Editing Nitrogen assimilation

'''Nitrogen assimilation''' is the formation of organic [[nitrogen]] compounds like [[amino acid]]s from  inorganic nitrogen compounds present in the environment. Organisms like [[plants]], [[fungi]] and certain [[bacteria]] that can [[nitrogen fixation|fix]] nitrogen gas (N<sub>2</sub>) depend on the ability to assimilate [[nitrate]] or [[ammonia]] for their needs. Other organisms, like animals, depend entirely on organic nitrogen from their food.

==Nitrogen assimilation in plants==
Plants absorb nitrogen from the soil in the form of nitrate (NO<sub>3</sub><sup>−</sup>) and ammonium (NH<sub>4</sub><sup>+</sup>). In aerobic soils where [[nitrification]] can occur, nitrate is usually the predominant form of available nitrogen that is absorbed.<ref name=Xu2012>{{Cite journal | last1 = Xu | first1 = G. | last2 = Fan | first2 = X. | last3 = Miller | first3 = A. J. | title = Plant Nitrogen Assimilation and Use Efficiency | doi = 10.1146/annurev-arplant-042811-105532 | journal = Annual Review of Plant Biology | volume = 63 | pages = 153–182 | year = 2012 | issue = 1 | pmid =  22224450| bibcode = 2012AnRPB..63..153X | s2cid = 20690850 }}</ref><ref name=Nadelhoffer1984>{{Cite journal| doi = 10.1007/BF02140039| issn = 0032-079X| volume = 80| issue = 3| pages = 321–335| last = Nadelhoffer| first = KnuteJ.|author2=JohnD. Aber |author3=JerryM. Melillo | title = Seasonal patterns of ammonium and nitrate uptake in ten temperate forest ecosystems| journal = Plant and Soil| date = 1984-10-01| bibcode = 1984PlSoi..80..321N| s2cid = 40749543}}</ref> However this is not always the case as ammonia can predominate in grasslands<ref name=Jackson1989>{{Cite journal | last1 = Jackson | first1 = L. E. | last2 = Schimel | first2 = J. P. | last3 = Firestone | first3 = M. K. | doi = 10.1016/0038-0717(89)90152-1 | title = Short-term partitioning of ammonium and nitrate between plants and microbes in an annual grassland | journal = Soil Biology and Biochemistry | volume = 21 | issue = 3 | pages = 409–415 | year = 1989 | bibcode = 1989SBiBi..21..409J }}</ref> and in flooded, anaerobic soils like [[paddy field|rice paddies]].<ref name=Ishi2011>{{Cite journal 
| last1 = Ishii | first1 = S. 
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| title = Nitrogen cycling in rice paddy environments: Past achievements and future challenges 
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| volume = 26 
| issue = 4 
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| year = 2011 
| pmid = 22008507 | doi=10.1264/jsme2.me11293
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}}</ref> Plant roots themselves can affect the abundance of various forms of nitrogen by changing the pH and secreting organic compounds or oxygen.<ref name=Li2008>{{Cite journal 
| last1 = Li | first1 = Y. L. N. 
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| journal = Plant, Cell & Environment 
| volume = 31 
| issue = 1 
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| year = 2007 
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| doi-access = free 
}}</ref> This influences microbial activities like the inter-conversion of various nitrogen species, the release of ammonia from organic matter in the soil and the fixation of nitrogen by [[Diazotroph|non-nodule-forming bacteria]].

Ammonium ions are absorbed by the plant via [[ammonia transporter]]s. Nitrate is taken up by several nitrate transporters that use a proton gradient to power the transport.<ref name=Sorgona2011>{{Cite journal | last1 = Sorgonà | first1 = A. | last2 = Lupini | first2 = A. | last3 = Mercati | first3 = F. | last4 = Di Dio | first4 = L. | last5 = Sunseri | first5 = F. | last6 = Abenavoli | first6 = M. R. | doi = 10.1111/j.1365-3040.2011.02311.x | title = Nitrate uptake along the maize primary root: An integrated physiological and molecular approach | journal = Plant, Cell & Environment | volume = 34 | issue = 7 | pages = 1127–1140 | year = 2011 | pmid =  21410710| doi-access = free | bibcode = 2011PCEnv..34.1127S }}</ref><ref name=Tischner>{{Cite journal | last1 = Tischner | first1 = R. | title = Nitrate uptake and reduction in higher and lower plants | doi = 10.1046/j.1365-3040.2000.00595.x | journal = Plant, Cell and Environment | volume = 23 | issue = 10 | pages = 1005–1024 | year = 2000 | doi-access = free | bibcode = 2000PCEnv..23.1005T }}</ref> Nitrogen is transported from the root to the shoot via the xylem in the form of nitrate, dissolved ammonia and amino acids. Usually<ref name="Scheurwater2002">{{Cite journal | last1 = Scheurwater | first1 = I. | last2 = Koren | first2 = M. | last3 = Lambers | first3 = H. | last4 = Atkin | first4 = O. K. | title = The contribution of roots and shoots to whole plant nitrate reduction in fast- and slow-growing grass species | doi = 10.1093/jxb/erf008 | journal = Journal of Experimental Botany | volume = 53 | issue = 374 | pages = 1635–1642 | year = 2002 | pmid =  12096102| doi-access = free }}</ref> (but not always<ref name="Stewart1986">{{Cite journal | last1 = Stewart | first1 = G. R. | last2 = Popp | first2 = M. | last3 = Holzapfel | first3 = I. | last4 = Stewart | first4 = J. A. | last5 = Dickie-Eskew | first5 = A. N. N. | title = Localization of Nitrate Reduction in Ferns and Its Relationship to Environment and Physiological Characteristics | doi = 10.1111/j.1469-8137.1986.tb02905.x | journal = New Phytologist | volume = 104 | issue = 3 | pages = 373–384 | year = 1986 | doi-access = free | bibcode = 1986NewPh.104..373S }}</ref>) most of the nitrate reduction is carried out in the shoots while the roots reduce only a small fraction of the absorbed nitrate to ammonia. Ammonia (both absorbed and synthesized) is incorporated into amino acids via the [[glutamine synthetase]]-[[glutamine oxoglutarate aminotransferase|glutamate synthase]] (GS-GOGAT) pathway.<ref name=Masclaux-Daubresse2006>{{Cite journal | last1 = Masclaux-Daubresse | first1 = C. | last2 = Reisdorf-Cren | first2 = M. | last3 = Pageau | first3 = K. | last4 = Lelandais | first4 = M. | last5 = Grandjean | first5 = O. | last6 = Kronenberger | first6 = J. | last7 = Valadier | first7 = M. H. | last8 = Feraud | first8 = M. | last9 = Jouglet | first9 = T. | last10 = Suzuki | first10 = A. | title = Glutamine Synthetase-Glutamate Synthase Pathway and Glutamate Dehydrogenase Play Distinct Roles in the Sink-Source Nitrogen Cycle in Tobacco | doi = 10.1104/pp.105.071910 | journal = Plant Physiology | volume = 140 | issue = 2 | pages = 444–456 | year = 2006 | pmid =  16407450| pmc =1361315 }}</ref> While nearly all<ref name=Kiyomiya2001>{{Cite journal 
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| title = Real time visualization of 13N-translocation in rice under different environmental conditions using positron emitting Ttacer imaging system 
| journal = Plant Physiology 
| volume = 125 
| issue = 4 
| pages = 1743–1753 
| year = 2001 
| pmid = 11299355 
| pmc = 88831
}}</ref> the ammonia in the root is usually incorporated into amino acids at the root itself, plants may transport significant amounts of ammonium ions in the xylem to be fixed in the shoots.<ref name=Schjoerring2002>{{Cite journal | last1 = Schjoerring | first1 = J. K. | last2 = Husted | first2 = S. | last3 = Mäck | first3 = G. | last4 = Mattsson | first4 = M. | title = The regulation of ammonium translocation in plants | doi = 10.1093/jexbot/53.370.883 | journal = Journal of Experimental Botany | volume = 53 | issue = 370 | pages = 883–890 | year = 2002 | pmid =  11912231| doi-access = free }}</ref> This may help avoid the transport of organic compounds down to the roots just to carry the nitrogen back as amino acids.

