Nitrification

Daniel J Arp, Oregon State University, Corvallis, Oregon, USA

Published online: September 2009

DOI: 10.1002/9780470015902.a0021154

Full Article on Wiley Online Library

Nitrification is the process whereby reduced forms of inorganic and organic nitrogen, particularly ammonium, are oxidized to nitrate. The process is mediated by microorganisms and contributes to the movement of nitrogen through the biogeochemical nitrogen cycle. Ammonia-oxidizing bacteria first oxidize ammonia to nitrite, followed by the oxidation of nitrite to nitrate by the nitrite-oxidizing bacteria. In both cases, these bacteria are able to derive energy for growth from the oxidation of these inorganic compounds and can use carbon dioxide as their sole carbon source. Crenarchaeota were recently shown to also be capable of deriving energy from the oxidation of ammonia to nitrite. Ammonia monooxygenase initiates the metabolism of ammonia and produces hydroxylamine. This intermediate is converted to nitrite by hydroxylamine oxidoreductase, a trimer of an octaheme subunit. Nitrite oxidation to nitrate is catalysed by nitrite oxidoreductase, a molybdenum-containing enzyme.

Key Concepts

Nitrification is the process whereby reduced forms of inorganic and organic nitrogen, primarily ammonia, are oxidized to nitrate.
Nitrification is mediated by microorganisms including Bacteria and Crenarchaeota and occurs in two steps. In the first step, ammonia is oxidized to nitrite and in the second step nitrite is oxidized to nitrate.
Ammonia-oxidizing bacteria and Crenarchaeota can derive energy for growth from the oxidation of ammonia to nitrite.
Nitrite-oxidizing bacteria derive energy for growth from the oxidation of nitrite to nitrate.
Many ammonia- and nitrite-oxidizing bacteria are autotrophs and assimilate carbon dioxide via the Calvin cycle.
Key enzymes involved in nitrification are ammonia monooxygenase, which catalyses the oxidation of ammonia to hydroxylamine, hydroxylamine oxidoreductase, which catalyses the oxidation of hydroxylamine to nitrite and nitrite oxidoreductase, which catalyses the oxidation of nitrite to nitrate.
Microorganisms involved in nitrification are broadly distributed in nature and found virtually everywhere that ammonia and oxygen are present.
The genomes of several representative ammonia- and nitrite-oxidizing bacteria reveal the presence of genes consistent with the autotrophic lifestyle and only limited genes to support growth on organic compounds, again consistent with their lifestyle.

Keywords: nitrification; ammonia-oxidizing bacteria; ammonia-oxidizing archaea; nitrite-oxidizing bacteria; ammonia monooxygenase

