activities decrease with depth. In contrast, oxidative enzymes, which are involved in the decay of recalcitrant organic material, are released from the microbial community especially in the bulk fraction of subsoil. This emphasizes the importance of subsoil for nutrient acquisition and gives evidence for a distinct spatial separation of microbes with diverging lifestyles.
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Scientific Article
Steinbach, A. ; Schulz, S. ; Giebler, J. ; Schulz, S. ; Pronk, G.J. ; Kögel-Knabner, I. ; Harms, H. ; Wick, L.Y. ; Schloter, M.
ISME J. 9, 1687-1691 (2015)
Clay minerals, charcoal and metal oxides are essential parts of the soil matrix and strongly influence the formation of biogeochemical interfaces in soil. We investigated the role of these parental materials for the development of functional microbial guilds using the example of alkane-degrading bacteria harbouring the alkane monooxygenase gene (alkB) in artificial mixtures composed of different minerals and charcoal, sterile manure and a microbial inoculum extracted from an agricultural soil. We followed changes in abundance and community structure of alkane-degrading microbial communities after 3 and 12 months of soil maturation and in response to a subsequent 2-week plant litter addition. During maturation we observed an overall increasing divergence in community composition. The impact of metal oxides on alkane-degrading community structure increased during soil maturation, whereas the charcoal impact decreased from 3 to 12 months. Among the clay minerals illite influenced the community structure of alkB-harbouring bacteria significantly, but not montmorillonite. The litter application induced strong community shifts in soils, maturated for 12 months, towards functional guilds typical for younger maturation stages pointing to a resilience of the alkane-degradation function potentially fostered by an extant 'seed bank'.
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Stempfhuber, B. ; Engel, M. ; Fischer, D. ; Neskovic-Prit, G. ; Wubet, T. ; Schöning, I. ; Gubry-Rangin, C. ; Kublik, S. ; Schloter-Hai, B. ; Rattei, T. ; Welzl, G. ; Nicol, G.W. ; Schrumpf, M. ; Buscot, F. ; Prosser, J.I. ; Schloter, M.
Microb. Ecol. 69, 879-883 (2015)
In this study, we investigated the impact of soil pH on the diversity and abundance of archaeal ammonia oxidizers in 27 different forest soils across Germany. DNA was extracted from topsoil samples, the amoA gene, encoding ammonia monooxygenase, was amplified; and the amplicons were sequenced using a 454-based pyrosequencing approach. As expected, the ratio of archaeal (AOA) to bacterial (AOB) ammonia oxidizers’ amoA genes increased sharply with decreasing soil pH. The diversity of AOA differed significantly between sites with ultra-acidic soil pH (<3.5) and sites with higher pH values. The major OTUs from soil samples with low pH could be detected at each site with a soil pH <3.5 but not at sites with pH >4.5, regardless of geographic position and vegetation. These OTUs could be related to the Nitrosotalea group 1.1 and the Nitrososphaera subcluster 7.2, respectively, and showed significant similarities to OTUs described from other acidic environments. Conversely, none of the major OTUs typical of sites with a soil pH >4.6 could be found in the ultra- and extreme acidic soils. Based on a comparison with the amoA gene sequence data from a previous study performed on agricultural soils, we could clearly show that the development of AOA communities in soils with ultra-acidic pH (<3.5) is mainly triggered by soil pH and is not influenced significantly by the type of land use, the soil type, or the geographic position of the site, which was observed for sites with acido-neutral soil pH.
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Scientific Article
Eisenhofer, S. ; Efendiyev, M.A. ; Otani, M. ; Schulz, S. ; Zischka, H.
Discrete Contin. Dyn. Syst.-Ser. B 20, 1031-1057 (2015)
Mitochondrial swelling has huge impact to multicellular organisms since it triggers apoptosis, the programmed cell death. In this paper we present a new mathematical model of this phenomenon. As a novelty it includes spatial effects, which are of great importance for the in vivo process. Our model considers three mitochondrial subpopulations varying in the degree of swelling. The evolution of these groups is dependent on the present calcium concentration and is described by a system of ODEs, whereas the calcium propagation is modeled by a reaction-diffusion equation taking into account spatial effects. We analyze the derived model with respect to existence and long-time behavior of solutions and obtain a complete mathematical classification of the swelling process.
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Scientific Article
Gschwendtner, S. ; Leberecht, M. ; Engel, M. ; Kublik, S. ; Dannenmann, M. ; Polle, A. ; Schloter, M.
Microb. Ecol. 69, 867-878 (2015)
Soil microbial community responses to elevated atmospheric CO2 concentrations (eCO2) occur mainly indirectly via CO2-induced plant growth stimulation leading to quantitative as well as qualitative changes in rhizodeposition and plant litter. In order to gain insight into short-term, site-specific effects of eCO2 on the microbial community structure at the plant-soil interface, young beech trees (Fagus sylvatica L.) from two opposing mountainous slopes with contrasting climatic conditions were incubated under ambient (360 ppm) CO2 concentrations in a greenhouse. One week before harvest, half of the trees were incubated for 2 days under eCO2 (1,100 ppm) conditions. Shifts in the microbial community structure in the adhering soil as well as in the root rhizosphere complex (RRC) were investigated via TRFLP and 454 pyrosequencing based on 16S ribosomal RNA (rRNA) genes. Multivariate analysis of the community profiles showed clear changes of microbial community structure between plants grown under ambient and elevated CO2 mainly in RRC. Both TRFLP and 454 pyrosequencing showed a significant decrease in the microbial diversity and evenness as a response of CO2 enrichment. While Alphaproteobacteria dominated by Rhizobiales decreased at eCO2, Betaproteobacteria, mainly Burkholderiales, remained unaffected. In contrast, Gammaproteobacteria and Deltaproteobacteria, predominated by Pseudomonadales and Myxococcales, respectively, increased at eCO2. Members of the order Actinomycetales increased, whereas within the phylum Acidobacteria subgroup Gp1 decreased, and the subgroups Gp4 and Gp6 increased under atmospheric CO2 enrichment. Moreover, Planctomycetes and Firmicutes, mainly members of Bacilli, increased under eCO2. Overall, the effect intensity of eCO2 on soil microbial communities was dependent on the distance to the roots. This effect was consistent for all trees under investigation; a site-specific effect of eCO2 in response to the origin of the trees was not observed.
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Scientific Article
Kastl, E.-M. ; Schloter-Hai, B. ; Buegger, F. ; Schloter, M.
Biol. Fertil. Soils 51, 57-64 (2015)
Exploitative fast-growing plants have higher demands for nutrients compared to conservative slow-growing plants. We presume that these differences in nutrient uptake highly influence the microbial performance mainly in the rhizosphere of nutrient-poor soils. In order to investigate the influence of plants with contrasting exploitation types on microbial communities at the root-soil interface, we performed a greenhouse experiment in a N-poor, sandy soil using the fast-growing plant Dactylis glomerata and the conservative, slow-growing plant Festuca rubra. We applied four different amounts of the inorganic fertilizer ammonium nitrate (0, 50, 100, and 200 kg NH4NO3 ha-1). After 6 weeks, the abundance of nitrifiers and denitrifiers was investigated in the root-rhizosphere complex (RRC) based on the quantification of the marker genes amoA, nirK, nirS, and nosZ. Furthermore, soil chemical properties and the plant biomass were determined. Independent from the investigated plant species, fertilizer applications up to 100 kg ha-1 resulted in a clear depletion of ammonium and nitrate in the RRC, with ammonium and nitrate concentrations <1 mg kg-1 dry weight (dw). Only the highest fertilizer rate increased both ammonium and nitrate concentrations in the RRC of both plants reaching concentrations of 9.5 mg kg-1 dw for ammonium and 92.5 mg kg-1 dw for nitrate. The abundance of bacterial ammonia oxidizers (AOB) followed this trend (increase in abundance in response to the highest fertilizer rate), and copy numbers up to 3.2 × 107 copies g-1 dw were measured in the RRC of treatments with F. rubra where 200 kg N ha-1 was applied. As the archaeal ammonia oxidizers (AOA) did respond neither to plant species nor to the fertilizer application, the AOA/AOB ratio decreased from 10 in the non-fertilized treatments to 2 in treatments with 200 kg N ha-1. Also the abundance of microbes involved in denitrification strongly increased in response to higher fertilization rates in the RRC of both plant species, although higher gene copy numbers were detected in the rhizosphere of D. glomerata mainly for nitrous oxide reducers (up to 2.7 × 108 copies g-1 dw). Surprisingly, the highest fertilization rates resulted in a 50 % decrease in abundance of microbes involved in nitrite as well as nitrous oxide reduction.
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Scientific Article
Lyubenova, L. ; Bipuah, H. ; Belford, E.J. ; Michalke, B. ; Winkler, B. ; Schröder, P.
Environ. Sci. Pollut. Res. 22, 657-666 (2015)
The present study focused on cupric sulphate and cupric nitrate uptake in Typha latifolia and the impact of these copper species on the plant's detoxification capacity. When the plants were exposed to 10, 50 and 100 μM cupric sulphate or cupric nitrate, copper accumulation in T. latifolia roots and shoots increased with rising concentration of the salts. Shoot to root ratios differed significantly depending on the form of copper supplementation, e.g. if it was added as cupric (II) sulphate or cupric (II) nitrate. After incubation with 100 μM of cupric sulphate, up to 450 mg Cu/kg fresh weight (FW) was accumulated, whereas the same concentration of cupric nitrate resulted in accumulation of 580 mg/kg FW. Furthermore, significant differences in the activity of some antioxidative enzymes in Typha roots compared to the shoots, which are essential in the plant's reaction to cope with metal stress, were observed. The activity of peroxidase (POX) in roots was increased at intermediate concentrations (10 and 50 μM) of CuSO4, whereas it was inhibited at the same Cu(NO3)2 concentrations. Ascorbate peroxidase (APOX) and dehydroascorbate reductase (DHAR) increased their enzyme activity intensely, which may be an indication for copper toxicity in T. latifolia plants. Besides, fluorodifen conjugation by glutathione S-transferases (GSTs) was increased up to sixfold, especially in roots.
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2014
Gschwendtner, S. ; Tejedor, J. ; Bimueller, C. ; Dannenmann, M. ; Knabner, I.K. ; Schloter, M.
PLoS ONE 9:e114278 (2014)
Ongoing climate change will lead to more extreme weather events, including severe drought periods and intense drying rewetting cycles. This will directly influence microbial nitrogen (N) turnover rates in soil by changing the water content and the oxygen partial pressure. Therefore, a space for time climate change experiment was conducted by transferring intact beech seedling-soil mesocosms from a northwest (NW) exposed site, representing today's climatic conditions, to a southwest (SW) exposed site, providing a model climate for future conditions with naturally occurring increased soil temperature (+0.8°C in average). In addition, severe drought and intense rainfall was simulated by a rainout shelter at SW and manual rewetting after 39 days drought, respectively. Soil samples were taken in June, at the end of the drought period (August), 24 and 72 hours after rewetting (August) and after a regeneration period of four weeks (September). To follow dynamics of bacterial and archaeal communities involved in N turnover, abundance and activity of nitrifiers, denitrifiers, N2-fixing microbes and N-mineralizers was analyzed based on marker genes and the related transcripts by qPCR from DNA and RNA directly extracted from soil. Abundance of the transcripts was reduced under climate change with most pronounced effects for denitrification. Our results revealed that already a transfer from NW to SW without further treatment resulted in decreased cnor and nosZ transcripts, encoding for nitric oxide reductase and nitrous oxide reductase, respectively, while nirK transcripts, encoding for nitrite reductase, remained unaffected. Severe drought additionally led to reduced nirK and cnor transcripts at SW. After rewetting, nirK transcripts increased rapidly at both sites, while cnor and nosZ transcripts increased only at NW. Our data indicate that the climate change influences activity pattern of microbial communities involved in denitrification processes to a different extend, which may impact emission rates of the greenhouse gas N2O.
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Scientific Article
Purahong, W. ; Schloter, M. ; Pecyna, M.J. ; Kapturska, D. ; Däumlich, V. ; Mital, S. ; Buscot, F. ; Hofrichter, M. ; Gutknecht, J.L. ; Krüger, D.
Sci. Rep. 4:7014 (2014)
The widespread paradigm in ecology that community structure determines function has recently been challenged by the high complexity of microbial communities. Here, we investigate the patterns of and connections between microbial community structure and microbially-mediated ecological function across different forest management practices and temporal changes in leaf litter across beech forest ecosystems in Central Europe. Our results clearly indicate distinct pattern of microbial community structure in response to forest management and time. However, those patterns were not reflected when potential enzymatic activities of microbes were measured. We postulate that in our forest ecosystems, a disconnect between microbial community structure and function may be present due to differences between the drivers of microbial growth and those of microbial function.
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Scientific Article
Bartha, B. ; Huber, C. ; Schröder, P.
Plant Sci. 227, 12-20 (2014)
The fate of pharmaceuticals in our environment is a very important issue for environmental and health research. Although these substances have been detected in environmental compartments in low concentration until now, they will pose considerable environmental risk to ecosystems, animals and human due to their biological activity. Alternative plant based removal technologies that make use of some potential wetland species like Phragmites or Typha within traditional wastewater treatment plants have to be established to cope with this "new generation" of pollutants. We investigated uptake and translocation of diclofenac (1mgl(-1)) in the macrophyte Typha latifolia L. during one week exposure in greenhouse experiments. Detoxification products and involved key enzymatic processes were identified. We also examined the oxidative stress induced by the treatment and the defense capacity of the plants. Rapid uptake and effective metabolism were observed, where glycoside and glutathione conjugates represent dominant metabolites. Up to seven-fold induction of glycosyltransferase activity was observed in roots, but not in shoots. Glutathione S-transferase activity was also induced, but to a lower extent. The activity changes of defense enzymes points to oxidative stress in the plants. Our results show that human pharmaceuticals can be metabolized by plants similar to xenobiotics, but that similarities to human metabolism are limited.
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Berg, G. ; Grube, M. ; Schloter, M. ; Smalla, K.
Front. Microbiol. 5:491 (2014)
The study of plant-microbe associations by new techniques has significantly improved our understanding of the structure and specificity of the plant microbiome. Yet, microbiome function and the importance of the plant’s microbiome in the context of human and plant health are largely unexplored. Comparable with our human microbiome, millions of microbes inhabit plants, forming complex ecological communities that influence plant growth and health through its collective metabolic activities and host interactions. Viewing the microbiota from an ecological perspective can provide insight into how to promote plant health and stress tolerance of their hosts or how to adapt to a changing climate by targeting this microbial community. Moreover, the plant microbiome has a substantial impact on human health by influencing our gut microbiome by eating raw plants such as lettuce and herbs and but also by influencing the microbiome of our environment through airflow. This research topic will highlight the current knowledge regarding plant microbiomes, their specificity, diversity and function. Especially welcome are articles focused on the microbiomes of fresh edible plants and their impact on human health. Furthermore all applied aspects studying the management of plant microbiomes to enhance plant growth, health quality and stress tolerance are encouraged.
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Scientific Article
Bimüller, C. ; Müller, C.W. ; Lützow, M. ; Kreyling, O. ; Kölbl, A. ; Haug, S. ; Schloter, M. ; Knabner, I.K.
Soil Biol. Biochem. 78, 263-273 (2014)
To better understand how carbon and nitrogen mineralization are linked in soils, we conducted a long-term incubation experiment and compared carbon and nitrogen dynamics in the bulk soil and in soil fractions. Topsoil of a Rendzic Leptosol from a beech forest site near Tuttlingen, Germany, was separated into three particle size classes: sand (2000–20 μm), silt (20–2 μm), and clay (<2 μm). Bulk soil and particle size fractions were incubated in replicate, allowing periodic destructive sampling of triplicates at day 0, 14, 42, 84, 140, 210, and 280. We monitored CO2–C respiration, NH3–N emissions, nitrogen mineralization, pool sizes of total and salt extractable (0.01 M CaCl2) organic carbon and nitrogen, and microbial biomass carbon and nitrogen. The chemical composition of selected samples was further characterized by 13C-NMR spectroscopy. Fractionation did not influence carbon mineralization (∑ fractions ≈ bulk soil), which decreased in the order sand > clay > silt. The fractions respired between 10.4% (sand fraction), 8.8% (clay fraction) and 4.4% (silt fraction) of total soil organic carbon. However, nitrogen mineralization was affected by the fractionation procedure (∑ fractions < bulk soil) and followed the order clay > silt > sand. Fractionation increased the surface area and hence provided accessory mineral surfaces, which allowed new binding of especially nitrogen-rich compounds, in addition to ammonium fixation via cation exchange. As indicated by lower metabolic quotients, microbial carbon mineralization was more efficient in the bulk soil compared to the calculated sum of fractions. In the clay fraction, carbon mineralization rates, salt extractable organic carbon contents, and microbial biomass carbon and nitrogen contents declined strongly towards the end of the incubation. This indicates that in the clay fraction, organic carbon was not available for microbial degradation and that microorganisms were strongly carbon-limited causing a subsequent inhibition of nitrogen immobilization. Density fractionation revealed that organic matter in the sand fraction consisted mainly of particulate organic matter present as light material containing partly decomposed plant remnants. The organic matter in the clay fraction was mostly adsorbed on mineral surfaces. Organic matter in the sand and in the clay fraction was dominated by O/N-alkyl C indicating low recalcitrance, but the C/N ratio of organic matter narrowed with decreasing particle size. Our results suggest that carbon and nitrogen mineralization are decoupled in the mineral-associated fractions of the soil. The specific interactions of both carbon and nitrogen containing components with the mineral matrix strongly modulate the mineralization dynamics. Therefore, isolated considerations of C/N or alkyl C to O/N-alkyl C ratios of organic matter are insufficient as indicators for decomposition in plant residues. The combined consideration of C/N and alkyl C to O/N-alkyl C ratios provides a first impression about the degree of decomposition in plant residues. However, bioavailability in fractions where organic matter is mainly stabilized by spatial inaccessibility and by organo-mineral interactions cannot be explained by these ratios, but can be examined by an incubation approach.
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Scientific Article
Babin, D. ; Vogel, C. ; Zühlke, S. ; Schloter, M. ; Pronk, G.J. ; Heister, K. ; Spiteller, M. ; Kögel-Knabner, I. ; Smalla, K.
PLoS ONE 9:e106865 (2014)
The fate of polycyclic aromatic hydrocarbons (PAHs) in soil is determined by a suite of biotic and abiotic factors, and disentangling their role in the complex soil interaction network remains challenging. Here, we investigate the influence of soil composition on the microbial community structure and its response to the spiked model PAH compound phenanthrene and plant litter. We used long-term matured artificial soils differing in type of clay mineral (illite, montmorillonite) and presence of charcoal or ferrihydrite. The soils received an identical soil microbial fraction and were incubated for more than two years with two sterile manure additions. The matured artificial soils and a natural soil were subjected to the following spiking treatments: (I) phenanthrene, (II) litter, (III) litter + phenanthrene, (IV) unspiked control. Total community DNA was extracted from soil sampled on the day of spiking, 7, 21, and 63 days after spiking. Bacterial 16S rRNA gene and fungal internal transcribed spacer amplicons were quantified by qPCR and subjected to denaturing gradient gel electrophoresis (DGGE). DGGE analysis revealed that the bacterial community composition, which was strongly shaped by clay minerals after more than two years of incubation, changed in response to spiked phenanthrene and added litter. DGGE and qPCR showed that soil composition significantly influenced the microbial response to spiking. While fungal communities responded only in presence of litter to phenanthrene spiking, the response of the bacterial communities to phenanthrene was less pronounced when litter was present. Interestingly, microbial communities in all artificial soils were more strongly affected by spiking than in the natural soil, which might indicate the importance of higher microbial diversity to compensate perturbations. This study showed the influence of soil composition on the microbiota and their response to phenanthrene and litter, which may increase our understanding of complex interactions in soils for bioremediation applications.
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Scientific Article
Legay, N. ; Baxendale, C. ; Grigulis, K. ; Krainer, U. ; Kastl, E.-M. ; Schloter, M. ; Bardgett, R.D. ; Arnoldi, C. ; Bahn, M. ; Dumont, M. ; Poly, F. ; Pommier, T. ; Clément, J.C. ; Lavorel, S.
Ann. Bot. 114, 1011-1021 (2014)
BACKGROUND AND AIMS: Abiotic properties of soil are known to be major drivers of the microbial community within it. Our understanding of how soil microbial properties are related to the functional structure and diversity of plant communities, however, is limited and largely restricted to above-ground plant traits, with the role of below-ground traits being poorly understood. This study investigated the relative contributions of soil abiotic properties and plant traits, both above-ground and below-ground, to variations in microbial processes involved in grassland nitrogen turnover. METHODS: In mountain grasslands distributed across three European sites, a correlative approach was used to examine the role of a large range of plant functional traits and soil abiotic factors on microbial variables, including gene abundance of nitrifiers and denitrifiers and their potential activities. KEY RESULTS: Direct effects of soil abiotic parameters were found to have the most significant influence on the microbial groups investigated. Indirect pathways via plant functional traits contributed substantially to explaining the relative abundance of fungi and bacteria and gene abundances of the investigated microbial communities, while they explained little of the variance in microbial activities. Gene abundances of nitrifiers and denitrifiers were most strongly related to below-ground plant traits, suggesting that they were the most relevant traits for explaining variation in community structure and abundances of soil microbes involved in nitrification and denitrification. CONCLUSIONS: The results suggest that consideration of plant traits, and especially below-ground traits, increases our ability to describe variation in the abundances and the functional characteristics of microbial communities in grassland soils.
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Scientific Article
Fuchslueger, L. ; Kastl, E.-M. ; Bauer, F. ; Kienzl, S. ; Hasibeder, R. ; Ladreiter-Knauss, T. ; Schmitt, M. ; Bahn, M. ; Schloter, M. ; Richter, A. ; Szukics, U.
Biogeosciences 11, 6003-6015 (2014)
Future climate scenarios suggest an increased frequency of summer drought periods in the European Alpine Region. Drought can affect soil nitrogen (N) cycling, by altering N transformation rates, as well as the abundances of ammonia-oxidizing bacteria and archaea. However, the extent to which drought affects N cycling under in situ conditions is still controversial. The goal of this study was to analyse effects of drought on soil N turnover and ammonia-oxidizer abundances. To this end we conducted a rain-exclusion experiment at two differently managed mountain grassland sites, an annually mown and occasionally fertilized meadow and an abandoned grassland. Soils were sampled before, during and after drought and were analysed for gross rates of N mineralization, microbial uptake of inorganic N, nitrification, and the abundances of bacterial and archaeal ammonia oxidizers based on gene copy numbers of the amoA gene (AOB and AOA, respectively). Our results showed that the response to drought differed between the two sites. Effects were stronger at the managed meadow, where NH4+ immobilization rates increased and AOA abundances decreased. At the abandoned site gross nitrification and NO3− immobilization rates decreased during drought, while neither AOB, nor AOA abundances were affected. The different responses of the two sites to drought were likely related to site specific differences, such as soil organic matter content, nitrogen pools and absolute soil water content, resulting from differences in land-management. At both sites rewetting after drought had only minor short-term effects on the parameters that had been affected by drought, and seven weeks after the drought no effects of drought were detectable anymore. Thus, our findings indicate that drought can have distinct transient effects on soil nitrogen cycling and ammonia-oxidizer abundances in mountain grasslands and that the effect strength could be modulated by grassland management.
Wissenschaftlicher Artikel
Scientific Article
Berg, G. ; Grube, M. ; Schloter, M. ; Smalla, K.
Front. Microbiol. 5:148 (2014)
Most eukaryotes develop close interactions with microorganisms that are essential for their performance and survival. Thus, eukaryotes and prokaryotes in nature can be considered as meta-organisms or holobionts. Consequently, microorganisms that colonize different plant compartments contain the plant’s second genome. In this respect, many studies in the last decades have shown that plant-microbe interactions are not only crucial for better understanding plant growth and health, but also for sustainable crop production in a changing world. This mini-review acting as editorial presents retrospectives and future perspectives for plant microbiome studies as well as information gaps in this emerging research field. In addition, the contribution of this research topic to the solution of various issues is discussed.
Review
Review
Radl, V. ; Chronakova, A. ; Cuhel, J. ; Simek, M. ; Elhottova, D. ; Welzl, G. ; Schloter, M.
Appl. Soil Ecol. 77, 68-71 (2014)
In areas used for cattle overwintering detrimental effects normally associated with grazing are intensified. Among the alterations observed, increases on the N availability and soil pH may highly influence structure of ammonia oxidizing microbes and thus influence nitrification pattern in soil. To evaluate this assumption, we assessed the abundance and diversity of ammonia oxidizing bacteria (AOB) and archaea (AOA) in three sites with different degrees of animal impact (severe, moderate or no impact) of an overwintering pasture by means of qPCR and T-RFLP of amoA genes. In areas where no animal impact could be identified AOA was dominating over AOB. However, AOB abundance increased as the degree of animal impact enhances, becoming most dominant in the severely impacted site. Interestingly, the diversity of AOB was the highest in the severely impacted area, where AOA diversity was the lowest. Obviously the pressure imposed by altered environmental conditions created by cattle husbandry lead to the selection of AOB and AOA populations, adapted to alkaline pH and higher ammonia concentration.
Wissenschaftlicher Artikel
Scientific Article
Uksa, M. ; Fischer, D. ; Welzl, G. ; Kautz, T. ; Köpke, U. ; Schloter, M.
Soil Biol. Biochem. 75, 197-201 (2014)
Spatial and temporal dynamics of microbial community structure and function in subsoils have been rarely studied in the past. In this paper we present data on how bacterial communities as well as selected functional groups of microbes change in the rhizosphere, the drilosphere, and in bulk soil over time in topsoil as well as in subsoil. We show that the overall richness of bacteria and abundance of nitrifiers and denitrifiers decreases in bulk soil with soil depth. However, these effects were not or to a much lower degree observed in the rhizosphere and the drilosphere. Temporal fluctuations contributed by far less than spatial factors to the dynamics of bacterial communities and abundance of nitrifiers and denitrifiers in all compartments independent from the soil depth.
Wissenschaftlicher Artikel
Scientific Article
Hanak, A.M. ; Nagler, M. ; Weinmaier, T. ; Sun, X. ; Fragner, L. ; Schwab, C. ; Rattei, T. ; Ulrich, K. ; Ewald, D. ; Engel, M. ; Schloter, M. ; Bittner, R. ; Schleper, C. ; Weckwerth, W.
Genome Announc. 2:e00276-14 (2014)
Paenibacillus sp. P22 is a Gram-negative facultative anaerobic endospore-forming bacterium isolated from poplar hybrid 741 (♀[Populus alba × (P. davidiana + P. simonii) × P. tomentosa]). This bacterium shows strong similarities to Paenibacillus humicus, and important growth-promoting effects on in vitro grown explants of poplar hybrid 741 have been described.
Wissenschaftlicher Artikel
Scientific Article
Dalkmann, P. ; Siebe, C. ; Amelung, W. ; Schloter, M. ; Siemens, J.
Environ. Sci. Technol. 48, 4963-4970 (2014)
Long-term irrigation with untreated wastewater may increase soil microbial adaptation to pollution load and lead to enhanced natural attenuation. We hypothesized that long-term wastewater irrigation accelerates the dissipation of pharmaceuticals. To test our hypothesis we performed an incubation experiment with soils from the Mezquital Valley, Mexico that were irrigated for 0, 14, or 100 years. The results showed that the dissipation half-lives (DT50) of diclofenac (<0.1-1.4 days), bezafibrate (<0.1-4.8 days), sulfamethoxazole (2-33 days), naproxen (6-19 days), carbamazepine (355-1,624 days), and ciprofloxacin were not affected by wastewater irrigation. Trimethoprim dissipation was even slower in soils irrigated for 100 years (DT50: 45-72 days) than in nonirrigated soils (DT50: 12-16 days), was negatively correlated with soil organic matter content and soil-water distribution coefficients, and was inhibited in sterilized soils. Applying a kinetic fate model indicated that long-term irrigation enhanced sequestration of cationic or uncharged trimethoprim and uncharged carbamazepine, but did not affect sequestration of fast-dissipating zwitterions or negatively charged pharmaceuticals. We conclude that microbial adaptation processes play a minor role for pharmaceutical dissipation in wastewater-irrigated soils, while organic matter accumulation in these soils can retard trimethoprim and carbamazepine dissipation.
Wissenschaftlicher Artikel
Scientific Article
Reichel, R. ; Radl, V. ; Rosendahl, I. ; Albert, A. ; Amelung, W. ; Schloter, M. ; Thiele-Bruhn, S.
Appl. Microbiol. Biotechnol. 89, 6487-6495 (2014)
Sulfadiazine (SDZ) is an antibiotic frequently administered to livestock, and it alters microbial communities when entering soils with animal manure, but understanding the interactions of these effects to the prevailing climatic regime has eluded researchers. A climatic factor that strongly controls microbial activity is soil moisture. Here, we hypothesized that the effects of SDZ on soil microbial communities will be modulated depending on the soil moisture conditions. To test this hypothesis, we performed a 49-day fully controlled climate chamber pot experiments with soil grown with Dactylis glomerata (L.). Manure-amended pots without or with SDZ contamination were incubated under a dynamic moisture regime (DMR) with repeated drying and rewetting changes of >20 % maximum water holding capacity (WHCmax) in comparison to a control moisture regime (CMR) at an average soil moisture of 38 % WHCmax. We then monitored changes in SDZ concentration as well as in the phenotypic phospholipid fatty acid and genotypic 16S rRNA gene fragment patterns of the microbial community after 7, 20, 27, 34, and 49 days of incubation. The results showed that strongly changing water supply made SDZ accessible to mild extraction in the short term. As a result, and despite rather small SDZ effects on community structures, the PLFA-derived microbial biomass was suppressed in the SDZ-contaminated DMR soils relative to the CMR ones, indicating that dynamic moisture changes accelerate the susceptibility of the soil microbial community to antibiotics.
Wissenschaftlicher Artikel
Scientific Article
Purahong, W. ; Kapturska, D. ; Pecyna, M.J. ; Schulz, E. ; Schloter, M. ; Buscot, F. ; Hofrichter, M. ; Kruger, D.
