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Earth's Systems / Biological processes / Terrestrial ecosystem functioning / Living soil system / Humification and SOM stabilization / Microbial necromass pathway to stable organic matter

Microbial necromass pathway to stable organic matter

Dead microbial cells release labile cytoplasm while cell wall remnants such as chitin, peptidoglycan and melanin persist. Necromass is recycled, sorbed to minerals, entombed in aggregates, or lost as carbon dioxide and dissolved carbon.

Boundary: where this process starts

Starts with: Cells die by starvation, viral lysis, grazing and drying-rewetting shock

Boundary: where it ends

Ends after: Sorption of necromass compounds to clay and Fe/Al oxides; Dissolved necromass leaches or respired during decay

PARTICIPANTSRESOURCESMicrobialnecromassSoil microbesMineralsurfacesBacteriophagesIron oxidesOtherparticipantsCarbonNitrogenChitinCarbon dioxideIron oxidesImpact +3 of 5. Click for details and evidence.DeathImpact +3 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.45% reuseImpact +4 of 5. Click for details and evidence.30% sorptionImpact +3 of 5. Click for details and evidence.13% entombmentImpact -2 of 5. Click for details and evidence.12% lossImpact +3 of 5. Click for details and evidence.↻ reinforces · moderate · 0.4 Recycled carboImpact +3 of 5. Click for details and evidence.Impact +2 of 5. Click for details and evidence.Impact +2 of 5. Click for details and evidence.Cell wall chemistry sets decImpact 02 of 5. Click for details and evidence.Impact +1 of 5. Click for details and evidence.Stable N supports growth onlImpact +4 of 5. Click for details and evidence.Mineral-stabilised carbonImpact -2 of 5. Click for details and evidence.Carbon lostImpact +3 of 5. Click for details and evidence.Impact +2 of 5. Click for details and evidence.Impact -3 of 5. Click for details and evidence.↻ balances · moderate · 0.25 As mineral surfCells die by starvation, viral lysis, grazing and drying-rewetting shock: makes CarbonmakesCells die by starvation, viral lysis, grazing and drying-rewetting shock: makes NitrogenmakesCytoplasm is released labile while cell wall remnants (peptidoglycan, chitin, melanin) resist decay: makes CarbonmakesCytoplasm is released labile while cell wall remnants (peptidoglycan, chitin, melanin) resist decay: makes NitrogenmakesCytoplasm is released labile while cell wall remnants (peptidoglycan, chitin, melanin) resist decay: uses ChitinNecromass fate: uses CarbonNecromass fate: uses NitrogenReuse by living microbes (necromass recycling): uses up Carbonuses upReuse by living microbes (necromass recycling): uses up Nitrogenuses upSorption of necromass compounds to clay and Fe/Al oxides: uses CarbonSorption of necromass compounds to clay and Fe/Al oxides: uses Iron oxidesEntombment in aggregates and as persistent fragments: uses CarbonDissolved necromass leaches or respired during decay: makes Carbon dioxidemakesFungal necromass (melanised, C:N about 10) decays more slowly than bacterial necromass in many soils: uses CarbonFungal necromass (melanised, C:N about 10) decays more slowly than bacterial necromass in many soils: uses ChitinNecromass nitrogen is conserved as organic N in stable matter: uses NitrogenCarbon use efficiency controls necromass production: uses CarbonCarbon use efficiency controls necromass production: uses Carbon dioxidereleased as cells dieCarbon: released as cells diereleased as cells dieNitrogen: released as cells diereleased as labilecytoplasmCarbon: released as labile cytoplasmreleased in labilecytoplasmNitrogen: released in labile cytoplasmresists decay as wallremnantChitin: resists decay as wall remnantfate determinespersistenceCarbon: fate determines persistencefate determinesavailabilityNitrogen: fate determines availabilityreused by livingmicrobesCarbon: reused by living microbesrecycled by livingmicrobesNitrogen: recycled by living microbessorbs onto mineralsurfacesCarbon: sorbs onto mineral surfacesbinds necromasscompoundsIron oxides: binds necromass compoundsentombed in aggregatesCarbon: entombed in aggregatesrespired during decayCarbon dioxide: respired during decaypersists longer infungal necromassCarbon: persists longer in fungal necromassdecays slowly asmelanised fragmentsChitin: decays slowly as melanised fragmentsconserved in stablematterNitrogen: conserved in stable mattersplit betweenrespiration and biomassCarbon: split between respiration and biomassreduced by higherefficiencyCarbon dioxide: reduced by higher efficiencyStart: Microbial cellsdieSTARTStart: Microbial cells dieEnd: Necromass carbonstored, recycled orlostENDEnd: Necromass carbon stored, recycled or lostCells die bystarvation, virallysis, grazing a…📄1Cells die by starvation, viral lysis, grazing and drying-rewetting shockCytoplasm is releasedlabile while cell wallremnan…📄1Cytoplasm is released labile while cell wall remnants (peptidoglycan, chitin, melanin) resist decayNecromass fate📄2Necromass fateReuse by livingmicrobes (necromassrecycling)📄1Reuse by living microbes (necromass recycling)Sorption of necromasscompounds to clay andFe/Al oxides📄1Sorption of necromass compounds to clay and Fe/Al oxidesEntombment inaggregates and aspersistent fragments📄1Entombment in aggregates and as persistent fragmentsDissolved necromassleaches or respiredduring decay📄1Dissolved necromass leaches or respired during decayFungal necromass(melanised, C:N about10) decays more slow…👍1📄1Fungal necromass (melanised, C:N about 10) decays more slowly than bacterial necromass in many soilsNecromass nitrogen isconserved as organic Nin stable matter📄1Necromass nitrogen is conserved as organic N in stable matterCarbon use efficiencycontrols necromassproduction↘📄1Carbon use efficiency controls necromass production
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.

