Editing Nitrogen fixation (section)

== Biological ==
Biological nitrogen fixation (BNF) occurs when atmospheric nitrogen is converted to ammonia by a [[nitrogenase]] enzyme.<ref name=Rees/> The overall reaction for BNF is:

{{chem2|N2 + 16ATP + 16H2O + 8e- + 8H+}} → {{chem2|2NH3 +H2 + 16ADP + 16P_{i}|}}

The process is coupled to the [[hydrolysis]] of 16 equivalents of [[adenosine triphosphate|ATP]] and is accompanied by the co-formation of one equivalent of {{chem|H|2}}. The conversion of {{chem|N|2}} into ammonia occurs at a [[metal cluster]] called [[FeMoco]], an abbreviation for the iron-[[molybdenum]] cofactor. The mechanism proceeds via a series of [[protonation]] and reduction steps wherein the FeMoco [[active site]] [[hydrogenate]]s the {{chem|N|2}} substrate.<ref name=Rees/> In free-living [[diazotroph]]s, nitrogenase-generated ammonia is assimilated into [[glutamate]] through the [[glutamine synthetase]]/glutamate synthase pathway. The microbial [[nif gene]]s required for nitrogen fixation are widely distributed in diverse environments.<ref>{{cite journal | vauthors = Gaby JC, Buckley DH | title = A global census of nitrogenase diversity | journal = Environmental Microbiology | volume = 13 | issue = 7 | pages = 1790–9 | date = July 2011 | pmid = 21535343 | doi = 10.1111/j.1462-2920.2011.02488.x | bibcode = 2011EnvMi..13.1790G }}</ref>

Nitrogenases are rapidly degraded by oxygen. For this reason, many bacteria cease production of the enzyme in the presence of oxygen. Many nitrogen-fixing organisms exist only in [[anaerobic organism|anaerobic]] conditions, respiring to draw down oxygen levels, or binding the oxygen with a [[protein]] such as [[leghemoglobin]].<ref name="postgate">{{cite book | vauthors = Postgate J |year=1998 |title= Nitrogen Fixation|edition= 3rd |publisher=Cambridge University Press|location= Cambridge}}</ref><ref>{{cite journal | vauthors = Streicher SL, Gurney EG, Valentine RC | title = The nitrogen fixation genes | journal = Nature | volume = 239 | issue = 5374 | pages = 495–9 | date = October 1972 | pmid = 4563018 | doi = 10.1038/239495a0 | bibcode = 1972Natur.239..495S | s2cid = 4225250 }}</ref>

=== Importance of nitrogen ===
{{biogeochemical cycle sidebar|nutrient}}
Atmospheric nitrogen cannot be metabolized by most organisms,<ref>{{cite book | vauthors = Delwiche CC | chapter = Cycling of Elements in the Biosphere|date=1983 | title = Inorganic Plant Nutrition|pages=212–238| veditors = Läuchli A, Bieleski RL |series=Encyclopedia of Plant Physiology|place=Berlin, Heidelberg|publisher=Springer|language=en|doi=10.1007/978-3-642-68885-0_8|isbn=978-3-642-68885-0 }}</ref> because its triple covalent bond is very strong. Most take up fixed nitrogen from various sources. For every 100 atoms of carbon, roughly 2 to 20 atoms of nitrogen are assimilated. The atomic ratio of carbon (C) : nitrogen (N) : phosphorus (P) observed on average in planktonic biomass was originally described by Alfred Redfield,<ref name="REDFIELD 1958 230A–221">{{Cite journal| vauthors = Redfield AC |title=The Biological Control of Chemical Factors in the Environment|date=1958|url=https://www.jstor.org/stable/27827150|journal=American Scientist|volume=46|issue=3|pages=230A–221|jstor=27827150|issn=0003-0996}}</ref> who determined the stoichiometric relationship between C:N:P atoms, The Redfield Ratio, to be 106:16:1.<ref name="REDFIELD 1958 230A–221"/>

