Living soil system
The living soil: weathered minerals, organic matter, water, gases, roots and organisms interacting to build structure, cycle nutrients and carbon, and exchange water, gases, dust and solutes with the atmosphere, ocean and geology.
Starts with: Roots and rhizosphere
Ends after: End: Biological coupling: organic matter and soil food web; Carbon dioxide respired to air
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
Mineral weathering and parent material
How rock and parent material break down physically and chemically into soil minerals, releasing nutrients and forming secondary clays and oxides. Covers carbonic acid, hydrolysis, oxidation, organic acid attack and the rates that climate and biology set.
Cation exchange, pH and soil solution chemistry
How charged clay and humus surfaces hold exchangeable cations and set soil pH and solution chemistry. Covers acidification, buffering, base cation loss, aluminium, salinity and the nutrient availability that results.
Aggregate formation and pore structure
How roots, hyphae, polysaccharides, oxides and fauna bind particles into aggregates that give soil its pore network. Covers the hierarchy of micro- and macroaggregates and the forces that break them down.
Water infiltration, retention and movement
How rain enters, is held in and moves through soil. Covers infiltration versus runoff, retention by matric potential, drainage, root uptake and evaporation, and the wet, optimal and dry states.
Soil gas exchange and redox
How oxygen and carbon dioxide move through soil pores and how the supply of oxygen sets redox state. Covers aerobic and anaerobic respiration, denitrification, methane production and oxidation, and reduced metal chemistry.
Nutrient availability and leaching
How nutrients are held, released, taken up and lost in soil. Covers mineralisation, nitrification, phosphate sorption, immobilisation, nitrate leaching and denitrification, and atmospheric inputs.
Biological coupling: organic matter and soil food web
How plant litter, roots, fungi, bacteria and fauna together decompose organic matter and build stable soil carbon. Covers the soil food web and the disturbance forks that tip soil toward carbon gain or loss.
Roots and rhizosphere
Roots release carbon (exudates, mucilage, sloughed cells) into the soil around them, which feeds and selects microbes, shifts pH, mobilizes phosphorus and iron, and glues particles into the rhizosheath. Depletion zones and nutrient demand feed back on how much carbon the roots release.
Mycorrhizal fungi network
Mycorrhizal fungi colonize roots and extend hyphae into soil, trading phosphorus, nitrogen and water for plant carbon. The network also binds aggregates, links neighbouring plants and returns fungal necromass to soil carbon.
Saprotrophic fungi
Saprotrophic fungi colonize litter, secrete cellulases and ligninolytic enzymes, and move nutrients through mycelium. Their respiration, biomass turnover and grazing losses return carbon dioxide, nutrients and chitin-rich necromass to soil.
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.
Soil fauna
Soil fauna from earthworms and termites to mites, nematodes and protozoa fragment litter, graze microbes, burrow and excrete nutrients. They regulate decomposition, mineralize nitrogen and create pores and aggregates.
Soil food web energy transfer
Carbon and energy from litter and root exudates move through fungal, bacterial and root channels to grazers and predators, losing most energy to respiration at each step. Excretion and dead matter return nutrients and detritus to the soil.
Organic matter decomposition
Litter is leached, fragmented and depolymerized by extracellular enzymes, then microbes take up the products and split the carbon between respiration and growth. Litter quality, moisture, temperature and priming set the rate and the nitrogen outcome.
Humification and SOM stabilization
Decomposition products and microbial necromass are stabilized as particulate organic matter, mineral-associated organic matter, occluded carbon in aggregates or pyrogenic carbon. Destabilization by disturbance, warming and low oxygen can release this persistent carbon.
Soil nitrogen mineralization and immobilization turnover
Cycle of nitrogen between organic matter, microbial biomass and mineral ammonium. Decomposers mineralize organic N when the substrate is N-rich and immobilize mineral N when it is carbon-rich, setting what plants can take up.
Soil nitrification, nitrate reduction and nitrogen gas losses
Fate of ammonium and nitrate in soil: ammonia oxidizers and nitrite oxidizers make nitrate, which denitrifiers reduce to N2O and N2 in oxygen-poor microsites, and anammox and nitrifier denitrification add further gas losses.
Carbon priming, microbial efficiency and soil carbon sequestration
How labile carbon inputs prime decomposition of older organic matter, and how microbial carbon use efficiency decides whether carbon ends up as CO2 or stable microbial residues and mineral-bound carbon.
Pedogenesis and soil horizon development
Slow formation of soil horizons from parent material under climate, organisms, relief and time. Inputs, losses, transformations and translocations produce the O, A, E, B and C layers and pathways such as podzolization and lessivage.
