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Earth's Systems / Biological processes / Terrestrial ecosystem functioning / Living soil system / Soil nitrification, nitrate reduction and nitrogen gas losses

Soil nitrification, nitrate reduction and nitrogen gas losses

Fate of ammonium and nitrate in soil: ammonia oxidizers and nitrite oxidizers make nitrate, which denitrifiers reduce to N2O and N2 in oxygen-poor microsites, and anammox and nitrifier denitrification add further gas losses.

Boundary: where this process starts

Starts with: Which ammonia oxidizer dominates this soil?

Boundary: where it ends

Ends after: Nitrate leaches below the root zone with drainage water; Ammonia volatilizes from high-pH soil surfaces

PARTICIPANTSRESOURCESDenitrifyingbacteriaNitrifyingbacteriaNitrifyingarchaeaAmmonia-oxidizingbacteriaAmmonia-oxidizingarchaeaOtherparticipantsAmmoniumNitrateOxygenNitriteNitrous oxideImpact +3 of 5. Click for details and evidence.Impact +3 of 5. Click for details and evidence.45% low ammonium or acid soiImpact +3 of 5. Click for details and evidence.40% high ammonium, fertilizeImpact +2 of 5. Click for details and evidence.15% oligotrophic, oxic condiImpact +3 of 5. Click for details and evidence.Impact +3 of 5. Click for details and evidence.Impact +3 of 5. Click for details and evidence.Impact +4 of 5. Click for details and evidence.Impact +3 of 5. Click for details and evidence.Impact -2 of 5. Click for details and evidence.↻ balances · weak · 0.2 Acidification slows Impact -3 of 5. Click for details and evidence.Inhibitors suppress ammonia Impact 03 of 5. Click for details and evidence.Impact 03 of 5. Click for details and evidence.Impact +3 of 5. Click for details and evidence.Impact 03 of 5. Click for details and evidence.Impact -4 of 5. Click for details and evidence.60% denitrificationImpact +3 of 5. Click for details and evidence.30% DNRAImpact -2 of 5. Click for details and evidence.10% anammox and otherImpact 03 of 5. Click for details and evidence.Impact -4 of 5. Click for details and evidence.25% acid pH, high nitrate, lImpact +3 of 5. Click for details and evidence.75% near-neutral pH, enough Impact -4 of 5. Click for details and evidence.Impact +3 of 5. Click for details and evidence.Impact +3 of 5. Click for details and evidence.↻ reinforces · weak · 0.2 Ammonium regained Impact +2 of 5. Click for details and evidence.Impact -3 of 5. Click for details and evidence.Impact -2 of 5. Click for details and evidence.Low O2 at the boundary diverImpact -4 of 5. Click for details and evidence.Impact -4 of 5. Click for details and evidence.Impact 01 of 5. Click for details and evidence.Impact -3 of 5. Click for details and evidence.Impact -3 of 5. Click for details and evidence.Impact +3 of 5. Click for details and evidence.Impact 02 of 5. Click for details and evidence.Impact -2 of 5. Click for details and evidence.Impact 02 of 5. Click for details and evidence.Impact 02 of 5. Click for details and evidence.Which ammonia oxidizer dominates this soil?: uses AmmoniumWhich ammonia oxidizer dominates this soil?: uses OxygenArchaea oxidize ammonia at low supply and in acid soils: uses up Ammoniumuses upArchaea oxidize ammonia at low supply and in acid soils: uses up Oxygenuses upArchaea oxidize ammonia at low supply and in acid soils: makes NitritemakesBacteria oxidize ammonia where ammonium is plentiful: uses up Ammoniumuses upBacteria oxidize ammonia where ammonium is plentiful: uses up Oxygenuses upBacteria oxidize ammonia where ammonium is plentiful: makes NitritemakesComammox Nitrospira oxidize ammonia all the way to nitrate: uses up Ammoniumuses upComammox Nitrospira oxidize ammonia all the way to nitrate: makes