=== Nitrogenase ===
{{Main|Nitrogenase}}
The protein complex nitrogenase is responsible for [[Catalysis|catalyzing]] the reduction of nitrogen gas (N<sub>2</sub>) to ammonia (NH<sub>3</sub>).<ref>{{cite journal |doi=10.1021/acs.chemrev.9b00556 |title=Reduction of Substrates by Nitrogenases |date=2020 |last1=Seefeldt |first1=Lance C. |last2=Yang |first2=Zhi-Yong |last3=Lukoyanov |first3=Dmitriy A. |last4=Harris |first4=Derek F. |last5=Dean |first5=Dennis R. |last6=Raugei |first6=Simone |last7=Hoffman |first7=Brian M. |journal=Chemical Reviews |volume=120 |issue=12 |pages=5082–5106 |pmid=32176472 |pmc=7703680 }}</ref><ref>{{cite journal |doi=10.1002/1873-3468.14534 |title=Biological nitrogen fixation in theory, practice, and reality: A perspective on the molybdenum nitrogenase system |date=2023 |last1=Threatt |first1=Stephanie D. |last2=Rees |first2=Douglas C. |journal=FEBS Letters |volume=597 |issue=1 |pages=45–58 |pmid=36344435 |pmc=10100503 }}</ref> In [[cyanobacteria]], this [[enzyme]] system is housed in a specialized cell called the [[heterocyst]].<ref>{{cite journal | vauthors = Peterson RB, Wolk CP | title = High recovery of nitrogenase activity and of Fe-labeled nitrogenase in heterocysts isolated from Anabaena variabilis | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 75 | issue = 12 | pages = 6271–6275 | date = December 1978 | pmid = 16592599 | pmc = 393163 | doi = 10.1073/pnas.75.12.6271 | doi-access = free | bibcode = 1978PNAS...75.6271P }}</ref> The production of the [[nitrogenase]] complex is genetically regulated, and the activity of the protein complex is dependent on ambient oxygen concentrations, and intra- and extracellular concentrations of ammonia and oxidized nitrogen species (nitrate and nitrite).<ref>{{cite journal | vauthors = Beversdorf LJ, Miller TR, McMahon KD | title = The role of nitrogen fixation in cyanobacterial bloom toxicity in a temperate, eutrophic lake | journal = PLOS ONE | volume = 8 | issue = 2 | pages = e56103 | date = 2013-02-06 | pmid = 23405255 | pmc = 3566065 | doi = 10.1371/journal.pone.0056103 | doi-access = free | bibcode = 2013PLoSO...856103B }}</ref><ref>{{Cite journal| vauthors = Gallon JR |date=2001-03-01|title=N2 fixation in phototrophs: adaptation to a specialized way of life |journal=Plant and Soil|language=en|volume=230|issue=1|pages=39–48 |doi=10.1023/A:1004640219659|bibcode=2001PlSoi.230...39G |s2cid=22893775|issn=1573-5036}}</ref><ref>{{cite journal | vauthors = Paerl H | title = The cyanobacterial nitrogen fixation paradox in natural waters | journal = F1000Research | volume = 6 | pages = 244 | date = 2017-03-09 | pmid = 28357051 | pmc = 5345769 | doi = 10.12688/f1000research.10603.1 | doi-access = free }}</ref> Additionally, the combined concentrations of both ammonium and nitrate are thought to inhibit N<sub>Fix</sub>, specifically when intracellular concentrations of 2-[[Ketoglutaric acid|oxoglutarate]] (2-OG) exceed a critical threshold.<ref>{{cite journal | vauthors = Li JH, Laurent S, Konde V, Bédu S, Zhang CC | title = An increase in the level of 2-oxoglutarate promotes heterocyst development in the cyanobacterium Anabaena sp. strain PCC 7120 | journal = Microbiology | volume = 149 | issue = Pt 11 | pages = 3257–3263 | date = November 2003 | pmid = 14600238 | doi = 10.1099/mic.0.26462-0 | doi-access = free }}</ref> The specialized heterocyst cell is necessary for the performance of nitrogenase as a result of its sensitivity to ambient oxygen.<ref>{{cite book | vauthors = Wolk CP, Ernst A, Elhai J | chapter = Heterocyst Metabolism and Development|date=1994 | title = The Molecular Biology of Cyanobacteria |pages=769–823| veditors = Bryant DA |series=Advances in Photosynthesis|place=Dordrecht|publisher=Springer Netherlands|language=en|doi=10.1007/978-94-011-0227-8_27|isbn=978-94-011-0227-8 }}</ref>

