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Publications of Our Institute


Young V, Dohai B, Thomas C. A. Hitch, Hyden P, Weller B, van Heusden NS, Saha D, Macgregor JF, Maseko SB, Chung-Wen Lin, Boujeant M, Choteau SA, Ober F, Schwehn P, Rothballer S,  Altmann M, Altmann S, Strobel A, Rothballer M, Tofaute M, Heinig M,  Clavel T, Twizere JC, Vincentelli R, Boes M, Krappmann D, Falter C,  Rattei T, Brun C, Zanzoni A, Falter-Braun P. bioRxiv 2023.09.25.559292; doi:

A gut meta-interactome map reveals modulation of human immunity by microbiome effectors

The molecular mechanisms by which the gut microbiome influences human health remain largely unknown. Pseudomonadota is the third most abundant phylum in normal gut microbiomes. Several pathogens in this phylum can inject so-called virulence effector proteins into host cells. We report the identification of intact type 3 secretion systems (T3SS) in 5 - 20% of commensal Pseudomonadota in normal human gut microbiomes. To understand their functions, we experimentally generated a high-quality protein-protein meta-interactome map consisting of 1,263 interactions between 289 bacterial effectors and 430 human proteins. Effector targets are enriched for metabolic and immune functions and for genetic variation of microbiome-influenced traits including autoimmune diseases. We demonstrate that effectors modulate NF-κB signaling, cytokine secretion, and adhesion molecule expression. Finally, effectors are enriched in metagenomes of Crohn’s disease, but not ulcerative colitis patients pointing toward complex contributions to the etiology of inflammatory bowel diseases. Our results suggest that effector-host protein interactions are an important regulatory layer by which the microbiome impacts human health.


Osborne R, Rehneke L, Lehmann S, Roberts J, Altmann M, Altmann S, Zhang Y, Köpff E, Dominguez-Ferreras A, Okechukwu E, Sergaki C, Rich-Griffin C, Ntoukakis V, Eichmann R, Shan W, Falter-Braun P, Schäfer P. Nat Commun. 2023 Jul 10;14(1):4065. doi: 10.1038/s41467-023-39885-5.PMID: 37429856 

Symbiont-host interactome mapping reveals effector-targeted modulation of hormone networks and activation of growth promotion.

Plants have benefited from interactions with symbionts for coping with challenging environments since the colonisation of land. The mechanisms of symbiont-mediated beneficial effects and similarities and differences to pathogen strategies are mostly unknown. Here, we use 106 (effector-) proteins, secreted by the symbiont Serendipita indica (Si) to modulate host physiology, to map interactions with Arabidopsis thaliana host proteins. Using integrative network analysis, we show significant convergence on target-proteins shared with pathogens and exclusive targeting of Arabidopsis proteins in the phytohormone signalling network. Functional in planta screening and phenotyping of Si effectors and interacting proteins reveals previously unknown hormone functions of Arabidopsis proteins and direct beneficial activities mediated by effectors in Arabidopsis. Thus, symbionts and pathogens target a shared molecular microbe-host interface. At the same time Si effectors specifically target the plant hormone network and constitute a powerful resource for elucidating the signalling network function and boosting plant productivity.


Weller B, Lin CW, Pogoutse O, Sauer M, Marin-de la Rosa N, Strobel A, Young V, Knapp JJ, Rayhan A, Falter C, Kim DK, Roth FP, Falter-Braun P. G3 (Bethesda). 2023 Jul 5;13(7):jkad105. doi: 10.1093/g3journal/jkad105.PMID: 37267226 

A resource of human coronavirus protein-coding sequences in a flexible, multipurpose Gateway Entry clone collection.

The COVID-19 pandemic has catalyzed unprecedented scientific data and reagent sharing and collaboration, which enabled understanding the virology of the SARS-CoV-2 virus and vaccine development at record speed. The pandemic, however, has also raised awareness of the danger posed by the family of coronaviruses, of which 7 are known to infect humans and dozens have been identified in reservoir species, such as bats, rodents, or livestock. To facilitate understanding the commonalities and specifics of coronavirus infections and aspects of viral biology that determine their level of lethality to the human host, we have generated a collection of freely available clones encoding nearly all human coronavirus proteins known to date. We hope that this flexible, Gateway-compatible vector collection will encourage further research into the interactions of coronaviruses with their human host, to increase preparedness for future zoonotic viral outbreaks.


Kim DK, Weller B, Lin CW, Sheykhkarimli D, Knapp JJ, Dugied G, Zanzoni A, Pons C, Tofaute MJ, Maseko SB, Spirohn K, Laval F, Lambourne L, Kishore N, Rayhan A, Sauer M, Young V, Halder H, la Rosa NM, Pogoutse O, Strobel A, Schwehn P, Li R, Rothballer ST, Altmann M, Cassonnet P, Coté AG, Vergara LE, Hazelwood I, Liu BB, Nguyen M, Pandiarajan R, Dohai B, Coloma PAR, Poirson J, Giuliana P, Willems L, Taipale M, Jacob Y, Hao T, Hill DE, Brun C, Twizere JC, Krappmann D, Heinig M, Falter C, Aloy P, Demeret C, Vidal M, Calderwood MA, Roth FP, Falter-Braun P. Nat Biotechnol. 2022 Oct 10. doi: 10.1038/s41587-022-01475-z. PMID: 36217029. IF 68.164

A proteome-scale map of the SARS-CoV-2-human contactome.

Understanding the mechanisms of coronavirus disease 2019 (COVID-19) disease severity to efficiently design therapies for emerging virus variants remains an urgent challenge of the ongoing pandemic. Infection and immune reactions are mediated by direct contacts between viral molecules and the host proteome, and the vast majority of these virus-host contacts (the 'contactome') have not been identified. Here, we present a systematic contactome map of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with the human host encompassing more than 200 binary virus-host and intraviral protein-protein interactions. We find that host proteins genetically associated with comorbidities of severe illness and long COVID are enriched in SARS-CoV-2 targeted network communities. Evaluating contactome-derived hypotheses, we demonstrate that viral NSP14 activates nuclear factor κB (NF-κB)-dependent transcription, even in the presence of cytokine signaling. Moreover, for several tested host proteins, genetic knock-down substantially reduces viral replication. Additionally, we show for USP25 that this effect is phenocopied by the small-molecule inhibitor AZ1. Our results connect viral proteins to human genetic architecture for COVID-19 severity and offer potential therapeutic targets.


McLellan H, Harvey SE, Steinbrenner J, Armstrong MR, He Q, Clewes R, Pritchard L, Wang W, Wang S, Nussbaumer T, Dohai B, Luo Q, Kumari P, Duan H, Roberts A, Boevink PC, Neumann C, Champouret N, Hein I, Falter-Braun P, Beynon J, Denby K, Birch PRJ. Proc Natl Acad Sci U S A. 2022 Aug 30;119(35):e2114064119. doi: 10.1073/pnas.2114064119. Epub 2022 Aug 22.

Exploiting breakdown in nonhost effector-target interactions to boost host disease resistance.

Plants are resistant to most microbial species due to nonhost resistance (NHR), providing broad-spectrum and durable immunity. However, the molecular components contributing to NHR are poorly characterised. We address the question of whether failure of pathogen effectors to manipulate nonhost plants plays a critical role in NHR. RxLR (Arg-any amino acid-Leu-Arg) effectors from two oomycete pathogens, Phytophthora infestans and Hyaloperonospora arabidopsidis, enhanced pathogen infection when expressed in host plants (Nicotiana benthamiana and Arabidopsis, respectively) but the same effectors performed poorly in distantly related nonhost pathosystems. Putative target proteins in the host plant potato were identified for 64 P. infestans RxLR effectors using yeast 2-hybrid (Y2H) screens. Candidate orthologues of these target proteins in the distantly related non-host plant Arabidopsis were identified and screened using matrix Y2H for interaction with RxLR effectors from both P. infestans and H. arabidopsidis. Few P. infestans effector-target protein interactions were conserved from potato to candidate Arabidopsis target orthologues (cAtOrths). However, there was an enrichment of H. arabidopsidis RxLR effectors interacting with cAtOrths. We expressed the cAtOrth AtPUB33, which unlike its potato orthologue did not interact with P. infestans effector PiSFI3, in potato and Nicotiana benthamiana. Expression of AtPUB33 significantly reduced P. infestans colonization in both host plants. Our results provide evidence that failure of pathogen effectors to interact with and/or correctly manipulate target proteins in distantly related non-host plants contributes to NHR. Moreover, exploiting this breakdown in effector-nonhost target interaction, transferring effector target orthologues from non-host to host plants is a strategy to reduce disease.

Kuhl T, Chowdhury SP, Uhl J, Rothballer M.

Genome-based characterization of plant-associated Rhodococcus qingshengii RL1 reveals stress tolerance and plant-microbe interaction traits.

Stress tolerant, plant-associated bacteria can play an important role in maintaining a functional plant microbiome and protecting plants against various (a)biotic stresses. Members of the stress tolerant genus Rhodococcus are frequently found in the plant microbiome. Rhodococcus qingshengii RL1 was isolated from Eruca sativa and the complete genome was sequenced, annotated and analyzed using different bioinformatic tools. A special focus was laid on functional analyses of stress tolerance and interactions with plants. The genome annotation of RL1 indicated that it contains a repertoire of genes which could enable it to survive under different abiotic stress conditions for e.g., elevated mercury concentrations, to interact with plants via root colonization, to produce phytohormones and siderophores, to fix nitrogen and to interact with bacterial signaling via a LuxR-solo and quorum quenching. Based on the identified genes, functional analyses were performed in vitro with RL1 under different growth conditions. The R. qingshengii type strain djl6 and a closely related Rhodococcus erythropolis BG43 were included in the experiments to find common and distinct traits between the strains. Genome based phylogenetic analysis of 15 available and complete R. erythropolis and R. qingshengii genome sequences revealed a separation of the R. erythropolis clade in two subgroups. First one harbors only R. erythropolis strains including the R. erythropolis type strain. The second group consisted of the R. qingshengii type strain and a mix of R. qingshengii and R. erythropolis strains indicating that some strains of the second group should be considered for taxonomic re-assignment. However, BG43 was clearly identified as R. erythropolis and RL1 clearly as R. qingshengii and the strains had most tested traits in common, indicating a close functional overlap of traits between the two species. Keywords: Rhodococcus qingshengii; mercury tolerance; nitrogen fixation; plant–microbe interaction; quorum quenching.

Babin D, Sommermann L, Chowdhury SP, Behr JH, Sandmann M, Neumann G, Nesme, J, Sørensen SJ, Schellenberg I, Rothballer M, Geistlinger J, Smalla K, Grosch R.

Distinct rhizomicrobiota assemblages and plant performance in lettuce grown in soils with different agricultural management histories.

A better understanding of factors shaping the rhizosphere microbiota is important for sustainable crop production. We hypothesized that the effect of agricultural management on the soil microbiota is reflected in the assemblage of the rhizosphere microbiota with implications for plant performance. We designed a growth chamber experiment growing the model plant lettuce under controlled conditions in soils of a long-term field experiment with contrasting histories of tillage (mouldboard plough vs cultivator tillage), fertilization intensity (intensive standard nitrogen (N) + pesticides/growth regulators vs extensive reduced N without fungicides/growth regulators), and last standing field crop (rapeseed vs winter wheat). High-throughput sequencing of bacterial and archaeal 16S rRNA genes and fungal ITS2 regions amplified from total community DNA showed that these factors shaped the soil and rhizosphere microbiota of lettuce, however, to different extents among the microbial domains. Pseudomonas and Olpidium were identified as major indicators for agricultural management in the rhizosphere of lettuce. Long-term extensive fertilization history of soils resulted in higher lettuce growth and increased expression of genes involved in plant stress responses compared to intensive fertilization. Our work adds to the increasing knowledge on how soil microbiota can be manipulated by agricultural management practices which could be harnessed for sustainable crop production.

Muendo BM, Shikuku VO, Getenga ZM, Lalah JO, Wandiga SO, Rothballer M.

Adsorption-desorption and leaching behavior of diuron on selected Kenyan agricultural soils.

In this work, the adsorption-desorption dynamics of diuron in three typical Kenyan agricultural soils, Nzoia (NZ), Thika (TH) and Machakos (MK) was investigated. The equilibrium adsorption data, tested against three classical nonlinear adsorption isotherms, was best described by the Freundlich model. The Freundlich adsorption constant, (KF), increased in the order MK > TH > NZ soil. Additionally, the negative Gibb's free energy values indicate the adsorption processes were thermodynamically spontaneous and physical. Multiple linear regression analysis indicated that the adsorption-desorption behavior was controlled by the clay and phosphorus contents of the soil. Phosphorus negatively affected the adsorption of diuron and promoted desorption. The groundwater ubiquity score (GUS) indicated that diuron movement rating in MK soil was 'moderate' while the movement in TH and NZ soils was 'high'.

Windisch S, Sommermann L, Babin D, Chowdhury SP, Grosch R, Moradtalab N, Walker F, Höglinger B, El-Hasan A, Armbruster W, Nesme J, Sørensen SJ, Schellenberg I, Geistlinger J, Smalla K, Rothballer M, Ludewig U, Neumann G.

Impact of long-term organic and mineral fertilization on rhizosphere metabolites, root-microbial interactions and plant health of lettuce.

Fertilization management can affect plant performance and soil microbiota, involving still poorly understood rhizosphere interactions. We hypothesized that fertilization practice exerts specific effects on rhizodeposition with consequences for recruitment of rhizosphere microbiota and plant performance. To address this hypothesis, we conducted a minirhizotron experiment using lettuce as model plant and field soils with contrasting properties from two long-term field experiments (HUB-LTE: loamy sand, DOK-LTE: silty loam) with organic and mineral fertilization history. Increased relative abundance of plant-beneficial arbuscular mycorrhizal fungi and fungal pathotrophs were characteristic of the rhizospheres in the organically managed soils (HU-org; BIODYN2). Accordingly, defense-related genes were systemically expressed in shoot tissues of the respective plants. As a site-specific effect, high relative occurrence of the fungal lettuce pathogen Olpidium sp. (76-90%) was recorded in the rhizosphere, both under long-term organic and mineral fertilization at the DOK-LTE site, likely supporting Olpidium infection due to a lower water drainage potential compared to the sandy HUB-LTE soils. However, plant growth depressions and Olpidium infection were exclusively recorded in the BIODYN2 soil with organic fertilization history. This was associated with a drastic (87-97%) reduction in rhizosphere abundance of potentially plant-beneficial microbiota (Pseudomonadaceae, Mortierella elongata) and reduced concentrations of the antifungal root exudate benzoate, known to be increased in presence of Pseudomonas spp. In contrast, high relative abundance of Pseudomonadaceae (Gammaproteobacteria) in the rhizosphere of plants grown in soils with long-term mineral fertilization (61-74%) coincided with high rhizosphere concentrations of chemotactic dicarboxylates (succinate, malate) and a high C (sugar)/N (amino acid) ratio, known to support the growth of Gammaproteobacteria. This was related with generally lower systemic expression of plant defense genes as compared with organic fertilization history. Our results suggest a complex network of belowground interactions among root exudates, site-specific factors and rhizosphere microbiota, modulating the impact of fertilization management with consequences for plant health and performance.

Bigott Y, Chowdhury SP, Pérez S, Montemurro N, Manasfi R, Schröder P.

Effect of the pharmaceuticals diclofenac and lamotrigine on stress responses and stress gene expression in lettuce (Lactuca sativa) at environmentally relevant concentrations.

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.

Ferreira NDS, Sant' AFH, Reis VM, Ambrosini A, Volpiano CG, Rothballer M, Schwab S, Baura VA, Balsanelli E, Pedrosa FDO, Pereira Passaglia LM, de Souza EM, Hartmann A, Cassan FD, Zilli JE,

Genome-based reclassification of Azospirillum brasilense Sp245 as the type strain of Azospirillum baldaniorum sp. nov.

Azospirillum sp. strain Sp245T, originally identified as belonging to Azospirillum brasilense, is recognized as a plant-growth-promoting rhizobacterium due to its ability to fix atmospheric nitrogen and to produce plant-beneficial compounds. Azospirillum sp. Sp245T and other related strains were isolated from the root surfaces of different plants in Brazil. Cells are Gram-negative, curved or slightly curved rods, and motile with polar and lateral flagella. Their growth temperature varies between 20 to 38 °C and their carbon source utilization is similar to other Azospirillum species. A preliminary 16S rRNA sequence analysis showed that the new species is closely related to A. brasilense Sp7T and A. formosense CC-Nfb-7T. Housekeeping genes revealed that Azospirillum sp. Sp245T, BR 12001 and Vi22 form a separate cluster from strain A. formosense CC-Nfb-7T, and a group of strains closely related to A. brasilense Sp7T. Overall genome relatedness index (OGRI) analyses estimated based on average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) between Azospirillum sp. Sp245T and its close relatives to other Azospirillum species type strains, such as A. brasilense Sp7T and A. formosense CC-Nfb-7T , revealed values lower than the limit of species circumscription. Moreover, core-proteome phylogeny including 1079 common shared proteins showed the independent clusterization of A. brasilense Sp7T, A. formosense CC-Nfb-7T and Azospirillum sp. Sp245T, a finding that was corroborated by the genome clustering of OGRI values and housekeeping phylogenies. The DNA G+C content of the cluster of Sp245T was 68.4-68.6 %. Based on the phylogenetic, genomic, phenotypical and physiological analysis, we propose that strain Sp245T together with the strains Vi22 and BR12001 represent a novel species of the genus Azospirillum, for which the name Azospirillum baldaniorum sp. nov. is proposed. The type strain is Sp245T (=BR 11005T=IBPPM 219T) (GCF_007827915.1, GCF_000237365.1, and GCF_003119195.2).

Parry G, Provart NJ, Brady SM, Uzilday B, Multinational Arabidopsis Steering Committee (Falter-Braun, P.), Multinational Arabidopsis Steering Committee (Mayer KFX).

Current status of the multinational Arabidopsis community.

The multinational Arabidopsis research community is highly collaborative and over the past thirty years these activities have been documented by the Multinational Arabidopsis Steering Committee (MASC). Here, we (a) highlight recent research advances made with the reference plant Arabidopsis thaliana; (b) provide summaries from recent reports submitted by MASC subcommittees, projects and resources associated with MASC and from MASC country representatives; and (c) initiate a call for ideas and foci for the "fourth decadal roadmap," which will advise and coordinate the global activities of the Arabidopsis research community.

Anderson AC, Rothballer M, Altenburger MJ, Wölber JP, Karygianni L, Lagkouvardos I, Hellwig E, Al-Ahmad A.

In-vivo shift of the microbiota in oral biofilm in response to frequent sucrose consumption.

Caries is associated with shifts of microbiota in dental biofilms and primarily driven by frequent sucrose consumption. Data on environmentally induced in vivo microbiota shifts are scarce therefore we investigated the influence of frequent sucrose consumption on the oral biofilm. Splint systems containing enamel slabs were worn for 3 × 7 days with 7-day intervals to obtain oral biofilm samples. After a three-month dietary change of sucking 10 g of sucrose per day in addition to the regular diet, biofilm was obtained again at the end of the second phase. The microbiota was analysed using Illumina MiSeq amplicon sequencing (v1-v2 region). In addition, roughness of the enamel surface was measured with laser scanning microscopy. The sucrose phase resulted in significant differences in beta-diversity and significantly decreased species richness. It was marked by a significant increase in abundance of streptococci, specifically Streptococcus gordonii, Streptococcus parasanguinis and Streptococcus sanguinis. Enamel surface roughness began to increase, reflecting initial impairment of dental enamel surface. The results showed that frequent sucrose consumption provoked compositional changes in the microbiota, leading to an increase of non-mutans streptococci, hence supporting the extended ecological plaque hypothesis and emphasizing the synergy of multiple bacterial species in the development of caries.

Poursarebani N, Trautewig C, Melzer M, Nussbaumer T, Lundqvist U, Rutten T, Schmutzer T, Brandt R, Himmelbach A, Altschmied L, Koppolu R, Youssef HM, Sibout R, Dalmais M, Bendahmane A, Stein N, Xin Z, Schnurbusch T.

COMPOSITUM 1 contributes to the architectural simplification of barley inflorescence via meristem identity signals.

