Gaseous oxygen is excluded from the reactions by physical containment. Anaerobes utilize electron acceptors from sources other than oxygen gas. These acceptors can be the organic material itself or may be supplied by inorganic oxides from within the input material. When the oxygen source in an anaerobic system is derived from the organic material itself, the 'intermediate' end products are primarily alcohols, aldehydes, and organic acids, plus carbon dioxide. In the presence of specialised methanogens, the intermediates are converted to the 'final' end products of methane, carbon dioxide, and trace levels of hydrogen sulfide.[19] In an anaerobic system, the majority of the chemical energy contained within the starting material is released by methanogenic bacteria as methane.[13]
Populations of anaerobic microorganisms typically take a significant period of time to establish themselves to be fully effective. Therefore, common practice is to introduce anaerobic microorganisms from materials with existing populations, a process known as "seeding" the digesters, typically accomplished with the addition of sewage sludge or cattle slurry.[20]