Nitrification

Abstract

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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References

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.

Beman JM, Popp BN and Francis CA (2008) Molecular and biogeochemical evidence for ammonia oxidation by marine Crenarchaeota in the Gulf of California. The ISME Journal 2: 429–441.

Caranto JD and Lancaster KM (2017) Nitric oxide is an obligate bacterial nitrification intermediate produced by hydroxylamine oxidoreductase. Proceedings of the National Academy of Sciences 114: 8217–8222.

Costa E, Pérez J and Kreft J (2006) Why is metabolic labour divided in nitrification? Trends in Microbiology 14: 213–219.

Daims H, Lebedeva EV, Pjevac P, et al. (2015) Complete nitrification by Nitrospira bacteria. Nature 528: 504–509.

Daims H, Lücker S and Wagner M (2016) A new perspective on microbes formerly known as nitrite‐oxidizing bacteria. Trends in Microbiology 24: 699–712.

Galloway JN, Leach AM, Bleeker A and Erisman JW (2013) A chronology of human understanding of the nitrogen cycle. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 368 (1621): 20130120.

Hayatsu M, Tago K, Uchiyama I, et al. (2017) An acid‐tolerant ammonia‐oxidizing gamma‐proteobacterium from soil. The ISME Journal 11: 1130–1141.

Hink L, Lycus P, Gubry‐Rangin Ce, et al. (2017) Kinetics of NH3‐oxidation, NO‐turnover, N2O‐production and electron flow during oxygen depletion in model bacterial and archaeal ammonia oxidisers. Environmental Microbiology 19: 4882–4896.

Hink L, Nicol GW and Prosser JI (2018) Archaea produce lower yields of N2O than bacteria during aerobic ammonia oxidation in soil. Environmental Microbiology 19: 4829–4837.

Hommes NG, Sayavedra‐Soto LA and Arp DJ (2003) Chemolithoorganotrophic growth of Nitrosomonas europaea on fructose. Journal of Bacteriology 185: 6809–6814.

Kerou M, Offre P, Valledor L, et al. (2016) Proteomics and comparative genomics of Nitrososphaera viennensis reveal the core genome and adaptations of archaeal ammonia oxidizers. Proceedings of the National Academy of Sciences 113: E7937–E7946.

van Kessel MAHJ, Speth DR, Albertsen M, et al. (2015) Complete nitrification by a single microorganism. Nature 528: 555–559.

Kim JG, Park SJ, Sinninghe Damsté JS, et al. (2016) Hydrogen peroxide detoxification is a key mechanism for growth of ammonia‐oxidizing archaea. Proceedings of the National Academy of Sciences 113: 7888–7893.

Kits KD, Sedlacek CJ, Lebedeva EV, et al. (2017) Kinetic analysis of a complete nitrifier reveals an oligotrophic lifestyle. Nature 549: 269–272.

Könneke M, Bernhard AE, de la Torre JR, Walker CB, Waterbury JB and Stahl DA (2005) Isolation of an autotrophic ammonia‐oxidizing marine archaeon Nature 437: 543–546.

Könneke M, Schubert DM, Brown PC, et al. (2014) Ammonia‐oxidizing archaea use the most energy‐efficient aerobic pathway for CO2 fixation. Proceedings of the National Academy of Sciences 111: 8239–8244.

Kozlowski JA, Price J and Stein LY (2014) Revision of N2O‐producing pathways in the ammonia‐oxidizing bacterium Nitrosomonas europaea ATCC 19718. Applied and Environmental Microbiology 80: 4930–4935.

Kozlowski JA, Kits KD and Stein LY (2016a) Comparison of nitrogen oxide metabolism among diverse ammonia‐oxidizing bacteria. Frontiers in Microbiology 7: 9.

Kozlowski JA, Stieglmeier M, Schleper C, Klotz MG and Stein LY (2016b) Pathways and key intermediates required for obligate aerobic ammonia‐dependent chemolithotrophy in bacteria and Thaumarchaeota. The ISME Journal 10: 1836–1845.

Levicnik Hofferle S, Nicol GW, Ausec L, Mandic‐Mulec I and Prosser JI (2012) Stimulation of thaumarchaeal ammonia oxidation by mineralised organic nitrogen, but not inorganic nitrogen. FEMS Microbiology Ecology 80: 114–123.

Li Y, Chapman SJ, Nicol GW and Yao H (2018) Nitrification and nitrifiers in acidic soils. Soil Biology and Biochemistry 116: 290–301.

Lücker S, Wagner M, Maixner F, et al. (2010) A Nitrospira metagenome illuminates the physiology and evolution of globally important nitrite‐oxidizing bacteria. Proceedings of the National Academy of Sciences 107: 13479–13484.

Lund MB, Smith JM and Francis CA (2012) Diversity, abundance and expression of nitrite reductase (nirK)‐like genes in marine thaumarchaea. The ISME Journal 6: 1966–1977.

Martens‐Habbena W, Berube PM, Urakawa H, de la Torre JR and Stahl DA (2009) Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria. Nature 461: 976–979.

