Editing Nitrification (section)

==Microbiology==

=== Ammonia oxidation ===
The process of nitrification begins with the first stage of ammonia oxidation, where ammonia (NH<sub>3</sub>) or ammonium (NH<sub>4</sub><sup>+</sup>) get converted into nitrite (NO<sub>2</sub><sup>−</sup>). This first stage is sometimes known as nitritation. It is performed by two groups of organisms, [[nitrifying bacteria|ammonia-oxidizing bacteria]] ('''AOB''') and ammonia-oxidizing [[archaea]] ('''AOA<ref name="Hatzenpichler R. 2012">{{cite journal | vauthors = Hatzenpichler R | title = Diversity, physiology, and niche differentiation of ammonia-oxidizing archaea | journal = Applied and Environmental Microbiology | volume = 78 | issue = 21 | pages = 7501–10 | date = November 2012 | pmid = 22923400 | pmc = 3485721 | doi = 10.1128/aem.01960-12 | bibcode = 2012ApEnM..78.7501H }}</ref>''').

====Ammonia-Oxidizing Bacteria====
Ammonia-Oxidizing Bacteria (AOB) are typically Gram-negative bacteria and belong to [[Betaproteobacteria]] and [[Gammaproteobacteria]]<ref>{{cite journal | vauthors = Purkhold U, Pommerening-Röser A, Juretschko S, Schmid MC, Koops HP, Wagner M | title = Phylogeny of all recognized species of ammonia oxidizers based on comparative 16S rRNA and amoA sequence analysis: implications for molecular diversity surveys | journal = Applied and Environmental Microbiology | volume = 66 | issue = 12 | pages = 5368–82 | date = December 2000 | pmid = 11097916 | pmc = 92470 | doi = 10.1128/aem.66.12.5368-5382.2000 | bibcode = 2000ApEnM..66.5368P }}</ref> including the commonly studied genera ''[[Nitrosomonas]]'' and ''[[Nitrococcus]]''. They are known for their ability to utilize ammonia as an energy source and are prevalent in a wide range of environments, such as soils, aquatic systems, and wastewater treatment plants.

AOB possess enzymes called [[ammonia monooxygenase]]s (AMOs), which are responsible for catalyzing the conversion of ammonia to hydroxylamine (NH<sub>2</sub>OH), a crucial intermediate in the process of nitrification.<ref>{{Cite journal |last1=Wright |first1=Chloë L. |last2=Schatteman |first2=Arne |last3=Crombie |first3=Andrew T. |last4=Murrell |first4=J. Colin |last5=Lehtovirta-Morley |first5=Laura E. |date=2020-04-17 |title=Inhibition of Ammonia Monooxygenase from Ammonia-Oxidizing Archaea by Linear and Aromatic Alkynes |url=http://dx.doi.org/10.1128/aem.02388-19 |journal=Applied and Environmental Microbiology |volume=86 |issue=9 |pages=e02388-19 |doi=10.1128/aem.02388-19 |pmid=32086308 |issn=0099-2240|pmc=7170481 |bibcode=2020ApEnM..86E2388W }}</ref> This enzymatic activity is sensitive to environmental factors, such as pH, temperature, and oxygen availability.

AOB play a vital role in soil nitrification, making them key players in [[nutrient cycling]]. They contribute to the transformation of ammonia derived from organic matter decomposition or fertilizers into nitrite, which subsequently serves as a substrate for nitrite-oxidizing bacteria (NOB).

