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Resource: used or used up in processesCarbon
Appears in 76 processs and 320 steps. Everything below is linked: open a process to see it in context.
Top processes
Bacteria and archaea
15 stepsRoots and rhizosphere
13 stepsLiving soil system
12 steps- Biological coupling: organic matter and soil food web
- Roots and rhizosphere
- Mycorrhizal fungi network
- and 9 more in this process
Mycorrhizal fungi network
12 stepsSoil food web energy transfer
12 stepsShow 70 more processes
- Only about 0.1-2% of cells in bulk soil are active at a given time, with a much higher active share near roots and fresh substrate
- Cell response to starvation or drying: sporulate, enter reversible non-spore dormancy, or die
- Sporulation (Bacillus, Clostridium, many Actinobacteria): endospores resist heat, UV and desiccation and survive for decades
- and 7 more in this process
- Dormant spore germinates in a wet, nutrient-rich pulse and sends out a germ tube
- Vegetative mycelium grows by tip extension and branching, penetrating particles and secreting hydrolases (chitinase, cellulase, xylanase)
- Resource depletion sensed: substrate mycelium partly lyses and the colony switches to aerial hyphae
- and 4 more in this process
- Organic carbon on mineral surfaces clusters near a monolayer-equivalent loading of 0.5-1.0 mg C per m2
- In acidic humid soils reactive Fe and Al phases (short-range-order oxides, Al-humus complexes) dominate retention by ligand exchange, and radiocarbon turnover times correlate with their content
- In neutral to alkaline soils exchangeable calcium and clay matter more than clay content alone, while reactive Al and Fe explain most variation in acidic soils
- and 4 more in this process
- Fate of gross primary production
- Net primary production builds biomass
- Fate of net primary production
- and 3 more in this process
Organic matter decomposition
6 stepsOcclusion in aggregates
6 steps- Passive efflux of sugars and amino acids down a concentration gradient of roughly 1000:1 from cytosol to soil solution
- Signalling compounds released: flavonoids, strigolactones, benzoxazinoids, coumarins
- Exudate compounds enter soil solution with half-lives of minutes to hours
- and 3 more in this process
- Soil holds roughly 10^7-10^10 virus-like particles per gram, often one to ten per bacterial cell
- Phage infection mode (estimate: more lysogeny than lysis in dry, nutrient-poor soil; range 30-70% lytic)
- Lytic phage adsorbs, replicates and bursts the host (burst size about 10-100 virions)
- and 3 more in this process
- 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
- Starvation and drying drive cells into dormancy: spores, fewer ribosomes, smaller cells and osmolyte accumulation
- Dormant cells cut maintenance metabolism to orders of magnitude below growth rates
- and 3 more in this process
Saprotrophic fungi
5 steps- Bacterial feeders (Rhabditidae, Cephalobidae) are fast-breeding opportunists (c-p 1-2) that boom after a bacterial flush
- Fungal feeders pierce hyphae with a stylet (Aphelenchoides, Tylenchidae) and increase under fungal-dominated decomposition
- Omnivore and predatory nematodes (Dorylaimida, Mononchida; c-p 4-5) breed slowly and are the first lost under disturbance
- and 2 more in this process
- Lloyd-Taylor function: respiration proportional to exp[309/(T-227)] gives Q10 about 3.3 near 0-10 C, 2.3 near 10-20 C and 1.9 near 20-30 C
- Warm soil speeds decomposition and nitrogen mineralisation and extends root and microbial activity
- Warming-driven soil carbon loss is estimated at about 55 Pg C by 2050 in the top metre
- and 2 more in this process
- Nitrogenase (Mo-Fe protein) reduces N2 using 16 ATP and 8 electrons per N2, with 1 H2 co-produced
- Nodule: leghemoglobin buffers free oxygen near 10-50 nM while supplying respiring bacteroids
- Free-living protection: Azotobacter respiratory protection, anaerobic microsites, or conformational shielding
- and 1 more in this process