Grasses have varying inflorescence shapes; however, little is known about the genetic mechanisms specifying such shapes among tribes. Here, we identify the grass-specific TCP transcription factor COMPOSITUM 1 (COM1) expressing in inflorescence meristematic boundaries of different grasses. COM1 specifies branch-inhibition in barley (Triticeae) versus branch-formation in non-Triticeae grasses. Analyses of cell size, cell walls and transcripts reveal barley COM1 regulates cell growth, thereby affecting cell wall properties and signaling specifically in meristematic boundaries to establish identity of adjacent meristems. COM1 acts upstream of the boundary gene Liguleless1 and confers meristem identity partially independent of the COM2 pathway. Furthermore, COM1 is subject to purifying natural selection, thereby contributing to specification of the spike inflorescence shape. This meristem identity pathway has conceptual implications for both inflorescence evolution and molecular breeding in Triticeae.

Anderson AC, Rothballer M, Altenburger MJ, Woelber JP, Karygianni L, Vach K, Hellwig E, Al-Ahmad A.

Long-term fluctuation of oral biofilm microbiota following different dietary phases.

Caries development is associated with shifts in the oral biofilm microbiota and primarily linked to frequent simple carbohydrate consumption. Different nutritional ingredients can either promote or prevent caries development. To investigate the effects of selected ingredients on the oral biofilm microbiota in situ, 11 study participants underwent 3-month-long dietary phases with intake of a regular diet (PI), additional frequent sucrose (PII), milk and yoghurt (PIII), and a diet rich in dietary fiber (PIV) and then returned to their regular diet (PV). Oral biofilm was sampled and analyzed applying 16S rRNA Illumina MiSeq sequencing. Additionally, the effect on the enamel was analyzed by measuring enamel surface roughness with laser scanning microscopy. The beta-diversity results showed that the microbiota in all the following phases differed significantly from PI and that the microbial community in PII was significantly different from all other phases. The abundance of the genus Streptococcus fluctuated over the course of the five phases, with a significant increase in PII (P = 0.01), decreasing in PIII and PIV (PIII and PIV versus PII: P < 0.00001) and increasing again toward PV. Other taxa showed various fluctuations of their abundances, with PV returning approximately to the levels of PI. In conclusion, while elevated sucrose consumption favored caries-promoting non-mutans streptococci, frequent milk and yoghurt intake caused a significant decrease in the abundance of these microbial taxa and in addition reduced enamel surface roughness. These results indicate that modulations of the oral biofilm microbiota can be attained even in adults through dietary changes and corresponding recommendations can be made for the prevention of caries development.IMPORTANCE Caries affects a large proportion of the population worldwide, resulting in high treatment costs. Its etiology can be ascribed to shifts of the microbiota in dental biofilms primarily driven by dietary factors. It is unclear how diet affects the microbial community of plaque biofilm in situ and whether it can be modulated to help prevent caries development. To address these issues, we analyzed changes of the in situ plaque microbiota following 3-month-long dietary changes involving elevated sucrose, dairy, and dietary fiber consumption over a period of 15 months. Applying high-throughput sequencing, we found non-mutans streptococci, a taxonomic group involved in the beginning stages toward microbial dysbiosis, in decreased abundance with elevated dairy and dietary fiber intake. Through analysis of the enamel surface roughness, these effects were confirmed. Therefore, correspondent dietary measures can be recommended for children as well as adults for caries prevention.

Kulich I, Vogler F, Bleckmann A, Cyprys P, Lindemeier M, Fuchs I, Krassini L, Schubert T, Steinbrenner J, Beynon J, Falter-Braun P, Längst G, Dresselhaus T, Sprunck S.

ARMADILLO REPEAT ONLY proteins confine Rho GTPase signalling to polar growth sites.

Polar growth requires the precise tuning of Rho GTPase signalling at distinct plasma membrane domains. The activity of Rho of plant (ROP) GTPases is regulated by the opposing action of guanine nucleotide-exchange factors (GEFs) and GTPase-activating proteins (GAPs). Whereas plant-specific ROPGEFs have been shown to be embedded in higher-level regulatory mechanisms involving membrane-bound receptor-like kinases, the regulation of GAPs has remained enigmatic. Here, we show that three Arabidopsis ARMADILLO REPEAT ONLY (ARO) proteins are essential for the stabilization of growth sites in root hair cells and trichomes. AROs interact with ROP1 enhancer GAPs (RENGAPs) and bind to the plasma membrane via a conserved polybasic region at the ARO amino terminus. The ectopic spreading of ROP2 in aro2/3/4 mutant root hair cells and the preferential interaction of AROs with active ROPs and anionic phospholipids suggests that AROs recruit RENGAPs into complexes with ROPs to confine ROP signalling to distinct membrane regions.

Zytynska SE, Eicher M, Rothballer M, Weisser WW.

Microbial-mediated plant growth promotion and pest suppression varies under climate change.

Climate change is altering the dynamics of crop pests and diseases resulting in reduced crop yields. Using beneficial soil bacterial to increase crop health is a quickly developing area in sustainable agriculture, but it is unknown if climate change or interactions with other species could alter their effect. The plant growth-promoting rhizobacterium Acidovorax radicis N35 is known to increase barley (Hordeum vulgare) plant growth under laboratory conditions, and we tested the stability of the plant-bacterial interactions when exposed to elevated carbon dioxide (CO2) and ozone (O3) levels while infesting the aboveground leaves with cereal aphids (Sitobion avenae) and the soil with beneficial earthworms. Acidovorax radicis N35 increased plant growth and reduced insect growth - with greatest effect in a high-stress elevated O3 environment, but reduced effects under elevated CO2. Earthworms promoted both plant and insect growth, but inoculation with A. radicis N35 alleviated some of the earthworm-mediated increase in pest abundance, particularly in the ambient environment. The consistency of these beneficial effects highlights the potential of exploiting local species interactions for predicting and mitigating climate change effects in managed systems. We conclude that microbial bioprotectants have high potential for benefiting agriculture via plant-growth promotion and pest suppression.

Alabid I, Hardt M, Imani J, Hartmann A, Rothballer, M, Li D, Uhl J, Schmitt-Kopplin P, Glaeser S, Kogel KH.

The N-acyl homoserine-lactone depleted Rhizobium radiobacter mutant RrF4NM13 shows reduced growth-promoting and resistance-inducing activities in mono- and dicotyledonous plants.

The Alphaproteobacterium Rhizobium radiobacter (syn. Agrobacterium tumefaciens, “A. fa brum”) can live in close association with the sebacinoid fungus Serendipita (syn. Piriformospora) indica that forms a mutualistic Sebacinalean symbiosis with a wide range of host plants. The endobacterial strain R. radiobacter F4 (RrF4), which was originally isolated from the fungus, has plant growth promotion and resistance-inducing activities resembling the beneficial activities known from the endobacteria-containing S. indica. The mechanism by which free endobacterial cells influence growth and disease resistance of colonized host plants is not fully understood. Here, we show that RrF4 produces a spectrum of quorum sensing-mediating N-acyl-homoserine lactones (AHLs) with acyl chains of C8, C10, and C12 as well as hydroxyl- or oxo-substitutions at the C3 position. In addition, and in line with previous findings showing that AHLs increase plant biomass and induce systemic resistance, the AHL-depleted lactonase-overexpressing transconjugant RrF4NM13 was partially compromised in promoting growth and inducing resistance against bacterial pathogens in both Arabidopsis thaliana and wheat (Triticum aestivum). Scanning and transmission electron microscopy proved that RrF4NM13, in contrast to RrF4, does not form cellulose-like fiber scaffolds for efficient root surface attachment. Moreover, RrF4NM13 does not penetrate into the intercellular space of the cortical tissue, which in contrast is strongly colonized by RrF4. We discuss the possibility that AHLs contribute to the outcome of the Sebacinalean symbiosis.

Escudero-Martinez C, Rodriguez PA, Liu S, Santos PA, Stephens J, Bos JIB.

An aphid effector promotes barley susceptibility through suppression of defence gene expression.

Aphids secrete diverse repertoires of effectors into their hosts to promote the infestation process. While 'omics' approaches facilitated the identification and comparison of effector repertoires from a number of aphid species, the functional characterization of these proteins has been limited to dicot (model) plants. The bird cherry-oat aphid Rhopalosiphum padi is a pest of cereal crops, including barley. Here, we extend efforts to characterize aphid effectors with regard to their role in promoting susceptibility to the R. padi-barley interaction. We selected three R. padi effectors based on sequence similarity to previously characterized Myzus persicae effectors and assessed their subcellular localization, expression, and role in promoting plant susceptibility. Expression of R. padi effectors RpC002 and Rp1 in transgenic barley lines enhanced plant susceptibility to R. padi but not M. persicae, for which barley is a poor host. Characterization of Rp1 transgenic barley lines revealed reduced gene expression of plant hormone signalling genes relevant to plant-aphid interactions, indicating that this effector enhances susceptibility by suppressing plant defences in barley. Our data suggest that some aphid effectors specifically function when expressed in host species, and feature activities that benefit their corresponding aphid species.

Garcia VJ, Xu S, Ravikumar R, Wang W, Elliott L, Gonzalez E, Fesenko M, Altmann M, Brunschweiger B, Falter-Braun P, Moore I, Burlingame A, Assaad FF, Wang Z.

TRIPP is a plant-specific component of the Arabidopsis TRAPPII membrane trafficking complex with important roles in plant development.

How the membrane trafficking system spatially organizes intracellular activities and intercellular signaling networks in plants is not well understood. Transport Protein Particle (TRAPP) complexes play key roles in the selective delivery of membrane vesicles to various subcellular compartments in yeast and animals but remain to be fully characterized in plants. Here, we investigated TRAPP complexes in Arabidopsis (Arabidopsis thaliana) using immunoprecipitation followed by quantitative mass spectrometry analysis of AtTRS33, a conserved core component of all TRAPP complexes. We identified 14 AtTRS33-interacting proteins, including homologs of all 13 TRAPP components in mammals and a protein that has homologs only in multicellular photosynthetic organisms and is thus named TRAPP-Interacting Plant Protein (TRIPP). TRIPP specifically associates with the TRAPPII complex through binary interactions with two TRAPPII-specific subunits. TRIPP colocalized with a subset of TRS33 compartments and trans-Golgi network markers in a TRS33-dependent manner. Loss-of-function tripp mutants exhibited dwarfism, sterility, partial photomorphogenesis in the dark, reduced polarity of the auxin transporter PIN2, incomplete cross wall formation, and altered localization of a TRAPPII-specific component. Therefore, TRIPP is a plant-specific component of the TRAPPII complex with important functions in trafficking, plant growth, and development.