====Ammonia-Oxidizing Archaea====
Prior to the discovery of archaea capable of ammonia oxidation, ammonia-oxidizing bacteria (AOB) were considered the only organisms capable of ammonia oxidation. Since their discovery in 2005,<ref>{{cite journal | vauthors = Treusch AH, Leininger S, Kletzin A, Schuster SC, Klenk HP, Schleper C | title = Novel genes for nitrite reductase and Amo-related proteins indicate a role of uncultivated mesophilic crenarchaeota in nitrogen cycling | journal = Environmental Microbiology | volume = 7 | issue = 12 | pages = 1985–95 | date = December 2005 | pmid = 16309395 | doi = 10.1111/j.1462-2920.2005.00906.x | bibcode = 2005EnvMi...7.1985T }}</ref> two isolates of AOAs have been cultivated: ''Nitrosopumilus maritimus''<ref name="Isolation of an autotrophic ammonia">{{cite journal | vauthors = Könneke M, Bernhard AE, de la Torre JR, Walker CB, Waterbury JB, Stahl DA | title = Isolation of an autotrophic ammonia-oxidizing marine archaeon | journal = Nature | volume = 437 | issue = 7058 | pages = 543–6 | date = September 2005 | pmid = 16177789 | doi = 10.1038/nature03911 | bibcode = 2005Natur.437..543K | s2cid = 4340386 }}</ref> and ''Nitrososphaera viennensis''.<ref>{{cite journal | vauthors = Tourna M, Stieglmeier M, Spang A, Könneke M, Schintlmeister A, Urich T, Engel M, Schloter M, Wagner M, Richter A, Schleper C | display-authors = 6 | title = Nitrososphaera viennensis, an ammonia oxidizing archaeon from soil | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 108 | issue = 20 | pages = 8420–5 | date = May 2011 | pmid = 21525411 | pmc = 3100973 | doi = 10.1073/pnas.1013488108 | bibcode = 2011PNAS..108.8420T | doi-access = free }}</ref> When comparing AOB and AOA, AOA dominate in both soils and marine environments,<ref name="Hatzenpichler R. 2012"/><ref>{{cite journal | vauthors = Karner MB, DeLong EF, Karl DM | title = Archaeal dominance in the mesopelagic zone of the Pacific Ocean | journal = Nature | volume = 409 | issue = 6819 | pages = 507–10 | date = January 2001 | pmid = 11206545 | doi = 10.1038/35054051 | bibcode = 2001Natur.409..507K | s2cid = 6789859 }}</ref><ref name="Isolation of an autotrophic ammonia"/><ref>{{cite journal | vauthors = Wuchter C, Abbas B, Coolen MJ, Herfort L, van Bleijswijk J, Timmers P, Strous M, Teira E, Herndl GJ, Middelburg JJ, Schouten S, Sinninghe Damsté JS | display-authors = 6 | title = Archaeal nitrification in the ocean | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 103 | issue = 33 | pages = 12317–22 | date = August 2006 | pmid = 16894176 | pmc = 1533803 | doi = 10.1073/pnas.0600756103 | bibcode = 2006PNAS..10312317W | doi-access = free }}</ref><ref name=LeiningerUrich2006>{{cite journal | vauthors = Leininger S, Urich T, Schloter M, Schwark L, Qi J, Nicol GW, Prosser JI, Schuster SC, Schleper C | display-authors = 6 | title = Archaea predominate among ammonia-oxidizing prokaryotes in soils | journal = Nature | volume = 442 | issue = 7104 | pages = 806–9 | date = August 2006 | pmid = 16915287 | doi = 10.1038/nature04983 | url = http://www.abdn.ac.uk/staffpages/uploads/mbi010/Nature%20442,%20806-809.pdf | s2cid = 4380804 | bibcode = 2006Natur.442..806L | author-link7 = James I. Prosser | access-date = 2016-05-18 | archive-date = 2016-06-11 | archive-url = https://web.archive.org/web/20160611030331/http://www.abdn.ac.uk/staffpages/uploads/mbi010/Nature%20442,%20806-809.pdf | url-status = live }}</ref><ref>{{cite journal | vauthors = Daebeler A, Abell GC, Bodelier PL, Bodrossy L, Frampton DM, Hefting MM, Laanbroek HJ | title = Archaeal dominated ammonia-oxidizing communities in Icelandic grassland soils are moderately affected by long-term N fertilization and geothermal heating | language = English | journal = Frontiers in Microbiology | volume = 3 | pages = 352 | date = 2012 | pmid = 23060870 | pmc = 3463987 | doi = 10.3389/fmicb.2012.00352 | doi-access = free }}</ref> suggesting that ''[[Nitrososphaerota]]'' (formerly ''Thaumarchaeota'') may be greater contributors to ammonia oxidation in these environments.<ref name="Hatzenpichler R. 2012"/>