Martens‐Habbena W, Qin W, Horak REA, et al. (2015) The production of nitric oxide by marine ammonia‐oxidizing archaea and inhibition of archaeal ammonia oxidation by a nitric oxide scavenger. Environmental Microbiology 17: 2261–2274.

Ni BJ, Peng L, Law YY, Guo JH and Yuan ZG (2014) Modeling of nitrous oxide production by autotrophic ammonia‐oxidizing bacteria with multiple production pathways. Environmental Science & Technology 48: 3916–3924.

van Niftrik L and Jetten MSM (2012) Anaerobic ammonium‐oxidizing bacteria: unique microorganisms with exceptional properties. Microbiology and Molecular Biology Reviews: MMBR 76: 585–596.

Norton JM (2011) Diversity and environmental distribution of ammonia‐oxidizing bacteria. In: Ward BB, Arp DJ and Klotz MG (eds) Nitrification, pp. 39–55. Washington, DC: ASM Press.

Nyerges G and Stein LY (2009) Ammonia co‐metabolism and product inhibition vary considerably among species of methanotrophic bacteria. FEMS Microbiology Letters 297: 131–136.

Offre P, Kerou M, Spang A and Schleper C (2014) Variability of the transporter gene complement in ammonia‐oxidizing archaea. Trends in Microbiology 22: 665–675.

Okabe S, Aoi Y, Satoh H and Suwa Y (2011) Nitrification in wastewater treatment. In: Ward BB, Arp DJ and Klotz MG (eds) Nitrification, pp. 405–433. Washington, DC: ASM Press.

Pachiadaki MG, Sintes E, Bergauer K, et al. (2017) Major role of nitrite‐oxidizing bacteria in dark ocean carbon fixation. Science 358: 1046–1050.

Prosser JI, Head IM and Stein LY (2014) The family Nitrosomonadaceae. In: Rosenberg E, DeLong E, Lory S, Stackebrandt E and Thompson F (eds) The Prokaryotes, pp. 901–918. Berlin/Heidelberg: Springer .

Prosser JI and Nicol GW (2016) Candidatus Nitrosotalea. In: Whitman PWB (ed.) Bergey's Manual of Systematics of Archaea and Bacteria. pp. 1–7. Wiley‐Blackwell. DOI: 10.1002/9781118960608.gbm01292

Sorokin DY, Lücker S, Vejmelkova D, et al. (2012) Nitrification expanded: discovery, physiology and genomics of a nitrite‐oxidizing bacterium from the phylum Chloroflexi. The ISME Journal 6: 2245–2256.

Starkenburg SR, Arp DJ and Bottomley PJ (2008) Expression of a putative nitrite reductase and the reversible inhibition of nitrite‐dependent respiration by nitric oxide in Nitrobacter winogradskyi NB‐255. Environmental Microbiology 10: 3036–3042.

Stein LY (2011) Heterotrophic nitrification and nitrifier denitrification. In: Ward BB, Arp DJ and Klotz MG (eds) Nitrification, pp. 95–114. Washington, DC: ASM Press.

Stein LY and Klotz MG (2011) Nitrifying and denitrifying pathways of methanotrophic bacteria. Biochemical Society Transactions 39: 1826–1831.

Stein LY and Klotz MG (2016) The nitrogen cycle. Current Biology 26: R94–R98.

Tavormina PL, Orphan VJ, Kalyuzhnaya MG, Jetten MSM and Klotz MG (2011) A novel family of functional operons encoding methane/ammonia monooxygenase‐related proteins in gammaproteobacterial methanotrophs. Environmental Microbiology Reports 3: 91–100.

Taylor AE, Vajrala N, Giguere AT, et al. (2013) Use of aliphatic n‐alkynes to discriminate soil nitrification activities of ammonia‐oxidizing thaumarchaea and bacteria. Applied and Environmental Microbiology 79: 6544–6551.

Vajrala N, Martens‐Habbena W, Sayavedra‐Soto LA, et al. (2013) Hydroxylamine as an intermediate in ammonia oxidation by globally abundant marine archaea. Proceedings of the National Academy of Sciences 110: 1006–1011.

Walker CB, de la Torre JR, Urakawa H, et al. (2010) The genome of Nitrosopumilus maritimus reveals a close functional relationship to the globally distributed marine Crenarchaeota. Proceedings of the National Academy of Sciences 107: 8818–8823.

Winogradsky S (1890) Recherches sur les organismes de la nitrification. Annals de l'lnstitut Pasteur 4: 213–231.

Winogradsky S (1892) Contributions à la morphologie des organismes de la nitrification. Archives de Sciences Biologiques (St. Petersbourg) 1: 88–137.

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.

Klotz MG and Stein LY (2008) Nitrifier genomics and evolution of the nitrogen cycle. FEMS Microbiology Letters 278: 146–156.

Popkin, G. (2015) Feeding the World in the 21st Century: Grand Challenges in the Nitrogen Cycle. National Science Foundation Award Number 1550842. https://www.nsf.gov/mps/che/workshops/nsf_nitrogen_report_int.pdf

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.

Trimmer M, Chronopoulou PM, Maanoja ST, et al. (2016) Nitrous oxide as a function of oxygen and archaeal gene abundance in the North Pacific. Nature Communications 7: 13451–13460.

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