Nitrification is the process by which ammonia () is converted to nitrate ().  Nitrification is actually the net result of two distinct processes: oxidation of ammonia to nitrite () by nitrosifying bacteria (e.g. Nitrosomonas) and oxidation of nitrite to nitrate by the nitrite-oxidizing bacteria (e.g. Nitrobacter).  Both of these processes are extremely energetically poor leading to very slow growth rates for both types of organisms.  Biochemically, ammonia oxidation occurs by the stepwise oxidation of ammonia to hydroxylamine () by the enzyme ammonia monooxygenase in the cytoplasm, followed by the oxidation of hydroxylamine to nitrite by the enzyme hydroxylamine oxidoreductase in the periplasm.
Electron and proton cycling are very complex but as a net result only one proton is translocated across the membrane per molecule of ammonia oxidized.  Nitrite oxidation is much simpler, with nitrite being oxidized by the enzyme nitrite oxidoreductase coupled to proton translocation by a very short electron transport chain, again leading to very low growth rates for these organisms.  Oxygen is required in both ammonia and nitrite oxidation, meaning that both nitrosifying and nitrite-oxidizing bacteria are aerobes.  As in sulfur and iron oxidation, NADH for carbon dioxide fixation using the Calvin cycle is generated by reverse electron flow, thereby placing a further metabolic burden on an already energy-poor process.
In 2015, two groups independently showed the microbial genus Nitrospira is capable of complete nitrification (Comammox).