Editing Soil (section)

===Humus===
Humus refers to organic matter that has been decomposed by soil microflora and fauna to the point where it is resistant to further breakdown.<ref>{{cite journal |last=Ponge |first=Jean-François |date=August 2022 |title=Humus: dark side of life or intractable “aether”? |journal=Pedosphere |volume=32 |issue=4 |pages=660–64 |url=https://www.researchgate.net/publication/360175852 |doi=10.1016/S1002-0160(21)60013-9 |access-date=13 April 2025 }}</ref> Humus usually constitutes only five percent of the soil or less by volume, but it is an essential source of nutrients and adds important textural qualities crucial to [[soil health]] and plant growth.<ref>{{cite web |url=https://humates.com/wp-content/uploads/2020/04/ORGANICMATTERPettit.pdf |last=Pettit |first=Robert E. |title=Organic matter, humus, humate, humic acid, fulvic acid and humin: their importance in soil fertility and plant health |access-date=13 April 2025 }}</ref> Humus also feeds arthropods, [[termite]]s and [[earthworm]]s which further improve the soil.<ref>{{cite journal |last1=Ji |first1=Rong |last2=Kappler |first2=Andreas |last3=Brune |first3=Andreas |year=2000 |title=Transformation and mineralization of synthetic <sup>14</sup>C-labeled humic model compounds by soil-feeding termites |journal=[[Soil Biology and Biochemistry]] |volume=32 |issue=8–9 |pages=1281–91 |doi=10.1016/S0038-0717(00)00046-8 |citeseerx=10.1.1.476.9400 |url=https://www.academia.edu/13008941 |access-date=20 April 2025 }}</ref> The end product, humus, is suspended in [[colloidal]] form in the soil solution and forms a [[weak acid]] that can attack silicate minerals by [[Chelation|chelating]] their iron and aluminum atoms.<ref>{{cite book |last1=Drever |first1=James I. |last2=Vance |first2=George F. |title=Organic acids in geological processes |chapter=Role of soil organic acids in mineral weathering processes |year=1994 |doi=10.1007/978-3-642-78356-2_6 |editor-last1=Pittman |editor-first1=Edward D. |editor-last2=Lewan |editor-first2=Michael D. |publisher=[[Springer Science+Business Media|Springer]] |location=Berlin, Germany |pages=138–61 |isbn=978-3-642-78356-2 |chapter-url=https://fr.1lib.sk/book/53559896/96a34d |access-date=20 April 2025 }}</ref> Humus has a high cation and anion exchange capacity that on a dry weight basis is many times greater than that of clay colloids. It also acts as a buffer, like clay, against changes in pH and soil moisture.<ref name="Piccolo1996">{{cite book |last=Piccolo |first=Alessandro |year=1996 |chapter=Humus and soil conservation |doi=10.1016/B978-044481516-3/50006-2 |title=Humic substances in terrestrial ecosystems |editor-first=Alessandro |editor-last=Piccolo |publisher= [[Elsevier]] |location=Amsterdam, the Netherlands |pages=225–264 |isbn=978-0-444-81516-3 |chapter-url=https://www.researchgate.net/publication/281451183 |access-date=20 April 2025 }}</ref>

[[Humic acid]]s and [[fulvic acid]]s, which begin as raw organic matter, are important constituents of humus. After the death of plants, animals, and microbes, microbes begin to feed on the residues through their production of extra-cellular soil enzymes, resulting finally in the formation of humus.<ref>{{cite journal |last1=Varadachari |first1=Chandrika |last2=Ghosh |first2=Kunal |year=1984 |title=On humus formation |journal=[[Plant and Soil]] |volume=77 |issue=2 |pages=305–13 |url=https://www.researchgate.net/publication/225528442 |doi=10.1007/BF02182933 |bibcode=1984PlSoi..77..305V |s2cid=45102095 |access-date=20 April 2025 }}</ref> As the residues break down, only molecules made of [[aliphatic compound|aliphatic]] and [[aromatic hydrocarbon|aromatic]] hydrocarbons, assembled and stabilized by oxygen and [[Hydrogen bond|hydrogen bonds]], remain in the form of complex molecular assemblages collectively called humus.<ref name="Piccolo2002"/> Humus is never pure in the soil, because it reacts with metals and clays to form complexes which further contribute to its stability and to soil structure.<ref name="Piccolo1996"/> Although the structure of humus has in itself few nutrients (with the exception of constitutive metals such as calcium, iron and aluminum) it is able to attract and link, by weak bonds, cation and anion nutrients that can further be released into the soil solution in response to selective root uptake and changes in soil pH, a process of paramount importance for the maintenance of fertility in tropical soils.<ref>{{cite journal |last1=Mendonça |first1=Eduardo S. |last2=Rowell |first2=David L. |year=1996 |title=Mineral and organic fractions of two oxisols and their influence on effective cation-exchange capacity |journal=[[Soil Science Society of America Journal]] |volume=60 |issue=6 |pages=1888–92 |url=https://fr.1lib.sk/book/55342950/7121f7 |doi=10.2136/sssaj1996.03615995006000060038x |bibcode=1996SSASJ..60.1888M |access-date=20 April 2025 }}</ref>