PLoS ONE 9:e93700 (2014)
Leaf litter decomposition is the key ecological process that determines the sustainability of managed forest ecosystems, however very few studies hitherto have investigated this process with respect to silvicultural management practices. The aims of the present study were to investigate the effects of forest management practices on leaf litter decomposition rates, nutrient dynamics (C, N, Mg, K, Ca, P) and the activity of ligninolytic enzymes. We approached these questions using a 473 day long litterbag experiment. We found that age-class beech and spruce forests (high forest management intensity) had significantly higher decomposition rates and nutrient release (most nutrients) than unmanaged deciduous forest reserves (P<0.05). The site with near-to-nature forest management (low forest management intensity) exhibited no significant differences in litter decomposition rate, C release, lignin decomposition, and C/N, lignin/N and ligninolytic enzyme patterns compared to the unmanaged deciduous forest reserves, but most nutrient dynamics examined in this study were significantly faster under such near-to-nature forest management practices. Analyzing the activities of ligninolytic enzymes provided evidence that different forest system management practices affect litter decomposition by changing microbial enzyme activities, at least over the investigated time frame of 473 days (laccase, P<0.0001; manganese peroxidase (MnP), P = 0.0260). Our results also indicate that lignin decomposition is the rate limiting step in leaf litter decomposition and that MnP is one of the key oxidative enzymes of litter degradation. We demonstrate here that forest system management practices can significantly affect important ecological processes and services such as decomposition and nutrient cycling.
Wissenschaftlicher Artikel
Scientific Article
Lyubenova, L. ; Yazici, A. ; Tutus, Y. ; Fuchs, C. ; Michalke, B. ; Schröder, P. ; Cakmak, I.
International Conference on Agronomic, Molecular Genetics and Human Nutrition Approaches for Improving the Nutritional Quality and Safety of Food Crops, 68-69 (2014)
Meeting abstract
Meeting abstract
Purahong, W. ; Hoppe, B. ; Kahl, T. ; Schloter, M. ; Schulze, E.-D. ; Bauhus, J. ; Buscot, F. ; Krüger, D.
J. Environ. Manage. 139, 109-119 (2014)
The impact of changes within a single land-use category or land-use intensity on microbial communities is poorly understood, especially with respect to fungi. Here we assessed how forest management regimes and a change in forest type affect the richness and community structure of wood-inhabiting fungi across Germany. We used molecular methods based on the length polymorphism of the internal transcribed spacers and the 5.8S rRNA gene to assess fungal operational taxonomic units (OTUs). A cloning/sequencing approach was used to identify taxonomic affinities of the fungal OTUs. Overall, 20–24% and 25–27% of native fungal OTUs from forest reserves and semi-natural forests became undetectable or were lost in managed and converted forests, respectively. Fungal richness was significantly reduced during a regeneration phase in age-class beech forests with a high level of wood extraction (P = 0.017), whereas fungal community structures were not significantly affected. Conversion of forests from native, deciduous to coniferous species caused significant changes in the fungal community structure (R = 0.64–0.66, P = 0.0001) and could reduce fungal richness (P < 0.05) which may depend on which coniferous species was introduced. Our results showed that Ascocoryne cylichnium, Armillaria sp., Exophiala moniliae, Hyphodontia subalutacea and Fomes fomentarius, all known for wood-decaying abilities were strongly reduced in their abundances when forests were converted from beech to coniferous. We conclude that changes within a single land-use category can be regarded as a major threat to fungal diversity in temperate forest ecosystems.
Wissenschaftlicher Artikel
Scientific Article
Ding, G.-C. ; Radl, V. ; Schloter-Hai, B. ; Jechalke, S. ; Heuer, H. ; Smalla, K. ; Schloter, M.
PLoS ONE 9:e92958 (2014)
Large amounts of manure have been applied to arable soils as fertilizer worldwide. Manure is often contaminated with veterinary antibiotics which enter the soil together with antibiotic resistant bacteria. However, little information is available regarding the main responders of bacterial communities in soil affected by repeated inputs of antibiotics via manure. In this study, a microcosm experiment was performed with two concentrations of the antibiotic sulfadiazine (SDZ) which were applied together with manure at three different time points over a period of 133 days. Samples were taken 3 and 60 days after each manure application. The effects of SDZ on soil bacterial communities were explored by barcoded pyrosequencing of 16S rRNA gene fragments amplified from total community DNA. Samples with high concentration of SDZ were analyzed on day 193 only. Repeated inputs of SDZ, especially at a high concentration, caused pronounced changes in bacterial community compositions. By comparison with the initial soil, we could observe an increase of the disturbance and a decrease of the stability of soil bacterial communities as a result of SDZ manure application compared to the manure treatment without SDZ. The number of taxa significantly affected by the presence of SDZ increased with the times of manure application and was highest during the treatment with high SDZ-concentration. Numerous taxa, known to harbor also human pathogens, such as Devosia, Shinella, Stenotrophomonas, Clostridium, Peptostreptococcus, Leifsonia, Gemmatimonas, were enriched in the soil when SDZ was present while the abundance of bacteria which typically contribute to high soil quality belonging to the genera Pseudomonas and Lysobacter, Hydrogenophaga, and Adhaeribacter decreased in response to the repeated application of manure and SDZ.
Wissenschaftlicher Artikel
Scientific Article
Hartmann, A. ; Rothballer, M. ; Hense, B.A. ; Schröder, P.
Front. Plant Sci. 5:131 (2014)
Interference of pathogenic as well as symbiotic microbes with the innate immune response via their MAMPS is fundamental for microbe-host interactions. In addition, a multitude of microbial effector molecules are modulating or even initiating specific mutualistic activities in host plants. It is hypothesized, that quorum sensing molecules, like the N-acyl-homoserine lactones of Gram-negative bacteria, should be regarded as important players or modulators of host-bacteria interactions. Other known or still structurally unknown quorum sensing compounds may also serve as central functional glue between root-colonizing / endophytic bacteria and their hosts. While the interactions of plants with pure/single effectors were studied in some detail, the interaction network with other elicitors and effectors of plant responses is still largely unexplored. Functional interaction studies of holobiotic plant systems, including the plant host and its associated microbes, may result in a more profound understanding of the complicated social network of basic innate immune responses with specific effector molecules, if quorum sensing compounds of endophytic bacteria are integrated. Plant - microbiome interactions in the light of the holobiontic concept Higher organisms evolved in the omnipresence of microbes, which could be of pathogenic or symbiotic nature. A framework of response patterns evolved which is known as innate immunity. A major part of this response is the recognition of microbial-associated molecular patterns (MAMP) such as chitin or lipochitooligosaccharides, peptidoglycan, lipopolysaccharides or flagellum structures and the initiation of efficient plant defence reactions (Janeway and Medzhitov, 2002; Jones and Dangl, 2006). However, there are many plant-associated endophytic bacteria known, which are living within plants without triggering persistent and apparent defence responses or visibly do not harm the plant. In some cases, even a stimulation of plant growth due to the presence of specific players within the plant microbiome was reported (Turner et al., 2013). It is now generally accepted, that plant performance and activities can only be characterized and understood completely, if the “holobiont”, the plant plus the intimately associated microbiota, is considered (Zilber-Rosenberg et al., 2008). The evolutionary advantage of an integrated holobiontic system is characterized by a much better adaptability and flexibility towards rapidly changing adverse environmental conditions. It is still mostly unknown, which particular plant genetic loci are controlling the interactions with the plant microbiome and which signals are steering this cooperativity. Mutualistic microbes are able to overcome or short-circuit plant defence responses to enable successful colonization of the host (Zamioudis and Pieterse, 2012; Alqueres et al., 2012). Beneficial associations with microbes other than mycorhiza or Rhizobia are also controlled by systemically regulated or autoregulated processes on top of the basic innate immunity response. The induction of systemic immunity responses like ISR (induced systemic resistance) by some beneficial rhizosphere bacteria or the SAR (systemic acquired resistance) response provoked by pathogens are results of multiple response cascades employed by the plant host to respond to microbial and other environmental interactions. However, the entire response network is by far not yet revealed. For example, bacteria-induced plant responses resulting in improved resistance towards pathogens can also be due to the perception of secondary metabolites, like the surfactin lipopeptide, produced by certain biocontrol Bacilli (Garcia-Gutiérrez et al., 2013) or volatile compounds of plant-associated microbes (Yi et al., 2010). The biocontrol activity of microbial inoculants is probably due to multiple effects of their secondary metabolites to achieve direct inhibition of the pathogenic counterpart as well as an increase of systemic resistance of the plant host. Bacterial quorum sensing molecules like N-acyl homoserine lactones modulate plant responses towards contact with bacteria It is hypothesized, that eukaryotic organisms developed ways to sense microbes in addition to the recognition of their MAMPs by their diffusible small molecules. A very ancient and basic feature of unicellular bacteria is their way of environmental sensing and social communication. In many Gram-negative bacteria the synthesis of autoinducers of the N-acyl-homoserine lactone (AHL) type is tightly regulated in response to cell density or the cell “quorum” (Eberl, 1999). These metabolites are released into the cellular environment to sense the quality of the ecological niche in terms of diffusion space and the density and distribution of their own population. This environmental sensing mechanism helps to adapt the regulation of their gene expression to the given conditions in their habitat and thus optimizes the fitness of the population. Therefore, the generally known term “quorum sensing” (QS) was supplemented by the more broadly defined concept of “efficiency sensing” (Hense et al., 2007). Since this optimization of in situ gene expression is of very basic importance, autoinducer QS-molecules are widespread among bacteria and have quite different molecular structures. N-acyl-homoserine lactones (AHL) are common in Gram-negative bacteria, while cyclic peptides as QS-signals are only to be found in Gram-positive bacteria. The detailed structure of the AHL-molecules can vary; the acyl side chain consists of 4 to 14 carbon atoms and may also contain double bonds. The C3-atom can be hydroxylated or oxidized to a carbonyl-carbon; thus, considerable information and quite different physicochemical properties can be present within these different AHL-structures. As is outlined below, also plants have obviously learned during their evolution to respond to these quorum sensing compounds in different specific ways. We speculate, that QS-compounds are early signals indicating that pathogens are in the surroundings to gather themselves for attack or that mutualists are about to interact with roots. The first demonstration of specific responses of a plant to bacterial N-acyl-homoserine lactones was demonstrated for the legume Medicago truncatula (Mathesius et al., 2003). AHLs from symbiotic (Sinorhizobium meliloti) or pathogenic (Pseudomonas aeruginosa) bacteria provoked at concentrations as low as nano- to micromolar significant changes in the accumulation of over 150 proteins. Auxin-responsive and flavonoid synthesis proteins were induced and also a secretion of plant metabolites that mimic quorum sensing compounds were found, which may have the potential to disrupt quorum sensing signalling by associated bacteria. In tomato plants, a specific induction of systemic resistance proteins after inoculation of the roots with C4- and C6-side chain AHL-producing Serratia liquefaciens MG1 was discovered independently (Hartmann et al., 2004; Schuhegger et al., 2006). The fungal leaf pathogen Alternaria alternata was much less effective, when S. liquefaciens MG 1 wild type had been inoculated to roots of tomato plants as compared to the AHL-negative mutant. It could be shown, that salicylic acid was increased as well as SA- and ethylene-dependent defence genes (i.e. PR1a) in MG1-inoculated plants. Furthermore, Serratia plymuthica HRO-C48, producing C4-/C6- and OHC4-/OHC6-homoserine lactones, is able to induce ISR-like systemic protection of bean and tomato plants against the fungal leaf pathogen Botrytis cinnera; this response was greatly reduced with mutants impaired in AHL-production (Liu et al., 2007; Pang et al., 2009). In contrast, Arabidopsis thaliana responds to short (C4- and C6-) N-acyl AHL-compounds in a different manner: C4- and C6- homoserine lactones alter the expression of selected hormonal regulated genes which results in changes of the plant´s hormone content, in particular an increased auxin / cytokinin ratio (von Rad et al., 2008). However, no systemic resistance response was found to be induced in A. thaliana when roots were stimulated with short side-chain AHLs. Ortiz-Castro et al. (2008) found that C10-homoserine lactone elicited developmental changes in the root system in Arabidopsis plants by altering the expression of cell division and differentiation-related genes. Furthermore, Liu et al. (2012) and Jin et al. (2012) demonstrated that the root stimulatory effect of C6- and C8- homoserine lactones in Arabidopsis plants is mediated through the G-protein coupled receptor encoded by AtGPA1. In mung bean, oxoC10-homoserine lactone activates auxin-induced adventitious root formation via H2O2- and NO-dependent cyclic GMP signaling (Bai et al., 2012). On the other hand, N-acyl-AHLs with C12- and C14- side chains induce systemic resistance to the obligate biotrophic fungus Golovinomyces orontii in A. thaliana and to Blumeria graminis f. sp. hordei in barley (Hordeum vulgare) (Schikora et al., 2011). This response is mediated through altered activation of AtMPK6. The mitogen-activated protein kinases AtMPK3 and AtMPK6 were stronger activated by the model elicitor flg22 in the presence of C12- or C14-AHL compounds which resulted in a higher expression of the defence-related transcription factors WRKY26 and WRKY29 as well as the PR1 gene (Schikora et al., 2011). Thus, AHLs with short and medium side lengths induce developmental effects on root architecture, while long side chain AHLs induce systemic resistance in A. thaliana (Schenk et al., 2012). Furthermore, it was shown, that better water soluble short side chain AHL-compounds are actively taken up into plant roots and transported along the roots into the shoot; in contrast, the lipophilic long acyl side chain AHLs are not transported in barley and A. thaliana. (Götz et al., 2007, von Rad et al., 2008, Sieper et al., 2014). However, no uptake was detected in the legume yam bean (Pachyrhizus erosus (L.) Urban) (Götz et al., 2007). The latter finding corroborates the report of Delalande et al. (2008) that legumes like Lotus corniculatus produce lactonases which degrade AHLs and prevents its uptake and transport. In barley, it could further be demonstrated that C8- and C10-AHLs are taken up in a cell energy dependent manner by ABC-transporters into the root and transported via the central cylinder into the shoot (Sieper et al., 2014). Interestingly, several plants have been demonstrated to produce AHL-mimic substances or to develop other activities influencing quorum sensing of plant associated bacteria (Gao et al., 2003; Bauer and Mathesius, 2004). Flavonoids released by legumes increase the expression of N-acyl-homoserine lactone synthesis genes in Rhizobia (Pérez-Montano et al., 2011): Indole acetic acid and cytokinin biosynthesis of Gypsophila was shown to influence QS, type III secretion system and gall formation activity by Pantoea plantarum (Chalupowicz et al., 2009). On the other hand, tobacco plants have been engineered to produce short- and long-side chain AHL-compounds which could be detected in substantial amounts at leaf and root surfaces as well as in soil (Scott et al., 2006). Constitutive expression of quorum sensing genes in transgenic tobacco plants leads to alteration in induced systemic resistance elicited by the rhizobacterium Serratia marcescens 90-166 (Ryu et al., 2013). Furthermore, transgenic tomato plants engineered to produce different AHL-compounds were demonstrated to alter the activity of plant growth promoting rhizobacteria and resulted e.g. in increased salt tolerance (Barriuso et al., 2008). We hypothesize, that quorum sensing in a plant-microbe holobiont system should be regarded in a bidirectional way with influences from the plant and the microbial partners. Uptake of AHL-compounds and specific perception of AHLs in animal cells were also studied intensively in recent years (Teplitski et al., 2011; Hartmann and Schikora, 2012). 3-oxo-C12-homoserine lactone (C12-AHL), the major AHL-compound of Pseudomonas aeruginosa, was shown to selectively impair the regulation of the nuclear transcription factor NF-κB which controls innate immune responses in mammalian cells (Kravchenko et al., 2008). C12-AHL also impaired human dendritic cell functions required for priming of T-cells (Bernatowicz et al., submitted). Since the response to AHL-compounds in mammalian systems is complicated due to the interferences with the adaptive immune system, plants provide an ideal model for the detailed interaction studies of basic innate immune responses and developmental processes with N-acylhomoserine lactones as modifying bacterial effector molecules. Interference of pathogenic as well as symbiotic microbes with the innate immune response via their MAMPS is fundamental for microbe-host interactions. In addition, a multitude of microbial effector molecules are modulating or even initiating specific mutualistic activities in host plants. It is hypothesized, that quorum sensing molecules, like the N-acyl-homoserine lactones of Gram-negative bacteria, should be regarded as important players or modulators of host-bacteria interactions. Other known or still structurally unknown quorum sensing compounds may also serve as central functional glue between root-colonizing / endophytic bacteria and their hosts. While the interactions of plants with pure/single effectors were studied in some detail, the interaction network with other elicitors and effectors of plant responses is still largely unexplored. Functional interaction studies of holobiotic plant systems, including the plant host and its associated microbes, may result in a more profound understanding of the complicated social network of basic innate immune responses with specific effector molecules, if quorum sensing compounds of endophytic bacteria are integrated. Plant - microbiome interactions in the light of the holobiontic concept Higher organisms evolved in the omnipresence of microbes, which could be of pathogenic or symbiotic nature. A framework of response patterns evolved which is known as innate immunity. A major part of this response is the recognition of microbial-associated molecular patterns (MAMP) such as chitin or lipochitooligosaccharides, peptidoglycan, lipopolysaccharides or flagellum structures and the initiation of efficient plant defence reactions (Janeway and Medzhitov, 2002; Jones and Dangl, 2006). However, there are many plant-associated endophytic bacteria known, which are living within plants without triggering persistent and apparent defence responses or visibly do not harm the plant. In some cases, even a stimulation of plant growth due to the presence of specific players within the plant microbiome was reported (Turner et al., 2013). It is now generally accepted, that plant performance and activities can only be characterized and understood completely, if the “holobiont”, the plant plus the intimately associated microbiota, is considered (Zilber-Rosenberg et al., 2008). The evolutionary advantage of an integrated holobiontic system is characterized by a much better adaptability and flexibility towards rapidly changing adverse environmental conditions. It is still mostly unknown, which particular plant genetic loci are controlling the interactions with the plant microbiome and which signals are steering this cooperativity. Mutualistic microbes are able to overcome or short-circuit plant defence responses to enable successful colonization of the host (Zamioudis and Pieterse, 2012; Alqueres et al., 2012). Beneficial associations with microbes other than mycorhiza or Rhizobia are also controlled by systemically regulated or autoregulated processes on top of the basic innate immunity response. The induction of systemic immunity responses like ISR (induced systemic resistance) by some beneficial rhizosphere bacteria or the SAR (systemic acquired resistance) response provoked by pathogens are results of multiple response cascades employed by the plant host to respond to microbial and other environmental interactions. However, the entire response network is by far not yet revealed. For example, bacteria-induced plant responses resulting in improved resistance towards pathogens can also be due to the perception of secondary metabolites, like the surfactin lipopeptide, produced by certain biocontrol Bacilli (Garcia-Gutiérrez et al., 2013) or volatile compounds of plant-associated microbes (Yi et al., 2010). The biocontrol activity of microbial inoculants is probably due to multiple effects of their secondary metabolites to achieve direct inhibition of the pathogenic counterpart as well as an increase of systemic resistance of the plant host. Bacterial quorum sensing molecules like N-acyl homoserine lactones modulate plant responses towards contact with bacteria It is hypothesized, that eukaryotic organisms developed ways to sense microbes in addition to the recognition of their MAMPs by their diffusible small molecules. A very ancient and basic feature of unicellular bacteria is their way of environmental sensing and social communication. In many Gram-negative bacteria the synthesis of autoinducers of the N-acyl-homoserine lactone (AHL) type is tightly regulated in response to cell density or the cell “quorum” (Eberl, 1999). These metabolites are released into the cellular environment to sense the quality of the ecological niche in terms of diffusion space and the density and distribution of their own population. This environmental sensing mechanism helps to adapt the regulation of their gene expression to the given conditions in their habitat and thus optimizes the fitness of the population. Therefore, the generally known term “quorum sensing” (QS) was supplemented by the more broadly defined concept of “efficiency sensing” (Hense et al., 2007). Since this optimization of in situ gene expression is of very basic importance, autoinducer QS-molecules are widespread among bacteria and have quite different molecular structures. N-acyl-homoserine lactones (AHL) are common in Gram-negative bacteria, while cyclic peptides as QS-signals are only to be found in Gram-positive bacteria. The detailed structure of the AHL-molecules can vary; the acyl side chain consists of 4 to 14 carbon atoms and may also contain double bonds. The C3-atom can be hydroxylated or oxidized to a carbonyl-carbon; thus, considerable information and quite different physicochemical properties can be present within these different AHL-structures. As is outlined below, also plants have obviously learned during their evolution to respond to these quorum sensing compounds in different specific ways. We speculate, that QS-compounds are early signals indicating that pathogens are in the surroundings to gather themselves for attack or that mutualists are about to interact with roots. The first demonstration of specific responses of a plant to bacterial N-acyl-homoserine lactones was demonstrated for the legume Medicago truncatula (Mathesius et al., 2003). AHLs from symbiotic (Sinorhizobium meliloti) or pathogenic (Pseudomonas aeruginosa) bacteria provoked at concentrations as low as nano- to micromolar significant changes in the accumulation of over 150 proteins. Auxin-responsive and flavonoid synthesis proteins were induced and also a secretion of plant metabolites that mimic quorum sensing compounds were found, which may have the potential to disrupt quorum sensing signalling by associated bacteria. In tomato plants, a specific induction of systemic resistance proteins after inoculation of the roots with C4- and C6-side chain AHL-producing Serratia liquefaciens MG1 was discovered independently (Hartmann et al., 2004; Schuhegger et al., 2006). The fungal leaf pathogen Alternaria alternata was much less effective, when S. liquefaciens MG 1 wild type had been inoculated to roots of tomato plants as compared to the AHL-negative mutant. It could be shown, that salicylic acid was increased as well as SA- and ethylene-dependent defence genes (i.e. PR1a) in MG1-inoculated plants. Furthermore, Serratia plymuthica HRO-C48, producing C4-/C6- and OHC4-/OHC6-homoserine lactones, is able to induce ISR-like systemic protection of bean and tomato plants against the fungal leaf pathogen Botrytis cinnera; this response was greatly reduced with mutants impaired in AHL-production (Liu et al., 2007; Pang et al., 2009). In contrast, Arabidopsis thaliana responds to short (C4- and C6-) N-acyl AHL-compounds in a different manner: C4- and C6- homoserine lactones alter the expression of selected hormonal regulated genes which results in changes of the plant´s hormone content, in particular an increased auxin / cytokinin ratio (von Rad et al., 2008). However, no systemic resistance response was found to be induced in A. thaliana when roots were stimulated with short side-chain AHLs. Ortiz-Castro et al. (2008) found that C10-homoserine lactone elicited developmental changes in the root system in Arabidopsis plants by altering the expression of cell division and differentiation-related genes. Furthermore, Liu et al. (2012) and Jin et al. (2012) demonstrated that the root stimulatory effect of C6- and C8- homoserine lactones in Arabidopsis plants is mediated through the G-protein coupled receptor encoded by AtGPA1. In mung bean, oxoC10-homoserine lactone activates auxin-induced adventitious root formation via H2O2- and NO-dependent cyclic GMP signaling (Bai et al., 2012). On the other hand, N-acyl-AHLs with C12- and C14- side chains induce systemic resistance to the obligate biotrophic fungus Golovinomyces orontii in A. thaliana and to Blumeria graminis f. sp. hordei in barley (Hordeum vulgare) (Schikora et al., 2011). This response is mediated through altered activation of AtMPK6. The mitogen-activated protein kinases AtMPK3 and AtMPK6 were stronger activated by the model elicitor flg22 in the presence of C12- or C14-AHL compounds which resulted in a higher expression of the defence-related transcription factors WRKY26 and WRKY29 as well as the PR1 gene (Schikora et al., 2011). Thus, AHLs with short and medium side lengths induce developmental effects on root architecture, while long side chain AHLs induce systemic resistance in A. thaliana (Schenk et al., 2012). Furthermore, it was shown, that better water soluble short side chain AHL-compounds are actively taken up into plant roots and transported along the roots into the shoot; in contrast, the lipophilic long acyl side chain AHLs are not transported in barley and A. thaliana. (Götz et al., 2007, von Rad et al., 2008, Sieper et al., 2014). However, no uptake was detected in the legume yam bean (Pachyrhizus erosus (L.) Urban) (Götz et al., 2007). The latter finding corroborates the report of Delalande et al. (2008) that legumes like Lotus corniculatus produce lactonases which degrade AHLs and prevents its uptake and transport. In barley, it could further be demonstrated that C8- and C10-AHLs are taken up in a cell energy dependent manner by ABC-transporters into the root and transported via the central cylinder into the shoot (Sieper et al., 2014). Interestingly, several plants have been demonstrated to produce AHL-mimic substances or to develop other activities influencing quorum sensing of plant associated bacteria (Gao et al., 2003; Bauer and Mathesius, 2004). Flavonoids released by legumes increase the expression of N-acyl-homoserine lactone synthesis genes in Rhizobia (Pérez-Montano et al., 2011): Indole acetic acid and cytokinin biosynthesis of Gypsophila was shown to influence QS, type III secretion system and gall formation activity by Pantoea plantarum (Chalupowicz et al., 2009). On the other hand, tobacco plants have been engineered to produce short- and long-side chain AHL-compounds which could be detected in substantial amounts at leaf and root surfaces as well as in soil (Scott et al., 2006). Constitutive expression of quorum sensing genes in transgenic tobacco plants leads to alteration in induced systemic resistance elicited by the rhizobacterium Serratia marcescens 90-166 (Ryu et al., 2013). Furthermore, transgenic tomato plants engineered to produce different AHL-compounds were demonstrated to alter the activity of plant growth promoting rhizobacteria and resulted e.g. in increased salt tolerance (Barriuso et al., 2008). We hypothesize, that quorum sensing in a plant-microbe holobiont system should be regarded in a bidirectional way with influences from the plant and the microbial partners. Uptake of AHL-compounds and specific perception of AHLs in animal cells were also studied intensively in recent years (Teplitski et al., 2011; Hartmann and Schikora, 2012). 3-oxo-C12-homoserine lactone (C12-AHL), the major AHL-compound of Pseudomonas aeruginosa, was shown to selectively impair the regulation of the nuclear transcription factor NF-κB which controls innate immune responses in mammalian cells (Kravchenko et al., 2008). C12-AHL also impaired human dendritic cell functions required for priming of T-cells (Bernatowicz et al., submitted). Since the response to AHL-compounds in mammalian systems is complicated due to the interferences with the adaptive immune system, plants provide an ideal model for the detailed interaction studies of basic innate immune responses and developmental processes with N-acylhomoserine lactones as modifying bacterial effector molecules. - See more at: http://journal.frontiersin.org/Journal/10.3389/fpls.2014.00131/full#sthash.vXVExt5S.dpuf
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Wallisch, S. ; Gril, T. ; Dong, X. ; Welzl, G. ; Bruns, C. ; Heath, E. ; Engel, M. ; Suhaldoc, M. ; Schloter, M.
Front. Microbiol. 5:96 (2014)
Alkane degrading microorganisms play an important role for the bioremediation of petrogenic contaminated environments. In this study, we investigated the effects of compost addition on the abundance and diversity of bacteria harboring the alkane monooxygenase gene (alkB) in an oil-contaminated soil originated from an industrial zone in Celje, Slovenia (Technosol). Soil without any amendments (control soil) and soil amended with two composts differing in their maturation stage and nutrient availability, were incubated under controlled conditions in a microcosm experiment and sampled after 0, 6, 12, and 36 weeks of incubation. As expected the addition of compost stimulated the degradation of alkanes in the investigated soil shortly after the addition. By using quantitative real-time PCR higher number of alkB genes were detected in soil samples amended with compost compared to the control soils. To get an insight into the composition of alkB harboring microbial communities, we performed next generation sequencing of amplicons of alkB gene fragment. Richness and diversity of alkB gene harboring prokaryotes was higher in soil mixed with compost compared to control soils with stronger effects of the less maturated, nutrient poor compost. The phylogenetic analysis of communities suggested that the addition of compost stimulated the abundance of alkB harboring Actinobacteria during the experiment independent from the maturation stage of the compost. AlkB harboring γ-proteobacteria like Shewanella or Hydrocarboniphaga as well as α-proteobacteria of the genus Agrobacterium responded also positively to the addition of compost to soil. The amendment of the less maturated, nutrient poor compost resulted in addition in a large increase of alkB harboring bacteria of the Cytophaga group (Microscilla) mainly at the early sampling time points. Our data indicates that compost amendments significantly change abundance and diversity pattern of alkB harboring microbes in Technosol and might be a useful agent to stimulate bioremediation of hydrocarbons in contaminated soils. - See more at: http://journal.frontiersin.org/Journal/10.3389/fmicb.2014.00096/abstract#sthash.kWHdc5jQ.dpuf
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Haesler, F. ; Hagn, A. ; Engel, M. ; Schloter, M.
Front. Microbiol. 5:36 (2014)
Many bacteria belonging to the phylum of Actinobacteria are known as antagonists against phytpathogenic microbes. This study aimed to analyze the effect of ozone on the actinobacterial community of the rhizosphere of four years old European beech (Fagus sylvatica L.) trees during different time points of the vegetation period. Effects of ozone on the total community structure of Actinobacteria were studied based on the analysis of 16S rRNA gene amplicons. In addition effects of the ozone treatment on the diversity of potential biocontrol active Actionobacteria being able to produce antibiotics were characterized by using the type II polyketide synthases (PKS) genes as marker. Season as well as ozone treatments had a significant effect on parts of the actinobacterial rhizosphere community of European beech. However on the basis of the performed analysis, the diversity of Actinobacteria possessing type II PKS genes is neither affected by seasonal changes nor by the ozone treatments, indicating no influence of the investigated treatments on the biocontrol active part of the actinobacterial community.
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Macherius, A. ; Seiwert, B. ; Schröder, P. ; Huber, C. ; Lorenz, W. ; Reemtsma, T.
J. Agric. Food Chem. 62, 1001-1009 (2014)
Plants can extensively transform contaminants after uptake through phase I and phase II metabolism to a large diversity of products. UPLC-QToF-MS was used to detect and identify metabolites of the bacteriostatic agent triclosan in a horseradish hairy root culture. Thirty-three metabolites of triclosan were recognized by a stepwise approach of mass defect filtering, multivariate data analysis, and isotope pattern filtering from a data set of several thousands of signals in the exposed culture. Structure proposals were elaborated for 23 triclosan metabolites on the basis of their MS data. The majority were identified as conjugates (phase II metabolites) such as saccharides or sulfosaccharides. Additionally, a disulfosaccharide was identified as a plant metabolite for the first time. Besides that, also conjugates of a phase I metabolite, hydroxytriclosan, were determined in horseradish tissue extracts. Dehalogenation products of triclosan were not observed. The large number of metabolites detected and identified in this study emphasizes the importance of a comprehensive analytical approach in studies on the uptake and fate of organic contaminants in plants.
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Oufdou, K. ; Benidire, L. ; Lyubenova, L. ; Daoui, K. ; El Abidine Fatemi, Z. ; Schröder, P.