Altmann M, Altmann S, Rodriguez PA, Weller B, Vergara LE, Palme J, la Rosa NM, Sauer M, Wenig M, Villaécija-Aguilar JA, Sales J, Lin CW, Pandiarajan R, Young V, Strobel A, Gross L, Carbonnel S, Kugler KG, Garcia-Molina A, Bassel GW, Falter C, Mayer KFX, Gutjahr C, Vlot AC, Grill E, Falter-Braun P.

Extensive signal integration by the phytohormone protein network.

Plant hormones coordinate responses to environmental cues with developmental programs1, and are fundamental for stress resilience and agronomic yield2. The core signalling pathways underlying the effects of phytohormones have been elucidated by genetic screens and hypothesis-driven approaches, and extended by interactome studies of select pathways3. However, fundamental questions remain about how information from different pathways is integrated. Genetically, most phenotypes seem to be regulated by several hormones, but transcriptional profiling suggests that hormones trigger largely exclusive transcriptional programs4. We hypothesized that protein-protein interactions have an important role in phytohormone signal integration. Here, we experimentally generated a systems-level map of the Arabidopsis phytohormone signalling network, consisting of more than 2,000 binary protein-protein interactions. In the highly interconnected network, we identify pathway communities and hundreds of previously unknown pathway contacts that represent potential points of crosstalk. Functional validation of candidates in seven hormone pathways reveals new functions for 74% of tested proteins in 84% of candidate interactions, and indicates that a large majority of signalling proteins function pleiotropically in several pathways. Moreover, we identify several hundred largely small-molecule-dependent interactions of hormone receptors. Comparison with previous reports suggests that noncanonical and nontranscription-mediated receptor signalling is more common than hitherto appreciated.

Nussbaumer T, Debnath O, Wagner C, Heidari P.

TraitCorr as a workbench for correlating gene expression measurements with phenotypic data.

Today, high-throughput transcriptome sequencing and microarray experiments can generate enormous amounts of data to profile gene expression. This expression data often associates with phenotypic information and thus sheds light on the roles of particular traits on genes. Here, we present the user-interface TraitCorr to establish genotype-phenotype relationships and to determine genes, which correlate significantly with a selected trait, using simple correlation and regression analysis. TraitCorr also includes user-friendly visualization and export features. Furthermore, TraitCorr allows identifying genes that are shared among different traits and thus provides new aspects of gene functions which could be useful to better understand the relationship between gene products and phenotype.

Wierbowski SD, Vo TV, Falter-Braun P, Jobe TO, Kruse LH, Wei X, Liang J, Meyer MJ, Akturk N, Rivera-Erick CA, Cordero NA, Paramo MI, Shayhidin EE, Bertolotti M, Tippens ND, Akther K, Sharma R, Katayose Y, Salehi-Ashtiani K, Hao T, Ronald PC, Ecker JR, Schweitzer PA, Kikuchi S, Mizuno H, Hill DE, Vidal M, Moghe GD, McCouch SR, Yu H,

A massively parallel barcoded sequencing pipeline enables generation of the first ORFeome and interactome map for rice.

Systematic mappings of protein interactome networks have provided invaluable functional information for numerous model organisms. Here we develop PCR-mediated Linkage of barcoded Adapters To nucleic acid Elements for sequencing (PLATE-seq) that serves as a general tool to rapidly sequence thousands of DNA elements. We validate its utility by generating the ORFeome for Oryza sativa covering 2,300 genes and constructing a high-quality protein-protein interactome map consisting of 322 interactions between 289 proteins, expanding the known interactions in rice by roughly 50%. Our work paves the way for high-throughput profiling of protein-protein interactions in a wide range of organisms.

Lantzouni O, Alkofer A, Falter-Braun P, Schwechheimer C

Growth-regulating factors interact with DELLAs and regulate growth in cold stress.

DELLA proteins are repressors of the gibberellin (GA) hormone signaling pathway that act mainly by regulating transcription factor activities in plants. GAs induce DELLA repressor protein degradation and thereby control a number of critical developmental processes as well as responses to stresses such as cold. The strong effect of cold temperatures on many physiological processes has rendered it difficult to assess, based on phenotypic criteria, the role of GA and DELLAs in plant growth during cold stress. Here, we uncover substantial differences in the GA transcriptomes between plants grown at ambient temperature (21°C) and plants exposed to cold stress (4°C) in Arabidopsis (Arabidopsis thaliana). We further identify over 250, to the largest extent previously unknown, DELLA-transcription factor interactions using the yeast two-hybrid system. By integrating both data sets, we reveal that most members of the nine-member GRF (GROWTH REGULATORY FACTOR) transcription factor family are DELLA interactors and, at the same time, that several GRF genes are targets of DELLA-modulated transcription after exposure to cold stress. We find that plants with altered GRF dosage are differentially sensitive to the manipulation of GA and hence DELLA levels, also after cold stress, and identify a subset of cold stress-responsive genes that qualify as targets of this DELLA-GRF regulatory module.

Mergner J, Frejno M, List M, Papacek M, Chen X, Chaudhary A, Samaras P, Richter S, Shikata H, Messerer M, Lang D, Altmann S, Cyprys P, Zolg DP, Mathieson T, Bantscheff M, Hazarika RR, Schmidt T, Dawid C, Dunkel A, Hofmann T, Sprunck S, Falter-Braun P, Johannes F, Mayer KFX, Jürgens G, Wilhelm M, Baumbach J, Grill E, Schneitz K, Schwechheimer C, Kuster B.

Mass-spectrometry-based draft of the Arabidopsis proteome.

Plants are essential for life and are extremely diverse organisms with unique molecular capabilities1. Here we present a quantitative atlas of the transcriptomes, proteomes and phosphoproteomes of 30 tissues of the model plant Arabidopsis thaliana. Our analysis provides initial answers to how many genes exist as proteins (more than 18,000), where they are expressed, in which approximate quantities (a dynamic range of more than six orders of magnitude) and to what extent they are phosphorylated (over 43,000 sites). We present examples of how the data may be used, such as to discover proteins that are translated from short open-reading frames, to uncover sequence motifs that are involved in the regulation of protein production, and to identify tissue-specific protein complexes or phosphorylation-mediated signalling events. Interactive access to this resource for the plant community is provided by the ProteomicsDB and ATHENA databases, which include powerful bioinformatics tools to explore and characterize Arabidopsis proteins, their modifications and interactions.

Omony J, Nussbaumer T, Gutzat R.

DNA methylation analysis in plants: review of computational tools and future perspectives.

Genome-wide DNA methylation studies have quickly expanded due to advances in next-generation sequencing techniques along with a wealth of computational tools to analyze the data. Most of our knowledge about DNA methylation profiles, epigenetic heritability and the function of DNA methylation in plants derives from the model species Arabidopsis thaliana. There are increasingly many studies on DNA methylation in plants-uncovering methylation profiles and explaining variations in different plant tissues. Additionally, DNA methylation comparisons of different plant tissue types and dynamics during development processes are only slowly emerging but are crucial for understanding developmental and regulatory decisions. Translating this knowledge from plant model species to commercial crops could allow the establishment of new varieties with increased stress resilience and improved yield. In this review, we provide an overview of the most commonly applied bioinformatics tools for the analysis of DNA methylation data (particularly bisulfite sequencing data). The performances of a selection of the tools are analyzed for computational time and agreement in predicted methylated sites for A. thaliana, which has a smaller genome compared to the hexaploid bread wheat. The performance of the tools was benchmarked on five plant genomes. We give examples of applications of DNA methylation data analysis in crops (with a focus on cereals) and an outlook for future developments for DNA methylation status manipulations and data integration.

Kuhl T, Felder M, Nussbaumer T, Fischer D, Kublik S, Chowdhury SP, Schloter M, Rothballer M.

De novo genome assembly of a plant-associated Rhodococcus qingshengii strain (RL1) isolated from Eruca sativa Mill. and showing plant growth-promoting properties.

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.

Platzer A, Nussbaumer T, Karonitsch T, Smolen JS, Aletaha D.

Analysis of gene expression in rheumatoid arthritis and related conditions offers insights into sex-bias, gene biotypes and co-expression patterns.

The era of next-generation sequencing has mounted the foundation of many gene expression studies. In rheumatoid arthritis research, this has led to the discovery of important candidate genes which offered novel insights into mechanisms and their possible roles in the cure of the disease. In the last years, data generation has outstripped data analysis and while many studies focused on specific aspects of the disease, a global picture of the disease is not yet accomplished. Here, we analyzed and compared a collection of gene expression information from healthy individuals and from patients suffering under different arthritis conditions from published studies containing the following clinical conditions: early and established rheumatoid arthritis, osteoarthritis and arthralgia. We show comprehensive overviews of this data collection and give new insights specifically on gene expression in the early stage, into sex-dependent gene expression, and we describe general differences in expression of different biotypes of genes. Many genes that are related to cytoskeleton changes (actin filament related genes) are differently expressed in early rheumatoid arthritis in comparison to healthy subjects; interestingly, eight of these genes reverse their expression ratio significantly between men and women compared early rheumatoid arthritis and healthy subjects. There are some slighter changes between men and woman between the conditions early and established rheumatoid arthritis. Another aspect are miRNAs and other gene biotypes which are not only promising candidates for diagnoses but also change their expression grossly in average at rheumatoid arthritis and arthralgia compared to the healthy condition. With a selection of intersecting genes, we were able to generate simple classification models to distinguish between healthy and rheumatoid arthritis as well as between early rheumatoid arthritis to other arthritides based on gene expression.

Kalde M, Elliott L, Ravikumar R, Rybak K, Altmann M, Klaeger S, Wiese C, Abele M, Al B, Kalbfuß N, Qi X, Steiner A, Meng C, Zheng H, Kuster B, Falter-Braun P, Ludwig C, Moore I, Assaad FF.

Interactions between Transport Protein Particle (TRAPP) complexes and Rab GTPases in Arabidopsis.

Transport Protein Particle II (TRAPPII) is essential for exocytosis, endocytosis, protein sorting and cytokinesis. In spite of a considerable understanding of its biological role, little information is known about Arabidopsis TRAPPII complex topology and molecular function. In this study, independent proteomic approaches initiated with TRAPP components or Rab-A GTPase variants converge on the TRAPPII complex. We show that the Arabidopsis genome encodes the full complement of 13 TRAPPC subunits, including four previously unidentified components. A dimerization model is proposed to account for binary interactions between TRAPPII subunits. Preferential binding to dominant negative (GDP-bound) versus wild-type or constitutively active (GTP-bound) RAB-A2a variants discriminates between TRAPPII and TRAPPIII subunits and shows that Arabidopsis complexes differ from yeast but resemble metazoan TRAPP complexes. Analyzes of Rab-A mutant variants in trappii backgrounds provide genetic evidence that TRAPPII functions upstream of RAB-A2a, allowing us to propose that TRAPPII is likely to behave as a guanine nucleotide exchange factor (GEF) for the RAB-A2a GTPase. GEFs catalyze exchange of GDP for GTP; the GTP-bound, activated, Rab then recruits a diverse local network of Rab effectors to specify membrane identity in subsequent vesicle fusion events. Understanding GEF-Rab interactions will be crucial to unravel the co-ordination of plant membrane traffic.

Heidari P, Ahmadizadeh M, Izanlo F, Nussbaumer T.

In silico study of the CESA and CSL gene family in Arabidopsis thaliana and Oryza sativa: Focus on post-translation modifications.

Cellulose is an important cell wall component and plays a key role in the environmental stress response. Cellulose synthase (CESA) genes along with cellulose synthase-like (CSL) genes are involved in cellulose biosynthesis and various studies have been carried out on phylogeny and clustering of the related cellulose synthase genes but there is no comparative investigation of factors that regulate the post-translation modification. Here, we have selected candidate genes in Arabidopsis and rice and investigated them by various bioinformatics tools to allow a precise dissection of the regulatory modification elements. According to multiple sequence alignments and the distribution of conserved motifs genes were classified into three major groups and LOC_Os11g13650, LOC_Os02g43440 and LOC_Os10g25740 were identified as members of Os-CSLC subfamily. The prominent differences between CESA and CSL genes were observed in terms of the post-translational modification and physicochemical properties of proteins in Arabidopsis (as dicotyledonous) and rice (as monocotyledonous). Moreover, the binding sites of common transcription factors such as MYB, WRKY and abscisic acid response element (ABRE) family were found in the promoter regions of CESA and CSL genes family, and expression patterns sharply showed differentially expression in Arabidopsis and rice tissues as response to biotic and abiotic stresses. The considerable outcome of the post-translation modification of studied genes demonstrated that CESA proteins were more phosphorylated than CSL proteins, and CESA proteins were more hydrophilic. It can be concluded that obtained results furnish further information about the genes which are involving in cellulose biosynthesis that will be useful for more dissection and functional analysis.

Rodriguez PA, Rothballer M, Chowdhury SP, Nussbaumer T, Gutjahr C, Falter-Braun P.

Systems biology of plant-microbiome interactions.

In natural environments, plants are exposed to diverse microbiota that they interact with in complex ways. While plant-pathogen interactions have been intensely studied to understand defense mechanisms in plants, many microbes and microbial communities can have substantial beneficial effects on their plant host. Such beneficial effects include improved acquisition of nutrients, accelerated growth, resilience against pathogens, and improved resistance against abiotic stress conditions such as heat, drought, and salinity. However, the beneficial effects of bacterial strains or consortia on their host are often cultivar and species specific, posing an obstacle to their general application. Remarkably, many of the signals that trigger plant immune responses are molecularly highly similar and often identical in pathogenic and beneficial microbes. Thus, it is unclear what determines the outcome of a particular microbe-host interaction and which factors enable plants to distinguish beneficials from pathogens. To unravel the complex network of genetic, microbial, and metabolic interactions, including the signaling events mediating microbe-host interactions, comprehensive quantitative systems biology approaches will be needed.

Hartmann A, Fischer D, Kinzel L, Chowdhury SP, Hofmann A, Baldani JI, Rothballer M.

Assessment of the structural and functional diversities of plant microbiota: Achievements and challenges - A review.

Analyses of the spatial localization and the functions of bacteria in host plant habitats through in situ identification by immunological and molecular genetic techniques combined with high resolving microscopic tools and 3D-image analysis contributed substantially to a better understanding of the functional interplay of the microbiota in plants. Among the molecular genetic methods, 16S-rRNA genes were of central importance to reconstruct the phylogeny of newly isolated bacteria and to localize them in situ. However, they usually do not allow resolution for phylogenetic affiliations below genus level. Especially, the separation of opportunistic human pathogens from plant beneficial strains, currently allocated to the same species, needs genome-based resolving techniques. Whole bacterial genome sequences allow to discriminate phylogenetically closely related strains. In addition, complete genome sequences enable strain-specific monitoring for biotechnologically relevant strains. In this mini-review we present high resolving approaches for analysis of the composition and key functions of plant microbiota, focusing on interactions of diazotrophic plant growth promoting bacteria, like Azospirillum brasilense, with non-legume host plants. Combining high resolving microscopic analyses with specific immunological detection methods and molecular genetic tools, including especially transcriptome analyses of both the bacterial and plant partners, enables new insights into key traits of beneficial bacteria-plant interactions in holobiontic systems.

Rodrigo Quejigo J, Tejedor-Sanz S, Schroll R., Esteve-Núñez A.

Electrodes boost microbial metabolism to mineralize antibiotics in manure.

Livestock manures are potential sources of antibiotics in the environment. Sulfamethazine (SMZ), frequently used in veterinary medicine, can enter the environment by using manure as soil fertilizer due to its incomplete absorption in the animal gut and its unmetabolized excretion. The objective of this study was to evaluate the mineralization of 14C-labelled SMZ in manure under a new redox scenario provided by microbial electrochemical reactors, termed microbial electroremediating cells (MERC). These devices aim to overcome the electron acceptor limitation in bacterial oxidative metabolism by means of using electrodes to enhance the biodegradation of pollutants in the environment. Our results revealed that the total degradation of 14C-SMZ reached 43.5% in short term batch laboratory scale experiments under reducing conditions (-400 mV vs. Ag/AgCl). Actually, SMZ mineralization was enhanced up to 10-fold in the early stages (after 2 weeks) in comparison with an electrode-free natural attenuation assay. Moreover, mineralization showed a dependence on electrode potential, with negligible results for conditions set to +400 mV vs Ag/AgCl. The impact of merging electrodes and microorganisms for manure bioremediation suggests a promising future for this emerging technology to treat polluted livestock wastes and prevent soil and groundwater pollution.

Jin X, Kengara FO, Yue X, Wang F, Schroll R, Munch JC, Gu C, Jiang X.

Shorter interval and multiple flooding-drying cycling enhanced the mineralization of C-14-DDT in a paddy soil.

DDT and its main metabolites (DDTs) are still the residual contaminants in soil. Sequential anaerobic-aerobic cycling has long been approved for enhancing the degradation of DDTs in soil. However, there is a lack of study investigating whether anaerobic-aerobic cycling would enhance the mineralization of DDT, and what a kind of anaerobic-aerobic management regimes would be optimal. To fill these gaps, the fate of 14C-DDT under different flooding-drying cycles was examined in a paddy soil by monitoring its mineralization and bioavailability. The results show the total mineralization of 14C-DDT in 314 days accounted for 1.01%, 1.30%, and 1.41%, individually for the treatments subjected to one, two, and three flooding-drying cycles. By comparison, the treatment subjected to the permanently aerobic phase had only 0.12% cumulative mineralization. Shorter intervals and multiple flooding-drying cycles enhanced the mineralization of 14C-DDT, however, reduced its bioavailability. Therefore, the enhanced mineralization was explained from an abiotic pathway as predicted by the one-electron reduction potential (E1), the Fukui function for nucleophilic attack (f+) and the steps for anaerobic decarboxylation. From a practical view, it is important to investigate how the anaerobic-aerobic interval and frequency would affect the degradation and mineralization of DDT, which is very essential in developing remediation strategies.

Chowdhury SP, Babin D, Sandmann M, Jacquiod S, Sommermann L, Sørensen SJ, Fliessbach A, Mäder P, Geistlinger J, Smalla K, Rothballer M, Grosch R.

Effect of long-term organic and mineral fertilization strategies on rhizosphere microbiota assemblage and performance of lettuce.

Long-term agricultural fertilization strategies gradually change soil properties including the associated microbial communities. Cultivated crops recruit beneficial microbes from the surrounding soil environment via root exudates. In this study, we aimed to investigate the effects of long-term fertilization strategies across field sites on the rhizosphere prokaryotic (Bacteria and Archaea) community composition and plant performance. We conducted growth chamber experiments with lettuce (Lactuca sativa L.) cultivated in soils from two long-term field experiments, each of which compared organic versus mineral fertilization strategies. 16S rRNA gene amplicon sequencing revealed the assemblage of a rhizosphere core microbiota shared in all lettuce plants across soils, going beyond differences in community composition depending on field site and fertilization strategies. The enhanced expression of several plant genes with roles in oxidative and biotic stress signalling pathways in lettuce grown in soils with organic indicates an induced physiological status in plants. Lettuce plants grown in soils with different fertilization histories were visibly free of stress symptoms and achieved comparable biomass. This suggests a positive aboveground plant response to belowground plant-microbe interactions in the rhizosphere. Besides effects of fertilization strategy and field site, our results demonstrate the crucial role of the plant in driving rhizosphere microbiota assemblage.

Marin De La Rosa NA, Lin C-W, Kang YJ, Dhondt S, Gonzalez N, Inzé D, Falter-Braun P.

Drought resistance is mediated by divergent strategies in closely related Brassicaceae.

Droughts cause severe crop losses worldwide and climate change is projected to increase their prevalence in the future. Similar to the situation for many crops, the reference plant Arabidopsis thaliana (Ath) is considered drought-sensitive, whereas, as we demonstrate, its close relatives Arabidopsis lyrata (Aly) and Eutrema salsugineum (Esa) are drought-resistant. To understand the molecular basis for this plasticity we conducted a deep phenotypic, biochemical and transcriptomic comparison using developmentally matched plants. We demonstrate that Aly responds most sensitively to decreasing water availability with early growth reduction, metabolic adaptations and signaling network rewiring. By contrast, Esa is in a constantly prepared mode as evidenced by high basal proline levels, ABA signaling transcripts and late growth responses. The stress-sensitive Ath responds later than Aly and earlier than Esa, although its responses tend to be more extreme. All species detect water scarcity with similar sensitivity; response differences are encoded in downstream signaling and response networks. Moreover, several signaling genes expressed at higher basal levels in both Aly and Esa have been shown to increase water-use efficiency and drought resistance when overexpressed in Ath. Our data demonstrate contrasting strategies of closely related Brassicaceae to achieve drought resistance.