Nitrate reduction is carried out in two steps. Nitrate is first reduced to [[nitrite]] (NO<sub>2</sub><sup>−</sup>) in the cytosol by [[nitrate reductase]] using NADH or NADPH.<ref name=Tischner/> Nitrite is then reduced to ammonia in the chloroplasts ([[plastid]]s in roots) by a [[ferredoxin]] dependent [[ferredoxin—nitrite reductase|nitrite reductase]]. In photosynthesizing tissues, it uses an isoform of ferredoxin (Fd1) that is reduced by [[photosystem I|PSI]] while in the root it uses a form of ferredoxin (Fd3) that has a less negative midpoint potential and can be reduced easily by NADPH.<ref name=Hanke2003>{{Cite journal | last1 = Hanke | first1 = G. T. | last2 = Kimata-Ariga | first2 = Y. | last3 = Taniguchi | first3 = I. | last4 = Hase | first4 = T. | title = A Post Genomic Characterization of Arabidopsis Ferredoxins | doi = 10.1104/pp.103.032755 | journal = Plant Physiology | volume = 134 | issue = 1 | pages = 255–264 | year = 2004 | pmid =  14684843| pmc =316305 }}</ref> In non photosynthesizing tissues, NADPH is generated by [[glycolysis]] and the [[pentose phosphate pathway]].

In the chloroplasts,<ref name=Tcherkez>{{Cite journal | last1 = Tcherkez | first1 = G. | last2 = Hodges | first2 = M. | doi = 10.1093/jxb/erm115 | title = How stable isotopes may help to elucidate primary nitrogen metabolism and its interaction with (photo)respiration in C3 leaves | journal = Journal of Experimental Botany | volume = 59 | issue = 7 | pages = 1685–1693 | year = 2007 | pmid =  17646207| doi-access = free }}</ref> glutamine synthetase incorporates this ammonia as the amide group of [[glutamine]] using [[glutamate]] as a substrate. Glutamate synthase ([[glutamate synthase (ferredoxin)|Fd-GOGAT]] and [[glutamate synthase (NADH)|NADH-GOGAT]]) transfer the amide group onto a 2-oxoglutarate molecule producing two glutamates. Further transaminations are carried out make other amino acids (most commonly [[asparagine]]) from glutamine. While the enzyme [[glutamate dehydrogenase]] (GDH) does not play a direct role in the assimilation, it protects the mitochondrial functions during periods of high nitrogen metabolism and takes part in nitrogen remobilization.<ref name=Lea2003>{{Cite journal | last1 = Lea | first1 = P. J. | last2 = Miflin | first2 = B. J. | doi = 10.1016/S0981-9428(03)00060-3 | title = Glutamate synthase and the synthesis of glutamate in plants | journal = Plant Physiology and Biochemistry | volume = 41 | issue = 6–7 | pages = 555–564 | year = 2003 | bibcode = 2003PlPB...41..555L }}</ref>

===pH and Ionic balance during nitrogen assimilation===
[[File:Nitrate ion balance-variants.png| thumb|upright=0.9 |Different plants use different pathways to different levels. Tomatoes take in a lot of K<sup>+</sup> and accumulate salts in their vacuoles, castor reduces nitrate in the roots to a large extent and excretes the resulting alkali. Soy bean plants moves a large amount of malate to the roots where they convert it to alkali while the potassium is recirculated.]]
Every nitrate ion reduced to ammonia produces one OH<sup>−</sup> ion. To maintain a pH balance, the plant must either excrete it into the surrounding medium or neutralize it with organic acids. This results in the medium around the plants roots becoming alkaline when they take up nitrate.