Eur. J. Soil Biol. 60, 98-103 (2014)
Grain legumes such as the faba bean (Vicia faba L.) used for human as well as animal nutrition, are of great importance especially in countries under Mediterranean climate like Morocco, which is mainly characterized by semi-arid and arid climates and by saline soils. The objective of the present study was to evaluate the effects of salt stress on growth, nodulation and the enzymes of the glutathione ascorbate cycle of faba bean plants (Moroccan cultivar "Aguadulce"). The experiments were carried out under greenhouse-conditions, where faba bean plants were grown under control (nutrient solution) or salt stress conditions (nutrient solution containing 75 mM or 150 mM of NaCl). The activity of enzymes of the glutathione ascorbate cycle was studied in leaves and roots of faba bean plants inoculated by rhizobia RhOF4 or RhOF6, isolated from nodules of faba bean cultures in the region of Marrakech. The growth of faba bean plants decreased with increasing salt concentrations. Total weight and length of shoots significantly decreased under NaCl stress (p < 0.05), especially at 150 mM. Also the nodulation of the roots was strongly decreased under salinity stress, with reductions of 91.35% and of 88.67% in the total nodule number of plants exposed to 150 mM of NaCl and inoculated by RhOF4 and by RhOF6 respectively. NaCl effects on the glutathione-ascorbate cycle were more pronounced in roots inoculated by RhOF6. Stress responding glutathione S-transferase (GST) activity was generally increased in roots inoculated by RhOF6 and submitted to salt stress. On the contrary, specific activities of glutathione peroxidase (GPOX), superoxide dismutase (SOD), ascorbate peroxidase (APOX) and monodehydroascorbate reductase (MDHAR) were reduced in roots of faba bean plants inoculated by RhOF6 exposed to saline treatment as compared to the controls. Our results show the importance of several enzymes of the ascorbate-glutathione cycle and the reduced glutathione (GSH) during some faba bean-rhizobia symbiotic combinations, in root defence and adaptation against salt stress conditions. (C) 2013 Elsevier Masson SAS. All rights reserved.
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Purahong, W. ; Kahl, T. ; Schloter, M. ; Bauhus, J. ; Buscot, F. ; Krüger, D.
Mycol. Prog. 13, 959-964 (2014)
Managing forests by selection cutting is a promising silvicultural technique for maintaining forest biodiversity. Despite the importance of fungi in decomposition and nutrient cycling in forest ecosystems, no study to date has investigated the effects of selection cutting on fungal communities, especially using a culture-independent molecular technique to assess more than just the species that are fruiting at the time of sampling. Based on operational taxonomic units (OTUs) found in coarse woody debris, we compared the richness and community composition of wood-inhabiting fungi from selection cutting, age-class, and unmanaged European beech-dominated forests. We found that fungal OTU richness in selection cutting and unmanaged forests was not significantly different (P > 0.05), but it was higher, in both cases, than that in the age-class forest (P = 0.0002). Fungal community composition was not significantly different among the three forest types (P > 0.05). Abundances of common, wood-inhabiting fungal OTUs in different forest types were significantly correlated: the highest and lowest correlations were found between unmanaged forests and selection cutting (ρ = 0.52, P < 0.0001, n = 94), and between unmanaged and age-class forests (ρ = 0.30, P = 0.0080, n = 79), respectively. © 2014 German Mycological Society and Springer-Verlag Berlin Heidelberg.
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Regan, K.M. ; Nunan, N. ; Boeddinghaus, R.S. ; Baumgartner, V. ; Berner, D. ; Boch, S. ; Oelmann, Y. ; Overmann, J. ; Prati, D. ; Schloter, M. ; Schmitt, B. ; Sorkau, E. ; Steffens, M. ; Kandeler, E. ; Marhan, S.
Soil Biol. Biochem. 71, 21-30 (2014)
Temporal dynamics create unique and often ephemeral conditions that can influence soil microbial biogeography at different spatial scales. This study investigated the relation between decimeter to meter spatial variability of soil microbial community structure, plant diversity, and soil properties at six dates from April through November. We also explored the robustness of these interactions over time. An historically unfertilized, unplowed grassland in southwest Germany was selected to characterize how seasonal variability in the composition of plant communities and substrate quality changed the biogeography of soil microorganisms at the plot scale (10 m × 10 m). Microbial community spatial structure was positively correlated with the local environment, i.e. physical and chemical soil properties, in spring and autumn, while the density and diversity of plants had an additional effect in the summer period. Spatial relationships among plant and microbial communities were detected only in the early summer and autumn periods when aboveground biomass increase was most rapid and its influence on soil microbial communities was greatest due to increased demand by plants for nutrients. Individual properties exhibited varying degrees of spatial structure over the season. Differential responses of Gram positive and Gram negative bacterial communities to seasonal shifts in soil nutrients were detected. We concluded that spatial distribution patterns of soil microorganisms change over a season and that chemical soil properties are more important controlling factors than plant density and diversity. Finer spatial resolution, such as the mm to cm scale, as well as taxonomic resolution of microbial groups, could help determine the importance of plant species density, composition, and growth stage in shaping microbial community composition and spatial patterns.
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Vogel, C. ; Mueller, C.W. ; Höschen, C. ; Buegger, F. ; Heister, K. ; Schulz, S. ; Schloter, M. ; Kögel-Knabner, I.
Nat. Commun. 5:2947 (2014)
The sequestration of carbon and nitrogen by clay-sized particles in soils is well established, and clay content or mineral surface area has been used to estimate the sequestration potential of soils. Here, via incubation of a sieved (<2 mm) topsoil with labelled litter, we find that only some of the clay-sized surfaces bind organic matter (OM). Surprisingly, <19% of the visible mineral areas show an OM attachment. OM is preferentially associated with organo-mineral clusters with rough surfaces. By combining nano-scale secondary ion mass spectrometry and isotopic tracing, we distinguish between new labelled and pre-existing OM and show that new OM is preferentially attached to already present organo-mineral clusters. These results, which provide evidence that only a limited proportion of the clay-sized surfaces contribute to OM sequestration, revolutionize our view of carbon sequestration in soils and the widely used carbon saturation estimates.
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Stempfhuber, B. ; Welzl, G. ; Wubet, T. ; Schöning, I. ; Marhan, S. ; Buscot, F. ; Kandeler, E. ; Schloter, M.
Soil Biol. Biochem. 69, 179-186 (2014)
In this study, drivers for ammonia-oxidation and the related microbial communities (ammonia-oxidizing bacteria and archaea) were investigated in grassland soils on the local as well as on the regional scale focusing on the role of land-use intensity (LUI). To this end, 150 sites from three distinct regions across Germany were selected, covering the whole range of LUI levels (from natural grasslands up to intensive managed meadows). Furthermore, the role of contrasting soil types was analyzed in one of the regions (high vs low organic matter content) for ammonia-oxidation. We revealed a significant increase in potential nitrification rates and abundance of ammonia-oxidizing microbes at two sites on the local level from extensively to intensively managed sites, which indicates that the response pattern of ammonia-oxidizing microbes in grassland soils is likely triggered to a large extent by LUI. However at a third site, where two different soil types were investigated, no correlation between LUI and potential nitrification rates was observed, and only a site-specific effect was apparent. At this site, on the one hand the specific soil type (Histosol) and the related continuous nutrient mobilization from the former peat matrix, as well as the high groundwater level, which could induce a high abundance of methane- oxidizing microbes in the top soil, may be of greater importance as a driver for potential nitrification rates and abundance of ammonia- oxidizing microbes than LUI. On the other hand, the mineral soils of this site were characterized by extreme water shortage, which may also explain the lack of potential nitrification and the abundance of ammonia-oxidizing bacteria and archaea. Thus any extrapolation of local data to regional predictions must be made with care, as factors other than LUI may be of importance if the nitrification potential of a soil is to be described.
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Meyer, A.H. ; Focks, A. ; Radl, V. ; Welzl, G. ; Schöning, I. ; Schloter, M.
Microb. Ecol. 67, 161-166 (2014)
In the present study, the influence of the land use intensity on the diversity of ammonia oxidizing bacteria (AOB) and archaea (AOA) in soils from different grassland ecosystems has been investigated in spring and summer of the season (April and July). Diversity of AOA and AOB was studied by TRFLP fingerprinting of amoA amplicons. The diversity from AOB was low and dominated by a peak that could be assigned to Nitrosospira. The obtained profiles for AOB were very stable and neither influenced by the land use intensity nor by the time point of sampling. In contrast, the obtained patterns for AOA were more complex although one peak that could be assigned to Nitrosopumilus was dominating all profiles independent from the land use intensity and the sampling time point. Overall, the AOA profiles were much more dynamic than those of AOB and responded clearly to the land use intensity. An influence of the sampling time point was again not visible. Whereas AOB profiles were clearly linked to potential nitrification rates in soil, major TRFs from AOA were negatively correlated to DOC and ammonium availability and not related to potential nitrification rates.
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Ollivier, J. ; Yang, S. ; Dörfer, C. ; Welzl, G. ; Kühn, P. ; Scholten, T. ; Wagner, D.E. ; Schloter, M.
Biol. Fertil. Soils 50, 555-559 (2014)
In this study, we assessed the abundance and diversity of bacterial communities by 16S rRNA gene-based qPCR and T-RFLP across different soil depths of three sites located on the Tibetan Plateau which are affected by discontinuous permafrost or characterized as seasonally frozen ground. Our data indicates that bacterial community structure was significantly influenced by soil depth mainly at the site affected by seasonal freezing and thawing. In contrast at sites affected by permafrost, diversity pattern of bacterial communities in the top soil and deeper soil layers changed to a far lower extend. This might be related to the fact that the investigated sites were not waterlogged at the permafrost layer, thus no processes that shifts towards bacterial communities, which require anoxic environments, could be expected. Overall, at all sites, labile and stable C as well as N pools act as main drivers for bacterial communities.
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Sieper, T. ; Forczek, S. ; Matucha, M. ; Krämer, P. ; Hartmann, A. ; Schröder, P.
New Phytol. 201, 545-555 (2014)
Bacteria communicate with each other in a population density-dependent process known as quorum sensing. N-acyl-homoserine lactones (HSLs) are the autoinducers of Gram-negative bacteria and the best-studied quorum sensing signals so far. HSLs induce various responses in plants, including systemic resistance and root development. Here, we used different methods, including tritium labelling, sensor strain assays and monoclonal antibodies (mAbs), to analyse the uptake and translocation of C8- and C10- homoserine lactones into barley (Hordeum vulgare cv Barke). Both HSLs were already systemically transported into the shoot at 2 h after application. HSL uptake could be inhibited by orthovanadate, demonstrating that ABC transporters are involved in the uptake. Root transport occurs predominantly via the central cylinder, which was shown by transport inhibition via KCl application and autoradiography of root cross-sections. Furthermore, a newly established detection method with mAbs allowed the first detection of a systemic transport of long-chain HSLs in plants. The coupled use of different HSL detection methods demonstrated that the uptake and transport of HSLs into barley does not occur passively, but relies, at least partially, on active processes in the plant.
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Kölbl, A. ; Schad, P. ; Jahn, R. ; Amelung, W. ; Bannert, A. ; Cao, Z.H. ; Fiedler, S. ; Kalbitz, K. ; Lehndorff, E. ; Müller-Niggemann, C. ; Schloter, M. ; Schwark, L. ; Vogelsang, V. ; Wissing, L. ; Kögel-Knaber, I.
Geoderma 228-229, 67-89 (2014)
Inundation of paddy soils for submerged rice production strongly impacts soil formation. Here we used chronosequences with up to 2000 years of cultivation history to compare soil formation in non-inundated (non-paddy) cropping systems with the formation of soils used for paddy rice production. This approach allowed us to identify the influence of agricultural management at different stages of pedogenesis. Soil samples were taken from two chronosequences derived from uniform parent material in the coastal region of the Zhejiang Province (P.R. China). One chronosequence consisted of paddy soils of different ages (50-2000 years), characterized by a yearly cropping sequence of rice cultivation under flooded conditions alternated with a non-inundated crop. The adjacent non-inundated (non-paddy) chronosequence was exclusively used for non-inundated crop production for 50-700 years. Lipid biomarkers revealed origin and homogeneity of the original coastal sediments and enabled the reconstruction of a consistent land use history for both chronosequences. The chronological development of soil properties and horizons suggested that the formation of paddy soils can be subdivided into three phases. The initial phase of paddy soil development takes only a few decades and is dominated by desalinization and formation of a compacted plow pan, leading from Fluvisols to Anthraquic Cambisols. During the next centuries (second phase), the differentiation between paddy and non-paddy management becomes increasingly obvious in terms of accelerated carbonate losses and constantly increasing organic carbon concentrations in paddy topsoils. In the third stage of paddy soil development (≥ 700 years), a (trans-)formation and redistribution of oxides is accompanied by clearly visible hydromorphic patterns in paddy subsoils, thus promoting further development from Cambisols to Hydragric Anthrosols. To account for the underlying processes we suggest modifying the depth and mottling criteria for the definitions of anthraquic and hydragric soil horizons in the classification of the World Reference Base for Soil Resources. The non-paddy chronosequence was characterized by a low degree of soil development in which decalcification-related processes dominated throughout 700 years of soil formation. Hence, soil formation under paddy management was accelerated relative to that under dryland cropping, even though the 2000-year-old paddy soils lacked evidence of an advanced stage of silicate weathering, formation of pedogenic clay minerals, or clay migration.
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Fuka, M.M. ; Engel, M. ; Skelin, A. ; Matijasic, B.B. ; Redzepovic, S. ; Schloter, M.
Food Technol. Biotechnol. 51, 414-421 (2014)
In order to preserve the specificity of artisanal cheese and to minimize variations in quality, real-time PCR can be applied to monitor the dynamics of autochthonous bacterial population throughout ripening. This may give the basis for the selection of species and strains that can be used to deliver safe products with balanced texture and flavour, and moreover, it can be applied to monitor the abundance of slow-growing or nonculturable species. The aim of this study is to evaluate the application of real-time PCR and plate count analysis in order to follow the dynamics of lactic acid bacteria (LAB) and enterobacteria during the ripening of traditional Istrian cheese. The abundance of all LAB was increased by prolonging the ripening time and reached the plateau after 90 days. The present study demonstrated that Lactococcus counts were closest to total bacterial count irrespective of the applied method, confirming Lactococcus spp. as one of the dominant bacterial groups associated with the ripening of Istrian cheese. Enterobacteria were mainly present at early phases of cheese ripening, whereas at later time a decrease was visible in samples from all farms.
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Schröder, P. ; Belis, C.A. ; Schnelle-Kreis, J. ; Herzig, R. ; Prévôt, A.S. ; Raveton, M. ; Kirchner, M. ; Catinon, M.
Environ. Sci. Pollut. Res. 21, 252-267 (2014)
In the middle of Europe, the Alps form a geographical and meteorological trap for atmospheric pollutants including volatile and semi-volatile organic compounds emitted in the surrounding lowlands. This is due to their barrier effects, high precipitation rates, and low ambient temperatures. Also the pollutants emitted in the cities inside the Alps spread in the region depending on orographic and meteorological conditions. Although a number of studies on the distribution and effect of pollutants in the Alps has been published, comprehensive information on potential hazards, and ways to improve this sensible environment are lacking. This opinion paper is the result of a discussion during the Winterseminar of the AlpsBioCluster project in Munich. It summarizes the current literature and presents some case studies on local pollution sources in the Alps, and the possibility of using biomonitoring techniques to assess critical pollution loads and distributions.
Review
Review
2013
Lyubenova, L. ; Kuhn, A. ; Höltkemeier, A. ; Bipuah, H. ; Belford, E. ; Schröder, P.
In: (16th International conference on Heavy Metals in the Environment, 23-27.09.2012, Rome). 2013.:08006 ( ; 1)
The major topic of the present experiment was the investigation of the antioxidative enzymes and the root exudate excretion after plant exposure to copper. The copper was added for each treatment as copper sulphate and copper nitrate in the concentrations of 10 μM, 50 μM and 100 μM, respectively. The plant species chosen for the study was Typha latifolia. The experiment gives insight into the plant responses to different copper supplies during the same conditions of exposure. Remarkable results were obtained during the time course about the excretion of organic acids from Typha latifolia roots during one week of copper exposure. Oxalic acid, malic acid, acetic acid and lactic acid were detected. Interestingly, not all organic acids are excreted from the roots in the first hours after copper addition.
Fuka, M.M. ; Wallisch, S. ; Engel, M. ; Welzl, G. ; Havranek, J. ; Schloter, M.
PLoS ONE 8:e80734 (2013)
Microbial communities play an important role in cheese ripening and determine the flavor and taste of different cheese types to a large extent. However, under adverse conditions human pathogens may colonize cheese samples during ripening and may thus cause severe outbreaks of diarrhoea and other diseases. Therefore in the present study we investigated the bacterial community structure of three raw ewe's milk cheese types, which are produced without the application of starter cultures during ripening from two production sites based on fingerprinting in combination with next generation sequencing of 16S rRNA gene amplicons. Overall a surprisingly high diversity was found in the analyzed samples and overall up to 213 OTU97 could be assigned. 20 of the major OTUs were present in all samples and include mostly lactic acid bacteria (LAB), mainly Lactococcus, and Enterococcus species. Abundance and diversity of these genera differed to a large extent between the 3 investigated cheese types and in response to the ripening process. Also a large number of non LAB genera could be identified based on phylogenetic alignments including mainly Enterobacteriaceae and Staphylococcacae. Some species belonging to these two families could be clearly assigned to species which are known as potential human pathogens like Staphylococcus saprophyticus or Salmonella spp. However, during cheese ripening their abundance was reduced. The bacterial genera, namely Lactobacillus, Streptococcus, Leuconostoc, Bifidobacterium, Brevibacterium, Corynebacterium, Clostridium, Staphylococcus, Thermoanerobacterium, E. coli, Hafnia, Pseudomonas, Janthinobacterium, Petrotoga, Kosmotoga, Megasphaera, Macrococcus, Mannheimia, Aerococcus, Vagococcus, Weissella and Pediococcus were identified at a relative low level and only in selected samples. Overall the microbial composition of the used milk and the management of the production units determined the bacterial community composition for all cheese types to a large extend, also at the late time points of cheese ripening.
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Hartmann, A. ; Schenk, S.T. ; Riedel, T. ; Schröder, P. ; Schikora, A.
In: de Brujin, F.J.* [Eds.]: Molecular Microbial Ecology of the Rhizosphere: Volume 2. Hoboken, USA: Wiley-Blackwell, 2013. 775-783
Gram-negative bacteria communicate within a population on species or even genus level using small autoinducer signal molecules of the N-acyl homoserine lactone (HSL) type, which occur in several structural variations. Plants colonized by these bacteria are exposed to these signaling molecules and are able to recognize and even distinguish between different quorum-sensing QS-active molecules. Plants responses to those molecules are manifold, ranging from modifications of the defense system to modulation of the immune response or changes in the hormonal status. The type of response is dependent on the structural features of the HSL molecule and the plant species. In some plants, the HSL molecules with side chain length up to C10 are taken up, while in other plants, lactonases efficiently hydrolyse the molecules. It appears that short side chain (C4–C10) and long side chain (C12 and C14) HSLs induce different types of responses by activating different perception mechanisms and response cascades. Plants and microbes evolved together and thus complex trans-kingdom assemblages were formed. Apparently, in addition to the microbe-associated molecular pattern (MAMP) recognition, multiple communication possibilities have been formed, many of them only poorly understood at the present. All these signals can be integrated within a “superorganism,” which is characterized by its healthy state and well-balanced “immunity homoeostasis.”
Rasche, F. ; Schloter, M. ; Lüders, T. ; Sessitsch, A.
In: de Brujin, F.J.* [Eds.]: Molecular Microbial Ecology of the Rhizosphere: Volume 1. Hoboken, USA: Wiley-Blackwell, 2013. 413-421
DNA-based stable isotope probing (SIP) was introduced as a powerful tool to achieve a deeper insight of microbial processes through identifying relevant organisms that determine nutrient cycling and metabolize plant-derived compounds. Since its advent, it has been mainly used for studying micro-organisms in terrestrial ecosystems including the rhizosphere, but the endosphere has not been considered so far. Here we present a baseline study in which we used a 13CO2 (99 atom-%, 350 ppm) pulse labeling incubation experiment to identify active bacterial endophytes in two Solanum tuberosum L. cultivars, Desirée and Merkur (Rasche et al., 2009). Active bacterial endophytes were determined by SIP along with 16S rRNA gene-based community analysis including terminal restriction fragment length polymorphism analysis and generation of gene libraries. Our results show that the 13C label shuttles from plant assimilates to the endophytic bacterial community. In the 13C-enriched SIP fractions, a specific terminal restriction fragment became abundant, which could be clearly affiliated with Acinetobacter and Acidovorax sp. in Merkur and Desirée, respectively, indicating cultivar-specific distinctions in the 13C label flow. In summary, the presented DNA-based SIP approach was clearly suited to determine active bacterial endophytes in potato shoots which led to the overall conclusion that DNA-based SIP studies possess a very high potential to advance our current understanding of the complex nature of plant-microbe interactions and plant-dependent microbial metabolisms in the endosphere. Finally, this book chapter highlights essential research needs and gaps to substantiate the necessity to extend SIP-based approaches for prospective studies within the active and multifaceted plant-microbe ecosystem.
Fischer, D. ; Uksa, M. ; Tischler, W. ; Kautz, T. ; Köpke, U. ; Schloter, M.
Biol. Fertil. Soils 49, 1243-1246 (2013)
The role of subsoils and their microbial communities for the nutrient supply for plants is to a large extent unknown, especially in comparison to well investigated topsoil layers. Therefore, in this study, the influence of three different plant species with different rooting systems and different N uptake strategies on ammonium and nitrate levels and microbial communities involved in ammonia oxidation and denitrification was investigated in different soil horizons. Overall, our results show a higher genetic potential for both processes in topsoils than in subsoils independent of the present plant. Although we found accumulation of N in top and subsoils in plots with legumes, we could not observe an impact of the higher nitrate content on the genetic potential of denitrification and ammonia oxidation. However, differences in the ratios of ammonia oxidizing archaea to bacteria and also between denitrifying bacteria harboring genes for copper- (nirK) or cytochrome- (nirS) dependent nitrite reductase in top and subsoil samples reveal different ecophysiologies of microbes involved in N turnover in top and subsoil habitats.
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Scientific Article
Zhang, X. ; Liu, W. ; Schloter, M. ; Zhang, G. ; Chen, Q. ; Huang, J. ; Li, L. ; Elser, J.J. ; Han, X.
PLoS ONE 8:e76500 (2013)
Multiple co-occurring environmental changes are affecting soil nitrogen cycling processes, which are mainly mediated by microbes. While it is likely that various nitrogen-cycling functional groups will respond differently to such environmental changes, very little is known about their relative responsiveness. Here we conducted four long-term experiments in a steppe ecosystem by removing plant functional groups, mowing, adding nitrogen, adding phosphorus, watering, warming, and manipulating some of their combinations. We quantified the abundance of seven nitrogen-cycling genes, including those for fixation (nifH), mineralization (chiA), nitrification (amoA of ammonia-oxidizing bacteria (AOB) or archaea (AOA)), and denitrification (nirS, nirK and nosZ). First, for each gene, we compared its sensitivities to different environmental changes and found that the abundances of various genes were sensitive to distinct and different factors. Overall, the abundances of nearly all genes were sensitive to nitrogen enrichment. In addition, the abundances of the chiA and nosZ genes were sensitive to plant functional group removal, the AOB-amoA gene abundance to phosphorus enrichment when nitrogen was added simultaneously, and the nirS and nirK gene abundances responded to watering. Second, for each single- or multi-factorial environmental change, we compared the sensitivities of the abundances of different genes and found that different environmental changes primarily affected different gene abundances. Overall, AOB-amoA gene abundance was most responsive, followed by the two denitrifying genes nosZ and nirS, while the other genes were less sensitive. These results provide, for the first time, systematic insights into how the abundance of each type of nitrogen-cycling gene and the equilibrium state of all these nitrogen-cycling gene abundances would shift under each single- or multi-factorial global change.
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Pereira e Silva, M.C. ; Schloter-Hai, B. ; Schloter, M. ; van Elsas, J.D. ; Falcao Salles, J.
PLoS ONE 8:e74500 (2013)
Background Despite the fact that the fixation of nitrogen is one of the most significant nutrient processes in the terrestrial ecosystem, a thorough study of the spatial and temporal patterns in the abundance and distribution of N-fixing communities has been missing so far. Methodology/Principal Findings In order to understand the dynamics of diazotrophic communities and their resilience to external changes, we quantified the abundance and characterized the bacterial community structures based on the nifH gene, using real-time PCR, PCR-DGGE and 454-pyrosequencing, across four representative Dutch soils during one growing season. In general, higher nifH gene copy numbers were observed in soils with higher pH than in those with lower pH, but lower numbers were related to increased nitrate and ammonium levels. Results from nifH gene pyrosequencing confirmed the observed PCR-DGGE patterns, which indicated that the N fixers are highly dynamic across time, shifting around 60%. Forward selection on CCA analysis identified N availability as the main driver of these variations, as well as of the evenness of the communities, leading to very unequal communities. Moreover, deep sequencing of the nifH gene revealed that sandy soils (B and D) had the lowest percentage of shared OTUs across time, compared with clayey soils (G and K), indicating the presence of a community under constant change. Cosmopolitan nifH species (present throughout the season) were affiliated with Bradyrhizobium, Azospirillum and Methylocistis, whereas other species increased their abundances progressively over time, when appropriate conditions were met, as was notably the case for Paenibacilus and Burkholderia. Conclusions Our study provides the first in-depth pyrosequencing analysis of the N-fixing community at both spatial and temporal scales, providing insights into the cosmopolitan and specific portions of the nitrogen fixing bacterial communities in soil.
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Meyer, A.H. ; Focks, A. ; Radl, V. ; Keil, D. ; Welzl, G. ; Schöning, I. ; Boch, S. ; Marhan, S. ; Kandeler, E. ; Schloter, M.
PLoS ONE 8:e73536 (2013)
Understanding factors driving the ecology of N cycling microbial communities is of central importance for sustainable land use. In this study we report changes of abundance of denitrifiers, nitrifiers and nitrogen-fixing microorganisms (based on qPCR data for selected functional genes) in response to different land use intensity levels and the consequences for potential turnover rates. We investigated selected grassland sites being comparable with respect to soil type and climatic conditions, which have been continuously treated for many years as intensely used meadows (IM), intensely used mown pastures (IP) and extensively used pastures (EP), respectively. The obtained data were linked to above ground biodiversity pattern as well as water extractable fractions of nitrogen and carbon in soil. Shifts in land use intensity changed plant community composition from systems dominated by s-strategists in extensive managed grasslands to c-strategist dominated communities in intensive managed grasslands. Along the different types of land use intensity, the availability of inorganic nitrogen regulated the abundance of bacterial and archaeal ammonia oxidizers. In contrast, the amount of dissolved organic nitrogen determined the abundance of denitrifiers (nirS and nirK). The high abundance of nifH carrying bacteria at intensive managed sites gave evidence that the amounts of substrates as energy source outcompete the high availability of inorganic nitrogen in these sites. Overall, we revealed that abundance and function of microorganisms involved in key processes of inorganic N cycling (nitrification, denitrification and N fixation) might be independently regulated by different abiotic and biotic factors in response to land use intensity.
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Schloter, M. ; Esperschütz, J. ; Munch, J.-C.
In: Hüttl, R.F.* ; Kögel-Knabner, I.* ; Schulin, R.* ; Gerwin, W.* [Eds.]: Structures and processes of the initial ecosystem development phase in an artificial water catchment (Final report CRC/TR 38). Cottbus: Brandenburgische Technische Universität, 2013. 51-61 (Ecosys. Development ; 4)
Zeyer, J. ; Munch, J.-C. ; Brankatschk, R. ; Schulz, S. ; Schloter, M.
Ecosys. Development 4, 63-75 (2013)
Lyubenova, L. ; Kuhn, A.J. ; Höltkemeier, A. ; Schröder, P.
Plant Soil 370, 187-195 (2013)
Aims: Typha latifolia L. is an aquatic plant that has been widely exploited for the aims of phytoremediation. The main reason why we have chosen this plant species for the current study is its capacity to accumulate and detoxify heavy metals. The main topic of the investigation focused on the root uptake of copper (II) nitrate and copper (II) sulfate and the impact of different chemical copper species on the excreted organic acids. Methods: Oxalic, malic, acetic and lactic acids were determined using capillary electrophoresis; a comparison between the concentration and the time course during 7 days of treatment was performed. Results: There is a correlation between the total copper (II) sulfate concentration in the roots and the total amount of the excreted organic acids. In addition to that organic acids are involved in the detoxification mechanisms of Typha latifolia for copper (II) nitrate and copper (II) sulfate. Conclusions: Different from so far investigated plant species the highest amounts of organic acids are excreted from T. latifolia roots not in the first hours after treatment, but up to 7 days later.
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Mouhamadou, B. ; Puissant, J. ; Personeni, E. ; Desclos-Theveniau, M. ; Kastl, E.-M. ; Schloter, M. ; Zinger, L. ; Roy, J. ; Geremia, R.A. ; Lavorel, S.
Biol. Fertil. Soils 49, 1131-1139 (2013)
Many studies have shown effects of plants species on fungal communities, but these are often confounded with soil effects. Thus, the specific role of plant species in structuring rhizospheric and soil fungal communities is poorly described. Our study used microcosms in which plants were grown under artificial conditions to bridge this gap. Two perennial grasses dominating subalpine grasslands, Festuca paniculata and Dactylis glomerata, were grown at two levels of fertilization on standard soil. Fungal communities were determined by 454 pyrosequencing of the internal transcribed spacer 1 region. Among the fungal communities characterized by the primers used, original communities were associated to each plant species and also diverged between rhizosphere and bulk soils within each plant species, though there were no significant fertilization effects. Differences regarded global composition of the fungal communities and abundant molecular operational taxonomic units (MOTUs). Both plant species and location effects were reflected more in the abundance than in the composition of MOTUs. The observed differences in fungal communities coincide with differing strategies of plant root growth, with D. glomerata having greater root mass, length, and area than F. paniculata. Our study, by dissociating soil effects from plant effects, demonstrated that plant species exert a key control on soil fungi. We suggest that such effects may be linked to inter-specific differences in root traits and their consequences on nitrogen uptake.
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Lyubenova, L. ; Pongrac, P. ; Vogel-Mikus, K. ; Mezek, G.K. ; Vavpetic, P. ; Grlj, N. ; Regvar, M. ; Pelicon, P. ; Schröder, P.