Fayeulle A, Veignie E, Schroll R, Munch JC, Rafin, C.

PAH biodegradation by telluric saprotrophic fungi isolated from aged PAH-contaminated soils in mineral medium and historically contaminated soil microcosms.

Remediation of contaminated soils is of high relevance considering losses of this limited resource in most countries through erosion or through destruction for societal purposes. Most physicochemical remediation techniques lead to soil destruction avoiding reuse of the sites and loss of soil functions including ecological services like water retention/filtration, plant needs, carbon sequestration, or atmosphere restoration. This study aims to find out efficient telluric PAH-degrading fungi to both remediate soils and preserve their functioning.

Polzin J, Arevalo P, Nussbaumer T, Polz MF, Bright M.

Polyclonal symbiont populations in hydrothermal vent tubeworms and the environment.

Horizontally transmitted symbioses usually house multiple and variable symbiont genotypes that are acquired from a much more diverse environmental pool via partner choice mechanisms. However, in the deep-sea hydrothermal vent tubeworm Riftia pachyptila (Vestimentifera, Siboglinidae), it has been suggested that the Candidatus Endoriftia persephone symbiont is monoclonal. Here, we show with high-coverage metagenomics that adult R. pachyptila house a polyclonal symbiont population consisting of one dominant and several low-frequency variants. This dominance of one genotype is confirmed by multilocus gene sequencing of amplified housekeeping genes in a broad range of host individuals where three out of four loci ( atpA, uvrD and recA) revealed no genomic differences, while one locus ( gyrB) was more diverse in adults than in juveniles. We also analysed a metagenome of free-living Endoriftia and found that the free-living population showed greater sequence variability than the host-associated population. Most juveniles and adults shared a specific dominant genotype, while other genotypes can dominate in few individuals. We suggest that although generally permissive, partner choice is selective enough to restrict uptake of some genotypes present in the environment.

Ravikumar R, Kalbfuß N, Gendre D, Steiner A, Altmann M, Altmann S, Rybak K, Edelmann H, Stephan F, Lampe M, Facher E, Wanner G, Falter-Braun P, Bhalerao RP, Assaad FF.

Independent yet overlapping pathways ensure the robustness and responsiveness of trans-Golgi network functions in Arabidopsis.

The trans-Golgi-network (TGN) has essential housekeeping functions in secretion, endocytosis and protein sorting, but also more specialized functions in plant development. How the robustness of basal TGN function is ensured while specialized functions are differentially regulated is poorly understood. Here, we investigate two key regulators of TGN structure and function, ECHIDNA and the Transport Protein Particle II (TRAPPII) tethering complex. An analysis of physical, network and genetic interactions suggests that two network communities are implicated in TGN function and that ECHIDNA and TRAPPII belong to distinct yet overlapping pathways. Whereas ECHIDNA and TRAPPII colocalized at the TGN in interphase cells, their localization diverged in dividing cells. Moreover, ECHIDNA and TRAPPII localization patterns were mutually independent. TGN structure, endocytosis and sorting decisions were differentially impacted in echidna and trappii mutants. Our analyses point to a partitioning of specialized TGN functions, with ECHIDNA being required for cell elongation and TRAPPII for cytokinesis. Two independent pathways able to compensate for each other might contribute to the robustness of TGN housekeeping functions and to the responsiveness and fine tuning of its specialized functions.

Anderson AC, Rothballer M, Altenburger MJ, Woelber JP, Karygianni L, Lagkouvardos I, Hellwig E, Al-Ahmad A.

In-vivo shift of the microbiota in oral biofilm in response to frequent sucrose consumption.

Caries is associated with shifts of microbiota in dental biofilms and primarily driven by frequent sucrose consumption. Data on environmentally induced in vivo microbiota shifts are scarce therefore we investigated the influence of frequent sucrose consumption on the oral biofilm. Splint systems containing enamel slabs were worn for 3 × 7 days with 7-day intervals to obtain oral biofilm samples. After a three-month dietary change of sucking 10 g of sucrose per day in addition to the regular diet, biofilm was obtained again at the end of the second phase. The microbiota was analysed using Illumina MiSeq amplicon sequencing (v1-v2 region). In addition, roughness of the enamel surface was measured with laser scanning microscopy. The sucrose phase resulted in significant differences in beta-diversity and significantly decreased species richness. It was marked by a significant increase in abundance of streptococci, specifically Streptococcus gordonii, Streptococcus parasanguinis and Streptococcus sanguinis. Enamel surface roughness began to increase, reflecting initial impairment of dental enamel surface. The results showed that frequent sucrose consumption provoked compositional changes in the microbiota, leading to an increase of non-mutans streptococci, hence supporting the extended ecological plaque hypothesis and emphasizing the synergy of multiple bacterial species in the development of caries.

Altmann M, Altmann S, Falter C, Falter-Braun P.

High-quality yeast-2-hybrid interaction network mapping.

In this article, we describe a Y2H interaction mapping protocol for systematically screening medium-to-large collections of open reading frames (ORFs) against each other. The protocol is well suited for analysis of focused networks, for modules of interest, assembling genome-scale interactome maps, and investigating host-microbe interactions. The four-step high-throughput protocol has a demonstrated low false-discovery rate that is essential for producing meaningful network maps. Following the assembly of yeast expression clones from an existing ORFeome collection, we describe in detail the four-step procedure that begins with the primary screen using minipools, followed by secondary verification of primary positives, identification of candidate interaction pairs by sequencing, and a final verification step using fresh inoculants. In addition to this core protocol, aspects of network mapping and quality control will be discussed briefly. © 2018 by John Wiley & Sons, Inc.

Kljujev I, Raicevic V, Jovicic-Petrovic J, Vujovic B, Mirkovic M, Rothballer M.

Listeria monocytogenes - Danger for health safety vegetable production.

The microbiologically contaminated vegetables represent a risk for consumers, especially vegetables without thermal processing. It is known that human pathogen bacteria, such as Listeria monocytogenes, could exist on fresh vegetables. The fresh vegetables could become Listeria-contaminated if they come in touch with contaminated soil, manure, irrigation water. The aim of this work was to investigate the presence of Listeria spp. and L. monocytogenes in different kind of vegetables grown in field and greenhouse condition as well as surface and endophytic colonization plant roots of different vegetables species by L. monocytogenes in laboratory conditions. The detection of Listeria spp. and L. monocytogenes in vegetable samples was done using ISO and PCR methods. The investigation of colonization vegetable roots and detection Listeria-cells inside plant root tissue was done using Fluorescence in situ hybridization (FISH) method in combination with confocal laser scanning microscopy (CLSM). The results showed that 25.58% vegetable samples were positive for Listeria spp. and only one sample (carrot) was positive for L. monocytogenes out of 43 samples in total collected from field and greenhouse. The strain L. monocytogenes EGD-E surface and endophytic colonized carrot root in highest degree while strain L. monocytogenes SV4B was the most represented at leafy vegetable plants, such at lettuce (1.68 × 106 cells/mm3 absolutely dry root) and spinach (1.39 × 106 cells/mm3 absolutely dry root) root surface. The cells of L. monocytogenes SV4B were visible as single cells in interior tissue of plant roots (celery and sweet corn roots) as well as in the interior of the plant root cell at sweet corn root. The cells of L. monocytogenes EGD-E bind to the surface of the plant root and they were less commonly found out on root hair. In the inner layers of the root, those bacterial cells were inhabited intercellular spaces mainly as single cells very close to the larval vessels of root. Our results suggest that L. monocytogenes is very good endophytic colonizer of vegetable plant roots.

Nguyen NK, Dörfler U, Welzl G, Munch JC, Schroll R, Suhadolc M.

Large variation in glyphosate mineralization in 21 different agricultural soils explained by soil properties.

Glyphosate and its main metabolite aminomethylphosphonic acid (AMPA) have frequently been detected in surface water and groundwaters. Since adequate glyphosate mineralization in soil may reduce its losses to environment, improved understanding of site specific factors underlying pesticide mineralization in soils is needed. The aim of this study was to investigate the relationship between soil properties and glyphosate mineralization. To establish a sound basis for resilient correlations, the study was conducted with a large number of 21 agricultural soils, differing in a variety of soil parameters, such as soil texture, soil organic matter content, pH, exchangeable ions etc. The mineralization experiments were carried out with 14C labelled glyphosate at a soil water tension of -15 kPa and at a soil density of 1.3 g cm-3 at 20 ± 1 °C for an incubation period of 32 days. The results showed that the mineralization of glyphosate in different agricultural soils varied to a great extent, from 7 to 70% of the amount initially applied. Glyphosate mineralization started immediately after application, the highest mineralization rates were observed within the first 4 days in most of the 21 soils. Multiple regression analysis revealed exchangeable acidity (H+ and Al3+), exchangeable Ca2+ ions and ammonium lactate extractable K to be the key soil parameters governing glyphosate mineralization in the examined soils. A highly significant negative correlation between mineralized glyphosate and NaOH-extractable residues (NaOH-ER) in soils strongly suggests that NaOH-ER could be used as a simple and reliable parameter for evaluating the glyphosate mineralization capacity. The NaOH-ER were composed of glyphosate, unknown 14C-residues, and AMPA (12%-65%, 3%-34%, 0%-11% of applied 14C, respectively). Our results highlighted the influential role of soil exchangeable acidity, which should therefore be considered in pesticide risk assessments and management to limit efficiently the environmental transfers of glyphosate.

Kljujev I, Raicevic V, Vujovic B, Rothballer M, Schmid, M.

Salmonella as an endophytic colonizer of plants - A risk for health safety vegetable production.

