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Earth's Systems / Biological processes / Terrestrial ecosystem functioning / Living soil system / Bacteria and archaea / Methane oxidation by methanotrophs: the upland soil sink

Methane oxidation by methanotrophs: the upland soil sink

How aerobic methane-oxidising bacteria in the upper soil consume atmospheric and locally produced methane using particulate methane monooxygenase. It covers the high-affinity and low-affinity guilds, diffusion and moisture control, ammonium inhibition, land-use legacy and the global soil sink.

Boundary: where this process starts

Starts with: Methane diffuses from the air or deeper soil into gas-filled pores toward oxidising cells

Boundary: where it ends

Ends after: Upland soils remove about 30-40 Tg CH4 per year, roughly 5% of the global methane sink

PARTICIPANTSRESOURCESMethanotrophicbacteriaMethylocystisUpland soilMethaneSoil poresOtherparticipantsMethaneOxygenPore spaceCarbonWaterImpact +3 of 5. Click for details and evidence.gas supplyImpact 02 of 5. Click for details and evidence.concentration setImpact +4 of 5. Click for details and evidence.70% atmospheric CH4Impact +4 of 5. Click for details and evidence.30% elevated CH4 hotspotImpact +4 of 5. Click for details and evidence.enzyme stepImpact +4 of 5. Click for details and evidence.enzyme stepImpact +3 of 5. Click for details and evidence.moisture sets gas diffusivitImpact -3 of 5. Click for details and evidence.ammonium competesImpact -3 of 5. Click for details and evidence.land-use legacyImpact +3 of 5. Click for details and evidence.rhizosphere oxidationImpact +3 of 5. Click for details and evidence.formaldehyde fateImpact +2 of 5. Click for details and evidence.growth on high CH4Impact +3 of 5. Click for details and evidence.↻ reinforces · moderate · 0.3 more oxidisingImpact 01 of 5. Click for details and evidence.summed across soilsImpact +3 of 5. Click for details and evidence.net CH4 removalMethane diffuses from the air or deeper soil into gas-filled pores toward oxidising cells: uses MethaneMethane diffuses from the air or deeper soil into gas-filled pores toward oxidising cells: uses Pore spaceMethane concentration regime selects the methanotroph guild at the microsite: uses MethaneHigh-affinity oxidisers (upland soil clusters, USC-alpha and USC-gamma, and a Methylocystis pMMO2) consume atmospheric methane: uses up Methaneuses upHigh-affinity oxidisers (upland soil clusters, USC-alpha and USC-gamma, and a Methylocystis pMMO2) consume atmospheric methane: uses up Oxygenuses upLow-affinity Type I and Type II methanotrophs oxidise elevated methane near wet soil, rice paddies and landfill covers: uses up Methaneuses upLow-affinity Type I and Type II methanotrophs oxidise elevated methane near wet soil, rice paddies and landfill covers: uses up Oxygenuses upParticulate methane monooxygenase (pMMO) oxidises CH4 to methanol using O2 and a reductant, then methanol dehydrogenase yields formaldehyde: uses up Methaneuses upParticulate methane monooxygenase (pMMO) oxidises CH4 to methanol using O2 and a reductant, then methanol dehydrogenase yields formaldehyde: uses up Oxygenuses upSoil moisture sets an optimum: dry soil limits cell activity, wet soil blocks diffusion: uses Pore spaceSoil moisture sets an optimum: dry soil limits cell activity, wet soil blocks diffusion: uses WaterAmmonium inhibits methane oxidation because the two substrates compete at the same enzyme family and nitrifiers co-oxidise: uses MethaneLand-use conversion from forest to arable cuts uptake, and recovery takes many decades: uses MethaneWetland and paddy roots and oxic surface layers oxidise a large part (often cited 20-90%) of methane produced below: uses up Methaneuses upWetland and paddy roots and oxic surface layers oxidise a large part (often cited 20-90%) of methane produced below: uses up Oxygenuses upOxidised carbon ends as CO2 (about 40-70% of the carbon) and as methanotroph biomass and EPS: uses up Methaneuses upOxidised carbon ends as CO2 (about 40-70% of the carbon) and as methanotroph biomass and EPS: makes CarbonmakesUpland soils remove about 30-40 Tg CH4 per year, roughly 5% of the global methane sink: uses up Methaneuses upAt methane hotspots, oxidation supports cell growth and more oxidising biomass until oxygen or methane runs short: uses up Methaneuses upAt methane hotspots, oxidation supports cell growth and more oxidising biomass until oxygen or methane runs short: uses up Oxygenuses upAt methane hotspots, oxidation supports cell growth