Soil biology

thumb|Soil biology is the study of microbial and faunal activity in the soil. This photo shows the activity of both.

'''Soil biology''' is the study of microbial and faunal activity and ecology in soil. '''Soil life''', '''soil biota''', '''soil fauna''', or '''edaphon''' is a collective term that encompasses all organisms that spend a significant portion of their life cycle within a soil profile, or at the soil-litter interface. These organisms include earthworms, nematodes, protozoa, fungi, bacteria, different arthropods, as well as some reptiles (such as snakes), and species of burrowing mammals like gophers, moles and prairie dogs.<ref>{{cite book |last1=Blume |first1=Hans-Peter |last2=Brümmer |first2=Gerhard W. |last3=Fleige |first3=Heiner |last4=Horn |first4=Rainer |last5=Kandeler |first5=Ellen |last6=Kögel-Knabner |first6=Ingrid |last7=Kretzschmar |first7=Ruben |last8=Stahr |first8=Karl |last9=Wilke |first9=Berndt-Michael |title=Scheffer/Schachtschabel Soil Science |date=25 November 2015 |publisher=Springer Nature |location=Berlin, Germany |isbn=978-3-642-30942-7 |editor-last1=Blume |editor-first1=Hans-Peter |editor-last2=Brümmer |editor-first2=Gerhard W. |editor-last3=Fleige |editor-first3=Heiner |editor-last4=Horn |editor-first4=Rainer |editor-last5=Kandeler |editor-first5=Ellen |editor-last6=Kögel-Knabner |editor-first6=Ingrid |editor-last7=Kretzschmar |editor-first7=Ruben |editor-last8=Stahr |editor-first8=Karl |editor-last9=Wilke |editor-first9=Berndt-Michael |pages=87–122 |chapter=Soil organisms and their habitat |doi=10.1007/978-3-642-30942-7_4 |access-date=14 July 2025 |chapter-url=https://fr.1lib.sk/book/79635103/611e88 }}</ref> Soil biology plays a vital role in determining many soil characteristics. The decomposition of organic matter by soil organisms has an immense influence on soil fertility, plant growth, soil structure, and carbon storage. As a relatively new science, much remains unknown about soil biology and its effect on soil ecosystems.<ref>{{cite journal |last=Huhta |first=Veikko |date=4 January 2007 |title=The role of soil fauna in ecosystems: a historical review |url=https://www.researchgate.net/publication/233427710 |journal=Pedobiologia |volume=50 |issue=6 |pages=489–95 |doi=10.1016/j.pedobi.2006.08.006 |bibcode=2007Pedob..50..489H |access-date=14 July 2025 }}</ref><ref>{{cite journal |last=Briones |first=María Jesús Iglesias |year=2014 |title=Soil fauna and soil functions: a jigsaw puzzle |journal=Frontiers in Environmental Science |volume=2 |issue=7 |doi=10.3389/fenvs.2014.00007 |bibcode=2014FrEnS...2....7B |doi-access=free }}</ref>

== Overview ==

The soil is home to circa 59% of the world's biodiversity.<ref>{{cite journal |last1=Anthony |first1=Mark A. |last2=Bender |first2=S. Franz |last3=Van der Heijden |first3=Marcel G. A. |date=7 August 2023 |title=Enumerating soil biodiversity |journal=Proceedings of the National Academy of Sciences of the United States of America |volume=120 |issue=33 |article-number=e2304663120 |doi=10.1073/pnas.2304663120 |pmid=37549278 |pmc=10437432 |bibcode=2023PNAS..12004663A |doi-access=free }}</ref> The links between soil organisms and soil functions are complex. The interconnectedness and complexity of this soil 'food web' means any appraisal of soil function must necessarily take into account interactions with the living communities that exist within the soil.<ref>{{cite journal |last1=Brussaard |first1=Lijbert |last2=Pulleman |first2=Mirjam M. |last3=Ouédraogo |first3=Élisée |last4=Mando |first4=Abdoulaye |last5=Six |first5=Johan |date=4 January 2007 |title=Soil fauna and soil function in the fabric of the food web |url=https://www.academia.edu/19774576 |journal=Pedobiologia |volume=50 |issue=6 |pages=447–62 |doi=10.1016/j.pedobi.2006.10.007 |bibcode=2007Pedob..50..447B |access-date=16 July 2025 }}</ref> Soil organisms break down organic matter, making nutrients available for uptake by plants and other organisms.<ref>{{cite journal |last1=Whalen |first1=Joann K. |last2=Hamel |first2=Chantal |date=20 October 2008 |title=Effects of key soil organisms on nutrient dynamics in temperate agroecosystems |url=https://fr.1lib.sk/book/87162712/254301 |journal=Journal of Crop Improvement |volume=11 |issue=1–2 |pages=175–207 |doi=10.1300/J411v11n01_09 |access-date=16 July 2025 }}</ref> The nutrients stored in the bodies of soil organisms prevent nutrient loss by leaching, in particular for nitrogen and phosphorus.<ref>{{cite journal |last1=Bender |first1=S. Franz |last2=Van der Heijden |first2=Marcel G. A. |date=February 2015 |title=Soil biota enhance agricultural sustainability by improving crop yield, nutrient uptake and reducing nitrogen leaching losses |journal=Journal of Applied Ecology |volume=52 |issue=1 |pages=228–39 |doi=10.1111/1365-2664.12351 |bibcode=2015JApEc..52..228B |doi-access=free }}</ref> Microbial exudates act to maintain soil structure,<ref>{{cite journal |last1=Czarnes |first1=Sonia |last2=Hallett |first2=Paul D. |last3=Bengough |first3=Anthony Glyn |last4=Young |first4=Iain |date=September 2000 |title=Root- and microbial-derived mucilages affect soil structure and water transport |url=https://www.researchgate.net/publication/225007955 |journal=European Journal of Soil Science |volume=51 |issue=3 |pages=435–43 |doi=10.1046/j.1365-2389.2000.00327.x |bibcode=2000EuJSS..51..435C |access-date=16 July 2025 }}</ref> and earthworms are important in bioturbation.<ref>{{cite journal |last1=Piron |first1=Denis |last2=Boizard |first2=Hubert |last3=Heddadj |first3=Djilali |last4=Pérès |first4=Guénola |last5=Hallaire |first5=Vincent |last6=Cluzeau |first6=Daniel |date=November 2017 |title=Indicators of earthworm bioturbation to improve visual assessment of soil structure |url=https://fr.1lib.sk/book/94406902/d33969 |journal=Soil and Tillage Research |volume=173 |pages=53–63 |doi=10.1016/j.still.2016.10.013 |bibcode=2017STilR.173...53P |access-date=16 July 2025 }}</ref> However, critical aspects about how these populations function and interact are unclear. The discovery of glomalin in 1996 indicates that the knowledge to correctly answer some of the most basic questions about the biogeochemical cycle in soils is lacking.<ref>{{cite journal |last1=Treseder |first1=Kathleen K. |last2=Turner |first2=Katie M. |date=July 2007 |title=Glomalin in ecosystems |url=https://www.academia.edu/7796139 |journal=Soil Science Society of America Journal |volume=71 |issue=4 |pages=1257–66 |doi=10.2136/sssaj2006.0377 |bibcode=2007SSASJ..71.1257T |access-date=16 July 2025 }}</ref> There is much work ahead to gain a better understanding of the ecological role of soil biological components in the biosphere.<ref>{{cite book |last=Souza |first=Tancredo |title=Soil biology in tropical ecosystems |date=20 May 2022 |publisher=Springer Nature |location=Berlin, Germany |isbn=978-3-031-00949-5 |editor-last=Souza |editor-first=Tancredo |pages=37–53 |chapter=Soil organisms and ecological processes |doi=10.1007/978-3-031-00949-5_3 |access-date=16 July 2025 |chapter-url=https://archive.org/details/souza-2022_202507 }}</ref>

