Soils host the most complex microbiomes on Earth and are vital resources that provide essential ecosystem services and food security to humankind. To illustrate their importance, the United Nations had declared 2015 the International Year of Soils. Due to the complexity of soils, many fundamental aspects of the role of microorganisms and their interactions with plants, both in agriculture and greenhouse gas emissions, are still unresolved. Using cultivation-independent approaches of the Meta-Omics toolbox we aim to gain (eco) system level insights into fundamental mechanisms of carbon and nitrogen cycling catalyzed by microbiomes in a number of soil types. This encompasses microbiomes of (1) arctic permafrost soils as globally important carbon stocks vulnerable to rapid climate change and of (2) wetland soils that emit large quantities of the greenhouse gas methane.

Ruminant animals such as cows rely on the activity of a complex assembly of symbiotic microorganisms to anaerobically degrade the ingested plant biomass. Using metatranscriptomics, we study these microbiomes in the rumen of cows to shed light on their taxonomic structure, activities and interactions leading to greenhouse gas production. This knowledge might be ultimately valuable for the development of new and potent methane mitigation strategies in agriculture. Work with human microbiomes focuses on gut microbiomes and their role in chronic inflammations caused by lifestyle or parasite infections.

We study a group of recently identified methanogens, the Methanomassiliicoccales, with the aim to better understand their physiology and energy metabolism, i.e. how they produce their metabolic end-product methane. Furthermore, we study their ecology and interactions with other microorganisms in wetland soils and ruminant animals, two globally important sources of the potent greenhouse gas methane.