Anaerobic sugar fermentation reactions by various bacteria produce different end products. The production of ethanol by yeasts has been exploited by the brewing industry for thousands of years and is used for fuel production. Specific bacteria carry out the oxidation of alcohol to acetic acid in the production of vinegar. Other fermentation processes make even more valuable products. Organic compounds, such as acetone, isopropanol, and butyric acid, are produced in fermentation by various Clostridium species and can been prepared on an industrial scale. Other bacterial products and reactions have been discovered in organisms from extreme environments. There is considerable interest in the enzymes isolated from thermophilic bacteria, in which reactions may be carried out at higher rates owing to the higher temperatures at which they can occur.

Deposits of insoluble ferric iron (iron in the +3 oxidation state) are common in many environments. Bacterial reduction of ferric iron is common in waterlogged soils, bogs, and anaerobic portions of lakes. When the soluble ferrous iron (iron in the +2 oxidation state) thus formed reaches aerobic regions under neutral pH, the ferrous iron spontaneously oxidizes to insoluble, brown ferric deposits. In an acidic environment, iron does not readily oxidize from the ferrous to the ferric state. However, this reaction is tremendously accelerated by the acidophilic lithotrophic bacterium Acidithiobacillus ferrooxidans. When pyritic (ferrous sulfide) deposits are exposed to the air by mining operations, there is slow spontaneous oxidation of pyrite to ferrous ions and sulfuric acid. When the production of sulfuric acid causes conditions to reach a certain level of acidity, A. ferrooxidans thrives and oxidizes ferrous iron to the ferric form, which in turn oxidizes more pyrite in a continuously increasing fashion, with the formation of substantial amounts of sulfuric acid. The acidity of the environment may increase to a level near a pH of 2, which is a better environment for the solubilization of many other metal ions, particularly aluminum. Some of the ferrous iron generated by the bacteria is carried away by groundwater into surrounding streams, making them acidic and loaded with iron, which precipitates and forms deposits of iron some distance downstream from the mine. Acid mine drainage would not develop in the absence of bacterial activity, and the only practical way to prevent its occurrence is to seal or cover the acid-bearing material to prevent exposure to air. (For more information of oxidation and reduction reactions, see oxidation-reduction reaction.)

Although bacterial oxidation of sulfide materials results in the undesirable formation of acid mine drainage, the same reaction has been put to use for microbial leaching of copper, uranium, and other valuable metals from low-grade sulfide-containing ores. These metals are released from the ore after their conversion to more soluble forms by the direct oxidation of the metal by the bacterium and by the indirect oxidation of the metals in the ore by the ferric iron that was formed by bacterial action.

Microbial decomposition of petroleum products by hydrocarbon-oxidizing bacteria and fungi is of considerable ecological importance. The microbial decomposition of petroleum is an aerobic process, which is prevented if the oil settles to the layer of anaerobic sediment at the bottom (natural oil deposits in anaerobic environments are millions of years old). Hydrocarbon-oxidizing bacteria attach to floating oil droplets on the water surface, where their action eventually decomposes the oil to carbon dioxide. It is becoming a common practice to spray such bacteria and their growth factors onto oil spills to enhance the rate of degradation of the nonvolatile aliphatic and aromatic hydrocarbons.