NitratemakesComammox Nitrospira oxidize ammonia all the way to nitrate: uses up Oxygenuses upNitrite-oxidizing bacteria convert nitrite to nitrate: makes NitratemakesNitrite-oxidizing bacteria convert nitrite to nitrate: uses up Oxygenuses upNitrite-oxidizing bacteria convert nitrite to nitrate: uses up Nitriteuses upNitrate pool in soil solution (mobile anion): uses NitrateNitrification releases protons and acidifies soil: uses up Ammoniumuses upRoots release biological nitrification inhibitors: uses AmmoniumOxygen and moisture window: nitrification peaks at moderate water-filled pore space: uses OxygenNitrate reaches anoxic microsites inside aggregates: uses NitrateNitrate reaches anoxic microsites inside aggregates: uses OxygenWhere does nitrate go in an anoxic microsite?: uses NitrateDenitrifiers reduce nitrate stepwise via nitrite and nitric oxide to nitrous oxide and dinitrogen: uses up Nitrateuses upDenitrifiers reduce nitrate stepwise via nitrite and nitric oxide to nitrous oxide and dinitrogen: makes NitritemakesDenitrifiers reduce nitrate stepwise via nitrite and nitric oxide to nitrous oxide and dinitrogen: makes Nitrous oxidemakesWhat is the nitrous oxide to dinitrogen ratio?: uses Nitrous oxideAcid or nitrate-rich, carbon-poor soil: N2O reductase fails and N2O is released: uses NitrateAcid or nitrate-rich, carbon-poor soil: N2O reductase fails and N2O is released: makes Nitrous oxidemakesNear-neutral, carbon-rich soil: reduction completes to dinitrogen: uses up Nitrous oxideuses upDNRA bacteria reduce nitrate back to ammonium and conserve nitrogen: makes AmmoniummakesDNRA bacteria reduce nitrate back to ammonium and conserve nitrogen: uses up Nitrateuses upAnammox bacteria combine ammonium and nitrite into dinitrogen: uses up Ammoniumuses upAnammox bacteria combine ammonium and nitrite into dinitrogen: uses up Nitriteuses upNitrifier denitrification and chemodenitrification make nitrous oxide at the oxic-anoxic boundary: uses up Nitriteuses upNitrifier denitrification and chemodenitrification make nitrous oxide at the oxic-anoxic boundary: makes Nitrous oxidemakesNitrate leaches below the root zone with drainage water: uses up Nitrateuses upAmmonia volatilizes from high-pH soil surfaces: uses up Ammoniumuses upNitrous oxide and dinitrogen escape to the atmosphere: makes Nitrous oxidemakesClay minerals fix ammonium in interlayers: uses up Ammoniumuses upsupply shapes oxidizeridentityAmmonium: supply shapes oxidizer identityconsumed by oxidizerOxygen: consumed by oxidizeroxidized at low supplyAmmonium: oxidized at low supplyconsumed by archaealoxidationOxygen: consumed by archaeal oxidationformed as intermediateNitrite: formed as intermediateoxidized at high supplyAmmonium: oxidized at high supplyconsumed by bacterialoxidationOxygen: consumed by bacterial oxidationformed as intermediateNitrite: formed as intermediateoxidized in completepathwayAmmonium: oxidized in complete pathwayformed as final productNitrate: formed as final productconsumed in fulloxidationOxygen: consumed in full oxidationformed as end productNitrate: formed as end productconsumed in oxidationOxygen: consumed in oxidationoxidized to nitrateNitrite: oxidized to nitratedissolved and mobile insolutionNitrate: dissolved and mobile in solutionoxidized as acid sourceAmmonium: oxidized as acid sourceprotected from oxidationAmmonium: protected from oxidationsupplied at moderatemoistureOxygen: supplied at moderate moisturereaches anoxic zonesinside aggregatesNitrate: reaches anoxic zones inside aggregatesdepleted insideaggregatesOxygen: depleted inside aggregatesreduced under anoxiaNitrate: reduced under anoxiareduced stepwiseNitrate: reduced stepwiseformed as intermediateNitrite: formed as intermediateformed as intermediateNitrous oxide: formed as intermediatecompared as end productsNitrous oxide: compared as end productsreduced incompletelyNitrate: reduced incompletelyreleased when reductionfailsNitrous oxide: released when reduction failsreduced to dinitrogenNitrous oxide: reduced to dinitrogenretained in soilAmmonium: retained in soilreduced to ammoniumNitrate: reduced to ammoniumcombined with nitriteAmmonium: combined with nitritecombined with ammoniumNitrite: combined with ammoniumtransformed at boundaryNitrite: transformed at boundaryproduced at oxic-anoxicboundaryNitrous oxide: produced at oxic-anoxic boundaryleached below root zoneNitrate: leached below root zonelost as gas at high pHAmmonium: lost as gas at high pHreleased to atmosphereNitrous oxide: released to atmospherefixed within clay layersAmmonium: fixed within clay layersStart: Soilnitrification, nitratereduction and nitrog…STARTStart: Soil nitrification, nitrate reduction and nitrogen gas lossesEnd: Soilnitrification, nitratereduction and nitrog…ENDEnd: Soil nitrification, nitrate reduction and nitrogen gas lossesWhich ammonia oxidizerdominates this soil?📄1Which ammonia oxidizer dominates this soil?Archaea oxidize ammoniaat low supply and inacid soils📄1Archaea oxidize ammonia at low supply and in acid soilsBacteria oxidizeammonia where ammoniumis plentiful📄1Bacteria oxidize ammonia where ammonium is plentifulComammox Nitrospiraoxidize ammonia all theway to nitrate📄1Comammox Nitrospira oxidize ammonia all the way to nitrateNitrite-oxidizingbacteria convertnitrite to nitrate📄1Nitrite-oxidizing bacteria convert nitrite to nitrateNitrate pool in soilsolution (mobile anion)📄1Nitrate pool in soil solution (mobile anion)Nitrification releasesprotons and acidifiessoil📄1Nitrification releases protons and acidifies soilRoots releasebiologicalnitrificati…📄1Roots release biological nitrification inhibitorsOxygen and moisturewindow: nitrificationpeaks at modera…📄1Oxygen and moisture window: nitrification peaks at moderate water-filled pore spaceNitrate reaches anoxicmicrosites insideaggregates📄1Nitrate reaches anoxic microsites inside aggregatesWhere does nitrate goin an anoxic microsite?👍1📄1Where does nitrate go in an anoxic microsite?Denitrifiers reducenitrate stepwise vianitrite and nitr…📄1Denitrifiers reduce nitrate stepwise via nitrite and nitric oxide to nitrous oxide and dinitrogenWhat is the nitrousoxide to dinitrogenratio?📄1What is the nitrous oxide to dinitrogen ratio?Acid or nitrate-rich,carbon-poor soil: N2Oreductase fails and N…📄1Acid or nitrate-rich, carbon-poor soil: N2O reductase fails and N2O is releasedNear-neutral,carbon-rich soil:reduction completes …📄1Near-neutral, carbon-rich soil: reduction completes to dinitrogenDNRA bacteria reducenitrate back toammonium and conser…👍1📄1DNRA bacteria reduce nitrate back to ammonium and conserve nitrogenAnammox bacteriacombine ammonium andnitrite into dinitrogen📄1Anammox bacteria combine ammonium and nitrite into dinitrogenNitrifierdenitrification andchemodenitrificati…📄1Nitrifier denitrification and chemodenitrification make nitrous oxide at the oxic-anoxic boundaryNitrate leaches belowthe root zone withdrainage water📄1Nitrate leaches below the root zone with drainage waterAmmonia volatilizesfrom high-pH soilsurfaces📄1Ammonia volatilizes from high-pH soil surfacesNitrous oxide anddinitrogen escape tothe atmosphere📄1Nitrous oxide and dinitrogen escape to the atmosphereClay minerals fixammonium in interlayers📄1Clay minerals fix ammonium in interlayers
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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⑂ Which ammonia oxidizer dominates this soil?
