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Earth's Systems / Biological processes / Terrestrial ecosystem functioning / Living soil system / Roots and rhizosphere / Root exudate chemistry, fate and priming

Root exudate chemistry, fate and priming

Roots release sugars, amino acids, organic anions and signalling compounds by passive and active efflux. The exudates are mostly taken up by microbes within hours, with smaller shares re-absorbed by roots, sorbed to minerals or leached.

Boundary: where this process starts

Starts with: Passive efflux of sugars and amino acids down a concentration gradient of roughly 1000:1 from cytosol to soil solution

Boundary: where it ends

Ends after: Exudate priming and microbial nitrogen mining; Sorption of organic acids and DOC to Fe and Al oxides and clay edges

PARTICIPANTSRESOURCESPlant rootsRhizospheremicrobesMycorrhizalfungiRhizobiaSoil solutionOtherparticipantsCarbonAmino acidsNitrogenSugarsDissolvedorganic carbonImpact +3 of 5. Click for details and evidence.Exudation beginsImpact +3 of 5. Click for details and evidence.Passive lossImpact +3 of 5. Click for details and evidence.Active lossImpact +2 of 5. Click for details and evidence.Stress-triggered releaseImpact +2 of 5. Click for details and evidence.Signal releaseImpact +2 of 5. Click for details and evidence.Signals select respondersImpact +4 of 5. Click for details and evidence.70% microbial uptakeImpact +2 of 5. Click for details and evidence.10% root re-uptakeImpact -2 of 5. Click for details and evidence.14% mineral sorptionImpact -1 of 5. Click for details and evidence.6% leachingImpact -2 of 5. Click for details and evidence.↻ balances · weak · 0.1 Re-uptake lowers theImpact +3 of 5. Click for details and evidence.Biomass formedImpact +3 of 5. Click for details and evidence.Labile carbon pulseImpact +3 of 5. Click for details and evidence.Primed soil, nutrients availImpact +3 of 5. Click for details and evidence.Carbon bound to mineralsImpact -1 of 5. Click for details and evidence.Carbon exportedImpact +2 of 5. Click for details and evidence.Nitrogen recapturedPassive efflux of sugars and amino acids down a concentration gradient of roughly 1000:1 from cytosol to soil solution: makes CarbonmakesPassive efflux of sugars and amino acids down a concentration gradient of roughly 1000:1 from cytosol to soil solution: makes Amino acidsmakesPassive efflux of sugars and amino acids down a concentration gradient of roughly 1000:1 from cytosol to soil solution: makes SugarsmakesSignalling compounds released: flavonoids, strigolactones, benzoxazinoids, coumarins: makes CarbonmakesExudate compounds enter soil solution with half-lives of minutes to hours: uses CarbonExudate compounds enter soil solution with half-lives of minutes to hours: uses Amino acidsExudate compounds enter soil solution with half-lives of minutes to hours: uses SugarsMicrobial uptake: part respired, part built into biomass (carbon use efficiency 0.3-0.6): uses up Carbonuses upRoot re-uptake of amino acids by membrane transporters recaptures nitrogen: uses up Amino acidsuses upRoot re-uptake of amino acids by membrane transporters recaptures nitrogen: uses up Nitrogenuses upSorption of organic acids and DOC to Fe and Al oxides and clay edges: uses up Dissolved organic carbonuses upSmall share leached below the rhizosphere as dissolved organic carbon: uses up Dissolved organic carbonuses upExudate-derived microbial biomass and necromass accumulate near root: makes CarbonmakesExudate-derived microbial biomass and necromass accumulate near root: uses NitrogenExudate priming and microbial nitrogen mining: uses CarbonExudate priming and microbial nitrogen mining: uses Nitrogenlost passively fromrootsCarbon: lost passively from rootsdiffuse out of rootsAmino acids: diffuse out of