In balanced soil, plants grow in an active and steady environment. The nutrient content of the soil and its structure are important for plant well-being, but it is soil life that powers nutrient cycles and provides soil fertility.<ref>{{cite book |last1=Stockdale |first1=Elizabeth A. |last2=Goulding |first2=Keith W. T. |last3=George |first3=Timothy S. |last4=Murphy |first4=Deniel V. |title=Soil conditions and plant growth |date=9 January 2013 |publisher=Wiley-Blackwell |location=Oxford, United Kingdom |isbn=978-1-118-33729-5 |editor-last1=Gregory |editor-first1=Peter J. |editor-last2=Nortcliff |editor-first2=Stephen |pages=49–85 |chapter=Soil fertility |doi=10.1002/9781118337295.ch3 |access-date=17 July 2025 |chapter-url=https://archive.org/details/stockdale-et-al.-2013 }}</ref> Without the activities of soil organisms, organic materials would accumulate as undecayed litter at the soil surface, and there would be no humus<ref>{{cite book |last1=Brussaard |first1=Lijbert |last2=Juma |first2=Noorallah G. |title=Humic substances in terrestrial ecosystems |year=1996 |publisher=Elsevier |location=Amsterdam, The Netherlands |isbn=978-0-444-81516-3 |editor-last=Piccolo |editor-first=Alessandro |pages=329–59 |chapter=Organisms and humus in soils |doi=10.1016/B978-044481516-3/50009-8 |access-date=17 July 2025 |chapter-url=https://fr.1lib.sk/book/68856839/e73098 }}</ref> and no nutrients available for plants.<ref>{{cite book |last1=Hopkins |first1=David W. |last2=Dungait |first2=Jennifer A. J. |title=Soil microbiology and sustainable crop production |date=4 August 2010 |publisher=Springer |location=Dordrecht, The Netherlands |isbn=978-90-481-9479-7 |editor-last1=Dixon |editor-first1=Geoffrey R. |editor-last2=Tilston |editor-first2=Emma L. |pages=59–80 |chapter=Soil microbiology and nutrient cycling |doi=10.1007/978-90-481-9479-7_3 |access-date=17 July 2025 |chapter-url=https://fr.1lib.sk/book/53687480/8d3a3d }}</ref>

The soil biota includes: *Megafauna: size range – 20 mm upward, e.g. moles, rabbits, and rodents. *Macrofauna: size range – 2 to 20 mm, e.g. woodlice, earthworms, beetles, millipedes, slugs, snails, ants, and harvestmen. *Mesofauna: size range – 100 micrometres to 2 mm, e.g. tardigrades, mites, enchytraeids and springtails. *Microfauna and Microflora: size range – 1 to 100 micrometres, e.g. yeasts, bacteria, archaea, fungi, protozoa, nematodes, and rotifers.

Of these, bacteria, archaea and fungi play key roles in maintaining a healthy soil.<ref>{{cite journal |last1=Fierer |first1=Noah |last2=Wood |first2=Stephen A. |last3=Bueno de Mesquita |first3=Clifton P. |date=February 2021 |title=How microbes can, and cannot, be used to assess soil health |url=https://projects.au.dk/fileadmin/projects/ejpsoil/WP5/PhD_School_material/Soil_Systems/Literature_meeting_II/Fierer_SBB_2021.pdf |journal=Soil Biology and Biochemistry |volume=153 |article-number=108111 |doi=10.1016/j.soilbio.2020.108111 |bibcode=2021SBiBi.15308111F |access-date=17 July 2025 }}</ref> They act as decomposers that break down organic materials to produce detritus and other breakdown products.<ref>{{cite book |last=DeAngelis |first=Don L. |title=Dynamics of nutrient cycling and food webs |year=1992 |publisher=Springer |location=Dordrecht, The Netherlands |isbn=978-94-011-2342-6 |editor-last=DeAngelis |editor-first=Don L. |pages=123–41 |chapter=Nutrient interactions of detritus and decomposers |doi=10.1007/978-94-011-2342-6_7 |series=Population and community biology series |issn=1367-5257 |volume=9 |access-date=18 July 2025 |chapter-url=https://archive.org/details/de-angelis-1992 }}</ref> Burrowing soil detritivores, like earthworms, known as ecosystem engineers, ingest detritus and decompose it, while building a good granular soil structure and offering a habitat for various soil organisms.<ref>{{cite journal |last1=Sharma |first1=Dinesh Kumar |last2=Tomar |first2=Sonam |last3=Chakraborty |first3=Debashis |date=25 September 2017 |title=Role of earthworm in improving soil structure and functioning |url=https://www.researchgate.net/publication/320034382 |journal=Current Science |volume=113 |issue=6 |pages=1064–71 |doi=10.18520/cs/v113/i06/1064-1071 |access-date=18 July 2025 }}</ref> Saprotrophs, well represented by fungi, archaea and bacteria, extract soluble nutrients from detritus and soil organic matter, in particular in the rhizosphere.<ref>{{cite journal |last1=Odelade |first1=Kehinde Abraham |last2=Babalola |first2=Olubukola Oluranti |date=12 October 2019 |title=Bacteria, fungi and archaea domains in rhizospheric soil and their effects in enhancing agricultural productivity |journal=International Journal of Environmental Research and Public Health |volume=16 |issue=20 |page=3873 |doi=10.3390/ijerph16203873 |pmid=31614851 |doi-access=free |pmc=6843647 }}</ref> All other organisms living in the soil, each at its position along interconnected trophic networks (also called foodwebs), contribute to good health of the soil ecosystem.<ref>{{cite journal |last1=Lehmann |first1=Johannes |last2=Bossio |first2=Deborah S. |last3=Kögel-Knabner |first3=Ingrid |last4=Rillig |first4=Matthias C. |date=25 August 2020 |title=The concept and future prospects of soil health |url=https://fr.1lib.sk/book/113580842/50f905 |journal=Nature Reviews Earth & Environment |volume=1 |issue=10 |pages=544–53 |doi=10.1038/s43017-020-0080-8 |pmid=33015639 |access-date=17 July 2025 |pmc=7116140 |bibcode=2020NRvEE...1..544L }}</ref>

== Scope ==

Soil biology involves work in the following areas: *Modelling of biological processes and population dynamics *Soil biology, physics and chemistry: occurrence of physicochemical parameters and surface properties on biological processes and population behavior *Population biology and molecular ecology: methodological development and contribution to study microbial and faunal populations; diversity and population dynamics; genetic transfers, influence of environmental factors *Community ecology and functioning processes: interactions between organisms and mineral or organic compounds; involvement of such interactions in soil pathogenicity; transformation of mineral and organic compounds, cycling of elements; soil structuration

Complementary disciplinary approaches are necessarily utilized which involve molecular biology, genetics, ecophysiology, biogeography, ecology, soil processes, organic matter, nutrient cycling<ref name="raul">{{cite journal |last1=Ochoa-Hueso |first1=Raul |last2=Delgado-Baquerizo |first2=Manuel |last3=King |first3=Paul T. A. |last4=Benham |first4=Merryn |last5=Arca |first5=Valentina |last6=Power |first6=Sally Anne |title=Ecosystem type and resource quality are more important than global change drivers in regulating early stages of litter decomposition |journal=Soil Biology and Biochemistry |date=February 2019 |volume=129 |pages=144–52 |doi=10.1016/j.soilbio.2018.11.009 |bibcode=2019SBiBi.129..144O |s2cid=92606851 |url=https://www.academia.edu/41490992 |access-date=18 July 2025 |hdl=10261/336676 |hdl-access=free }}</ref> and landscape ecology.

