Editing Nitrification (section)

== Ecology ==
{{biogeochemical cycle sidebar|nutrient}}
Both steps are producing energy to be coupled to ATP synthesis. Nitrifying organisms are [[chemotroph|chemoautotroph]]s, and use [[carbon dioxide]] as their [[carbon]] source for growth. Some AOB possess the enzyme, [[urease]], which catalyzes the conversion of the urea molecule to two ammonia molecules and one carbon dioxide molecule. ''Nitrosomonas europaea'', as well as populations of soil-dwelling AOB, have been shown to assimilate the carbon dioxide released by the reaction to make [[biomass (ecology)|biomass]] via the [[Calvin Cycle]], and harvest energy by oxidizing ammonia (the other product of urease) to nitrite. This feature may explain enhanced growth of AOB in the presence of urea in acidic environments.<ref>{{cite journal | vauthors = Marsh KL, Sims GK, Mulvaney RL | year = 2005 | title = Availability of urea to autotrophic ammonia-oxidizing bacteria as related to the fate of <sup>14</sup>C- and <sup>15</sup>N-labeled urea added to soil | journal = Biol. Fert. Soil. | volume = 42 | issue = 2| pages = 137–145 | doi=10.1007/s00374-005-0004-2| bibcode = 2005BioFS..42..137M | s2cid = 6245255 }}</ref>

In most environments, organisms are present that will complete both steps of the process, yielding nitrate as the final product. However, it is possible to design systems in which nitrite is formed (the ''[[SHARON Wastewater Treatment|Sharon process]]'').

Nitrification is important in agricultural systems, where fertilizer is often applied as ammonia. Conversion of this ammonia to nitrate increases nitrogen leaching because nitrate is more water-soluble than ammonia.

Nitrification also plays an important role in the removal of [[nitrogen]] from municipal [[wastewater]]. The conventional removal is nitrification, followed by [[denitrification]]. The cost of this process resides mainly in [[aeration]] (bringing oxygen in the reactor) and the addition of an external carbon source (e.g., [[methanol]]) for the denitrification.

Nitrification can also occur in drinking water. In distribution systems where [[chloramines]] are used as the secondary disinfectant, the presence of free ammonia can act as a substrate for ammonia-oxidizing microorganisms. The associated reactions can lead to the depletion of the disinfectant residual in the system.<ref>{{cite journal | vauthors = Zhang Y, Love N, Edwards M | year = 2009 | title = Nitrification in Drinking Water Systems | journal = Critical Reviews in Environmental Science and Technology | volume = 39 | issue = 3| pages = 153–208 | doi = 10.1080/10643380701631739 | bibcode = 2009CREST..39..153Z | s2cid = 96988652 }}</ref> The addition of chlorite ion to chloramine-treated water has been shown to control nitrification.<ref>{{cite journal|doi=10.1002/j.1551-8833.1999.tb08715.x|title=Using chlorite ion to control nitrification|journal=Journal - American Water Works Association|volume=91|issue=10|pages=52–61|year=1999| vauthors = McGuire MJ, Lieu NI, Pearthree MS |bibcode=1999JAWWA..91j..52M |s2cid=93321500 }}</ref><ref>{{cite journal|doi=10.1002/j.1551-8833.2009.tb09970.x|title=Prevention of nitrification using chlorite ion: Results of a demonstration project in Glendale, Calif|journal=Journal - American Water Works Association|volume=101|issue=10|pages=47–59|year=2009| vauthors = McGuire MJ, Wu X, Blute NK, Askenaizer D, Qin G |bibcode=2009JAWWA.101j..47M |s2cid=101973325 }}</ref>

Together with [[ammonification]], nitrification forms a [[mineralization (soil)|mineralization]] process that refers to the complete decomposition of organic material, with the release of available nitrogen compounds. This replenishes the [[nitrogen cycle]].

