Microbes CaN cycle



In our research we focus on the composition, diversity, and function of microbial communities with the objective to elucidate ecological relations between microorganisms and their role in biogeochemical cycles. Of particular interest in previous and current research projects are nitrifying and methane-oxidising microbes. Studying these organisms in their natural habitats, in controlled microcosm experiments as well as in culture we focus on their physiological capabilities and on their responses to changing environmental conditions, i.e. their ecophysiology. Through these lines of research we aim to determine explanations for abundance and activity patterns, (micro)diversity, niche specilisations, and to quantify ecological importance of these guilds for biochemical cycles in various environments.




Open positions

Currently there are no open positions in our team.

We always welcome motivated M.Sc./ B.Sc. students to join our team for short-term internships or thesis projects. Please contact Anne and let her know about your ideas/expectations.

Research projects

Illuminating the interactions between nitrification and methane oxidation and the ensuing ecological impacts

Financial suppport: Czech Science Foundation (GACR); Duration: 2021-2025

Principal Investigator: Anne Daebeler

Team members: Magdalena Wutkowska, Anna Prokhorova, Justus Nweze, Renata Kruzikova


Nitrifiers and methanotrophs are microbial guilds responsible for aerobic transformation of reactive nitrogen and oxidation of methane, respectively. Both processes are fundamental ecosystem functions linked to nutrient cycling and global change. We hypothesize that interactions between these two guilds substantially contribute to the modulation of process rates. However, such interactions have hardly been investigated. The proposed line of research will expose the cause and nature of interactions between nitrifiers and methanotrophs and quantify their ecological impact. The project will employ a unique combination of multidisciplinary techniques, i.e. next generation sequencing, stable isotope incubations with integrated approaches of metagenomics and metatranscriptomics, single cell sorting, and metaproteomics with synthetic microbial consortia. Collectively, these approaches are poised to gather a deep understanding of the links between carbon and nitrogen cycling to eventually be able to predict and mitigate climate change and protect Earths ecosystems.

The project will resolve interactions between nitrifiers and methane oxidizers, quantify their ecological implications, and develop models for predictions. It will fill knowledge gaps on microbial ecogenomics and -physiology, and isolate new organisms.

TIMPAOMP project - The IMPortance of Anaerobic Oxidation of Methane in Peatlands

Financial suppport: Czech Science Foundation (GACR); Duration: 2023-2025

Principal Investigator: Vojtech Tlaskal

Team members: Renata Kruzikova


Ecosystem management of natural wetlands is an important tool of human land use practises that often have untargeted impacts on greenhouse gas (GHG) emissions such as methane. Systems such as northern peatlands are very sensitive to management practises and at the same time have the potential to release large amounts of GHGs due to their large storage of organic matter. As a result of practised clear-cutting of peatland forests the water table rises. At the same time, anoxic conditions in peat are expanding, creating a new niche for microbial greenhouse gas producers, but also for anaerobic methanotrophs that depend on substantial methane production and the presence of oxidised electron acceptors. There is a lack of knowledge about the proportion of anaerobically oxidised methane, the identity of the bacteria and archaea that carry out such process, their electron acceptors and nitrogen sources in peatlands. Filling these knowledge gaps, which are urgently needed to improve ecosystem models and reduce GHG emissions, is the subject of this project.


Biology Centre CAS
Institute of Soil Biology and Biogeochemistry
Na Sádkách 702/7
370 05 České Budějovice

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