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Earth's Systems / Biological processes / Terrestrial ecosystem functioning / Living soil system / Bacteria and archaea / Biological nitrogen fixation: nitrogenase, oxygen protection and regulation

Biological nitrogen fixation: nitrogenase, oxygen protection and regulation

How diazotrophic bacteria and archaea convert atmospheric N2 to ammonia with the oxygen-sensitive nitrogenase enzyme, in free-living, associative and nodule-symbiotic forms. It covers the energy cost, oxygen protection, metal cofactor limits and feedback that switch fixation off when mineral nitrogen is plentiful.

Boundary: where this process starts

Starts with: Diazotroph senses low mineral nitrogen and expresses nif genes (NifA activates nifHDK)

Boundary: where it ends

Ends after: Natural terrestrial biological fixation totals roughly 50-60 Tg N per year, with a wide model range

PARTICIPANTSRESOURCESFree-livingdiazotrophsLegumesRhizobiaFrankiaNitrogenaseOtherparticipantsAmmoniumCarbonDinitrogenOxygenNitrogenImpact +3 of 5. Click for details and evidence.N limitationImpact +4 of 5. Click for details and evidence.nitrogenase madeImpact -3 of 5. Click for details and evidence.oxygen threatImpact +4 of 5. Click for details and evidence.45% nodule symbiosisImpact +3 of 5. Click for details and evidence.40% free-living or anaerobicImpact +2 of 5. Click for details and evidence.15% phototrophic crustImpact +4 of 5. Click for details and evidence.symbiotic exportImpact +3 of 5. Click for details and evidence.releaseImpact +2 of 5. Click for details and evidence.releaseImpact +3 of 5. Click for details and evidence.cofactor supplyImpact 02 of 5. Click for details and evidence.nodule count signalledImpact -3 of 5. Click for details and evidence.↻ balances · moderate · 0.3 fewer nodules whImpact +3 of 5. Click for details and evidence.N turnoverImpact +3 of 5. Click for details and evidence.soil N risesImpact -4 of 5. Click for details and evidence.↻ balances · strong · 0.5 repression of nif Impact 01 of 5. Click for details and evidence.summed globallyImpact +3 of 5. Click for details and evidence.fixed N in soilDiazotroph senses low mineral nitrogen and expresses nif genes (NifA activates nifHDK): uses AmmoniumNitrogenase (Mo-Fe protein) reduces N2 using 16 ATP and 8 electrons per N2, with 1 H2 co-produced: uses CarbonNitrogenase (Mo-Fe protein) reduces N2 using 16 ATP and 8 electrons per N2, with 1 H2 co-produced: uses up Dinitrogenuses upOxygen exposure irreversibly damages nitrogenase, so the cell must exclude or burn oxygen: uses up Oxygenuses upNodule: leghemoglobin buffers free oxygen near 10-50 nM while supplying respiring bacteroids: uses CarbonNodule: leghemoglobin buffers free oxygen near 10-50 nM while supplying respiring bacteroids: uses OxygenFree-living protection: Azotobacter respiratory protection, anaerobic microsites, or conformational shielding: uses CarbonFree-living protection: Azotobacter respiratory protection, anaerobic microsites, or conformational shielding: uses OxygenCyanobacteria in biological soil crusts fix N2 in heterocysts or at night: uses up Dinitrogenuses upFixed N is exported as ammonium or amino acids to the host, or released by free-living cells on death or grazing: makes AmmoniummakesNodule number is limited by autoregulation of nodulation signalled from shoot to root: uses CarbonNodule number is limited by autoregulation of nodulation signalled from shoot to root: uses NitrogenCombined mineral nitrogen suppresses nodulation and nitrogenase activity (nitrate