- Lytic cycle: phage takes over the host, replicates and bursts the cell, with a burst of tens to hundreds of particles
- Phage-encoded auxiliary metabolic genes (glycoside hydrolases and others) rewire host carbon metabolism during infection
- Viral shunt: lysate (labile carbon, amino acids, nucleotides, ammonium) goes back to the dissolved pool instead of up the grazer food web
- and 1 more in this process
- Nitrogenase reduces Dinitrogen to Ammonia at about 16 ATP per N2 (N2 + 8 H+ + 8 e- + 16 ATP gives 2 NH3 + H2)
- Free-living heterotrophic fixers add only about 1-5 kg N per ha per year in most ecosystems
- Bacteroids assimilate ammonia by GS-GOGAT and the plant exports it as amides or ureides (asparagine; allantoin and allantoic acid in soybean)
- and 1 more in this process
- Soil-borne pathogens (Fusarium oxysporum, Gaeumannomyces tritici, Rhizoctonia solani) infect roots
- Pseudomonas fluorescens make 2,4-diacetylphloroglucinol (DAPG) that inhibits Gaeumannomyces; suppression needs about 10^5 DAPG-producing cfu per g root
- Take-all decline: disease falls after a few seasons of wheat monoculture as DAPG producers build up
- and 1 more in this process
- Cord-forming basidiomycetes (Phanerochaete velutina, Hypholoma fasciculare) explore soil as fans of fine hyphae from a resource base
- Cords and rhizomorphs translocate carbon, nitrogen and phosphorus over decimetres to metres, driven by source-sink gradients
- Unused links are pruned and their contents recycled, concentrating flux on productive paths
- and 1 more in this process
- Hyphae of one fungal genet can connect the roots of different plants, forming a common mycorrhizal network
- Isotope labelling showed net carbon transfer from paper birch to Douglas-fir through ectomycorrhizal hyphae, but soil and other routes are hard to exclude
- Seedlings connected to mature trees survived or grew better in some field experiments
- and 1 more in this process
- Bdellovibrio enters the periplasm, forms a bdelloplast, grows as a filament and lyses the prey after about 3-4 h releasing several progeny
- Myxobacteria lyse prey outside the cell and take up the soluble products
- Starved Myxococcus aggregate (about 10^5 cells) into fruiting bodies and form dormant myxospores
- and 1 more in this process
Soil fauna
3 stepsSoil sulfur cycling
3 steps- Soil CO2 efflux reaches about 98 Pg C per year globally, far above fossil emissions of about 9 Pg C
- Warming-driven CO2 release adds to atmospheric CO2; models suggest tens of Pg C lost by 2050 (central estimate about 55 Pg C with similar uncertainty)
- Labile carbon is used up, so respiration per unit soil falls after several years of warming (Harvard Forest soil warming, 5 degrees)
- Gut mucus supplies easily used carbon that activates dormant soil microbes (the Sleeping Beauty effect) while digestion is partly mutualistic
- Casts dry or age into compact, water-stable aggregates that physically protect organic carbon
- Non-native Lumbricus and Amynthas worms invading northern hardwood forests consume the forest floor and reduce its mass and thickness
- Fungi retain much of the mined nitrogen and pass only part to the tree when fungal N demand is high, aggravating tree N limitation
- Ecosystems dominated by ectomycorrhizal and ericoid plants store about 70% more soil carbon per unit nitrogen than arbuscular-dominated ones
- Carbon cost to the host: roughly 10-20% of net primary production goes to ectomycorrhizal fungi (estimate)
Biochar and charcoal in soil
2 steps- Colonizer-persister scale: c-p 1 enrichment opportunists reproduce within days; c-p 5 predators and omnivores have long generations and are disturbance sensitive
- Plant-parasitic nematodes (root-knot Meloidogyne, cyst Heterodera and Globodera) feed on roots; root-knot nematodes induce giant cells that act as nutrient sinks
Decomposition
2 stepsOften found with
Nitrogen 86Soil microbes 56Soil organic matter 33Plant roots 29Soil organic matter 25Soil bacteria 24Water 23Phosphorus 22Carbon dioxide 22Plants 20Decomposers 18Mycorrhizal fungi 17
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