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Earth's Systems / Biological processes / Terrestrial ecosystem functioning / Living soil system / Bacteria and archaea / Biological nitrogen fixation: free-living and symbiotic

Biological nitrogen fixation: free-living and symbiotic

How diazotrophic bacteria and archaea turn atmospheric dinitrogen into ammonia with nitrogenase, what they need (energy, molybdenum, low oxygen), and how fixed nitrogen is returned to soil. Covers the carbon cost to host plants and the nitrate feedback that throttles fixation.

Boundary: where this process starts

Starts with: Nitrogenase reduces Dinitrogen to Ammonia at about 16 ATP per N2 (N2 + 8 H+ + 8 e- + 16 ATP gives 2 NH3 + H2)

Boundary: where it ends

Ends after: Free-living heterotrophic fixers add only about 1-5 kg N per ha per year in most ecosystems; Nodule senescence, root turnover and rhizodeposition return fixed nitrogen to soil (below-ground N is about 4-70% of legume plant N across studies)

PARTICIPANTSRESOURCESLegume plantDiazotrophsRhizobiaNodulesNitrogenaseOtherparticipantsCarbonNitrogenDinitrogenAmmoniumMolybdenumImpact +3 of 5. Click for details and evidence.Impact +2 of 5. Click for details and evidence.Impact +3 of 5. Click for details and evidence.Cofactors availableImpact +3 of 5. Click for details and evidence.Oxygen sensitivity forces shImpact +2 of 5. Click for details and evidence.Free-living routeImpact +4 of 5. Click for details and evidence.Shielded enzyme delivers NH3Impact -3 of 5. Click for details and evidence.Plant pays carbonImpact +4 of 5. Click for details and evidence.Scales to ecosystem inputImpact -2 of 5. Click for details and evidence.Cost limits the symbiosis toImpact +3 of 5. Click for details and evidence.Fixed N returns through resiImpact +3 of 5. Click for details and evidence.Returned N raises soil minerImpact -3 of 5. Click for details and evidence.↻ balances · moderate · 0.3 High nitrate inhImpact +2 of 5. Click for details and evidence.Small inputImpact +4 of 5. Click for details and evidence.Nitrogen delivered to soilNitrogenase reduces Dinitrogen to Ammonia at about 16 ATP per N2 (N2 + 8 H+ + 8 e- + 16 ATP gives 2 NH3 + H2): uses CarbonNitrogenase reduces Dinitrogen to Ammonia at about 16 ATP per N2 (N2 + 8 H+ + 8 e- + 16 ATP gives 2 NH3 + H2): uses up Dinitrogenuses upNitrogenase reduces Dinitrogen to Ammonia at about 16 ATP per N2 (N2 + 8 H+ + 8 e- + 16 ATP gives 2 NH3 + H2): makes AmmoniummakesNitrogenase needs molybdenum, iron and phosphorus; Mo limits free-living fixation in some tropical forest litter: uses MolybdenumFree-living heterotrophic fixers add only about 1-5 kg N per ha per year in most ecosystems: uses CarbonFree-living heterotrophic fixers add only about 1-5 kg N per ha per year in most ecosystems: makes NitrogenmakesFree-living heterotrophic fixers add only about 1-5 kg N per ha per year in most ecosystems: uses up Dinitrogenuses upBacteroids assimilate ammonia by GS-GOGAT and the plant exports it as amides or ureides (asparagine; allantoin and allantoic acid in soybean): uses CarbonBacteroids assimilate ammonia by GS-GOGAT and the plant exports it as amides or ureides (asparagine; allantoin and allantoic acid in soybean): uses up Ammoniumuses upCarbon cost: the legume pays roughly 4-7 g carbon per g nitrogen fixed (estimate; midpoint 5): uses up Carbonuses upLegume symbioses supply tens to over 100 kg N per ha per year; agricultural fixation totals about 50-70 Tg N per year: makes NitrogenmakesLegume symbioses supply tens to over 100 kg N per ha per year; agricultural fixation totals about 50-70 Tg N per year: uses up Dinitrogenuses upNodule