==Bacteria==

Bacteria are single-cell organisms and the most numerous denizens of agricultural fields, with populations ranging from 100 million to 3 billion in a 'teaspoon' of productive soil.<ref>{{cite web |last=Hoorman |first=James J. |year=2011 |title=The role of soil bacteria |url=https://symbio.co.uk/uploads/PDFs/The%20Role%20of%20Soil%20bacteria.pdf |publisher=Ohio State University |location=Columbus, Ohio |access-date=18 July 2025 }}</ref> They are capable of very rapid reproduction by binary fission (dividing into two) in favourable conditions. When in its exponential phase of growth ''Escherichia coli'' is thus capable of producing 1 milliard more in just 1 hour.<ref>{{cite journal |last=Hagen |first=Stephen J. |date=1 December 2010 |title=Exponential growth of bacteria: constant multiplication through division |url=https://fr.1lib.sk/book/53812741/69d35d |journal=American Journal of Physics |volume=78 |issue=12 |pages=1290–6 |doi=10.1119/1.3483278 |bibcode=2010AmJPh..78.1290H |access-date=18 July 2025 }}</ref> Most soil bacteria live close to plant roots in the rhizosphere and are often referred to as rhizobacteria, helping plants to grow.<ref>{{cite journal |last1=Lugtenberg |first1=Ben |last2=Kamilova |first2=Faina |date=October 2009 |title=Plant-growth-promoting rhizobacteria |url=https://fr.1lib.sk/book/47795051/2e02ce |journal=Annual Review of Microbiology |volume=63 |pages=541–56 |doi=10.1146/annurev.micro.62.081307.162918 |pmid=19575558 |access-date=18 July 2025 }}</ref> Bacteria live in soil water, including the film of moisture surrounding soil particles, where some are able to swim by means of flagella.<ref>{{cite journal |last1=Ramoneda |first1=Josep |last2=Fan |first2=Kunkun |last3=Lucas |first3=Jane M. |last4=Chu |first4=Haiyan |last5=Bissett |first5=Andrew |last6=Strickland |first6=Michael S. |last7=Fierer |first7=Noah |date=January 2024 |title=Ecological relevance of flagellar motility in soil bacterial communities |url=https://www.researchgate.net/publication/380007739 |journal=The ISME Journal |volume=18 |issue=1 |article-number=wrae067 |doi=10.1093/ismejo/wrae067 |pmid=38648266 |access-date=18 July 2025 |pmc=11095265 }}</ref> The majority of the beneficial soil-dwelling bacteria need oxygen (and are thus termed aerobic bacteria), whilst those that do not require air are referred to as anaerobic, and tend to cause putrefaction of dead organic matter.<ref>{{cite book |last=Forbes |first=Shari L. |title=Soil analysis in forensic taphonomy: chemical and biological effects of buried human remains |year=2008 |publisher=CRC Press |location=Boca Raton, Florida |isbn=978-0-429-24949-5 |editor-last1=Tibbett |editor-first1=Mark |editor-last2=Carter |editor-first2=Davisd O. |pages=203–23 |chapter=Decomposition chemistry in a burial environment |doi=10.1201/9781420069921.ch8 |access-date=18 July 2025 |chapter-url=https://fr.1lib.sk/book/86969282/c01208 }}</ref> Aerobic bacteria are most active in a soil that is moist (but not saturated, as this will deprive aerobic bacteria of the air that they require), and neutral soil pH, and where there is plenty of food (carbohydrates and micronutrients from organic matter) available.<ref>{{cite journal |last1=Linn |first1=D. M. |last2=Doran |first2=John W. |date=July–August 1984 |title=Aerobic and anaerobic microbial populations in no-till and plowed soils |url=https://fr.1lib.sk/book/55339465/ba26c5 |journal=Soil Science Society of America Journal |volume=48 |issue=4 |pages=794–9 |doi=10.2136/sssaj1984.03615995004800040019x |bibcode=1984SSASJ..48..794L |access-date=18 July 2025 }}</ref> Hostile conditions will not completely kill bacteria; rather, the bacteria will stop growing and get into a dormant stage, often in the form of clay-coated quiescent colonies,<ref>{{cite journal |last1=England |first1=Laura S. |last2=Lee |first2=Hung |last3=Trevors |first3=Jack T. |date=May 1993 |title=Bacterial survival in soil: effect of clays and protozoa |url=https://www.academia.edu/67564243 |journal=Soil Biology and Biochemistry |volume=25 |issue=5 |pages=525–31 |doi=10.1016/0038-0717(93)90189-I |bibcode=1993SBiBi..25..525E |access-date=18 July 2025 }}</ref> and those individuals with pre-adaptive mutations or rapidly evolving better-adapted traits may compete better in the new conditions.<ref>{{cite journal |last1=Pekkonen |first1=Minna |last2=Ketola |first2=Tarmo |last3=Laakso |first3=Jouni T. |date=30 September 2013 |title=Resource availability and competition shape the evolution of survival and growth ability in a bacterial community |journal=PLOS One |volume=8 |issue=9 |article-number=e76471 |doi=10.1371/journal.pone.0076471 |pmid=24098791 |doi-access=free |pmc=3787024 |bibcode=2013PLoSO...876471P }}</ref> Some Gram-positive bacteria (e.g. ''Bacillus'', ''Clostridium'') produce spores in order to wait for more favourable circumstances,<ref>{{cite journal |last1=Stephenson |first1=Keith |last2=Lewis |first2=Richard J. |date=April 2005 |title=Molecular insights into the initiation of sporulation in Gram-positive bacteria: new technologies for an old phenomenon |journal=FEMS Microbiology Reviews |volume=29 |issue=2 |pages=281–301 |doi=10.1016/j.fmrre.2004.10.003 |pmid=15808745 |doi-access=free }}</ref> and Gram-negative bacteria get into a "nonculturable" resting stage.<ref>{{cite journal |last1=Navarro Llorens |first1=Juana María |last2=Tormo |first2=Antonio |last3=Martínez-García |first3=Esteban |date=July 2010 |title=Stationary phase in gram-negative bacteria |url=https://www.academia.edu/93793235 |journal=FEMS Microbiology Reviews |volume=34 |issue=4 |pages=476–95 |doi=10.1111/j.1574-6976.2010.00213.x |pmid=20236330 |access-date=21 July 2025 }}</ref> Bacteria are colonized by persistent viral agents (bacteriophages) that replicate in bacterial hosts and promote gene transfer,<ref>{{cite journal |last1=Penadés |first1=José R. |last2=Chen |first2=John |last3=Quiles-Puchalt |first3=Nuria |last4=Carpena |first4=Nuria |last5=Novick |first5=Richard P. |date=February 2015 |title=Bacteriophage-mediated spread of bacterial virulence genes |url=https://fr.1lib.sk/book/66937053/67f429 |journal=Current Opinion in Microbiology |volume=23 |pages=171–8 |doi=10.1016/j.mib.2014.11.019 |pmid=25528295 |access-date=21 July 2025 }}</ref> a property of bacteria-virus relationships now currently used in genetic engineering.<ref>{{cite journal |last1=Pires |first1=Diana P. |last2=Cleto |first2=Sara |last3=Sillankorva |first3=Sanna |last4=Azeredo |first4=Joana |last5=Lu |first5=Timothy K. |date=1 June 2016 |title=Genetically engineered phages: a review of advances over the last decade |url=https://fr.1lib.sk/book/86396708/fdda82 |journal=Microbiology and Molecular Biology Reviews |volume=80 |issue=3 |pages=523–43 |doi=10.1128/mmbr.00069-15 |pmid=27250768 |access-date=21 July 2025 |pmc=4981678 |hdl=1822/43301 }}</ref>