To maintain ionic balance, every NO<sub>3</sub><sup>−</sup> taken into the root must be accompanied by either the uptake of a cation or the excretion of an anion. Plants like tomatoes take up metal ions like K<sup>+</sup>, Na<sup>+</sup>, Ca<sup>2+</sup> and Mg<sup>2+</sup> to exactly match every nitrate taken up and store these as the salts of organic acids like [[malate]] and [[oxalate]].<ref>{{Cite journal
| doi = 10.1104/pp.60.3.349| pmid = 16660091| issn = 0032-0889| volume = 60| issue = 3| pages = 349–353| last = Kirkby| first = Ernest A.|author2=Alistair H. Knight | title = Influence of the Level of Nitrate Nutrition on Ion Uptake and Assimilation, Organic Acid Accumulation, and Cation-Anion Balance in Whole Tomato Plants| journal = Plant Physiology| date = 1977-09-01| pmc = 542614}}</ref> Other plants like the soybean balance most of their NO<sub>3</sub><sup>−</sup> intake with the excretion of OH<sup>−</sup> or HCO<sub>3</sub><sup>−</sup>.<ref>{{Cite journal| doi = 10.1104/pp.88.3.605| pmid = 16666356| issn = 0032-0889| volume = 88| issue = 3| pages = 605–612| last = Touraine| first = Bruno|author2=Nicole Grignon |author3=Claude Grignon | title = Charge Balance in NO3−-Fed Soybean Estimation of K+ and Carboxylate Recirculation| journal = Plant Physiology| date = 1988-11-01| pmc = 1055632}}</ref>

Plants that reduce nitrates in the shoots and excrete alkali from their roots need to transport the alkali in an inert form from the shoots to the roots. To achieve this they synthesize malic acid in the leaves from neutral precursors like carbohydrates. The potassium ions brought to the leaves along with the nitrate in the xylem are then sent along with the malate to the roots via the phloem. In the roots, the malate is consumed. When malate is converted back to malic acid prior to use, an OH<sup>−</sup> is released and excreted. (RCOO<sup>−</sup> + H<sub>2</sub>O -> RCOOH +OH<sup>−</sup>) The potassium ions are then recirculated up the xylem with fresh nitrate. Thus the plants avoid having to absorb and store excess salts and also transport the OH<sup>−</sup>.<ref>{{Cite journal| doi = 10.1104/pp.99.3.1118| pmid = 16668978| issn = 0032-0889| volume = 99| issue = 3| pages = 1118–1123| last = Touraine| first = Bruno|author2=Bertrand Muller |author3=Claude Grignon | title = Effect of Phloem-Translocated Malate on NO3− Uptake by Roots of Intact Soybean Plants| journal = Plant Physiology| date = 1992-07-01| pmc = 1080591}}</ref>

Plants like castor reduce a lot of nitrate in the root itself, and excrete the resulting base. Some of the base produced in the shoots is transported to the roots as salts of organic acids while a small amount of the carboxylates are just stored in the shoot itself.<ref>{{Cite journal| doi = 10.1093/jxb/38.4.580| issn = 0022-0957| volume = 38| issue = 4| pages = 580–596| last = Allen| first = Susan|author2=J. A. Raven | title = Intracellular pH Regulation in Ricinus communis Grown with Ammonium or Nitrate as N Source: The Role of Long Distance Transport| journal = Journal of Experimental Botany| date = 1987-04-01}}</ref>