Nitrogenase consist of two proteins, a catalytic iron-dependent protein, commonly referred to as MoFe protein and a reducing iron-only protein (Fe protein). Three iron-dependent proteins are known: [[molybdenum]]-dependent, [[vanadium]]-dependent, and [[iron]]-only, with all three nitrogenase protein variations containing an iron protein component. Molybdenum-dependent nitrogenase is most common.<ref name=Rees/> The different types of nitrogenase can be determined by the specific iron protein component.<ref>{{cite book | vauthors = Schneider K, Müller A | title = Catalysts for Nitrogen Fixation| chapter = Iron-Only Nitrogenase: Exceptional Catalytic, Structural and Spectroscopic Features|date=2004 |pages=281–307| veditors = Smith BE, Richards RL, Newton WE |series=Nitrogen Fixation: Origins, Applications, and Research Progress|place=Dordrecht|publisher=Springer Netherlands|language=en|doi=10.1007/978-1-4020-3611-8_11|isbn=978-1-4020-3611-8 }}</ref> Nitrogenase is highly conserved. [[Gene expression]] through [[DNA sequencing]] can distinguish which protein complex is present in the microorganism and potentially being expressed. Most frequently, the [[Nif gene|''nif''H gene]] is used to identify the presence of molybdenum-dependent nitrogenase, followed by closely related nitrogenase reductases (component II) ''vnf''H and ''anf''H representing vanadium-dependent and iron-only nitrogenase, respectively.<ref>{{Cite journal| vauthors = Knoche KL, Aoyama E, Hasan K, Minteer SD |date=2017|title=Role of Nitrogenase and Ferredoxin in the Mechanism of Bioelectrocatalytic Nitrogen Fixation by the Cyanobacteria Anabaena variabilis SA-1 Mutant Immobilized on Indium Tin Oxide (ITO) Electrodes|url=https://www.cheric.org/research/tech/periodicals/view.php?seq=1531452|journal=Electrochimica Acta|language=ko|volume=232|pages=396–403|doi=10.1016/j.electacta.2017.02.148}}</ref> In studying the ecology and evolution of [[Diazotroph|nitrogen-fixing bacteria]], the ''nifH'' gene is the [[biomarker]] most widely used.<ref>{{cite journal | vauthors = Raymond J, Siefert JL, Staples CR, Blankenship RE | title = The natural history of nitrogen fixation | journal = Molecular Biology and Evolution | volume = 21 | issue = 3 | pages = 541–554 | date = March 2004 | pmid = 14694078 | doi = 10.1093/molbev/msh047 | doi-access = free | author4-link = Robert E. Blankenship }}</ref> ''nif''H has two similar genes ''anf''H and vnfH that also encode for the nitrogenase reductase component of the nitrogenase complex.<ref>{{cite journal | vauthors = Schüddekopf K, Hennecke S, Liese U, Kutsche M, Klipp W | title = Characterization of anf genes specific for the alternative nitrogenase and identification of nif genes required for both nitrogenases in Rhodobacter capsulatus | journal = Molecular Microbiology | volume = 8 | issue = 4 | pages = 673–684 | date = May 1993 | pmid = 8332060 | doi = 10.1111/j.1365-2958.1993.tb01611.x | s2cid = 42057860 }}</ref>

=== Evolution of nitrogenase ===
Nitrogenase is thought to have evolved sometime between 1.5-2.2 billion years ago (Ga),<ref>{{Cite journal |last1=Garcia |first1=Amanda K. |last2=McShea |first2=Hanon |last3=Kolaczkowski |first3=Bryan |last4=Kaçar |first4=Betül |date=May 2020 |title=Reconstructing the evolutionary history of nitrogenases: Evidence for ancestral molybdenum-cofactor utilization |journal=Geobiology |language=en |volume=18 |issue=3 |pages=394–411 |doi=10.1111/gbi.12381 |issn=1472-4677 |pmc=7216921 |pmid=32065506|bibcode=2020Gbio...18..394G }}</ref><ref>{{Cite journal |last1=Boyd |first1=E. S. |last2=Anbar |first2=A. D. |last3=Miller |first3=S. |last4=Hamilton |first4=T. L. |last5=Lavin |first5=M. |last6=Peters |first6=J. W. |date=May 2011 |title=A late methanogen origin for molybdenum-dependent nitrogenase |url=https://onlinelibrary.wiley.com/doi/10.1111/j.1472-4669.2011.00278.x |journal=Geobiology |language=en |volume=9 |issue=3 |pages=221–232 |doi=10.1111/j.1472-4669.2011.00278.x |pmid=21504537 |bibcode=2011Gbio....9..221B |issn=1472-4677}}</ref> although some isotopic support showing nitrogenase evolution as early as around 3.2 Ga.<ref>{{Cite journal |last1=Stüeken |first1=Eva E. |last2=Buick |first2=Roger |last3=Guy |first3=Bradley M. |last4=Koehler |first4=Matthew C. |date=April 2015 |title=Isotopic evidence for biological nitrogen fixation by molybdenum-nitrogenase from 3.2 Gyr |url=https://www.nature.com/articles/nature14180 |journal=Nature |language=en |volume=520 |issue=7549 |pages=666–669 |doi=10.1038/nature14180 |pmid=25686600 |bibcode=2015Natur.520..666S |issn=0028-0836}}</ref> Nitrogenase appears to have evolved from [[maturase]]-like proteins, although the function of the preceding protein is currently unknown.<ref>{{Cite journal |last1=Garcia |first1=Amanda K |last2=Kolaczkowski |first2=Bryan |last3=Kaçar |first3=Betül |date=2022-03-02 |editor-last=Archibald |editor-first=John |title=Reconstruction of Nitrogenase Predecessors Suggests Origin from Maturase-Like Proteins |journal=Genome Biology and Evolution |language=en |volume=14 |issue=3 |doi=10.1093/gbe/evac031 |issn=1759-6653 |pmc=8890362 |pmid=35179578}}</ref>

