Glossary
The terms of the field, defined once.
Carbon Biome Project uses these words the same way on every page and in every publication. Each entry gives a definition, an example and where the term is at work on the site. Where a term is debated, the entry says who argues what.
What living things leave behind
- Soil organic matter
What living things leave in the soil: plant residues, roots, the carbon roots release, and the bodies and by-products of microbes and soil animals, at every stage of decomposition.1,3
Example. A fallen leaf, the fine roots that died last season and the remains of the bacteria that fed on them all count, from whole pieces down to fragments too small to see.1
Where organic matter comes from- Decomposition
The breakdown of organic material by soil animals, bacteria and fungi: into ever smaller pieces, and through microbial respiration back to carbon dioxide. Microbes take up only small fragments, typically under about 600 daltons, so larger material is broken down outside the cell first.1,3,4
Example. Earthworms, mites and springtails shred leaf litter; fungi and bacteria then colonise the pieces.3,4
A leaf becoming soil- Particulate organic matter
Physical fragments of decomposing litter in the soil.4
Example. Pieces of leaf and root that can still be picked out of the soil, before they have been broken down further.4
- Microbial necromass
The dead cells and remains of microbes. Part of it persists on mineral surfaces.5
Example. In laboratory model soils given simple substrates and no plant litter, microbes produced organic matter that resembled soil organic matter.5
Microbes as builders of soil- Soil organic carbon
The carbon held in soil organic matter.6,7
Example. Down to two metres the world’s soils hold about 2,060 billion tonnes of it, by one estimate, more than the air and all vegetation together. Figures differ with the depth counted and with how permafrost is treated.6,7
The planet’s carbon, on the Science page- Persistence
How long organic matter remains in soil. It is set by the surroundings more than by the chemistry of the material: minerals, aggregates and inaccessible pores that shelter it from decomposers, and cold or waterlogged ground where decomposers work slowly.1,7
Example. Dissolved compounds that attach to clay are protected from decomposers. What keeps them is where they sit, more than what they are made of.1,4
The dark fractions
- Humic substances
Dark organic material found in soils, natural waters and organic deposits such as peat and brown coal, defined by how it behaves in an alkaline extraction. It is a mixture of many compounds, not one molecule.8,9
Example. Whether it exists in soil as a separate natural class is argued over. Lehmann and Kleber argue that it does not, and that the extract is made by the procedure; Olk and colleagues reply that the extracted fractions still track real environmental and agricultural behaviour.1,9,10
The debate, on the Science page- Humic acid fraction
The part of an alkaline extract that settles out as a dark solid when the extract is acidified to about pH 1 to 2.8,11
Example. In a glass, the brown material that gathers and sinks once acid is added.11
The separation, on the Science page- Fulvic acid fraction
The part that stays dissolved at that pH, purified further on a resin. On average it is more oxygen-rich and more acidic than the humic acid fraction.11,12,13
Example. IHSS counts 13.24 milliequivalents of carboxyl groups per gram of carbon in its Elliott soil fulvic acid, against 8.28 in the humic acid from the same soil.12
The separation, on the Science page- Humin
The part of the organic matter that alkali never dissolves.8,11
Example. What is left of the organic matter after both the alkali and the acid steps.8
- Leonardite
Oxidised lignite.16
Example. IHSS keeps a leonardite humic acid among its standard samples, beside river, peat and soil samples. It carries 7.46 milliequivalents of carboxyl groups per gram of carbon.12,14
Soils, waters and buried ground- Lignite
Brown coal, one of the organic deposits that hold humic substances.8
Example. Lignite and peat are both among the sources of the humic materials tested on plants.15
- Peat
An organic deposit, one of those that hold humic substances.8
Example. IHSS draws one of its standard humic acids from Pahokee peat.12,14
- Preparation
A specific material made from a source by specific processing steps.17
Example. Two products sold as humic acid can differ widely in composition, and some differ from their own labels, so a result travels only with the preparation that produced it.17
What needs to match before a finding can travel
Charge, ions and water
- Charge
The electrical property that makes particles attract or repel one another: opposite charges attract. A particle can carry a positive charge, a negative charge or none.10,18
Example. An acidic group on organic matter is uncharged while it holds its hydrogen ion (COOH). Once it lets the hydrogen ion go (COO−) it carries one negative charge, and can hold a positive ion near it.10,18