=== Nitrification in the marine environment ===
In the [[marine environment]], nitrogen is often the [[limiting nutrient]], so the [[nitrogen cycle]] in the ocean is of particular interest.<ref name="zehr1">{{cite journal |vauthors=Zehr JP, Kudela RM |year=2011 |title=Nitrogen cycle of the open ocean: from genes to ecosystems |journal=Annual Review of Marine Science |volume=3 |pages=197–225 |bibcode=2011ARMS....3..197Z |doi=10.1146/annurev-marine-120709-142819 |pmid=21329204 |s2cid=23018410}}</ref><ref name="Denitrification 1996 pp. 247-261">{{cite journal |vauthors=Ward BB |date=November 1996 |title=Nitrification and Denitrification: Probing the Nitrogen Cycle in Aquatic Environments |url=https://www.princeton.edu/nitrogen/publications/pdfs/Ward_1996_Probing.pdf |journal=Microbial Ecology |volume=32 |issue=3 |pages=247–61 |doi=10.1007/BF00183061 |pmid=8849421 |bibcode=1996MicEc..32..247W |s2cid=11550311 |access-date=2018-10-18 |archive-date=2017-10-19 |archive-url=https://web.archive.org/web/20171019062459/https://www.princeton.edu/nitrogen/publications/pdfs/Ward_1996_Probing.pdf |url-status=live }}</ref>   The nitrification step of the cycle is of particular interest in the ocean because it creates [[nitrate]], the primary form of nitrogen responsible for [[F-ratio (oceanography)|"new" production]].  Furthermore, as the ocean becomes enriched in [[Human impact on the environment|anthropogenic]] [[Carbon dioxide|CO<sub>2</sub>]], the resulting decrease in [[pH]] could lead to decreasing rates of nitrification.  Nitrification could potentially become a "bottleneck" in the nitrogen cycle.<ref>{{cite journal |vauthors=Hutchins D, Mulholland M, Fu F |year=2009 |title=Nutrient cycles and marine microbes in a CO<sub>2</sub>-enriched ocean |url=https://digitalcommons.odu.edu/cgi/viewcontent.cgi?article=1024&context=oeas_fac_pubs |journal=Oceanography |volume=22 |issue=4 |pages=128–145 |doi=10.5670/oceanog.2009.103 |doi-access=free |access-date=2018-10-18 |archive-date=2018-10-18 |archive-url=https://web.archive.org/web/20181018201544/https://digitalcommons.odu.edu/cgi/viewcontent.cgi?article=1024&context=oeas_fac_pubs |url-status=live }}</ref>

Nitrification, as stated above, is formally a two-step process; in the first step [[ammonia]] is [[oxidized]] to [[nitrite]], and in the second step nitrite is oxidized to nitrate.  Diverse microbes are responsible for each step in the marine environment.  Several groups of [[ammonia-oxidizing bacteria]] (AOB) are known in the marine environment, including ''[[Nitrosomonas]]'', ''[[Nitrospira]]'', and ''[[Nitrosococcus]]''.  All contain the functional gene [[ammonia monooxygenase]] ('''AMO''') which, as its name implies, is responsible for the oxidation of ammonia.<ref name="Hatzenpichler R. 2012" /><ref name="Denitrification 1996 pp. 247-261" />  Subsequent [[metagenomic]] studies and cultivation approaches have revealed that some [[Thermoproteota]] (formerly Crenarchaeota) possess AMO. Thermoproteota are abundant in the ocean and some species have a 200 times greater affinity for ammonia than AOB, contrasting with the previous belief that AOB are primarily responsible for nitrification in the ocean.<ref>{{cite journal |vauthors=Martens-Habbena W, Berube PM, Urakawa H, de la Torre JR, Stahl DA |date=October 2009 |title=Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria |journal=Nature |volume=461 |issue=7266 |pages=976–9 |bibcode=2009Natur.461..976M |doi=10.1038/nature08465 |pmid=19794413 |s2cid=1692603}}</ref><ref name="zehr1" /> Furthermore, though nitrification is classically thought to be vertically separated from [[primary production]] because the oxidation of nitrate by [[bacteria]] is inhibited by light, nitrification by AOA does not appear to be light inhibited, meaning that nitrification is occurring throughout the [[water column]], challenging the classical definitions of [[F-ratio (oceanography)|"new" and "recycled" production]].<ref name="zehr1" />

In the second step, nitrite is oxidized to nitrate.  In the oceans, this step is not as well understood as the first, but the bacteria ''[[Nitrospina]]''<ref name=":0" /><ref>{{cite journal |vauthors=Sun X, Kop LF, Lau MC, Frank J, Jayakumar A, Lücker S, Ward BB |date=October 2019 |title=Uncultured Nitrospina-like species are major nitrite oxidizing bacteria in oxygen minimum zones |journal=The ISME Journal |volume=13 |issue=10 |pages=2391–2402 |doi=10.1038/s41396-019-0443-7 |pmc=6776041 |pmid=31118472|bibcode=2019ISMEJ..13.2391S }}</ref> and ''[[Nitrobacter]]'' are known to carry out this step in the ocean.<ref name="zehr1" />