Over the past two decades, our concept about the distribution of life on Earth has fundamentally changed. Microorganisms (bacteria and archaea) colonize not only the upper soil layers, but the underlying sediments and rocks as well. Previous estimates assumed that up to 94 % of all microorganisms live in deep subsurface sediments, but recent findings show that microbial abundance in the marine subsurface is much lower than previously estimated. However, these deeply buried communities are as important as the surface biosphere for driving carbon and nutrient cycling and catalyzing a multitude of reactions between rocks, sediments, and fluids. Due to their low abundance and low metabolic rates, studies of deep biosphere microorganisms require special analytical procedures. Therefore we developed an integrated research strategy, which connects geochemical measurements of sediment properties with microbiological/molecular biological analyses of microbial communities and modeling of microbial pathways/ networks. Our ongoing studies in sediments of the El’gygytgyn Crater Lake and of the South Pacific Gyre show the importance of microorganisms for the element cycles in these extreme environments. The composition of microbial communities, their role in major biogeochemical cycles and their response to changing environmental conditions, however, are still largely unknown. The future research of the German Centre for Geosciences GFZ will extend our knowledge on the role of microorganisms mainly in continental deposits, especially their impact on biogeochemical cycles, mineral weathering as well as on the quality and stability of reservoirs in the broadest sense.