Charge and exchange, scene 1 on the Science pageIllustration, not to scale. A stretch of organic matter in water, with a few of its acidic groups drawn schematically. - Ion
An atom or group of atoms that carries an electrical charge. A positive ion is a cation; a negative ion is an anion.18
Example. Common cations in soil water include calcium (Ca²⁺), magnesium (Mg²⁺), potassium (K⁺), ammonium (NH₄⁺), sodium (Na⁺) and hydrogen (H⁺). Common anions include nitrate, sulfate and chloride.18
Ions at a charged surface, on the Science page- pH
A measure of how acidic or alkaline water is, set by its concentration of hydrogen ions. The lower the number, the more acidic the water.10,18
Example. Most soils lie between about pH 4 and 7. Across that range the carboxyl group of a simple fatty acid goes from about 11 percent charged at pH 4 to 99 percent at pH 7. Alkaline extraction runs at pH 13.10
The pH control in scene 1, on the Science page- Ions, dissolved compounds and colloids
Three different forms that material takes in water. An ion is a single charged atom or small charged group, such as Ca²⁺. A dissolved compound is a whole molecule spread through the water, such as a sugar or a fulvic fragment. A colloid is a particle larger than a molecule but small enough not to settle.8,18,19
Example. In soil water, calcium travels as an ion, a fulvic fragment as a dissolved compound, and fine clay with organic matter attached as a colloid. Only the ion takes part in cation exchange; the other two are held and carried in other ways, so naming the form matters.10,18
Illustration, not to scale. The same glass of soil water can hold all three. - Colloid
A particle larger than most simple molecules yet small enough not to settle out of water. Colloids are large enough to scatter light, which can make water look cloudy.19
Example. In soil, a small amount of organic matter is spread through a much larger mass of colloidal-sized minerals, and forms associations with them.10
- Dissolved organic matter
Organic matter dissolved in water: a mixture of many compounds. In rivers, about half of it is humic substances, which affect the water’s pH and alkalinity.8
Example. The Suwannee River, a blackwater stream, carries 30 to 80 milligrams of dissolved organic carbon per litre at a pH below 4. IHSS draws its standard river samples from it.9,12
Humic material in soils and waters
What it does in soil and water
- Cation exchange
The holding and swapping of positively charged nutrients on negatively charged surfaces of clay and organic matter, including the acidic groups of humic material.12,18
Example. A calcium ion (Ca²⁺) can take the place of two hydrogen ions (H⁺) on a surface, so the total charge stays balanced.18
Charge and exchange, scene 1 on the Science page- Cation exchange capacity
A measure of how much negative charge a soil carries, and so how many positive ions it can hold for exchange. It is reported in milliequivalents per 100 grams, the same as centimoles of charge per kilogram.18
Example. The part contributed by organic matter rises with pH, because more of its acidic groups let go of their hydrogen ions. The part from clay is fixed by the mineral’s structure.18
- Binding
A general word for one substance holding on to another. In soil and water it covers several different kinds of association, including attraction between opposite charges, coordination to a metal ion (complexation) and weaker forces such as hydrogen bonding.9
Example. Binding does not by itself mean uptake or benefit. Humic material binds some persistent organic pollutants, which makes them less bioavailable to organisms.9
Three interactions kept apart, on the Science pageIllustration, not to scale. Binding is association. It does not by itself mean that a plant or an animal takes the substance up. - Adsorption
The holding of a substance at a surface, rather than throughout a material.9,18
Example. Water chemists isolate humic and fulvic fractions by passing acidified river water through a resin, where they adsorb. In soil, positive ions are held close to the surfaces of clay.9,18
- Desorption
The release of an adsorbed substance from a surface back into the water around it. Together with adsorption, it is what makes holding at a surface reversible.9,18
Example. Humic and fulvic fractions held on a resin are desorbed with an alkaline solution. In a soil test, ammonium displaces the cations held by the soil into the extracting solution, where they are measured.9,18
- Complexation
The bonding of a metal ion to a ligand, a molecule or ion that supplies a pair of electrons to bond with it, to form a complex. In soils, much of the hold on plant-available metal ions comes from the weakly acidic groups of humic material.9,20
Example. Iron held by a water-soluble humic fraction from peat: cucumber roots reduced the iron at their surface and took it up, more at pH 6.0 than at 7.5. Being complexed and being taken up are separate steps.21
