Bacteria living in the first few millimeters to meter of sediment live via chemoautrophic reactions after all available oxygen has been utilized (eg. Jorgensen 1982, Ravenschlag et al. 2000).  First, nitrate is reduced, then manganese and next iron are oxidized.  However, less is known about the energy sources of bacteria the deeper one moves in the sediment column.  Types of bacteria identified thus far, categorized by their chemoautotrophic energy source include: aerobic ammonifers; nitrate-reducers, both to ammonia and nitrogen; fermentative anaerobic heterotrophs; sulfate reducers, including acetate, lactate, and methane utilizers that produce CO₂ from CH₄ in initial enrichments but for which activity was not sustained on subcultures; methanogens; acetogens; and anaerobic hexadecane oxidizers (Parkes et al. 2000).

            As mentioned in the introduction, sulfate reduction was long considered to be the final step in the reduction of organic material as one moved down the sediment column.  However, it appears that the “last step” of chemoautotrophic or chemosynthetic life in the sediments may change depending on a variety of factors and therefore be different from locality to locality.  D’Hondt et al. 2002 claimed that SO₄² reduction, methanogenesis, and fermentation are the principal degradative metabolic processes in subsurface (>1.5 mbsf) marine sediments for three reasons: First, at the sediment-water interface, concentrations of dissolved SO₄² are more than 50 times as great as concentrations of all electron acceptors with higher standard free energies combined. Second, external electron acceptors, such as iron and manganese, which yield more energy than SO₄² typically disappear within the first few centimeters to tens of meters of sediment depth.  Thirdly, once all SO₄² has been reduced, methanogenesis and fermentation are the principal remaining avenues of metabolic activity (D'Hondt et al. 2002).

            Methanogenesis can be achieved through two different reactions:  H₂/CO₂ where HCO₃^– is reduced to CH₄, and acetate oxidation (Wellsbury and Parkes 2000, Parkes et al. 2000).  It is believed t sulfate reducing bacteria can out compete methanogens for organic carbon down to sulfate concentrations of about 3mM.  Below this concentration, methanogenesis dominates.  However, methane can be used in sulfate reduction as well.  These organisms keep methane concentrations low through the sediment column in comparison to sulfate.  At two gas hydrate zones, the Peru Margin and the Japan Sea, both H₂/CO₂ methanogenesis and acetate methanogensis levels are elevated by about two orders of magnitude both at the hydrate level and below (Parkes et al. 2000).  Methane oxidation occurs throughout the sediment column, including at gas hydrate sites, even below, as well as above the sulfate reducing zone.  However, no organism that can anaerobically consume methane has been isolated from the sediments (Parkes et al. 2000).