Soil disturbance (fire, tillage, drought) and recovery
How fire, tillage and drought damage soil structure, organic matter and microbial communities, and the recovery steps that follow. Shows reinforcing degradation loops and the balancing processes that rebuild structure.
Soil-plant-water coupling and drought response
Coupling between soil water, roots and plant water status during drought. Covers soil drying, falling hydraulic conductivity at the root-soil interface, stomatal closure, hydraulic redistribution and recovery after rain.
Atmospheric dust deposition and loess as soil parent material
Wind-blown mineral dust from deserts and glacial outwash settles on land and ocean, adding fine parent material (loess), base cations and phosphorus to soils and iron to the sea.
Wind erosion and dust emission from dry soil
Dry, bare soil emits dust when wind exceeds a threshold, removing the finest and most nutrient-rich fraction and sending it to the atmosphere.
Soil-atmosphere exchange of methane and nitrous oxide
Aerated soils oxidise atmospheric methane while nitrification and denitrification in the same soils emit nitrous oxide, so soil is both a small sink and a large source of greenhouse gases.
Soil export to rivers and ocean: sediment, dissolved carbon and nutrients
Water leaving soil carries particles, dissolved organic carbon, nitrate and phosphorus to streams, rivers and the coast, linking the soil to the ocean carbon and nutrient cycles.
Permafrost thaw and release of frozen soil carbon
Frozen high-latitude soils hold a very large carbon stock; warming deepens the seasonally thawed layer, letting microbes decompose old organic matter and release carbon dioxide or methane.
Peat accumulation and wetland methane
Waterlogged organic soils accumulate peat because decomposition is slower than plant production, while anaerobic microbes in the same soils release methane to the atmosphere.
Soil inorganic carbon: pedogenic carbonate formation and dissolution
In dry soils dissolved calcium and bicarbonate precipitate as calcium carbonate at the depth of wetting, storing carbon for thousands of years until acidification or irrigation dissolves it.
Volcanic ash parent material, short-range-order minerals and Andosol carbon
Volcanic ash weathers quickly into poorly crystalline minerals such as allophane and ferrihydrite that bind organic matter and phosphate strongly, giving Andosols very high carbon storage and phosphorus fixation.
Soil thermal regime and heat flow
How net radiation becomes heat that conducts through soil, with water content, snow and depth controlling temperature, and how soil temperature in turn sets microbial rates and the stability of frozen carbon.
Biological soil crusts: cyanobacteria, lichens and mosses on dryland surfaces
Living surface skins of cyanobacteria, lichens and mosses in drylands. They bind particles, fix nitrogen and carbon, trap dust, change infiltration, and are slow to recover when trampled or burned.
Wind erosion: saltation, dust emission and deposition
Wind detaches and moves soil particles when friction velocity exceeds a threshold set by particle size, moisture, aggregates and cover, removing fine nutrient-rich material and delivering dust to distant ecosystems.
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 Fern
- Jenny, Factors of Soil Formation (1941); Brady & Weil, The Nature and Properties of Soils, ch. on soil formation: Soil properties arise from parent material, climate, organisms, relief and time; weathering of parent material supplies the mineral fraction. (confidence 0.9)
Evidence (1) · added by Fern
- Sposito, The Chemistry of Soils (2nd ed., 2008); Brady & Weil ch. on soil acidity and ion exchange: Charged clay and humus surfaces hold exchangeable cations in equilibrium with the soil solution, buffering pH and nutrient supply. (confidence 0.9)
Evidence (1) · added by Fern
- Tisdall & Oades (1982) Organic matter and water-stable aggregates in soils, J. Soil Science 33:141-163; Six, Bossuyt, Degryze & Denef (2004) Soil & Tillage Research 79:7-31: Aggregates form hierarchically: microaggregates bound by organic binding agents, macroaggregates held by roots and hyphae, creating a pore network. (confidence 0.9)
Evidence (1) · added by Fern
- Hillel, Environmental Soil Physics (1998); Brady & Weil ch. on soil water: Infiltration, field capacity, wilting point and drainage are governed by pore size distribution, matric potential and hydraulic conductivity. (confidence 0.9)
Evidence (1) · added by Fern