Complexation, scene 2 on the Science page- Chelation
A particular form of complexation in which one binding partner holds a metal ion at more than one site, the way a claw holds a marble.20
Example. Heme holds an iron ion at four sites, and EDTA, used in detergents, holds a metal ion at six. Models of humic material allow a metal ion with two positive charges to be held at one site or at two.9,20
Complexation, scene 2 on the Science page- Bioavailability
How much of a substance a living thing can take up and use, in a given setting. It depends on the substance’s form, the conditions and the organism, so it is measured in a named system rather than assumed from being dissolved.8,9
Example. Binding can lower it as well as raise it: humic material makes some persistent organic pollutants less bioavailable. Iron from one peat humate reached cucumber and barley by different routes.9,21
- Electron transfer
The passing of electrons from one substance to another. In respiration, a cell takes electrons from its food and passes them on to an acceptor.22,24
Example. In laboratory cultures, the iron-reducing bacterium Geobacter metallireducens used humic substances in place of iron as the acceptor. Here humic material takes the electrons; it is not the food.22,23
Electron transfer, scene 3 on the Science pageIllustration, not to scale. Iron-reducing bacteria in laboratory culture (Lovley 1996; Coates 1998). The electrons move; the humic material is the go-between, not the food. - Electron shuttling
Electron transfer by way of a go-between. In laboratory cultures, some bacteria pass electrons from their respiration to humic material, which can pass them on to iron minerals. A different role from supplying carbon.22,24
Example. Microbes also reduced humic material in solid form, not only dissolved, so the go-between need not be in solution.24
Electron transfer, scene 3 on the Science page
The living ground
- Rhizosphere
The zone of soil influenced by a living root.2
Example. Microbes crowd the soil around a living root, where the carbon compounds it releases land.2
The root environment, Soil and plants- Root exudates
Carbon compounds released by living roots, which feed the microbes around them.2,25
Example. Recently fixed plant carbon reaches soil microbes both through roots directly and through mycorrhizal fungi.25
Roots feed the soil’s microbes- Mycorrhizal fungi
Fungi that live in partnership with plant roots. Their threads take carbon from the root and pass nutrients back.25,26
Example. In root-organ culture, the fungus took carbon from the root and passed nitrogen back.26
Roots feed the soil’s microbes- Endophyte
A microbe living inside plant tissue.27,28
Example. In stevia leaves, the endophyte community shifted with growth stage and with fulvic acid; in tomato roots, it shifted with a humic product.27,28
Open questions, on the Science page- Microbial community
The microbes living together in one place, such as a root zone or a gut.
Digestion
- Fermentation (digestive)
Microbial breakdown of plant fibre and other feed in part of the gut, such as the rumen or the horse’s hindgut.29,30
Equine biology, Horses- Rumen
The largest compartment of a cattle stomach, a major microbial fermentation environment.30
Livestock- Hindgut
The caecum and colon. In the horse, where forage is fermented by microbes.29
Equine biology, Horses- Caecum (cecum)
A blind pouch at the start of the large intestine. In the horse it holds about three times the volume of the stomach.29
The framework and the evidence
- Microbiome Management
The practice of examining and supporting the environmental conditions in which microbial communities function.33
The Microbiome Management Framework- The Microbiome Management Framework
The project’s model connecting three things in any living system: environmental conditions, microbial activity and observable function.33
The model, on the Framework page- Environmental conditions
Resources, physical conditions and management.33
Example. The framework begins here: describe the environment, including recent transitions in the system, before deciding what to change.33
Applying the framework- Microbial activity
Functions and interactions within the community.33
- Observable function
What can be measured in the host or wider system.33
- Digestive Stability
In digestive systems, appropriate digestive function and the capacity to adapt through change. A working concept within the framework, not a diagnosis or a single validated score.33
Digestive Stability, on the Framework page- Published study, research report, background biology
The three kinds of record in the evidence library: a peer-reviewed paper; an unpublished report, with who supplied it; and a study that tested no humic or fulvic material but explains the biology.16
How the library reads evidence- Open question
A question the studies in this collection have not answered. On this site it is drawn as a dotted line that stops.
