Biogenic methane is an important end-product of biogeochemical processes associated with the bacterial remineralization of labile organic matter. Organic matter remineralization in typical soils and sediments proceeds through a series of reactions in which the available oxidant that yields the greatest free energy determines the dominant process at a particular horizon. If O₂ is present, aerobic decomposition is the major pathway. Upon depletion of dissolved O₂, organic matter degradation shifts to nitrate reduction. Once nitrate is fully utilized, metal oxides (MnO₂ and Fe₂O₃) serve as oxidants. When metal oxides are no longer available, organic matter remineralization proceeds through sulfate reduction. The final reaction in the series, methane production, generally occurs after the sulfate pool has been exhausted. In sediments prone to gas production, sulfate reduction and methane production are likely to be the dominant decomposition reactions due to limited supply of other oxidants.

The occurrence of methane production and other decomposition reactions in soils and sediments is ultimately controlled by the flux of reactive organic matter, however, the rates, and thus depth distribution, of these reactions vary dramatically in response to seasonal variations in temperature. Following its production, the distribution of methane in sediments is further modified by consumption (oxidation) and transport processes which may also exhibit pronounced seasonality in their absolute rates and relative importance. The production and transport of dissolved and gas bubble methane from organic-rich sediments can be predicted by simple mass conservation models in which reaction rates are balanced by diffusive and advective transport. Reactive organic matter input rates, concentrations of sulfate and other oxidants, temperature, transport mechanisms, and pressure exert primary control on resulting fluxes and distributions.

Biogenic methane is generally distinguished from thermally generated gas through its relatively depleted stable carbon isotopic composition as well as >1000-fold higher concentration than other light hydrocarbons. However, time-course incubation experiments at room temperature with natural sediments reveal a large range in isotopic composition of bacterially produced methane which overlaps values for thermally-produced methane found in hydrothermal environments. Heating of organic matter in hydrothermal sediments generates relatively C-13-enriched methane and C-1/C-2+C-3 light hydrocarbon ratios less than 100. Large quantities of short chain organic acids such as acetate which may serve as microbial substrates are also generated during such thermal alteration. We have much to learn about microbial versus thermal controls on the concentrations and isotopic composition of light hydrocarbons during their production and oxidation.