and more oxidising biomass until oxygen or methane runs short: uses Carbondiffuses into gas-filledporesMethane: diffuses into gas-filled porestransports gas towardoxidisersPore space: transports gas toward oxidisersconcentration selectsguildMethane: concentration selects guildconsumed byhigh-affinity oxidisersMethane: consumed by high-affinity oxidisersused in oxidationOxygen: used in oxidationoxidised near wet soilsMethane: oxidised near wet soilsused in oxidationOxygen: used in oxidationhydroxylated to methanolMethane: hydroxylated to methanolco-substrate in pMMOreactionOxygen: co-substrate in pMMO reactiongas diffusion blockedwhen wetPore space: gas diffusion blocked when wetsets optimal activityWater: sets optimal activityoxidation suppressed bycompetitionMethane: oxidation suppressed by competitionuptake reduced byconversionMethane: uptake reduced by conversionoxidised in wetlandrootsMethane: oxidised in wetland rootssupplied by roots andsurfacesOxygen: supplied by roots and surfacesoxidised into carbonproductsMethane: oxidised into carbon productsincorporated intobiomass and EPSCarbon: incorporated into biomass and EPSremoved by upland soilsMethane: removed by upland soilsoxidised to supportgrowthMethane: oxidised to support growthlimits growth whendepletedOxygen: limits growth when depletedassimilated into biomassCarbon: assimilated into biomassStart: Methane reachesoxic soilSTARTStart: Methane reaches oxic soilEnd: Methane convertedto CO2 and biomassENDEnd: Methane converted to CO2 and biomassMethane diffuses fromthe air or deeper soilinto gas-filled por…📄1Methane diffuses from the air or deeper soil into gas-filled pores toward oxidising cellsMethane concentrationregime selects themethanotroph guild …📄1Methane concentration regime selects the methanotroph guild at the micrositeHigh-affinity oxidisers(upland soil clusters,USC-alpha a…📄1High-affinity oxidisers (upland soil clusters, USC-alpha and USC-gamma, and a Methylocystis pMMO2) consume atmospheric methaneLow-affinity Type I andType II methanotrophsoxidise elevat…📄1Low-affinity Type I and Type II methanotrophs oxidise elevated methane near wet soil, rice paddies and landfill coversParticulate methanemonooxygenase (pMMO)oxidises CH4 …📄1Particulate methane monooxygenase (pMMO) oxidises CH4 to methanol using O2 and a reductant, then methanol dehydrogenase yields formaldehydeSoil moisture sets anoptimum: dry soillimits cell activit…📄1Soil moisture sets an optimum: dry soil limits cell activity, wet soil blocks diffusionAmmonium inhibitsmethane oxidationbecause the t…📄1Ammonium inhibits methane oxidation because the two substrates compete at the same enzyme family and nitrifiers co-oxidiseLand-use conversionfrom forest to arablecuts uptake, a…📄1Land-use conversion from forest to arable cuts uptake, and recovery takes many decadesWetland and paddy rootsand oxic surface layersoxidise a large pa…📄1Wetland and paddy roots and oxic surface layers oxidise a large part (often cited 20-90%) of methane produced belowOxidised carbon ends asCO2 (about 40-70% ofthe carbon) and …📄1Oxidised carbon ends as CO2 (about 40-70% of the carbon) and as methanotroph biomass and EPSUpland soils removeabout 30-40 Tg CH4 peryear, roughly 5% of t…📄1Upland soils remove about 30-40 Tg CH4 per year, roughly 5% of the global methane sinkAt methane hotspots,oxidation supports cellgrowth and mo…📄1At methane hotspots, oxidation supports cell growth and more oxidising biomass until oxygen or methane runs short
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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Methane diffuses from the air or deeper soil into gas-filled pores toward oxidising cells
MethaneSoil poresAtmosphereMethanePore space
Evidence (1) · added by Ember-C
  • Smith et al. 2003, European Journal of Soil Science 54:779-791 (Exchange of greenhouse gases between soil and atmosphere: interactions of soil physical factors and biological processes): Gas diffusivity through air-filled pore space controls CH4 uptake rate in well-drained soils. (confidence 0.85)
⑂ Methane concentration regime selects the methanotroph guild at the microsite
Methanotrophic bacteriaMethane
Evidence (1) · added by Ember-C
  • Conrad 1996, Microbiological Reviews 60:609-640 (Soil microorganisms as controllers of atmospheric trace gases): Ambient-air soils oxidise CH4 at about 1.8-1.9 ppmv with kinetics distinct from soils exposed to high CH4. Shares are an estimate: most aerated upland area is at atmospheric concentration. (confidence 0.5)