From the organic gardener's point of view, the important roles that bacteria play are:

thumb|350px|right|The nitrogen cycle

===Nitrification===

Nitrification is a vital part of the nitrogen cycle, wherein certain chemolithotrophic nitrifying bacteria (e.g. ''Nitrosomonas''), called autotrophic nitrifiers (manufacturing their own carbohydrate supply without using the process of photosynthesis) are able to transform nitrogen in the form of ammonium, which is produced by the decomposition of proteins, into nitrates, available to growing plants and once again converted to proteins.<ref>{{cite journal |last=Prosser |first=James Ivor |year=1990 |title=Autotrophic nitrification in bacteria |url=https://fr.1lib.sk/book/63711198/aa7b3f |journal=Advances in Microbial Physiology |volume=30 |pages=125–81 |doi=10.1016/S0065-2911(08)60112-5 |pmid=2700538 |isbn=978-0-12-027730-8 |access-date=21 July 2025 }}</ref> Other nitrifying bacteria (e.g. ''Arthrobacter'') are able of heterotrophic nitrification, a still badly known biochemical process of soil nitrogen transformation.<ref>{{cite journal |last1=Brierley |first1=Euan D. R. |last2=Wood |first2=Martin |date=August 2001 |title=Heterotrophic nitrification in an acid forest soil: isolation and characterisation of a nitrifying bacterium |url=https://fr.1lib.sk/book/49826656/b82024 |journal=Soil Biology and Biochemistry |volume=33 |issue=10 |pages=1403–9 |doi=10.1016/S0038-0717(01)00045-1 |bibcode=2001SBiBi..33.1403B |access-date=21 July 2025 }}</ref>

===Nitrogen fixation===

In another part of the nitrogen cycle, the process of nitrogen fixation constantly puts additional nitrogen into biological circulation. This is carried out by free-living nitrogen-fixing (diazotroph) bacteria in the soil or water such as ''Azotobacter'' and heterocyst-bearing cyanobacteria (blue-green algae), or by those that live in close symbiosis with legumes, such as rhizobia, or with actinorhizal plants, such as ''Frankia''. These form colonies in nodules they create on the roots of peas, beans, ''Casuarina'' and related flowering plants. Nitrogen-fixing bacteria are able to convert nitrogen from the atmosphere into nitrogen-containing organic substances,<ref>{{cite journal |last1=Franche |first1=Claudine |last2=Lindström |first2=Kristina |last3=Elmerich |first3=Claudine |date=3 December 2008 |title=Nitrogen-fixing bacteria associated with leguminous and non-leguminous plants |url=https://www.researchgate.net/publication/225535435 |journal=Plant and Soil |volume=321 |issue=1–2 |pages=35–59 |doi=10.1007/s11104-008-9833-8 |access-date=21 July 2025 }}</ref> and thus play a decisive role in incipient soil formation.<ref>{{cite journal |last1=Schulz |first1=Stefanie |last2=Brankatschk |first2=Robert |last3=Dümig |first3=Alexander |last4=Kögel-Knabner |first4=Ingrid |last5=Schloter |first5=Michael |last6=Zeyer |first6=Josef |date=18 June 2013 |title=The role of microorganisms at different stages of ecosystem development for soil formation |journal=Biogeosciences |volume=10 |issue=6 |pages=3983–96 |doi=10.5194/bg-10-3983-2013 |bibcode=2013BGeo...10.3983S |doi-access=free |hdl=20.500.11850/70776 |hdl-access=free }}</ref>

===Denitrification===

While nitrogen fixation converts nitrogen from the atmosphere into organic compounds, a series of processes called denitrification returns some amount of nitrogen to the atmosphere. Denitrifying bacteria tend to be anaerobes, or facultatively anaerobes (can alter between the oxygen dependent and oxygen independent types of metabolisms), including ''Achromobacter'' and ''Pseudomonas''. The denitrification process caused by oxygen-free conditions converts nitrates and nitrites in soil into nitrogen gas or into gaseous compounds such as nitrous oxide or nitric oxide. In excess, denitrification can lead to overall losses of available soil nitrogen and subsequent loss of soil fertility.<ref>{{cite journal |last=Groffman |first=Peter M. |date=8 November 2012 |title=Terrestrial denitrification: challenges and opportunities |journal=Ecological Processes |volume=1 |issue=11 |article-number=11 |doi=10.1186/2192-1709-1-11 |bibcode=2012EcoPr...1...11G |doi-access=free }}</ref> An excess of nitrogen fertilizers may cause denitrification<ref>{{cite journal |last1=Mulvaney |first1=Richard L. |last2=Khan |first2=Shahoor ad |last3=Mulvaney |first3=C. S. |date=February 1997 |title=Nitrogen fertilizers promote denitrification |url=https://fr.1lib.sk/book/39392824/310392 |journal=Biology and Fertility of Soils |volume=24 |issue=2 |pages=211–20 |doi=10.1007/s003740050233 |bibcode=1997BioFS..24..211M |access-date=22 July 2025 }}</ref> in addition to nitrate loss by percolation to the aquifer.<ref>{{cite journal |last1=Burkart |first1=Michael R. |last2=Stoner |first2=Jeffrey D. |date=1 May 2002 |title=Nitrate in aquifers beneath agricultural systems |url=https://fr.1lib.sk/book/95148789/fa3a0e |journal=Water Science and Technology |volume=45 |issue=9 |pages=19–29 |doi=10.2166/wst.2002.0195 |pmid=12079102 |bibcode=2002WSTec..45Q..19B |access-date=22 July 2025 |url-access=subscription }}</ref> However, fixed nitrogen may circulate many times between organisms and the soil before denitrification returns it to the atmosphere, as shown by the diagram above illustrating the nitrogen cycle.

===Actinomycetota===

Actinomycetota (actinomycetes, actinobacteria) are critical in the decomposition of organic matter and in humus formation. They specialize in breaking down cellulose and lignin<ref>{{cite journal |last1=Mason |first1=J. Clark |last2=Richards |first2=Michelle |last3=Zimmermann |first3=Wolfgang |last4=Broda |first4=Paul |date=May 1988 |title=Identification of extracellular proteins from actinomycetes responsible for the solubilisation of lignocellulose |url=https://fr.1lib.sk/book/37544245/a6cb16 |journal=Applied Microbiology and Biotechnology |volume=28 |issue=3 |pages=276–80 |doi=10.1007/BF00250455 |access-date=22 July 2025 }}</ref> along with the tough chitin<ref>{{cite journal |last1=Lacombe-Harvey |first1=Marie-Ève |last2=Brzezinski |first2=Ryszard |last3=Beaulieu |first3=Carole |date=21 June 2018 |title=Chitinolytic functions in actinobacteria: ecology, enzymes, and evolution |url=https://www.researchgate.net/publication/325917137 |journal=Applied Microbiology and Biotechnology |volume=102 |issue=17 |pages=7219–30 |doi=10.1007/s00253-018-9149-4 |pmid=29931600 |access-date=22 July 2025 |pmc=6097792 }}</ref> found in the exoskeletons of arthropods. Their various production of volatile metabolites is responsible for the sweet ''earthy'' aroma associated with a good healthy soil.<ref>{{cite journal |last1=Schöller |first1=Charlotte E. G. |last2=Gürtier |first2=Hanne |last3=Pedersen |first3=Rita |last4=Molin |first4=Søren |last5=Wilkins |first5=Ken |date=27 March 2002 |title=Volatile metabolites from actinomycetes |url=https://fr.1lib.sk/book/53465747/873720 |journal=Journal of Agricultural and Food Chemistry |volume=50 |issue=9 |pages=2615–21 |doi=10.1021/jf0116754 |pmid=11958631 |bibcode=2002JAFC...50.2615S |access-date=22 July 2025 }}</ref> They require plenty of air and a pH between 6.0 and 7.5, but are more tolerant of dry conditions than most other bacteria and fungi.<ref>{{cite web |url=https://www.the-compost-gardener.com/actinomycetes.html |title=Actinomycetes: remarkable antibiotic, nitrogen fixing, decomposer bacteria |website=www.the-compost-gardener.com |access-date=22 July 2025 }}</ref>

