Nitrifying bacteria are chemoautotrophic or chemolithotrophs depending on the genera (Nitrosomonas, Nitrosococcus, Nitrobacter, Nitrococcus) bacteria that grow by consuming inorganic nitrogen compounds. Many species of nitrifying bacteria have complex internal membrane systems that are the location for key enzymes in nitrification: ammonia monooxygenase which oxidizes ammonia to hydroxylamine, and nitrite oxidoreductase, which oxidizes nitrite to nitrate.
Nitrifying bacteria are widespread in the environment, and are found in highest numbers where considerable amounts of ammonia are present (areas with extensive protein decomposition, and sewage treatment plants). Nitrifying bacteria thrive in lakes and streams with high inputs of sewage and wastewater because of the high ammonia content.
Oxidation of ammonia to nitrate 
Nitrification in nature is a two-step oxidation process of ammonium (NH4+ or ammonia NH3) to nitrate (NO3-) catalyzed by two ubiquitous bacterial groups. The first reaction is oxidation ammonium to nitrite by ammonium oxidizing bacteria (AOB) represented by Nitrosomonas species. The second reaction is oxidation nitrite (NO2-) to nitrate by nitrite-oxidizing bacteria (NOB), represented by Nitrobacter species  . First step nitrification - molecular mechanism
Ammonia oxidation in autotrophic nitrification is a complex process that requires several enzymes, proteins and presence of oxygen. The key enzymes, necessary to obtaining energy during oxidation ammonium to nitrite are ammonia monooxygenase (AMO) and hydroxylamine oxidoreductase (HAO). First is a transmembrane copper protein which catalyzes the oxidation of ammonium to hydroxylamine (1.1) taking two electrons directly from the quinone pool. This reaction requires O2. In the second step (1.2), a trimeric multiheme c-type HAO converts hydroxylamine into nitrite in the periplasm with production of four electrons. The stream of four electron are channelled through cytochrome c554 to a membrane-bound cytochrome c552. Two of the electrons are routed back to AMO, where they are used for the oxidation of ammonia (quinol pool). Rest two electrons are used to generate a proton motive force and reduce NAD(P) through reverse electron transport. (Figure 1.)
- NH3 + O2 → NO−
2 + 3H+ + 2e− (1)
- NH3 + O2 + 2H+ + 2e− → NH2OH + H2O (1.1)
- NH2OH + H2O → NO−
2 + 5H+ + 4e− (1.2)
Second step nitrification - molecular mechanism
Nitrite produced in first step autotrophic nitrification is oxidized to nitrate by nitrite oxidoreductase (NXR)(2). It is a membrane-associated iron-sulfur molybdoprotein, and is part of an electron transfer chain which channels electrons from nitrite to molecular oxygen. The molecular mechanism of oxidation nitrite is less described than oxidation ammonium. In new research (e.g. Woźnica A. et al., 2013) proposed new hypothetical model of NOB electron transport chain and NXR mechanism (Figure 2.). It should be noted that, in contrast to earlier models  the NXR acts on the outside of the plasma membrane, directly contributing to postulated by Spieck  and coworkers mechanism of proton gradient generation. Nevertheless, the molecular mechanism of nitrite oxidation is an open question.
2 + H2O → NO−
3 + 2H+ + 2e− (2)
|Nitrifying bacteria that oxidize ammonia
|Nitrifying bacteria that oxidize nitrite
See also 
- Root nodule
- Denitrifying bacteria
- Nitrogen cycle
- Nitrogen deficiency
- Nitrogen fixation
- Electron transport chain - nitrifying bacteria
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