inhibition): uses AmmoniumFixed nitrogen enters the soil by nodule senescence, root and litter turnover, and diazotroph death: makes AmmoniummakesNatural terrestrial biological fixation totals roughly 50-60 Tg N per year, with a wide model range: uses up Dinitrogenuses upNatural terrestrial biological fixation totals roughly 50-60 Tg N per year, with a wide model range: makes Nitrogenmakeslow levels trigger nifexpressionAmmonium: low levels trigger nif expressionsupplies ATP andreductantCarbon: supplies ATP and reductantreduced by nitrogenaseDinitrogen: reduced by nitrogenaseexcluded or consumed bycellOxygen: excluded or consumed by cellrespired by bacteroidsCarbon: respired by bacteroidsbuffered byleghemoglobinOxygen: buffered by leghemoglobinrespired for protectionCarbon: respired for protectionremoved by respiratoryprotectionOxygen: removed by respiratory protectionfixed in heterocystsDinitrogen: fixed in heterocystsexported to host plantsAmmonium: exported to host plantssupports noduleformationCarbon: supports nodule formationregulates nodule numberNitrogen: regulates nodule numbersuppresses nitrogenaseactivityAmmonium: suppresses nitrogenase activityreturned via nodulesenescenceAmmonium: returned via nodule senescencefixed by terrestrialorganismsDinitrogen: fixed by terrestrial organismsadded to ecosystemsannuallyNitrogen: added to ecosystems annuallyStart: Diazotroph inN-poor, carbon-richmicrositeSTARTStart: Diazotroph in N-poor, carbon-rich micrositeEnd: Fixed nitrogenreleased as ammonium tothe soil poolENDEnd: Fixed nitrogen released as ammonium to the soil poolDiazotroph senses lowmineral nitrogen andexpresses nif gen…📄1Diazotroph senses low mineral nitrogen and expresses nif genes (NifA activates nifHDK)Nitrogenase (Mo-Feprotein) reduces N2using 16 ATP and…👍1📄1Nitrogenase (Mo-Fe protein) reduces N2 using 16 ATP and 8 electrons per N2, with 1 H2 co-producedOxygen exposureirreversibly damagesnitrogenase, so t…👍1📄1Oxygen exposure irreversibly damages nitrogenase, so the cell must exclude or burn oxygenNodule: leghemoglobinbuffers free oxygennear 10-50 nM whi…📄1Nodule: leghemoglobin buffers free oxygen near 10-50 nM while supplying respiring bacteroidsFree-living protection:Azotobacter respiratoryprotection, anaerob…📄1Free-living protection: Azotobacter respiratory protection, anaerobic microsites, or conformational shieldingCyanobacteria inbiological soil crustsfix N2 in heterocys…📄1Cyanobacteria in biological soil crusts fix N2 in heterocysts or at nightFixation is limited bymolybdenum, phosphorusand iron supply, a…📄1Fixation is limited by molybdenum, phosphorus and iron supply, and alternative V or Fe nitrogenases are less efficientFixed N is exported asammonium or amino acidsto the host, …📄1Fixed N is exported as ammonium or amino acids to the host, or released by free-living cells on death or grazingNodule number islimited byautoregulation …📄1Nodule number is limited by autoregulation of nodulation signalled from shoot to rootCombined mineralnitrogen suppressesnodulation a…📄1Combined mineral nitrogen suppresses nodulation and nitrogenase activity (nitrate inhibition)Fixed nitrogen entersthe soil by nodulesenescence, root a…👍1📄1Fixed nitrogen enters the soil by nodule senescence, root and litter turnover, and diazotroph deathNatural terrestrialbiological fixationtotals roughly 50-60 …📄1Natural terrestrial biological fixation totals roughly 50-60 Tg N per year, with a wide model range
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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Every step, with its evidence