Contamination of vegetables and fruits is the result of presence of human pathogen bacteria which can contaminate products in any part of production chain. There is an evidence of presence of: Salmonella spp. on the fresh vegetables and Salmonellosis is connected with tomato, sprouts, cantaloupe etc. The goal of this research is transmission of pathogen bacteria from irrigation water to plants and studying/monitoring the ability of the Salmonella spp. to colonize the surface and interior (endophytic colonization) of root at different vegetable species. Transmission of three Salmonella spp. strains from irrigation water to plants, as well as colonization of plants by these bacteria was investigated by using Fluorescence In Situ Hybridization (FISH) in combination with confocal laser scanning microscopy (CLSM). All tested Salmonella spp. strains showed ability to more or less colonize the surface and interior niches of the root, stem and leaf of the investigated plant species. These bacteria also were found in plant cells cytoplasm, although the mechanism of their entrance has not been clarified yet.

Queligo JR, Domínguez-Garay A, Dörfler U, Schroll R, Esteve-Núñez A.

Anodic shifting of the microbial community profile to enhance oxidative metabolism in soil.

The biodegradation of pollutants in soil is limited by the availability of terminal electron acceptors required to support microbial respiration. Microbial Electroremediating Cells (MERCs) consist of a variety of bioelectrochemical devices that aim to overcome electron acceptor limitation and maximize the biodegradation of pollutants in the environment. This electrode-based method to stimulate the oxidative metabolism of environmental microbial populations is referred to as bioelectroventing. The current research uses MERCs principles, under different configurations, for stimulating native soil bacteria to achieve the complete removal of the herbicide isoproturon (IPU). Our studies conclude that the application of a high anodic potential (+600 mV versus Ag/AgCl) to contaminated soils increases, not only IPU-removal, but also leads to an effective clean-up as demonstrated by soil ecotoxicological analysis after treatment. Furthermore, electrode potential differences induced taxonomical shifts in the microbial community as exposed by the high-throughput sequencing analysis. We also used microbial community diversity as reporter of the electrode's influence. Our results showed that the electrode impacted the communities as far as 0.5 cm away. The data provided here is evidence that polarized electrodes are a cost-effective and environmentally friendly strategy to select microbial communities for the successfully bioremediation of isoproturon-polluted soils.

Zhu X, Schroll R, Dörfler U, Chen B.

Inoculation of soil with an Isoproturon degrading microbial community reduced the pool of "real non-extractable" Isoproturon residues.

During pesticides degradation, biogenic non-extractable residues (“apparent NER”) may not share the same environmental fate and risks with the “real NER” that are bound to soil matrix. It is not clear how microbial community (MC) inoculation for pesticides degradation would influence the NER composition. To investigate degradation efficiency of pesticides Isoproturon (IPU) and NER composition following MC inoculation, clay particles harboring MC that contains the IPU degrading strain, Sphingomonas sp., were inoculated into soil receiving 14C-labeled IPU addition. Mineralization of IPU was greatly enhanced with MC inoculation that averagely 55.9% of the applied 14C-IPU was consumed up into 14CO2 during 46 days soil incubation. Isoproturon degradation was more thorough with MC than that in the control: much less amount of metabolic products (4.6% of applied IPU) and NER (35.4%) formed in MC treatment, while the percentages were respectively 30.3% for metabolites and 49.8% for NER in the control. Composition of NER shifted with MC inoculation, that relatively larger amount of IPU was incorporated into the biogenic “apparent NER” in comparison with “real NER”. Besides its well-recognized role on enhancing mineralization, MC inoculation with clay particles benefits soil pesticides remediation in term of reducing “real NER” formation, which has been previously underestimated.

Rothballer M, Uhl J, Kunze J, Schmitt-Kopplin P, Hartmann A.

Detection of the bacterial quorum-sensing signaling molecules N-Acyl-Homoserine Lactones (HSL) and N-Acyl-Homoserine (HS) with an Enzyme-Linked Immunosorbent Assay (ELISA) and via Ultrahigh-Performance Liquid Chromatography Coupled to Mass Spectrometry (UHPLC-MS).

Quick and reliable quantitative methods requiring low amounts of sample volume are needed for the detection of N-acyl-homoserine lactones (HSL) and their degradation products N-acyl-homoserines (HS) in order to elucidate the occurrence and dynamics of these prevalent quorum-sensing molecules of Gram-negative bacteria in natural samples and laboratory model experiments. A combination of ELISA and UHPLC-MS is presented here which has proven to meet these requirements. Both methods can not only precisely detect and quantify HSLs but also their degradation products HS and thereby enable studying signaling dynamics in quorum sensing, which have been identified to play an essential role in bacterial communication.

Jin X, Kengara FO, Wang F, Gu C, Yang X, Dörfler U, Schroll R,Munch JC, Jiang X.

Natural attenuation of ~(14)C-HCB and ~(14)C-DDT in Kenya paddy soil and sugarcane field soil.

Objective: Contamination of farmland soils with persistent organic pollutants (POPs) is still a problem of environmental concerns. Take hexachlorobenzene (HCB) and 1,1,1-trichloro-2,2-bis-4-chlorophenyl ethane (DDT) for example, pollution of farmland soils is generally characterized by being low in concentration and vast in area, and new pollutants flow in unceasingly from non-point sources. Farmland soils are rich in microorganisms, which potentially play a significant role in degrading such POPs. Method: In this study, HCB and DDT were selected as representative of highly chlorinated and low chlorinated POPs, respectively, and soils were collected from a years-long paddy field and a years-long sugarcane field for use to study potentials of the soils naturally attenuating HCB and DDT. C-labeled HCB and C-labeled DDT were used for tracing mineralization, volatilization, metabolites, and bound residues to overcome the shortage of the traditional methods for studying the degradation of compounds. Traditional methods merely monitor the concentrations of the mother compound and/or the metabolites which may be sheltered in soil matrix via adsorption, and result in overestimating of the degradation extent. Result: Results showed that C-HCB and C-DDT were spiked respectively into the paddy soil and the sugarcane field soil, and then incubated aerobically under the optimal water content (63% for paddy soil, 35% for sugarcane field soil) in an attempt to get the highest mineralization rate. Both the 14CO2 and the 14C-volatiles were trapped by specific liquid in a closed system and measured with a scintillation counter. 14CO2 production corresponds to mineralization degree of the compounds. After 84 days of incubation, only 0.14% of 14C-HCB and 3% of C-DDT were mineralized. ASE extraction showed that penta-chlorobenzene was the only detected metabolites of HCB. DDD, DDE and DDMU were found to be the main metabolites of DDT. In the paddy soil samples, DDD was relatively higher in concentration, whereas in the sugarcane field soil samples DDE was. The extremely low mineralization extents indicate that soils are very low in potential of attenuating HCB and DDT naturally. Mere aerobic treatment is not adequate to remove HCB and DDT from soil. It is thereby inferred that it is necessary to treat the polluted soil anaerobically to remove such compounds, because in anaerobic incubation HCB would undergo reductive dechlorination which favors aerobic hydroxylation of benzene rings by dioxygenase or lignoltic enzymes, and anaerobic incubation may probably promote the growth of potential DDT degraders, like the benzene-and phenol-mineralization microorganisms that can trigger ring-cleavage reaction. Comparison between HCB and DDT in the total mineralization indicates that under aerobic conditions, high chlorinated compounds are much more persistent than the lower chlorinated compounds. HCB and DDT were quite low in volatilization, being in the range 0.1%-0.6%, which indicates volatilization is not an important process of HCB and DDT in environment. Besides, compost from garden waste was introduced into the DDT incubation experiment to simulate effects of exogenous carbon on mineralization and volatilization of DDT. Results show that the compost increased the mineralization and the non-extractable bound residues of DDT, but reduced the volatilization of the substance; however, the effects were not statistically significant. From an engineering application view, the use of compost to enhancing DDT mineralization was not cost effective. Conclusion: All the findings in this study may serve as reference of good reasons for understanding the natural attenuation of the chlorinated organic compounds in natural soils, and for remediation of soils polluted with such compounds. Since paddy soil and sugarcane field soil have their own specific dominant degradation mechanisms, it is more advisable to design case-specific strategies, anaerobic, aerobic or anaerobic-aerobic alternation, to have the pollutants degraded the most efficiently.

Friesner J, Assmann SM, Bastow R, Bailey-Serres J, Beynon J, Brendel V, Buell CR, Bucksch A, Busch W, Demura T, Dinneny JR, Doherty CJ, Eveland AL, Falter-Braun P, Gehan MA, Gonzales M, Grotewold E, Gutiérrez RA, Krämer U, Krouk G, Ma SL, Markelz RJC, Megraw M, Meyers BC, Murray JAH, Provart NJ, Rhee S, Smith R, Spalding EP, Taylor C, Teal TK, Torii KU, Town C, Vaughn M, Vierstra R, Ware D, Wilkins O, Williams C, Brady SM.

The next generation of training for arabidopsis researchers: Bioinformatics and quantitative biology.

Training for experimental plant biologists needs to combine bioinformatics, quantitative approaches, computational biology, and training in the art of collaboration, best achieved through fully integrated curriculum development. It has been more than 50 years since Arabidopsis (Arabidopsis thaliana) was first introduced as a model organism to understand basic processes in plant biology. A well-organized scientific community has used this small reference plant species to make numerous fundamental plant biology discoveries (Provart et al., 2016). Due to an extremely well-annotated genome and advances in high-throughput sequencing, our understanding of this organism and other plant species has become even more intricate and complex. Computational resources, including CyVerse,3 Araport,4 The Arabidopsis Information Resource (TAIR),5 and BAR,6 have further facilitated novel findings with just the click of a mouse. As we move toward understanding biological systems, Arabidopsis researchers will need to use more quantitative and computational approaches to extract novel biological findings from these data. Here, we discuss guidelines, skill sets, and core competencies that should be considered when developing curricula or training undergraduate or graduate students, postdoctoral researchers, and faculty. A selected case study provides more specificity as to the concrete issues plant biologists face and how best to address such challenges.

Garcia-Molina A, Altmann M, Alkofer A, Epple PM, Dangl JL, Falter-Braun P.

LSU network hubs integrate abiotic and biotic stress responses via interaction with the superoxide dismutase FSD2.

In natural environments, plants often experience different stresses simultaneously, and adverse abiotic conditions can weaken the plant immune system. Interactome mapping revealed that the LOW SULPHUR UPREGULATED (LSU) proteins are hubs in an Arabidopsis protein interaction network that are targeted by virulence effectors from evolutionarily diverse pathogens. Here we show that LSU proteins are up-regulated in several abiotic and biotic stress conditions, such as nutrient depletion or salt stress, by both transcriptional and post-translational mechanisms. Interference with LSU expression prevents chloroplastic reactive oxygen species (ROS) production and proper stomatal closure during sulphur stress. We demonstrate that LSU1 interacts with the chloroplastic superoxide dismutase FSD2 and stimulates its enzymatic activity in vivo and in vitro. Pseudomonas syringae virulence effectors interfere with this interaction and preclude re-localization of LSU1 to chloroplasts. We demonstrate that reduced LSU levels cause a moderately enhanced disease susceptibility in plants exposed to abiotic stresses such as nutrient deficiency, high salinity, or heavy metal toxicity, whereas LSU1 overexpression confers significant disease resistance in several of these conditions. Our data suggest that the network hub LSU1 plays an important role in co-ordinating plant immune responses across a spectrum of abiotic stress conditions.

Alessandrini F, Vennemann A, Gschwendtner S, Neumann AU, Rothballer M, Seher T, Wimmer M, Kublik S,Traidl-Hoffmann C, Schloter M, Wiemann M, Schmidt-Weber CB.

Pro-Inflammatory versus immunomodulatory effects of silver nanoparticles in the lung: The critical role of dose, size and surface modification.

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.

Tanwer P, Bauer S, Heinrichs E, Panda G, Saluja D, Rudel T, Beier D.

Post-transcriptional regulation of target genes by the sRNA FnrS in Neisseria gonorrhoeae.

Small non-coding RNAs (sRNAs) are well-established post-transcriptional regulators of gene expression in bacteria that respond to a variety of environmental stimuli. They usually act by base-pairing with their target mRNAs, which is commonly facilitated by the RNA chaperone Hfq. In this study we initiated the analysis of the sRNA FnrS of Neisseria gonorrhoeae, which is induced under anaerobic conditions. We identified four putative FnrS target genes using bioinformatics approaches and validated these target genes using translational reporter gene fusions in both Escherichia coli and N. gonorrhoeae, thereby demonstrating their downregulation by direct base-pairing between the respective mRNA and FnrS. We demonstrate deregulation of target mRNAs upon deletion of fnrS and provide evidence that the isc gene cluster required for iron-sulfur cluster biosynthesis, which harbours iscS, which is a direct target of FnrS, is coordinately downregulated by the sRNA. By mutational analysis we show that, surprisingly, three distinct regions of FnrS are employed for interaction with different target genes.

Sheng H, Harir M, Boughner LA, Jiang X, Schmitt-Kopplin P, Schroll R, Wang F.

N-acyl-homoserine lactone dynamics during biofilm formation of a 1,2,4-trichlorobenzene mineralizing community on clay.

In Gram-negative bacteria, quorum sensing systems are based on the N-acyl-homoserine lactone (AHL) molecule. The objective of this study was to investigate the role of quorum sensing systems during biofilm formation by a microbial community while degrading the pollutant. Our model system included 1,2,4-trichlorobenzene (1,2,4-TCB) and its mineralizing Gram-negative bacterial community to investigate the relationships between AHL dynamics, cell growth and pollutant degradation. Biomineralization of 1,2,4-TCB was monitored for both the planktonic bacterial community with and without sterile clay particles in liquid cultures. The bacterial growth and production of AHLs were quantified by fluorescent in situ hybridization and immunoassay analysis, respectively. A rapid production of AHLs which occurred coincided with the biofilm formation and the increase of mineralization rate of 1,2,4-TCB in liquid cultures. There is a positive correlation between the cell density of Bodertella on the clay particles and mineralization rate of 1,2,4-TCB. 3-oxo-C12:1-HSL appears to be the dominant AHL with the highest intensity and rapidly degraded by the bacterial community via two main consecutive reactions (lactone hydrolysis and decarboxylic reaction). These findings suggest that the integrated AHLs and their degraded products play a crucial role in biofilm formation and biomineralization of 1,2,4-TCB in culture.

Sun H, Koal P, Gerl G, Schroll R, Joergensen RG, Munch JC.

Water-extractable organic matter and its fluorescence fractions in response to minimum tillage and organic farming in a Cambisol.

Abstract Background Minimum tillage (MT) and organic farming (OF) are increasingly conducted in agricultural managements from the interest of optimizing soil conditions and developing sustainable agriculture. Our understanding of their effects on water-extractable organic matter (WEOM) is still insufficient. Methods To study the effects of MT and OF on WEOM, we analyzed soil materials sampled at two depths (0–8-cm-upper soil and 12–25-cm-deeper soil) from long-term field experiments using different farming and tillage methods. The content, composition, and quality of WEOM were examined. Results The results showed organic farming significantly decreased water-extractable organic carbon and nitrogen, but had positive effect on WEOM humic-like components revealed by parallel factor analysis with excitation–emission matrix, soil organic carbon (SOC), total nitrogen (TN), as well as SOC/TN. In addition, organic farming increased the aromaticity and condensation of WEOM as indicated by specific UV absorption and humification index. MT had no effect on WEOM both quantitatively and qualitatively but significantly decreased SOC and TN of the whole investigated soil profile. The depth effect was significant with strong stratification of WEOM, WEOM components as well as SOC and total N in upper soil. Moreover, the WEOM spectroscopic quality showed sharp differences between the upper and deeper soils. Conclusions The results indicated that in the combined presence both tillage management and farming management, farming management imposed more influence on WEOM than tillage, and organic farming may facilitate the transformation of WEOM and lead to formation of WEOM with high stability. MT significantly changed the distribution of SOC and WEOM in soil, profile but did not increase the contents of SOC and WEOM in the site of the present study. However, the presence of larger pool of WEOM in MT + OF treatment at upper soil is likely to fuel possibly greater microbial activity and more rapid nutrient cycling in soil which can be favorable practice with potential in improving soil conditions in view of developing a sustainable ecosystem in the studied site

Domínguez-Garay A, Quejigo JR, Dörfler U, Schroll R, Esteve-Núñez A.

Bioelectroventing: An electrochemical-assisted bioremediation strategy for cleaning-up atrazine-polluted soils.

The absence of suitable terminal electron acceptors (TEA) in soil might limit the oxidative metabolism of environmental microbial populations. Bioelectroventing is a bioelectrochemical strategy that aims to enhance the biodegradation of a pollutant in the environment by overcoming the electron acceptor limitation and maximizing metabolic oxidation. Microbial electroremediating cells (MERCs) are devices that can perform such a bioelectroventing. We also report an overall profile of the 14 C-ATR metabolites and 14 C mass balance in response to the different treatments. The objective of this work was to use MERC principles, under different configurations, to stimulate soil bacteria to achieve the complete biodegradation of the herbicide 14 C-atrazine (ATR) to 14 CO2 in soils. Our study concludes that using electrodes at a positive potential [+600 mV (versus Ag/AgCl)] ATR mineralization was enhanced by 20-fold when compared to natural attenuation in electrode-free controls. Furthermore, ecotoxicological analysis of the soil after the bioelectroventing treatment revealed an effective clean-up in < 20 days. The impact of electrodes on soil bioremediation suggests a promising future for this emerging environmental technology.

Liu D, Keiblinger KM, Schindlbacher A, Wegner U, Sun H, Fuchs S, Lassek C, Riedel K, Zechmeister-Boltenstern S.

Microbial functionality as affected by experimental warming of a temperate mountain forest soil—A metaproteomics survey.

Soil microbes play an important role in terrestrial carbon (C) cycling, but their functional response to global warming remains yet unclear. Soil metaproteomics has the potential to contribute to a better understanding of warming effects on soil microbes as proteins specifically represent active microbes and their physiological functioning. To quantify warming effects on microbial proteins and their distribution among different functional and phylogenetic groups, we sampled forest soil that had been artificially warmed (+4 °C) during seven consecutive growing seasons and analyzed its metaproteomic fingerprint and linked to soil respiration as a fundamental ecosystem service. Bacterial protein abundances largely exceeded fungal abundances at the study site but protein abundances showed only subtle differences among control and warmed soil at the phylum and class level, i.e. a temperature-induced decrease in Firmicutes, an increase in Agaricomycetes and Actinobacteria, and a decrease in the Asco/Basidiomycota ratio. Community function in warmed soil showed a clear trend towards increased proteins involved in microbial energy production and conversion, related to the increased CO2 efflux from warmed soil as a result of stress environmental conditions. The differences in community function could be related to specific phyla using metaproteomics, indicating that microbial adaptation to long-term soil warming mainly changed microbial functions, which is related to enhanced soil respiration. The response of soil respiration to warming (+35% soil CO2 efflux during sampling) has not changed over time. Accordingly, potential long-term microbial adaptations to soil warming were too subtle to affect soil respiration rates or, were overlaid by other co-varying factors (e.g. substrate availability).

Sun H, Koal P, Gerl G, Schroll R, Joergensen RG, Munch JC.

Response of water extractable organic matter and its fluorescence fractions to organic farming and tree species in poplar and robinia-based alley cropping agroforestry systems.

Organic farming and agroforestry both have the potential to develop sustainable and environmental-friendly agroecosystems and to sequester more soil organic C (SOC). In a long-term field trial, we evaluated the effect of 21-year organic farming and 4-year agroforestry (Robinia and Poplar-based alley cropping system) on water extractable organic matter (WEOM). The technique combining excitation emission matrix (EEM) spectra with parallel factor analysis (PARAFAC) was used to reveal the components of WEOM. In addition, WEOM was characterized by UV absorbance and fluorescence spectra. Organic farming generally increased SOC and total N contents but decreased the WEOM content as well as the WEOM components indicated by the maximum fluorescence intensity (Fmax). Specific UV absorbance (SUVA) and humification index (HIX) of WEOM in organic farming implied WEOM in the organic farming had more components with aromatic structure but less humified. Higher fluorescence (FI) and freshness indices (BIX) of WEOM in organic farming system indicated that a higher percentage of WEOM was microbial-derived in the organic than in the integrated farming system. Robinia showed positive effect on SOC and total N contents in comparison with poplar and had stronger effects on the WEOM components, although the WEOM content did not differ between the two tree species. The significant farming × trees interactions on SOC and water extractable organic carbon (WEOC) indicated that the robinia effects were more pronounced in the organic farming system. Thus, the change of SOC was the result of interactive effect of farming and hedgerow trees in an agroforestry system. The low-input organic farming and robinia tended to result in change of quality of WEOM and led to enrichment of substances of high stability in WEOM. From above, the combination of organic farming and robinia trees is an important means for developing sustainable agricultural systems and soil carbon sequestration.