J. Hazard. Mater. 248, 371-378 (2013)
Understanding the uptake, accumulation and distribution of toxic elements in plants is crucial to the design of effective phytoremediation strategies, especially in the case of complex multi-element pollution. Using micro-proton induced X-ray emission, the spatial distribution of Na, Mg, Al, Si, P, S, Cl, K, Ca, Mn, Fe, Zn, As, Br, Rb, Sr, Cd and Pb have been quantitatively resolved in roots and rhizomes of an obligate wetland plant species, Typha latifolia, treated with a mixture of 100 mu M each of As, Cd and Pb, together. The highest concentrations of As, Cd and Pb were found in the roots of the T. latifolia, with tissue-specific distributions. The As was detected in the root rhizodermis, and in the rhizome the majority of the As was within the vascular tissues, which indicates the high mobility of As within T. latifolia. The Cd was detected in the root exodermis, and in the vascular bundle and epidermis of the rhizome. The highest Pb concentrations were detected in the root rhizodermis and exodermis, and in the epidermis of the rhizome. These data represent an essential step in the resolution of fundamental questions in plant ionomics.
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Ziegler, M. ; Engel, M. ; Welzl, G. ; Schloter, M.
J. Microbiol. Methods 94, 30-36 (2013)
The plant root interface is a hot spot for microbial activities. Root exudates are the key compounds that drive microbial performance. However quality and amount of root exudates are highly dynamic in time and space, thus a direct influence of a single compound on a microbial community composition is fairly impossible to study in nature. Therefore it was the aim of this project to develop an artificial root model (ARM), and investigate the influence of three compounds which have often been described as root exudates acting as model compounds for carbohydrates, organic acids and amino acids (glucose, malic acid and serine) on the development of bacterial communities and time on the ARM based on 16S rRNA derived TRFLP pattern. The ARM consisted of a slide covered with low melting agarose, where 8 different compounds which have been described as typical root exudates were embedded. The ARMs were incubated in soil for 2, 5, 9 and 20days, before the analysis of the developed bacterial community structure was done. The bacterial community composition was in good agreement after 9days of incubation of the ARM in soil with the root associated microflora of Arabidopsis thaliana shortly before flowering. The single compounds of the exudates mix had different effects on the development of ARM derived bacterial communities. Whereas the experiments where glucose was omitted gave no significant differences in the development of bacterial communities over time compared to the ARM where the standard mixture of exudates had been applied, there was a pronounced effect visible mainly after two days of incubation of the ARM in the experiments where no malic acid was added to the exudate mixture. At later time points ARMs with standard exudates' mixture and those where malic acid had been omitted, the bacterial community composition did not differ. The experiments where serine was omitted mainly induced shifts in the bacterial community composition compared to the ARM with standard exudates' mixture at the latest sampling time point (20days of incubation).
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Giebler, J. ; Wick, L.Y. ; Schloter, M. ; Harms, H. ; Chatzinotas, A.
Appl. Environ. Microbiol. 79, 3129-3132 (2013)
Sequence and terminal restriction fragment length polymorphism (T-RFLP) analyses revealed multiple alkB gene copies/cell in soil bacterial isolates and an apparently high genetic mobility among various phylogenetic groups. Identifying alkane degraders by alkB terminal restriction fragments (T-RFs) and sequences is strongly biased, as the phylogenetic trees based on 16S rRNA and alkB gene sequences were highly inconsistent.
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Le Roux, X. ; Schmid, B. ; Poly, F. ; Barnard, R.L. ; Niklaus, P.A. ; Guillaumaud, N. ; Habekost, M. ; Oelmann, Y. ; Philippot, L. ; Salles, J.F. ; Schloter, M. ; Steinbeiss, S. ; Weigelt, A.
PLoS ONE 8:e61069 (2013)
Random reductions in plant diversity can affect ecosystem functioning, but it is still unclear which components of plant diversity (species number – namely richness, presence of particular plant functional groups, or particular combinations of these) and associated biotic and abiotic drivers explain the observed relationships, particularly for soil processes. We assembled grassland communities including 1 to 16 plant species with a factorial separation of the effects of richness and functional group composition to analyze how plant diversity components influence soil nitrifying and denitrifying enzyme activities (NEA and DEA, respectively), the abundance of nitrifiers (bacterial and archaeal amoA gene number) and denitrifiers (nirK, nirS and nosZ gene number), and key soil environmental conditions. Plant diversity effects were largely due to differences in functional group composition between communities of identical richness (number of sown species), though richness also had an effect per se. NEA was positively related to the percentage of legumes in terms of sown species number, the additional effect of richness at any given legume percentage being negative. DEA was higher in plots with legumes, decreased with increasing percentage of grasses, and increased with richness. No correlation was observed between DEA and denitrifier abundance. NEA increased with the abundance of ammonia oxidizing bacteria. The effect of richness on NEA was entirely due to the build-up of nitrifying organisms, while legume effect was partly linked to modified ammonium availability and nitrifier abundance. Richness effect on DEA was entirely due to changes in soil moisture, while the effects of legumes and grasses were partly due to modified nitrate availability, which influenced the specific activity of denitrifiers. These results suggest that plant diversity-induced changes in microbial specific activity are important for facultative activities such as denitrification, whereas changes in microbial abundance play a major role for non-facultative activities such as nitrification.
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Bischoff, J. ; Mangelsdorf, K. ; Gattinger, A. ; Schloter, M. ; Kurchatova, A.N. ; Herzschuh, U. ; Wagner, D.E.
Global Biogeochem. Cycles 27, 305-317 (2013)
In order to investigate the link between the methane dynamics in permafrost deposits and climate changes in the past, we studied the abundance, composition, and methane production of methanogenic communities in Late Pleistocene and Holocene sediments of the Siberian Arctic. We detected intervals of increased methane concentrations in Late Pleistocene and Holocene deposits along a 42 ka old permafrost sequence from Kurungnakh Island in the Lena Delta (northeast Siberia). Increased amounts of archaeal life markers (intact phospholipid ethers) and a high variety in genetic fingerprints detected by 16S ribosomal ribonucleic acid gene analyses of methanogenic archaea suggest presently living and presumably active methanogenic archaea in distinct layers predominantly in Holocene deposits, but also in deep frozen ground at 17 m depth. Potential methanogenic activity was confirmed by incubation experiments. By comparing methane concentrations, microbial incubation experiments, gene analysis of methanogens, and microbial life markers (intact phospholipid esters and ethers) to already partly degraded membrane lipids, such as archaeol and isoprenoid glycerol dialkyl glycerol tetraethers, we demonstrated that archaeol likely represents a signal of past methanogenic archaea. The archaeol signal was used to reconstruct the response of methanogenic communities to past temperature changes in the Siberian Arctic, and the data suggest higher methane emissions occurred during warm periods, particularly during an interval in the Late Pleistocene and during the Holocene. This new data on present and past methanogenic communities in the Siberian terrestrial permafrost imply that these microorganisms will respond to the predicted future temperature rise in the Arctic with increasing methane production, as demonstrated in previous warmer periods.
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Fischer, D. ; Pagenkemper, S. ; Nellesen, J. ; Peth, S. ; Horn, R. ; Schloter, M.
J. Microbiol. Methods 93, 121-123 (2013)
In this study the influence of X-ray computed tomography (XRCT) on the microbial community structure and function in soils has been investigated. Our results clearly indicate that XRCT of soil samples has a strong impact on microbial communities and changes structure and function significantly due to the death of selected microbial groups as a result of the treatment.
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Holbeck, B. ; Amelung, W. ; Wolf, A. ; Südekum, K.-H. ; Schloter, M. ; Welp, G.
Soil Tillage Res. 130, 120-127 (2013)
Frequently, organic fertilizers are applied to maintain or to increase soil fertility and plant yields. However, as the N availability of organic fertilizers is difficult to calculate, applied fertilizer N may be subject to loss, particularly through leaching. The objective of this study was to evaluate the fate of fertilizer N from two common organic manures (chicken manure, mushroom compost) in arable topsoil during one winter cover cropping and cropping season. For this purpose, 15N-labelled fertilizers were produced by feeding chicken with 15N-labelled maize pellets and by incubating a mushroom substrate with 15N-labelled mineral fertilizer, respectively. Thereafter, the 15N uptake by a mustard winter cover crop, its release to the main crop (sugar beet), and its retention in soil were investigated in two differently textured soils under otherwise identical conditions during a period of 400 days. Mineral K15NO3 fertilizer served as control. In the surface soil (0–10 cm), only 20–40% of the applied 15N was recovered after the first 50–60 days, which was the period of mustard growth. Thereafter, the amount of 15N recovered in the soil increased again until day 259, reflecting the re-release of the fertilizer N from the winter cover crop in all treatments. The fertilizer N recovery in the winter cover crop itself was highest for mushroom compost (60%), followed by mineral fertilizer (50%) whereas it was almost not detectable for chicken manure (3%). Soil texture did not affect the overall retention of the fertilizer N in soil, and even after 400 days we recovered 67% of the fertilizer N from mushroom compost, 37% from chicken manure and 28% from the mineral fertilizer (0–30 cm). The following main crop, sugar beet, still utilized between 7 and 13% of the initial fertilizer addition from the previous summer. We conclude that mustard winter cover cropping after organic fertilization is efficient in retaining available N during winter time, and mushroom compost is better than mineral N-fertilizer and chicken manure in respect of being a slow and sustainable N fertilizer source for the plants at reduced N losses.
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Ollivier, J. ; Schacht, D. ; Kindler, R. ; Groeneweg, J. ; Engel, M. ; Wilke, B.-M. ; Kleineidam, K. ; Schloter, M.
Front. Microbiol. 4:22 (2013)
In a field experiment, the impact of repeated application of the antibiotic sulfadiazine (SDZ)-contaminated pig manure was assessed on functional microbial communities involved in ammonia and nitrite oxidation in the root-rhizosphere complexes (RRCs) of diverse plants composing a pasture. We surveyed the abundance of ammonia-oxidizing archaea (AOA) and bacteria (AOB) as well as Nitrobacter- and Nitrospira-like nitrite-oxidizing bacteria (NOB) by quantitative PCR (qPCR), and the diversity of amoA AOA and Nitrobacter-like nxrA amplicons using a cloning-sequencing approach. Whereas the first SDZ-contaminated manure application caused only slight effects on the investigated microbial communities and did not change the diversity and abundance pattern significantly, the second application of SDZ-contaminated manure induced an up to 15-fold increased ratio of AOA:AOB and a reduction of nrxA genes. The diversity of AOA amoA increased after the second application of SDZ-contaminated manure compared to the control treatment whereas a clear reduction of nrxA OTUs was visible in the same samples. The results indicate that the application of SDZ may principally affect nitrite oxidation by NOB and alternative pathways like nitrite reduction might be favored under these conditions.
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Schulz, S. ; Brankatschk, R. ; Dümig, A. ; Kögel-Knabner, I. ; Schloter, M. ; Zeyer, J.
Biogeosciences 10, 3983-3996 (2013)
Soil formation is the result of a complex network of biological as well as chemical and physical processes. Mainly the role of soil microbes is of high interest in this respect, as they are responsible for most transformations and drive the development of stable and labile carbon and nutrient pools in soil, which facilitate the basis for the subsequent establishment of plant communities. Glacier forefields, which provide a chronosequence of soils of different age due to the continuous retreat of the ice layer as a consequence of the increasing annual temperature since the last centuries, are a nice play ground to study the interaction of bacteria, fungi and archaea with their abiotic environment at different stages of soil formation. In this review we give insights into the role of microbes for soil development on the basis of investigations which have been performed at the Damma glacier in Switzerland in the frame of two international network projects Big Link (http://www.cces.ethz.ch/projects/clench/BigLink/) and DFG SFB/TRR 38 (http://www.tu-cottbus.de/ecosystem/). The review focusses on the microbiology of three major steps of soil formation including weathering of the parental material, the development of basic nutrient cycles, the formation of soil crusts and biofilms as initial microbial network structures and the occurrence of plants respectively the setup of plant communities.
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Grigulis, K. ; Lavorel, S. ; Krainer, U. ; Legay, N. ; Baxendale, C. ; Dumont, M. ; Kastl, E.-M. ; Arnoldi, C. ; Bardgett, R.D. ; Poly, F. ; Pommier, T. ; Schloter, M. ; Tappeiner, U. ; Bahn, M. ; Clément, J.-C.
J. Ecol. 101, 47-57 (2013)
Summary Plant functional diversity and soil microbial community composition are tightly coupled. Changes in these interactions may influence ecosystem functioning. Links between plant functional diversity, soil microbial communities and ecosystem functioning have been demonstrated in experiments using plant monocultures and mixtures, using broad plant and microbial functional groups, but have not been examined in diverse natural plant communities. We quantified the relative effects of plant and microbial functional properties on key ecosystem functions. We measured plant functional diversity, soil microbial community composition and parameters associated with nitrogen (N) cycling and key nutrient cycling processes at three grassland sites in different parts of Europe. Because plant structure and function strongly influence soil microbial communities, we determined relationships between ecosystem properties, plant traits and soil community characteristics following a sequential approach in which plant traits were fitted first, followed by the additional effects of soil micro-organisms. We identified a continuum from standing green biomass and standing litter, linked mostly with plant traits, to potential N mineralization and potential leaching of soil inorganic N, linked mostly with microbial properties. Plant and microbial functional parameters were equally important in explaining % organic matter content in soil. A parallel continuum ran from plant height, linked with above-ground biomass, to plant quality effects captured by the leaf economics spectrum, which were linked with the recycling of carbon (C) and N. More exploitative species (higher specific leaf area, leaf N concentrations and lower leaf dry matter content) and taller swards, along with soil microbial communities dominated by bacteria, with rapid microbial activities, were linked with greater fodder production, but poor C and N retention. Conversely, dominance by conservative species (with opposite traits) and soil microbial communities dominated by fungi, and bacteria with slow activities, were usually linked with low production, but greater soil C storage and N retention. Synthesis – Grassland production, C sequestration and soil N retention are jointly related to plant and microbial functional traits. Managing grasslands for selected, or multiple, ecosystem services will thus require a consideration of the joint effects of plant and soil communities. Further understanding of the mechanisms that link plant and microbial functional traits is essential to achieve this.  
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Schulz, S. ; Engel, M. ; Fischer, D. ; Buegger, F. ; Elmer, M. ; Welzl, G. ; Schloter, M.
Biogeosciences 10, 1183-1192 (2013)
Legumes can be considered as pioneer plants during ecosystem development, as they form a symbiosis with different nitrogen fixing rhizobia species, which enable the plants to grow on soils with low available nitrogen content. In this study we compared the abundance and diversity of nitrogen fixing microbes based on the functional marker gene nifH, which codes for a subunit of the Fe-protein of the dinitrogenase reductase, in nodules of different size classes of Trifolium arvense (L.). Additionally, carbon and nitrogen contents of the bulk soil and plant material were measured. Plants were harvested from different sites, reflecting 2 (2a) and 5 (5a) yr of ecosystem development, of an opencast lignite mining area in the south of Cottbus, Lower Lusatia (Germany) where the artificial catchment "Chicken Creek" was constructed to study the development of terrestrial ecosystems. Plants from the 5a site revealed higher amounts of carbon and nitrogen, although nifH gene abundances in the nodules and carbon and nitrogen contents between the two soils did not differ significantly. Analysis of the nifH clone libraries showed a significant effect of the nodule size on the community composition of nitrogen fixing microbes. Medium sized nodules (2–5 mm) contained a uniform community composed of Rhizobium leguminosarum bv. trifolii, whereas the small nodules (< 2 mm) consisted of a diverse community including clones with non-Rhizobium nifH gene sequences. Regarding the impact of the soil age on the community composition a clear distinction between the small and the medium nodules can be made. While clone libraries from the medium nodules were pretty similar at both soil ages, soil age had a significant effect on the community compositions of the small nodules, where the proportion of R. leguminosarum bv. trifolii increased with soil age.
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Kautz, T. ; Amelung, W. ; Ewert, F. ; Gaiser, T. ; Horn, R. ; Jahn, R. ; Javaux, M. ; Kemna, A. ; Kuzyakov, Y. ; Munch, J.-C. ; Pätzold, S. ; Peth, S. ; Scherer, H.W. ; Schloter, M. ; Schneider, H. ; Vanderborght, J. ; Vetterlein, D. ; Walter, A. ; Wiesenberg, G.L.B. ; Köpke, U.
Soil Biol. Biochem. 57, 1003-1022 (2013)
In arable farming systems, the term ‘subsoil’ refers to the soil beneath the tilled or formerly tilled soil horizon whereas the latter one is denoted as ‘topsoil’. To date, most agronomic and plant nutrition studies have widely neglected subsoil processes involved in nutrient acquisition by crop roots. Based on our current knowledge it can be assumed that subsoil properties such as comparatively high bulk density, low air permeability, and poverty of organic matter, nutrients and microbial biomass are obviously adverse for nutrient acquisition, and sometimes subsoils provide as little as less than 10% of annual nutrient uptake in fertilised arable fields. Nevertheless, there is also strong evidence indicating that subsoil can contribute to more than two-thirds of the plant nutrition of N, P and K, especially when the topsoil is dry or nutrient-depleted. Based on the existing literature, nutrient acquisition from arable subsoils may be conceptualised into three major process components: (I) mobilisation from the subsoil, (II) translocation to the shoot and long-term accumulation in the Ap horizon and (III) re-allocation to the subsoil. The quantitative estimation of nutrient acquisition from the subsoil requires the linking of field experiments with mathematical modelling approaches on different spatial scales including Process Based Models for the field scale and FunctionaleStructural Plant Models for the plant scale. Possibilities to modify subsoil properties by means of agronomic management are limited, but ‘subsoiling’ e i.e. deep mechanical loosening e as well as the promotion of biopore formation are two potential strategies for increasing access to subsoil resources for crop roots in arable soils. The quantitative role of biopores in the nutrient acquisition from the subsoil is still unclear, and more research is needed to determine the bioaccessibility of nutrients in subsoil horizons.
Review
Review
San Miguel, A. ; Schröder, P. ; Harpaintner, R. ; Gaude, T. ; Ravanel, P. ; Raveton, M.
Environ. Sci. Pollut. Res. 20, 3464-3471 (2013)
Mixed pollution is a characteristic of many industrial sites and constructed wetlands. Plants possessing an enzymatic detoxifying system that is able to handle xenobiotics seems to be a viable option for the removal of mixed persistent contaminants such organochlorines (OCs:  monochlorobenzene (MCB), 1,4-dichlorobenzene (DCB), 1,2,4-trichlorobenzene (TCB), γ-hexachlorocyclohexane (HCH)). In this study, Phragmites australis plants were exposed to sublethal concentrations of OCs (7 days), in single-exposure (0.8 to 10 mgl−1) and in mixture of OCs (0.2 mgl−1 MCB+0.2 mgl−1 DCB+2.5 mgl−1 TCB+0.175 mgl−1 HCH). Studies were conducted on the detoxification phase II enzymes; glutathione Stransferases (GST), and glucosyltransferases (UGT). Measurements of GST and UGT activities revealed that OCs may be buffered by glutathione and glucose conjugation. There appeared to be a correlation between the effects on phase II enzymes and the degree of chlorination of the benzene ring with, for example, the greatest effects being obtained for HCH exposure. In the case of mixed pollution, the induction of some GST isoenzymes (CDNB, 35 % non-significant) and UGT (118 %) in leaves and the inhibition of phase II enzymes in the other organs were measured. UGTs appear to be key enzymes in the detoxification of OCs.
Wissenschaftlicher Artikel
Scientific Article
Esperschütz, J. ; Zimmermann, C. ; Dümig, A. ; Welzl, G. ; Buegger, F. ; Elmer, M. ; Munch, J.-C. ; Schloter, M.
Biogeosciences 10, 5155-5124 (2013)
In initial ecosystems concentrations of all macro- and micronutrients can be considered as extremely low. Plant litter therefore strongly influences the development of a degraders' food web and is an important source for C and N input into soil in such ecosystems. In the present study, a 13C litter decomposition field experiment was performed for 30 weeks in initial soils from a post-mining area near the city of Cottbus (Germany). Two of this regions' dominant but contrasting pioneering plant species (Lotus corniculatus L. and Calamagrostis epigejos L.) were chosen to investigate the effects of litter quality on the litter decomposing microbial food web in initially nutrient-poor substrates. The results clearly indicate the importance of litter quality, mainly the amount of N stored in the litter material and its bioavailability for the degradation process and the development of microbial communities in the detritusphere and bulk soil. Whereas the degradation process of the L. corniculatus litter which had a low C/N ratio was fast and most pronounced changes in the microbial community structure were observed 1–4 weeks after litter addition, the degradation of the C. epigejos litter material was slow and microbial community changes mainly occurred at between 4 and 30 weeks after litter addition to the soil. However for both litter materials a clear indication for the importance of fungi for the degradation process was observed both on the abundance level as well as on the level of 13C incorporation (activity).
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Scientific Article
Pérez-de-Mora, A. ; Reuter, B. ; Lucio, M. ; Ahne, A. ; Schloter, M. ; Pritsch, K.
Mycorrhiza 23, 185-197 (2013)
The ecological and biogeochemical relevance of hydrolytic enzymes associated with the fungal cell wall has been poorly studied in ectomycorrhizal (ECM) fungi. We used a modified sequential extraction procedure to investigate the activity of various hydrolytic enzymes (β-glucosidase, acid-phosphatase, leucine-aminopeptidase, chitinase, xylanase and glucuronidase) and their association with the cell wall of three ECM fungi (Rhizopogon roseolus, Paxillus involutus and Piloderma croceum). Fungi were grown on C-rich solid medium under three different P concentrations (3.7, 0.37 and 0.037 mM). The sequential extraction procedure classifies enzymes as: (a) cytosolic, (b) loosely bound, (c) hydrophobically bound, (d) ionically bound and (e) covalently bound. Results showed that for the same fungus absolute enzymatic activity was affected by P concentration, whilst enzymatic compartmentalization among the cytosol and the cell wall fractions was not. The association of enzymes with the cell wall was fungus- and enzyme-specific. Our data indicate also that enzymes best known for being either extracellular or cytosolic or both, do act in muro as well. The ecological implications of cell wall-bound enzymes and the potential applications and limitations of sequential extractions are further discussed.
Wissenschaftlicher Artikel
Scientific Article
2012
Fuka, M.M. ; Radl, V. ; Matijasic, B.B. ; Schloter, M.
Afr. J. Biotechnol. 11, 16650-16654 (2012)
Denaturing gradient gel electrophoresis (DGGE) is a powerful method used to study structure of bacterial communities, without cultivation, based on the diversity of the genes coding for ribosomal RNA. However, the results are strongly dependent on the respective target region of the used primer systems. Therefore, three primer pairs that amplify different variable regions of the 16S rRNA gene (V1, V3 and V6 to V8) were tested in order to investigate the bacterial diversity existent in Istrian cheese. We found that primer set extremely influenced DGGE analysis. V3 primers were most efficient when 15 cheese associated isolates were resolved by DGGE. However, for Istrian cheese analysis, the best separation and highest number of bands in DGGE patterns were noticed for V6 to V8 primer pairs.
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Scientific Article
Steffens, M. ; Leu, C. ; Ruppert, A.K. ; Zara, F. ; Striano, P. ; Robbiano, A. ; Capovilla, G. ; Tinuper, P. ; Gambardella, A. ; Bianchi, A. ; La Neve, A. ; Crichiutti, G. ; de Kovel, C.G.F. ; Trenite, D.K.N. ; de Haan, G.J. ; Lindhout, D. ; Gaus, V. ; Schmitz, B. ; Janz, D. ; Weber, Y.G. ; Becker, F. ; Lerche, H. ; Steinhoff, B.J. ; Kleefuss-Lie, A.A. ; Kunz, W.S. ; Surges, R. ; Elger, C.E. ; Muhle, H. ; von Spiczak, S. ; Ostertag, P. ; Helbig, I. ; Stephani, U. ; Moller, R.S. ; Hjalgrim, H. ; Dibbens, L.M. ; Bellows, S. ; Oliver, K. ; Mullen, S. ; Scheffer, I.E. ; Berkovic, S.F. ; Everett, K.V. ; Gardiner, M.R. ; Marini, C. ; Guerrini, R. ; Lehesjoki, A.E. ; Siren, A. ; Guipponi, M. ; Malafosse, A. ; Thomas, P. ; Nabbout, R. ; Baulac, S. ; Leguern, E. ; Guerrero, R. ; Serratosa, J.M. ; Reif, P.S. ; Rosenow, F. ; Morzinger, M. ; Feucht, M. ; Zimprich, F. ; Kapser, C. ; Schankin, C.J. ; Suls, A. ; Smets, K. ; de Jonghe, P. ; Jordanova, A. ; Caglayan, H. ; Yapici, Z. ; Yalcin, D.A. ; Baykan, B. ; Bebek, N. ; Ozbek, U. ; Gieger, C. ; Wichmann, H.-E. ; Balschun, T. ; Ellinghaus, D. ; Franke, A. ; Meesters, C. ; Becker, T. ; Wienker, T.F. ; Hempelmann, A. ; Schulz, S. ; Ruschendorf, F. ; Leber, M. ; Pauck, S.M. ; Trucks, H. ; Toliat, M.R. ; Nürnberg, P. ; Avanzini, G. ; Koeleman, B.P.C. ; Sander, T. ; EPICURE Consortium () ; EMINet Consortium ()
Hum. Mol. Genet. 21, 5359-5372 (2012)
Genetic generalized epilepsies (GGEs) have a lifetime prevalence of 0.3 and account for 2030 of all epilepsies. Despite their high heritability of 80, the genetic factors predisposing to GGEs remain elusive. To identify susceptibility variants shared across common GGE syndromes, we carried out a two-stage genome-wide association study (GWAS) including 3020 patients with GGEs and 3954 controls of European ancestry. To dissect out syndrome-related variants, we also explored two distinct GGE subgroups comprising 1434 patients with genetic absence epilepsies (GAEs) and 1134 patients with juvenile myoclonic epilepsy (JME). Joint Stage-1 and 2 analyses revealed genome-wide significant associations for GGEs at 2p16.1 (rs13026414, P-meta 2.5 10(9), OR[T] 0.81) and 17q21.32 (rs72823592, P-meta 9.3 10(9), OR[A] 0.77). The search for syndrome-related susceptibility alleles identified significant associations for GAEs at 2q22.3 (rs10496964, P-meta 9.1 10(9), OR[T] 0.68) and at 1q43 for JME (rs12059546, P-meta 4.1 10(8), OR[G] 1.42). Suggestive evidence for an association with GGEs was found in the region 2q24.3 (rs11890028, P-meta 4.0 10(6)) nearby the SCN1A gene, which is currently the gene with the largest number of known epilepsy-related mutations. The associated regions harbor high-ranking candidate genes: CHRM3 at 1q43, VRK2 at 2p16.1, ZEB2 at 2q22.3, SCN1A at 2q24.3 and PNPO at 17q21.32. Further replication efforts are necessary to elucidate whether these positional candidate genes contribute to the heritability of the common GGE syndromes.
Wissenschaftlicher Artikel
Scientific Article
Schulz, S. ; Yukunkina, T. ; Pagel, H. ; Wick, L.Y. ; Poll, C. ; Streck,T. ; Kanddeler, E. ; Schloter, M.
Biol. Fertil. Soils 48, 933-940 (2012)
In the present study, the temporal and spatial variation of the abundance of the alkane monooxygenase gene alkB and 16S rRNA genes in different soil compartments was analysed in the presence or absence of 2-methyl- 4-chlorophenoxyacetic acid (MCPA) after the addition of pea litter to soil in a microcosm study. Samples were analysed shortly after litter addition (T0) and 1 week (T1), 3 weeks (T3) and 6 weeks (T6) after the addition of litter. In addition also, the quantity and quality of litter-derived alkanes was analysed and measured. The results revealed a fast and complete degradation of MCPA in all compartments throughout the experiment. Nevertheless, significant changes in the distribution patterns of short- andmiddle-chained alkanes suggest an interaction of MCPA and alkane degradation. alkB gene copy numbers were highly influenced by the time point of analysis and by the investigated soil compartment. Overall, an increase in alkB gene copy numbers from T0 to T3 was visible in the upper soil compartments whereas a decrease compared to T0 was measured in the deeper soil compartments. MCPA addition resulted in an increase of alkB abundance at T6. Gene copy numbers of 16S rRNA were not influenced by sampling time and soil compartment. In contrast to the control treatments, a slight increase in 16S rRNA gene copy numbers was visible at T1 and T3 compared to T0 in all soil compartments.
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Scientific Article
Yevdokimov, I.V. ; Gattinger, A. ; Buegger, F. ; Schloter, M. ; Munch, J.-C.
Microbiology 81, 743-749 (2012)
The changes in the structure and activity of a soil microbial community caused by addition of moderate andd high rates of the mineral nitrogen fertilizer (KNO3) were studied in a laboratory incubation experiment. The structure of the microbial community was evaluated from the phospholipid fatty acid (PLFA) profile; specific growth rate of the microorganisms was determined by the method of the kinetics of substrate-induced respiration; the total pool of microbial carbon was estimate by the fumigation-extraction method. The amounts of nitrogen fertilizer applied in three treatments of the experiment were 0 (contol), 100, and 2000 μg N/g soil. Even in the absence of assitional sources of organi carbon, a considerable portion of the added 15N (up to 74%) was immobilized. No significant inrease in the amount of microbial carbon was observed during incubation. The specific growth rate of the microbial community in soil supplemented with glucose deccreased twofold after addition of 2000 μg N/g soil. In this treatment, the ratio of cyclic fatty acids to their monoenoic precursors also increased, indicating the adaptation of microbial cells to extremely high amounts of nitrogfen fertilizer. Moreover, consierable changes in the structure of the soil microbial community, such as an increase in the ratio of fungal- to bacterial markers and a decrease in the ratio between PLFA of gram-positive and gram-negative bacteria, were observed in the treatment with addition of 2000 μg N/g soil. Our data clearly indicate that mineral nitrogen fertilization of soil under carbon limitation has a pronounced impact on the structure and activity of soil microbial communities.
Wissenschaftlicher Artikel
Scientific Article
Huber, C. ; Bartha, B. ; Schröder, P.