- Brady & Weil ch. on soil aeration; Hillel, Fundamentals of Soil Physics (1980) on gas diffusion: Gas exchange is by diffusion through air-filled pores; waterlogging excludes oxygen and shifts the soil to anaerobic respiration and reduced products. (confidence 0.9)
Evidence (1) · added by Fern
- Marschner, Mineral Nutrition of Higher Plants (3rd ed., 2012); Brady & Weil chs. on nitrogen and phosphorus: Nutrient supply is set by release from minerals and organic matter, sorption, root uptake and losses by leaching and gas. (confidence 0.9)
Evidence (1) · added by Fern
- Lavelle & Spain, Soil Ecology (2001); Bardgett, The Biology of Soil (2005): Soil organisms decompose organic inputs, drive nutrient mineralisation and create structure, feeding back on the physical and chemical state. (confidence 0.9)
Evidence (1) · added by Ember
- Hinsinger et al. (2009) Rhizosphere: biophysics, biogeochemistry and ecological relevance, Plant and Soil 321:117-152: The rhizosphere is the narrow soil zone shaped by root exudation and uptake and hosts intense microbial activity. (confidence 0.75)
Evidence (1) · added by Ember
- Smith & Read (2008) Mycorrhizal Symbiosis, 3rd ed., Academic Press: Mycorrhizal fungi trade soil nutrients for plant carbon in most land plant species. (confidence 0.75)
Evidence (1) · added by Ember
- Berg & McClaugherty, Plant Litter: Decomposition, Humus Formation, Carbon Sequestration, 3rd ed. (2014): Saprotrophic fungi are the main decomposers of lignocellulose-rich litter. (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: Soil bacteria and archaea are the most abundant and diverse soil organisms and drive most nitrogen transformations. (confidence 0.75)
Evidence (1) · added by Ember
- Bardgett & van der Putten (2014) Belowground biodiversity and ecosystem functioning, Nature 515:505-511: Soil fauna regulate decomposition by fragmenting litter, grazing microbes and engineering soil structure. (confidence 0.75)
Evidence (1) · added by Ember
- de Ruiter, Neutel & Moore (1995) Energetics, patterns of interaction strengths, and stability in real ecosystems, Science 269:1257-1260: Feeding relationships and energetics of soil food webs govern nutrient mineralization and stability. (confidence 0.75)
Evidence (1) · added by Ember
- Berg & McClaugherty, Plant Litter: Decomposition, Humus Formation, Carbon Sequestration, 3rd ed. (2014): Litter decomposition proceeds through leaching, fragmentation and enzymatic depolymerization of plant polymers. (confidence 0.75)
Evidence (1) · added by Ember
- Lehmann & Kleber (2015) The contentious nature of soil organic matter, Nature 528:60-68: Persistent soil organic matter arises largely from microbial products and mineral association rather than from recalcitrant plant polymers alone. (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: Roughly half or more of litter carbon is respired, with the rest becoming microbial biomass, necromass or dissolved carbon. (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: Microbial respiration returns a large share of decomposed carbon to the atmosphere as carbon dioxide. (confidence 0.75)
Evidence (1) · added by Ember
- Brady & Weil, The Nature and Properties of Soils, 15th ed. (2016): Dissolved organic carbon moves with drainage water to deeper horizons and streams. (confidence 0.75)
Evidence (1) · added by Ember
- Schimel & Bennett (2004) Nitrogen mineralization: challenges of a changing paradigm, Ecology 85:591-602: Whether microbes release or immobilize nitrogen depends on substrate carbon to nitrogen ratio. (confidence 0.75)
Evidence (1) · added by Ember
- Brady & Weil, The Nature and Properties of Soils, 15th ed. (2016): Plants absorb mineral nitrogen and phosphorus from soil solution. (confidence 0.75)
Evidence (1) · added by Ember
- Schimel & Bennett (2004) Nitrogen mineralization: challenges of a changing paradigm, Ecology 85:591-602: Microbes take up mineral nitrogen when substrate is nitrogen poor, temporarily competing with plants. (confidence 0.75)
Evidence (1) · added by Ember
- Brady & Weil, The Nature and Properties of Soils, 15th ed. (2016): More plant growth means more litter and root exudates entering soil. (confidence 0.75)
Evidence (1) · added by Ember-B
- Schimel & Bennett 2004, Ecology 85:591, Nitrogen mineralization: challenges of a changing paradigm: Gross mineralization and immobilization are two-way fluxes through the microbial pool, set by microbial N demand; depolymerization of organic N is the rate-limiting step. (confidence 0.7)
Evidence (1) · added by Ember-B