Nitrogenase has three different forms (''Nif, Anf, and Vnf'') that correspond with the metal found in the active site of the protein (molybdenum, iron, and vanadium respectively).<ref>{{Cite journal |last=Eady |first=Robert R. |date=1996-01-01 |title=Structure−Function Relationships of Alternative Nitrogenases |url=https://pubs.acs.org/doi/10.1021/cr950057h |journal=Chemical Reviews |language=en |volume=96 |issue=7 |pages=3013–3030 |doi=10.1021/cr950057h |pmid=11848850 |issn=0009-2665}}</ref> Marine metal abundances over Earth's geologic timeline are thought to have driven the relative abundance of which form of nitrogenase was most common.<ref>{{Cite journal |last1=Anbar |first1=A. D. |last2=Knoll |first2=A. H. |date=2002-08-16 |title=Proterozoic Ocean Chemistry and Evolution: A Bioinorganic Bridge? |url=https://www.science.org/doi/10.1126/science.1069651 |journal=Science |language=en |volume=297 |issue=5584 |pages=1137–1142 |doi=10.1126/science.1069651 |pmid=12183619 |bibcode=2002Sci...297.1137A |issn=0036-8075}}</ref> Currently, there is no conclusive agreement on which form of nitrogenase arose first.

===Microorganisms===
{{Main|Diazotroph}}
Diazotrophs are widespread within domain [[Bacteria]] including [[cyanobacteria]] (e.g. the highly significant ''[[Trichodesmium]]'' and ''[[Cyanothece]]''), [[green sulfur bacteria]], [[purple sulfur bacteria]], [[Azotobacteraceae]], [[rhizobia]] and ''[[Frankia]].''<ref>{{Cite web|url=https://scitechdaily.com/nitrogen-inputs-in-the-ancient-ocean-underappreciated-bacteria-step-into-the-spotlight/|title=Nitrogen Inputs in the Ancient Ocean: Underappreciated Bacteria Step Into the Spotlight|first=Max Planck|last=Institute|date=6 August 2021}}</ref><ref name="Mus-2016">{{cite journal | vauthors = Mus F, Crook MB, Garcia K, Garcia Costas A, Geddes BA, Kouri ED, Paramasivan P, Ryu MH, Oldroyd GE, Poole PS, Udvardi MK, Voigt CA, Ané JM, Peters JW | title = Symbiotic Nitrogen Fixation and the Challenges to Its Extension to Nonlegumes | journal = Applied and Environmental Microbiology | volume = 82 | issue = 13 | pages = 3698–3710 | date = July 2016 | pmid = 27084023 | pmc = 4907175 | doi = 10.1128/AEM.01055-16 | bibcode = 2016ApEnM..82.3698M | veditors = Kelly RM }}</ref> Several obligately anaerobic bacteria fix nitrogen including many (but not all) ''[[Clostridium]]'' spp. Some [[archaea]] such as ''[[Methanosarcina acetivorans]]'' also fix nitrogen,<ref>{{cite journal | vauthors = Dhamad AE, Lessner DJ | title = A CRISPRi-dCas9 System for Archaea and Its Use To Examine Gene Function during Nitrogen Fixation by Methanosarcina acetivorans | journal = Applied and Environmental Microbiology | volume = 86 | issue = 21 | pages = e01402–20 | date = October 2020 | pmid = 32826220 | pmc = 7580536 | doi = 10.1128/AEM.01402-20 | bibcode = 2020ApEnM..86E1402D | veditors = Atomi H }}</ref> and several other [[methanogen]]ic [[taxa]], are significant contributors to nitrogen fixation in oxygen-deficient soils.<ref>{{cite journal | vauthors = Bae HS, Morrison E, Chanton JP, Ogram A | title = Methanogens Are Major Contributors to Nitrogen Fixation in Soils of the Florida Everglades | journal = Applied and Environmental Microbiology | volume = 84 | issue = 7 | pages = e02222–17 | date = April 2018 | pmid = 29374038 | pmc = 5861825 | doi = 10.1128/AEM.02222-17 | bibcode = 2018ApEnM..84E2222B }}</ref>

