Microbial Systems Ecology

Members of the group "Microbial Systems Ecology" (left to right): Upper Row - Andreas Kölsch, René Kallies, Anke Kuppardt, Anja Narr, Bärbel Kiesel, Nicole Steinbach; Middle Row - Anett Heidtmann, Verena Jaschik, Santa Claus, Antonis Chatzinotas; Lower Row - Julia Johnke (Canan Karakoc on sampling campaign...).

Research Topics

Microorganisms play a crucial role in ecosystem performance and functioning. They are ubiquitous, possess enormous genetic, metabolic and physiological potential and are responsible for virtually all biogeochemical cycling processes. Ecosystems are composed of several trophic levels which interact with each other. In order to understand the link between biodiversity and ecosystem functioning, we thus need to take into account these multiple trophic levels.

The aim of the Microbial Interaction Ecology group is to gain a better understanding of the ecology of microbial systems and the importance of microbial biodiversity for ecosystem functioning by incorporating the interactions within and between trophic levels. Next to applying a variety of molecular biological tools for field samples (PCR-based screening, next-generation sequencing, FISH, stable-isotope probin, -omics..) this also requires testing established ecological theories with microbial systems. Our group focuses on the interactions of all major microbial players (prokaryotes, viruses, protists and fungi) and on plant-microbe interactions. The interactions among these groups are the basis for (microbial) food webs, the transfer of nutrients to higher trophic levels and the stability and resilience of microbial systems and processes.

The research topics of the group cover:

  • the importance of biotic/chemical interactions between bacteria, viruses (bacteriophages), protists,fungi and plants for ecosystem services,
  • the resilience and stability of prokaryotic ecosystem services,
  • the biodiversity of prokaryotes, protists and phages,
  • the use of microbial model systems to address ecological theory,
  • the transfer and establishment of degradative traits and antibiotic resistance via plasmids.


Dr. René Kallies
Dr. Bärbel Kiesel
Dr. Anke Kuppardt (Wackwitz)

PhD Students

Julia Johnke
Canan Karakoç
Anja Narr
Peter Hofmann

Judit Laufer


Anett Heidtmann
Nicole Steinbach


Guest Scientists


  • Isolation and purification of DNA, RNA, plasmids from environmental samples
  • High throughput sequencing (phylogenetic and functional marker genes)
  • Quantitative PCR
  • Community fingerprinting (T-RFLP, SNuPE) and fluorescence in situ hybridization (FISH)
  • Phylogenetic analysis, probe and primer design
  • Cultivation of protists, bacteria and phages
  • Gene transfer (conjugation, transduction, classical transformation and electroporation, monitoring of gene transfer events)
  • Stable isotope probing (DNA-/RNA-SIP)
  • Multivariate statistics (PCA, RDA, nm-MDS, CCA)
  • Laboratory-based microbial model systems
  • Analysis of plant metabolites as a response to rhizosphere interactions (collaboration with Dr. Fester)

Please visit the webpages of the group leader Antonis Chatzinotas or the group members for information on research projects and cooperations.


To see our publications, please visit our personal web pages.

Open PhD, Master-/Bachelorpositions and Internships of our group you can find at
Jobs and Education