J. Hazard. Mater. 243, 250-256 (2012)
Pharmaceuticals from human or veterinary medication form a new class of micropollutants that poses a serious threat to our aquatic environment and its organisms. The intensively used nonsteroidal anti-inflammatory drug diclofenac is found in the environment worldwide due to its poor elimination during waste water treatment processes. In order to test phytoremediation as a tool for the removal of this drug from waste water, the uptake of the compound into plant tissues and its metabolic pathway was addressed using Hordeum vulgare (barley) and a hairy root cell culture of Armoracia rusticana (horse radish) as model species. Diclofenac is taken up by plants and undergoes rapid metabolization; already after 3 h of exposure the drug and its metabolites could be detected in the plant tissues. Similar to its fate in mammalian cells the drug is activated in a phase I reaction resulting in the hydroxylated metabolite 4′OH-diclofenac which is conjugated subsequently in phase II to a glucopyranoside, a typical plant specific metabolite. After exposure to 10 and 100 μM diclofenac a concentration dependent formation of the hydroxylated metabolite was observed, while the formation of the phase II metabolite OH-diclofenac glucopyranoside was not positively affected by the higher concentration. To our knowledge this is the first time these two human painkiller metabolites are shown to occur in plant tissues.
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Scientific Article
Bannert, A. ; Bogen, C. ; Esperschütz, J. ; Koubová, A. ; Buegger, F. ; Fischer, D. ; Radl, V. ; Fuß, R. ; Chronakova, A. ; Elhottova, D. ; Simek, M. ; Schloter, M.
Biogeosciences 9, 3891-3899 (2012)
While the importance of anaerobic methane oxidation has been reported for marine ecosystems, the role of this process in soils is still questionable. Grasslands used as pastures for cattle-overwintering show an increase in anaerobic soil micro-sites caused by animal treading and excrement deposition. Therefore anaerobic potential methane oxidation activity of severely impacted soil from a cattle winter pasture was investigated in an incubation experiment under anaerobic conditions using 13C-labeled methane. We were able to detect a high microbial activity utilizing CH4 as nutrient source shown by the respiration of 13CO2. Measurements of possible terminal electron acceptors for anaerobic oxidation of methane were carried out. Soil sulfate concentrations were too low to explain the oxidation of the amount of methane added, but enough nitrate and iron(III) were detected. However, only nitrate was consumed during the experiment. 13C-PLFA analyses clearly showed the utilization of CH4 as nutrient source mainly by organisms harbouring 16:1ω7 PLFAs. These lipids were found in Gram-negative microorganisms and anaerobes. The fact that these lipids are also typical for type I methanotrophs, known as aerobic methane oxidizers, might indicate a link between aerobic and anaerobic methane oxidation.
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Scientific Article
Agerer, R. ; Hartmann, A. ; Pritsch, K. ; Raidl, S. ; Schloter, M. ; Verma, R. ; Weigt, R.
In: Matyssek, R.* ; Schnyder, H.* ; Oßwald, W.* ; Ernst, D.* ; Munch, J.-C.* ; Pretzsch, H.* [Eds.]: Growth and Defence in Plants. Berlin: Springer, 2012. 213-242 (Ecol. Stud. ; 220)
The ectomycorrhizosphere is a heterogeneous and variable micro-environment, predominantly established by variously formed extramatrical mycelia (EMM) that emanate from the hyphal mantle of ectomycorrhizae that envelopes the short roots. The mycelia differ fungal species-dependent regarding range, density and differentiation. Contingent upon the amount of sugars available for the ectomycorrhizal fungi — controlled, e.g. by elevated above-ground concentrations of ozone or carbon dioxide exposure to host trees — an ectomycorrhizal community can change its total amount of EMM, leading to changes in space occupation, and consequently, to alterations in its capacity to explore and exploit soil resources. We quantify the exploration type specific space occupation under the influence of twice-ambient ozone concentrations and estimate the carbon cost the tree has to pay for. Further, we address enzymatic capacities of ectomycorrhizal communities and focus on bacteria being associated with the mycelium. Finally we discuss the impact of soil micro-niches on ectomycorrhizal communities and mention briefly the ectomycorrhizal competition with each other and with saprotrophic fungi.
Larionova, A.A. ; Stulin, A.F. ; Zanina, O.G. ; Yevdokimov, I.V. ; Khokhlova, O.S. ; Buegger, F. ; Schloter, M. ; Kudeyaro, V.N.
Eurasian Soil Sci. 45, 768-778 (2012)
The distribution of carbon in an agrochernozem’s profile was studied by the natural 13C abun dance method during the C3–C4 vegetation transition and the analysis of the soil phytolith complex under a continuous corn monoculture. A young pool of soil organic matter (SOM) formed during 43 years of monoc ulture growing was detected by the isotope analysis in the 0 to 60cm layer, while the analysis of the phytolith complex identified this pool deeper: corn phytoliths were detected in the 0 to 80cm layer. The maximum size of the young pool was found in the upper soil horizon; it reached 6.4% of the SOM in the 0 to 20cm layer. The apparent time of the SOM turnover was 635 and 2225 years in the 0 to 20 and 40 to 60cm layers, respectively. The high values of the mean residence time were related to the low input of plant residues to the soil at the growing of corn for silage and the high initial content of organic carbon in the chernozem. The changes in the isotope composition after the decalcification of the soil to remove carbonates and the variation of the δ13C in the corn biomass during the vegetation period significantly affected the calculated value of the mean residence time.
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Scientific Article
Kuffner, M. ; Hai, B. ; Rattei, T. ; Melodelima, C. ; Schloter, M. ; Zechmeister-Boltenstern, S. ; Jandl, R. ; Schindlbacher, A. ; Sessitsch, A.
FEMS Microbiol. Ecol. 82, 551-562 (2012)
Climate warming may induce shifts in soil microbial communities possibly altering the long-term carbon mineralization potential of soils. We assessed the response of the bacterial community in a forest soil to experimental soil warming (+4 °C) in the context of seasonal fluctuations. Three experimental plots were sampled in the fourth year of warming in summer and winter and compared to control plots by 16S rRNA gene pyrosequencing. We sequenced 17 308 amplicons per sample and analysed operational taxonomic units at genetic distances of 0.03, 0.10 and 0.25, with respective Good's coverages of 0.900, 0.977 and 0.998. Diversity indices did not differ between summer, winter, control or warmed samples. Summer and winter samples differed in community structure at a genetic distance of 0.25, corresponding approximately to phylum level. This was mainly because of an increase of Actinobacteria in winter. Abundance patterns of dominant taxa (> 0.06% of all reads) were analysed individually and revealed, that seasonal shifts were coherent among related phylogenetic groups. Seasonal community dynamics were subtle compared to the dynamics of soil respiration. Despite a pronounced respiration response to soil warming, we did not detect warming effects on community structure or composition. Fine-scale shifts may have been concealed by the considerable spatial variation.
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Scientific Article
Sharma, S. ; Mehta, R. ; Gupta, R. ; Schloter, M.
J. Microbiol. Methods 91, 62-64 (2012)
An improved protocol for extraction of prokaryotic mRNA from soil samples was developed by modifying the extraction procedure to obtain higher yields of mRNA and to reduce co-extraction of humic acids. The modified protocol was found to be more robust and efficient compared to the original protocol by Griffiths et al. (2000) without compromising with the quality and quantity of RNA.
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Scientific Article
Ollivier, J. ; Wanat, N. ; Austruy, A. ; Hitmi, A. ; Joussein, E. ; Welzl, G. ; Munch, J.-C. ; Schloter, M.
Microb. Ecol. 64, 1038-1046 (2012)
Mine wastes have been considered as a source of heavy metal (HM) contamination in the environment and negatively impact many important ecosystem services provided by soils. Plants like Miscanthus, which tolerate high HM concentrations in soil, are often used for phytoremediation and provide the possibility to use these soils at least for the production of energy crops. However, it is not clear if plant growth at these sites is limited by the availability of nutrients, mainly nitrogen, as microbes in soil might be affected by the contaminant. Therefore, in this study, we investigated in a greenhouse experiment the response of ammonia-oxidizing microbes in the root-rhizosphere complex of Miscanthus × giganteus grown in soils with different levels of long-term arsenic (As) and lead (Pb) contamination. Quantitative PCR of the ammonia monooxigenease gene (amoA) was performed to assess the abundance of ammonia-oxidizing bacteria (AOB) and archaea (AOA) at two different points of plant growth. Furthermore, bulk soil samples before planting were analyzed. In addition, terminal restriction fragment length polymorphism (T-RFLP) analysis was used to investigate the diversity of archaeal amoA amplicons. Whereas high concentrations of As and Pb in soil (83 and 15 g/kg, respectively) resulted independent from plant growth in a clear reduction of AOA and AOB compared to the control soils with lower HM contents, in soils with contamination levels of 10 g/kg As and 0.2 g/kg Pb, only AOB were negatively affected in bulk soil samples. Diversity analysis of archaeal amoA genes revealed clear differences in T-RFLP patterns in response to the degree of HM contamination. Therefore, our results could clearly prove the different response patterns of AOA and AOB in HM-contaminated soils and the development of archaeal amoA phylotypes which are more tolerant towards HMs in soil samples from the areas that were impacted the most by mining waste, which could contribute to functional redundancy of ammonia-oxidizing microbes in soils and stability of nitrification pattern.
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Scientific Article
Enowashu, E. ; Kandeler, E. ; Schloter, M. ; Rasche, F. ; Engel, M.
J. Microbiol. Methods 91, 14-21 (2012)
A new set of primers was developed allowing the specific detection of the pepN gene (coding for alanine aminopeptidase) from Gram-negative bacteria. The primers were designed in silico by sequence alignments based on available DNA sequence data. The PCR assay was validated using DNA from selected pure cultures. The analysis of gene libraries from extracted DNA from different soil samples revealed a high diversity of pepN related sequences mainly related to α-Proteobacteria. Most sequences obtained from clone libraries were closely related to already published sequences (<80% homology on amino acid level), which may be related to the conserved character of the amplified region of pepN. By linking the diversity data obtained by the clone library studies to potential enzymatic activities of alanine aminopeptidase, lowest diversity of pepN was found in those soil samples which displayed lowest activity levels, which confirms the importance of diversity for the ecosystem function mainly when transformation processes of complex molecules are studied.
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Scientific Article
Birkhofer, K. ; Schöning, I. ; Alt, F. ; Herold, N. ; Klarner, B. ; Maraun, M. ; Marhan, S. ; Oelmann, Y. ; Wubet, T. ; Yurkov, A. ; Begerow, D. ; Berner, D. ; Buscot, F. ; Daniel, R. ; Diekötter, T. ; Ehnes, R. B. ; Erdmann, G. ; Fischer, C. ; Fösel, B. ; Groh, J. ; Gutknecht, J. ; Kandeler, E. ; Lang, C. ; Lohaus, G. ; Meyer, A.H. ; Nacke, H. ; Näther, A. ; Overmann, J. ; Polle, A. ; Pollierer, M. M. ; Scheu, S. ; Schloter, M. ; Schulze, E.-D. ; Schulze, W. ; Weinert, J. ; Weisser, W. W. ; Wolters, V. ; Schrumpf, M.
PLoS ONE 7:e43292 (2012)
Very few principles have been unraveled that explain the relationship between soil properties and soil biota across large spatial scales and different land-use types. Here, we seek these general relationships using data from 52 differently managed grassland and forest soils in three study regions spanning a latitudinal gradient in Germany. We hypothesize that, after extraction of variation that is explained by location and land-use type, soil properties still explain significant proportions of variation in the abundance and diversity of soil biota. If the relationships between predictors and soil organisms were analyzed individually for each predictor group, soil properties explained the highest amount of variation in soil biota abundance and diversity, followed by land-use type and sampling location. After extraction of variation that originated from location or land-use, abiotic soil properties explained significant amounts of variation in fungal, meso- and macrofauna, but not in yeast or bacterial biomass or diversity. Nitrate or nitrogen concentration and fungal biomass were positively related, but nitrate concentration was negatively related to the abundances of Collembola and mites and to the myriapod species richness across a range of forest and grassland soils. The species richness of earthworms was positively correlated with clay content of soils independent of sample location and land-use type. Our study indicates that after accounting for heterogeneity resulting from large scale differences among sampling locations and land-use types, soil properties still explain significant proportions of variation in fungal and soil fauna abundance or diversity. However, soil biota was also related to processes that act at larger spatial scales and bacteria or soil yeasts only showed weak relationships to soil properties. We therefore argue that more general relationships between soil properties and soil biota can only be derived from future studies that consider larger spatial scales and different land-use types.
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Scientific Article
Schulz, S. ; Giebler, J. ; Chatzinotas, A. ; Wick, L.Y. ; Fetzer, I. ; Welzl, G. ; Harms, H. ; Schloter, M.
ISME J. 6, 1763-1774 (2012)
Alkanes are major constituents of plant-derived waxy materials. In this study, we investigated the abundance, community structure and activity of bacteria harbouring the alkane monooxygenase gene alkB, which catalyses a major step in the pathway of aerobic alkane degradation in the litter layer, the litter-soil interface and in bulk soil at three time points during the degradation of maize and pea plant litter (2, 8 and 30 weeks) to improve our understanding about drivers for microbial performance in different soil compartments. Soil cores of different soil textures (sandy and silty) were taken from an agricultural field and incubated at constant laboratory conditions. The abundance of alkB genes and transcripts (by qPCR) as well as the community structure (by terminal restriction fragment polymorphism fingerprinting) were measured in combination with the concentrations and composition of alkanes. The results obtained indicate a clear response pattern of all investigated biotic and abiotic parameters depending on the applied litter material, the type of soil used, the time point of sampling and the soil compartment studied. As expected the distribution of alkanes of different chain length formed a steep gradient from the litter layer to the bulk soil. Mainly in the two upper soil compartments community structure and abundance patterns of alkB were driven by the applied litter type and its degradation. Surprisingly, the differences between the compartments in one soil were more pronounced than the differences between similar compartments in the two soils studied. This indicates the necessity for analysing processes in different soil compartments to improve our mechanistic understanding of the dynamics of distinct functional groups of microbes.
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Scientific Article
Lyubenova, L. ; Pongrac, P. ; Vogel-Mikus, K. ; Mezek, G.K. ; Vavpetic, P. ; Grlj, N. ; Kump, P. ; Necemer, M. ; Regvar, M. ; Pelicon, P. ; Schröder, P.
Metallomics 4, 333-341 (2012)
Typha latifolia is a plant species widely used for phytoremediation. Accumulation, localization and distribution of Pb and mineral nutrients were investigated in roots, rhizomes and leaves of Typha latifolia grown at 0, 50, 100 and 250 mu M Pb concentrations in a pot experiment under controlled conditions. Bulk elemental concentrations were determined by X-ray fluorescence (XRF) spectroscopy whereas micro-proton-induced X-ray emission (micro-PIXE) was used for element localization in root and rhizome tissues. Gradual increase in bulk Pb concentrations was observed in Typha latifolia roots and rhizomes treated with increasing Pb concentrations, however in rhizomes Pb concentrations were an order of magnitude lower than in roots. In leaves Pb concentrations were around the limit of detection for XRF (similar to 20 mu g g(-1)). An increase in concentration of K and Ca in roots, rhizomes and leaves, of iron and zinc in roots and leaves, and of Mn in rhizomes was observed either at 50 and/or 100 mu M Pb treatments, whereas for K and Ca in roots, rhizomes and leaves, Fe and Zn in roots and leaves and Mn in rhizomes, or at 250 mu M Pb treatment the increase was seen for concentrations of Fe and Zn in rhizomes and Cu in roots. Mn concentrations decreased with Pb treatments in roots and leaves. Element localization using micro-PIXE analysis demonstrated Pb accumulation in epidermal and cortical tissues of treated roots and rhizomes, while in endodermis and vascular tissues Pb was not detected. A displacement of Ca from epidermal to cortical tissues was observed in Pb treated roots and rhizomes, pointing to cell wall immobilization of Pb as one of the tolerance mechanisms in Typha latifolia. High level of colocalization of Pb with P (r = 0.60), S (r = 0.37) and Zn (r = 0.70) was observed in Pb treated roots, while in rhizomes colocalization with the mentioned elements was still positive, but not that prominent. These results indicate that Pb may form complexes with phosphorus and sulfur compounds in roots and rhizomes, which may also represent attraction sites for binding Zn. Because of its large root and rhizome surface area acting as main sites for Pb adsorption, Typha latifolia may represent potentially efficient plant species for phytoremediation of Pb contaminated soils and waters.
Wissenschaftlicher Artikel
Scientific Article
Heuer, H. ; Kopmann, C. ; Zimmerling, U. ; Krögerrecklenfort, E. ; Kleineidam, K. ; Schloter, M. ; Top, E.M. ; Smalla, K.
In: Kenn, P.L.* ; Montforts, M.H.* [Eds.]: Antimicrobial Resistance in the Environment. Hoboken, NJ: Wiley-Blackwell, 2012. 453-463
  no Abstract
Timmers, R.A. ; Rothballer, M. ; Strik, D.P. ; Engel, M. ; Schulz, S. ; Schloter, M. ; Hartmann, A. ; Hamelers, B. ; Buisman, C.
Appl. Microbiol. Biotechnol. 94, 537-548 (2012)
The plant microbial fuel cell (PMFC) is a technology in which living plant roots provide electron donor, via rhizodeposition, to a mixed microbial community to generate electricity in a microbial fuel cell. Analysis and localisation of the microbial community is necessary for gaining insight into the competition for electron donor in a PMFC. This paper characterises the anode-rhizosphere bacterial community of a Glyceria maxima (reed mannagrass) PMFC. Electrochemically active bacteria (EAB) were located on the root surfaces, but they were more abundant colonising the graphite granular electrode. Anaerobic cellulolytic bacteria dominated the area where most of the EAB were found, indicating that the current was probably generated via the hydrolysis of cellulose. Due to the presence of oxygen and nitrate, short-chain fatty acid-utilising denitrifiers were the major competitors for the electron donor. Acetate-utilising methanogens played a minor role in the competition for electron donor, probably due to the availability of graphite granules as electron acceptors.
Wissenschaftlicher Artikel
Scientific Article
Elhottova, D. ; Koubová, A. ; Simek, M. ; Cajthaml, T. ; Jirout, J. ; Esperschütz, J.A. ; Schloter, M. ; Gattinger, A.
Appl. Soil Ecol. 58, 56-65 (2012)
The present field study documents substantial changes in the soil microbial community (SMC) and organic matter (SOM) in an upland pasture soil resulting from 10 years of “cattle outdoor over-wintering practice”. Soils from a long-term investigated pasture area were compared under three different levels of cattle impact (SI – severe, MI – moderate, NI – no impact). Extended polar lipids analysis (PLA) confirmed a qualitatively new microbial community profile and a several-fold increase of the microbial biomass in the impacted soils (SI) compared to the control NI soil. The new SMC was derived from cattle intestine microorganisms, typical by increased content of archaeal phospholipid ether lipids and by new fatty acids indicative for bacterial and fungal fecal anaerobes. A quality of the SI-SOM, evaluated by the relative content of the pyrolytic fragments profile was more similar to the cattle excrements than to the MI and NI soils, and an organic carbon content of the SI soil was not more than three times higher in comparison to the control NI soil. The quality and quantity of the SOM as well as the SMC in both, the most impacted SI and the control NI soils, were stable in contrast to the moderately impacted MI soil. During the growing season, the MI soil lost 75% of the Corg and 65% of the soil microbial biomass that had accumulated during winter; its aromatic-rich-SOM showed transformation into SOM, enriched by N, P-organic derivates. This transformation was positively correlated to a significant recovery of the actinobacteria and reduction of anaerobic microorganisms during the vegetation season. Results in this study showed that the stability of the soil microbial changes due to the cattle outdoor over-wintering husbandry depended on the stability of the quantitative and qualitative changes of the SOM.
Wissenschaftlicher Artikel
Scientific Article
Müller-Niggemann, C. ; Bannert, A. ; Schloter, M. ; Lehndorff, E. ; Schwark, L.
Biogeosciences 9, 1237-1251 (2012)
In order to assess the intrinsic heterogeneity of paddy soils, a set of biogeochemical soil parameters was investigated in five field replicates of seven paddy fields (50, 100, 300, 500, 700, 1000, and 2000 yr of wetland rice cultivation), one flooded paddy nursery, one tidal wetland (TW), and one freshwater site (FW) from a coastal area at Hangzhou Bay, Zhejiang Province, China. All soils evolved from a marine tidal flat substrate due to land reclamation. The biogeochemical parameters based on their properties were differentiated into (i) a group behaving conservatively (TC, TOC, TN, TS, magnetic susceptibility, soil lightness and colour parameters, δ13C, δ15N, lipids and n-alkanes) and (ii) one encompassing more labile properties or fast cycling components (Nmic, Cmic, nitrate, ammonium, DON and DOC). The macroscale heterogeneity in paddy soils was assessed by evaluating intra- versus inter-site spatial variability of biogeochemical properties using statistical data analysis (descriptive, explorative and non-parametric). Results show that the intrinsic heterogeneity of paddy soil organic and minerogenic components per field is smaller than between study sites. The coefficient of variation (CV) values of conservative parameters varied in a low range (10% to 20%), decreasing from younger towards older paddy soils. This indicates a declining variability of soil biogeochemical properties in longer used cropping sites according to progress in soil evolution. A generally higher variation of CV values (>20–40%) observed for labile parameters implies a need for substantially higher sampling frequency when investigating these as compared to more conservative parameters. Since the representativeness of the sampling strategy could be sufficiently demonstrated, an investigation of long-term carbon accumulation/sequestration trends in topsoils of the 2000 yr paddy chronosequence under wetland rice cultivation restricted was conducted. Observations cannot be extrapolated to global scale but with coastal paddy fields developed on marine tidal flat substrates after land reclamation in the Zhejiang Province represent a small fraction (<1%) of the total rice cropping area. The evolutionary trend showed that the biogeochemical signatures characteristic for paddy soils were fully developed in less than 300 yr since onset of wetland rice cultivation. A six-fold increase of topsoil TOC suggests a substantial gain in CO2 sequestration potential when marine tidal wetland substrate developed to 2000 yr old paddy soil.
Wissenschaftlicher Artikel
Scientific Article
Li, D. ; Rothballer, M. ; Engel, M. ; Hoser, J.D.S. ; Schmidt, T. ; Kuttler, C. ; Schmid, M. ; Schloter, M. ; Hartmann, A.
FEMS Microbiol. Ecol. 79, 751-762 (2012)
Acidovorax radicis N35, isolated from surface-sterilized wheat roots (Triticum aestivum), showed irreversible phenotypic variation in nutrient broth, resulting in a differing colony morphology. In addition to the wild-type form (rough colony type), a phenotypic variant form (smooth colony type) appeared at a frequency of 3.2 × 10(-3) per cell per generation on NB agar plates. In contrast to the N35 wild type, the variant N35v showed almost no cell aggregation and had lost its flagella and swarming ability. After inoculation, only the wild-type N35 significantly promoted the growth of soil-grown barley plants. After co-inoculation of axenically grown barley seedlings with differentially fluorescently labeled N35 and N35v cells, decreased competitive endophytic root colonization in the phenotypic variant N35v was observed using confocal laser scanning microscopy. In addition, 454 pyrosequencing of both phenotypes revealed almost identical genomic sequences. The only stable difference noted in the sequence of the phenotype variant N35v was a 16-nucleotide deletion identified in a gene encoding the mismatch repair protein MutL. The deletion resulted in a frameshift that revealed a new stop codon resulting in a truncated MutL protein missing a functional MutL C-terminal domain. The mutation was consistent in all investigated phenotype variant cultures and might be responsible for the observed phenotypic variation in A. radicis N35.
Wissenschaftlicher Artikel
Scientific Article
Fischer, D. ; Pfitzner, B. ; Schmid, M. ; Simoes-Araujo, J.L. ; Reis, V.M. ; Pereira, W. ; Ormeno-Orrillo, E. ; Hai, B. ; Hofmann, A. ; Schloter, M. ; Martinez-Romero, E. ; Baldani, J.I. ; Hartmann, A.
Plant Soil 356, 83-99 (2012)
To identify active diazotrophs in sugarcane, 16S rRNA and nifH transcript analyses were applied. This should help to better understand the basis of the biological nitrogen fixation (BNF) activity of a high nitrogen fixing sugarcane variety. A field experiment using the sugarcane variety RB 867515 was conducted in Seropédica, RJ, Brazil, receiving the following treatments: unfertilised and fertilised controls without inoculation, unfertilised with inoculation. The five-strain mixture developed by EMBRAPA-CNPAB was used as inoculum. Root and leaf sheath samples were harvested in the third year of cultivation to analyse the 16S rRNA and nifH transcript diversity. In addition to nifH expression from Gluconacetobacter spp. and Burkholderia spp., a wide diversity of nifH sequences from previously uncharacterised Ideonella/Herbaspirillum related phylotypes in sugarcane shoots as well as Bradyrhizobium sp. and Rhizobium sp. in roots was found. These results were confirmed using 16S cDNA analysis. From the inoculated bacteria, only nifH transcripts from G. diazotrophicus and B. tropica were detected in leaf sheaths and roots. Known as well as yet uncultivated diazotrophs were found active in sugarcane roots and stems using molecular analyses. Two strains of the inoculum mix were identified at the late summer harvest.
Wissenschaftlicher Artikel
Scientific Article
Nehnevajova, E. ; Lyubenova, L. ; Herzig, R. ; Schröder, P. ; Schwitzguébel, J.-P. ; Schmülling, T.
Environ. Exp. Bot. 76, 39-48 (2012)
Sunflower mutant lines with an enhanced tolerance and metal accumulation capacity obtained by mutation breeding have been proposed for Zn, Cd and Cu removal from metal-contaminated soils in previous studies. However, soils contaminated with trace elements induce various biochemical alterations in plants leading to oxidative stress. There is a lack of knowledge concerning the metal accumulation and antioxidant responses during the growth and development of sunflowers. This study, therefore, aimed to characterise metal accumulation and possible metal detoxification mechanisms in young seedlings and adult sunflowers. Beside the inbred line, two mutant lines with an improved growth and enhanced metal uptake capacity on a metal contaminated soil were investigated in more detail. Sunflowers cultivated on a metal-contaminated soil in the greenhouse showed a decrease in shoot biomass and chlorophyll concentration in two different developmental stages. Adult sunflowers showed a lower sensitivity to metal toxicity than young seedlings, whereas mutant lines were more tolerant to metal stress than the control. Mutant lines also produced a higher amount of carotenoids on a metal contaminated soil than on the control soil, indicating a possible protective mechanism of sunflower mutants against oxidative stress caused by Cd and excess Zn. Heavy metals primarily increased the activity of antioxidant enzymes involved in the ascorbate–glutathione cycle in sunflower leaves. Activity of dehydroascorbate reductase (DHAR), monodehydroascorbate reductase (MDHAR) and glutathione reductase (GR) was strongly increased in young seedlings exposed to heavy metals. The enzyme activities were even more pronounced in mutant lines. A significantly increased ascorbate peroxidase (APOX) activity in adult sunflowers exposed to heavy metals indicated an elevated use of ascorbate after a longer exposure to metal stress. An increased antioxidant level corresponded to a high Cd and Zn accumulation in young and adult sunflowers.Metal distribution, zinc translocation in particular, from the root into the shoot tissue obviously increased during sunflower growth and ripening. Altogether, these results suggest that sunflower plants, primarily the mutant lines, possess an efficient defence mechanism against oxidative stress caused by metal toxicity. A good tolerance of sunflowers toward heavy metals coupled with an increased metal accumulation capacity might contribute to an efficient removal of heavy metals from a polluted area.
Wissenschaftlicher Artikel
Scientific Article
2011
Gubry-Rangin, C. ; Hai, B. ; Quince, C. ; Engel, M. ; Thomson, B.C. ; James, P. ; Schloter, M. ; Griffiths, R.I. ; Prosser, J.I. ; Nicol, G.W.
Proc. Natl. Acad. Sci. U.S.A. 108, 21206-21211 (2011)
Soil pH is a major determinant of microbial ecosystem processes and potentially a major driver of evolution, adaptation, and diversity of ammonia oxidizers, which control soil nitrification. Archaea are major components of soil microbial communities and contribute significantly to ammonia oxidation in some soils. To determine whether pH drives evolutionary adaptation and community structure of soil archaeal ammonia oxidizers, sequences of amoA, a key functional gene of ammonia oxidation, were examined in soils at global, regional, and local scales. Globally distributed database sequences clustered into 18 well-supported phylogenetic lineages that dominated specific soil pH ranges classified as acidic (pH <5), acido-neutral (5≤ pH <7), or alkalinophilic (pH ≥7). To determine whether patterns were reproduced at regional and local scales, amoA gene fragments were amplified from DNA extracted from 47 soils in the United Kingdom (pH 3.5-8.7), including a pH-gradient formed by seven soils at a single site (pH 4.5-7.5). High-throughput sequencing and analysis of amoA gene fragments identified an additional, previously undiscovered phylogenetic lineage and revealed similar pH-associated distribution patterns at global, regional, and local scales, which were most evident for the five most abundant clusters. Archaeal amoA abundance and diversity increased with soil pH, which was the only physicochemical characteristic measured that significantly influenced community structure. These results suggest evolution based on specific adaptations to soil pH and niche specialization, resulting in a global distribution of archaeal lineages that have important consequences for soil ecosystem function and nitrogen cycling.
Wissenschaftlicher Artikel
Scientific Article
Peters, A. ; Döring, A. ; Ladwig, K.-H. ; Meisinger, C. ; Linkohr, B. ; Autenrieth, C. ; Baumeister, S.E. ; Behr, J. ; Bergner, A. ; Bickel, H. ; Bidlingmaier, M. ; Dias, A. ; Emeny, R.T. ; Fischer, B. ; Grill, E. ; Gorzelniak, L. ; Hänsch, H. ; Heidbreder, S. ; Heier, M. ; Horsch, A. ; Huber, D. ; Huber, R.M. ; Jörres, R.A. ; Kääb, S. ; Karrasch, S. ; Kirchberger, I. ; Klug, G. ; Kranz, B. ; Kuch, B. ; Lacruz, M.E. ; Lang, O. ; Mielck, A. ; Nowak, D. ; Perz, S. ; Schneider, A.E. ; Schulz, S. ; Müller, M. ; Seidl, H. ; Strobl, R. ; Thorand, B. ; Wende, R. ; Weidenhammer, W. ; Zimmermann, A.-K. ; Wichmann, H.-E. ; Holle, R.