==Fungi==

A gram of garden soil can contain around one million fungi, such as yeasts and moulds, and around 700 km fungal hyphae can live in 1 g of soil.<ref>{{cite journal |last1=Bridge |first1=Paul |last2=Spooner |first2=Brian |date=May 2001 |title=Soil fungi: diversity and detection |url=https://fr.1lib.sk/book/43238146/626729 |journal=Plant and Soil |volume=232 |issue=1–2 |pages=147–54 |doi=10.1023/A:1010346305799 |bibcode=2001PlSoi.232..147B |access-date=22 July 2025 }}</ref> Fungi have no chlorophyll, and are not able to photosynthesise. They cannot use atmospheric carbon dioxide as a source of carbon, therefore they are chemo-heterotrophic, meaning that, like animals, they require a chemical source of energy rather than being able to use light as an energy source, as well as organic substrates to get carbon for growth and development. Given these requirements and the development of a dense hyphal network (mycelium) they actively participate to the degradation of freshly deposited organic remains and their transformation in humus (humification) and carbon dioxide (mineralization).<ref>{{cite book |last=Guggenberger |first=Georg |title=Microorganisms in soils: roles in genesis and functions |year=2005 |publisher=Springer-Verlag |location=Berlin, Germany |isbn=978-3-540-26609-9 |editor-last1=Varma |editor-first1=Ajit |editor-last2=Buscot |editor-first2=François |pages=85–106 |chapter=Humification and mineralization in soils |series=Soil Biology |volume=3 |doi=10.1007/3-540-26609-7_4 |access-date=22 July 2025 |chapter-url=https://fr.1lib.sk/book/47776478/0227be }}</ref>

Many fungi are parasitic, often causing disease to their living host plant, although some have beneficial relationships with living plants, as illustrated below. In terms of soil and humus creation, the most important fungi tend to be saprotrophic; that is, they live on dead or decaying organic matter, thus breaking it down and converting it to mineral forms (e.g. nitrate, ammonium, phosphate) that are available to the higher plants. A succession of fungi species will colonise the dead matter, beginning with those that use sugars and starches, which are succeeded by those that are able to break down cellulose and lignins.<ref>{{cite book |last1=Kjøller |first1=Annelise H. |last2=Struwe |first2=Sten |title=Enzymes in the environment: activity, ecology, and applications |year=2002 |publisher=CRC Press |location=Boca Raton, Florida |isbn=978-0-429-20757-0 |editor-last1=Burns |editor-first1=Richard G. |editor-last2=Dick |editor-first2=Richard P. |pages=267–84 |chapter=Fungal communities, succession, enzymes, and decomposition |access-date=22 July 2025 |chapter-url=https://archive.org/details/kjoller-struwe-2002 }}</ref>

Fungi spread underground by sending long thin threads known as mycelium throughout the soil; these threads can be observed throughout many soils and compost heaps. From the mycelia the fungi is able to throw up its fruiting bodies, the visible part above the soil (e.g., mushrooms, toadstools, and puffballs), which may contain millions of spores. When the fruiting body bursts, these spores are dispersed through the air to settle in fresh environments, and are able to lie dormant for up to years until the right conditions for their activation arise or the right food is made available.<ref>{{cite journal |last1=Feofilova |first1=E. P. |last2=Ivashechkin |first2=Aleksey A. |last3=Alekhin |first3=A. I. |last4=Sergeeva |first4=Yana E. |date=29 December 2011 |title=Fungal spores: dormancy, germination, chemical composition, and role in biotechnology (review) |url=https://fr.1lib.sk/book/53053083/0bc5ee |journal=Applied Biochemistry and Microbiology |volume=48 |issue=1 |pages=1–11 |doi=10.1134/S0003683812010048 |access-date=22 July 2025 }}</ref> Fungal spores are dispersed by wind,<ref>{{cite book |last1=McCartney |first1=Alastair |last2=West |first2=Jon |title=Food mycology: a multifaceted approach to fungi and food |date=26 June 2007 |publisher=CRC Press |location=Boca Raton, Florida |isbn=978-0-429-18901-2 |editor-last1=Dijksterhuis |editor-first1=Jan |editor-last2=Samson |editor-first2=Robert A. |pages=65–81 |chapter=Dispersal of fungal spores through the air |access-date=23 July 2025 |chapter-url=https://archive.org/details/mc-cartney-west-2007 }}</ref> water,<ref>{{cite journal |last1=Golan |first1=Jacob J. |last2=Pringle |first2=Anne |date=14 July 2017 |title=Long-distance dispersal of fungi |url=https://www.researchgate.net/publication/318455657 |journal=Microbiology Spectrum |volume=5 |issue=4 |pages=1–24 |article-number=5.4.03 |doi=10.1128/microbiolspec.funk-0047-2016 |pmid=28710849 |access-date=23 July 2025 |pmc=11687522 }}</ref> but also by a variety of fungal-feeding animals, from small invertebrates (e.g. springtails)<ref>{{cite journal |last=Dromph |first=Karsten M. |year=2001 |title=Dispersal of entomopathogenic fungi by collembolans |url=https://fr.1lib.sk/book/49826737/af7f3e |journal=Soil Biology and Biochemistry |volume=33 |issue=15 |pages=2047–51 |doi=10.1016/S0038-0717(01)00130-4 |bibcode=2001SBiBi..33.2047D |access-date=23 July 2025 }}</ref> to big mammals (e.g. wild boars),<ref>{{cite journal |last1=Piattoni |first1=Federica |last2=Oir |first2=Francesca |last3=Morara |first3=Marco |last4=Iotti |first4=Mirco |last5=Zambonelli |first5=Alessandra |year=2012 |title=The role of wild boars in spore dispersal of hypogeous fungi |journal=Acta Mycologica |volume=47 |issue=2 |pages=145–53 |doi=10.5586/am.2012.017 |doi-access=free }}</ref> helping them to colonize new, sometimes remote environments, hence the cosmopolitan distribution of many fungal species.<ref>{{cite journal |last1=Sato |first1=Hirotoshi |last2=Tsujino |first2=Riyou |last3=Kurita |first3=Kazuki |last4=Yokoyama |first4=Kazumasa |last5=Agata |first5=Kiyokazu |date=November 2012 |title=Modelling the global distribution of fungal species: new insights into microbial cosmopolitanism |journal=Molecular Ecology |volume=21 |issue=22 |pages=5599–612 |doi=10.1111/mec.12053 |pmid=23062148 |bibcode=2012MolEc..21.5599S |url=https://fr.1lib.sk/book/53049966/b58e99 |access-date=23 July 2025 |url-access=subscription }}</ref>

