All ecosystems on planet Earth are populated by microbes, which are massively entangled in all biogeochemical cycles. In ecosystems relevant to human society, microbes fulfill important functions, resulting in ecosystem services. One important ecosystem service is carbon fixation, i.e., the conversion of inorganic carbon into organic molecules necessary for life. Ecosystem services are a central aspect of ecosystem health, one of the three pillars of the One Health concept.

The Probst Lab focuses on healthy and diseased ecosystems and the role that microbes play therein. We are particularly interested in bacteria, archaea, small eukarya, and viruses that infect these organisms. Since most microbes escape cultivation techniques in the laboratory, we use a community sequencing approach called metagenomics (also environmental genomics) to determine the DNA sequences of entire communities, which we disentangle at the (population) genome level. We bioinformatically pair metagenomics with other techniques like RNA sequencing, proteomics, or lipidomics. The combination of these ‘omics techniques provides information on the status of different microbes in healthy and diseased ecosystems. To investigate the ecophysiology of microbes in situ, we also apply metagenomics-informed correlative microscopy techniques, including fluorescence in situ hybridization (FISH) to visualize specific viruses.

Our research questions are mostly related to aquatic ecosystems and how microbes interact with and mediate nutrient turnover therein. Our favorite ecosystems include rivers, lakes, deep and shallow groundwater, oil reservoirs, and deep sediments.