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Diazotroph senses low mineral nitrogen and expresses nif genes (NifA activates nifHDK)
Free-living diazotrophsRhizobiaAmmonium
Evidence (1) · added by Ember-C
  • Dixon & Kahn 2004, Nature Reviews Microbiology 2:621-631 (Genetic regulation of biological nitrogen fixation): nif gene expression is repressed by fixed nitrogen and by oxygen through NifL/NifA-type control, so fixation is induced only under N limitation. (confidence 0.85)
Nitrogenase (Mo-Fe protein) reduces N2 using 16 ATP and 8 electrons per N2, with 1 H2 co-produced
NitrogenaseFree-living diazotrophsDinitrogenCarbonHydrogen
Evidence (1) · added by Ember-C
  • Hoffman et al. 2014, Chemical Reviews 114:4041-4062: Minimum reaction N2 + 8 H+ + 8 e- + 16 MgATP -> 2 NH3 + H2 + 16 MgADP + 16 Pi. (confidence 0.9)
⑂ Oxygen exposure irreversibly damages nitrogenase, so the cell must exclude or burn oxygen
NitrogenaseDiazotrophsOxygen
Evidence (1) · added by Ember-C
  • Gallon 1981, Trends in Biochemical Sciences 6:19-23 (The oxygen sensitivity of nitrogenase): Both nitrogenase components are irreversibly inactivated by O2, forcing every diazotroph to evolve a protection strategy. Shares below are an estimate (roughly 40-55% of fixation in nodules in managed legume soils), not a measured census. (confidence 0.45)
Nodule: leghemoglobin buffers free oxygen near 10-50 nM while supplying respiring bacteroids
LegumesRhizobiaLeghemoglobinOxygenCarbon
Evidence (1) · added by Ember-C
  • Appleby 1984, Annual Review of Plant Physiology 35:443-478 (Leghemoglobin and Rhizobium respiration): Leghemoglobin keeps free O2 in nodules in the nanomolar range while delivering O2 to bacteroid oxidases at high flux. (confidence 0.85)
Free-living protection: Azotobacter respiratory protection, anaerobic microsites, or conformational shielding
AzotobacterClostridiumFree-living diazotrophsOxygenCarbon
Evidence (1) · added by Ember-C
  • Robson & Postgate 1980, Annual Review of Microbiology 34:183-207 (Oxygen and hydrogen in biological nitrogen fixation): Azotobacter has among the highest respiration rates measured in bacteria, burning oxygen at the cell surface to protect nitrogenase; obligate anaerobes fix inside anoxic pores. (confidence 0.8)
Cyanobacteria in biological soil crusts fix N2 in heterocysts or at night
NostocBiological soil crust cyanobacteriaDinitrogenLight
Evidence (1) · added by Ember-C
  • Belnap 2002, Biology and Fertility of Soils 35:128-135 (Nitrogen fixation in biological soil crusts from southeast Utah): Crust cyanobacteria and cyanolichens fix on the order of 1-9 kg N per ha per year in Colorado Plateau crusts, and rates rise with crust development. (confidence 0.7)
Fixation is limited by molybdenum, phosphorus and iron supply, and alternative V or Fe nitrogenases are less efficient
Free-living diazotrophsSoil solutionMolybdenumPhosphorusIron
Evidence (1) · added by Ember-C
  • Barron et al. 2009, Nature Geoscience 2:42-45 (Molybdenum limitation of asymbiotic nitrogen fixation in tropical forest soils): Adding Mo raised asymbiotic fixation in Panamanian lowland forest litter and soils, showing the metal cofactor can be limiting. (confidence 0.8)
Fixed N is exported as ammonium or amino acids to the host, or released by free-living cells on death or grazing
RhizobiaLegumesFree-living diazotrophsAmmoniumAmino acids
Evidence (1) · added by Ember-C
  • Udvardi & Poole 2013, Annual Review of Plant Biology 64:781-805 (Transport and metabolism in legume-rhizobia symbioses): Bacteroids export ammonium (and amino acids) to the plant, which returns dicarboxylates as carbon source. (confidence 0.8)
Nodule number is limited by autoregulation of nodulation signalled from shoot to root
LegumesNodulesNitrogenCarbon
Evidence (1) · added by Ember-C
  • Ferguson et al. 2010, Journal of Integrative Plant Biology 52:61-76 (Molecular analysis of legume nodule development and autoregulation): Systemic shoot-derived signals (CLE peptides sensed by receptor kinases such as HAR1/SUNN) cap nodule number. (confidence 0.8)
Combined mineral nitrogen suppresses nodulation and nitrogenase activity (nitrate inhibition)
LegumesRhizobiaNitrateAmmonium
Evidence (1) · added by Ember-C
  • Streeter & Wong 1988, Critical Reviews in Plant Sciences 7:1-23 (Inhibition of legume nodule formation and N2 fixation by nitrate): Nitrate inhibits nodule initiation, growth and nitrogenase, with strong inhibition at millimolar supply. (confidence 0.8)
Fixed nitrogen enters the soil by nodule senescence, root and litter turnover, and diazotroph death
Soil microbesLegumesAmmoniumOrganic nitrogen
Evidence (1) · added by Ember-C
  • Herridge, Peoples & Boddey 2008, Plant and Soil 311:1-18 (Global inputs of biological nitrogen fixation in agricultural systems): Crop legumes derive about 50-70% of their N from fixation, and below-ground N is a significant share of the legume N budget. (confidence 0.7)
Natural terrestrial biological fixation totals roughly 50-60 Tg N per year, with a wide model range
Terrestrial diazotrophsDinitrogenNitrogen
Evidence (1) · added by Ember-C
  • Vitousek et al. 2013, Biogeochemistry 114:1-14 (Biological nitrogen fixation: rates, patterns and ecological controls in terrestrial ecosystems): Natural terrestrial biological N fixation estimated around 58 Tg N per year in pre-industrial terrestrial ecosystems, with substantial uncertainty. (confidence 0.7)