==Nitrogen use efficiency==
'''Nitrogen use efficiency''' (NUE) is the proportion of nitrogen present that a plant absorbs and uses. Improving nitrogen use efficiency and thus fertilizer efficiency is important to make agriculture more sustainable,<ref name="SBC">{{cite web |url=http://sbc.ucdavis.edu/Biotech_for_Sustain_pages/Nitrogen_Use_Efficiency/ |title=Nitrogen Use Efficiency |author=<!--Not stated--> |website=Seed Biotechnology Center |publisher=UC Davis |access-date=2019-11-23 |url-status=dead|archive-url=https://web.archive.org/web/20210516055840/http://sbc.ucdavis.edu/Biotech_for_Sustain_pages/Nitrogen_Use_Efficiency/|archive-date=2021-05-16}}</ref> by reducing pollution ([[fertilizer runoff]]) and production cost and increasing yield. Worldwide, crops generally have less than 50% NUE.<ref name="Fageria">{{cite journal |last1=Fageria |first1=N.K. |last2=Baligar |first2=V.C. |date=2005 |title=Enhancing Nitrogen Use Efficiency in Crop Plants |journal=Advances in Agronomy |volume=88 |pages=97–185 |doi=10.1016/S0065-2113(05)88004-6 |isbn=9780120007868 }}</ref> Better fertilizers, improved crop management,<ref name="Fageria"/> selective breeding,<ref>{{cite journal |last1=Sharma |first1=Narendra |last2=Sinha |first2=Vimlendu Bhushan |last3=Prem Kumar |first3=N. Arun |last4=Subrahmanyam |first4=Desiraju |last5=Neeraja |first5=C. N. |last6=Kuchi |first6=Surekha |last7=Jha |first7=Ashwani |last8=Parsad |first8=Rajender |last9=Sitaramam |first9=Vetury |last10=Raghuram |first10=Nandula |title=Nitrogen Use Efficiency Phenotype and Associated Genes: Roles of Germination, Flowering, Root/Shoot Length and Biomass |journal=Frontiers in Plant Science |date=20 January 2021 |volume=11 |pages=587464 |doi=10.3389/fpls.2020.587464 |pmid=33552094 |pmc=7855041 |doi-access=free|bibcode=2021FrPS...1187464S }}</ref> and [[genetic engineering]]<ref name="SBC"/><ref>{{cite journal |last1=Melino |first1=Vanessa J |last2=Tester |first2=Mark A |last3=Okamoto |first3=Mamoru |title=Strategies for engineering improved nitrogen use efficiency in crop plants via redistribution and recycling of organic nitrogen |journal=Current Opinion in Biotechnology |date=February 2022 |volume=73 |pages=263–269 |doi=10.1016/j.copbio.2021.09.003 |pmid=34560475 |url=https://www.researchgate.net/publication/313799536|hdl=10754/672009 |s2cid=237626832 |hdl-access=free }}</ref> can increase NUE.

Nitrogen use efficiency can be measured at various levels: the crop plant, the soil, by fertilizer input, by ecosystem productivity, etc.<ref>{{cite journal |last1=Congreves |first1=Kate A. |last2=Otchere |first2=Olivia |last3=Ferland |first3=Daphnée |last4=Farzadfar |first4=Soudeh |last5=Williams |first5=Shanay |last6=Arcand |first6=Melissa M. |title=Nitrogen Use Efficiency Definitions of Today and Tomorrow |journal=Frontiers in Plant Science |date=4 June 2021 |volume=12 |pages=637108 |doi=10.3389/fpls.2021.637108 |pmid=34177975 |pmc=8220819 |doi-access=free|bibcode=2021FrPS...1237108C }}</ref> At the level of photosynthesis in leaves, it is termed '''photosynthetic nitrogen use efficiency''' (PNUE).<ref name="McKinley">{{cite journal |last1=McKinley |first1=Duncan C. |last2=Blair |first2=John M. |date=2008 |title=Woody Plant Encroachment by ''Juniperus virginiana'' in a Mesic Native Grassland Promotes Rapid Carbon and Nitrogen Accrual |journal=Ecosystems |volume=11 |issue=3 |pages=454–468 |doi=10.1007/s10021-008-9133-4 |bibcode=2008Ecosy..11..454M |s2cid=23911766 }}</ref><ref name="Funk">{{cite journal |last1=Funk |first1=Jennifer L. |date=2008-10-15 |title=Differences in plasticity between invasive and native plants from a low resource environment |journal=Journal of Ecology |volume=96 |issue=6 |pages=1162–1173 |doi=10.1111/j.1365-2745.2008.01435.x |bibcode=2008JEcol..96.1162F |s2cid=84336174 }}</ref>

==References==
{{reflist}}

{{Plant nutrition}}

[[Category:Nitrogen cycle|Assimilation]]
[[Category:Nitrogen|Assimilation]]
[[Category:Metabolism]]
[[Category:Plant physiology]]