Editing Nitrogen cycle (section)

== Processes ==
{{biogeochemical cycle sidebar|nutrient}}
Nitrogen is present in the environment in a wide variety of chemical forms including organic nitrogen, [[ammonium]] ({{chem2|NH4+}}), [[nitrite]] ({{chem2|NO2-}}), [[nitrate]] ({{chem2|NO3-}}), [[nitrous oxide]] ({{chem2|N2O}}), [[nitric oxide]] (NO) or inorganic nitrogen gas ({{chem2|N2}}). Organic nitrogen may be in the form of a living organism, [[humus]] or in the intermediate products of organic matter decomposition. The processes in the nitrogen cycle is to transform nitrogen from one form to another. Many of those processes are carried out by [[microorganism|microbes]], either in their effort to harvest energy or to accumulate nitrogen in a form needed for their growth. For example, the [[metabolic waste#Nitrogen wastes|nitrogenous wastes]] in animal [[urine]] are broken down by [[nitrifying bacteria]] in the soil to be used by plants. The diagram alongside shows how these processes fit together to form the nitrogen cycle.

=== Nitrogen fixation ===
{{Main|Nitrogen fixation}}
The conversion of nitrogen gas ({{chem2|N2}}) into nitrates and nitrites through atmospheric, industrial and biological processes is called nitrogen fixation. Atmospheric nitrogen must be processed, or "[[nitrogen fixation|fixed]]", into a usable form to be taken up by plants. Between 5 and 10 billion kg per year are fixed by [[lightning]] strikes, but most fixation is done by free-living or [[symbiosis|symbiotic]] [[bacterium|bacteria]] known as [[diazotrophs]]. These bacteria have the [[nitrogenase]] [[enzyme]] that combines gaseous nitrogen with [[hydrogen]] to produce [[ammonia]], which is converted by the bacteria into other [[organic compound]]s. Most biological nitrogen fixation occurs by the activity of [[molybdenum]] (Mo)-nitrogenase, found in a wide variety of bacteria and some [[Archaea]]. Mo-nitrogenase is a complex two-component [[enzyme]] that has multiple metal-containing prosthetic groups.<ref name="Moir 2011" /> An example of free-living bacteria is ''[[Azotobacter]]''. Symbiotic nitrogen-fixing bacteria such as ''[[Rhizobium]]'' usually live in the root nodules of [[legumes]] (such as peas, alfalfa, and locust trees). Here they form a [[Mutualism (biology)|mutualistic]] relationship with the plant, producing ammonia in exchange for [[carbohydrate]]s. Because of this relationship, legumes will often increase the nitrogen content of nitrogen-poor soils. A few non-legumes can also form such [[symbiosis|symbioses]]. Today, about 30% of the total fixed nitrogen is produced industrially using the [[Haber-Bosch]] process,<ref name="Smith 2004" /> which uses high temperatures and pressures to convert nitrogen gas and a hydrogen source (natural gas or petroleum) into ammonia.<ref name="Smil 2000" />

=== Assimilation ===
{{Main|Assimilation (biology)|Nitrogen assimilation}}
Plants can absorb nitrate or ammonium from the soil by their root hairs. If nitrate is absorbed, it is first reduced to nitrite ions and then ammonium ions for incorporation into amino acids, nucleic acids, and chlorophyll. In plants that have a symbiotic relationship with rhizobia, some nitrogen is assimilated in the form of ammonium ions directly from the nodules. It is now known that there is a more complex cycling of amino acids between ''Rhizobia'' bacteroids and plants. The plant provides amino acids to the bacteroids so ammonia assimilation is not required and the bacteroids pass amino acids (with the newly fixed nitrogen) back to the plant, thus forming an interdependent relationship.<ref name="Willey 2011" /> While many animals, fungi, and other [[heterotrophic]] organisms obtain nitrogen by ingestion of [[amino acid]]s, [[nucleotide]]s, and other small organic molecules, other heterotrophs (including many [[bacteria]]) are able to utilize inorganic compounds, such as ammonium as sole N sources.  Utilization of various N sources is carefully regulated in all organisms.

