Systems for enhanced in-situ or perhaps even ex-situ biogenic methane production from hydrocarbon-bearing formations (1) including coal seam, oil shale, coal, coal derivates and the like are presented in embodiments such as but not limited to: increasing and perhaps even selection of microbial populations (2), amending CBM water and other microbe-containing media, diminishing sulfate reduction competition, enhancing organic matter concentrations and generation of biogenic methane (10), universally treating hydrocarbon-bearing formations, and introducing amendments (3) to hydrocarbon-bearing formations.