Earth's Systems / Biological processes / Terrestrial ecosystem functioning / Living soil system / Bacteria and archaea / Soil viruses and bacteriophages: lysis, lysogeny and the viral shunt
Soil viruses and bacteriophages: lysis, lysogeny and the viral shunt
How bacteriophages and other soil viruses infect bacterial and archaeal hosts, either killing them (lytic) or integrating as prophage (lysogenic), and how their lysate returns carbon and nitrogen to the microbial pool. It covers host resistance and coevolution, phage-encoded metabolic genes, and clay adsorption.
Boundary: where this process starts
Starts with: Virus-like particles number about 10^8-10^9 per gram dry soil, usually exceeding or matching bacterial counts
Boundary: where it ends
Ends after: Phages in microcosms raised soil nitrate and ammonium availability and reshaped the bacterial community; Resistant hosts (receptor mutation, CRISPR-Cas, restriction) survive, and phage evolve counter-infectivity in an arms race
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.
Virus-like particles number about 10^8-10^9 per gram dry soil, usually exceeding or matching bacterial counts
Evidence (1) · added by Ember-C
- Williamson, Radosevich & Wommack 2005, Applied and Environmental Microbiology 71:3119-3125 (Abundance and diversity of viruses in six Delaware soils): Direct counts of 1.5x10^8 to 1.1x10^9 virus-like particles per gram of dry soil across six soils, with virus-to-bacterium ratios near 1-8 in most. (confidence 0.8)
Contact is limited to connected water films; clay and organic matter adsorb phage and can protect or inactivate them
Evidence (1) · added by Ember-C
- Kimura, Jia, Nakayama & Asakawa 2008, Soil Science and Plant Nutrition 54:1-32 (Ecology of viruses in soils: past, present and future perspectives): Soil viruses adsorb to clay and organic colloids, which limits their transport to hosts and affects persistence of infectivity. (confidence 0.75)
⑂ Infection outcome: lytic cycle, lysogeny, or failed infection by host defence
Evidence (1) · added by Ember-C
- Williamson et al. 2007, Environmental Microbiology 9:2563-2574 (Incidence of lysogeny within temperate and extreme soil environments): Inducible prophage were detected in a large share of soil bacteria in many temperate and extreme soils, so both strategies occur. Shares below are estimates (about 35-65% lytic) and not measured in situ. (confidence 0.4)
Lytic cycle: phage takes over the host, replicates and bursts the cell, with a burst of tens to hundreds of particles
Evidence (1) · added by Ember-C
- Kuzyakov & Mason-Jones 2018, Soil Biology and Biochemistry 127:305-317: Lytic phage destroy host cells and release new virions together with the cell contents. (confidence 0.7)
Phage-encoded auxiliary metabolic genes (glycoside hydrolases and others) rewire host carbon metabolism during infection
Evidence (1) · added by Ember-C
- Emerson et al. 2018, Nature Microbiology 3:870-880 (Host-linked soil viral ecology along a permafrost thaw gradient): Of 1,907 viral populations recovered from Stordalen Mire, genes for carbon degradation such as glycoside hydrolases were found on soil viruses. (confidence 0.85)
Viral shunt: lysate (labile carbon, amino acids, nucleotides, ammonium) goes back to the dissolved pool instead of up the grazer food web
Evidence (1) · added by Ember-C
- Suttle 2007, Nature Reviews Microbiology 5:801-812 (Marine viruses, major leaders in the global ecosystem): The viral shunt concept: lysis converts particulate cell carbon and nutrients into dissolved pools, increasing respiration and nutrient recycling. Defined for the ocean, applied to soil by Kuzyakov & Mason-Jones 2018. (confidence 0.7)
Phages in microcosms raised soil nitrate and ammonium availability and reshaped the bacterial community
Evidence (1) · added by Ember-C
- Braga et al. 2020, Microbiome 8:52 (Impact of phages on soil bacterial communities and nitrogen availability under different assembly scenarios): Adding a phage mix to soil microcosms changed bacterial community composition and increased available nitrogen in some assembly scenarios. (confidence 0.75)
Lysogeny: prophage integrates in the host genome, giving immunity to related phage and passing to daughter cells
Evidence (1) · added by Ember-C
- Williamson et al. 2007, Environmental Microbiology 9:2563-2574: Inducible prophage detected in bacterial isolates from soil, indicating a stable lysogenic state. (confidence 0.75)
Stress (DNA damage, starvation, drying and rewetting) can induce prophage and switch cells to the lytic cycle
Evidence (1) · added by Ember-C
- Williamson et al. 2007, Environmental Microbiology 9:2563-2574: Mitomycin C and other induction agents triggered lytic release of prophage in soil bacterial assemblages. (confidence 0.7)
Resistant hosts (receptor mutation, CRISPR-Cas, restriction) survive, and phage evolve counter-infectivity in an arms race
Evidence (1) · added by Ember-C
- Gomez & Buckling 2011, Science 332:106-109 (Bacteria-phage antagonistic coevolution in soil): In soil, Pseudomonas fluorescens and phage showed antagonistic coevolution, with phages driving rapid bacterial resistance evolution and soil-specific limits on the dynamics. (confidence 0.8)
Dominant hosts are infected most often, which caps their abundance (kill-the-winner) and preserves diversity
Evidence (1) · added by Ember-C
- Thingstad 2000, Limnology and Oceanography 45:1320-1328 (Elements of a theory for the mechanisms controlling abundance, diversity, and biogeochemical role of lytic bacterial viruses in aquatic systems): Lytic viral attack scaled to host abundance suppresses the best competitors; mostly shown in aquatic systems and not proven for soil. (confidence 0.55)