[[Cyanobacteria]], commonly known as blue-green algae, inhabit nearly all illuminated environments on Earth and play key roles in the carbon and [[nitrogen cycle]] of the [[biosphere]]. In general, cyanobacteria can use various inorganic and organic sources of combined nitrogen, such as [[nitrate]], [[nitrite]], [[ammonium]], [[urea]], or some [[amino acid]]s. Several cyanobacteria strains are also capable of diazotrophic growth, an ability that may have been present in their last common ancestor in the [[Archean]] eon.<ref>{{cite journal | vauthors = Latysheva N, Junker VL, Palmer WJ, Codd GA, Barker D | title = The evolution of nitrogen fixation in cyanobacteria | journal = Bioinformatics | volume = 28 | issue = 5 | pages = 603–606 | date = March 2012 | pmid = 22238262 | doi = 10.1093/bioinformatics/bts008 | doi-access = free }}</ref> Nitrogen fixation not only naturally occurs in soils but also aquatic systems, including both freshwater and marine.<ref name="Pierella Karlusich-2021">{{cite journal | vauthors = Pierella Karlusich JJ, Pelletier E, Lombard F, Carsique M, Dvorak E, Colin S, Picheral M, Cornejo-Castillo FM, Acinas SG, Pepperkok R, Karsenti E, de Vargas C, Wincker P, Bowler C, Foster RA | title = Global distribution patterns of marine nitrogen-fixers by imaging and molecular methods | journal = Nature Communications | volume = 12 | issue = 1 | pages = 4160 | date = July 2021 | pmid = 34230473 | pmc = 8260585 | doi = 10.1038/s41467-021-24299-y | bibcode = 2021NatCo..12.4160P }}</ref><ref>{{Cite journal| vauthors = Ash C |date=2021-08-13| veditors = Ash C, Smith J |title=Some light on diazotrophs |journal=Science|language=en|volume=373|issue=6556|pages=755.7–756|doi=10.1126/science.373.6556.755-g|bibcode=2021Sci...373..755A|s2cid=238709371|issn=0036-8075}}</ref> Indeed, the amount of nitrogen fixed in the ocean is at least as much as that on land.<ref>{{cite journal | vauthors = Kuypers MM, Marchant HK, Kartal B | title = The microbial nitrogen-cycling network | journal = Nature Reviews. Microbiology | volume = 16 | issue = 5 | pages = 263–276 | date = May 2018 | pmid = 29398704 | doi = 10.1038/nrmicro.2018.9 | hdl-access = free | s2cid = 3948918 | hdl = 21.11116/0000-0003-B828-1 }}</ref> The colonial marine cyanobacterium ''[[Trichodesmium]]'' is thought to fix nitrogen on such a scale that it accounts for almost half of the nitrogen fixation in marine systems globally.<ref>{{cite journal | vauthors = Bergman B, Sandh G, Lin S, Larsson J, Carpenter EJ | title = Trichodesmium--a widespread marine cyanobacterium with unusual nitrogen fixation properties | journal = FEMS Microbiology Reviews | volume = 37 | issue = 3 | pages = 286–302 | date = May 2013 | pmid = 22928644 | pmc = 3655545 | doi = 10.1111/j.1574-6976.2012.00352.x }}</ref> Marine surface lichens and non-photosynthetic bacteria belonging in Proteobacteria and Planctomycetes fixate significant atmospheric nitrogen.<ref>{{Cite web|url=https://www.sciencedaily.com/releases/2018/06/180611133453.htm|title=Large-scale study indicates novel, abundant nitrogen-fixing microbes in surface ocean|website=ScienceDaily|access-date=8 June 2019|archive-url=https://web.archive.org/web/20190608024940/https://www.sciencedaily.com/releases/2018/06/180611133453.htm|archive-date=8 June 2019|url-status=live}}</ref> Species of nitrogen fixing cyanobacteria in fresh waters include: ''[[Aphanizomenon]]'' and [[Dolichospermum flosaquae|''Dolichospermum'']] (previously Anabaena).<ref>{{Cite journal| vauthors = Rolff C, Almesjö L, Elmgren R |date=2007-03-05|title=Nitrogen fixation and abundance of the diazotrophic cyanobacterium Aphanizomenon sp. in the Baltic Proper|url=http://www.int-res.com/abstracts/meps/v332/p107-118/|journal=Marine Ecology Progress Series|language=en|volume=332|pages=107–118|doi=10.3354/meps332107 |bibcode=2007MEPS..332..107R|doi-access=free}}</ref> Such species have specialized cells called [[Heterocyst|heterocytes]], in which nitrogen fixation occurs via the nitrogenase enzyme.<ref>{{Cite journal| vauthors = Carmichael WW |date=12 Oct 2001|title=Health Effects of Toxin-Producing Cyanobacteria: "The CyanoHABs" |journal=Human and Ecological Risk Assessment|language=en|volume=7|issue=5|pages=1393–1407|doi=10.1080/20018091095087|bibcode=2001HERA....7.1393C |s2cid=83939897|issn=1080-7039}}</ref><ref>{{cite journal | vauthors = Bothe H, Schmitz O, Yates MG, Newton WE | title = Nitrogen fixation and hydrogen metabolism in cyanobacteria | journal = Microbiology and Molecular Biology Reviews | volume = 74 | issue = 4 | pages = 529–551 | date = December 2010 | pmid = 21119016 | pmc = 3008169 | doi = 10.1128/MMBR.00033-10 }}</ref>

