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Earth's Systems / Biological processes / Terrestrial ecosystem functioning / Living soil system / Bacteria and archaea / Microbial dormancy, the seed bank and reactivation after rewetting

Microbial dormancy, the seed bank and reactivation after rewetting

Most soil microbial cells are dormant at any moment. This subprocess traces how starvation and drying push cells into dormancy, how a seed bank preserves diversity, and how rewetting or substrate pulses wake cells and produce a respiration flush.

Boundary: where this process starts

Starts with: Only about 0.1-2% of soil microbial cells are active at one time in bulk soil; the share is higher near roots and fresh litter

Boundary: where it ends

Ends after: Reactivated cells grow on lysed-cell and exudate carbon until substrate is used up, which re-triggers dormancy

PARTICIPANTSRESOURCESSoil microbesDormant cellsSpore formersRare taxaRainCarbonWaterDissolvedorganic carbonCarbon dioxideImpact +3 of 5. Click for details and evidence.Impact +3 of 5. Click for details and evidence.Cells below threshold go dorImpact -3 of 5. Click for details and evidence.Metabolism is shut downImpact +3 of 5. Click for details and evidence.Persistence builds a seed baImpact +3 of 5. Click for details and evidence.Rewetting wakes the bankImpact +2 of 5. Click for details and evidence.Signals and substrates spreaImpact +3 of 5. Click for details and evidence.Reactivated cells growImpact -3 of 5. Click for details and evidence.↻ balances · moderate · 0.4 Substrate exhausImpact +3 of 5. Click for details and evidence.Active fraction and respiratOnly about 0.1-2% of soil microbial cells are active at one time in bulk soil; the share is higher near roots and fresh litter: uses CarbonStarvation and drying drive cells into dormancy: spores, fewer ribosomes, smaller cells and osmolyte accumulation: uses CarbonStarvation and drying drive cells into dormancy: spores, fewer ribosomes, smaller cells and osmolyte accumulation: uses WaterDormant cells cut maintenance metabolism to orders of magnitude below growth rates: uses CarbonThe dormant seed bank preserves rare taxa for years and lets the community rebound after disturbance: uses CarbonRewetting dry soil wakes cells within minutes to hours: Carbon dioxide pulse and Dissolved organic carbon flush (Birch effect): uses WaterRewetting dry soil wakes cells within minutes to hours: Carbon dioxide pulse and Dissolved organic carbon flush (Birch effect): makes Dissolved organic carbonmakesRewetting dry soil wakes cells within minutes to hours: Carbon dioxide pulse and Dissolved organic carbon flush (Birch effect): makes Carbon dioxidemakesResuscitation-promoting factors and substrate pulses wake neighbouring cells; waking is uneven, so community composition shifts after each pulse: uses CarbonReactivated cells grow on lysed-cell and exudate carbon until substrate is used up, which re-triggers dormancy: uses up Carbonuses upReactivated cells grow on lysed-cell and exudate carbon until substrate is used up, which re-triggers dormancy: uses up Dissolved organic carbonuses upmostly held in dormantcellsCarbon: mostly held in dormant cellsconserved in dormantcellsCarbon: conserved in dormant cellsdrying drives dormancyWater: drying drives dormancymetabolised at traceratesCarbon: metabolised at trace ratesstored in seed bankCarbon: stored in seed bankrewetting triggers pulseWater: rewetting triggers pulseflushed from dried soilDissolved organic carbon: flushed from dried soilpulse released onrewettingCarbon dioxide: pulse released on rewettingreleased by substratepulsesCarbon: released by substrate pulsesconsumed until exhaustedCarbon: consumed until exhaustedconsumed by reactivatedcellsDissolved organic carbon: consumed by reactivated cellsStart: Microbialdormancy, the seed bankand reactivation aft…STARTStart: Microbial dormancy, the seed bank and reactivation after rewettingEnd: Microbialdormancy, the seed bankand reactivation aft…ENDEnd: Microbial dormancy, the seed bank and reactivation after rewettingOnly about 0.1-2% ofsoil microbial cellsare active at one ti…📄1Only about 0.1-2% of soil microbial cells are active at one time in bulk soil; the share is higher near roots and fresh litterStarvation and dryingdrive cells intodormancy: spores, few…📄1Starvation and drying drive cells into dormancy: spores, fewer ribosomes, smaller cells and osmolyte accumulationDormant cells cutmaintenance metabolismto orders of magnitu…📄1Dormant cells cut maintenance metabolism to orders of magnitude below growth ratesThe dormant seed bankpreserves rare taxa foryears and lets t…📄1The dormant seed bank preserves rare taxa for years and lets the community rebound after disturbanceRewetting dry soilwakes cells withinminutes to hour…📄1Rewetting dry soil wakes cells within minutes to hours: Carbon dioxide pulse and Dissolved organic carbon flush (Birch effect)Resuscitation-promotingfactors and substratepulses wa…📄1Resuscitation-promoting factors and substrate pulses wake neighbouring cells; waking is uneven, so community composition shifts after each pulseReactivated cells growon lysed-cell andexudate carbon unt…📄1Reactivated cells grow on lysed-cell and exudate carbon until substrate is used up, which re-triggers dormancy
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.