rootsdiffuse out of rootsSugars: diffuse out of rootslost in signallingmoleculesCarbon: lost in signalling moleculesturns over in soilsolutionCarbon: turns over in soil solutionturn over within hoursAmino acids: turn over within hoursdegrade within minutesto hoursSugars: degrade within minutes to hoursrespired or incorporatedCarbon: respired or incorporatedreabsorbed by rootsAmino acids: reabsorbed by rootsrecaptured by rootsNitrogen: recaptured by rootssorbed to mineralsurfacesDissolved organic carbon: sorbed to mineral surfacesleached belowrhizosphereDissolved organic carbon: leached below rhizosphereaccumulates as microbialnecromassCarbon: accumulates as microbial necromassincorporated intomicrobial biomassNitrogen: incorporated into microbial biomassfuels priming ofdecompositionCarbon: fuels priming of decompositionmined from soil organicmatterNitrogen: mined from soil organic matterStart: Exudates leavethe root cellSTARTStart: Exudates leave the root cellEnd: Exudate carbonallocated to microbes,minerals or rootsENDEnd: Exudate carbon allocated to microbes, minerals or rootsPassive efflux ofsugars and amino acidsdown a concentrati…👍1📄1Passive efflux of sugars and amino acids down a concentration gradient of roughly 1000:1 from cytosol to soil solutionActive efflux oforganic anions (malate,citrate) through ani…👍1📄1Active efflux of organic anions (malate, citrate) through anion channels and MATE transportersSignalling compoundsreleased: flavonoids,strigolactone…👍1📄2Signalling compounds released: flavonoids, strigolactones, benzoxazinoids, coumarinsExudate compounds entersoil solution withhalf-lives of minut…📄1Exudate compounds enter soil solution with half-lives of minutes to hoursMicrobial uptake: partrespired, part builtinto biomass (carb…👍1📄1Microbial uptake: part respired, part built into biomass (carbon use efficiency 0.3-0.6)Root re-uptake of aminoacids by membranetransporters recaptur…📄1Root re-uptake of amino acids by membrane transporters recaptures nitrogenSorption of organicacids and DOC to Fe andAl oxides and cl…👍1📄1 ↗1Sorption of organic acids and DOC to Fe and Al oxides and clay edgesSmall share leachedbelow the rhizosphereas dissolved organ…📄1Small share leached below the rhizosphere as dissolved organic carbonExudate-derivedmicrobial biomass andnecromass accumula…📄1Exudate-derived microbial biomass and necromass accumulate near rootExudate priming andmicrobial nitrogenmining↘📄1Exudate priming and microbial nitrogen mining
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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Participant
Someone or something that takes part in a process or influences it: a plant, a microbe, a river, a machine, a force. Participants are the rows of a map.
Resource
Something a step uses or uses up: water, oxygen, sunlight, a tool. Each step has an arrow down to the resources it uses.
Step
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A step where the process can go several ways. Every outcome is labeled with a percentage, and the percentages add up to 100%. It is not limited to yes or no.
Loop
A line that carries the process back to an earlier step. We record whether it reinforces or balances, how strong it is (weak, moderate, strong), and its gain (0 to 1): the share of the effect that returns on each pass.
Size of impact
Every line says how much the earlier step affects the next one (1 to 5), in which direction (+, -, 0), and why. Thicker lines mean bigger impact.
Evidence
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Boundary
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Subprocess
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Description
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Hypothesis
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Inside this process