=== Ammonification ===
When a plant or animal dies or an animal expels waste, the initial form of nitrogen is [[Organic matter|organic]], present in forms such as amino acids and DNA.<ref>{{Cite web |title=The Nitrogen Cycle: Processes, Players, and Human Impact {{!}} Learn Science at Scitable |url=https://www.nature.com/scitable/knowledge/library/the-nitrogen-cycle-processes-players-and-human-15644632/ |access-date=2025-02-13 |website=www.nature.com |language=en}}</ref> Bacteria and fungi convert this organic nitrogen into [[ammonia]] and sometimes ammonium through a series of processes called ammonification or [[Mineralization (soil)|mineralization]]. This is the last step in the nitrogen cycle step involving organic compounds.<ref>{{Citation |last=Strock |first=J.S. |title=Ammonification |date=2008 |pages=162–165 |url=https://www.sciencedirect.com/topics/earth-and-planetary-sciences/ammonification |access-date=2025-02-13 |publisher=Elsevier |language=en |doi=10.1016/B978-008045405-4.00256-1 |isbn=978-0-08-045405-4 |encyclopedia=Encyclopedia of Ecology|url-access=subscription }}</ref> Myriad enzymes are involved including [[Dehydrogenase|dehydrogenases]], [[Protease|proteases]], and [[Deamination|deaminases]] such as [[glutamate dehydrogenase]] and [[glutamine synthetase]].<ref name=":2">{{Citation |last=Cabello |first=P. |title=Nitrogen Cycle |date=2009-01-01 |work=Encyclopedia of Microbiology (Third Edition) |pages=299–321 |editor-last=Schaechter |editor-first=Moselio |url=https://www.sciencedirect.com/science/article/abs/pii/B9780123739445000559 |access-date=2025-03-18 |place=Oxford |publisher=Academic Press |isbn=978-0-12-373944-5 |last2=Roldán |first2=M. D. |last3=Castillo |first3=F. |last4=Moreno-Vivián |first4=C.}}</ref> Nitrogen mineralization and ammonification have a positive correlation with organic nitrogen in the soil,<ref>{{Cite journal |last=Marion |first=G. M. |last2=Black |first2=C. H. |date=1988 |title=Potentially Available Nitrogen and Phosphorus Along a Chaparral Fire Cycle Chronosequence |url=https://acsess.onlinelibrary.wiley.com/doi/abs/10.2136/sssaj1988.03615995005200040048x?getft_integrator=sciencedirect_contenthosting&src=getftr&utm_source=sciencedirect_contenthosting |journal=Soil Science Society of America Journal |language=en |volume=52 |issue=4 |pages=1155–1162 |doi=10.2136/sssaj1988.03615995005200040048x |issn=1435-0661|url-access=subscription }}</ref> soil microbial biomass, and average annual precipitation.<ref name=":3">{{Cite journal |last=Li |first=Zhaolei |last2=Tian |first2=Dashuan |last3=Wang |first3=Bingxue |last4=Wang |first4=Jinsong |last5=Wang |first5=Song |last6=Chen |first6=Han Y. H. |last7=Xu |first7=Xiaofeng |last8=Wang |first8=Changhui |last9=He |first9=Nianpeng |last10=Niu |first10=Shuli |date=2019 |title=Microbes drive global soil nitrogen mineralization and availability |url=https://onlinelibrary.wiley.com/doi/abs/10.1111/gcb.14557?getft_integrator=sciencedirect_contenthosting&src=getftr&utm_source=sciencedirect_contenthosting |journal=Global Change Biology |language=en |volume=25 |issue=3 |pages=1078–1088 |doi=10.1111/gcb.14557 |issn=1365-2486|url-access=subscription }}</ref> They also respond closely to changes in temperature.<ref>{{Cite journal |last=Pierre |first=S. |last2=Hewson |first2=I. |last3=Sparks |first3=J. P. |last4=Litton |first4=C. M. |last5=Giardina |first5=C. |last6=Groffman |first6=P. M. |last7=Fahey |first7=T. J. |date=2017 |title=Ammonia oxidizer populations vary with nitrogen cycling across a tropical montane mean annual temperature gradient |url=https://esajournals.onlinelibrary.wiley.com/doi/abs/10.1002/ecy.1863?getft_integrator=sciencedirect_contenthosting&src=getftr&utm_source=sciencedirect_contenthosting |journal=Ecology |language=en |volume=98 |issue=7 |pages=1896–1907 |doi=10.1002/ecy.1863 |issn=1939-9170|url-access=subscription }}</ref> However, these processes slow in the presence of vegetation with high carbon to nitrogen ratios<ref>{{Cite journal |last=Gosz |first=J. R. |date=1981 |title=Nitrogen Cycling in Coniferous Ecosystems |url=https://www.jstor.org/stable/45128679 |journal=Ecological Bulletins |issue=33 |pages=405–426 |issn=0346-6868}}</ref><ref>{{Cite journal |last=Vitousek |first=Peter M. |last2=Gosz |first2=James R. |last3=Grier |first3=Charles C. |last4=Melillo |first4=Jerry M. |last5=Reiners |first5=William A. |date=1982 |title=A Comparative Analysis of Potential Nitrification and Nitrate Mobility in Forest Ecosystems |url=https://esajournals.onlinelibrary.wiley.com/doi/abs/10.2307/1942609?getft_integrator=sciencedirect_contenthosting&src=getftr&utm_source=sciencedirect_contenthosting |journal=Ecological Monographs |language=en |volume=52 |issue=2 |pages=155–177 |doi=10.2307/1942609 |issn=1557-7015|url-access=subscription }}</ref> and fertilization with sugar.<ref>{{Cite journal |last=Zagal |first=Erick |last2=Persson |first2=Jan |date=1994-10-01 |title=Immobilization and remineralization of nitrate during glucose decomposition at four rates of nitrogen addition |url=https://www.sciencedirect.com/science/article/abs/pii/0038071794902127 |journal=Soil Biology and Biochemistry |volume=26 |issue=10 |pages=1313–1321 |doi=10.1016/0038-0717(94)90212-7 |issn=0038-0717|url-access=subscription }}</ref><ref>{{Cite journal |last=DeLuca |first=T. H. |last2=Keeney |first2=D. R. |date=1993-01-01 |title=Glucose-induced nitrate assimilation in prairie and cultivated soils |url=https://link.springer.com/article/10.1007/BF00001116 |journal=Biogeochemistry |language=en |volume=21 |issue=3 |pages=167–176 |doi=10.1007/BF00001116 |issn=1573-515X|url-access=subscription }}</ref>