=== Algae ===
One type of [[organelle]], originating from [[cyanobacteria]]l [[endosymbiont]]s called [[UCYN-A]]2,<ref name="Thompson_2012" /><ref>{{Cite journal |last1=Thompson |first1=Anne |last2=Carter |first2=Brandon J. |last3=Turk-Kubo |first3=Kendra |last4=Malfatti |first4=Francesca |last5=Azam |first5=Farooq |last6=Zehr |first6=Jonathan P. |date=October 2014 |title=Genetic diversity of the unicellular nitrogen-fixing cyanobacteria UCYN-A and its prymnesiophyte host: UCYN-A genetic diversity |url=https://cloudfront.escholarship.org/dist/prd/content/qt4687q7k8/qt4687q7k8.pdf?t=nx0365 |journal=Environmental Microbiology |language=en |volume=16 |issue=10 |pages=3238–3249 |doi=10.1111/1462-2920.12490 |pmid=24761991 |s2cid=24822220}}</ref> can turn nitrogen gas into a biologically available form. This [[nitroplast]] was discovered in [[algae]], particularly in the marine algae [[Braarudosphaera bigelowii]].<ref>{{Cite journal |last=Wong |first=Carissa |date=2024-04-11 |title=Scientists discover first algae that can fix nitrogen — thanks to a tiny cell structure |url=https://www.nature.com/articles/d41586-024-01046-z |journal=Nature |volume=628 |issue=8009 |page=702 |language=en |doi=10.1038/d41586-024-01046-z|pmid=38605201 |bibcode=2024Natur.628..702W }}</ref>

[[Diatom]]s in the family ''Rhopalodiaceae'' also possess [[cyanobacteria]]l [[endosymbiont]]s called spheroid bodies or diazoplasts.<ref>{{cite journal |last1=Moulin |first1=Solène L. Y. |last2=Frail |first2=Sarah |last3=Braukmann |first3=Thomas |last4=Doenier |first4=Jon |last5=Steele-Ogus |first5=Melissa |last6=Marks |first6=Jane C. |last7=Mills |first7=Matthew M. |last8=Yeh |first8=Ellen |date=15 April 2024 |title=The endosymbiont of Epithemia clementina is specialized for nitrogen fixation within a photosynthetic eukaryote |journal=ISME Communications |volume=4 |pages=ycae055 |doi=10.1093/ismeco/ycae055 |pmc=11070190 |pmid=38707843 |doi-access=free}}</ref> These endosymbionts have lost photosynthetic properties, but have kept the ability to perform nitrogen fixation, allowing these diatoms to fix atmospheric nitrogen.<ref>{{Cite journal |last1=Schvarcz |first1=Christopher R. |last2=Wilson |first2=Samuel T. |last3=Caffin |first3=Mathieu |last4=Stancheva |first4=Rosalina |last5=Li |first5=Qian |last6=Turk-Kubo |first6=Kendra A. |last7=White |first7=Angelicque E. |last8=Karl |first8=David M. |last9=Zehr |first9=Jonathan P. |last10=Steward |first10=Grieg F. |date=2022-02-10 |title=Overlooked and widespread pennate diatom-diazotroph symbioses in the sea |journal=Nature Communications |language=en |volume=13 |issue=1 |pages=799 |bibcode=2022NatCo..13..799S |doi=10.1038/s41467-022-28065-6 |issn=2041-1723 |pmc=8831587 |pmid=35145076}}</ref><ref>{{Cite journal |pmc=4128115 |year=2014 |last1=Nakayama |first1=T. |title=Complete genome of a nonphotosynthetic cyanobacterium in a diatom reveals recent adaptations to an intracellular lifestyle |journal=Proceedings of the National Academy of Sciences of the United States of America |volume=111 |issue=31 |pages=11407–11412 |last2=Kamikawa |first2=R. |last3=Tanifuji |first3=G. |last4=Kashiyama |first4=Y. |last5=Ohkouchi |first5=N. |last6=Archibald |first6=J. M. |last7=Inagaki |first7=Y. |pmid=25049384 |doi=10.1073/pnas.1405222111 |bibcode=2014PNAS..11111407N |doi-access=free}}</ref> Other diatoms in symbiosis with nitrogen-fixing cyanobacteria are among the genera ''Hemiaulus'', ''Rhizosolenia'' and ''Chaetoceros''.<ref>{{Cite journal |last1=Pierella Karlusich |first1=Juan José |last2=Pelletier |first2=Eric |last3=Lombard |first3=Fabien |last4=Carsique |first4=Madeline |last5=Dvorak |first5=Etienne |last6=Colin |first6=Sébastien |last7=Picheral |first7=Marc |last8=Cornejo-Castillo |first8=Francisco M. |last9=Acinas |first9=Silvia G. |last10=Pepperkok |first10=Rainer |last11=Karsenti |first11=Eric |date=2021-07-06 |title=Global distribution patterns of marine nitrogen-fixers by imaging and molecular methods |journal=Nature Communications |language=en |volume=12 |issue=1 |pages=4160 |doi=10.1038/s41467-021-24299-y |issn=2041-1723 |pmc=8260585 |pmid=34230473 |bibcode=2021NatCo..12.4160P}}</ref>