Ammonia-oxidizing archaeaAmmonia-oxidizing bacteriaComammox NitrospiraAmmoniumOxygen
Evidence (1) · added by Ember-B
  • Prosser & Nicol 2012, Trends in Microbiology 20:523, Archaeal and bacterial ammonia-oxidisers in soil: AOA tend to dominate low-ammonium, acidic soils and AOB high-ammonium fertilized soils; comammox share is poorly quantified, so these shares are rough estimates. (confidence 0.7)
Archaea oxidize ammonia at low supply and in acid soils
Ammonia-oxidizing archaeaAmmoniumOxygenNitrite
Evidence (1) · added by Ember-B
  • Leininger et al. 2006, Nature 442:806, Archaea predominate among ammonia-oxidizing prokaryotes in soils: Archaeal amoA genes outnumber bacterial amoA in many soils and archaea grow at low NH3 supply. (confidence 0.7)
Bacteria oxidize ammonia where ammonium is plentiful
Ammonia-oxidizing bacteriaAmmoniumOxygenNitrite
Evidence (1) · added by Ember-B
  • Prosser & Nicol 2012, Trends in Microbiology 20:523, Archaeal and bacterial ammonia-oxidisers in soil: AOB respond to high ammonium (fertilizer, manure urine patches) and are more active at neutral pH. (confidence 0.7)
Comammox Nitrospira oxidize ammonia all the way to nitrate
Comammox NitrospiraAmmoniumOxygenNitrate
Evidence (1) · added by Ember-B
  • Daims et al. 2015, Nature 528:504, Complete nitrification by Nitrospira bacteria: Single Nitrospira cells can complete both oxidation steps, the comammox pathway. (confidence 0.7)
Nitrite-oxidizing bacteria convert nitrite to nitrate
Nitrite-oxidizing bacteriaNitriteNitrateOxygen
Evidence (1) · added by Ember-B
  • Kuypers, Marchant & Kartal 2018, Nature Reviews Microbiology 16:263, The microbial nitrogen-cycling network: Nitrobacter and Nitrospira oxidize nitrite to nitrate so that nitrite rarely accumulates. (confidence 0.7)
Nitrate pool in soil solution (mobile anion)
Soil solutionNitrateWater
Evidence (1) · added by Ember-B
  • Brady & Weil 2016, The Nature and Properties of Soils, 15th ed., Pearson: Nitrate is negatively charged, is weakly retained by most soils and moves with drainage water. (confidence 0.7)
Nitrification releases protons and acidifies soil
Nitrifying bacteriaNitrifying archaeaHydrogen ionsAmmonium
Evidence (1) · added by Ember-B
  • Brady & Weil 2016, The Nature and Properties of Soils, 15th ed., Pearson: Oxidation of one NH4+ yields two H+, a major acidifying process in fertilized soils. (confidence 0.7)
Roots release biological nitrification inhibitors
Plant rootsAmmoniumOrganic acids
Evidence (1) · added by Ember-B
  • Subbarao et al. 2006, Critical Reviews in Plant Sciences 25:303, Scope and strategies for regulation of nitrification in agricultural systems: Some grasses such as Brachiaria release compounds that suppress nitrifiers, slowing nitrate formation. (confidence 0.7)
Oxygen and moisture window: nitrification peaks at moderate water-filled pore space
Soil waterSoil poresOxygenWater
Evidence (1) · added by Ember-B
  • Stark & Firestone 1995, Applied and Environmental Microbiology 61:218, Mechanisms for soil moisture effects on activity of nitrifying bacteria: Nitrifier activity is limited by substrate diffusion when dry and by oxygen when wet, peaking at intermediate moisture. (confidence 0.7)
Nitrate reaches anoxic microsites inside aggregates
Soil aggregatesSoil waterNitrateOxygenWater
Evidence (1) · added by Ember-B
  • Firestone & Davidson 1989, Microbiological basis of NO and N2O production and consumption in soil, in Exchange of Trace Gases between Terrestrial Ecosystems and the Atmosphere: Anoxic microsites form where respiration outpaces oxygen diffusion, often in wet aggregates with high carbon supply. (confidence 0.7)
⑂ Where does nitrate go in an anoxic microsite?
Denitrifying bacteriaDNRA bacteriaAnammox bacteriaNitrateOrganic carbon
Evidence (1) · added by Ember-B
  • Rutting et al. 2011, Ecological Applications 21:3, Assessment of the importance of dissimilatory nitrate reduction to ammonium for the terrestrial nitrogen cycle: Denitrification usually dominates, DNRA is favoured at high carbon to nitrate ratios and strongly reducing conditions, anammox is minor in most soils; shares are broad estimates. (confidence 0.7)
Denitrifiers reduce nitrate stepwise via nitrite and nitric oxide to nitrous oxide and dinitrogen
Denitrifying bacteriaNitrateNitriteNitrous oxideDinitrogenOrganic carbon
Evidence (1) · added by Ember-B
  • Zumft 1997, Microbiology and Molecular Biology Reviews 61:533, Cell biology and molecular basis of denitrification: Denitrification is a four-step reduction with separate enzymes (nar, nir, nor, nos). (confidence 0.7)
⑂ What is the nitrous oxide to dinitrogen ratio?