Example. Whether the carbon in fulvic material feeds the microbes that live inside a plant.
Open questions, on the Science page
Suggest a term, or a correction.
The glossary grows with the evidence. Where a source would sharpen an entry, tell us.
Sources
- Lehmann J, Kleber M. The contentious nature of soil organic matter. Nature 528:60 to 68. 2015. doi.org/10.1038/nature16069
- USDA Natural Resources Conservation Service. Soil Health Management. www.nrcs.usda.gov/conservation-basics/soil/soil-health/soil-health-management
- USDA Natural Resources Conservation Service. Soil Biology Primer. www.nrcs.usda.gov/resources/education-and-teaching-materials/soil-biology-primer
- Cotrufo MF, et al. Formation of soil organic matter via biochemical and physical pathways of litter mass loss. Nature Geoscience 8:776 to 779. 2015. doi.org/10.1038/ngeo2520
- Kallenbach CM, Frey SD, Grandy AS. Direct evidence for microbial-derived soil organic matter formation and its ecophysiological controls. Nature Communications 7:13630. 2016. doi.org/10.1038/ncomms13630
- Batjes NH. Harmonized soil property values for broad-scale modelling (WISE30sec) with estimates of global soil carbon stocks. Geoderma 269:61 to 68. 2016. Abstract read. doi.org/10.1016/j.geoderma.2016.01.034
- Canadell JG, Monteiro PMS, Costa MH, et al. Global carbon and other biogeochemical cycles and feedbacks. In: Climate Change 2021: The Physical Science Basis. Contribution of Working Group I to the Sixth Assessment Report of the IPCC, pp. 673 to 816. Cambridge University Press. 2021. Figure 5.12 and Box 5.1. doi.org/10.1017/9781009157896.007
- International Humic Substances Society. What are humic substances. Read 22 October 2026. humic-substances.org/what-are-humic-substances-2/
- Olk DC, et al. Environmental and agricultural relevance of humic fractions extracted by alkali from soils and natural waters. Journal of Environmental Quality 48:217 to 232. 2019. Full text read 22 October 2026. doi.org/10.2134/jeq2019.02.0041
- Kleber M, Lehmann J. Humic substances extracted by alkali are invalid proxies for the dynamics and functions of organic matter in terrestrial and aquatic ecosystems. Journal of Environmental Quality 48:207 to 216. 2019. Full text read 22 October 2026. doi.org/10.2134/jeq2019.01.0036
- International Humic Substances Society. Isolation of IHSS soil fulvic and humic acids, adapted from Swift 1996. humic-substances.org/isolation-of-ihss-soil-fulvic-and-humic-acids/
- International Humic Substances Society. Acidic functional groups of IHSS samples. Read 22 October 2026. humic-substances.org/acidic-functional-groups-of-ihss-samples/
- International Humic Substances Society. Elemental compositions and stable isotopic ratios of IHSS samples.
