Microbiology of Anaerobic Systems


Research Topics

Anaerobic microorganisms, among them the oldest life-forms on Earth, display the most manifold metabolic pathways and lifestyles that have been ever invented by evolution, such as various mechanisms for energy conservation, carbon fixation, elemental cycling, fermentative conversion of organic matter and syntrophic interactions, enabling life on the thermodynamic edge. Anaerobic microbial communities play essential roles in biogeochemical cycles, natural attenuation of contaminated sites and various biotechnological processes, such as wastewater treatment, anaerobic digestion of organic waste and fermentative formation of valuable products.

The MicAS group studies the microbial ecology and physiology of anaerobic microbial communities in natural and engineered environments in order to identify microbial key players and their functions and to elucidate carbon and energy flows as well as microbial interactions. We aim at the biotechnological application of anaerobic microbiota, a deeper understanding of their functions in microbial ecosystem services, and novel insights into the ecophysiology of not yet cultured microbes (microbial dark matter).

In engineered systems such as anaerobic biorectors we develop microbiological strategies to optimize the production of biogas and other fermentation products by open mixed cultures (reactor microbiomes). The main objectives are i) to identify microbial parameters for process control and ii) to exploit novel feedstocks and microbial resources for the production of chemical building blocks and biofuels from renewable resources.

In environmental systems such as contaminated subsurface systems, we aim at the identification of microbial key players in biogeochemical cycles and contaminant degradation as well as the elucidation of the ecophysiological role of not yet cultured microbes.

Our research topics in detail:

  • Anaerobic digestion of lignocellulosic and nitrogen-rich waste
  • Bioaugmentation of anaerobic bioreactors
  • Trace elements in anaerobic digestion
  • Biotechnological application of anaerobic fermentations (carboxylate platform, syngas platform)
  • Biomethanation of hydrogen from excess electricity (Power-to-Gas)
  • Process monitoring based on biogas isotopic signature
  • Carbon flow and syntrophic interactions in anaerobic consortia
  • Metagenome-based analysis of metabolic networks in anaerobic consortia
  • Microbial ecology of hydrocarbon-contaminated aquifers

MicAS November 2016

PhD students

Fabian Bonk
Tarek M.M. Hamed Elzamel
Andreas Hardy Keller
Bin Liu
Washington Logroño
Rico Lucas
Emine Gözde Özbayram
Babett Wintsche


Elke Häusler
Ute Lohse
Lisa-Marie Bangen (apprentice)


Antonia Aalders
Jonathan Andrén
Aslınur ÇalIsiyor
Dennis Dockendorf
Shruthi Meenakshisundaram


  • Anaerobic cultivation
  • Lab-scale bioreactors (in collaboration with the DBFZ)
  • Process and cultivation analytics (HPLC, GC, etc.)
  • PCR-based community fingerprinting (T-RFLP) on the DNA- and RNA-level targeting phylogenetic and functional marker genes
  • Cloning, sequencing (Sanger – capillary electrophoresis) and phylogenetic analysis of PCR-amplified genes
  • Quantitative PCR
  • Next generation sequencing (shot gun and amplicon sequencing)
  • Genome and metagenome analysis and annotation using the Genoscope platform
  • Epifluorescence microscopy, FISH, CARD-FISH
  • Stable isotope fingerprinting (in collaboration with the Dept. Isotope Biogeochemistry)
  • Stable isotope probing of nucleic acids (DNA-/RNA-SIP)
  • Protein-SIP (in collaboration with the Dept. Molecular Systems Biology)