Z. Gerontol. Geriatr. 44, Suppl. 2, 2, 41-54 (2011)
Hintergrund. Das KORA-Age-Verbundprojekt hat zum Ziel, die Determinanten und Folgen von Multimorbidität im Alter zu ermitteln und nach Faktoren des erfolgreichen Alterns in der Allgemeinbevölkerung zu suchen. Material und Methoden. Die KORA-Age-Kohorte besteht aus 9197 Personen, die 1943 oder früher geboren wurden und Teilnehmer der KORA-Kohorte (KORA: Kooperative Gesundheitsforschung in der Region Augsburg) zwischen 1984 und 2001 waren. In der randomisierten Interventionsstudie KORINNA (Koronarinfarktnachbehandlung im Alter) wurde ein von Krankenschwestern durchgeführtes Case-Management-Programm mit 338 Herzinfarktpatienten getestet und gesundheitsökonomisch bewertet. Ergebnisse. In der KORA-Age-Kohorte wurden 2734 Todesfälle registriert, 4565 Personen nahmen an einer schriftlichen Befragung und 4127 Personen an einem Telefoninterview teil (Teilnahme: 76,2% bzw. 68,9%). Zusätzlich wurde eine alters- und geschlechtsstratifizierte Stichprobe von 1079 Personen untersucht (Teilnahme: 53,8%). Schlussfolgerung. Das KORA-Age-Verbundprojekt untersuchte eine große bevölkerungsbezogene Stichprobe älterer Menschen, die Aufschluss über die Verteilung und Determinanten von Multimorbidität und erfolgreichem Altern gibt.
Wissenschaftlicher Artikel
Scientific Article
Schloter, M.
In: Huang, P.M.* ; Li, Y.* ; Sumner, M.E.* [Eds.]: Handbook of soil sciences. Properties and processes. 2nd Edition. Boca Raton: CRC Press, 2011. 24.11-24.18
no abstract
Rothballer, M. ; Engel, M. ; Strik, D.P. ; Timmers, R. ; Schloter, M. ; Hartmann, A.
Commun. Agric. Appl. Biol. Sci. 76, 31-32 (2011)
Wissenschaftlicher Artikel
Scientific Article
Matucha, M. ; Schröder, P.
In: Schröder, P.* ; Collins, C.D.* [Eds.]: Organic Xenobiotics and Plants. From Mode of Action to Ecophysiology. Dordrecht: Springer, 2011. 87-103 (Plant Ecophysiology ; 8, Part 2)
Trichloroacetic acid (TCA) is a ubiquitous phytotoxic substance that oeeurs at various levels in the environment. The last eentury, it was produeed and used in agriculture as herbicide against perennial grasses for same time, before it was found as seeondary atmospherie pollutant. It was considered a reason of coniferous forest decline. TCA was further found among produets of disinfeetion of drinking water and of delignifieation of cellulose pulp by chlorine. In addition to these anthropogenie sources of TCA, is has been found to be formed in the forest ecosystem as a result of microbial chlorination of humic substances that subsequently yield TCA in the soil. TCA may be eonsidered important intermediate of soil organic matter degradation and belongs thus to naturally-produeed organohalogens and at thc same time to relevant xenobiotics and stressors affecting plants in thc fafest ecosystem. Hs role in the fafest ecosystem is clearly shown.
Schröder, P. ; Hesselmann, K. ; Protivova, V. ; Stampfl, A. ; Debus, R.
In: Proceedings (12th International Conference on Environmental Science and Technology, 8-10 Sept 2011, Rhodes, Greece). Athens: Global NEST, 2011.:A-1679
Particles in nanometre size - called ultrafine or nanoparticles - enter the environment from diesel exhausts, printer dusts, with fty ashes, and industrial emissions. A growing proportion is even prepared artificially lor their advantageous leatures lor electronics, biomedicine, cosmetics and car manufacturing. Their uncontrolled emission from a plethora 01 sources has lead to an elevation 01 their concentralion in the atmosphere. Concem has been voiced that lhey may influence human heallh, and lhe health 01 the environment. Whereas medical studies have begun to identify positive and negative effects 01 UFP, until now dala on lheir influence on plants are scarce. Regarding their ubiquitous presence, a positive or negative influence on plants can not be excluded Plant cells were exposed to nanoparticles (TiO" SiO" carbon black (Printex P9lJ)) in !wo concentrations each. UFP effects on root elongation and pollen tube growlh were invesligated. The results indicate varying impacts 01 the UFPs. Root elongation showed a substantial inhibition under lhe treatment 01 TiO, and AerosiL Printex had no visible effect The pollen tube growlh test didn't detect any significant phylotoxicily for all UFPs Furthermore, stress enzyme activity in mesophylls after ovemight incubation with nanoparticles was detected spectrophotometrically The enzymes under test were glutathione S - transIerase (GST), glutathione reductase (GR), peroxidase (POX) and catalase (CAT) Higher activilies 01 stress enzymes were detected especially in treated sampies 01 barley leal mesophyll. In the epidermis of onion, TiO, nanoparticles caused higher activity 01 GST (substrate CONS} compared to controls Further studies are underway to elucidate the selective plant stress reaction and to quantify detrimental effects on crops and ornamental plants.
Bartha, B. ; Huber, C. ; Schröder, P.
In: Proceedings (12th International Conference on Environmental Science and Technology, 08-10 September 2011, Rhodes, Greece). Athen: Global NEST, 2011.:A-166
Personal care products, medicaments and !tIeir metabolites are delected ubiquitously in the aquatic environment and increasingty polluling our drinking waler supplies. Allhough the need lor high quality drinking water has been recognized as one 01 the most challenging problems of our times, onty litlle knowledge exists on the impact of pharmaceuticals on eoosyslems, animals and man Paracetamol is one of lhe oompounds that can be regularty lound in the European waler cyde and are delecled in Iow 1-'9L-' levels in influents and effluents of waste water treatment plants and surfuce walers as weiL It is a non steroidal anti-inflammatory drug, extensivety used in human medication and tends to be relativety persistent in the environment We invesligated the late and metabolism 01 paracetamol in plantlissues using the typical wetland macrophyte Typha latifolia. Dur resutts indicate that T. lalilolia is able to lake up and detoxify pharmaceuticals we delected the drug in different plant tissues and idenlified ils metabolites with LeiMS analysis The formalion 01 !wo independentty lormed metabolites in plants again revealed strong similarilies be!ween plant and mammalian detoxification systems. The deloxificalion via glucuronisation in mammals is minored by gluoosidation 01 xenobiotics in plants. Furthermore a glulathione oonjugate is lormed, that is described also in mammalians These findings under1ine the great potential 01 plants lor wasle waler treatments in oonstructed weUands and again show the f1exibility of plants in the process.
Bannert, A. ; Kleineidam, K. ; Wissing, L. ; Mueller-Niggemann, C. ; Vogelsang, V. ; Welzl, G. ; Cao, Z. ; Schloter, M.
Appl. Environ. Microbiol. 77, 6109-6116 (2011)
In many areas of China, tidal wetlands have been converted into agricultural land for rice cultivation. However, the consequences of land use changes for soil microbial communities are poorly understood. Therefore, we investigated bacterial and archaeal communities involved in inorganic nitrogen turnover (nitrogen fixation, nitrification, and denitrification) based on abundances and relative species richness of the corresponding functional genes along a soil chronosequence ranging between 50 and 2,000 years of paddy soil management compared to findings for a tidal wetland. Changes in abundance and diversity of the functional groups could be observed, reflecting the different chemical and physical properties of the soils, which changed in terms of soil development. The tidal wetland was characterized by a low microbial biomass and relatively high abundances of ammonia-oxidizing microbes. Conversion of the tidal wetlands into paddy soils was followed by a significant increase in microbial biomass. Fifty years of paddy management resulted in a higher abundance of nitrogen-fixing microbes than was found in the tidal wetland, whereas dominant genes of nitrification and denitrification in the paddy soils showed no differences. With ongoing rice cultivation, copy numbers of archaeal ammonia oxidizers did not change, while that of their bacterial counterparts declined. The nirK gene, coding for nitrite reductase, increased with rice cultivation time and dominated its functionally redundant counterpart, nirS, at all sites under investigation. Relative species richness showed significant differences between all soils with the exception of the archaeal ammonia oxidizers in the paddy soils cultivated for 100 and 300 years. In general, changes in diversity patterns were more pronounced than those in functional gene abundances.
Wissenschaftlicher Artikel
Scientific Article
Pérez-de-Mora, A. ; Engel, M. ; Schloter, M.
Microb. Ecol. 62, 959-972 (2011)
Unraveling functional genes related to biodegradation of organic compounds has profoundly improved our understanding of biological remediation processes, yet the ecology of such genes is only poorly understood. We used a culture-independent approach to assess the abundance and diversity of bacteria catalyzing the degradation of n-alkanes with a chain length between C(5) and C(16) at a forest site co-contaminated with mineral oil hydrocarbons and metals for nearly 60 years. The alkB gene coding for a rubredoxin-dependent alkane monooxygenase enzyme involved in the initial activation step of aerobic aliphatic hydrocarbon metabolism was used as biomarker. Within the area of study, four different zones were evaluated: one highly contaminated, two intermediately contaminated, and a noncontaminated zone. Contaminant concentrations, hydrocarbon profiles, and soil microbial respiration and biomass were studied. Abundance of n-alkane-degrading bacteria was quantified via real-time PCR of alkB, whereas genetic diversity was examined using molecular fingerprints (T-RFLP) and clone libraries. Along the contamination plume, hydrocarbon profiles and increased respiration rates suggested on-going natural attenuation at the site. Gene copy numbers of alkB were similar in contaminated and control areas. However, T-RFLP-based fingerprints suggested lower diversity and evenness of the n-alkane-degrading bacterial community in the highly contaminated zone compared to the other areas; both diversity and evenness were negatively correlated with metal and hydrocarbon concentrations. Phylogenetic analysis of alkB denoted a shift of the hydrocarbon-degrading bacterial community from Gram-positive bacteria in the control zone (most similar to Mycobacterium and Nocardia types) to Gram-negative genotypes in the contaminated zones (Acinetobacter and alkB sequences with little similarity to those of known bacteria). Our results underscore a qualitative rather than a quantitative response of hydrocarbon-degrading bacteria to the contamination at the molecular level.
Wissenschaftlicher Artikel
Scientific Article
Roth, P.J. ; Lehndorff, E. ; Cao, Z.H. ; Zhuang, S.Y. ; Bannert, A. ; Wissing, L. ; Schloter, M. ; Kögel-Knabner, I. ; Amelung, W.
Glob. Change Biol. 17, 3405-3417 (2011)
Lowland rice paddy soils may accumulate significant amounts of organic matter. Our aim was to investigate the role of prolonged paddy management on the nitrogen (N) status of the soils, and to elucidate the contribution of bacteria and fungi to long-term N accumulation processes. For this purpose, we sampled a chronosequence of 0-2000 years of rice cropping with adjacent non-paddy systems in the Bay of Hangzhou, China. The samples were analyzed for bulk density, total, mineral and microbial N (N(mic)), and amino sugars as markers for microbial residues. The results showed that during the first 100 years of land embankment, both paddy and non-paddy soils accumulated N at a rate of up to 61 and 77 kg ha(-1) per annum, reaching steady-state conditions after 110-172 years, respectively. Final N stocks in paddy fields exceeded those of the non-paddies by a factor of 1.3. The contribution of amino sugars to total N increased to a maximum of 34 g N kg(-1) N in both land-use systems, highlighting a significant accumulation of N in microbial residues of the surface soils. Correspondingly, the ratio of N(mic) to microbial residue-N decreased to a constant value. In the paddy subsoils, we found that bacterial residues particularly contributed to the pool of microbial residue-N. Nevertheless, the absolute contents of amino sugars in paddy subsoils decreased during the last 1700 years of the chronosequence. We conclude that under paddy cultivation, soil microorganisms may accumulate parts of this N in their residues despite low overall N availability. However, this N accumulation is limited to initial stages of paddy soil development and restricted to the surface horizons, thus challenging its sustainability with future land-use changes.
Wissenschaftlicher Artikel
Scientific Article
Soler Artigas, M. ; Wain, L.V. ; Repapi, E. ; Obeidat, M. ; Sayers, I. ; Burton, P.R ; Johnson, T. ; Zhao, J.H. ; Albrecht, E. ; Dominiczak, A.F. ; Kerr, S.M. ; Smith, B.H. ; Cadby, G. ; Hui, J. ; Palmer, L.J. ; Hingorani, A.D. ; Wannamethee, S.G. ; Whincup, P.H. ; Ebrahim, S. ; Smith, G.D. ; Barroso, I. ; Loos, R.J. ; Wareham, N.J. ; Cooper, C. ; Dennison, E. ; Shaheen, S.O. ; Liu, J.Z. ; Marchini, J ; Medical Research Council NSHD Respiratory Study Team () ; Dahgam, S. ; Naluai, A.T. ; Olin, A.C. ; Karrasch, S. ; Heinrich, J. ; Schulz, S. ; McKeever, T.M. ; Pavord, I.D. ; Heliövaara, M. ; Ripatti, S. ; Surakka, I. ; Blakey, J.D. ; Kähönen, M. ; Britton, J.R. ; Nyberg, F. ; Holloway, J.W. ; Lawlor, D.A. ; Morris, R.W. ; James, A.L. ; Jackson, C.M. ; Hall, I.P. ; Tobin, M.D ; SpiroMeta Consortium ()
Am. J. Respir. Crit. Care Med. 184, 786-795 (2011)
RATIONALE: Genomic loci are associated with FEV1 or the ratio of FEV1 to FVC in population samples, but their association with chronic obstructive pulmonary disease (COPD) has not yet been proven, nor have their combined effects on lung function and COPD been studied. OBJECTIVES: To test association with COPD of variants at five loci (TNS1, GSTCD, HTR4, AGER, and THSD4) and to evaluate joint effects on lung function and COPD of these single-nucleotide polymorphisms (SNPs), and variants at the previously reported locus near HHIP. METHODS: By sampling from 12 population-based studies (n = 31,422), we obtained genotype data on 3,284 COPD case subjects and 17,538 control subjects for sentinel SNPs in TNS1, GSTCD, HTR4, AGER, and THSD4. In 24,648 individuals (including 2,890 COPD case subjects and 13,862 control subjects), we additionally obtained genotypes for rs12504628 near HHIP. Each allele associated with lung function decline at these six SNPs contributed to a risk score. We studied the association of the risk score to lung function and COPD. MEASUREMENTS AND MAIN RESULTS: Association with COPD was significant for three loci (TNS1, GSTCD, and HTR4) and the previously reported HHIP locus, and suggestive and directionally consistent for AGER and TSHD4. Compared with the baseline group (7 risk alleles), carrying 10-12 risk alleles was associated with a reduction in FEV1 (β = -72.21 ml, P = 3.90 × 10(-4)) and FEV1/FVC (β = -1.53%, P = 6.35 × 10(-6)), and with COPD (odds ratio = 1.63, P = 1.46 × 10(-5)) CONCLUSIONS: Variants in TNS1, GSTCD, and HTR4 are associated with COPD. Our highest risk score category was associated with a 1.6-fold higher COPD risk than the population average score.
Wissenschaftlicher Artikel
Scientific Article
Jentsch, A. ; Kreyling, J. ; Elmer, M. ; Gellesch, E. ; Glaser, B. ; Grant, K. ; Hein, R. ; Lara, M. ; Mirzae, H. ; Nadler, S.E. ; Nagy, L. ; Otieno, D. ; Pritsch, K. ; Rascher, U. ; Schadler, M. ; Schloter, M. ; Singh, B.K. ; Stadler, J. ; Walter, J. ; Wellstein, C. ; Wöllecke, J. ; Beierkuhnlein, C.
J. Ecol. 99, 689-702 (2011)
P>1. Studying the effects of climate or weather extremes such as drought and heat waves on biodiversity and ecosystem functions is one of the most important facets of climate change research. In particular, primary production is amounting to the common currency in field experiments world-wide. Rarely, however, are multiple ecosystem functions measured in a single study in order to address general patterns across different categories of responses and to analyse effects of climate extremes on various ecosystem functions. We set up a long-term field experiment, where we applied recurrent severe drought events annually for five consecutive years to constructed grassland communities in central Europe. The 32 response parameters studied were closely related to ecosystem functions such as primary production, nutrient cycling, carbon fixation, water regulation and community stability.Surprisingly, in the face of severe drought, above- and below-ground primary production of plants remained stable across all years of the drought manipulation. 4. Yet, severe drought significantly reduced below-ground performance of microbes in soil indicated by reduced soil respiration, microbial biomass and cellulose decomposition rates as well as mycorrhization rates. Furthermore, drought reduced leaf water potential, leaf gas exchange and leaf protein content, while increasing maximum uptake capacity, leaf carbon isotope signature and leaf carbohydrate content. With regard to community stability, drought induced complementary plant-plant interactions and shifts in flower phenology, and decreased invasibility of plant communities and primary consumer abundance. Synthesis. Our results provide the first field-based experimental evidence that climate extremes initiate plant physiological processes, which may serve to regulate ecosystem productivity. A potential reason for different dynamics in various ecosystem services facing extreme climatic events may lie in the temporal hierarchy of patterns of fast versus slow response. Such data on multiple response parameters within climate change experiments foster the understanding of mechanisms of resilience, of synergisms or decoupling of biogeochemical processes, and of fundamental response dynamics to drought at the ecosystem level including potential tipping points and thresholds of regime shift. Future work is needed to elucidate the role of biodiversity and of biotic interactions in modulating ecosystem response to climate extremes.
Wissenschaftlicher Artikel
Scientific Article
Pritsch, K. ; Courty, .P.E. ; Churin, J.L. ; Cloutier-Hurteau, B. ; Ali, MA. ; Damon, C. ; Duchemin, M. ; Egli, S. ; Ernst, J. ; Fraissinet-Tachet, L. ; Kuhar, F. ; Legname, E. ; Marmeisse, R. ; Müller, A. ; Nikolova, P. ; Peter, M. ; Plassard, C. ; Richard, F. ; Schloter, M. ; Selosse, M.A. ; Franc, A. ; Garbaye, J.
Mycorrhiza 21, 589-600 (2011)
The aim of a joint effort by different research teams was to provide an improved procedure for enzyme activity profiling of field-sampled ectomycorrhizae, including recommendations on the best conditions and maximum duration for storage of ectomycorrhizal samples. A more simplified and efficient protocol compared to formerly published procedures was achieved by using manufactured 96-filter plates in combination with a vacuum manifold and by optimizing incubation times. Major improvements were achieved by performing the series of eight enzyme assays with a single series of root samples instead of two series, reducing the time needed for sample preparation, minimizing error-prone steps such as pipetting and morphotyping, and facilitating subsequent DNA analyses due to the reduced sequencing effort. The best preservation of samples proved to be storage in soil at 4-6 °C in the form of undisturbed soil cores containing roots. Enzyme activities were maintained for up to 4 weeks under these conditions. Short-term storage of washed roots and ectomycorrhizal tips overnight in water did not cause substantial changes in enzyme activity profiles. No optimal means for longer-term storage by freezing at -20 °C or storage in 100% ethanol were recommended.
Wissenschaftlicher Artikel
Scientific Article
Artigas, M.S. ; Loth, D.W. ; Wain, L.V. ; Gharib, S.A. ; Obeidat, M. ; Tang, W. ; Zhai, G. ; Zhao, J.H. ; Smith, A.V. ; Huffman, J.E. ; Albrecht, E. ; Jackson, C.M. ; Evans, D.M. ; Cadby, G. ; Fornage, M. ; Manichaikul, A. ; Lopez, L.M. ; Johnson, T. ; Aldrich, M.C. ; Aspelund, T. ; Barroso, I. ; Campbell, H. ; Cassano, P.A. ; Couper, D.J. ; Eiriksdottir, G. ; Franceschini, N. ; Garcia, M. ; Gieger, C. ; Gislason, G.K. ; Grkovic, I. ; Hammond, C.J. ; Hancock, D.B. ; Harris, T.B. ; Ramasamy, A. ; Heckbert, S.R. ; Heliövaara, M. ; Homuth, G. ; Hysi, P.G. ; James, A.L. ; Jankovic, S. ; Joubert, B.R. ; Karrasch, S. ; Klopp, N. ; Koch, B. ; Kritchevsky, S.B. ; Launer, L.J. ; Liu, Y. ; Loehr, L.R. ; Lohman, K. ; Loos, R.J. ; Lumley, T. ; Al Balushi, K.A. ; Ang, W.Q. ; Barr, R.G. ; Beilby, J. ; Blakey, J.D. ; Boban, M. ; Boraska, V. ; Brisman, J. ; Britton, J.R. ; Brusselle, G.G. ; Cooper, C. ; Curjuric, I. ; Dahgam, S. ; Deary, I.J. ; Ebrahim, S. ; Eijgelsheim, M. ; Francks, C. ; Gaysina, D. ; Granell, R. ; Gu, X. ; Hankinson, J.L. ; Hardy, R. ; Harris, SE. ; Henderson, J. ; Henry, A. ; Hingorani, A.D. ; Hofman, A. ; Holt, P.G. ; Hui, J. ; Hunter, M.L. ; Imboden, M. ; Jameson, K.A. ; Kerr, S.M. ; Kolcic, I. ; Kronenberg, F. ; Liu, J.Z. ; Marchini, J. ; McKeever, T. ; Morris, A.D. ; Olin, A.C. ; Porteous, D.J. ; Postma, D.S. ; Rich, S.S. ; Ring, S.M. ; Rivadeneira, F. ; Rochat, T. ; Sayer, A.A. ; Sayers, I. ; Sly, P.D. ; Smith, G.D. ; Sood, A. ; Starr, J.M. ; Uitterlinden, A.G. ; Vonk, J.M. ; Wannamethee, S.G. ; Whincup, P.H. ; Wijmenga, C. ; Williams, O.D. ; Wong, A. ; Mangino, M. ; Marciante, K.D. ; McArdle, W.L. ; Meibohm, B. ; Morrison, A.C. ; North, K.E. ; Omenaas, E. ; Palmer, L.J. ; Pietiläinen, K.H. ; Pin, I. ; Polasek, O. ; Pouta, A. ; Psaty, B.M. ; Hartikainen, A.L. ; Rantanen, T. ; Ripatti, S. ; Rotter, J.I. ; Rudan, I. ; Rudnicka, A.R. ; Schulz, S. ; Shin, S.Y. ; Spector, T.D. ; Surakka, I. ; Vitart, V. ; Völzke, H. ; Wareham, N.J. ; Warrington, N.M. ; Wichmann, H.-E. ; Wild, S.H. ; Wilk, J.B. ; Wjst, M. ; Wright, A.F. ; Zgaga, L. ; Zemunik, T. ; Pennell, C.E. ; Nyberg, F. ; Kuh, D. ; Holloway, J.W. ; Boezen, H.M. ; Lawlor, D.A. ; Morris, R.W. ; Probst-Hensch, N ; International Lung Cancer Consortium () ; GIANT Consortium (Gieger, C. ; Heid, I.M. ; Thiering, E. ; Grallert, H. ; Illig, T. ; Peters, A. ; Heinrich, J. ; Wichmann, H.-E.) ; Kaprio, J. ; Wilson, J.F. ; Hayward, C. ; Kähönen, M. ; Heinrich, J. ; Musk, A.W. ; Jarvis, D.L. ; Gläser, S. ; Jarvelin, M.R. ; Stricker, B.H.C. ; Elliott, P. ; O'Connor, G.T. ; Strachan, D.P. ; London, S.J. ; Hall, I.P. ; Gudnason, V. ; Tobin, M.D.
Nat. Genet. 43, 1082-1090 (2011)
Pulmonary function measures reflect respiratory health and are used in the diagnosis of chronic obstructive pulmonary disease. We tested genome-wide association with forced expiratory volume in 1 second and the ratio of forced expiratory volume in 1 second to forced vital capacity in 48,201 individuals of European ancestry with follow up of the top associations in up to an additional 46,411 individuals. We identified new regions showing association (combined P < 5 × 10(-8)) with pulmonary function in or near MFAP2, TGFB2, HDAC4, RARB, MECOM (also known as EVI1), SPATA9, ARMC2, NCR3, ZKSCAN3, CDC123, C10orf11, LRP1, CCDC38, MMP15, CFDP1 and KCNE2. Identification of these 16 new loci may provide insight into the molecular mechanisms regulating pulmonary function and into molecular targets for future therapy to alleviate reduced lung function.
Wissenschaftlicher Artikel
Scientific Article
Graw, J. ; Welzl, G. ; Ahmad, N. ; Klopp, N. ; Heier, M. ; Wulff, A. ; Heinrich, J. ; Döring, A. ; Karrasch, S. ; Nowak, D. ; Schulz, S. ; Rathmann, W. ; Illig, T. ; Peters, A. ; Holle, R. ; Meisinger, C. ; Wichmann, H.-E.
Invest. Ophthalmol. Vis. Sci. 52, 7778-7786 (2011)
Purpose: The population-based KORA (Cooperative Health Research in the Region of Augsburg [Germany]) study was used to evaluate the prevalence of eye diseases and potential interactions with general health status, laboratory data, medication, and genetic background. Methods. In all, 2593 probands, ranging in age from 32 to 71 years (mean: 52 years), were asked in a standardized interview for the presence of cataracts, glaucoma, and corneal or retinal disorders; positive answers were validated and specified by treating ophthalmologists. Additional data came from a questionnaire or from laboratory data. Results. We validated 10 probands with corneal diseases (validation rate: 32%), 26 with retinal diseases (validation rate: 60%), 40 with glaucoma (validation rate: 75%), and 100 participants with cataracts (validation rate: 88%). Glaucoma was significantly associated with increasing age, diabetes and its treatment, and the use of drugs in airway diseases. Cataracts were significantly associated with increasing age, female sex, hypertension, and diabetes. In females, cataracts were particularly associated with the use of ophthalmological corticosteroids, some antihypertensives, and antidiabetics. In contrast, cataracts in males were associated only with the use of angiotensin-converting enzyme inhibitors. We also tested some polymorphic markers; two (GJA8, CRYBB3) were significantly associated with cataracts. Conclusions. Self-reported ocular diagnoses by questionnaire showed varying degrees of accuracy; this method of data collection is valid, providing confirmation is obtained from treating ophthalmologists. It revealed a similar profile of major risk factors for cataracts (age, female sex, and diabetes) in Germany like that of other international studies. The reported associations between medical treatment and genetic polymorphisms in early-onset cataract merit further functional study.
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Scientific Article
Dosnon-Olette, R. ; Schröder, P. ; Bartha, B. ; Aziz, A. ; Couderchet, M. ; Eullaffroy, P.
Environ. Sci. Pollut. Res. 18, 1015-1021 (2011)
Purpose Plants can absorb a diversity of natural and man-made toxic compounds for which they have developed diverse detoxification mechanisms. Plants are able to metabolize and detoxify a wide array of xenobiotics by oxidation, sugar conjugation, glutathione conjugation, and more complex reactions. In this study, detoxification mechanisms of dimethomorph, a fungicide currently found in aquatic media were investigated in Elodea canadensis. Methods Cytochrome P450 (P450) activity was measured by an oxygen biosensor system, glucosyltransferases (GTs) by HPLC, glutathione S-transferases (GSTs), and ascorbate peroxidase (APOX) were assayed spectrophotometrically.Results Incubation of Elodea with dimethomorph induced an increase of the P450 activity. GST activity was not stimulated by dimethomorph suggesting that GST does not participate in dimethomorph detoxification. In plants exposed to dimethomorph, comparable responses were observed for GST and APOX activities showing that the GST was more likely to play a role in response to oxidative stress. Preincubation with dimethomorph induced a high activity of O- and N-GT, it is therefore likely that both enzymes participate in the phase II (conjugation) of dimethomorph detoxification process. Conclusions For the first time in aquatic plants, P450 activity was shown to be induced by a fungicide suggesting a role in the metabolization of dimethomorph. Moreover, our finding is the first evidence of dimethomorph and isoproturon activation of cytochrome P450 multienzyme family in an aquatic plant, i.e., Elodea (isoproturon was taken here as a reference molecule). The detoxification of dimetomorph seems to proceed via hydroxylation, and subsequent glucosylation, and might yield soluble as well as cell wall bound residues.
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Scientific Article
Baldrian, P. ; Head, I.M. ; Prosser, J.I. ; Schloter, M. ; Smalla, K. ; Tebbe, C.C.
FEMS Microbiol. Ecol. 78, 1-2 (2011)
no Abstract
Editorial
Editorial
Ollivier, J. ; Töwe, S. ; Bannert, A. ; Hai, B. ; Kastl, E.-M. ; Meyer, A.H. ; Su, M. ; Kleineidam, K. ; Schloter, M.
FEMS Microbiol. Ecol. 78, 3-16 (2011)
Nitrogen management in soils has been considered as key to the sustainable use of terrestrial ecosystems and a protection of major ecosystem services. However, the microorganisms driving processes like nitrification, denitrification, N-fixation and mineralization are highly influenced by changing climatic conditions, intensification of agriculture and the application of new chemicals to a so far unknown extent. In this review, the current knowledge concerning the influence of selected scenarios of global change on the abundance, diversity and activity of microorganisms involved in nitrogen turnover, notably in agricultural and grassland soils, is summarized and linked to the corresponding processes. In this context, data are presented on nitrogen-cycling processes and the corresponding microbial key players during ecosystem development and changes in functional diversity patterns during shifts in land use. Furthermore, the impact of increased temperature, carbon dioxide and changes in precipitation regimes on microbial nitrogen turnover is discussed. Finally, some examples of the effects of pesticides and antibiotics after application to soil for selected processes of nitrogen transformation are also shown.
Review
Review
Bannert, A. ; Mueller-Niggemann, C. ; Kleineidam, K. ; Wissing, L. ; Cao, Z.-H. ; Schwark, L. ; Schloter, M.
Biol. Fertil. Soils 47, 839-843 (2011)
In the last years, archaea have been identified as key players in global N cycling, especially in nitrification. Ammonia-oxidizing archaea (AOA) are postulated tobelong to the new phylum Thaumarchaeota for which the lipid crenarchaeol should be specific. The ratios between two independent markers for AOA, the ammonia monooxygenase gene and crenarchaeol have been studied in different aerated soils, but so far not in flooded soils. This study investigated ammonia-oxidizing archaea in four paddy soils and a tidal wetland. Ratios were significantly higher in the paddy soils compared to the tidal wetland and in general higher as in upland soils, leading to the assumption that archaeal ammonia oxidizers different from crenarchaeol-containing Thaumarchaeota may play an important role in paddy soils.
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Scientific Article
Upadhyay, S. ; Elder, A. ; Cascio, W.E. ; Schulz, S.
In: Cassee, F.R.* ; Mills, N.L.* ; Newby, D.* [Eds.]: Cardiovascular Effects of Inhaled Ultrafine and Nanosized Particles. Hoboken, NJ: Wiley-Blackwell, 2011. 441-466
no abstract
Ganguly, K. ; Upadhyay, S. ; Irmler, M. ; Takenaka, S. ; Pukelsheim, K. ; Beckers, J. ; Hrabě de Angelis, M. ; Hamelmann, E. ; Stöger, T. ; Schulz, S.