[[Crenarchaeol]], which is generally thought to be produced exclusively by AOA (specifically Nitrososphaerota), has been proposed as a biomarker for AOA and ammonia oxidation. Crenarchaeol abundance has been found to track with seasonal blooms of AOA, suggesting that it may be appropriate to use crenarchaeol abundances as a proxy for AOA populations<ref>{{Cite journal|last1=Pitcher|first1=Angela|last2=Wuchter|first2=Cornelia|last3=Siedenberg|first3=Kathi|last4=Schouten|first4=Stefan|last5=Sinninghe Damsté|first5=Jaap S.|date=2011|title=Crenarchaeol tracks winter blooms of ammonia-oxidizing Thaumarchaeota in the coastal North Sea|journal=Limnology and Oceanography|volume=56|issue=6|pages=2308–2318|doi=10.4319/lo.2011.56.6.2308|issn=0024-3590|bibcode=2011LimOc..56.2308P|url=http://www.vliz.be/imisdocs/publications/49/256149.pdf|doi-access=free|access-date=2022-08-27|archive-date=2023-05-22|archive-url=https://web.archive.org/web/20230522172309/https://www.vliz.be/imisdocs/publications/49/256149.pdf|url-status=live}}</ref> and thus ammonia oxidation more broadly. However the discovery of Nitrososphaerota that are not obligate ammonia-oxidizers<ref name=":5">{{cite journal|vauthors=Mussmann M, Brito I, Pitcher A, Sinninghe Damsté JS, Hatzenpichler R, Richter A, Nielsen JL, Nielsen PH, Müller A, Daims H, Wagner M, Head IM|date=October 2011|title=Thaumarchaeotes abundant in refinery nitrifying sludges express amoA but are not obligate autotrophic ammonia oxidizers|journal=Proceedings of the National Academy of Sciences of the United States of America|volume=108|issue=40|pages=16771–6|bibcode=2011PNAS..10816771M|doi=10.1073/pnas.1106427108|pmc=3189051|pmid=21930919|doi-access=free }}</ref> complicates this conclusion,<ref name=":6">{{cite journal | vauthors = Rush D, Sinninghe Damsté JS | title = Lipids as paleomarkers to constrain the marine nitrogen cycle | journal = Environmental Microbiology | volume = 19 | issue = 6 | pages = 2119–2132 | date = June 2017 | pmid = 28142226 | pmc = 5516240 | doi = 10.1111/1462-2920.13682 | bibcode = 2017EnvMi..19.2119R }}</ref> as does one study that suggests that crenarchaeol may be produced by Marine Group II Euryarchaeota.<ref name=":7">{{cite journal | vauthors = Lincoln SA, Wai B, Eppley JM, Church MJ, Summons RE, DeLong EF | title = Planktonic Euryarchaeota are a significant source of archaeal tetraether lipids in the ocean | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 111 | issue = 27 | pages = 9858–63 | date = July 2014 | pmid = 24946804 | pmc = 4103328 | doi = 10.1073/pnas.1409439111 | bibcode = 2014PNAS..111.9858L | doi-access = free }}</ref>

