Molecular Microbe Ecology

In the working group Molecular Microbial Ecology the genetic prerequisites and molecular mechanisms for the interaction of rhizosphere microorganisms with their plant host are analyzed with special focus on the differences between beneficial and pathogenic interrelations. In achieving a broader understanding of these interactions we extend our research area also to other habitats for bacterial communities like human gut, teeth, lung, skin etc., as well as the transmission paths of health related microorganisms from the plant to human beings. Negative effects on human health can occur indirectly via e.g. pollen, whose allergenic potential is influenced by colonizing microbes, or directly by the infection with human pathogens, that are able to colonize crop plants epi- or even endophytically.

A special focus is on bacterial signalling substances controlling important properties in microbial communities and biofilms, which can provoke specific reactions in microorganisms, as well as plants and other higher organisms (including humans). Bacterial signaling substances are analyzed as important controlling factors in the interaction of human pathogens and toxin producing bacteria with their eukaryotic host (plant, animal). Analytical methods, including monoclonal antibodies, are developed and applied for studying the ecology of bacterial signaling substance of the N-acyl homoserine lactone type in different matrices and organismic habitats.



HMGU Projects

  • Isolation and characterization of novel plant growth promoting rhizobacteria (PGPR)
  • Phylogenetic analysis of epi- and / or endophytic rhizosphere bacteria
  • Characterization of diazotrophs in the rhizosphere and functional gene analysis (nifH)
  • Development of specific oligonucleotide probes for FISH analyses in combination with confocal laser scanning microscopy (CLSM) for the analysis of 3D structures of microbial communities
  • Interactions of human pathogenic bacteria like Salmonella, Listeria or Clostridia with fodder and crop plants. Plants as alternative ecological niche for pathogens
  • Isolation and characterization of signalling molecules (especially N-Acyl-Homoserinlactones) by root associated bacteria, in cooperation with Prof. Dr. Philippe Schmitt-Kopplin, Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, German Center for Environmental Health (GmbH)
  • Interactions of EHEC O104:H4 with fenugreek, in cooperation with Dr. Ingrid Huber, Bayrisches Landesamt für Gesundheit und Lebensmittelsicherheit (LGL)
  • Bacterial Quorum Sensing in the lung, in cooperation with Dr. Burkhard Hense, Institute of Computational Biology, Helmholtz Zentrum München, German Center for Environmental Health (GmbH), und Prof. Dr. Christian Kuttler, Zentrum Mathematik - M6, Technische Universität München,
  • Influence of nutritional change on the oral microbiome, in cooperation with Prof. Dr. Ali Al-Ahmad, Dr. Annette Carola Anderson, Klinik für Zahnerhaltungskunde und Parodontologie, Albert-Ludwigs-Universität, Freiburg, Germany,

Externally funded projects

  • The functional relevance of plant-microbe-insect interactions in a cereal crop system, DFG 2018 - 2021
  • Soil as a Sustainable Resource for the Bioeconomy – BonaRes: Implications of soil management practices and application of biocontrol strains on soil disease suppressiveness for improved soil health and sustainable plant production (DiControl), Bundesministerium für Bildung und Forschung (BMBF), 2015 - 2019


  • Prof. Dr. Helge Böhnel and Dr. Frank Gessler Institute for Applied Biotechnology in the Tropics, Georg-August University Goettingen, Goettingen,Germany
  • Prof Dr. Bart Currie, Dr. Mirjam Kaestli, Menzies School of Health Research, Tropical and Emerging Infectious Diseases Division, Royal Darwin Hospital Campus, Casuarina, Australia
  • Prof. Dr. Yoav Bashan, Dr. Luz Bashan, Environmental Microbiology Group, Centro de Investigaciones Biologicas del Noroeste (CIBNOR), La Paz, Baja California Sur, Mexico
  • Prof. Dr. Bhavanath Jha, Marine Biotechnology and Ecology Division, CSIR-Central Salt and Marine Chemicals Research, Institute, Bhavnagar, Gujarat, India
  • Prof. Dr. Dirk Haller, Dr. Thomas Clavel, Technische Universität München, Z I E L - Zentralinstitut für Ernährungs- und Lebensmittelforschung- Abteilung Biofunktionalität Freising-Weihenstephan, Germany
  • Prof. Dr. Elhafid Nabti, Leila Bensidhoum, Laboratory of Renewable Energies, Group of Biomass and Environment, University of Bejaia, Bejaïa, Algeria
  • Prof. Dr. Claudia Traidl-Hoffmann, Dr. Stefanie Gilles, Institute of Environmental Medicine, UNIKA-T, Technische Universität München, Augsburg, Germany
  • Dr. Christoph Keel, Université de Lausanne, Département de Microbiologie Fondamentale (DMF), Lausanne, Switzerland
  • Prof. Dr. Jose Ivo Baldani. Dr. Luc Rouws, Laboratorio de Genetica e Bioquımica, Pavilhao Johanna Dobereiner, Embrapa Agrobiologia, Seropedica, Rio de Janeiro, Brazil
  • Dr. Ali Al-Ahmad, Dr. Annette Carola Anderson, Department of Operative Dentistry and Periodontology, Albert-Ludwigs-University, Freiburg, Germany
  • Prof. Dr. Fabio Oliveira Pedrosa, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
  • Dr. Ingrid Huber, Bavarian Health and Food Safety Authority (LGL), Oberschleißheim, Germany

Master / doctoral thesises

Doktorarbeiten (seit 2017)

Ludwig-Maximilians-Universität München, Fakultät für Biologie

  • Theresa Kuhl, Characterization of bacteria isolated from crop plants in terms of biocontrol, plant growth promotion and healthy human nutritio, Start 2018
  • Sophia Klink, The functional relevance of plant-microbe-insect interactions in a cereal crop system, Start 2018


  • DNA, RNA isolation also from complex microbial habitats
  • PCR, rt-PCR, q-PCR
  • tRFLP analyses
  • Various cloning techniques and strategies
  • Sequencing of amplicons, transcriptomes, genomes and metagenomes (454, MiSeq)
  • Phylogenetic anaylses of microbial communities
  • Probe development for FISH experiments
  • Epifluorescence and 3D confocal laser scanning microscopy (CLSM)
  • Isolation and characterization of signalling molecules (AHL-type, cyclic peptides, boratdiester)
  • Construction of  gfp and/or yfp, rfp labeled sensor strains for functional assays
  • Competitive ELISA for quantitative detection of AHL signalling molecules and their degradation product