Editing Denitrification (section)

=== Conditions of denitrification ===
In nature, denitrification can take place in both terrestrial and marine [[ecosystem]]s.<ref name=":0">{{cite journal|last1=Seitzinger|first1=S.|last2=Harrison|first2=J. A.|last3=Bohlke|first3=J. K.|last4=Bouwman|first4=A. F.|last5=Lowrance|first5=R.|last6=Peterson|first6=B.|last7=Tobias|first7=C.|last8=Drecht|first8=G. V.|year=2006|title=Denitrification Across Landscapes and Waterscapes: A Synthesis|journal=Ecological Applications|volume=16|issue=6|pages=2064–2090|doi=10.1890/1051-0761(2006)016[2064:dalawa]2.0.co;2|pmid=17205890|hdl=1912/4707|hdl-access=free}}</ref> Typically, denitrification occurs in anoxic environments, where the concentration of dissolved and freely available oxygen is depleted. In these areas, nitrate (NO<sub>3</sub><sup>−</sup>) or nitrite ({{chem|NO|2}}<sup>−</sup>) can be used as a substitute terminal electron acceptor instead of [[oxygen]] (O<sub>2</sub>), a more energetically favourable electron acceptor. Terminal electron acceptor is a compound that gets reduced in the reaction by receiving electrons. Examples of anoxic environments can include [[soil]]s,<ref name=":1">{{cite journal|last1=Scaglia|first1=J.|last2=Lensi|first2=R.|last3=Chalamet|first3=A.|s2cid=20602996|year=1985|title=Relationship between photosynthesis and denitrification in planted soil|journal=Plant and Soil|volume=84|issue=1|pages=37–43|doi=10.1007/BF02197865|bibcode=1985PlSoi..84...37S }}</ref> [[groundwater]],<ref name=":2">{{cite journal|last=Korom|first=Scott F.|year=1992|title=Natural Denitrification in the Saturated Zone: A Review|journal=Water Resources Research|volume=28|issue=6|pages=1657–1668|bibcode=1992WRR....28.1657K|doi=10.1029/92WR00252}}</ref> [[wetlands]], oil reservoirs,<ref name=":3">{{Cite journal|last1=Cornish Shartau|first1=S. L.|last2=Yurkiw|first2=M.|last3=Lin|first3=S.|last4=Grigoryan|first4=A. A.|last5=Lambo|first5=A.|last6=Park|first6=H. S.|last7=Lomans|first7=B. P.|last8=Van Der Biezen|first8=E.|last9=Jetten|first9=M. S. M.|year=2010|title=Ammonium Concentrations in Produced Waters from a Mesothermic Oil Field Subjected to Nitrate Injection Decrease through Formation of Denitrifying Biomass and Anammox Activity|journal=Applied and Environmental Microbiology|volume=76|issue=15|pages=4977–4987|doi=10.1128/AEM.00596-10|pmc=2916462|pmid=20562276|last10=Voordouw|first10=G.|bibcode=2010ApEnM..76.4977C}}</ref> poorly ventilated corners of the ocean and [[seafloor sediments]].

Furthermore, denitrification can occur in oxic environments as well. High activity of denitrifiers can be observed in the intertidal zones, where the tidal cycles cause fluctuations of oxygen concentration in sandy coastal sediments.<ref>{{Cite journal|last=Merchant|display-authors=et al|date=2017|title=Denitrifying community in coastal sediments performs aerobic and anaerobic respiration simultaneously|pmid=28463234|pmc=5520038|journal=The ISME Journal|volume=11|issue=8|pages=1799–1812|doi=10.1038/ismej.2017.51|bibcode=2017ISMEJ..11.1799M }}</ref> For example, the bacterial species ''Paracoccus denitrificans'' engages in denitrification under both oxic and anoxic conditions simultaneously. Upon oxygen exposure, the bacteria is able to utilize [[Nitrous-oxide reductase|nitrous oxide reductase]], an enzyme that catalyzes the last step of denitrification.<ref>{{Cite journal|last=Qu|display-authors=et al|date=2016|title=Transcriptional and metabolic regulation of denitrification in Paracoccus denitrificans allows low but significant activity of nitrous oxide reductase under oxic conditions|pmid=26568281|journal=Environmental Microbiology|volume=18|issue=9|pages=2951–63|doi=10.1111/1462-2920.13128|bibcode=2016EnvMi..18.2951Q }}</ref> Aerobic denitrifiers are mainly Gram-negative bacteria in the phylum Proteobacteria. Enzymes NapAB, NirS, NirK and NosZ are located in the periplasm, a wide space bordered by the cytoplasmic and the outer membrane in Gram-negative bacteria.<ref name=":4">{{Cite journal|last1=Ji|first1=Bin|last2=Yang|first2=Kai|last3=Zhu|first3=Lei|last4=Jiang|first4=Yu|last5=Wang|first5=Hongyu|last6=Zhou|first6=Jun|last7=Zhang|first7=Huining|s2cid=85744076|date=2015|title=Aerobic denitrification: A review of important advances of the last 30 years|journal=Biotechnology and Bioprocess Engineering|volume=20|issue=4|pages=643–651|doi=10.1007/s12257-015-0009-0}}</ref>

A variety of environmental factors can influence the rate of denitrification on an ecosystem-wide scale. For example, temperature and pH have been observed to impact denitrification rates. In the bacterial species, ''[[Pseudomonas mandelii]],'' expression of denitrifying genes was reduced at temperatures below 30&nbsp;°C and a pH below 5, while activity was largely unaffected between a pH of 6–8.<ref name=":02">{{Cite journal |last1=Saleh-Lakha |first1=Saleema |last2=Shannon |first2=Kelly E. |last3=Henderson |first3=Sherri L. |last4=Goyer |first4=Claudia |last5=Trevors |first5=Jack T. |last6=Zebarth |first6=Bernie J. |last7=Burton |first7=David L. |date=2009-06-15 |title=Effect of pH and Temperature on Denitrification Gene Expression and Activity in Pseudomonas mandelii |journal=Applied and Environmental Microbiology |volume=75 |issue=12 |pages=3903–3911 |doi=10.1128/AEM.00080-09 |issn=0099-2240 |pmc=2698340 |pmid=19376915|bibcode=2009ApEnM..75.3903S }}</ref> Organic carbon as an electron donor is a common limiting nutrient for denitrification as observed in benthic sediments and wetlands.<ref name=":12">{{Cite journal |last1=Starr |first1=Robert C. |last2=Gillham |first2=Robert W. |date=November 1993 |title=Denitrification and Organic Carbon Availability in Two Aquifers |url=https://ngwa.onlinelibrary.wiley.com/doi/10.1111/j.1745-6584.1993.tb00867.x |journal=Groundwater |volume=31 |issue=6 |pages=934–947 |doi=10.1111/j.1745-6584.1993.tb00867.x |bibcode=1993GrWat..31..934S |issn=0017-467X|url-access=subscription }}</ref><ref name=":22">{{Cite journal |last1=Sirivedhin |first1=Tanita |last2=Gray |first2=Kimberly A. |date=February 2006 |title=Factors affecting denitrification rates in experimental wetlands: Field and laboratory studies |url=https://doi.org/10.1016/j.ecoleng.2005.09.001 |journal=Ecological Engineering |volume=26 |issue=2 |pages=167–181 |doi=10.1016/j.ecoleng.2005.09.001 |bibcode=2006EcEng..26..167S |issn=0925-8574|url-access=subscription }}</ref> Nitrate and oxygen can also be potential limiting factors for denitrification,  although the latter only has an observed limiting effect in wet soils.<ref name=":32">{{Cite journal |last1=Burgin |first1=Amy J. |last2=Groffman |first2=Peter M. |last3=Lewis |first3=David N. |date=September 2010 |title=Factors Regulating Denitrification in a Riparian Wetland |url=https://acsess.onlinelibrary.wiley.com/doi/10.2136/sssaj2009.0463 |journal=Soil Science Society of America Journal |volume=74 |issue=5 |pages=1826–1833 |doi=10.2136/sssaj2009.0463 |bibcode=2010SSASJ..74.1826B |issn=0361-5995|url-access=subscription }}</ref> Oxygen likely affects denitrification in multiple ways—because most denitrifiers are facultative, oxygen can inhibit rates, but it can also stimulate denitrification by facilitating nitrification and the production of nitrate. In wetlands as well as deserts,<ref name=":42">{{Cite journal |last1=Peterjohn |first1=William T. |last2=Schlesinger |first2=William H. |date=November 1991 |title=Factors Controlling Denitrification in a Chihuahuan Desert Ecosystem |url=https://acsess.onlinelibrary.wiley.com/doi/10.2136/sssaj1991.03615995005500060032x |journal=Soil Science Society of America Journal |volume=55 |issue=6 |pages=1694–1701 |doi=10.2136/sssaj1991.03615995005500060032x |bibcode=1991SSASJ..55.1694P |issn=0361-5995|url-access=subscription }}</ref> moisture is an environmental limitation to rates of denitrification.