===Root nodule symbioses===
{{Main|Root nodule}}

====Legume family====
[[Image:Root nodules on fava bean plant.jpg|thumb|right|Nodules are visible on this broad bean root]]
Plants that contribute to nitrogen fixation include those of the [[legume]] [[family (biology)|family]]—[[Fabaceae]]— with [[taxa]] such as [[kudzu]], [[clover]], [[soybean]], [[alfalfa]], [[lupin]], [[peanut]] and [[rooibos]].<ref name="Mus-2016" /> They contain [[symbiosis|symbiotic]] [[rhizobia]] bacteria within [[root nodule|nodules]] in their [[root|root systems]], producing nitrogen compounds that help the plant to grow and compete with other plants.<ref>{{cite journal | vauthors = Kuypers MM, Marchant HK, Kartal B | title = The microbial nitrogen-cycling network | journal = Nature Reviews. Microbiology | volume = 16 | issue = 5 | pages = 263–276 | date = May 2018 | pmid = 29398704 | doi = 10.1038/nrmicro.2018.9 | hdl = 21.11116/0000-0003-B828-1 | s2cid = 3948918 | hdl-access = free }}</ref> When the plant dies, the fixed nitrogen is released, making it available to other plants; this helps to fertilize the [[soil]].<ref name=postgate/><ref>{{cite book | vauthors = Smil V |year=2000 |title=Cycles of Life |publisher=Scientific American Library}}</ref> The great majority of legumes have this association, but a few [[genera]] (e.g., ''[[Styphnolobium]]'') do not. In many traditional farming practices, fields are [[Crop Rotation|rotated]] through various types of crops, which usually include one consisting mainly or entirely of [[clover]].{{citation needed|date=August 2019}}

Fixation efficiency in soil is dependent on many factors, including the [[legume]] and air and soil conditions. For example, nitrogen fixation by red clover can range from {{convert|50|to|200|lb/acre|abbr=on}}.<ref>{{Cite web|url=http://www1.foragebeef.ca/$Foragebeef/frgebeef.nsf/all/frg90/$FILE/fertilitylegumefixation.pdf|title=Nitrogen Fixation and Inoculation of Forage Legumes|archive-url=https://web.archive.org/web/20161202170130/http://www1.foragebeef.ca/$Foragebeef/frgebeef.nsf/all/frg90/$FILE/fertilitylegumefixation.pdf|archive-date=2 December 2016|url-status=dead}}</ref>

==== Non-leguminous ====
[[Image:A sectioned alder root nodule gall.JPG|right|thumb|A sectioned alder tree root nodule]]

The ability to fix nitrogen in nodules is present in [[actinorhizal plant]]s such as [[alder]] and [[bayberry]], with the help of ''[[Frankia]]'' bacteria. They are found in 25 genera in the [[order (biology)|order]]s [[Cucurbitales]], [[Fagales]] and [[Rosales]], which together with the [[Fabales]] form a ''nitrogen-fixing clade'' of [[eurosid]]s. The ability to fix nitrogen is not universally present in these families. For example, of 122 [[Rosaceae]] genera, only four fix nitrogen. Fabales were the first lineage to branch off this nitrogen-fixing clade; thus, the ability to fix nitrogen may be [[plesiomorphic]] and subsequently lost in most descendants of the original nitrogen-fixing plant; however, it may be that the basic [[genetics|genetic]] and [[physiological]] requirements were present in an incipient state in the [[most recent common ancestor]]s of all these plants, but only evolved to full function in some of them.<ref>{{cite book | vauthors = Dawson JO | chapter = Ecology of Actinorhizal Plants |title=Nitrogen-fixing Actinorhizal Symbioses |volume=6 |pages=199–234 |doi=10.1007/978-1-4020-3547-0_8 |year=2008 |publisher=Springer |series=Nitrogen Fixation: Origins, Applications, and Research Progress |isbn=978-1-4020-3540-1 }}</ref>

In addition, ''[[Trema (plant)|Trema]]'' (''Parasponia''), a tropical genus in the family [[Cannabaceae]], is unusually able to interact with rhizobia and form nitrogen-fixing nodules.<ref>{{cite journal | vauthors = Op den Camp R, Streng A, De Mita S, Cao Q, Polone E, Liu W, Ammiraju JS, Kudrna D, Wing R, Untergasser A, Bisseling T, Geurts R | title = LysM-type mycorrhizal receptor recruited for rhizobium symbiosis in nonlegume Parasponia | journal = Science | volume = 331 | issue = 6019 | pages = 909–12 | date = February 2011 | pmid = 21205637 | doi = 10.1126/science.1198181 | author-link11 = Ton Bisseling | s2cid = 20501765 | bibcode = 2011Sci...331..909O }}</ref>