senescence, root turnover and rhizodeposition return fixed nitrogen to soil (below-ground N is about 4-70% of legume plant N across studies): makes NitrogenmakesSoil mineral nitrogen inhibits nodulation and nodule activity, so fixation falls as nitrate rises: uses Nitrogenfuels ATP-drivenreductionCarbon: fuels ATP-driven reductionreduced to ammoniaDinitrogen: reduced to ammoniaproduced as ammoniaAmmonium: produced as ammoniacofactor for nitrogenaseMolybdenum: cofactor for nitrogenasefuels heterotrophicfixersCarbon: fuels heterotrophic fixersadded to ecosystemsupplyNitrogen: added to ecosystem supplyfixed by heterotrophs atlow ratesDinitrogen: fixed by heterotrophs at low ratessupplies carbonskeletonsCarbon: supplies carbon skeletonsassimilated into aminoacidsAmmonium: assimilated into amino acidsspent on nitrogenfixationCarbon: spent on nitrogen fixationadded to agriculturalsoilsNitrogen: added to agricultural soilsfixed by legumesymbiosesDinitrogen: fixed by legume symbiosesreturned via rootturnoverNitrogen: returned via root turnoverreduces nodule activityNitrogen: reduces nodule activityStart: Biologicalnitrogen fixation:free-living a…STARTStart: Biological nitrogen fixation: free-living and symbioticEnd: Biologicalnitrogen fixation:free-living a…ENDEnd: Biological nitrogen fixation: free-living and symbioticNitrogenase reducesDinitrogen to Ammoniaat about 16 ATP per …📄1Nitrogenase reduces Dinitrogen to Ammonia at about 16 ATP per N2 (N2 + 8 H+ + 8 e- + 16 ATP gives 2 NH3 + H2)Nitrogenase needsmolybdenum, iron andphosphorus; Mo limi…📄1Nitrogenase needs molybdenum, iron and phosphorus; Mo limits free-living fixation in some tropical forest litterOxygen irreversiblydamages nitrogenase, sofixers shield …📄1Oxygen irreversibly damages nitrogenase, so fixers shield it (leghemoglobin holds free O2 near 10 nM in nodules; heterocysts; respiratory protection)Free-livingheterotrophic fixersadd only about 1-5 kg…👍1📄1Free-living heterotrophic fixers add only about 1-5 kg N per ha per year in most ecosystemsBacteroids assimilateammonia by GS-GOGAT andthe plant exports it …📄1Bacteroids assimilate ammonia by GS-GOGAT and the plant exports it as amides or ureides (asparagine; allantoin and allantoic acid in soybean)Carbon cost: the legumepays roughly 4-7 gcarbon per g nitrog…📄1Carbon cost: the legume pays roughly 4-7 g carbon per g nitrogen fixed (estimate; midpoint 5)Legume symbioses supplytens to over 100 kg Nper ha per yea…📄1Legume symbioses supply tens to over 100 kg N per ha per year; agricultural fixation totals about 50-70 Tg N per yearNodule senescence, rootturnover andrhizodeposition retu…📄1Nodule senescence, root turnover and rhizodeposition return fixed nitrogen to soil (below-ground N is about 4-70% of legume plant N across studies)Soil mineral nitrogeninhibits nodulation andnodule activity, …📄1Soil mineral nitrogen inhibits nodulation and nodule activity, so fixation falls as nitrate rises
Line thickness = size of impact (1 to 5)% on a line = chance a fork takes that branch📄 = pieces of evidence on a stepNegative effectLoops backHypothesisResource used up (arrow into the step)Resource used, not used upResource made or released (arrow out of the step)
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Nitrogenase reduces Dinitrogen to Ammonia at about 16 ATP per N2 (N2 + 8 H+ + 8 e- + 16 ATP gives 2 NH3 + H2)
DiazotrophsNitrogenaseDinitrogenAmmoniumCarbon
Evidence (1) · added by Ember
  • Hoffman, Lukoyanov, Yang, Dean & Seefeldt 2014, Chemical Reviews 114:4041: Canonical stoichiometry of the Mo nitrogenase is 16 MgATP and 8 electrons per N2 reduced, with one H2 evolved. (confidence 0.9)
