Biodegradation of petroleum is a selective metabolism of special organic compounds by an ensemble of microorganisms. It apparently starts under aerobic conditions, which are provided in areas invaded by surface-derived, oxygen-rich formation waters. Bacteria introduced into an oil pool with meteoric waters apparently utilize dissolved oxygen for consumption of certain types of hydrocarbons. The selective removal of hydrocarbons seems to occur in the following sequence: n-alkanes, isoprenoid alkanes, naphthenes, and aromatics. Under anaerobic conditions, bacterial growth is possible if supplies of aerobic synthesized metabolites are available or else by reduction of dissolved sulfate, which results at least in the production of reduced sulfur compounds.

The fate of the synthesized microbial material is at present unclear. Part of the more stable and oil-soluble compounds may be dissolved in the crude oil and increase the fraction of nonhydrocarbons, especially asphaltenes. The microbial alteration processes yielding heavy oils are an effect of the selective depletion of light components coupled with enrichment of heavy NSO compounds, especially sulfur compounds.