=== Nitrite oxidation ===
The second step of nitrification is the oxidation of nitrite into nitrate. This process is sometimes known as nitratation. Nitrite oxidation is conducted by nitrite-oxidizing bacteria ('''NOB''') from the taxa ''[[Nitrospirota]]'',<ref>{{cite journal | vauthors = Daims H, Nielsen JL, Nielsen PH, Schleifer KH, Wagner M | title = In situ characterization of ''Nitrospira''-like nitrite-oxidizing bacteria active in wastewater treatment plants | journal = Applied and Environmental Microbiology | volume = 67 | issue = 11 | pages = 5273–84 | date = November 2001 | pmid = 11679356 | pmc = 93301 | doi = 10.1128/AEM.67.11.5273-5284.2001 | bibcode = 2001ApEnM..67.5273D | url = }}</ref> ''[[Nitrospinota]]'',<ref name=":0">{{cite journal | vauthors = Beman JM, Leilei Shih J, Popp BN | title = Nitrite oxidation in the upper water column and oxygen minimum zone of the eastern tropical North Pacific Ocean | journal = The ISME Journal | volume = 7 | issue = 11 | pages = 2192–205 | date = November 2013 | pmid = 23804152 | pmc = 3806268 | doi = 10.1038/ismej.2013.96 | bibcode = 2013ISMEJ...7.2192B }}</ref> ''[[Pseudomonadota]]''<ref>{{cite journal | vauthors = Poly F, Wertz S, Brothier E, Degrange V | title = First exploration of Nitrobacter diversity in soils by a PCR cloning-sequencing approach targeting functional gene nxrA | journal = FEMS Microbiology Ecology | volume = 63 | issue = 1 | pages = 132–40 | date = January 2008 | pmid = 18031541 | doi = 10.1111/j.1574-6941.2007.00404.x | doi-access =  | bibcode = 2008FEMME..63..132P }}</ref> and ''[[Chloroflexota]]''.<ref>{{cite journal | vauthors = Spieck E, Spohn M, Wendt K, Bock E, Shively J, Frank J, Indenbirken D, Alawi M, Lücker S, Hüpeden J | display-authors = 6 | title = Extremophilic nitrite-oxidizing Chloroflexi from Yellowstone hot springs | journal = The ISME Journal | volume = 14 | issue = 2 | pages = 364–379 | date = February 2020 | pmid = 31624340 | pmc = 6976673 | doi = 10.1038/s41396-019-0530-9 | bibcode = 2020ISMEJ..14..364S }}</ref> NOB are typically present in soil, geothermal springs, freshwater and marine ecosystems.

=== Complete ammonia oxidation ===
{{main|Comammox}}
Ammonia oxidation to nitrate in a single step within one organism was predicted in 2006<ref>{{cite journal | vauthors = Costa E, Pérez J, Kreft JU | title = Why is metabolic labour divided in nitrification? | journal = Trends in Microbiology | volume = 14 | issue = 5 | pages = 213–9 | date = May 2006 | pmid = 16621570 | doi = 10.1016/j.tim.2006.03.006 | url = https://linkinghub.elsevier.com/retrieve/pii/S0966842X06000758 | access-date = 2021-01-21 | archive-date = 2020-10-19 | archive-url = https://web.archive.org/web/20201019214506/https://linkinghub.elsevier.com/retrieve/pii/S0966842X06000758 | url-status = live | url-access = subscription }}</ref> and discovered in 2015 in the species ''[[Nitrospira inopinata]]''. A pure culture of the organism was obtained in 2017,<ref>{{cite journal | vauthors = Kits KD, Sedlacek CJ, Lebedeva EV, Han P, Bulaev A, Pjevac P, Daebeler A, Romano S, Albertsen M, Stein LY, Daims H, Wagner M | display-authors = 6 | title = Kinetic analysis of a complete nitrifier reveals an oligotrophic lifestyle | journal = Nature | volume = 549 | issue = 7671 | pages = 269–272 | date = September 2017 | pmid = 28847001 | pmc = 5600814 | doi = 10.1038/nature23679 | bibcode = 2017Natur.549..269K | url = }}</ref> representing a revolution in our understanding of the nitrification process.