Only about 0.1-2% of soil microbial cells are active at one time in bulk soil; the share is higher near roots and fresh litter
Soil microbesCarbon
Evidence (1) · added by Ember
  • Blagodatskaya & Kuzyakov 2013, Soil Biology and Biochemistry 67:192, Active microorganisms in soil: critical review of estimation criteria and approaches: Active microorganisms are roughly 0.1-2% of total cells in bulk soil, with larger shares in hotspots. (confidence 0.7)
Starvation and drying drive cells into dormancy: spores, fewer ribosomes, smaller cells and osmolyte accumulation
Soil microbesSpore formersWaterCarbon
Evidence (1) · added by Ember
  • Lennon & Jones 2011, Nature Reviews Microbiology 9:119: Sporulation and other dormancy states are triggered by starvation and desiccation cues. (confidence 0.85)
Dormant cells cut maintenance metabolism to orders of magnitude below growth rates
Dormant cellsCarbon
Evidence (1) · added by Ember
  • Price & Sowers 2004, PNAS 101:4631, Temperature dependence of metabolic rates for microbial growth, maintenance, and survival: Basal survival metabolic rates are many orders of magnitude lower than growth rates. (confidence 0.7)
The dormant seed bank preserves rare taxa for years and lets the community rebound after disturbance
Rare taxaDormant cellsCarbon
Evidence (1) · added by Ember
  • Lennon & Jones 2011, Nature Reviews Microbiology 9:119: Seed banks buffer populations against environmental change and maintain diversity. (confidence 0.8)
Rewetting dry soil wakes cells within minutes to hours: Carbon dioxide pulse and Dissolved organic carbon flush (Birch effect)
Soil microbesRainWaterCarbon dioxideDissolved organic carbon
Evidence (1) · added by Ember
  • Birch 1958, Plant and Soil 10:9, The effect of soil drying on humus decomposition and nitrogen availability: Drying then rewetting causes a flush of mineralization and CO2 well above steady rates. (confidence 0.8)
Resuscitation-promoting factors and substrate pulses wake neighbouring cells; waking is uneven, so community composition shifts after each pulse
Soil microbesRpf proteinsCarbon
Evidence (1) · added by Ember
  • Mukamolova, Kaprelyants, Young & Kell 1998, PNAS 95:8916, A bacterial cytokine: A secreted protein from Micrococcus luteus resuscitates dormant cells at picomolar concentrations. (confidence 0.75)
Reactivated cells grow on lysed-cell and exudate carbon until substrate is used up, which re-triggers dormancy
Soil microbesDissolved organic carbonCarbon
Evidence (1) · added by Ember
  • Blagodatskaya & Kuzyakov 2013, Soil Biology and Biochemistry 67:192: Substrate addition raises the active fraction from under 5% to tens of percent for hours to days, then it declines. (confidence 0.6)