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Earth's Systems / Biological processes / Terrestrial ecosystem functioning / Living soil system / Roots and rhizosphere / Disease-suppressive soils and the rhizosphere cry for help

Disease-suppressive soils and the rhizosphere cry for help

How a root microbiome protects plants from soil-borne pathogens: infected plants recruit antagonists through exudates, Pseudomonas that make DAPG and siderophores suppress pathogens, resident microbes compete generally, and rhizobacteria prime plant defences.

Boundary: where this process starts

Starts with: Soil-borne pathogens (Fusarium oxysporum, Gaeumannomyces tritici, Rhizoctonia solani) infect roots

Boundary: where it ends

Ends after: Take-all decline: disease falls after a few seasons of wheat monoculture as DAPG producers build up; Pyoverdine siderophores sequester Iron, starving pathogens, especially in neutral to alkaline soil where Fe is scarce

PARTICIPANTSRESOURCESPlant rootsPathogenicfungiAntagonisticbacteriaRhizobacteriaPseudomonasfluorescensOtherparticipantsCarbonRoot exudatesIronRoot tissueOrganic acidsImpact -3 of 5. Click for details and evidence.Impact +2 of 5. Click for details and evidence.Resident communityImpact +3 of 5. Click for details and evidence.Infection changes exudationImpact +3 of 5. Click for details and evidence.Recruited consortium assemblImpact +3 of 5. Click for details and evidence.Producers of antibiotics enrImpact +3 of 5. Click for details and evidence.Consortium primes plant defeImpact -4 of 5. Click for details and evidence.↻ balances · strong · 0.5 DAPG producers supImpact +3 of 5. Click for details and evidence.Suppression builds with monoImpact +3 of 5. Click for details and evidence.Competition includes iron seImpact +4 of 5. Click for details and evidence.Disease suppressedImpact +3 of 5. Click for details and evidence.Pathogen iron-starvedImpact +3 of 5. Click for details and evidence.Plant primed for defenceSoil-borne pathogens (Fusarium oxysporum, Gaeumannomyces tritici, Rhizoctonia solani) infect roots: uses CarbonSoil-borne pathogens (Fusarium oxysporum, Gaeumannomyces tritici, Rhizoctonia solani) infect roots: uses up Root tissueuses upInfected plants change exudates (for example malic acid) that recruit antagonists such as Bacillus subtilis: the cry for help: makes Root exudatesmakesInfected plants change exudates (for example malic acid) that recruit antagonists such as Bacillus subtilis: the cry for help: makes Organic acidsmakesDisease-induced assembly: a consortium of Stenotrophomonas, Xanthomonas and Microbacterium is enriched in the rhizosphere after downy-mildew infection: uses Root exudatesPseudomonas fluorescens make 2,4-diacetylphloroglucinol (DAPG) that inhibits Gaeumannomyces; suppression needs about 10^5 DAPG-producing cfu per g root: uses CarbonTake-all decline: disease falls after a few seasons of wheat monoculture as DAPG producers build up: uses CarbonGeneral suppression: high microbial biomass and activity compete for carbon and Iron; pasteurized soil loses suppression: uses up Carbonuses upGeneral suppression: high microbial biomass and activity compete for carbon and Iron; pasteurized soil loses suppression: uses IronPyoverdine siderophores sequester Iron, starving pathogens, especially in neutral to alkaline soil where Fe is scarce: uses up Ironuses upconsumed by pathogengrowthCarbon: consumed by pathogen growthinfected by soilbornepathogensRoot tissue: infected by soilborne pathogenschanged to recruitantagonistsRoot exudates: changed to recruit antagonistsproduced to recruitantagonistsOrganic acids: produced to recruit antagonistsshape a rhizosphereconsortiumRoot exudates: shape a rhizosphere consortiumchannelled into DAPGproductionCarbon: channelled into DAPG productionchannelled intosuppressive producersCarbon: channelled into suppressive producerscompeted for by microbesCarbon: competed for by microbescontested by microbialcompetitorsIron: contested by microbial competitorssequestered, starvingpathogensIron: sequestered, starving pathogensStart:Disease-suppressivesoils and t…STARTStart: Disease-suppressive soils and the rhizosphere cry for helpEnd:Disease-suppressivesoils and t…ENDEnd: Disease-suppressive soils and the rhizosphere cry for helpSoil-borne pathogens(Fusarium oxysporum,Gaeumannomyces tritic…📄1Soil-borne pathogens (Fusarium oxysporum, Gaeumannomyces tritici, Rhizoctonia solani) infect rootsInfected plants changeexudates (for examplemalic acid) th…📄1Infected plants change exudates (for example malic acid) that recruit antagonists such as Bacillus subtilis: the cry for helpDisease-inducedassembly: a consortiumof Stenotrophomona…📄1Disease-induced assembly: a consortium of Stenotrophomonas, Xanthomonas and Microbacterium is enriched in the rhizosphere after downy-mildew infectionPseudomonas fluorescensmake2,4-diacetylphloroglu…📄1Pseudomonas fluorescens make 2,4-diacetylphloroglucinol (DAPG) that inhibits Gaeumannomyces; suppression needs about 10^5 DAPG-producing cfu per g rootTake-all decline:disease falls after afew seasons of whe…📄1Take-all decline: disease falls after a few seasons of wheat monoculture as DAPG producers build upGeneral suppression:high microbial biomassand activity compe…📄1General suppression: high microbial biomass and activity compete for carbon and Iron; pasteurized soil loses suppressionPyoverdine siderophoressequester Iron,starving pathogen…📄1Pyoverdine siderophores sequester Iron, starving pathogens, especially in neutral to alkaline soil where Fe is scarceInduced systemicresistance:rhizobacteria pri…📄1Induced systemic resistance: rhizobacteria prime plant defences through jasmonate and ethylene signalling without direct antagonism
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)
What am I looking at? The concepts on every map
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
One thing that happens in a process. Every step has at least one participant and carries evidence.
Decision fork
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
The support for a claim: a source and what it shows. Every step, line, change and vote needs it. Click any step or line to read its evidence.
Boundary
Where a process starts and where it ends. Every process, and every subprocess, has a start and an end.
Subprocess
A step that is itself a whole process, with its own boundary, steps and lines. Click a step marked ↘ to open it. Subprocesses nest as deep as the evidence goes.
Description
A plain-language summary of what a process is and what it covers.
Hypothesis
A proposed new connection between two parts of the map that nobody has linked. It carries a prediction, a way to test it, and a count of papers on each topic and on both. It is an unverified idea until someone tests it.