Respir. Res. 12, 94 (2011)
BACKGROUND: Declined lung function is a risk factor for particulate matter associated respiratory diseases like asthma and chronic obstructive pulmonary disease (COPD). Carbon nanoparticles (CNP) are a prominent component of outdoor air pollution that causes pulmonary toxicity mainly through inflammation. Recently we demonstrated that mice (C3H/HeJ) with higher than normal pulmonary function resolved the elicited pulmonary inflammation following CNP exposure through activation of defense and homeostasis maintenance pathways. To test whether CNP-induced inflammation is affected by declined lung function, we exposed JF1/Msf (JF1) mice with lower than normal pulmonary function to CNP and studied the pulmonary inflammation and its resolution. METHODS: 5 μg, 20 μg and 50 μg CNP (Printex 90) were intratracheally instilled in JF1 mice to determine the dose response and the time course of inflammation over 7 days (20 μg dosage). Inflammation was assessed using histology, bronchoalveolar lavage (BAL) analysis and by a panel of 62 protein markers. RESULTS: 24 h after instillation, 20 μg and 50 μg CNP caused a 25 fold and 19 fold increased polymorphonuclear leucocytes (PMN) respectively while the 5 μg represented the 'no observable adverse effect level' as reflected by PMN influx (9.7 × 10E3 vs 8.9 × 10E3), and BAL/lung concentrations of pro-inflammatory cytokines. Time course assessment of the inflammatory response revealed that compared to day1 the elevated BAL PMN counts (246.4 × 10E3) were significantly decreased at day 3 (72.9 × 10E3) and day 7 (48.5 × 10E3) but did not reach baseline levels indicating slow PMN resolution kinetics. Strikingly on day 7 the number of macrophages doubled (455.0 × 10E3 vs 204.7 × 10E3) and lymphocytes were 7-fold induced (80.6 × 10E3 vs 11.2 × 10E3) compared to day1. At day 7 elevated levels of IL1B, TNF, IL4, MDC/CCL22, FVII, and vWF were detected in JF1 lungs which can be associated to macrophage and lymphocyte activation. CONCLUSION: This explorative study indicates that JF1 mice with impaired pulmonary function also exhibits delayed resolution of particle mediated lung inflammation as evident from elevated PMN and accumulation of macrophages and lymphocytes on day 7. It is plausible that elevated levels of IL1B, IL4, TNF, CCL22/MDC, FVII and vWF counteract defense and homeostatic pathways thereby driving this phenomenon.
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Scientific Article
Esperschütz, J. ; Welzl, G. ; Schreiner, K. ; Buegger, F. ; Munch, J.-C. ; Schloter, M.
FEMS Microbiol. Lett. 320, 48-55 (2011)
Initial ecosystems are characterized by a low availability of nutrients and a low soil organic matter content. Interactions of plants and microorganisms in such environments, particularly in relation to litter decomposition, are very important for further ecosystem development. In a litter decomposition study using an initial substrate from a former mining area, we applied the litter of two contrasting pioneer plant species (legume vs. pasture plants), Lotus corniculatus and Calamagrostis epigejos, which are commonly observed in the study area. Litter decomposition was investigated and carbon (C) translocation from litter into soil microorganisms was described by following (13) C from labelled plant litter materials into the fraction of phospholipid fatty acids. Labile C compounds of both plant litter types were easily degraded during the first 4 weeks of litter decomposition. In contrast to climax ecosystems, where the importance of fungi for litter degradation has been shown in many studies, in our experiment, data clearly indicate an outcompetition of fungi by Gram-positive bacteria as soon as available nitrogen is limited in the detritusphere.
Wissenschaftlicher Artikel
Scientific Article
Schnabel, E. ; Karrasch, S. ; Schulz, S. ; Gläser, S. ; Meisinger, C. ; Heier, M. ; Peters, A. ; Wichmann, H.-E. ; Behr, J. ; Huber, R.M. ; Heinrich, J.
Respir. Res. 12:50 (2011)
BACKGROUND: Several studies showed that blood pressure and lung function are associated. Additionally, a potential effect of antihypertensive medication, especially beta-blockers, on lung function has been discussed. However, side effects of beta-blockers have been investigated mainly in patients with already reduced lung function. Thus, aim of this analysis is to determine whether hypertension and antihypertensive medication have an adverse effect on lung function in a general adult population. METHODS: Within the population-based KORA F4 study 1319 adults aged 40-65 years performed lung function tests and blood pressure measurements. Additionally, information on anthropometric measurements, medical history and use of antihypertensive medication was available. Multivariable regression models were applied to study the association between blood pressure, antihypertensive medication and lung function. RESULTS: High blood pressure as well as antihypertensive medication were associated with lower forced expiratory volume in one second (p=0.02 respectively p=0.05; R2: 0.65) and forced vital capacity values (p=0.01 respectively p=0.05, R2: 0.73). Furthermore, a detailed analysis of antihypertensive medication pointed out that only the use of beta-blockers was associated with reduced lung function, whereas other antihypertensive medication had no effect on lung function. The adverse effect of beta-blockers was significant for forced vital capacity (p=0.04; R2: 0.65), while the association with forced expiratory volume in one second showed a trend toward significance (p=0.07; R2: 0.73). In the same model high blood pressure was associated with reduced forced vital capacity (p=0.01) and forced expiratory volume in one second (p=0.03) values, too. CONCLUSION: Our analysis indicates that both high blood pressure and the use of beta-blockers, but not the use of other antihypertensive medication, are associated with reduced lung function in a general adult population.
Wissenschaftlicher Artikel
Scientific Article
Keil, D. ; Meyer, A.H. ; Berner, D. ; Poll, C. ; Schützenmeister, A. ; Piepho, H.P. ; Vlasenko, A. ; Philippot, L. ; Schloter, M. ; Kandeler, E. ; Marhan, S.
FEMS Microbiol. Ecol. 77, 95-106 (2011)
A geostatistical approach using replicated grassland sites (10 m × 10 m) was applied to investigate the influence of grassland management, i.e. unfertilized pastures and fertilized mown meadows representing low and high land-use intensity (LUI), on soil biogeochemical properties and spatial distributions of ammonia-oxidizing and denitrifying microorganisms in soil. Spatial autocorrelations of the different N-cycling communities ranged between 1.4 and 7.6 m for ammonia oxidizers and from 0.3 m for nosZ-type denitrifiers to scales >14 m for nirK-type denitrifiers. The spatial heterogeneity of ammonia oxidizers and nirS-type denitrifiers increased in high LUI, but decreased for biogeochemical properties, suggesting that biotic and/or abiotic factors other than those measured are driving the spatial distribution of these microorganisms at the plot scale. Furthermore, ammonia oxidizers (amoA ammonia-oxidizing archaea and amoA ammonia-oxidizing bacteria) and nitrate reducers (napA and narG) showed spatial coexistence, whereas niche partitioning was found between nirK- and nirS-type denitrifiers. Together, our results indicate that spatial analysis is a useful tool to characterize the distribution of different functional microbial guilds with respect to soil biogeochemical properties and land-use management. In addition, spatial analyses allowed us to identify distinct distribution ranges indicating the coexistence or niche partitioning of N-cycling communities in grassland soil.
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Scientific Article
Dong, X. ; Meisel, B. ; Block, A. ; Graßmann, J. ; Radl, V. ; Weinert, N. ; Meincke, R. ; Berg, G. ; Wenzel, G. ; Schloter, M. ; Mohler, V.
Transgenic Plant J. 5, 35-42 (2011)
Two genetically engineered (GE) zeaxanthin-rich potato (Solanum tuberosum L.) clones, derived from potato cultivar ‘Baltica’ were evaluated under open-field conditions with respect to agronomic performance, stability and tuber-specific expression of the inserted zeaxanthin epoxidase (zep) gene. Data collected from two field sites totalling four environments in Germany demonstrated that general morphology and tuber yield of GE potato clones were not impaired by the metabolic changes in tuber tissue. Quantitative real-time PCR analysis of zep gene expression in leaves, roots and tubers collected at three different developmental stages from the two GE potato clones and the conventional counterpart clone ‘Baltica’ showed that the transgene maintained its ability to induce the accumulation of zeaxanthin in tubers, while no significant zep expression changes were found in leaves and roots. The results clearly demonstrated that the tuber-specific promoter led to a strict tissue-specific expression of the inserted gene in the two GE potato clones in each of the four environments. Additionally, HPLC measurement showed that the tubers from two GE clones contained 19.5 to 58.7 µg/g dw of zeaxanthin, while the zeaxanthin content in the tubers of ‘Baltica’ was under detection level. HPLC results together with qRT-PCR results confirmed the inverse relationship between zep expression level and the accumulation of zeaxanthin in GE tubers. Furthermore, zep expression analysis of four other conventional cultivars showed that gene expression differed in a similar or even greater range among the four conventional cultivars investigated than the variation between GE clones and ‘Baltica’.
Wissenschaftlicher Artikel
Scientific Article
Esperschütz, J. ; Pérez-de-Mora, A. ; Schreiner, K. ; Welzl, G. ; Buegger, F. ; Zeyer, J. ; Hagedorn, F. ; Munch, J.-C. ; Schloter, M.
Biogeosciences 8, 3283-3294 (2011)
Microbial food webs are critical for efficient nutrient turnover providing the basis for functional and stable ecosystems. However, the successional development of such microbial food webs and their role in "young" ecosystems is unclear. Due to a continuous glacier retreat since the middle of the 19th century, glacier forefields have expanded offering an excellent opportunity to study food web development at differently developed soils. In the present study, litter degradation and the corresponding C fluxes into microbial communities were investigated along the forefield of the Damma glacier (Switzerland). 13C-enriched litter of the pioneering plant Leucanthemopsis alpina (L.) Heywood was incorporated into the soil at sites that have been free from ice for approximately 10, 60, 100 and more than 700 years. The structure and function of microbial communities were identified by 13C analysis of phospholipid fatty acids (PLFA) and phospholipid ether lipids (PLEL). Results showed increasing microbial diversity and biomass, and enhanced proliferation of bacterial groups as ecosystem development progressed. Initially, litter decomposition proceeded faster at the more developed sites, but at the end of the experiment loss of litter mass was similar at all sites, once the more easily-degradable litter fraction was processed. As a result incorporation of 13C into microbial biomass was more evident during the first weeks of litter decomposition. 13C enrichments of both PLEL and PUFA biomarkers following litter incorporation were observed at all sites, suggesting similar microbial foodwebs at all stages of soil development. Nonetheless, the contribution of bacteria and actinomycetes to litter turnover became more pronounced as soil age increased in detriment of archaea, fungi and protozoa, more prominent in recently deglaciated terrain.
Wissenschaftlicher Artikel
Scientific Article
Gschwendtner, S. ; Esperschütz, J. ; Buegger, F. ; Reichmann, M. ; Müller, M. ; Munch, J.-C. ; Schloter, M.
FEMS Microbiol. Ecol. 76, 564-575 (2011)
A high percentage of photosynthetically assimilated carbon is released into soil via root exudates, which are acknowledged as the most important factor for the development of microbial rhizosphere communities. As quality and quantity of root exudates are dependent on plant genotype, the genetic engineering of plants might also influence carbon partitioning within the plant and thus microbial rhizosphere community structure. In this study, the carbon allocation patterns within the plant-rhizosphere system of a genetically modified amylopectin-accumulating potato line (Solanum tuberosum L.) were linked to microbial degraders of root exudates under greenhouse conditions, using (13)C-CO(2) pulse-chase labelling in combination with phospholipid fatty acid (PLFA) analysis. In addition, GM plants were compared with the parental cultivar as well as a second potato cultivar obtained by classical breeding. Rhizosphere samples were obtained during young leaf developmental and flowering stages. (13)C allocation in aboveground plant biomass, water-extractable organic carbon, microbial biomass carbon and PLFA as well as the microbial community structure in the rhizosphere varied significantly between the natural potato cultivars. However, no differences between the GM line and its parental cultivar were observed. Besides the considerable impact of plant cultivar, the plant developmental stage affected carbon partitioning via the plant into the rhizosphere and, subsequently, microbial communities involved in the transformation of root exudates.
Wissenschaftlicher Artikel
Scientific Article
Tourna, M. ; Stieglmeier, M. ; Spang, A. ; Könneke, M. ; Schintlmeister, A. ; Urich, T. ; Engel, M. ; Schloter, M. ; Wagner, M. ; Richter, A. ; Schleper, C.
Proc. Natl. Acad. Sci. U.S.A. 108, 8420-8425 (2011)
Genes of archaea encoding homologues of ammonia monooxygenases have been found on a widespread basis and in large amounts in almost all terrestrial and marine environments, indicating that ammonia oxidizing archaea (AOA) might play a major role in nitrification on Earth. However, only one pure isolate of this group from a marine environment has so far been obtained, demonstrating archaeal ammonia oxidation coupled with autotrophic growth similar to the bacterial counterparts. Here we describe the cultivation and isolation of an AOA from soil. It grows on ammonia or urea as an energy source and is capable of using higher ammonia concentrations than the marine isolate, Nitrosopumilus maritimus. Surprisingly, although it is able to grow chemolithoautotrophically, considerable growth rates of this strain are obtained only upon addition of low amounts of pyruvate or when grown in coculture with bacteria. Our findings expand the recognized metabolic spectrum of AOA and help explain controversial results obtained in the past on the activity and carbon assimilation of these globally distributed organisms.
Wissenschaftlicher Artikel
Scientific Article
Kotzerke, A. ; Fulle, M. ; Sharma, S. ; Kleineidam, K. ; Welzl, G. ; Lamshöft, M. ; Schloter, M. ; Wilke, B.M.
J. Plant Nutr. Soil Sci. 174, 56-64 (2011)
Most veterinary drugs enter the environment via manure application. However, ecotoxic effects of antibiotics are varying as a function of their physicochemical characteristics and for most antibiotics it is still unclear how these substances interact with soil biota. It was the aim of the present study to investigate effects of manure containing different concentrations of the antibiotic amoxicillin (AMX) on microbial-community function in two different soils over an incubation time of 18 d. Therefore, soil respiration, potential nitrification, and the products of N turnover were measured. We could show that CaCl2-extractable amounts of AMX in soil are low, even shortly after the application of high doses together with manure. Thus, not surprisingly basal respiration in soil was not influenced by the addition of the antibiotic with manure. In contrast, mainly shortly after manure addition the kinetic of substrate-induced respiration was clearly shifted by the treatments depending on the presence of AMX in the manure: Potential nitrification rates in the two different soils were not significantly affected when data were related to the overall incubation time by the application of AMX to the manure. However, shortly after the addition of the manure containing AMX, a tendency to lower turnover rates was visible compared to the application of pure manure.
Wissenschaftlicher Artikel
Scientific Article
Horsch, M. ; Seeburg, PH. ; Adler, T. ; Aguilar-Pimentel, J.A. ; Becker, L. ; Calzada-Wack, J. ; Garrett, L. ; Götz, A. ; Hans, W. ; Higuchi, M. ; Hölter, S.M. ; Naton, B. ; Prehn, C. ; Puk, O. ; Rácz, I. ; Rathkolb, B. ; Rozman, J. ; Schrewe, A. ; Adamski, J. ; Busch, D.H. ; Esposito, I. ; Graw, J. ; Ivandic, B. ; Klingenspor, M. ; Klopstock, T. ; Mempel, M. ; Ollert, M. ; Schulz, S. ; Wolf, E. ; Wurst, W. ; Zimmer, A. ; Gailus-Durner, V. ; Fuchs, H. ; Hrabě de Angelis, M. ; Beckers, J.
J. Biol. Chem. 286, 18614-18622 (2011)
ADAR2, an RNA editing enzyme that converts specific adenosines to inosines in certain pre-mRNAs, often leading to amino acid substitutions in the encoded proteins, is mainly expressed in brain. Of all ADAR2-mediated edits, a single one in the pre-mRNA of the AMPA receptor subunit GluA2 is essential for survival. Hence, early postnatal death of mice lacking ADAR2 is averted when the critical edit is engineered into both GluA2 encoding Gria2 alleles. Adar2(-/-)/Gria2(R/R) mice display normal appearance and life span, but the general phenotypic effects of global lack of ADAR2 have remained unexplored. Here we have employed the Adar2(-/-)/Gria2(R/R) mouse line, and Gria2(R/R) mice as controls, to study the phenotypic consequences of loss of all ADAR2-mediated edits except the critical one in GluA2. Our extended phenotypic analysis covering ∼320 parameters identified significant changes related to absence of ADAR2 in behavior, hearing ability, allergy parameters and transcript profiles of brain.
Wissenschaftlicher Artikel
Scientific Article
Kleineidam, K. ; Kosmrlj, K. ; Kublik, S. ; Palmer, I. ; Pfab, H. ; Ruser, R. ; Fiedler, S. ; Schloter, M.
Chemosphere 84, 182-186 (2011)
In agricultural plant production nitrification inhibitors like 3,4-dimethylpyrazole phosphate (DMPP) are used to retard the microbial nitrification process of fertilized ammonium to enhance the nitrogen supply for cultivated crops and to reduce nitrogen losses from the production system. Besides the well-known ammonia-oxidizing bacteria (AOB) it is known for a few years that also ammonia-oxidizing archaea (AOA) are able to perform the first step in nitrification, hence being also a target for a nitrification inhibitor. However, so far no information are available concerning the effectiveness of DMPP and its extent towards AOB and AOA, neither in bulk soil nor in the root-rhizosphere complex. We investigated in a field experiment performed according to agricultural practice the effect of DMPP on the abundance of AOB and AOA two, four and eight weeks after fertilization. We observed impaired abundances of AOB but not of AOA in both soil compartments that were still visible eight weeks after application, possibly indicating a reduced effectiveness of the nitrification inhibitor in our study.
Wissenschaftlicher Artikel
Scientific Article
Kilinc, E. ; Schulz, S. ; Kuiper, G.J. ; Spronk, H.M.H. ; ten Cate, H. ; Upadhyay, S. ; Ganguly, K. ; Stöger, T. ; Semmler-Behnke, M. ; Takenaka, S. ; Kreyling, W.G. ; Pitz, M. ; Reitmeir, P. ; Peters, A. ; Eickelberg, O. ; Wichmann, H.-E.
Part. Fibre Toxicol. 8:12 (2011)
Inhalation of fine particulate matter (<2.5 μm; fine PM) has been shown to increase the risk for cardiovascular events. In this letter, we reappraise the role of tissue factor (TF) antigen and we also summarize changes in measured coagulation proteins in humans and rodents by other studies with fine PM. By considering all studies including ours, we conclude that monitoring the overall coagulation state by measuring capacity assays such as thrombin generation, and quantification of TF activity would be more suitable than determining single coagulation proteins (such as TF antigen) in order to better assess the systemic prothrombotic effects of fine PM.
Letter to the Editor
Letter to the Editor
Vargas Gil, S. ; Meriles, J. ; Conforto, C. ; Basanta, M. ; Radl, V. ; Hagn, A. ; Schloter, M. ; March, G.J.
Eur. J. Soil Biol. 47, 55-60 (2011)
Argentina is the world's third most important soybean producer; hence, there is an urgent need to preserve soil health by applying appropriate agricultural practices to maintain sustainable production in the upcoming years. Because productivity of agricultural systems largely depends on soil microbial processes, the influence of different management strategies on soil microbial community structure was analyzed in a long-term field trial started in 1992. The experimental design was a split-plot arrangement of treatments, consisting in two tillage treatments: zero tillage (it) and reduced tillage (RT), in combination with two crop rotation treatments: soybean monoculture (SS) and corn-soybean (CS). Phospholipid fatty acid (PLFA) profiles were used to assess total microbial community structure. Denaturing gradient gel electrophoresis (DGGE) profiles of 18S rRNA were generated to describe the influence of crop practices on fungal communities. Total PLFA content was lowest in soil under reduced tillage and soybean monoculture; therefore the use of reduced tillage-soybean monoculture in agroecosystems might produce important reductions in total microbial biomass. The structure of total microbial communities, as estimated by PLFA, was affected by crop rotation. Moreover, the fungal communities, as estimated by DGGE analysis, were influenced by combined effects of crop rotation and tillage system.
Wissenschaftlicher Artikel
Scientific Article
Melero, S. ; Pérez-de-Mora, A. ; Murillo, M. ; Buegger, F. ; Kleineidam, K. ; Kublik, S. ; Vanderlinden, K. ; Moreno, F. ; Schloter, M.
Appl. Soil Ecol. 47, 221-225 (2011)
The impact of tillage practices on microbial N transformations in Vertisols is poorly understood and data from long-term field experiments are scarce, particularly in semiarid regions. We evaluated the effects of traditional tillage (TT) vs no-tillage (NT) on denitrification in a long-term field experiment under a rainfed crop rotation system (cereal-sunflower-legumes) on a Vertisol (SW Spain). In general, the abundance of denitrifiers and the respective potential denitrification rates was higher under NT compared to TT during the vegetation period, but not after harvesting. However differences in denitrifier numbers were within the same order of magnitude (0.5-3 x 10(7) copies g soil dw). The abundance of nitrite reducers and N2O reducers was relatively similar. In addition, N2O/N-2 ratios between 1 and 2 were found for both treatments. These results emphasize that NT has a limited impact on denitrification in Vertisols under fertilizer regime and legume-crop rotation and thus losses of N2O are expected to be comparable to those of traditional tillage systems.
Wissenschaftlicher Artikel
Scientific Article
Töwe, S. ; Wallisch, S. ; Bannert, A. ; Fischer, D. ; Hai, B. ; Haesler, F. ; Kleineidam, K. ; Schloter, M.
J. Microbiol. Methods 84, 406-412 (2011)
We developed an improved protocol, allowing the simultaneous extraction of DNA and RNA from soil using phenol-chloroform with subsequent column-based separation of DNA and RNA (PCS). We compared this new approach with the well established protocol published by Griffiths et al. (2000), where DNA and RNA are separated by selective enzymatic digestions and two commercial kits used for DNA or RNA extraction, respectively, using four different agricultural soils. We compared yield and purity of the nucleic acids as well as abundance and diversity profiles of the soil bacterial communities targeting the nosZ gene via quantitative real-time PCR and terminal restriction fragment length polymorphism on DNA and RNA level. The newly developed protocol provided purer nucleic acid extracts compared to the used kit-based protocols. All protocols were suitable for DNA- and RNA-based gene quantification, however high variations between replicates were obtained for RNA samples using the original Griffiths protocol. Diversity patterns of nosZ were highly influenced by the extraction protocol used both on the DNA and RNA level. Finally, our data showed that the new protocol allows a simultaneous and reproducible extraction and separation of DNA and RNA, which were suitable for reliable analyses of gene and transcript copy numbers and diversity pattern.
Wissenschaftlicher Artikel
Scientific Article
Petric, I. ; Philippot, L. ; Abbate, C. ; Bispo, A. ; Chesnot, T. ; Hallin, S. ; Laval, K. ; Lebeau, T. ; Lemanceau, P. ; Leyval, C. ; Lindström, K. ; Pandard, P. ; Romero, E. ; Sarr, A. ; Schloter, M. ; Simonet, P. ; Smalla, K. ; Wilke, B.M. ; Martin-Laurent, F.
J. Microbiol. Methods 84, 454-460 (2011)
Extracting DNA directly from micro-organisms living in soil is a crucial step for the molecular analysis of soil microbial communities. However, the use of a plethora of different soil DNA extraction protocols, each with its own bias, makes accurate data comparison difficult. To overcome this problem, a method for soil DNA extraction was proposed to the International Organization for Standardization (ISO) in 2006. This method was evaluated by 13 independent European laboratories actively participating in national and international ring tests. The reproducibility of the standardized method for molecular analyses was evaluated by comparing the amount of DNA extracted, as well as the abundance and genetic structure of the total bacterial community in the DNA extracted from 12 different soils by the 13 laboratories. High quality DNA was successfully extracted from all 12 soils, despite different physical and chemical characteristics and a range of origins from arable soils, through forests to industrial sites. Quantification of the 16S rRNA gene abundances by real time PCR and analysis of the total bacterial community structure by automated ribosomal intergenic spacer analysis (A-RISA) showed acceptable to good levels of reproducibility. Based on the results of both ring-tests, the method was unanimously approved by the ISO as an international standard method and the normative protocol will now be disseminated within the scientific community. Standardization of a soil DNA extraction method will improve data comparison, facilitating our understanding of soil microbial diversity and soil quality monitoring.
Wissenschaftlicher Artikel
Scientific Article
Weinert, N. ; Piceno, Y. ; Ding, G.C. ; Meincke, R. ; Heuer, H. ; Berg, G. ; Schloter, M. ; Andersen, G. ; Smalla, K.
FEMS Microbiol. Ecol. 75, 497-506 (2011)
The phylogenetic composition of bacterial communities in the rhizosphere of three potato cultivars grown at two distant field sites was analysed. Ribosomal gene fragments amplified from total community DNA were hybridized to PhyloChips. A total of 2432 operational taxonomic units (OTUs) were detected by the PhyloChips, of which 65% were found in the rhizosphere of all cultivars at both field sites. From all detected OTUs, 9% revealed a cultivar-dependent abundance at the one or the other field site and 4% at both sites. Differential abundance on the three cultivars was mainly observed for OTUs belonging to the Pseudomonadales, Actinomycetales and Enterobacteriales. More than 40% of OTUs belonging to Bradyrhizobiales, Sphingomonadales, Burkholderiales, Rhodocyclales, Xanthomonadales and Actinomycetales differed significantly in their abundance between the sites. A sequence analysis of six 16S rRNA gene clone libraries corresponded well with the taxonomic community structure evidenced by the PhyloChip hybridization. Most ribotypes matched OTUs detected by the PhyloChip. Those OTUs that responded to the potato cultivar at both field sites might be of interest in view of cultivar-specific effects on bacterial biocontrol strains and pathogens.
Wissenschaftlicher Artikel
Scientific Article
Heuer, H. ; Solehati, Q. ; Zimmerling, U. ; Kleineidam, K. ; Schloter, M. ; Müller, T. ; Focks, A. ; Thiele-Bruhn, S. ; Smalla, K.
Appl. Environ. Microbiol. 77, 2527-2530 (2011)
Two soils were amended three times with pig manure. The abundance of sulfonamide resistance genes was determined by quantitative PCR 2 months after each application. In both soils treated with sulfadiazine-containing manure, the numbers of copies of sul1 and sul2 significantly increased compared to numbers after treatments with antibiotic-free manure or a control and accumulated with repeated applications.
Wissenschaftlicher Artikel
Scientific Article
Koch, B. ; Schäper, C. ; Ewert, R. ; Völzke, H. ; Obst, A. ; Friedrich, N. ; Felix, S.B. ; Vogelmeier, C.F. ; Schnabel, E. ; Karrasch, S. ; Wichmann, H.-E. ; Schäfer, T. ; Schulz, S. ; Heinrich, J. ; Gläser, S.
Respir. Med. 105, 352-362 (2011)
Spirometry is a frequently performed lung function test and an important tool in medical surveillance examinations of pulmonary diseases. The interpretation of lung function relies on the comparison to reference values derived from a healthy population. The study aim was to compare the lung function data of three representative population-based German studies (Study of Health in Pomerania [SHIP-1], Cooperative Health Research in the Region of Augsburg [KORA-S3] and European Community Respiratory Health Survey Erfurt [ECRHS-I Erfurt]) with existing European spirometry reference values and to establish a new set of comprehensive German prediction equations. METHODS:Spirometry was performed in 4133 participants of three population-based surveys using almost identical standardised methods. Current and former smokers, subjects with cardiopulmonary disorders or on medication with potential influence on lung function were excluded. Sex specific prediction equations were established by quantile regression analyses. Comparison was performed to existing European reference values. RESULTS: The healthy reference sample consisted of 1302 (516 male) individuals, aged 20-80 years. Sex specific comprehensive prediction equations adjusted for age and height are provided. Significant differences were found in comparison to previous studies with pronounced lower values of the current population if applying historic prediction equations. CONCLUSION: The results contribute to the interpretation of lung function examination in providing a comprehensive set of spirometry reference values obtained in a large number of healthy volunteers. Whereas the differences in between the investigated studies are negligible, striking divergence was detected in comparison to historic and recent European spirometry prediction values.
Wissenschaftlicher Artikel
Scientific Article
Bartling, J. ; Esperschütz, J. ; Wilke, B.M. ; Schloter, M.
J. Hazard. Mater. 187, 488-494 (2011)
Ethyl tert butyl ether (ETBE) and tert amyl methyl ether (TAME) are oxygenates used in gasoline in order to reduce emissions from vehicles. The present study investigated their impact on a soil microflora that never was exposed to any contamination before. Therefore, soil was artificially contaminated and incubated over 6 weeks. Substrate induced respiration (SIR) measurements and phospholipid fatty acid (PLFA) analysis indicated shifts in both, microbial function and structure during incubation. The results showed an activation of microbial respiration in the presence of ETBE and TAME, suggesting biodegradation by the microflora. Furthermore, PLFA concentrations decreased in the presence of ETBE and TAME and Gram-positive bacteria became more dominant in the microbial community.
Wissenschaftlicher Artikel
Scientific Article
Clarke, N. ; Gryndler, M. ; Liste, H.-H. ; Schroll, R. ; Schröder, P. ; Matucha, M.
In: Schröder, P.* ; Collins, C.D.* [Eds.]: Organic Xenobiotics and Plants: From Mode of Action to Ecophysiology. Dordrecht: Springer Science+Business Media B.V., 2011. 17-45 (Plant Ecophysiology ; 8)
The halogens, most importantly fluorine, chlorine, bromine, and iodine, occur in nature as ions and compounds, including organic compounds. Halogenated organic substances (haloorganics) were long considered purely anthropogenic products; however, they are in addition a commonly occurring and important part of natural ecosystems. Natural haloorganics are produced largely by living organisms, although abiotic production occurs as well. A survey is given of processes of formation, transport, and degradation of haloorganics in temperate and boreal forests, predominantly in Europe. More work is necessary in order to understand the environmental impact of haloorganics in temperate and boreal forest soils. This includes both further research, especially to understand the key processes of formation and degradation of halogenated compounds, and monitoring of the substances in question in forest ecosystems. It is also important to understand the effect of various forest management techniques on haloorganics, as management can be used to produce desired effects.
Kotzerke, A. ; Hammesfahr, U. ; Kleineidam, K. ; Lamshöft, M. ; Thiele-Bruhn, S. ; Schloter, M. ; Wilke, B.M.
