One of the primary unknowns in subsurface energy storage is the impact caused by microbial communities that are naturally present in underground reservoirs at a broad range of environmental conditions. H₂ is an energetic electron donor, supplying energy for a wide variety of subsurface microorganisms, many of which have been documented to exist naturally in the geologic units that are targets for H₂ gas storage. Even at low concentrations, hydrogen has been found to be a suitable electron donor when coupled with iron (III) reduction, sulfate reduction, sulfur reduction, and methanogenesis in subsurface reservoirs with a broad range of salinities and temperatures as high as 90 ℃.

Recent studies have recognized this knowledge gap, and strongly recommended research and laboratory tests to investigate the effect of H₂ on the subsurface microbial community before initiating any large scale H₂ injections. This lack of understanding was a further concern of the European Gas Research Group, which stated that of 20 potential reservoir phenomena that will negatively impact H₂ gas storage, the most serious potential issues are due the activity of bacteria.  Major expected microbial driven reactions are:

• Methanogenesis: In this reaction, microorganisms called methanogens oxidize hydrogen and reduce carbon dioxide to produce methane. Gaz de France previously found the microbially induced methanogenesis reaction to rapidly consume 50% of stored hydrogen gas, producing methane.
• Hydrogen Sulfide Production: A hazardous mechanism of H₂ consumption might occur through sulfate and sulfur reducers (SRBs). Gaz de France, documented technical challenges associated with SRBs producing hydrogen sulfide gas (H₂S). Town gas storage fields (~ 45-60% H₂) in the Czech Republic have reported significant consumption of stored H₂ coupled to H₂S production. Lastly, several models demonstrate reservoirs that are current targets of hydrogen storage have a high risk of H₂S production from SRBs.
• Microbiological Corrosion: Microbially induced corrosion of steel has previously been documented to occur in the anoxic environment after introduction of H₂ to the subsurface. Hydrogen-consuming microorganisms have been implicated in causing corrosion at temperatures up to 90 °C and high salinities.
• Secondary Effects: The shifting microbial community may lead to other unexpected byproducts, such as organic acids or even calcium carbonate scaling. The presence of microbial communities adapted to reducing, H₂-rich environments may contribute to corrosive mineral reactions through local pH changes and co-production of various acids.

Large-scale hydrogen storage will not be possible without the delineation of expected microbial activity in these systems. Before hydrogen can be safely and securely stored in underground reservoirs, the effect of gas injection on the naturally occurring microbial community and the associated change in chemistry needs to be assessed.