- International Humic Substances Society. Source materials for IHSS samples. humic-substances.org/source-materials-for-ihss-samples/
- Rose MT, Patti AF, Little KR, Brown AL, Jackson WR, Cavagnaro TR. A meta-analysis and review of plant-growth response to humic substances: practical implications for agriculture. Advances in Agronomy 124:37 to 89. 2014. doi.org/10.1016/B978-0-12-800138-7.00002-4
- Carbon Biome Project evidence library: the records of studies that used preparations extracted from oxidised lignite. carbonbiomeproject.com/evidence/
- Lyons G, Genc Y. Commercial humates in agriculture: real substance or smoke and mirrors? Agronomy 6:50. 2016. doi.org/10.3390/agronomy6040050
- Franzen D. Cation exchange and cation exchange capacity. Chapter 7 of the North Dakota State University Extension soil fertility ebook. Read 22 October 2026. www.ndsu.edu/agriculture/sites/default/files/ebook/Franzen/Chp_7.html
- OpenStax. Chemistry 2e, section 11.5, Colloids. Read 22 October 2026. openstax.org/books/chemistry-2e/pages/11-5-colloids
- OpenStax. Chemistry 2e, section 19.2, Coordination chemistry of transition metals. Read 22 October 2026. openstax.org/books/chemistry-2e/pages/19-2-coordination-chemistry-of-transition-metals
- Cesco S, Nikolic M, Römheld V, Varanini Z, Pinton R. Uptake of 59Fe from soluble 59Fe-humate complexes by cucumber and barley plants. Plant and Soil 241:121 to 128. 2002. Abstract read. doi.org/10.1023/A:1016061003397
- Lovley DR, Coates JD, Blunt-Harris EL, Phillips EJP, Woodward JC. Humic substances as electron acceptors for microbial respiration. Nature 382:445 to 448. 1996. doi.org/10.1038/382445a0
- Coates JD, Ellis DJ, Blunt-Harris EL, Gaw CV, Roden EE, Lovley DR. Recovery of humic-reducing bacteria from a diversity of environments. Applied and Environmental Microbiology 64:1504 to 1509. 1998. doi.org/10.1128/AEM.64.4.1504-1509.1998
- Roden EE, Kappler A, Bauer I, et al. Extracellular electron transfer through microbial reduction of solid-phase humic substances. Nature Geoscience 3:417 to 421. 2010. doi.org/10.1038/ngeo870
- Kaiser C, et al. Exploring the transfer of recent plant photosynthates to soil microbes: mycorrhizal pathway vs direct root exudation. New Phytologist. 2014 online, 2015 in print. doi.org/10.1111/nph.13138
- Fellbaum CR, et al. Carbon availability triggers fungal nitrogen uptake and transport in arbuscular mycorrhizal symbiosis. PNAS 109:2666 to 2671. 2012. doi.org/10.1073/pnas.1118650109
- Yu X, Yang J, Wang E, Li B, Yuan H. Effects of growth stage and fulvic acid on the diversity and dynamics of endophytic bacterial community in Stevia rebaudiana Bertoni leaves. Frontiers in Microbiology 6:867. 2015. doi.org/10.3389/fmicb.2015.00867
- Lengrand S, Dubois B, Pesenti L, Debode F, Legrève A. Humic substances increase tomato tolerance to osmotic stress while modulating vertically transmitted endophytic bacterial communities. Frontiers in Plant Science 15:1488671. 2024. doi.org/10.3389/fpls.2024.1488671
- Easley J. Introduction to digestive disorders of horses. Merck Veterinary Manual, horse owners. Reviewed 2019. www.merckvetmanual.com/horse-owners/digestive-disorders-of-horses/introduction-to-digestive-disorders-of-horses
- Mississippi State University Extension. Understanding the ruminant animal digestive system. extension.msstate.edu/publications/understanding-the-ruminant-animal-digestive-system
- Gloor GB, Macklaim JM, Pawlowsky-Glahn V, Egozcue JJ. Microbiome datasets are compositional: and this is not optional. Frontiers in Microbiology 8:2224. 2017. doi.org/10.3389/fmicb.2017.02224
- Zhang Z, Qu Y, Li S, et al. Soil bacterial quantification approaches coupling with relative abundances reflecting the changes of taxa. Scientific Reports 7:4837. 2017. doi.org/10.1038/s41598-017-05260-w
- Carbon Biome Project. The Microbiome Management Framework. carbonbiomeproject.com/framework/
Prepared by Carbon Biome Project, 22 October 2026. External scientific review of this page has not been completed. Entries with no source number are the project’s own definitions or standard usage. Citing the International Humic Substances Society, the IPCC, the USDA, OpenStax and the Merck Veterinary Manual does not imply their endorsement of the project.