Additionally, environmental factors can also influence whether denitrification proceeds to completion, characterized by the complete reduction of NO<sub>3</sub><sup>−</sup> to N<sub>2</sub> rather than releasing N<sub>2</sub>O as an end product. Soil pH and texture are both factors that can moderate denitrification, with higher pH levels driving the reaction more to completion.<ref name=":5">{{Cite journal |last1=Foltz |first1=Mary E. |last2=Alesso |first2=Agustín |last3=Zilles |first3=Julie L. |date=2023 |title=Field soil properties and experimental nutrient additions drive the nitrous oxide ratio in laboratory denitrification experiments: a systematic review |journal=Frontiers in Soil Science |volume=3 |doi=10.3389/fsoil.2023.1194825 |doi-access=free |issn=2673-8619}}</ref> Nutrient composition, particularly the ratio of carbon to nitrogen, is a strong contributor to complete denitrification,<ref name=":6">{{Cite journal |last1=Yang |first1=Xinping |last2=Wang |first2=Shimei |last3=Zhou |first3=Lixiang |date=January 2012 |title=Effect of carbon source, C/N ratio, nitrate and dissolved oxygen concentration on nitrite and ammonium production from denitrification process by Pseudomonas stutzeri D6 |url=https://doi.org/10.1016/j.biortech.2011.10.026 |journal=Bioresource Technology |volume=104 |pages=65–72 |doi=10.1016/j.biortech.2011.10.026 |pmid=22074905 |bibcode=2012BiTec.104...65Y |issn=0960-8524|url-access=subscription }}</ref> with a 2:1 ratio of C:N being able to facilitate full nitrate reduction regardless of temperature or carbon source.<ref name=":7">{{Cite journal |last1=Elefsiniotis |first1=P. |last2=Li |first2=D. |date=2006-02-15 |title=The effect of temperature and carbon source on denitrification using volatile fatty acids |url=https://www.sciencedirect.com/science/article/pii/S1369703X05003463 |journal=Biochemical Engineering Journal |volume=28 |issue=2 |pages=148–155 |doi=10.1016/j.bej.2005.10.004 |bibcode=2006BioEJ..28..148E |issn=1369-703X|url-access=subscription }}</ref> Copper, as a co-factor for [[nitrite reductase]] and [[nitrous-oxide reductase]], also promoted complete denitrification when added as a supplement.<ref name=":8">{{Cite journal |last1=Moloantoa |first1=Karabelo M. |last2=Khetsha |first2=Zenzile P. |last3=Kana |first3=Gueguim E. B. |last4=Maleke |first4=Maleke M. |last5=Van Heerden |first5=Esta |last6=Castillo |first6=Julio C. |last7=Cason |first7=Errol D. |date=2023 |title=Metagenomic assessment of nitrate-contaminated mine wastewaters and optimization of complete denitrification by indigenous enriched bacteria |journal=Frontiers in Environmental Science |volume=11 |doi=10.3389/fenvs.2023.1148872 |doi-access=free |bibcode=2023FrEnS..1148872M |issn=2296-665X}}</ref> Besides nutrients and terrain, microbial community composition can also affect the ratio of complete denitrification, with prokaryotic phyla [[Actinomycetota]] and [[Thermoproteota]] being responsible for greater release of N<sub>2</sub> than N<sub>2</sub>O compared to other prokaryotes.<ref name=":9">{{Cite journal |last1=Deveautour |first1=C. |last2=Rojas-Pinzon |first2=P.A. |last3=Veloso |first3=M. |last4=Rambaud |first4=J. |last5=Duff |first5=A.M. |last6=Wall |first6=D. |last7=Carolan |first7=R. |last8=Philippot |first8=L. |last9=Richards |first9=K.G. |last10=O'Flaherty |first10=V. |last11=Brennan |first11=F. |date=May 2022 |title=Biotic and abiotic predictors of potential N2O emissions from denitrification in Irish grasslands soils: A national-scale field study |journal=Soil Biology and Biochemistry |volume=168 |pages=108637 |doi=10.1016/j.soilbio.2022.108637 |issn=0038-0717|doi-access=free }}</ref>

Denitrification can lead to a condition called [[Isotope fractionation|isotopic fractionation]] in the soil environment. The two stable isotopes of nitrogen, <sup>14</sup>N and <sup>15</sup>N are both found in the sediment profiles. The lighter isotope of nitrogen, <sup>14</sup>N, is preferred during denitrification, leaving the heavier nitrogen isotope, <sup>15</sup>N, in the residual matter. This selectivity leads to the enrichment of <sup>14</sup>N in the biomass compared to <sup>15</sup>N.<ref>{{Cite journal|author=Dähnke K. |author2=Thamdrup B.|date=2013|title=Nitrogen isotope dynamics and fractionation during sedimentary denitrification in Boknis Eck, Baltic Sea|journal=Biogeosciences|volume=10|issue=5|pages=3079–3088|via=Copernicus Publications|doi=10.5194/bg-10-3079-2013|bibcode=2013BGeo...10.3079D|doi-access=free}}</ref> Moreover, the relative abundance of <sup>14</sup>N can be analyzed to distinguish denitrification apart from other processes in nature.