Microbial transformation involved in the planetary biogeochemical cycles

Among representatives of planet-impacting microbes are methanogens, contributing to half of global methane emissions by munching on a range of carbon sources (i.e., CO2, methylamines, lignin derivatives…). On the other side, specialized microbes “burn” hydrocarbons without oxygen, acting as filters that prevent alkanes from reaching the atmosphere or contaminating the environment. For instance, it is estimated that 50 to 70% of the emitted methane is converted back to CO2 through their metabolism. These anaerobic microbes, capable of juggling carbon via astounding chemistry, are key actors in the biosphere by orchestrating the final steps in the degradation of biological matter, providing biological nitrogen, or sustaining trophic chains through sulfur cycling coupling.

Our work is to understand the chemical reactions from their energy metabolism by isolating and characterizing their enzymes. Due to the complexity of these (metallo)-enzymes and their unknown secrets (e.g., new type of cofactors), we directly use native microbes, even if they are part of the so-called “microbial dark matter”. How do we solve the extreme challenge of isolating one enzyme among so many others from the microbial consortium? Through protein crystallization! Then we rely on all available tools in our lab and on the EPN campus to obtain as much biological information as possible from these crystals.

For instance, we recently used anaerobic microbial enrichments containing methanotrophs to snapshot the enzyme that captures methane. The structures solved at atomic resolution highlight the native metallocofactor containing nickel, together with the coenzymes used in the reactions and seven post-translational modifications.

Selected publications

  • Jawadekar D, Lemaire ON, Wagner T. New Frontiers in short-chain Alkyl-Coenzyme M Reductases. Current Opinion in Microbiology. 2025. doi: 10.1016/j.mib.2025.102665
  • Müller M-C, Wissink M, Mukherjee P, Von Possel N, Laso-Pérez R, Engilberge S, Carpentier P, Kahnt J, Wegener G, Welte CU, Wagner T. Atomic resolution structures of key enzyme MCR in anaerobic methanotrophy reveal novel and extensive post-translational modifications. Nat. Comm. 2025. doi: 10.1038/s41467-025-63387-1
  • Wagner T, Toffin L, Borrel G. Les archées méthanogènes. Chapter for an Archaea book dedicated to BsC and MsC students. 2024. Book chapter available in French and English.
  • Lemaire ON, Wegener G, Wagner T. F420 reduction as a cellular driver for anaerobic ethanotrophy. Nat. Commun. 2024. doi: 10.1038/s41467-024-53338-7
  • Lemaire ON, and Wagner T. A Structural View of Alkyl-Coenzyme M Reductases, the First Step of Alkane Anaerobic Oxidation Catalyzed by Archaea. Biochemistry. 2022. doi: 10.1021/acs.biochem.2c00135.
  • Kurth JM, Nobu MK, Tamaki H, de Jonge N, Berger S, Jetten MSM, Yamamoto K, Mayumi D, Sakata S, Bai L, Cheng L, Nielsen JL, Kamagata Y, Wagner T, Welte CU. Methanogenic archaea use a bacteria-like methyltransferase system to demethoxylate aromatic compounds. ISME J. 2021. doi: 10.1038/s41396-021-01025-6.
  • Hahn CJ, Lemaire ON, Kahnt J, Engilberge S, Wegener G, Wagner T. Crystal structure of a key enzyme for anaerobic ethane activation. Science. 2021. doi: 10.1126/science.abg1765.
  • Kurth JM, Müller MC, Welte CU, Wagner T. Structural Insights into the Methane-Generating Enzyme from a Methoxydotrophic Methanogen Reveal a Restrained Gallery of Post-Translational Modifications. Microorganisms. 2021. doi: 10.3390/microorganisms9040837.

External collaborations

  • Dr. Gunter Wegener (MPI Bremen, Germany)
  • Prof. Dr. Cornelia Welte (Radboud University, The Netherlands)
  • Anna Schevchenko (MPI Dresden, Germany)
  • Prof. Dr. Julia Kurth (Münster University, Germany)
  • Dr. Ingo Zebger (Technical University Berlin, Gemany)