High-affinity oxidisers (upland soil clusters, USC-alpha and USC-gamma, and a Methylocystis pMMO2) consume atmospheric methane
High-affinity methanotrophsMethylocystisMethaneOxygen
Evidence (1) · added by Ember-C
  • Baani & Liesack 2008, PNAS 105:10203-10208 (Two isozymes of particulate methane monooxygenase with different methane oxidation kinetics in Methylocystis sp. strain SC2): A second pMMO isozyme with a much lower Km allowed oxidation of CH4 at atmospheric mixing ratios. (confidence 0.85)
Low-affinity Type I and Type II methanotrophs oxidise elevated methane near wet soil, rice paddies and landfill covers
MethylococcaceaeMethylocystaceaeMethaneOxygen
Evidence (1) · added by Ember-C
  • Bender & Conrad 1992, FEMS Microbiology Ecology 101:261-270 (Kinetics of CH4 oxidation in oxic soils exposed to ambient air or high CH4 mixing ratios): Soils exposed to high CH4 develop a low-affinity oxidation with a Km and Vmax orders of magnitude higher than ambient-air soils. (confidence 0.8)
Particulate methane monooxygenase (pMMO) oxidises CH4 to methanol using O2 and a reductant, then methanol dehydrogenase yields formaldehyde
Methanotrophic bacteriapMMOMethaneOxygen
Evidence (1) · added by Ember-C
  • Hanson & Hanson 1996, Microbiological Reviews 60:439-471: pMMO is a copper-containing membrane enzyme; CH4 + O2 + 2 e- + 2 H+ -> CH3OH + H2O. (confidence 0.9)
Soil moisture sets an optimum: dry soil limits cell activity, wet soil blocks diffusion
Soil waterMethanotrophic bacteriaWaterPore space
Evidence (1) · added by Ember-C
  • Del Grosso et al. 2000, Global Biogeochemical Cycles 14:999-1019 (General CH4 oxidation model and comparisons of CH4 oxidation in natural and managed systems): Modelled CH4 oxidation depends on water-filled pore space through gas diffusivity and on soil water stress, peaking at intermediate moisture. (confidence 0.8)
Ammonium inhibits methane oxidation because the two substrates compete at the same enzyme family and nitrifiers co-oxidise
Methanotrophic bacteriaNitrifying bacteriaAmmoniumMethane
Evidence (1) · added by Ember-C
  • Bedard & Knowles 1989, Microbiological Reviews 53:68-84 (Physiology, biochemistry, and specific inhibitors of CH4, NH4+, and CO oxidation by methanotrophs and nitrifiers): Methane monooxygenase oxidises NH4+ and ammonia monooxygenase oxidises CH4, giving mutual competitive inhibition. (confidence 0.85)
Land-use conversion from forest to arable cuts uptake, and recovery takes many decades
Land managersMethanotrophic bacteriaMethane
Evidence (1) · added by Ember-C
  • Priemé et al. 1997, Soil Biology and Biochemistry 29:1269-1273 (Slow increase in rate of methane oxidation in soils with time following land use change from arable agriculture to woodland): Methane oxidation rose only slowly after arable fields were afforested, taking on the order of a century to approach old-forest rates. (confidence 0.75)
Wetland and paddy roots and oxic surface layers oxidise a large part (often cited 20-90%) of methane produced below
Methanotrophic bacteriaWetland plant rootsMethaneOxygen
Evidence (1) · added by Ember-C
  • Segers 1998, Biogeochemistry 41:23-51 (Methane production and methane consumption: a review of processes underlying wetland methane fluxes): Oxidation in the oxic surface and rhizosphere removes a variable but often large fraction of produced CH4 before it escapes. (confidence 0.7)
Oxidised carbon ends as CO2 (about 40-70% of the carbon) and as methanotroph biomass and EPS
Methanotrophic bacteriaMethaneCarbon dioxideCarbon
Evidence (1) · added by Ember-C
  • Hanson & Hanson 1996, Microbiological Reviews 60:439-471: Carbon conversion efficiency into biomass differs between RuMP (Type I) and serine-cycle (Type II) methanotrophs, the remainder being respired as CO2. (confidence 0.6)
Upland soils remove about 30-40 Tg CH4 per year, roughly 5% of the global methane sink
Upland soilsMethanotrophic bacteriaMethane
Evidence (1) · added by Ember-C
  • Saunois et al. 2020, Earth System Science Data 12:1561-1623 (The global methane budget 2000-2017): Soil uptake is estimated around 30-35 Tg CH4 per year with a wide range, a small term next to OH oxidation in the atmosphere. (confidence 0.8)
At methane hotspots, oxidation supports cell growth and more oxidising biomass until oxygen or methane runs short
Methanotrophic bacteriaMethaneOxygenCarbon
Evidence (1) · added by Ember-C
  • Conrad 1996, Microbiological Reviews 60:609-640: Low-affinity methanotroph populations grow when exposed to high CH4, raising the oxidation capacity of the soil. (confidence 0.65)