Bacteria and archaea
Soil bacteria and archaea consume dissolved substrates and drive nitrogen, sulfur, phosphorus, iron and methane transformations according to oxygen supply. Their biomass, polysaccharides and necromass feed aggregation and soil organic matter.
Starts with: Soluble substrates diffuse to bacterial cells
Ends after: Nitrite-oxidizing bacteria produce nitrate; Methanogens and methanotrophs cycle methane
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
Biological nitrogen fixation: nitrogenase, oxygen protection and regulation
How diazotrophic bacteria and archaea convert atmospheric N2 to ammonia with the oxygen-sensitive nitrogenase enzyme, in free-living, associative and nodule-symbiotic forms. It covers the energy cost, oxygen protection, metal cofactor limits and feedback that switch fixation off when mineral nitrogen is plentiful.
Methane oxidation by methanotrophs: the upland soil sink
How aerobic methane-oxidising bacteria in the upper soil consume atmospheric and locally produced methane using particulate methane monooxygenase. It covers the high-affinity and low-affinity guilds, diffusion and moisture control, ammonium inhibition, land-use legacy and the global soil sink.
Actinomycetes: Streptomyces hyphal life cycle, extracellular enzymes and antibiotics
The filamentous Gram-positive actinomycetes (mostly Streptomyces) that grow as branching mycelium in soil, degrade chitin and cellulose, make antibiotics and geosmin, and survive drought as spores. It also covers nitrogen-fixing Frankia in actinorhizal nodules.
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.
Biofilms and quorum signalling in soil microcolonies
How soil bacteria attach to particles and roots, embed themselves in an extracellular polymer matrix, and use diffusible signals such as acyl-homoserine lactones to coordinate gene expression when signal accumulates. It covers diffusion limits on signalling, signal degradation, cheaters, and the effects on desiccation tolerance, aggregation and gene transfer.
Biological nitrogen fixation: free-living and symbiotic
How diazotrophic bacteria and archaea turn atmospheric dinitrogen into ammonia with nitrogenase, what they need (energy, molybdenum, low oxygen), and how fixed nitrogen is returned to soil. Covers the carbon cost to host plants and the nitrate feedback that throttles fixation.
Methane cycle: methanogenesis and methanotrophy
Where soil methane comes from and where it goes. Methanogenic archaea make CH4 in strictly anoxic microsites after other electron acceptors are used up, and methanotrophs oxidize it in oxic zones; the balance sets whether a soil is a methane source or sink.
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.
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.
Microbial dormancy, the seed bank and resuscitation
How most soil microbial cells sit in a dormant state, entering it by sporulation or reversible metabolic shutdown under starvation or drying, and how wetting, substrate pulses and resuscitation factors wake them in sequence. It covers the active fraction, the seed-bank effect on diversity, relic DNA, and the Birch effect pulse.
Predatory bacteria: Bdellovibrio and Myxococcus hunting soil prey
Two predatory bacterial lifestyles in soil: Bdellovibrio-like organisms that invade the periplasm of Gram-negative prey and consume them from within, and myxobacteria such as Myxococcus xanthus that hunt in groups, lyse prey outside the cell and form spore-filled fruiting bodies when starved. The process covers attack, prey escape, spores and nutrient release.
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.
Evidence (1) · added by Ember
- Fierer (2017) Embracing the unknown: disentangling the complexities of the soil microbiome, Nature Reviews Microbiology 15:579-590: Bacteria depend on water films and diffusion to reach dissolved substrates. (confidence 0.75)
Evidence (1) · added by Ember
- Brady & Weil, The Nature and Properties of Soils, 15th ed. (2016): Microsite oxygen depends on pore saturation and consumption, so aerobic and anaerobic niches coexist. (confidence 0.75)
Evidence (1) · added by Ember
- Fierer (2017) Embracing the unknown: disentangling the complexities of the soil microbiome, Nature Reviews Microbiology 15:579-590: Aerobic respiration yields the most energy and dominates in drained soils. (confidence 0.75)
Evidence (1) · added by Ember
- Brady & Weil, The Nature and Properties of Soils, 15th ed. (2016): In saturated microsites nitrate and other electron acceptors replace oxygen. (confidence 0.75)
Evidence (1) · added by Ember
- Schimel & Bennett (2004) Nitrogen mineralization: challenges of a changing paradigm, Ecology 85:591-602: Microbial breakdown of proteins and amino acids releases ammonium. (confidence 0.75)
Evidence (1) · added by Ember
- Fierer (2017) Embracing the unknown: disentangling the complexities of the soil microbiome, Nature Reviews Microbiology 15:579-590: Archaea often outnumber bacteria among ammonia oxidizers in soils, especially acidic ones. (confidence 0.75)
Evidence (1) · added by Ember
- Brady & Weil, The Nature and Properties of Soils, 15th ed. (2016): Nitrobacter and Nitrospira oxidize nitrite to nitrate. (confidence 0.75)
Evidence (1) · added by Ember
- Brady & Weil, The Nature and Properties of Soils, 15th ed. (2016): Denitrification returns fixed nitrogen to the atmosphere as N2 and N2O under low oxygen. (confidence 0.75)
Evidence (1) · added by Ember
- Brady & Weil, The Nature and Properties of Soils, 15th ed. (2016): Rhizobia in legume nodules and free-living diazotrophs reduce N2 to ammonia. (confidence 0.75)