Biol. Fertil. Soils 47, 177-186 (2011)
Difloxacin (DIF) belongs to the fluoroquinolones, a frequently detected group of antibiotics in the environment. It is excreted in pig manure to a large extent and may consequently reach soils in potentially effective concentrations via manuring. The aim of this study was to assess the effects of DIF-spiked manure on microbial communities and selected functions in soils in a microcosm experiment up to 1 month after application. To test a dose dependency of the effects, three different concentrations of DIF (1, 10 and 100 mg/kg of soil) were used. Microcosms with application of pure manure, as well as untreated microcosms served as control. The addition of pure manure resulted in an increase of microbial biomass and soil respiration as well as a reduced bacteria/fungi ratio. Due to the fast and strong immobilisation of DIF, effects of the antbiotic compound were only visible up to 8 days after application (microbial biomass; respiration; potential denitrification; ratio of bacteria/fungi). As expected these short-term effects resulted in reduced potential denitrification rates as well as a reduced bacteria/fungal ratio in the treatments were DIF has been applied. Surprisingly, microbial biomass values as well as respiration rates were increased by DIF application. Other parameters like nitrate and ammonium content in soil were not influenced by DIF application at any time point. Long-term effects (32 days after application) were only visible for the potential nitrification rates. For those parameters that were influenced by the DIF application a clear dose dependency could not be described.
Wissenschaftlicher Artikel
Scientific Article
Schaaf, W. ; Bens, O. ; Fischer, A. ; Gerke, H.H. ; Gerwin, W. ; Grünewald, U. ; Holländer, H.M. ; Kögel-Knabner, I. ; Mutz, M. ; Schloter, M. ; Schulin, R. ; Veste, M. ; Winter, S. ; Hüttl, R.F.
J. Plant Nutr. Soil Sci. 174, 229-239 (2011)
Ecosystems are characterized as complex systems with abiotic and biotic processes interacting between the various components that have evolved over long-term periods. Most ecosystem studies so far have been carried out in mature systems. Only limited knowledge exists on the very initial phase of ecosystem development. Concepts on the development of ecosystems are often based on assumptions and extrapolations with respect to structure process interactions in the initial stage. To characterize the effect of this initial phase on structure and functioning of ecosystems in later stages, it is necessary to disentangle the close interaction of spatial and temporal patterns of ecosystem structural assemblages with processes of ecosystem development. The study of initial, less complex systems could help to better identify and characterize coupled patterns and processes. This paper gives an overview of concepts for the initial development of different ecosystem compartments and identifies open questions and research gaps. The artificial catchment site Chicken Creek is introduced as a new research approach to investigate these patterns and processes of initial ecosystem development under defined boundary conditions. This approach allows to integrate the relevant processes with related pattern and structure development over temporal and spatial scales and to derive thresholds and stages in state and functioning of ecosystems at the catchment level
Wissenschaftlicher Artikel
Scientific Article
Brankatsch, R. ; Töwe, S. ; Kleineidam, K. ; Schloter, M. ; Zeyer, J.
ISME J. 5, 1025-1037 (2011)
Glacier forefields are ideal ecosystems to study the development of nutrient cycles as well as single turnover processes during soil development. In this study, we examined the ecology of the microbial nitrogen (N) cycle in bulk soil samples from a chronosequence of the Damma glacier, Switzerland. Major processes of the N cycle were reconstructed on the genetic as well as the potential enzyme activity level at sites of the chronosequence that have been ice-free for 10, 50, 70, 120 and 2000 years. In our study, we focused on N fixation, mineralization (chitinolysis and proteolysis), nitrification and denitrification. Our results suggest that mineralization, mainly the decomposition of deposited organic material, was the main driver for N turnover in initial soils, that is, ice-free for 10 years. Transient soils being ice-free for 50 and 70 years were characterized by a high abundance of N fixing microorganisms. In developed soils, ice-free for 120 and 2000 years, significant rates of nitrification and denitrification were measured. Surprisingly, copy numbers of the respective functional genes encoding the corresponding enzymes were already high in the initial phase of soil development. This clearly indicates that the genetic potential is not the driver for certain functional traits in the initial phase of soil formation but rather a well-balanced expression of the respective genes coding for selected functions.
Wissenschaftlicher Artikel
Scientific Article
Karrasch, S. ; Ernst, K. ; Behr, J. ; Heinrich, J. ; Huber, R.M. ; Nowak, D. ; Wichmann, H.-E. ; Baumeister, S.E. ; Meisinger, C. ; Ladwig, K.-H. ; Holle, R. ; Jörres, R.A. ; Schulz, S. ; KORA Study Group (Wichmann, H.-E. ; Holle, R. ; John, J. ; Illig, T. ; Peters, A. ; Meisinger, C. ; Ladwig, K.-H.)
Respir. Med. 105, 713-718 (2011)
The aim of the current study was to determine the impact and interaction of important influencing factors on the fraction of exhaled nitric oxide (FeNO). FeNO was measured in a population-based sample of 1250 middle-aged subjects from the KORA F4 cohort (Augsburg, Germany). Analysis of covariance models was performed including the factors age, height, FVC, FEV(1), sex, current smoking status, recent respiratory tract infection, and respiratory allergy. Geometric mean (SD as factor; 95% confidence interval as factor) FeNO was 13.9 (1.9; 1.033) ppb. FeNO significantly depended on age, height, smoking, infection and allergy. Smoking reduced FeNO by 21%, while infection and allergy led to increases by 9 and 11%, respectively. Increases in age by 10 years and in height by 10 cm were associated with increases of FeNO by 15 and 10%, respectively. Non-smokers demonstrated independent multiplicative superposition of factors affecting FeNO while the effect of allergy was virtually eliminated in smokers without infection. We conclude that in middle-aged non-smokers the effects of infection, age and height can be easily taken into account and do not significantly disturb the effect of respiratory tract allergies on FeNO. In current smokers, however, effects were heterogeneous and information on smoking intensity seems to be useful for better adjustment.
Wissenschaftlicher Artikel
Scientific Article
Fuchs, H. ; Gailus-Durner, V. ; Adler, T. ; Aguilar-Pimentel, J.A. ; Becker, L. ; Calzada-Wack, J. ; Da Silva-Buttkus, P. ; Neff, F. ; Götz, A.A. ; Hans, W. ; Hölter, S.M. ; Horsch, M. ; Kastenmüller, G. ; Kemter, E. ; Lengger, C. ; Maier, H. ; Matloka, M. ; Möller, G. ; Naton, B. ; Prehn, C. ; Puk, O. ; Rácz, I. ; Rathkolb, B. ; Römisch-Margl, W. ; Rozman, J. ; Wang-Sattler, R. ; Schrewe, A. ; Stöger, C. ; Tost, M. ; Adamski, J. ; Aigner, B. ; Beckers, J. ; Behrendt, H. ; Busch, D.H. ; Esposito, I. ; Graw, J. ; Illig, T. ; Ivandic, B. ; Klingenspor, M. ; Klopstock, T. ; Kremmer, E. ; Mempel, M. ; Neschen, S. ; Ollert, M. ; Schulz, S. ; Suhre, K. ; Wolf, E. ; Wurst, W. ; Zimmer, A. ; Hrabě de Angelis, M.
Methods 53, 120-135 (2011)
Model organisms like the mouse are important tools to learn more about gene function in man. Within the last 20years many mutant mouse lines have been generated by different methods such as ENU mutagenesis, constitutive and conditional knock-out approaches, knock-down, introduction of human genes, and knock-in techniques, thus creating models which mimic human conditions. Due to pleiotropic effects, one gene may have different functions in different organ systems or time points during development. Therefore mutant mouse lines have to be phenotyped comprehensively in a highly standardized manner to enable the detection of phenotypes which might otherwise remain hidden. The German Mouse Clinic (GMC) has been established at the Helmholtz Zentrum München as a phenotyping platform with open access to the scientific community (www.mousclinic.de; [1]). The GMC is a member of the EUMODIC consortium which created the European standard workflow EMPReSSslim for the systemic phenotyping of mouse models (http://www.eumodic.org/[2]).
Review
Review
Lyubenova, L. ; Schröder, P.
Bioresour. Technol. 102, 996-1004 (2011)
Upon treatment with Cd and As cattail (Typha latifolia) showed induced catalase, monodehydroascorbate reductase and ascorbate peroxidase activities in leaves but strong inhibition in rhizomes. Peroxidase activity in leaves of the same plants was inhibited whereas linear increase was detected after Cd treatment in rhizomes. Glutathione S-transferase measurements resulted in identical effects of the trace elements on the substrates CDNB, DCNB, NBC, NBoC, fluorodifen. When GST was assayed with the model substrate DCNB, a different pattern of activity was observed, with strongly increasing activities at increasing HM concentrations. Consequently, to improve the success rates, future phytoremediation plans need to preselect plant species with high antioxidative enzyme activities and an alert GST pattern capable of detoxifying an array of organic xenobiotics.
Wissenschaftlicher Artikel
Scientific Article
2010
Kaymakanova, M. ; Lyubenova, L. ; Schröder, P. ; Stoeva, N. ; Balabanova, D.
Agric. Sci. 2, 41-44 (2010)
The effect of salt stress on the activity of antioxidative enzymes was studied in leaves and roots of bean plants (Phaseolus vulgaris L.), grown under control (nutrient solution) and salt stress (nutrient solution containing 100 mM NaCl and Na2SO4) conditions. In the leaves of salt-stressed plants, ascorbate connected enzymes (APX, MDHAR and DHAR) demonstrated increased activity and at the same time their activity was decreased the in roots. The increase of the enzyme activity was more pronounced under sodium sulfate compared with the chloride treatment in the bean leaves. In saltstressed roots the Na2SO4 application reduced the activity at a higher degree. As a result of the two salt treatments of bean plants the CAT activity were increased in the roots and decreased in the leaves as compared with the control. The observed differences in the enzyme activities show the specific reaction in the different organs of the bean plants as well as the dependence on the kind of the applied salts.
Wissenschaftlicher Artikel
Scientific Article
Lyubenova, L. ; Schröder, P.
In: Sherameti, I.* ; Varma, A.* [Eds.]: Soil Heavy Metals. Berlin: Springer, 2010. 65-85 (Soil Biol. ; 19)
Schröder, P. ; Lyubenova, L. ; Huber, C.
Desalin. Water Treat. 23, 95-100 (2010)
Multiple sites of moderate to low pollution with heavy metals or organic xenobiotics have been identified throughout Europe, and those where no immediate pressure exists for further use, may well be remediated by plant based technologies. Hence, phytoremediation has become a green sustainable technology that has gained increasing attention during the last decade. Municipal and industrial wastewater treatment plants can be optimized by the addition of lagoons with aquatic macrophytes. However, it is obvious, that quite a number of remediation projects failed due to insuf¬ficient plant performance. In this paper, we present evidence that Typha and Phragmites, two widely used plant species in phytoremediation, are capable of removal and metabolism of heavy metals and organic pollutants from water and sediments to some extent, but will fail at higher concentrations. We show also that pollution with heavy metals will interfere with both, the oxidative stress defence in plants, and with their ability to conjugate and detoxify organic xenobiotics. Despite plant species dependent differences, the general reactions seem to include oxidative stress and an induction of antioxidative enzymes. Both species respond to trace elements with oxidative stress and decay of central physiological functions. In non-hyperaccumulators like the chosen species, photosynthesis, growth, but also defense will cease at higher concentrations or prolonged exposure to heavy metals. Interestingly, defense reactions against organic xenobiotics, so far considered unrelated to heavy metal stress will also be impaired by mixed pollution, especially cadmium. Here, direct interac¬tions with enzyme proteins are possible, but influence on transcription is frequently observed. For the practical use of plants in phytoremediation, it is discussed that only species with proven stress resistance or mixed plant consortia with differential resistances and uptake can be recommended.
Wissenschaftlicher Artikel
Scientific Article
Alessandrini, F. ; Weichenmeier, I. ; van Miert, E. ; Takenaka, S. ; Karg, E.W. ; Blume, C. ; Mempel, M. ; Schulz, S. ; Bernard, A. ; Behrendt, H.
Part. Fibre Toxicol. 7:11 (2010)
Clara cell protein (CC16), the main secretory product of bronchiolar Clara cells, plays an important protective role in the respiratory tract against oxidative stress and inflammation. The purpose of the study was to investigate the role of elemental carbon ultrafine particles (EC-UFP)-induced oxidative stress on Clara cells and CC16 in a mouse model of allergic lung inflammation.METHODS: Ovalbumin (OVA)-sensitized mice were exposed to EC-UFP (507 microg/m(3) for 24 h) or filtered air immediately prior to allergen challenge and systemically treated with N-acetylcysteine (NAC) or vehicle prior and during EC-UFP inhalation. CC16 was measured up to one week after allergen challenge in bronchoalveolar lavage fluid (BALF) and in serum. The relative expression of CC16 and TNF-alpha mRNA were measured in lung homogenates. A morphometrical analysis of mucus hypersecretion and electron microscopy served to investigate goblet cell metaplasia and Clara cell morphological alterations.RESULTS: In non sensitized mice EC-UFP inhalation caused alterations in CC16 concentration, both at protein and mRNA level, and induced Clara cell hyperplasia. In sensitized mice, inhalation of EC-UFP prior to OVA challenge caused most significant alterations of BALF and serum CC16 concentration, BALF total protein and TNF-alpha relative expression compared to relevant controls; their Clara cells displayed the strongest morphological alterations and strongest goblet cell metaplasia occurred in the small airways. NAC strongly reduced both functional and morphological alterations of Clara cells.CONCLUSION: Our findings demonstrate that oxidative stress
Wissenschaftlicher Artikel
Scientific Article
Ollivier, J. ; Kleineidam, K. ; Reichel, R. ; Thiele-Bruhn, S. ; Kotzerke, A. ; Kindler, R. ; Wilke, B.-M. ; Schloter, M.
Appl. Environ. Microbiol. 76, 7903-7909 (2010)
The antibiotic sulfadiazine (SDZ) can enter the environment by application of manure from antibiotic-treated animals to arable soil. Because antibiotics are explicitly designed to target microorganisms, they likely affect microbes in the soil ecosystem, compromising important soil functions and disturbing processes in nutrient cycles. In a greenhouse experiment, we investigated the impact of sulfadiazine-contaminated pig manure on functional microbial communities involved in key processes of the nitrogen cycle in the root-rhizosphere complexes (RRCs) of maize (Zea mays) and clover (Trifolium alexandrinum). At both the gene and transcript level, we performed real-time PCR using nifH, amoA (in both ammonia-oxidizing bacteria and archaea), nirK, nirS, and nosZ as molecular markers for nitrogen fixation, nitrification, and denitrification. Sampling was performed 10, 20, and 30 days after the application. SDZ affected the abundance pattern of all investigated genes in the RRCs of both plant species (with stronger effects in the RRC of clover) 20 and 30 days after the addition. Surprisingly, effects on the transcript level were less pronounced, which might indicate that parts of the investigated functional groups were tolerant or resistant against SDZ or, as in the case of nifH and clover, have been protected by the nodules.
Wissenschaftlicher Artikel
Scientific Article
Upadhyay, S. ; Ganguly, K. ; Stöger, T. ; Semmler-Behnke, M. ; Takenaka, S. ; Kreyling, W.G. ; Pitz, M. ; Reitmeir, P. ; Peters, A. ; Eickelberg, O. ; Wichmann, H.-E. ; Schulz, S.
Part. Fibre Toxicol. 7:27 (2010)
RATIONALE: Several epidemiological studies associated exposure to increased levels of particulate matter in Augsburg, Germany with cardiovascular mortality and morbidity. To elucidate the mechanisms of cardiovascular impairments we investigated the cardiopulmonary responses in spontaneously hypertensive rats (SHR), a model for human cardiovascular diseases, following intratracheal instillation of dust samples from Augsburg. METHODS: 250 μg, 500 μg and 1000 μg of fine ambient particles (aerodynamic diameter <2.5 μm, PM₂(.)₅-AB) collected from an urban background site in Augsburg during September and October 2006 (PM₂(.)₅ 18.2 μg/m³, 10,802 particles/cm3) were instilled in 12 months old SHRs to assess the inflammatory response in bronchoalveolar lavage fluid (BALF), blood, lung and heart tissues 1 and 3 days post instillation. Radio-telemetric analysis was performed to investigate the cardiovascular responses following instillation of particles at the highest dosage based on the inflammatory response observed. RESULTS: Exposure to 1000 μg of PM₂(.)₅-AB was associated with a delayed increase in delta mean blood pressure (ΔmBP) during 2(nd)-4(th) day after instillation (10.0 ± 4.0 vs. -3.9 ± 2.6 mmHg) and reduced heart rate (HR) on the 3rd day post instillation (325.1 ± 8.8 vs. 348.9 ± 12.5 bpm). BALF cell differential and inflammatory markers (osteopontin, interleukin-6, C-reactive protein, and macrophage inflammatory protein-2) from pulmonary and systemic level were significantly induced, mostly in a dose-dependent way. Protein analysis of various markers indicate that PM₂(.)₅-AB instillation results in an activation of endothelin system (endothelin1), renin-angiotensin system (angiotensin converting enzyme) and also coagulation system (tissue factor, plasminogen activator inhibitor-1) in pulmonary and cardiac tissues during the same time period when alternation in ΔmBP and HR have been detectedd. CONCLUSIONS: Our data suggests that high concentrations of PM₂(.)₅-AB exposure triggers low grade PM mediated inflammatory effects in the lungs but disturbs vascular homeostasis in pulmonary tissues and on a systemic level by affecting the renin angiotensin system, the endothelin system and the coagulation cascade. These findings are indicative for promotion of endothelial dysfunction, atherosclerotic lesions, and thrombogeneis and, thus, provide plausible evidence that susceptible-predisposed individuals may develop acute cardiac events like myocardial infarction when repeatedly exposed to high pollution episodes as observed in epidemiological studies in Augsburg, Germany.
Wissenschaftlicher Artikel
Scientific Article
Töwe, S. ; Albert, A. ; Kleineidam, K. ; Brankatschk, R. ; Dümig, A. ; Welzl, G. ; Munch, J.-C. ; Zeyer, J. ; Schloter, M.
Microb. Ecol. 60, 762-770 (2010)
Glacier forefields are an ideal playground to investigate the role of development stages of soils on the formation of plant-microbe interactions as within the last decades, many alpine glaciers retreated, whereby releasing and exposing parent material for soil development. Especially the status of macronutrients like nitrogen differs between soils of different development stages in these environments and may influence plant growth significantly. Thus, in this study, we reconstructed major parts of the nitrogen cycle in the rhizosphere soil/root system of Leucanthemopsis alpina (L.) HEYWOOD: as well as the corresponding bulk soil by quantifying functional genes of nitrogen fixation (nifH), nitrogen mineralisation (chiA, aprA), nitrification (amoA AOB, amoA AOA) and denitrification (nirS, nirK and nosZ) in a 10-year and a 120-year ice-free soil of the Damma glacier forefield. We linked the results to the ammonium and nitrate concentrations of the soils as well as to the nitrogen and carbon status of the plants. The experiment was performed in a greenhouse simulating the climatic conditions of the glacier forefield. Samples were taken after 7 and 13 weeks of plant growth. Highest nifH gene abundance in connection with lowest nitrogen content of L. alpina was observed in the 10-year soil after 7 weeks of plant growth, demonstrating the important role of associative nitrogen fixation for plant development in this soil. In contrast, in the 120-year soil copy numbers of genes involved in denitrification, mainly nosZ were increased after 13 weeks of plant growth, indicating an overall increased microbial activity status as well as higher concentrations of nitrate in this soil.
Wissenschaftlicher Artikel
Scientific Article
Bartha, B. ; Huber, C. ; Harpaintner, R. ; Schröder, P.
Environ. Sci. Pollut. Res. 17, 1553-1562 (2010)
PURPOSE: Besides classical organic pollutants and pesticides, pharmaceuticals and their residues have nowadays become recognized as relevant environmental contaminants. The risks of these chemicals for aquatic ecosystems are well known, but information about the pharmaca-plant interactions and metabolic pathways is scarce. Therefore, we investigate the process of uptake of acetaminophen (N-Acetyl-4-aminophenol) by Brassica juncea, drug-induced defense responses and detoxification mechanisms in different plant parts. MATERIAL AND METHODS: Hydroponically grown Indian mustard (Brassica juncea L. Czern.) plants were treated with acetaminophen and root and leaf samples were collected after 24, 72, and 168 h of treatment. The uptake of acetaminophen and the formation of its metabolites were analyzed using LC-MS/MS technique and enzyme activities including glutathione S-transferases (GSTs) as well as several plant defense enzymes like catalase, ascorbat peroxidase, peroxidase, and glutathione reductase were assayed spectrophotometrically. RESULTS: We determined the uptake and the translocation of acetaminophen, and we tried to identify the steps of the detoxification process by assaying typical enzymes, supposing the involvement of the same- or similar enzymes and reactions as in the mammalian detoxification process. After 24-h exposure, effective uptake and translocation were observed to the upper part of plants followed by two independent conjugative detoxification pathways. Changes in antioxidant defense enzyme activities connected to the defense pathway towards reactive oxygen species indicate an additional oxidative stress response in the plants. CONCLUSIONS: The major metabolic pathways in mammals are conjugation with activated sulfate and glucuronic acid, while a small amount of acetaminophen forms a chemically reactive and highly toxic, hydroxylated metabolite. We identified a glutathionyl and a glycoside conjugate, which refer to the similarities to mammalian detoxification. Increased GST activities in leaf tissues were observed correlated with the appearance of the acetaminophen-glutathione conjugate which shows the involvement of this enzyme group in the metabolism of acetaminophen in plants to organic pollutants and xenobiotics. High acetaminophen concentrations lead to oxidative stress and irreversible damages in the plants, which necessitates further investigations using lower drug concentrations for the deeper understanding of the induced detoxification-and defense processes.
Wissenschaftlicher Artikel
Scientific Article
Kleineidam, K. ; Sharma, S. ; Kotzerke, A. ; Heuer, H. ; Thiele-Bruhn, S. ; Smalla, K. ; Wilke, B.-M. ; Schloter, M.
Microb. Ecol. 60, 703-707 (2010)
Sulfadiazine (SDZ) is an antibiotic frequently used in agricultural husbandry. Via manuring of excrements of medicated animals, the drug reaches the soil and might impair important biochemical transformation processes performed by microbes, e.g., the nitrogen turnover. We studied the effect of pig manure and SDZ-spiked pig manure on denitrifying bacteria by quantifying nirK and nirS nitrite reductase genes in two arable soils. Addition of manure entailed mainly an increase of nirK-harboring denitrifiers in both soils, whereas in the SDZ-amended treatments, primarily the nirS denitrifiers increased in abundance after the bioavailable SDZ had declined. However, the community composition of nirS nitrite reducers investigated by denaturing gradient gel electrophoresis did not change despite the observed alterations in abundance.
Wissenschaftlicher Artikel
Scientific Article
Carrasco, L. ; Gattinger, A. ; Fliessbach, A. ; Roldan, A. ; Schloter, M. ; Caravaca, F.
Microb. Ecol. 60, 265-271 (2010)
The objective of this study was to compare the microbial community composition and biomass associated with the rhizosphere of a perennial gramineous species (Lygeum spartum L.) with that of an annual (Piptatherum miliaceum L.), both growing in semiarid mine tailings. We also established their relationship with the contents of potentially toxic metals as well as with indicators of soil quality. The total phospholipid fatty acid (PLFA) amount was significantly higher in the rhizosphere soil of the annual species than in the rhizosphere soil of the perennial species. The fungal/bacterial PLFA ratio was significantly greater in the perennial species compared to the annual species. The fatty acid 16:1ω5c, the fungal/bacterial PLFA ratio and monounsaturated/saturated PLFA ratio were correlated negatively with the soluble contents of toxic metals. The cyc/prec (cy17:0 + cy19:0/16:1ω7 + 18:1ω7) ratio was correlated positively with the soluble contents of Pb, Zn, Al, Ni, Cd, and Cu. The results of the PLFA analysis for profiling microbial communities and their stress status of both the plant species indicate that perennial and annual gramineous species appear equally suitable for use in programmes of revegetation of semiarid mine tailings.
Wissenschaftlicher Artikel
Scientific Article
Kaymakanova, M. ; Lyubenova, L. ; Schröder, P. ; Stoeva, N.
Gen. Appl. Plant Physiol. 36, 55-59 (2010)
The effects of two salts, NaCl and Na2SO4, applied at a concentration of 100 mM each in the root medium, оn the antioxidant enzymes (GR, GPX and GST) and glutathione (GSH) homeostasis of hydroponically grown bean plants (Phaseolus vulgaris L.) were studied. An increased GPX activity as well as decreased GSH content in both root and leaf of salt-treated plants were well expressed. The other enzymes studied (GR and GST) responded organ- and salt-specifically. The results obtained showed that both salts provoked oxidative stress responses in the treated bean plants.
Wissenschaftlicher Artikel
Scientific Article
Pritsch, K. ; Becerra, A. ; Polme, S. ; Tedersoo, L. ; Schloter, M. ; Agerer, R.
Mycologia 102, 1263-1273 (2010)
The objective of this study was to describe the morphological and anatomical features of five unidentified ectomycorrhizal types of Alnus acuminata and to complement their identification based on ITS-rDNA sequence analysis. The combined approach of morphotyping and sequence analysis based on ITS sequence comparison with sequences contained in GenBank and the UNITE database let us assign three of the five field-collected ectomycorrhiza morphotypes to the tomentella-thelephora lineage that closely matched European and North American species. The sequencing results within Tomentella point toward alder specific clades within T. sublilacina, T. ellisii and T. stuposa sensu lato. The two other EcM morphotypes matched Lactarius omphaliiformis and a Russula sp. Better focused, concomitant fruit body surveys are needed for accurate identification of South American ectomycorrhizal fungi because of the evidence of cryptic speciation in both agaricoid and resupinate mycobionts.
Wissenschaftlicher Artikel
Scientific Article
Philippot, L. ; Abbate, C. ; Bispo, A. ; Chesnot, T. ; Hallin, S. ; Lemanceau, P. ; Lindström, K. ; Pandard, P. ; Romero, E. ; Schloter, M. ; Somonet, P. ; Smalla, K. ; Wilke, B.-W. ; Petric, I. ; Martin-Laurent, F.
J. Soils Sediments 10, 1344-1345 (2010)
Review
Review
Weinert, N. ; Meincke, R. ; Gottwald, C. ; Heuer, H. ; Schloter, M. ; Berg, G. ; Smalla, K.
FEMS Microbiol. Ecol. 74, 114-123 (2010)
The surface of tubers might be a reservoir for bacteria that are disseminated with seed potatoes or that affect postharvest damage. The numbers of culturable bacteria and their antagonistic potential, as well as bacterial community fingerprints were analysed from tubers of seven field-grown potato genotypes, including two lines with tuber-accumulated zeaxanthin. The plant genotype significantly affected the number of culturable bacteria only at one field site. Zeaxanthin had no effect on the bacterial plate counts. In dual culture, 72 of 700 bacterial isolates inhibited at least one of the potato pathogens Rhizoctonia solani, Verticillium dahliae or Phytophthora infestans, 12 of them suppressing all three. Most of these antagonists were identified as Bacillus or Streptomyces. From tubers of two plant genotypes, including one zeaxanthin line, higher numbers of antagonists were isolated. Most antagonists showed glucanase, cellulase and protease activity, which could represent mechanisms for pathogen suppression. PCR-DGGE fingerprints of the 16S rRNA genes of bacterial communities from the tuber surfaces revealed that the potato genotype significantly affected the Pseudomonas community structure at one site. However, the genotypes showed nearly identical fingerprints for Bacteria, Actinobacteria, Alphaproteobacteria, Betaproteobacteria, Bacillus and Streptomycetaceae. In conclusion, tuber-associated bacteria were only weakly affected by the plant genotype.
Wissenschaftlicher Artikel
Scientific Article
Mench, M. ; Lepp, N. ; Bert, V. ; Schwitzguébel, J.P. ; Gawronski, S. ; Schröder, P. ; Vangronsveld, J.
J. Soils Sediments 10, 1039-1070 (2010)
Many agricultural and brownfield soils are polluted and more have become marginalised due to the introduction of new, risk-based legislation. The European Environment Agency estimates that there are at least 250,000 polluted sites in the member states that require urgent remedial action. There is also significant volumes of wastewaters and dredged polluted sediments. Phytotechnologies potentially offer a cost-effective in situ alternative to conventional technologies for remediation of low to medium-contaminated matrices, e.g. soils, sediments, tailings, solid wastes and waters. For further development, social and commercial acceptance, there is a clear requirement for up-to-date information on successes and failures of these technologies based on evidence from the field. This review reports the outcomes from several integrated experimental attempts to address this at both field and market level in the 29 countries participating in COST Action 859. This review offers insight into the deployment of promising and emergent in situ phytotechnologies, for sustainable remediation and management of contaminated soils and water, that integrative research findings produced between 2004 and 2009 by members of COST Action 859. Many phytotechnologies are at the demonstration level, but relatively few have been applied in practice on large sites. They are not capable of solving all problems. Those options that may prove successful at market level are (a) phytoextraction of metals, As and Se from marginally contaminated agricultural soils, (b) phytoexclusion and phytostabilisation of metal- and As-contaminated soils, (c) rhizodegradation of organic pollutants and (d) rhizofiltration/rhizodegradation and phytodegradation of organics in constructed wetlands. Each incidence of pollution in an environmental compartment is different and successful sustainable management requires the careful integration of all relevant factors, within the limits set by policy, social acceptance and available finances. Many plant stress factors that are not evident in short-term laboratory experiments can limit the effective deployment of phytotechnologies at field level. The current lack of knowledge on physicochemical and biological mechanisms that underpin phytoremediation, the transfer of contaminants to bioavailable fractions within the matrices, the long-term sustainability and decision support mechanisms are highlighted to identify future R&D priorities that will enable potential end-users to identify particular technologies to meet both statutory and financial requirements. Multidisciplinary research teams and a meaningful partnership between stakeholders are primary requirements that determine long-term ecological, ecotoxicological, social and financial sustainability of phytotechnologies and to demonstrate their efficiency for the solution of large-scale pollution problems. The gap between research and development for the use of phytoremediation options at field level is partly due to a lack of awareness by regulators and problem owners, a lack of expertise and knowledge by service providers and contractors, uncertainties in long-term effectiveness and difficulties in the transfer of particular metabolic pathways to productive and widely available plants. Networks such as COST Action 859 are highly relevant to the integration of research activity, maintenance of projects that demonstrate phytoremediation at a practical field scale and to inform potential end-users on the most suitable techniques. Biomass for energy and other financial returns, biodiversity and ecological consequences, genetic isolation and transfer of plant traits, management of plant-microorganism consortia in terrestrial systems and constructed wetlands, carbon sequestration and soil and water multi-functionality are identified as key areas that need to be incorporated into existing phytotechnologies.
Wissenschaftlicher Artikel
Scientific Article
Gschwendtner, S. ; Reichmann, M. ; Müller, M. ; Radl, V. ; Munch, J.-C. ; Schloter, M.
Plant Soil 335, 413-422 (2010)
In this study, the potential effects of a