===Mycorrhizae===

Those fungi that are able to live symbiotically with living plants, creating a relationship that is beneficial to both, are known as mycorrhizae (from ''myco'' meaning fungus and ''rhiza'' meaning root). In mycorrhizae plant roots are invaded by the mycelia of the mycorrhizal fungus, which lives partly in the soil and partly in the root, and may either penetrate the root cortex without entering its cells (forming the Hartig net) and cover the root as a sheath (ectomycorrhizae) or be present in cortical cells in the form of arbuscules (arbuscular mycorrhizae). The mycorrhizal fungus obtains the carbohydrates that it requires from the root,<ref>{{cite book |last1=Hampp |first1=Rüdiger |last2=Schaeffer |first2=Christoph |title=Mycorrhiza: structure, function, molecular biology and biotechnology |year=1999 |publisher=Springer |location=Berlin, Germany |edition=second |isbn=978-3-662-03779-9 |editor-last1=Varma |editor-first1=Ajit |editor-last2=Hock |editor-first2=Bertold |pages=273–303 |chapter=Mycorrhiza: carbohydrate and energy metabolism |access-date=24 July 2025 |chapter-url=https://archive.org/details/hampp-schaeffer-1999 |doi=10.1007/978-3-662-03779-9_12 }}</ref> in return providing the plant with nutrients, including nitrogen<ref>{{cite journal |last1=Govindarajulu |first1=Manjula |last2=Pfeffer |first2=Philip E. |last3=Jin |first3=Hairu |last4=Abubaker |first4=Jehad |last5=Douds |first5=David D. |last6=Allen |first6=James W. |last7=Bücking |first7=Heike |last8=Lammers |first8=Peter J. |last9=Shachar-Hill |first9=Yair |date=9 June 2005 |title=Nitrogen transfer in the arbuscular mycorrhizal symbiosis |url=https://www.researchgate.net/publication/7797122 |journal=Nature |volume=435 |issue=7043 |pages=819–23 |doi=10.1038/nature03610 |pmid=15944705 |bibcode=2005Natur.435..819G |access-date=24 July 2025 }}</ref> and phosphorus,<ref>{{cite journal |last1=Plassard |first1=Claude |last2=Becquer |first2=Adeline |last3=Garcia |first3=Kevin |date=September 2019 |title=Phosphorus transport in mycorrhiza: how far are we? |url=https://www.academia.edu/105159639 |journal=Trends in Plant Science |volume=24 |issue=9 |pages=794–801 |doi=10.1016/j.tplants.2019.06.004 |pmid=31272899 |bibcode=2019TPS....24..794P |access-date=24 July 2025 }}</ref> and with moisture.<ref>{{cite journal |last1=Plamboeck |first1=Agneta H. |last2=Dawson |first2=Todd E. |last3=Egerton-Warburton |first3=Louise M. |last4=North |first4=Malcolm |last5=Bruns |first5=Thomas D. |last6=Querejeta |first6=José Ignacio |date=1 March 2007 |title=Water transfer via ectomycorrhizal fungal hyphae to conifer seedlings |url=https://www.researchgate.net/publication/6473985 |journal=Mycorrhiza |volume=17 |issue=5 |pages=439–47 |doi=10.1007/s00572-007-0119-4 |pmid=17333298 |bibcode=2007Mycor..17..439P |access-date=24 July 2025 }}</ref> Later the plant roots will also absorb the mycelium into its own tissues.<ref>{{cite journal |last1=Gutjahr |first1=Caroline |last2=Parniske |first2=Martin |date=5 June 2017 |title=Control of partner lifetime in a plant-fungus relationship |journal=Current Biology |volume=27 |issue=11 |pages=R420–R423 |doi=10.1016/j.cub.2017.04.020 |pmid=28586667 |doi-access=free }}</ref> In some cases mycorrhizae could provide their host, either directly or indirectly, with nutrients issued from the degradation of more complex soil organic matter (humus).<ref>{{cite journal |last1=Wu |first1=Songlin |last2=Fu |first2=Wei |last3=Rillig |first3=Matthias C. |last4=Chen |first4=Baodong |last5=Zhu |first5=Yong-Guan |last6=Huang |first6=Longbin |date=May 2024 |title=Soil organic matter dynamics mediated by arbuscular mycorrhizal fungi: an updated conceptual framework |journal=New Phytologist |volume=242 |issue=4 |pages=1417–25 |doi=10.1007/s00572-007-0119-4 |pmid=17333298 |bibcode=2007Mycor..17..439P |doi-access=free }}</ref> Mycorrhizae can also benefit nutrients (other than sugar carbon) and moisture from the host,<ref>{{cite journal |last1=Wang |first1=Wanxiao |last2=Shi |first2=Jincai |last3=Xie |first3=Qiujin |last4=Jiang |first4=Yina |last5=Yu |first5=Nan |last6=Wang |first6=Ertao |date=12 September 2017 |title=Nutrient exchange and regulation in arbuscular mycorrhizal symbiosis |journal=Molecular Plant |volume=10 |issue=9 |pages=1147–58 |doi=10.1016/j.molp.2017.07.012 |pmid=28782719 |bibcode=2017MPlan..10.1147W |doi-access=free }}</ref><ref>{{cite journal |last1=Querejeta |first1=José |last2=Egerton-Warburton |first2=Louise M. |last3=Allen |first3=Michael F. |date=January 2003 |title=Direct nocturnal water transfer from oaks to their mycorrhizal symbionts during severe soil drying |url=https://www.academia.edu/65856381 |journal=Oecologia |volume=134 |issue=1 |pages=55–64 |doi=10.1007/s00442-002-1078-2 |pmid=12647179 |bibcode=2003Oecol.134...55Q |access-date=25 July 2025 }}</ref> and exchange nutrients (including carbon) and moisture between plants through common mycorrhizal networks.<ref>{{cite journal |last1=Fitter |first1=Alastair H. |last2=Graves |first2=J. D. |last3=Watkins |first3=N. K. |last4=Robinson |first4=David |last5=Scrimgeour |first5=Charlie |date=June 1998 |title=Carbon transfer between plants and its control in networks of arbuscular mycorrhizas |journal=Functional Ecology |volume=12 |issue=3 |pages=406–12 |doi=10.1046/j.1365-2435.1998.00206.x |bibcode=1998FuEco..12..406F |doi-access=free }}</ref><ref>{{cite journal |last1=He |first1=Xin-Hua |last2=Critchley |first2=Christa |last3=Bledsoe |first3=Caroline |date=18 June 2010 |title=Nitrogen transfer within and between plants through Common Mycorrhizal Networks (CMNs) |url=https://fr.1lib.sk/book/50938261/c5a155 |journal=Critical Reviews in Plant Sciences |volume=22 |issue=6 |pages=531–67 |doi=10.1080/713608315 |access-date=25 July 2025 |url-access=subscription }}</ref><ref>{{cite journal |last1=Egerton-Warburton |first1=Louise M. |last2=Querejeta |first2=José Ignacio |last3=Allen |first3=Michael F. |date=April 2007 |title=Common mycorrhizal networks provide a potential pathway for the transfer of hydraulically lifted water between plants |url=https://www.researchgate.net/publication/6455980 |journal=Journal of Experimental Botany |volume=58 |issue=6 |pages=1473–83 |doi=10.1093/jxb/erm009|pmid=17350936 |access-date=25 July 2025 }}</ref> Chemical signalling between plants through common mycorrhizal networks, although a beautiful concept, is still a matter of conjecture, more research being needed.<ref>{{cite journal |last1=Barto |first1=E. Kathryn |last2=Weidenhamer |first2=Jeffrey D. |last3=Cipollini |first3=Don |last4=Rillig |first4=Matthias C. |date=November 2012 |title=Fungal superhighways: do common mycorrhizal networks enhance below ground communication? |url=https://www.researchgate.net/publication/229434864 |journal=Trends in Plant Science |volume=17 |issue=11 |pages=633–7 |doi=10.1016/j.tplants.2012.06.007 |pmid=22818769 |bibcode=2012TPS....17..633B |access-date=25 July 2025 }}</ref><ref>{{cite journal |last1=Rillig |first1=Matthias C. |last2=Lehmann |first2=Anika |last3=Lanfranco |first3=Luisa |last4=Caruso |first4=Tancredi |last5=Johnson |first5=David |date=June 2025 |title=Clarifying the definition of common mycorrhizal networks |journal=Functional Ecology |volume=39 |issue=6 |pages=1411–7 |doi=10.1111/1365-2435.14545 |bibcode=2025FuEco..39.1411R |doi-access=free }}</ref>