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.

Soil-borne pathogens (Fusarium oxysporum, Gaeumannomyces tritici, Rhizoctonia solani) infect roots
Pathogenic fungiPlant rootsRoot tissueCarbon
Evidence (1) · added by Ember
  • Mendes et al. 2011, Science 332:1097, Deciphering the rhizosphere microbiome for disease-suppressive bacteria: A Rhizoctonia-suppressive soil was dissected to identify the bacterial taxa that protect sugar beet. (confidence 0.7)
Infected plants change exudates (for example malic acid) that recruit antagonists such as Bacillus subtilis: the cry for help
Infected rootsBacillus subtilisOrganic acidsRoot exudates
Evidence (1) · added by Ember
  • Rudrappa, Czymmek, Pare & Bais 2008, Plant Physiology 148:1547, Root-secreted malic acid recruits beneficial soil bacteria: Arabidopsis infected by Pseudomonas syringae secreted malic acid that recruited Bacillus subtilis FB17 and protected leaves. (confidence 0.85)
Disease-induced assembly: a consortium of Stenotrophomonas, Xanthomonas and Microbacterium is enriched in the rhizosphere after downy-mildew infection
Arabidopsis rootsRhizobacteriaRoot exudates
Evidence (1) · added by Ember
  • Berendsen et al. 2018, ISME Journal 12:1496, Disease-induced assemblage of a plant-beneficial bacterial consortium: Infection enriched a three-member consortium that induced resistance and protected the next plant generation. (confidence 0.85)
Pseudomonas fluorescens make 2,4-diacetylphloroglucinol (DAPG) that inhibits Gaeumannomyces; suppression needs about 10^5 DAPG-producing cfu per g root
Pseudomonas fluorescensGaeumannomyces triticiCarbon
Evidence (1) · added by Ember
  • Raaijmakers & Weller 1998, Molecular Plant-Microbe Interactions 11:144, Natural plant protection by 2,4-diacetylphloroglucinol-producing Pseudomonas spp. in take-all decline: Take-all decline soils carried at least about 10^5 cfu DAPG producers per g wheat root. (confidence 0.8)
Take-all decline: disease falls after a few seasons of wheat monoculture as DAPG producers build up
WheatPseudomonas fluorescensCarbon
Evidence (1) · added by Ember
  • Weller et al. 2002, Annual Review of Phytopathology 40:309: Take-all decline arises with continued wheat monoculture and is transferable to conducive soil. (confidence 0.65)
General suppression: high microbial biomass and activity compete for carbon and Iron; pasteurized soil loses suppression
Resident soil microbesCarbonIron
Evidence (1) · added by Ember
  • Weller et al. 2002, Annual Review of Phytopathology 40:309: General suppression is lost on sterilization and scales with total microbial activity. (confidence 0.8)
Pyoverdine siderophores sequester Iron, starving pathogens, especially in neutral to alkaline soil where Fe is scarce
PseudomonasPathogenic fungiIronSiderophores
Evidence (1) · added by Ember
  • Kloepper, Leong, Teintze & Schroth 1980, Current Microbiology 4:317, Pseudomonas siderophores: a mechanism explaining disease-suppressive soils: Siderophore-producing pseudomonads reduced Fusarium wilt in soils; effect reversed with added iron. (confidence 0.75)
Induced systemic resistance: rhizobacteria prime plant defences through jasmonate and ethylene signalling without direct antagonism
RhizobacteriaPlant rootsJasmonateEthylene
Evidence (1) · added by Ember
  • Pieterse, Zamioudis, Berendsen, Weller, Van Wees & Bakker 2014, Annual Review of Phytopathology 52:347, Induced systemic resistance by beneficial microbes: Beneficial rhizobacteria prime the whole plant for faster defence activation. (confidence 0.85)