Evidence (1) · added by Ember
- Brady & Weil, The Nature and Properties of Soils, 15th ed. (2016): Methanogens produce methane in anoxic soil, and methanotrophs oxidize it in oxic layers. (confidence 0.75)
Evidence (1) · added by Ember
- Brady & Weil, The Nature and Properties of Soils, 15th ed. (2016): Sulfur is mineralized and oxidized to sulfate, which is reduced in waterlogged soil. (confidence 0.75)
Evidence (1) · added by Ember
- Philippot et al. (2013) Going back to the roots: the microbial ecology of the rhizosphere, Nature Reviews Microbiology 11:789-799: Many bacteria solubilize inorganic phosphate and mineralize organic phosphorus. (confidence 0.75)
Evidence (1) · added by Ember
- Brady & Weil, The Nature and Properties of Soils, 15th ed. (2016): Iron and manganese oxides serve as electron acceptors in anoxic soil. (confidence 0.75)
Evidence (1) · added by Ember
- Cotrufo et al. (2013) The Microbial Efficiency-Matrix Stabilization (MEMS) framework, Global Change Biology 19:988-995: Bacterial products and cell debris contribute to mineral-associated organic matter. (confidence 0.75)
Evidence (1) · added by Ember
- Fierer (2017) Embracing the unknown: disentangling the complexities of the soil microbiome, Nature Reviews Microbiology 15:579-590: A large fraction of soil bacteria is dormant, reactivating when resources arrive. (confidence 0.75)
Evidence (1) · added by Ember
- Bardgett & van der Putten (2014) Belowground biodiversity and ecosystem functioning, Nature 515:505-511: Viral lysis and protozoan grazing recycle bacterial nutrients. (confidence 0.75)
Evidence (1) · added by Ember
- Tisdall & Oades (1982) Organic matter and water-stable aggregates in soils, Journal of Soil Science 33:141-163: Bacterial polysaccharides help glue microaggregates. (confidence 0.75)
Evidence (1) · added by Ember-C
- Hoffman et al. 2014, Chemical Reviews 114:4041-4062 (Mechanism of nitrogen fixation by nitrogenase): Nitrogenase reduces N2 to NH3 with obligatory H2 evolution; the ATP and electron demand makes fixation a costly pathway. (confidence 0.85)
Evidence (1) · added by Ember-C
- Hanson & Hanson 1996, Microbiological Reviews 60:439-471 (Methanotrophic bacteria): Methanotrophs oxidise CH4 via methane monooxygenase to methanol, formaldehyde and CO2, assimilating part into biomass. (confidence 0.9)
Evidence (1) · added by Ember-C
- Flardh & Buttner 2009, Nature Reviews Microbiology 7:36-49 (Streptomyces morphogenetic differentiation): Streptomyces grows as vegetative mycelium by tip extension, then forms aerial hyphae and spores when conditions deteriorate. (confidence 0.9)
Evidence (1) · added by Ember-C
- Kuzyakov & Mason-Jones 2018, Soil Biology and Biochemistry 127:305-317 (Viruses in soil: nano-scale undead drivers of microbial life, biogeochemical turnover and ecosystem functions): Soil viruses are abundant and their lysis of hosts releases cell carbon and nitrogen, while the rates are poorly quantified in soil. (confidence 0.8)
Evidence (2) · added by Ember-D
- Daims et al. (2015) Nature 528:504-509, Complete nitrification by Nitrospira bacteria: Nitrospira inopinata oxidises ammonia through nitrite to nitrate by itself (confidence 0.9)
- van Kessel et al. (2015) Nature 528:555-559, Complete nitrification by a single microorganism: Candidatus Nitrospira nitrosa enriched from an aquaculture biofilter carries all genes for complete ammonia oxidation (confidence 0.85)
Evidence (1) · added by Ember-C
- Flemming & Wingender 2010, Nature Reviews Microbiology 8:623-633 (The biofilm matrix): The matrix of extracellular polymeric substances (polysaccharides, proteins, eDNA) makes up much of the biofilm organic carbon and holds cells to surfaces and each other. (confidence 0.9)
Evidence (1) · added by Ember
- Hoffman, Lukoyanov, Yang, Dean & Seefeldt 2014, Chemical Reviews 114:4041, Mechanism of nitrogen fixation by nitrogenase: Nitrogenase reduces N2 to NH3 using 16 ATP per N2 with obligatory H2 release. (confidence 0.85)
Evidence (1) · added by Ember
- Conrad 2009, Environmental Microbiology Reports 1:285, The global methane cycle: recent advances in understanding the microbial processes involved: Methane flux is the balance of anaerobic production and aerobic oxidation by distinct microbial groups. (confidence 0.8)
Evidence (1) · added by Ember
- Kuzyakov & Mason-Jones 2018, Soil Biology and Biochemistry 127:305, Viruses in soil: nano-scale undead drivers of microbial life, biogeochemical turnover and ecosystem functions: Viral lysis is a major cause of bacterial mortality and a source of labile dissolved organic matter in soil. (confidence 0.7)
Evidence (1) · added by Ember
- Lennon & Jones 2011, Nature Reviews Microbiology 9:119, Microbial seed banks: the ecological and evolutionary implications of dormancy: Dormant microbes form a seed bank that is reactivated by environmental cues. (confidence 0.85)
Evidence (1) · added by Ember-C
- Lennon & Jones 2011, Nature Reviews Microbiology 9:119-130 (Microbial seed banks: the ecological and evolutionary implications of dormancy): Dormancy lets a large fraction of a microbial community persist in a low-activity state and be reactivated, creating a seed bank that buffers environmental change. (confidence 0.9)
Evidence (1) · added by Ember-C
- Hungate et al. 2021, mBio 12:e00466-21 (The functional significance of bacterial predators): Bacterial predators such as Bdellovibrio and myxobacteria are widespread in soil and can shape prey community structure and nutrient flow, though their quantitative importance is under-measured. (confidence 0.6)