In the anaerobic state, both biological and electrochemical activities are found. There is a gradient in soils with an aerobic zone on top, an oxidizing layer, and an anaerobic zone on the bottom. As plant material decays, the carbon in the aerobic zone is broken up by microorganisms into dissolved organic carbon. In the anaerobic zone fermentation occurs. In this process, microorganisms convert dissolved organic carbon into lactic acid or ethanol.
Methanogenic organisms work in the anaerobic zone to convert dissolved organic carbon into methane.
In both the aerobic and fermentation processes, CO2 is generated. This process also affects the pH of the water. The production of methane is much more common in freshwater systems. This ion is used by plants or is washed away by runoff. Nitrosomonas is the species of bacteria responsible for the conversion of ammonia to nitrite, and Nitrobacter converts nitrite to nitrate.