Nitrogenase needs molybdenum, iron and phosphorus; Mo limits free-living fixation in some tropical forest litter
DiazotrophsSoil solutionMolybdenumIronPhosphorus
Evidence (1) · added by Ember
  • Barron, Purves, Hedin 2009, Nature Geoscience 2:42, Molybdenum limitation of asymbiotic nitrogen fixation in tropical forest soils: Adding Mo, but not P, raised asymbiotic fixation in lowland Panamanian forest litter and soil. (confidence 0.8)
Oxygen irreversibly damages nitrogenase, so fixers shield it (leghemoglobin holds free O2 near 10 nM in nodules; heterocysts; respiratory protection)
RhizobiaCyanobacteriaAzotobacterOxygen
Evidence (1) · added by Ember
  • Appleby 1984, Annual Review of Plant Physiology 35:443, Leghemoglobin and Rhizobium respiration: Leghemoglobin buffers free O2 in infected nodule cells at nanomolar levels while carrying the O2 flux for bacteroid respiration. (confidence 0.8)
Free-living heterotrophic fixers add only about 1-5 kg N per ha per year in most ecosystems
Free-living diazotrophsDinitrogenCarbonNitrogen
Evidence (1) · added by Ember
  • Reed, Cleveland & Townsend 2011, Annual Review of Ecology, Evolution, and Systematics 42:489, Functional ecology of free-living nitrogen fixation: Free-living fixation rates are typically a few kg N/ha/yr, far below legume symbioses; range across biomes roughly 1-20. (confidence 0.7)
Bacteroids assimilate ammonia by GS-GOGAT and the plant exports it as amides or ureides (asparagine; allantoin and allantoic acid in soybean)
BacteroidsLegume plantAmmoniumCarbon
Evidence (1) · added by Ember
  • Udvardi & Poole 2013, Annual Review of Plant Biology 64:781, Transport and metabolism in legume-rhizobia symbioses: Fixed NH3 is assimilated via glutamine synthetase and exported as amides or ureides depending on legume species. (confidence 0.85)
Carbon cost: the legume pays roughly 4-7 g carbon per g nitrogen fixed (estimate; midpoint 5)
Legume plantNodulesCarbonSugars
Evidence (1) · added by Ember
  • Minchin & Witty 2005, in Werner & Newton (eds), Nitrogen Fixation in Agriculture, Forestry, Ecology and the Environment, Springer, respiratory and carbon costs of symbiotic N2 fixation in legumes: Reported carbon cost of nodulated N2 fixation is a few grams of C per gram of N, estimates vary with method. (confidence 0.5)
Legume symbioses supply tens to over 100 kg N per ha per year; agricultural fixation totals about 50-70 Tg N per year
Legume plantRhizobiaNitrogenDinitrogen
Evidence (1) · added by Ember
  • Herridge, Peoples & Boddey 2008, Plant and Soil 311:1, Global inputs of biological nitrogen fixation in agricultural systems: Crop and forage legumes plus other agricultural fixers are estimated to fix about 50-70 Tg N per year globally. (confidence 0.7)
Nodule senescence, root turnover and rhizodeposition return fixed nitrogen to soil (below-ground N is about 4-70% of legume plant N across studies)
Legume plantSoil microbesNitrogenSoil organic matter
Evidence (1) · added by Ember
  • Fustec, Mariotti, Grandgirard & Amarger 2010, Agronomy for Sustainable Development 30:57, Nitrogen rhizodeposition of legumes. A review: Below-ground N of legumes spans a very wide range (roughly 4-70% of plant N), depending on species and method. (confidence 0.6)
Soil mineral nitrogen inhibits nodulation and nodule activity, so fixation falls as nitrate rises
Legume plantNodulesNitrateNitrogen
Evidence (1) · added by Ember
  • Streeter 1988, Critical Reviews in Plant Sciences 7:1, Inhibition of legume nodule formation and N2 fixation by nitrate: Nitrate suppresses nodule initiation, growth and nitrogenase activity, with inhibition increasing with nitrate supply. (confidence 0.85)