{| class="wikitable"
|+Non-legumious nodulating plants
!Family
!Genera
!Species
|-
|[[Betulaceae]]
|{{plainlist|
* [[Alnus]] (alders)
}}
|Most or all species
|-
|[[Boraginaceae]]
|{{plainlist|
* [[Phacelia]]
}}
|{{plainlist|
* [[Phacelia tanacetifolia]]
}}
|-
|[[Cannabaceae]]
|{{plainlist|
* [[Trema (plant)|Trema (Parasponia)]]
}}
|{{plainlist|
* [[Trema orientale]]
* [[Trema lamarckiana]]
}}
|-
|[[Casuarinaceae]]
|{{plainlist|
* [[Allocasuarina]]
* [[Casuarina]]
* [[Ceuthostoma]]
* [[Gymnostoma]]
}}
|
|-
|[[Coriariaceae]]
|{{plainlist|
* [[Coriaria]]
}}
|{{plainlist|
* [[Coriaria arborea]]
* [[Coriaria myrtifolia]]
}}
|-
|[[Datiscaceae]]
|{{plainlist|
* [[Datisca]]
}}
|
|-
|[[Elaeagnaceae]]
|{{plainlist|
* [[Elaeagnus]] (silverberries)
* [[Hippophae]] (sea-buckthorns)
* [[Shepherdia]] (buffaloberries)
}}
|
|-
|[[Myricaceae]]
|{{plainlist|
* [[Comptonia (plant)|Comptonia]] (sweetfern)
* [[Myrica]] (babyberries)
}}
|
|-
|[[Posidoniaceae]]
|{{plainlist|
* [[Posidonia]] (seagrass)
}}
|
|-
|[[Rhamnaceae]]
|{{plainlist|
* [[Ceanothus]]
* [[Colletia]]
* [[Discaria]]
* [[Kentrothamnus]]
* [[Retanilla]]
* [[Talguenea]]
* [[Trevoa]]
}}
|
|-
|[[Rosaceae]]
|{{plainlist|
* [[Cercocarpus]] (mountain mahoganies)
* [[Chamaebatia]] (mountain miseries)
* [[Dryas (plant)|Dryas]]
* [[Purshia]]/Cowania (bitterbrushes/cliffroses)
}}
|
|}

=== Other plant symbionts ===
Some other plants live in association with a [[cyanobiont]] (cyanobacteria such as ''[[Nostoc]]'') which fix nitrogen for them:
* Some lichens such as ''[[Lobaria]]'' and ''[[Peltigera]]''
* [[Mosquito fern]] (''[[Azolla]]'' species)
* [[Cycad]]s<ref>{{Cite web|title=Cycad biology, Article 1: Corraloid roots of cycads|url=http://www1.biologie.uni-hamburg.de/b-online/library/cycads/corraloid.htm|access-date=2021-10-14|website=www1.biologie.uni-hamburg.de}}</ref>
* ''[[Gunnera]]''
* ''[[Blasia]]'' ([[liverwort]])
* [[Hornwort]]s<ref>{{Cite journal| vauthors = Rai AN |date=2000|title=Cyanobacterium-plant symbioses|journal=New Phytologist|volume=147|issue=3|pages=449–481|doi=10.1046/j.1469-8137.2000.00720.x|pmid=33862930|doi-access=free}}</ref>

Some symbiotic relationships involving agriculturally-important plants are:<ref>{{cite journal | vauthors = Van Deynze A, Zamora P, Delaux PM, Heitmann C, Jayaraman D, Rajasekar S, Graham D, Maeda J, Gibson D, Schwartz KD, Berry AM, Bhatnagar S, Jospin G, Darling A, Jeannotte R, Lopez J, Weimer BC, Eisen JA, Shapiro HY, Ané JM, Bennett AB | title = Nitrogen fixation in a landrace of maize is supported by a mucilage-associated diazotrophic microbiota | journal = PLOS Biology | volume = 16 | issue = 8 | pages = e2006352 | date = August 2018 | pmid = 30086128 | pmc = 6080747 | doi = 10.1371/journal.pbio.2006352 | doi-access = free }}</ref>
* [[Sugarcane]] and unclear [[endophyte]]s
* [[Foxtail millet]] and ''[[Azospirillum brasilense]]''
* [[Kallar grass]] and ''[[Azoarcus]]'' sp. strain BH72
* [[Rice]] and ''[[Herbaspirillum seropedicae]]''
* [[Wheat]] and ''[[Klebsiella pneumoniae]]''
* [[Maize]] landrace '[[Sierra Mixe corn|Sierra Mixe]]' / 'olotón'<ref>{{cite web | vauthors = Pskowski M |date=July 16, 2019|title=Indigenous Maize: Who Owns the Rights to Mexico's 'Wonder' Plant? |url=https://e360.yale.edu/features/indigenous-maize-who-owns-the-rights-to-mexicos-wonder-plant |website=Yale E360}}</ref> and various [[Bacteroidota]] and [[Pseudomonadota]]