Beneficial mycorrhizal associations (either ectomycorrhizae or arbuscular mycorrhizae) are to be found in many of our edible and flowering crops, to the exception of Brassicaceae (e.g. cabbage, turnip) as well as in the majority of tree species, especially in forests and woodlands, with Ericaceae (e.g. bracken, bilberry) harbouring a special type, called ericoid mycorrhizae.<ref>{{cite journal |last1=Newman |first1=Edward I. |last2=Reddell |first2=Paul |date=August 1987 |title=The distribution of mycorrhizas among families of vascular plants |journal=New Phytologist |volume=106 |issue=4 |pages=745–51 |doi=10.1111/j.1469-8137.1987.tb00175.x |pmid=33874079 |bibcode=1987NewPh.106..745N |doi-access=free }}</ref> Tree mycorrhizae create a fine underground mesh that extends greatly beyond the limits of the tree's roots, greatly increasing their feeding range and actually causing neighbouring trees to become physically interconnected.<ref>{{cite journal |last1=Selosse |first1=Marc-André |last2=Richard |first2=Franck |last3=He |first3=Xinhua |last4=Simard |first4=Suzanne W. |date=November 2006 |title=Mycorrhizal networks: ''des liaisons dangereuses''? |url=https://fr.1lib.sk/book/49512111/1ad94a |journal=Trends in Ecology and Evolution |volume=21 |issue=11 |pages=621–8 |doi=10.1016/j.tree.2006.07.003 |pmid=16843567 |bibcode=2006TEcoE..21..621S |access-date=25 July 2025 }}</ref> The benefits of mycorrhizal relations to their plant partners are not limited to nutrients, but can be essential for plant reproduction. In situations where little light is able to reach the forest floor, a young seedling cannot obtain sufficient light to photosynthesise for itself and will not grow properly, causing a deficit of regeneration.<ref>{{cite journal |last1=Nicotra |first1=Adrienne B. |last2=Chazdon |first2=Robin L. |last3=Iriarte |first3=Silvia V. B. |date=September 1999 |title=Spatial heterogeneity of light and woody seedling regeneration in tropical wet forests |url=https://www.academia.edu/33974229 |journal=Ecology |volume=80 |issue=6 |page=1908–26 |doi=10.1890/0012-9658(1999)080[1908:SHOLAW]2.0.CO;2 |access-date=25 July 2025 }}</ref> But, if the ground is underlain by a mycorrhizal mat, then the developing seedling will throw down roots that can link with the fungal threads and through them obtain the nutrients it needs.<ref>{{cite journal |last1=Högberg |first1=Peter |last2=Högberg |first2=Mona N. |date=15 July 2022 |title=Does successful forest regeneration require the nursing of seedlings by nurse trees through mycorrhizal interconnections? |url=https://pub.epsilon.slu.se/29156/1/hogberg-p-et-al-20221007.pdf |journal=Forest Ecology and Management |volume=516 |issue=2 |article-number=120252 |doi=10.1016/j.foreco.2022.120252 |bibcode=2022ForEM.51620252H |access-date=25 July 2025 }}</ref>

David Attenborough points out the plant, fungi, animal relationship that creates a "three way harmonious trio" to be found in forest ecosystems, wherein the plant/fungi symbiosis is enhanced by animals such as the wild boar, deer, mice, or flying squirrel, which feed upon the fungi's fruiting bodies, including truffles, and cause their further spread.<ref>{{cite web |last=Attenborough |first=David |year=1995 |title=The private life of plants, a BBC nature documentary series written and presented by David Attenborough |url=https://archive.org/details/the-private-life-of-plants-e-04-the-social-struggle |access-date=28 July 2025 }}</ref> A greater understanding of the complex relationships that pervade natural systems is one of the major justifications of the organic gardener, in refraining from the use of artificial chemicals and the damage these might cause.<ref>{{cite journal |last1=George |first1=Nirmal Philip |last2=Ray |first2=Joseph George |date=24 February 2023 |title=The inevitability of arbuscular mycorrhiza for sustainability in organic agriculture: a critical review |journal=Frontiers in Sustainable Food Systems |volume=7 |article-number=1124688 |doi=10.3389/fsufs.2023.1124688 |bibcode=2023FrSFS...724688G |doi-access=free }}</ref>

Recent research has shown that arbuscular mycorrhizal fungi produce glomalin, a protein that binds soil particles and stores both carbon and nitrogen. These glomalin-related soil proteins are an important part of soil organic matter.<ref name=usda02>{{cite journal |url=https://agresearchmag.ars.usda.gov/AR/archive/2002/Sep/soil0902.pdf |title=Glomalin: hiding place for a third of the world's stored soil carbon |date=September 2002 |first=Don |last=Comis |journal=Agricultural Research |volume=50 |issue=9 |pages=4–7 |access-date=28 July 2025 }}</ref>

==Invertebrates== {{main|Soil animals}} Soil fauna affect soil formation and soil organic matter dynamically on many spatiotemporal scales.<ref>{{cite journal |date=15 December 2018 |title=Effects of soil macro- and mesofauna on litter decomposition and soil organic matter stabilization |journal=Geoderma |language=en |volume=332 |pages=161–172 |doi=10.1016/j.geoderma.2017.08.039|issn=0016-7061 |last1=Frouz |first1=Jan |bibcode=2018Geode.332..161F |s2cid=135319222 |url=https://fr.1lib.sk/book/98524669/a7baf3 |access-date=28 July 2025 }}</ref> Earthworms, ants and termites, known as ecosystem engineers, mix the soil as they burrow, significantly affecting soil formation and organic matter dynamics.<ref>{{cite journal |last1=Franco |first1=André L. C. |last2=Cherubin |first2=Mauricio R. |last3=Cerri |first3=Carlos E. P. |last4=Six |first4=Johan |last5=Wall |first5=Diana H. |last6=Cerri |first6=Carlos C. |date=November 2020 |title=Linking soil engineers, structural stability, and organic matter allocation to unravel soil carbon responses to land-use change |url=https://fr.1lib.sk/book/113809717/e15380 |journal=Soil Biology and Biochemistry |volume=150 |article-number=107998 |doi=10.1016/j.soilbio.2020.107998 |bibcode=2020SBiBi.15007998F |access-date=28 July 2025 }}</ref> Earthworms ingest soil particles and organic residues, enhancing the availability of plant nutrients in the material that passes through and out of their bodies.<ref>{{cite journal |last1=Bhadauria |first1=Tunira |last2=Saxena |first2=Krishan Gopal |date=14 December 2009 |title=Role of earthworms in soil fertility maintenance through the production of biogenic structures |journal=Applied and Environmental Soil Science |volume=2010 |page=ID 816073 |doi=10.1155/2010/816073 |doi-access=free }}</ref> By aerating and stirring the soil, and by increasing the stability of soil aggregates, these organisms help to assure the ready infiltration of water.<ref>{{cite journal |last1=Bouché |first1=Marcel B. |last2=Al-Addan |first2=Fathel |date=March–April 1997 |title=Earthworms, water infiltration and soil stability: some new assessments |url=https://fr.1lib.sk/book/49827228/4e5c48 |journal=Soil Biology and Biochemistry |volume=29 |issue=3–4 |pages=441–452 |doi=10.1016/S0038-0717(96)00272-6 |bibcode=1997SBiBi..29..441B |access-date=28 July 2025 |url-access=subscription }}</ref> These organisms in the soil also help improve pH levels, by buffering them around neutrality, an equilibrating process (negative feedback loop) by which fungal activity is favoured in alkaline soils<ref>{{cite journal |last1=Gong |first1=Xing |last2=Wang |first2=Shuai |last3=Wang |first3=Zhenwei |last4=Jiang |first4=Yuji |last5=Hu |first5=Zhengkun |last6=Zheng |first6=Yong |last7=Chen |first7=Xiaoyun |last8=Li |first8=Huixin |last9=Hu |first9=Feng |last10=Liu |first10=Manqiang |last11=Scheu |first11=Stefan |date=1 August 2019 |title=Earthworms modify soil bacterial and fungal communities through enhancing aggregation and buffering pH |url=https://fr.1lib.sk/book/106332794/300dda |journal=Geoderma |volume=347 |pages=59–69 |doi=10.1016/j.geoderma.2019.03.043 |bibcode=2019Geode.347...59G |access-date=28 July 2025 }}</ref> while bacterial activity is favoured in acid soils.<ref>{{cite journal |last1=Dempsey |first1=Mark A. |last2=Fisk |first2=Melany C. |last3=Fahey |first3=Timothy J. |date=October 2011 |title=Earthworms increase the ratio of bacteria to fungi in northern hardwood forest soils, primarily by eliminating the organic horizon |url=https://fr.1lib.sk/book/46056188/c274a5 |journal=Soil Biology and Biochemistry |volume=43 |issue=10 |pages=2135–41 |doi=10.1016/j.soilbio.2011.06.017 |bibcode=2011SBiBi..43.2135D |access-date=28 July 2025 }}</ref>