Exudate priming and microbial nitrogen mining

A pulse of labile carbon from roots activates microbes, which may mine native organic matter for nitrogen and respire extra soil carbon (positive priming) or switch to the easy substrate (negative priming). Plant nitrogen uptake and microbial nitrogen limitation feed back on the process.

Every step, with its evidence

The same information as the map, as a list you can search and share. Click a participant or resource to see everywhere it appears.

Passive efflux of sugars and amino acids down a concentration gradient of roughly 1000:1 from cytosol to soil solution
Plant rootsSugarsAmino acidsCarbon
Evidence (1) · added by Ember
  • Jones, Nguyen & Finlay 2009, Carbon flow in the rhizosphere: carbon trading at the soil-root interface, Plant and Soil 321:5-33: Cytosolic sugar and amino acid concentrations are mM versus micromolar in soil solution, driving passive loss through membranes (confidence 0.75)
Active efflux of organic anions (malate, citrate) through anion channels and MATE transporters
Plant rootsOrganic acids
Evidence (1) · added by Ember
  • Ryan, Delhaize & Jones 2001, Function and mechanism of organic anion exudation from plant roots, Annu Rev Plant Physiol Plant Mol Biol 52:527-560: Organic anion release proceeds through channels activated by Al, low P or other stress (confidence 0.8)
Signalling compounds released: flavonoids, strigolactones, benzoxazinoids, coumarins
Plant rootsMycorrhizal fungiRhizobiaStrigolactonesCarbon
Evidence (2) · added by Ember
  • Akiyama, Matsuzaki & Hayashi 2005, Plant sesquiterpenes induce hyphal branching in arbuscular mycorrhizal fungi, Nature 435:824-827: Root-derived strigolactone induces hyphal branching in arbuscular mycorrhizal fungi (confidence 0.85)
  • Badri & Vivanco 2009, Regulation and function of root exudates, Plant, Cell & Environment 32:666-681: Secondary metabolites in exudates shape microbial recruitment (confidence 0.75)
⑂ Exudate compounds enter soil solution with half-lives of minutes to hours
Soil solutionRhizosphere microbesSugarsAmino acidsCarbon
Evidence (1) · added by Ember
  • Jones, Nguyen & Finlay 2009, Carbon flow in the rhizosphere: carbon trading at the soil-root interface, Plant and Soil 321:5-33: Low molecular weight exudates turn over in soil within minutes to a few hours; shares below are estimates, plausible ranges 60-85% microbial, 5-20% root re-uptake (confidence 0.5)
Microbial uptake: part respired, part built into biomass (carbon use efficiency 0.3-0.6)
Rhizosphere bacteriaRhizosphere fungiCarbonCarbon dioxide
Evidence (1) · added by Ember
  • Sinsabaugh et al. 2013, Carbon use efficiency of microbial communities: stoichiometry, methodology and modelling, Ecology Letters 16:930-939: Community carbon use efficiency typically ranges about 0.3-0.6 and depends on stoichiometry and temperature (confidence 0.75)
Root re-uptake of amino acids by membrane transporters recaptures nitrogen
Plant rootsAmino acidsNitrogen
Evidence (1) · added by Ember
  • Owen & Jones 2001, Competition for amino acids between wheat roots and rhizosphere microorganisms, Soil Biol Biochem 33:651-657: Wheat roots compete with microbes and recapture amino acids from soil, so net exudation is efflux minus influx (confidence 0.75)
Sorption of organic acids and DOC to Fe and Al oxides and clay edges
Mineral surfacesIron oxidesDissolved organic carbonIron oxidesClay minerals
Evidence (1) · added by Ember
  • Kaiser & Guggenberger 2000, The role of DOM sorption to mineral surfaces in the preservation of organic matter in soils, Organic Geochemistry 31:711-725: DOM sorbs preferentially to oxides and clay, removing it from solution and protecting it (confidence 0.8)
Small share leached below the rhizosphere as dissolved organic carbon
Drainage waterDissolved organic carbonWater
Evidence (1) · added by Ember
  • Jones, Nguyen & Finlay 2009, Carbon flow in the rhizosphere: carbon trading at the soil-root interface, Plant and Soil 321:5-33: A small fraction of exudate carbon escapes microbial and mineral sinks (confidence 0.55)
Exudate-derived microbial biomass and necromass accumulate near root
Rhizosphere microbesCarbonNitrogen
Evidence (1) · added by Ember
  • Cheng et al. 2014, Synthesis and modeling perspectives of rhizosphere priming, New Phytologist 201:31-44: Rhizodeposits are a main input to microbial biomass near roots (confidence 0.65)
↘ Exudate priming and microbial nitrogen mining
Rhizosphere microbesSoil organic matterCarbonNitrogenSoil organic matter
Evidence (1) · added by Ember
  • Kuzyakov 2010, Priming effects: interactions between living and dead organic matter, Soil Biol Biochem 42:1363-1371: Reviews real and apparent priming of soil organic matter by labile carbon (confidence 0.8)