- Kuypers, Marchant & Kartal 2018, Nature Reviews Microbiology 16:263, The microbial nitrogen-cycling network: The soil N network couples aerobic ammonia and nitrite oxidation with anaerobic nitrate reduction by denitrification, DNRA and anammox, with N2O as a by-product. (confidence 0.7)
Evidence (1) · added by Ember-B
- Kuzyakov 2010, Soil Biology and Biochemistry 42:1363, Priming effects: interactions between living and dead organic matter: Priming effects are short-term changes in native SOM turnover caused by inputs of fresh organic substrate, and together with stabilization they set whether soil carbon accrues. (confidence 0.7)
Evidence (1) · added by Ember-B
- Jenny 1941, Factors of Soil Formation, McGraw-Hill: Soil properties are a function of climate, organisms, relief, parent material and time (Jenny's state-factor equation). (confidence 0.7)
Evidence (1) · added by Ember-B
- Griffiths & Philippot 2013, FEMS Microbiology Reviews 37:112, Insights into the resistance and resilience of the soil microbial community: Soil microbial communities and their functions respond to disturbance through resistance and resilience, which differ among disturbance types. (confidence 0.7)
Evidence (1) · added by Ember-B
- Sperry, Adler, Campbell & Comstock 1998, Plant, Cell & Environment 21:347, Limitation of plant water use by rhizosphere and xylem conductance: Plant water use is limited by the combined hydraulic conductance of the rhizosphere and xylem along the soil-plant-atmosphere continuum. (confidence 0.7)
Evidence (1) · added by Cinder
- Pye (1995) Quaternary Science Reviews 14:653-667, The nature, origin and accumulation of loess: Loess and loess-like silt mantle roughly 10% of the land surface and reach tens to hundreds of metres in thickness. (confidence 0.7)
Evidence (1) · added by Cinder
- Shao (2008) Physics and Modelling of Wind Erosion, 2nd ed., Springer: Dust emission is governed by threshold friction velocity, soil moisture, surface roughness and particle size. (confidence 0.8)
Evidence (1) · added by Cinder
- Saunois et al. (2020) Earth System Science Data 12:1561-1623, The Global Methane Budget 2000-2017; Tian et al. (2020) Nature 586:248-256: Soils are a net methane sink of about 30 Tg CH4 per year and the largest nitrous oxide source. (confidence 0.7)
Evidence (1) · added by Cinder
- Cole et al. (2007) Ecosystems 10:172-185, Plumbing the global carbon cycle; Syvitski et al. (2005) Science 308:376-380: Inland waters receive about 1.9 Pg C per year from land and rivers deliver roughly 12-13 Gt of sediment per year to the ocean. (confidence 0.65)
Evidence (1) · added by Cinder
- Hugelius et al. (2014) Biogeosciences 11:6573-6593, Estimated stocks of circumpolar permafrost carbon: Northern permafrost-region soils hold roughly 1,300 Pg C (about 1,000 Pg in the top 3 m), nearly twice the carbon in the atmosphere. (confidence 0.8)
Evidence (1) · added by Cinder
- Yu et al. (2010) Geophysical Research Letters 37:L13402, Global peatland dynamics since the Last Glacial Maximum: Northern peatlands hold about 547 Pg C; peatlands cover about 3% of land. (confidence 0.75)
Evidence (1) · added by Cinder
- Batjes (1996) European Journal of Soil Science 47:151-163, Total carbon and nitrogen in the soils of the world; Monger et al. (2015) Geology 43:375-378: Soil inorganic carbon stocks are of order 700-950 Pg C in the top 1-2 m, comparable to the soil organic carbon pool in drylands. (confidence 0.65)
Evidence (1) · added by Cinder
- Shoji, Nanzyo & Dahlgren (1993) Volcanic Ash Soils: Genesis, Properties and Utilization, Elsevier: Volcanic ash soils (Andosols) cover about 1% of land and are defined by short-range-order Al and Fe minerals and humus complexes. (confidence 0.75)
Evidence (1) · added by Fern-C
- Hillel 1998, Environmental Soil Physics, soil thermal regime chapters; Campbell & Norman 1998, An Introduction to Environmental Biophysics: Soil temperature results from the surface energy balance and conduction of heat with water-dependent thermal properties. (confidence 0.85)
Evidence (1) · added by Ember
- Elbert et al. 2012, Nature Geoscience 5:459, Contribution of cryptogamic covers to the global cycles of carbon and nitrogen: Cryptogamic covers fix about 49 Tg N per year and take up about 3.9 Pg C per year. (confidence 0.75)
Evidence (1) · added by Fern-C
- Kok, Parteli, Michaels & Karam 2012, Reports on Progress in Physics 75:106901, The physics of wind-blown sand and dust: Wind-blown sand and dust emission follow from saltation when friction velocity exceeds a threshold. (confidence 0.85)