The global nitrogen cycle is initiated by the fixation of atmospheric N2, by either natural or chemical processes, to bioavailable ammonium (NH4+). Nitrification is the oxidative process that transforms this ammonium to nitrate, via a nitrite intermediate. Nitrification is performed solely by microorganisms: ammonia‐oxidising bacteria and archaea oxidise ammonia to nitrite, nitrite‐oxidising bacteria oxidise nitrite to nitrate and comammox bacteria oxidise ammonia to nitrate. Nitrifiers (and anammox) are distinguished from other microorganisms as they can grow solely from the oxidation of inorganic nitrogenous molecules and fix carbon dioxide as their sole carbon source, although many can also grow using alternative catabolic processes, by cross‐feeding, and/or by mixotrophy. Key enzymes to the nitrification process include ammonia monooxygenase, hydroxylamine dehydrogenase and nitrite oxidoreductase. A putative enzyme catalysing nitric oxide oxidation to nitrite is currently uncharacterised. Essential intermediates to nitrification include hydroxylamine, nitric oxide and nitrite. As well as performing a required component of the global nitrogen cycle, nitrifying microorganisms are also responsible for the loss of nitrogen‐based fertilisers in soil and play a critical role in emission of the potent greenhouse gas, nitrous oxide, as mediated by production and consumption of nitric oxide in their metabolism.

Key Concepts

  • Nitrification is an oxidative process that transforms reduced nitrogen, primarily ammonia, to nitrate.
  • Fluxes in nitrogen transformations associated with nitrification activity have accelerated greatly over the past century owing to the production and application of inorganic ammonium‐based fertilisers.
  • Microorganisms involved in nitrification are ubiquitously distributed in nature and found virtually everywhere that ammonia and oxygen are present.
  • Nitrification is mediated by bacteria and archaea and is performed by either two (ammonia and nitrite oxidisers) or one (comammox) canonical functional group.
  • Autotrophic pathways of ammonia‐ and nitrite‐oxidising bacteria are the Calvin cycle or reverse TCA cycle; ammonia‐oxidising archaea assimilate carbon dioxide via the 3‐hydroxypropionate/4‐hydroxybutyrate pathway.
  • Key enzymes of nitrification are ammonia monooxygenase, hydroxylamine dehydrogenase, nitric oxide oxidase (putative) and nitrite oxidoreductase.
  • Methanotrophic and heterotrophic microorganisms can carry out parts of nitrification but cannot grow from oxidising reduced nitrogen compounds.
  • Mechanisms for the production of nitric oxide and nitrous oxide are distinct among nitrifying microorganisms.
  • Comparative genome analysis and the use of differential inhibitors can assist in determining differences in physiology and niche preference among nitrifying microorganisms.
  • There is substantial physiological diversity within individual functional groups (e.g. ammonia oxidisers) which results in niche differentiation both within and between taxonomic groups of nitrifiers.

Keywords: nitrification; ammonia‐oxidising bacteria; ammonia‐oxidising archaea; nitrite‐oxidising bacteria; Nitrospira; comammox; ammonia monooxygenase; nitric oxide; nitrous oxide

Figure 1. The microbially mediated process of nitrification. NH3 is oxidised to NO3 via two stages (1) by ammonia‐oxidising archaea (AOA) plus ammonia‐oxidising bacteria (AOB) and nitrite oxidising bacteria (NOB) or in one stage (2) by comammox bacteria. The oxidation of NH3 also results in the production of the N2O by different enzymatic or abiotic mechanisms.
Figure 2. Electron micrograph of Nitrosomonas europaea. Note the multiple layers of membranes pressed against the cell wall.
Figure 3. Metabolism of ammonia to nitrite by ammonia‐oxidising bacteria. The oxidation of ammonia to hydroxylamine is catalysed by ammonia monooxygenase (AMO). The oxidation of hydroxylamine to nitric oxide is catalysed by hydroxylamine dehydrogenase (HAO). The oxidation of nitric oxide to nitrite is catalysed by an unknown enzyme.
Figure 4. Metabolism of ammonia to nitrite by ammonia‐oxidising Thaumarchaeota. The oxidation of ammonia to hydroxylamine is catalysed by ammonia monooxygenase (AMO). The second step is speculative and based on evidence that AOA oxidise hydroxylamine to nitrite and that NO is an essential intermediate in the pathway. The reduction of nitrite to NO is presumably catalysed by NirK, the copper‐based nitrite reductase, that is highly expressed in AOA cultures, enrichments and in metatranscriptomes of abundant AOA populations.
Figure 5. Metabolism of nitrite to nitrate by nitrite‐oxidising bacteria. The oxidation of nitrite to nitrate is catalysed in a single step by nitrite oxidoreductase, NXR.
Figure 6. Metabolism of complete ammonia oxidation to nitrate (comammox). AMO, HAO and NXR enzymes have been identified in the genome sequence of Nitrospira inopinata. The role of NO metabolism is yet to be elucidated, but is hypothesised to resemble the pathway of AOB.


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Further Reading

Dworkin M (2011) Sergei Winogradsky: a founder of modern microbiology and the first microbial ecologist. FEMS Microbiology Reviews 36: 364–379.

Erisman JW, Sutton MA, Galloway J, Klimont Z and Winiwarter W (2008) How a century of ammonia synthesis changed the world. Nature Geoscience 1: 636–639.

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Popkin, G. (2015) Feeding the World in the 21st Century: Grand Challenges in the Nitrogen Cycle. National Science Foundation Award Number 1550842.

Prosser JI and Nicol GW (2012) Archaeal and bacterial ammonia‐oxidisers in soil: the quest for niche specialisation and differentiation. Trends in Microbiology 20: 523–531.

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Stein, Lisa Y, and Nicol, Graeme W(Apr 2018) Nitrification. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0021154.pub2]