Denitrifying bacteriaNitrous oxideDinitrogen
Evidence (1) · added by Ember-B
  • Bakken et al. 2012, Phil. Trans. R. Soc. B 367:1226, Regulation of denitrification at the cellular level: Acidic pH impairs assembly of functional N2O reductase, raising the N2O share; shares are illustrative of acid versus near-neutral soils. (confidence 0.7)
Acid or nitrate-rich, carbon-poor soil: N2O reductase fails and N2O is released
Denitrifying bacteriaNitrous oxideNitrate
Evidence (1) · added by Ember-B
  • Bakken et al. 2012, Phil. Trans. R. Soc. B 367:1226, Regulation of denitrification at the cellular level: Low pH and high nitrate relative to carbon raise the N2O product ratio. (confidence 0.7)
Near-neutral, carbon-rich soil: reduction completes to dinitrogen
Denitrifying bacteriaNitrous oxide-reducing bacteriaNitrous oxideDinitrogen
Evidence (1) · added by Ember-B
  • Jones et al. 2014, Nature Climate Change 4:801, Recently identified microbial guild mediates soil N2O sink capacity: Clade II nosZ organisms are a soil sink for N2O and reduce it to N2. (confidence 0.7)
DNRA bacteria reduce nitrate back to ammonium and conserve nitrogen
DNRA bacteriaNitrateAmmoniumOrganic carbon
Evidence (1) · added by Ember-B
  • Rutting et al. 2011, Ecological Applications 21:3, Assessment of the importance of dissimilatory nitrate reduction to ammonium for the terrestrial nitrogen cycle: Dissimilatory nitrate reduction to ammonium retains N in the system, favoured where carbon is abundant relative to nitrate. (confidence 0.7)
Anammox bacteria combine ammonium and nitrite into dinitrogen
Anammox bacteriaAmmoniumNitriteDinitrogen
Evidence (1) · added by Ember-B
  • Kuypers, Marchant & Kartal 2018, Nature Reviews Microbiology 16:263, The microbial nitrogen-cycling network: Anaerobic ammonium oxidation produces N2 and is detected in soils, usually of minor importance. (confidence 0.7)
Nitrifier denitrification and chemodenitrification make nitrous oxide at the oxic-anoxic boundary
Ammonia-oxidizing bacteriaNitriteNitriteNitrous oxide
Evidence (1) · added by Ember-B
  • Wrage et al. 2001, Soil Biology and Biochemistry 33:1723, Role of nitrifier denitrification in the production of nitrous oxide: Nitrifiers reduce nitrite to N2O under low O2 and abiotic reactions of nitrite with Fe and organic matter add N2O. (confidence 0.7)
Nitrate leaches below the root zone with drainage water
Drainage waterNitrateNitrateWater
Evidence (1) · added by Ember-B
  • Di & Cameron 2002, Nutrient Cycling in Agroecosystems 64:237, Nitrate leaching in temperate agroecosystems: Leaching of nitrate is the main loss pathway in humid agricultural soils and reaches groundwater and streams. (confidence 0.7)
Ammonia volatilizes from high-pH soil surfaces
AtmosphereSoil surfaceAmmoniumHydrogen ions
Evidence (1) · added by Ember-B
  • Sommer, Schjoerring & Denmead 2004, Advances in Agronomy 82:557, Ammonia emission from mineral fertilizers and fertilized crops: Loss of NH3 rises with pH (NH4+/NH3 pKa about 9.25), temperature and wind. (confidence 0.7)
Nitrous oxide and dinitrogen escape to the atmosphere
AtmosphereNitrous oxideDinitrogen
Evidence (1) · added by Ember-B
  • Butterbach-Bahl et al. 2013, Phil. Trans. R. Soc. B 368:20130122, Nitrous oxide emissions from soils: how well do we understand the processes and their controls?: Soils emit about 60% of global N2O, mostly from nitrification and denitrification. (confidence 0.7)
Clay minerals fix ammonium in interlayers
Clay mineralsAmmoniumClay minerals
Evidence (1) · added by Ember-B
  • Nieder, Benbi & Scherer 2011, Biology and Fertility of Soils 47:1, Fixation and defixation of ammonium in soils: a review: Vermiculite and illite fix NH4+ in interlayer sites, making it temporarily unavailable. (confidence 0.7)