References
	Arp DJ, Chain PSG and Klotz MG (2007) The impact of genome analyses on our understanding of ammonia-oxidizing bacteria. Annual Review of Microbiology 61: 503–528.
	Arp DJ and Stein LY (2003) Metabolism of inorganic N compounds by ammonia-oxidizing bacteria. Critical Reviews in Biochemistry and Molecular Biology 38: 471–495.
	Chain P, Lamerdin J, Larimer F et al. (2003) Complete genome sequence of the ammonia-oxidizing bacterium and obligate chemolithoautotroph Nitrosomonas europaea. Journal of Bacteriology 185: 2759–2773.
	book Ferguson SJ, Richardson DJ and van Spanning RJM (2007) "Biochemistry and molecular biology of nitrification". In: Bothe H, Ferguson SJ and Newton WE (eds) Biology of the Nitrogen Cycle, pp. 209–222. Amsterdam: Elsevier BV.
	Galloway JN and Cowling EB (2002) Reactive nitrogen and the world: 200 years of change. Ambio 31: 64–71.
	Klotz MG, Schmid MC, Strous M et al. (2008) Evolution of an octahaem cytochrome c protein family that is key to aerobic and anaerobic ammonia oxidation by bacteria. Environmental Microbiology 10: 3150–3163.
	Könneke M, Bernhard AE, de la Torre JR et al. (2005) Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 437: 543–546.
	Nicol GW and Schleper C (2006) Ammonia-oxidising crenarchaeota: important players in the nitrogen cycle? Trends in Microbiology 14: 207–212.
	book Prosser JI (2007) "The ecology of nitrifying bacteria". In: Bothe H, Ferguson SJ and Newton WE (eds) Biology of the Nitrogen Cycle, pp. 223–243. Amsterdam: Elsevier BV.
	Starkenburg SR, Chain PS, Sayavedra-Soto LA et al. (2006) Genome sequence of the chemolithoautrophic nitrite-oxidizing bacterium Nitrobacter winogradskyi Nb-255. Applied and Environmental Microbiology 72: 2050–2063.
Further Reading
	book Abeliovich A (2006) "Nitrite-oxidizing bacteria". In: Dworkin M, Falkow S, Rosenberg E, Schleifer K-H and Stackebrandt E (eds) The Prokaryotes – 3rd Edition, vol. 5, pp. 861–872. New York: Springer.
	book Bock E and Wagner M (2006) "Oxidation of inorganic nitrogen compounds as an energy source". In: Dworkin M, Falkow S, Rosenberg E, Schleifer K-H and Stackebrandt E (eds) The Prokaryotes – 3rd Edition, vol. 2, pp. 457–495. New York: Springer.
	Galloway JN, Townsend AR, Erisman JW et al. (2008) Transformation of the nitrogen cycle: recent trends, questions, and potential solutions. Science 320: 889–892.
	Hommes NG, Kurth EG, Sayavedra-Soto LA and Arp DJ (2006) Disruption of sucA, which encodes the E1 subunit of alpha-ketoglutarate dehydrogenase, affects the survival of Nitrosomonas europaea in stationary phase. Journal of Bacteriology 188: 343–347.
	Klotz MG, Arp DJ, Chain PS et al. (2006) Complete genome sequence of the marine, chemolithoautotrophic, ammonia-oxidizing bacterium Nitrosococcus oceani ATCC 19707. Applied and Environmental Microbiology 72: 6299–6315.
	Klotz MG and Stein LY (2008) Nitrifier genomics and evolution of the nitrogen cycle. FEMS Microbiology Letters 278: 146–156.
	book Koops H-P, Purkhold U, Pommerening-Roeser A, Timmermann G and Wagner M (2006) "The lithoautotrophic ammonia-oxidizing bacteria". In: Dworkin M, Falkow S, Rosenberg E, Schleifer K-H and Stackebrandt E (eds) The Prokaryotes – 3rd Edition, vol. 5, pp. 778–811. New York: Springer.
	Lieberman RL and Rosenzweig AC (2005) Crystal structure of a membrane-bound metalloenzyme that catalyses the biological oxidation of methane. Nature 434: 177–182.
	Treusch AH, Leininger S, Kletzin A et al. (2005) Novel genes for nitrite reductase and AMO-related proteins indicate a role of uncultivated mesophilic crenarchaeota in nitrogen cycling. Environmental Microbiology 7: 1985–1989.
	Zehr JP and Ward BB (2002) Nitrogen cycling in the ocean: new perspectives on processes and paradigms. Applied and Environmental Microbiology 68: 1015–1024.

Article Title:	Nitrification
* Name:
* E-mail:
* Note:

	Figure 1. Electron micrograph of Nitrosomonas europaea. Note the multiple layers of membranes pressed against the cell wall.
	Figure 2. Metabolism of ammonia to nitrite by ammonia-oxidizing bacteria. The oxidation of ammonia to hydroxylamine is catalysed by ammonia monooxygenase (AMO). The oxidation of hydroxylamine to nitrite is catalysed by hydroxylamine oxidoreductase (HAO).
	Figure 3. Metabolism of nitrite to nitrate by nitrite-oxidizing bacteria. The oxidation of nitrite to nitrate is catalysed by nitrite oxidase (also referred to as nitrite oxidoreductase).

Nitrification

Key Concepts

Related Sub-Topics: