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Earth's Systems / Biological processes / Terrestrial ecosystem functioning / Living soil system / Bacteria and archaea / Viral shunt: phage lysis recycles bacterial carbon and nitrogen

Viral shunt: phage lysis recycles bacterial carbon and nitrogen

How bacteriophages kill soil bacteria and release their cell contents as dissolved organic matter that other microbes re-use. Includes the lytic versus lysogenic choice, viral genes that boost host metabolism, and the density-dependent control of dominant strains.

Boundary: where this process starts

Starts with: Soil holds roughly 10^7-10^10 virus-like particles per gram, often one to ten per bacterial cell

Boundary: where it ends

Ends after: Surviving microbes take up the lysate and mineralize part of it; the rest sorbs to minerals or becomes necromass (the viral shunt)

PARTICIPANTSRESOURCESBacteriophagesSoil bacteriaDormant hostsLytic phageActive bacteriaOtherparticipantsCarbonNitrogenDissolvedorganic carbonPolysaccharidesAmmoniumImpact +3 of 5. Click for details and evidence.Impact +3 of 5. Click for details and evidence.Host state decides infectionImpact -3 of 5. Click for details and evidence.40% lytic infection of activImpact 02 of 5. Click for details and evidence.60% lysogeny in slow or dormImpact -2 of 5. Click for details and evidence.Stress induces lysis of a smImpact +2 of 5. Click for details and evidence.Prophage genes are expressedImpact -4 of 5. Click for details and evidence.Burst releases cell contentsImpact +1 of 5. Click for details and evidence.Boosted degradation adds to Impact +4 of 5. Click for details and evidence.Lysate is re-usedImpact -3 of 5. Click for details and evidence.Lysis cuts the dominant straImpact +3 of 5. Click for details and evidence.Growth on lysate rebuilds hoImpact +3 of 5. Click for details and evidence.↻ balances · moderate · 0.3 Higher density rImpact +4 of 5. Click for details and evidence.Nutrients recycledSoil holds roughly 10^7-10^10 virus-like particles per gram, often one to ten per bacterial cell: uses CarbonPhage infection mode (estimate: more lysogeny than lysis in dry, nutrient-poor soil; range 30-70% lytic): uses CarbonLytic phage adsorbs, replicates and bursts the host (burst size about 10-100 virions): uses up Carbonuses upLytic phage adsorbs, replicates and bursts the host (burst size about 10-100 virions): uses up Nitrogenuses upLysogenic phage integrates as prophage; drought, nutrient pulses or other stress can induce lysis: uses CarbonLysis releases cytoplasm, rich in labile carbon and nitrogen (cell C:N about 4-6), as Dissolved organic carbon: makes NitrogenmakesLysis releases cytoplasm, rich in labile carbon and nitrogen (cell C:N about 4-6), as Dissolved organic carbon: makes Dissolved organic carbonmakesViral auxiliary metabolic genes (for example glycoside hydrolases) may boost host carbon degradation: uses up Carbonuses upViral auxiliary metabolic genes (for example glycoside hydrolases) may boost host carbon degradation: uses up Polysaccharidesuses upSurviving microbes take up the lysate and mineralize part of it; the rest sorbs to minerals or becomes necromass (the viral shunt): uses up Dissolved organic carbonuses upSurviving microbes take up the lysate and mineralize part of it; the rest sorbs to minerals or becomes necromass (the viral shunt): makes AmmoniummakesHost density of the dominant strain rises on recycled nutrients and invites more infection (kill the winner): uses Carbonheld as virus-likeparticlesCarbon: held as virus-like particlespartitioned betweenlysis and lysogenyCarbon: partitioned between lysis and lysogenyburst releases cellcarbonCarbon: burst releases cell carbonburst releases cellnitrogenNitrogen: burst releases cell nitrogenheld in lysogenicprophageCarbon: held in lysogenic prophagereleased from burstcellsNitrogen: released from burst cellsreleased from burstcellsDissolved organic carbon: released from burst cellsdegraded by phage geneproductsCarbon: degraded by phage gene productsdegraded by phageenzymesPolysaccharides: degraded by phage enzymestaken up by survivingmicrobesDissolved organic carbon: taken up by surviving microbesreleased bymineralisationAmmonium: released by mineralisationrecycled to dominanthostCarbon: recycled to dominant hostStart: Viral shunt:phage lysis recyclesbacterial carbon a…STARTStart: Viral shunt: phage lysis recycles bacterial carbon and nitrogenEnd: Viral shunt: phagelysis recyclesbacterial carbon a…ENDEnd: Viral shunt: phage lysis recycles bacterial carbon and nitrogenSoil holds roughly10^7-10^10 virus-likeparticles per gra…📄1Soil holds roughly 10^7-10^10 virus-like particles per gram, often one to ten per bacterial cellPhage infection mode(estimate: morelysogeny than lysis …📄1Phage infection mode (estimate: more lysogeny than lysis in dry, nutrient-poor soil; range 30-70% lytic)Lytic phage adsorbs,replicates and burststhe host (burst si…📄1Lytic phage adsorbs, replicates and bursts the host (burst size about 10-100 virions)Lysogenic phageintegrates as prophage;drought, nutrie…📄1Lysogenic phage integrates as prophage; drought, nutrient pulses or other stress can induce lysisLysis releasescytoplasm, rich inlabile carbon a…📄1Lysis releases cytoplasm, rich in labile carbon and nitrogen (cell C:N about 4-6), as Dissolved organic carbonViral auxiliarymetabolic genes (forexample glycosi…👍1📄1Viral auxiliary metabolic genes (for example glycoside hydrolases) may boost host carbon degradationSurviving microbes takeup the lysate andmineralize part of i…📄1Surviving microbes take up the lysate and mineralize part of it; the rest sorbs to minerals or becomes necromass (the viral shunt)Host density of thedominant strain riseson recycled nutrien…📄1Host density of the dominant strain rises on recycled nutrients and invites more infection (kill the winner)
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 holds roughly 10^7-10^10 virus-like particles per gram, often one to ten per bacterial cell
BacteriophagesSoil bacteriaCarbon
Evidence (1) · added by Ember
  • Williamson, Radosevich & Wommack 2017, Annual Review of Virology 4:201, Viruses in soil ecosystems: an unknown quantity within an unexplored territory: Soil viral abundance ranges about 10^7-10^10 per g dry soil with virus-to-bacteria ratios of order 1-10. (confidence 0.65)
⑂ Phage infection mode (estimate: more lysogeny than lysis in dry, nutrient-poor soil; range 30-70% lytic)
BacteriophagesDormant hostsCarbon
Evidence (1) · added by Ember
  • Williamson, Radosevich & Wommack 2017, Annual Review of Virology 4:201: Lysogeny is common in soil bacteria and appears favoured when hosts are slow-growing; the lytic share is poorly constrained (estimate 30-70%, midpoint 50 shifted to 40 for dry soil). (confidence 0.4)
Lytic phage adsorbs, replicates and bursts the host (burst size about 10-100 virions)
Lytic phageActive bacteriaCarbonNitrogen
Evidence (1) · added by Ember
  • Kuzyakov & Mason-Jones 2018, Soil Biology and Biochemistry 127:305: Active host cells lyse, releasing tens of progeny virions per cell and the cell contents. (confidence 0.65)
Lysogenic phage integrates as prophage; drought, nutrient pulses or other stress can induce lysis
ProphageSoil bacteriaCarbon
Evidence (1) · added by Ember
  • Williamson, Radosevich & Wommack 2017, Annual Review of Virology 4:201: Prophage induction by environmental stress converts lysogens to lytic infections. (confidence 0.65)
Lysis releases cytoplasm, rich in labile carbon and nitrogen (cell C:N about 4-6), as Dissolved organic carbon
Lysed cellsDissolved organic carbonNitrogen
Evidence (1) · added by Ember
  • Kuzyakov & Mason-Jones 2018, Soil Biology and Biochemistry 127:305: Lysates are small, labile and N-rich compared with plant litter. (confidence 0.65)
Viral auxiliary metabolic genes (for example glycoside hydrolases) may boost host carbon degradation
BacteriophagesHost bacteriaCarbonPolysaccharides
Evidence (1) · added by Ember
  • Emerson et al. 2018, Nature Microbiology 3:870, Host-linked soil viral ecology along a permafrost thaw gradient: Soil viral genomes along a thaw gradient encoded glycoside hydrolases and other carbon-processing genes. (confidence 0.8)
Surviving microbes take up the lysate and mineralize part of it; the rest sorbs to minerals or becomes necromass (the viral shunt)
Soil microbesMineralsDissolved organic carbonAmmoniumCarbon dioxide
Evidence (1) · added by Ember
  • Wilhelm & Suttle 1999, BioScience 49:781, Viruses and nutrient cycles in the sea: Defines the viral shunt: lysis diverts biomass from higher trophic levels back into the dissolved pool for microbial re-use (marine concept applied to soil by Kuzyakov & Mason-Jones 2018). (confidence 0.65)
Host density of the dominant strain rises on recycled nutrients and invites more infection (kill the winner)
Dominant bacterial strainsBacteriophagesCarbon
Evidence (1) · added by Ember
  • Thingstad 2000, Limnology and Oceanography 45:1320, Elements of a theory for the mechanisms controlling abundance, diversity and biogeochemical role of lytic bacterial viruses in aquatic systems: Density-dependent infection caps the abundance of the best competitor and sustains diversity; soil evidence is limited. (confidence 0.55)