The purpose of this study was to identify and quantify the fate and speciation of carbon that can occur in mixtures of geological media (crushed rock) and autotrophic microbial communities. A sulfate reducing bacterium (Desulfotomaculum geothermicum) and a methanogenic archaeon (Methanothermococcus thermolithotrophicus) were both tested separately and together, with and without crushed sedimentary rock (carbonaceous sandstone) for different CO2 partial pressures (0.22, 0.88, 3.52, and 8 bar) at 54 degrees C in saline artificial groundwater. In order to quantify the respective metabolic activities, the inorganic gases of interest (H-2, CH4, H2S and CO2) were measured and the speciation of carbon was assessed by measuring volatile, non-purgeable, total and dissolved organic carbon as well as total and dissolved inorganic carbon. Despite a protective effect of the mineral matrix, the results showed a high sensitivity of autotrophic microorganisms to the stress induced by pressures of CO2 superior to one bar and revealed that a part of this stress was due to direct toxic effects. M. thermolithotrophicus demonstrated a better tolerance to CO2 and was dominating the consortia. This ascendancy was interpreted as resulting from equilibrium displacement due to transport effects of methane between the liquid and gas phases. Abiotic dissolution was observed but some biomineralization processes of carbonates were also identified for D. geothermicum. Both strains displayed very different patterns in their conversion of inorganic carbon: while M. thermolithotrophicus was mainly producing methane, D. geothermicum induced the formation of biomass. The availability of crushed rock increased the proportion of sessile biofilms. All these results were analyzed in correlation with a successful PHREEQC simulation and demonstrate the strong influence of the microbial activities and diversity on the carbon fate in the immediate surroundings of geological CCS storage zones.