Inside this process

Carbon use efficiency controls necromass production

Carbon use efficiency sets how much taken-up carbon becomes biomass and necromass rather than carbon dioxide. Substrate quality, nutrient limitation and temperature change it, with warming and acclimation shaping the soil carbon response.

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.

Cells die by starvation, viral lysis, grazing and drying-rewetting shock
Soil microbesBacteriophagesCarbonNitrogen
Evidence (1) · added by Ember
  • Kallenbach, Frey & Grandy 2016, Direct evidence for microbial-derived soil organic matter formation and its ecophysiological controls, Nature Communications 7:13630: Microbial turnover generates necromass continuously, with turnover of days to months (confidence 0.65)
Cytoplasm is released labile while cell wall remnants (peptidoglycan, chitin, melanin) resist decay
Microbial necromassChitinCarbonNitrogen
Evidence (1) · added by Ember
  • Miltner et al. 2012, SOM genesis: microbial biomass as a significant source, Biogeochemistry 111:41-55: Cell envelope residues accumulate and persist while protein and cytoplasm turn over fast (confidence 0.7)
⑂ Necromass fate
Microbial necromassSoil microbesMineral surfacesCarbonNitrogen
Evidence (2) · added by Ember
  • Kaestner et al. 2021, Microbial necromass in soils: linking microbes to soil processes and carbon turnover, Frontiers in Environmental Science 9:756378: Review of necromass pathways: reuse by living microbes, mineral association, occlusion; shares are estimates (confidence 0.45)
  • Cotrufo et al. 2013, The Microbial Efficiency-Matrix Stabilization (MEMS) framework integrates plant litter decomposition with soil organic matter stabilization, Global Change Biology 19:988-995: MEMS framework: labile microbial products form mineral-associated matter efficiently (confidence 0.65)
Reuse by living microbes (necromass recycling)
Soil microbesCarbonNitrogen
Evidence (1) · added by Ember
  • Kaestner et al. 2021, Microbial necromass in soils: linking microbes to soil processes and carbon turnover, Frontiers in Environmental Science 9:756378: A large part of necromass is recycled in the microbial food web (confidence 0.6)
Sorption of necromass compounds to clay and Fe/Al oxides
Mineral surfacesIron oxidesClay mineralsCarbonIron oxidesClay minerals
Evidence (1) · added by Ember
  • Kallenbach, Frey & Grandy 2016, Direct evidence for microbial-derived soil organic matter formation and its ecophysiological controls, Nature Communications 7:13630: Microbial-derived compounds were preferentially retained in mineral-associated fractions (confidence 0.75)
Entombment in aggregates and as persistent fragments
Soil aggregatesMicrobial necromassCarbon
Evidence (1) · added by Ember
  • Kaestner et al. 2021, Microbial necromass in soils: linking microbes to soil processes and carbon turnover, Frontiers in Environmental Science 9:756378: Necromass in aggregates and particles persists as an entombing effect (confidence 0.6)
Dissolved necromass leaches or respired during decay
Drainage waterDecomposersDissolved organic carbonCarbon dioxide
Evidence (1) · added by Ember
  • Kaestner et al. 2021, Microbial necromass in soils: linking microbes to soil processes and carbon turnover, Frontiers in Environmental Science 9:756378: Not all necromass is stabilized; some is respired or exported as DOC (confidence 0.55)
Fungal necromass (melanised, C:N about 10) decays more slowly than bacterial necromass in many soils
Fungal hyphaeSoil bacteriaChitinCarbon
Evidence (1) · added by Ember
  • Fernandez, Langley, Chapman, McCormack & Koide 2016, The decomposition of ectomycorrhizal fungal necromass, Soil Biol Biochem 93:38-49: Melanin and cell wall chemistry slow decomposition of ectomycorrhizal fungal necromass (confidence 0.75)
Necromass nitrogen is conserved as organic N in stable matter
Microbial necromassNitrogen
Evidence (1) · added by Ember
  • Miltner et al. 2012, SOM genesis: microbial biomass as a significant source, Biogeochemistry 111:41-55: Necromass is rich in N, amino sugars and amino acids, and drives stable organic N (confidence 0.6)
↘ Carbon use efficiency controls necromass production
Soil microbesTemperatureCarbonCarbon 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: Reviews stoichiometric and temperature controls on carbon use efficiency (confidence 0.85)