A significant fraction (~ 20%) of microbial life is found in the terrestrial deep subsurface, yet 17 the metabolic processes extant in those environments are poorly understood. Here we show that 18 H2, injected into the Opalinus Clay formation in a borehole located 300 meters below the 19 surface, fuels a community of microorganisms with interconnected metabolisms. Metagenomic 20 binning and metaproteomic analysis reveal a complete carbon cycle, driven by autotrophic 21 hydrogen oxidizers. Dead biomass from these organisms is a substrate for a fermenting 22 bacterium that produces acetate as a product. In turn, complete oxidizer heterotrophic sulfate-23 reducing bacteria utilize acetate and oxidize it to CO2, closing the cycle. This metabolic 24 reconstruction sheds light onto a hydrogen-driven carbon cycle, and a sunlight-independent 25 ecosystem in the deep subsurface.