Ants and termites are also often referred to as ''soil engineers'' because, when they create their nests, there are several chemical and physical changes made to the soil.<ref>{{cite book |last1=de Souza |first1=Henrique Jesus |last2=Delabie |first2=Jacques Hubert Charles |title=Encyclopedia of social insects |year=2019 |publisher=Springer |location=Berlin, Germany |isbn=978-3-319-90306-4 |editor-last=Starr |editor-first=Christopher K. |chapter=Ecosystem engineers, ants and termites |access-date=29 July 2025 |chapter-url=https://archive.org/details/de-souza-delabie-2020 |doi=10.1007/978-3-319-90306-4_186-2 }}</ref> Among these changes are increasing presence of the most essential elements like carbon, nitrogen, and phosphorus, elements needed for plant growth.<ref>{{cite journal |last1=Evans |first1=Theodore A. |last2=Dawes |first2=Tracy Z. |last3=Ward |first3=Philip R. |last4=Lo |first4=Nathan |date=29 March 2011 |title=Ants and termites increase crop yield in a dry climate |journal=Nature Communications |volume=2 |article-number=262 |doi=10.1038/ncomms1257 |pmid=21448161 |pmc=3072065 |bibcode=2011NatCo...2..262E |doi-access=free }}</ref> They also can gather soil particles from differing depths of soil and deposit them in other places, leading to the mixing of soil so it is richer with nutrients and other elements.<ref>{{cite journal |last1=Muon |first1=Ratha |last2=Ket |first2=Pinnara |last3=Sebag |first3=David |last4=Boukbida |first4=Hanane Aroui |last5=Podwojewski |first5=Pascal |last6=Hervé |first6=Vincent |last7=Ann |first7=Vannak |last8=Jouquet |first8=Pascal |date=June 2023 |title=Termite constructions as patches of soil fertility in Cambodian paddy fields |url=https://hal.science/hal-04098870v1/file/Termite.pdf |journal=Geoderma Regional |volume=33 |article-number=e00640 |doi=10.1016/j.geodrs.2023.e00640 |bibcode=2023GeodR..3300640M |access-date=29 July 2025 }}</ref><ref>{{cite journal |last1=Eldridge |first1=David J. |last2=Pickard |first2=John |year=1994 |title=Effects of ants on sandy soils in semi-arid eastern Australia. II. Relocation of nest entrances and consequences for bioturbation |url=https://www.researchgate.net/publication/248884625 |journal=Soil Research |volume=32 |issue=2 |pages=323–33 |doi=10.1071/SR9940323 |bibcode=1994SoilR..32..323E |access-date=29 July 2025 }}</ref>

==Vertebrates== {{main|Soil animals}} thumb|Gopher sticking out of burrow The soil is also important to many mammals. Gophers, moles, prairie dogs, and other burrowing animals rely on this soil for protection and food.<ref>{{cite journal |last=Kinlaw |first=Al |date=February 1999 |title=A review of burrowing by semi-fossorial vertebrates in arid environments |url=https://www.academia.edu/48388183 |journal=Journal of Arid Environments |volume=41 |issue=2 |pages=127–45 |doi=10.1006/jare.1998.0476 |bibcode=1999JArEn..41..127K |access-date=29 July 2025 }}</ref> The animals even give back to the soil as their burrowing creates nutrient-rich patches and allows more water to infiltrate the soil by increasing porosity, thus decreasing runoff along slopes.<ref>{{cite journal |last1=Platt |first1=Brian F. |last2=Kolb |first2=Dakota J. |last3=Kunhardt |first3=Christian G. |last4=Milo |first4=Scott P. |last5=New |first5=Lee G. |date=March–April 2016 |title=Burrowing through the literature: the impact of soil-disturbing vertebrates on physical and chemical properties of soil |url=https://fr.1lib.sk/book/91044921/0459bd |journal=Soil Science |volume=181 |issue=3–4 |pages=175–91 |doi=10.1097/SS.0000000000000150 |access-date=29 July 2025 }}</ref>

==Table of soil life==

== See also == {{div col|colwidth=30em}} *Agricultural soil science *Agroecology *Biogeochemical cycle *Compost *Nitrification *Nitrogen cycle * Potting soil *Soil food web *Soil microbiology * Soil science {{div col end}}

== Notes == {{notelist}}

== References == {{Reflist}}

== Bibliography == * Alexander, 1977, Introduction to Soil Microbiology, 2nd edition, John Wiley * Alexander, 1994, Biodegradation and Bioremediation, Academic Press * Bardgett, R.D., 2005, The Biology of Soil: A Community and Ecosystem Approach, Oxford University Press * Burges, A., and Raw, F., 1967, Soil Biology: Academic Press * Coleman D.C. et al., 2004, Fundamentals of Soil Ecology, 2nd edition, Academic Press * Coyne, 1999, Soil Microbiology: An Exploratory Approach, Delmar * Doran, J.W., D.C. Coleman, D.F. Bezdicek and B.A. Stewart. 1994. Defining soil quality for a sustainable environment. Soil Science Society of America Special Publication Number 35, ASA, Madison Wis. * Paul, P.A. and F.E. Clark. 1996, Soil Microbiology and Biochemistry, 2nd edition, Academic Press * Richards, 1987, The Microbiology of Terrestrial Ecosystems, Longman Scientific & Technical * Sylvia et al., 1998, Principles and Applications of Soil Microbiology, Prentice Hall * Soil and Water Conservation Society, 2000, Soil Biology Primer. * Tate, 2000, Soil Microbiology, 2nd edition, John Wiley * van Elsas et al., 1997, Modern Soil Microbiology, Marcel Dekker * Wood, 1995, Environmental Soil Biology, 2nd edition, Blackie A & P *Vats, Rajeev & Sanjeev, Aggarwal. (2019). Impact of termite activity and its effect on soil composition.

== External links == *[https://web.archive.org/web/20060821031646/http://www.safs.msu.edu/soilecology/soilbiology.htm Michigan State University – Soil Ecology and Management: Soil Biology] *[https://www.dpi.nsw.gov.au/agriculture/soils/guides/soil-biology/biology New South Wales – Soil Biology] *[https://web.archive.org/web/20060519054209/http://www.extension.umn.edu/distribution/cropsystems/components/7403_02.html University of Minnesota – Soil Biology and Soil Management] * [http://www.soil-net.com Soil-Net.com] A free schools-age educational site, featuring much on soil biology and teaching about soil and its importance. *[https://web.archive.org/web/20140318111103/http://organic-fertilizer.info/organic-fertilizer.php Why organic fertilizers are a good choice for healthy soil] *[https://web.archive.org/web/20120729020746/http://www.gmo-safety.eu/results/619.effects-beyond-normal-varietal-differences.html Effects of transgenic zeaxanthin potatoes on soil quality] Biosafety research project funded by the BMBF *[https://nature.berkeley.edu/soilmicro/methods/BalserPLFA.pdf Phospholipid fatty-acid analysis protocol] A method for analyzing the soil microbial community (pdf file) * [https://www.nrcs.usda.gov/resources/education-and-teaching-materials/soil-biology-primer USDA-NRCS – Soil Biology Primer]

{{DEFAULTSORT:Soil Life}} Category:Soil biology Category:Soil science