[[Lignin]] is resistant to breakdown and accumulates within the soil. It also reacts with [[proteins]],<ref>{{cite journal |last1=Heck |first1=Tobias |last2=Faccio |first2=Greta |last3=Richter |first3=Michael |last4=Thöny-Meyer |first4=Linda |year=2013 |title=Enzyme-catalyzed protein crosslinking |journal=[[Applied Microbiology and Biotechnology]] |volume=97 |issue=2 |pages=461–75 |url=https://www.researchgate.net/publication/233769618 |doi=10.1007/s00253-012-4569-z |pmid=23179622 |pmc=3546294 |access-date=27 April 2025 }}</ref> which further increases its resistance to decomposition, including enzymatic decomposition by microbes.<ref>{{cite journal |last1=Lynch |first1=D. L. |last2=Lynch |first2=C. C. |year=1958 |title=Resistance of protein–lignin complexes, lignins and humic acids to microbial attack |journal=[[Nature (journal)|Nature]] |volume=181 |issue=4621 |pages=1478–79 |url=https://fr.1lib.sk/book/42467876/142898 |doi=10.1038/1811478a0 |pmid=13552710 |bibcode=1958Natur.181.1478L |s2cid=4193782 |access-date=27 April 2025 }}</ref> [[Fat]]s and [[wax]]es from plant matter have still more resistance to decomposition and persist in soils for thousand years, hence their use as tracers of past vegetation in buried soil layers.<ref>{{cite journal |last1=Dawson |first1=Lorna A. |last2=Hillier |first2=Stephen |year=2010 |title=Measurement of soil characteristics for forensic applications |journal=[[Surface and Interface Analysis]] |volume=42 |issue=5 |pages=363–77 |url=https://www.academia.edu/128162468 |doi=10.1002/sia.3315 |s2cid=54213404 |access-date=27 April 2025 |archive-date=8 May 2021 |archive-url=https://web.archive.org/web/20210508065204/https://people.ok.ubc.ca/robrien/soil%20characteristics.pdf |url-status=live }}</ref> Clay soils often have higher organic contents that persist longer than soils without clay as the organic molecules adhere to and are stabilised by the clay.<ref>{{cite journal |last1=Manjaiah |first1=Kanchikeri Math |last2=Kumar |first2=Sarvendra |last3=Sachdev |first3=M. S. |last4=Sachdev |first4=P. |last5=Datta |first5=Samar Chandra |year=2010 |title=Study of clay–organic complexes |journal=[[Current Science]] |volume=98 |issue=7 |pages=915–21 |url=https://www.researchgate.net/publication/228867334 |access-date=27 April 2025 }}</ref> Proteins normally decompose readily, to the exception of [[scleroproteins]], but when bound to clay particles they become more resistant to decomposition.<ref>{{cite journal |last=Theng |first=Benny K.G. |year=1982 |title=Clay-polymer interactions: summary and perspectives |journal=Clays and Clay Minerals |volume=30 |issue=1 |pages=1–10 |doi=10.1346/CCMN.1982.0300101 |bibcode=1982CCM....30....1T |citeseerx=10.1.1.608.2942 |s2cid=98176725 |url=https://www.researchgate.net/publication/238684938 |access-date=27 April 2025 }}</ref> As for other proteins clay particles absorb the enzymes exuded by microbes, decreasing [[enzyme activity]] while protecting [[extracellular enzymes]] from degradation.<ref>{{cite journal |last1=Tietjen |first1=Todd |last2=Wetzel |first2=Robert G. |year=2003 |title=Extracellular enzyme-clay mineral complexes: enzyme adsorption, alteration of enzyme activity, and protection from photodegradation |journal=Aquatic Ecology |volume=37 |issue=4 |pages=331–39 |doi=10.1023/B:AECO.0000007044.52801.6b |bibcode=2003AqEco..37..331T |s2cid=6930871 |url=https://www.vliz.be/imisdocs/publications/ocrd/54440.pdf |access-date=24 April 2025 }}</ref> The addition of organic matter to clay soils can render that organic matter and any added nutrients inaccessible to plants and microbes for many years.<ref>{{cite journal |last1=Tahir |first1=Shermeen |last2=Marschner |first2=Petra |year=2017 |title=Clay addition to sandy soil: influence of clay type and size on nutrient availability in sandy soils amended with residues differing in C/N ratio |journal=[[Pedosphere]] |volume=27 |issue=2 |pages=293–305 |url=https://www.researchgate.net/publication/314221508 |doi=10.1016/S1002-0160(17)60317-5 |bibcode=2017Pedos..27..293T |access-date=24 April 2025 }}</ref> A study showed increased soil fertility following the addition of mature compost to a clay soil.