[[File:Nitrogen Cycle - Reactions and Enzymes.svg|thumb|upright=1.5| {{center|'''Microbial nitrogen cycle'''{{hsp}}<ref name="Sparacino-Watkins 2013" /><ref name="Simon 2013" />}} [[Anammox|ANAMMOX]] is anaerobic ammonium oxidation, [[Dissimilatory nitrate reduction to ammonium|DNRA]] is dissimilatory nitrate reduction to ammonium, and [[Comammox|COMAMMOX]] is complete ammonium oxidation.]]

=== Nitrification ===
{{Main|Nitrification}}
The conversion of ammonium to nitrate is performed primarily by soil-living bacteria and other nitrifying bacteria. In the primary stage of nitrification, the oxidation of ammonium ({{chem2|NH4+}}) is performed by bacteria such as the ''[[Nitrosomonas]]'' species, which converts ammonia to [[nitrites]] ({{chem2|NO2-}}). Other bacterial species such as ''[[Nitrobacter]]'', are responsible for the oxidation of the nitrites ({{chem2|NO2-}}) into [[nitrates]] ({{chem2|NO3-}}). It is important for the [[ammonia]] ({{chem2|NH3}}) to be converted to nitrates or nitrites because ammonia gas is toxic to plants.

Due to their very high [[solubility]] and because soils are highly unable to retain [[anions]], nitrates can enter [[groundwater]]. Elevated nitrate in groundwater is a concern for drinking water use because nitrate can interfere with blood-oxygen levels in infants and cause [[methemoglobinemia]] or blue-baby syndrome.<ref name="Vitousek 1997" /> Where groundwater recharges stream flow, nitrate-enriched groundwater can contribute to [[eutrophication]], a process that leads to high algal population and growth, especially blue-green algal populations. While not directly toxic to fish life, like ammonia, nitrate can have indirect effects on fish if it contributes to this eutrophication. Nitrogen has contributed to severe eutrophication problems in some water bodies. Since 2006, the application of nitrogen [[fertilizer]] has been increasingly controlled in Britain and the United States. This is occurring along the same lines as control of phosphorus fertilizer, restriction of which is normally considered essential to the recovery of eutrophied waterbodies.

=== Denitrification ===
{{Main|Denitrification}}
Denitrification is the reduction of nitrates back into nitrogen gas ({{chem|N|2}}), completing the nitrogen cycle. This process is performed by bacterial species such as ''[[Pseudomonas]]'' and [[Paracoccus denitrificans|''Paracoccus'']], under anaerobic conditions. They use the nitrate as an electron acceptor in the place of oxygen during respiration. These facultatively (meaning optionally) anaerobic bacteria can also live in aerobic conditions. Denitrification happens in anaerobic conditions e.g. waterlogged soils. The denitrifying bacteria use nitrates in the soil to carry out respiration and consequently produce nitrogen gas, which is inert and unavailable to plants. Denitrification occurs in free-living microorganisms as well as obligate symbionts of anaerobic ciliates.<ref>{{cite journal |last1=Graf |first1=Jon S. |last2=Schorn |first2=Sina |last3=Kitzinger |first3=Katharina |last4=Ahmerkamp |first4=Soeren |last5=Woehle |first5=Christian |last6=Huettel |first6=Bruno |last7=Schubert |first7=Carsten J. |last8=Kuypers |first8=Marcel M. M. |last9=Milucka |first9=Jana |title=Anaerobic endosymbiont generates energy for ciliate host by denitrification |journal=Nature |date=3 March 2021 |volume=591 |issue=7850 |pages=445–450 |doi=10.1038/s41586-021-03297-6| issn=0028-0836|pmid=33658719 |pmc=7969357 |bibcode=2021Natur.591..445G |doi-access=free }}</ref>

