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Abstract: Microbial methane in sedimentary basins comprises approximately 20% of global natural gas resources, yet little is known about the environmental requirements and metabolic rates of these subsurface microbial communities. The Illinois Basin, located in the midcontinent of the United States, is an ideal location to investigate hydrogeochemical factors controlling methanogenesis as microbial methane accumulations occur: (1) in three organic-rich reservoirs of different geologic ages and organic matter types – Upper Devonian New Albany Shale (up to 900m depth), Pennsylvanian coals (up to 600m depth), and Quaternary glacial sediments (shallow aquifers); (2) across steep salinity gradients; and (3) with variable concentrations of . For all three organic-rich reservoirs aqueous geochemical conditions are favorable for microbial methanogenesis, with near neutral pH, concentrations <2mM, and Cl− concentrations <3M. Also, carbon isotopic fractionation of CH4, CO2, and DIC is consistent with microbial methanogenesis, and increased carbon isotopic fractionation with average reservoir depth corresponds to a decrease of groundwater flushing rates with average depth of reservoir. Plots of stable isotopes of water and Cl− show mixing between a brine endmember and freshwater, suggesting that meteoric groundwater recharge has affected all microbial methanogenic systems. Additionally, similar methanogenic communities are present in all three reservoirs with comparable cell counts (8.69E3–2.58E6cells/mL). TRFLP results show low numbers of archaea species with only two dominant groups of base pairs in coals, shale, and limestone aquifers. These results compare favorably with other methanogen-containing deep subsurface environments. Individual hydrogeochemical parameters that have a Spearman correlation coefficient greater than 0.3 to variations in methanogenic species include stable isotopes of water (δ18O and δD), type of substrate (i.e. coals versus shale), pH, and Cl− concentration. The matching of variations between methanogenic TRFLP data and conservative tracers suggests that deep circulation of meteoric waters influenced archaeal communities in the Illinois Basin. In addition, coalification and burial estimates suggest that in the study area, coals and shale reservoirs were previously sterilized (>80°C in nutrient poor environments), necessitating the re-introduction of microbes into the subsurface via groundwater transport. [Copyright &y& Elsevier]