<ref>{{cite journal |last1=Melero |first1=Sebastiana |last2=Madejón |first2=Engracia |last3=Ruiz |first3=Juan Carlos |last4=Herencia |first4=Juan Francisco |year=2007 |title=Chemical and biochemical properties of a clay soil under dryland agriculture system as affected by organic fertilization |journal=European Journal of Agronomy |volume=26 |issue=3 |pages=327–34 |url=https://fr.1lib.sk/book/45675038/0dbbc0 |doi=10.1016/j.eja.2006.11.004 |bibcode=2007EuJAg..26..327M |access-date=24 April 2025 }}</ref> High soil [[tannin]] content can cause nitrogen to be sequestered as resistant tannin-protein complexes.<ref>{{cite journal |last1=Joanisse |first1=Gilles D. |last2=Bradley |first2=Robert L. |last3=Preston |first3=Caroline M. |last4=Bending |first4=Gary D. |title=Sequestration of soil nitrogen as tannin–protein complexes may improve the competitive ability of sheep laurel (Kalmia angustifolia) relative to black spruce (Picea mariana) |journal=[[New Phytologist]] |year=2009 |volume=181 |pages=187–98 |doi=10.1111/j.1469-8137.2008.02622.x |issue=1 |pmid=18811620 |doi-access=free |bibcode=2009NewPh.181..187J }}</ref><ref name=Fierer2001>{{cite journal |last1=Fierer |first1=Noah |last2=Schimel |first2=Joshua P. |last3=Cates |first3=Rex G. |last4=Zou |first4=Jiping |title=Influence of balsam poplar tannin fractions on carbon and nitrogen dynamics in Alaskan taiga floodplain soils |journal=[[Soil Biology and Biochemistry]] |year=2001 |volume=33 |pages=1827–39 |doi=10.1016/S0038-0717(01)00111-0 |issue=12–13 |bibcode=2001SBiBi..33.1827F |url=https://www.academia.edu/12814037 |access-date=24 April 2025 }}</ref>

Humus formation is a process dependent on the amount of plant material added each year and the type of base soil. Both are affected by climate and the type of organisms present.<ref name="Ponge2003"/> Soils with humus can vary in nitrogen content but typically have 3 to 6&nbsp;percent nitrogen. Raw organic matter, as a reserve of nitrogen and phosphorus, is a vital component affecting [[Fertile soil|soil fertility]].<ref name="Foth1984"/> Humus also absorbs water, and expands and shrinks between dry and wet states to a higher extent than clay, increasing soil porosity.<ref>{{cite journal |last1=Peng |first1=Xinhua |last2=Horn |first2=Rainer |title=Anisotropic shrinkage and swelling of some organic and inorganic soils |journal=European Journal of Soil Science |year=2007 |volume=58 |issue=1 |pages=98–107 |doi=10.1111/j.1365-2389.2006.00808.x |bibcode=2007EuJSS..58...98P |url=https://www.academia.edu/56639603 |access-date=4 May 2025 }}</ref> Humus is less stable than the soil's mineral constituents, as it is reduced by microbial [[decomposition]], and over time its concentration diminishes without the addition of new organic matter. However, humus in its most stable forms may persist over centuries if not millennia.<ref>{{cite journal |last1=Wang |first1=Yang |last2=Amundson |first2=Ronald |last3=Trumbmore |first3=Susan |title=Radiocarbon dating of soil organic matter |journal=[[Quaternary Research]] |year=1996 |volume=45 |issue=3 |pages=282–88 |doi=10.1006/qres.1996.0029 |bibcode=1996QuRes..45..282W |s2cid=73640995 |url=https://escholarship.org/content/qt6b14h4bv/qt6b14h4bv.pdf |access-date=4 May 2025 }}</ref> [[Charcoal]] is a source of highly stable humus, called [[black carbon]],<ref>{{cite journal |last1=Brodowski |first1=Sonja |last2=Amelung |first2=Wulf |last3=Haumaier |first3=Ludwig |last4=Zech |first4=Wolfgang |title=Black carbon contribution to stable humus in German arable soils |journal=Geoderma |year=2007 |volume=139 |issue=1–2 |pages=220–28 |doi=10.1016/j.geoderma.2007.02.004 |bibcode=2007Geode.139..220B |url=https://www.academia.edu/33858429 |access-date=4 May 2025 }}</ref> which had been used traditionally to improve the fertility of nutrient-poor tropical soils. This very ancient practice, as ascertained in the genesis of [[Amazonian dark earths]], has been renewed and became popular under the name of [[biochar]]. It has been suggested that biochar could be used to sequester more carbon in the fight against the greenhouse effect.<ref>{{cite journal |last1=Criscuoli |first1=Irene |last2=Alberti |first2=Giorgio |last3=Baronti |first3=Silvia |last4=Favilli |first4=Filippo |last5=Martinez |first5=Cristina |last6=Calzolari |first6=Costanza |last7=Pusceddu |first7=Emanuela |last8=Rumpel |first8=Cornelia |last9=Viola |first9=Roberto |last10=Miglietta |first10=Franco |title=Carbon sequestration and fertility after centennial time scale incorporation of charcoal into soil |journal=[[PLOS ONE]] |year=2014 |volume=9 |issue=3 |pages=e91114 |doi=10.1371/journal.pone.0091114 |pmc=3948733 |pmid=24614647|bibcode=2014PLoSO...991114C |doi-access=free }}</ref>