<gallery mode=packed style=float:left heights=270px>
File:Nitrogen cycle.jpg| Classical representation of nitrogen cycle
File:Nitrogen Cycle 2.svg|alt=Diagram of nitrogen cycle above and below ground. Atmospheric nitrogen goes to nitrogen-fixing bacteria in legumes and the soil, then ammonium, then nitrifying bacteria into nitrites then nitrates (which is also produced by lightning), then back to the atmosphere or assimilated by plants, then animals. Nitrogen in animals and plants become ammonium through decomposers (bacteria and fungi).|Flow of nitrogen through the ecosystem. Bacteria are a key element in the cycle, providing different forms of nitrogen compounds able to be assimilated by higher organisms
</gallery>

<gallery mode=packed style=float:right heights=400px>
File:The Nitrogen Cycle.png| Simple representation of the nitrogen cycle. Blue represent nitrogen storage, green is for processes moving nitrogen from one place to another, and red is for the bacteria involved
</gallery>

{{clear left}}

=== Dissimilatory nitrate reduction to ammonium ===
{{Main|Dissimilatory nitrate reduction to ammonium}}
Dissimilatory nitrate reduction to ammonium&nbsp;(DNRA), or nitrate/nitrite ammonification, is an [[anaerobic respiration]] process. Microbes which undertake DNRA oxidise organic matter and use nitrate as an electron acceptor, reducing it to [[nitrite]], then [[ammonium]] ({{chem2|NO3- -> NO2- -> NH4+}}).<ref name="Lam 2011" /> Both denitrifying and nitrate ammonification bacteria will be competing for nitrate in the environment, although DNRA acts to conserve bioavailable nitrogen as soluble ammonium rather than producing dinitrogen gas.<ref name="Marchant 2014" />

=== Anaerobic ammonia oxidation ===
{{Main|Anammox}}
The <u>AN</u>aerobic <u>AMM</u>onia <u>OX</u>idation process is also known as the [[Anammox|ANAMMOX]] process, an abbreviation coined by joining the first [[syllable]]s of each of these three words. This biological process is a [[redox]] [[comproportionation]] reaction, in which [[ammonia]] (the [[reducing agent]] giving electrons) and [[nitrite]] (the [[oxidizing agent]] accepting electrons) transfer three [[electron]]s and are converted into one molecule of [[diatomic]] [[nitrogen]] ({{chem|N|2}}) gas and two water molecules. This process makes up a major proportion of nitrogen conversion in the [[ocean]]s. The [[stoichiometry|stoichiometrically]] balanced formula for the ANAMMOX chemical reaction can be written as following, where an [[ammonium]] [[ion]] includes the ammonia molecule, its [[Conjugate (acid-base theory)|conjugated]] [[Base (chemistry)|base]]:  

: {{chem2|NH4+ + NO2- -> N2 + 2 H2O}} (Δ''G''° = {{val|-357 |u=kJ.mol-1}}).<ref name="Anammox" />

This an [[exergonic process]] (here also an [[exothermic reaction]]) releasing energy, as indicated by the negative value of Δ''G''°, the difference in [[Gibbs free energy]] between the products of reaction and the reagents.

=== Other processes ===
Though nitrogen fixation is the primary source of plant-available nitrogen in most [[ecosystem]]s, in areas with nitrogen-rich [[bedrock]], the breakdown of this rock also serves as a nitrogen source.<ref name="NPR 2011" /><ref name="Schuur 2011" /><ref name="Morford 2011" /> Nitrate reduction is also part of the [[iron cycle]], under anoxic conditions Fe(II) can donate an electron to {{chem2|NO3-}} and is oxidized to Fe(III) while {{chem2|NO3-}} is reduced to {{chem2|NO2-, N2O, N2}}, and {{chem2|NH4+}} depending on the conditions and microbial species involved.<ref name="Burgin 2011" /> The [[Whale feces|fecal plumes of cetaceans]] also act as a junction in the marine nitrogen cycle, concentrating nitrogen in the epipelagic zones of ocean environments before its dispersion through various marine layers, ultimately enhancing oceanic primary productivity.<ref name="roman2010">{{cite journal | title = The Whale Pump: Marine Mammals Enhance Primary Productivity in a Coastal Basin | last1 = Roman | first1 = J. | last2 = McCarthy | first2 = J.J. | journal = PLOS ONE | volume = 5 | issue = 10 | page = e13255 |  pmc=2952594| doi = 10.1371/journal.pone.0013255 | date = 2010| pmid = 20949007 | bibcode = 2010PLoSO...513255R | doi-access = free }}</ref>