The soil is home to circa 59% of the world'sbiodiversity.[4] The links between soil organisms and soil functions are complex. The interconnectedness and complexity of thissoil 'food web' means any appraisal of soil function must necessarily take into account interactions with the livingcommunities that exist within the soil.[5]Soil organisms break downorganic matter, makingnutrients available for uptake by plants and other organisms.[6] The nutrients stored in the bodies of soil organisms prevent nutrient loss byleaching, in particular for nitrogen and phosphorus.[7] Microbial exudates act to maintainsoil structure,[8] andearthworms are important inbioturbation.[9] However, critical aspects about how these populations function and interact are unclear. The discovery ofglomalin in 1996 indicates that the knowledge to correctly answer some of the most basic questions about thebiogeochemical cycle in soils is lacking.[10] There is much work ahead to gain a better understanding of theecological role of soil biological components in thebiosphere.[11]
In balanced soil, plants grow in an active and steady environment. Thenutrient content of the soil and itsstructure are important for plant well-being, but it is soil life that powersnutrient cycles and providessoil fertility.[12] Without the activities of soil organisms,organic materials would accumulate as undecayed litter at the soil surface, and there would be nohumus[13] and nonutrients available for plants.[14]
Of these, bacteria, archaea and fungi play key roles in maintaining a healthy soil.[15] They act asdecomposers that break down organic materials to producedetritus and other breakdown products.[16] Burrowing soildetritivores, likeearthworms, known asecosystem engineers, ingest detritus and decompose it, while building a good granularsoil structure and offering a habitat for various soil organisms.[17]Saprotrophs, well represented by fungi, archaea and bacteria, extract soluble nutrients from detritus andsoil organic matter, in particular in therhizosphere.[18] All other organisms living in the soil, each at its position along interconnected trophic networks (also calledfoodwebs), contribute to good health of the soil ecosystem.[19]
Bacteria are single-cell organisms and the most numerous denizens ofagricultural fields, with populations ranging from 100 million to 3 billion in a 'teaspoon' of productive soil.[21] They are capable of very rapid reproduction bybinary fission (dividing into two) in favourable conditions. When in itsexponential phase of growthEscherichia coli is thus capable of producing 1milliard more in just 1 hour.[22] Most soil bacteria live close to plant roots in therhizosphere and are often referred to asrhizobacteria, helping plants to grow.[23] Bacteria live insoil water, including the film of moisture surrounding soil particles, where some are able to swim by means offlagella.[24] The majority of the beneficial soil-dwelling bacteria need oxygen (and are thus termedaerobic bacteria), whilst those that do not require air are referred to asanaerobic, and tend to causeputrefaction of dead organic matter.[25] Aerobic bacteria are most active in asoil that is moist (but not saturated, as this will deprive aerobic bacteria of the air that they require), and neutralsoil pH, and where there is plenty of food (carbohydrates andmicronutrients from organic matter) available.[26] 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,[27] and those individuals withpre-adaptivemutations or rapidly evolving better-adaptedtraits may compete better in the new conditions.[28] SomeGram-positive bacteria (e.g.Bacillus,Clostridium) produce spores in order to wait for more favourable circumstances,[29] andGram-negative bacteria get into a "nonculturable" resting stage.[30] Bacteria are colonized by persistentviral agents (bacteriophages) that replicate in bacterial hosts and promotegene transfer,[31] a property of bacteria-virus relationships now currently used ingenetic engineering.[32]
From theorganic gardener's point of view, the important roles that bacteria play are:
In another part of thenitrogen cycle, the process ofnitrogen 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 asAzotobacter andheterocyst-bearingcyanobacteria (blue-green algae), or by those that live in closesymbiosis withlegumes, such asrhizobia, or withactinorhizal plants, such asFrankia. These form colonies in nodules they create on the roots ofpeas,beans,Casuarina and relatedflowering plants. Nitrogen-fixing bacteria are able to convert nitrogen from the atmosphere into nitrogen-containing organic substances,[35] and thus play a decisive role in incipient soil formation.[36]
While nitrogen fixation converts nitrogen from theatmosphere into organic compounds, a series of processes calleddenitrification returns some amount of nitrogen to the atmosphere.Denitrifying bacteria tend to beanaerobes, orfacultatively anaerobes (can alter between the oxygen dependent and oxygen independent types of metabolisms), includingAchromobacter andPseudomonas. The denitrification process caused by oxygen-free conditions converts nitrates and nitrites in soil into nitrogen gas or into gaseous compounds such asnitrous oxide ornitric oxide. In excess, denitrification can lead to overall losses of available soil nitrogen and subsequent loss ofsoil fertility.[37] An excess of nitrogenfertilizers may cause denitrification[38] in addition tonitrate loss bypercolation to theaquifer.[39] 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 thenitrogen cycle.
Actinomycetota (actinomycetes, actinobacteria) are critical in the decomposition oforganic matter and inhumus formation. They specialize in breaking downcellulose andlignin[40] along with the toughchitin[41] found in theexoskeletons ofarthropods. Their various production ofvolatilemetabolites is responsible for the sweetearthy aroma associated with a good healthy soil.[42] 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.[43]
A gram of garden soil can contain around one millionfungi, such asyeasts andmoulds, and around 700 km fungalhyphae can live in 1 g of soil.[44] Fungi have nochlorophyll, and are not able tophotosynthesise. They cannot use atmospheric carbon dioxide as a source of carbon, therefore they arechemo-heterotrophic, meaning that, likeanimals, 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 inhumus (humification) andcarbon dioxide (mineralization).[45]
Many fungi areparasitic, often causingdisease 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 besaprotrophic; 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 usesugars andstarches, which are succeeded by those that are able to break downcellulose andlignins.[46]
Fungi spread underground by sending long thin threads known asmycelium throughout the soil; these threads can be observed throughout many soils andcompost heaps. From the mycelia the fungi is able to throw up its fruiting bodies, the visible part above the soil (e.g.,mushrooms,toadstools, andpuffballs), which may contain millions ofspores. When thefruiting body bursts, these spores are dispersed through the air to settle in fresh environments, and are able to liedormant for up to years until the right conditions for their activation arise or the right food is made available.[47] Fungal spores are dispersed by wind,[48] water,[49] but also by a variety of fungal-feeding animals, from small invertebrates (e.g. springtails)[50] to big mammals (e.g. wild boars),[51] helping them to colonize new, sometimes remote environments, hence the cosmopolitan distribution of many fungal species.[52]
Those fungi that are able to livesymbiotically with living plants, creating a relationship that is beneficial to both, are known asmycorrhizae (frommyco meaningfungus andrhiza meaningroot). In mycorrhizae plant roots are invaded by themycelia of the mycorrhizal fungus, which lives partly in the soil and partly in the root, and may either penetrate the rootcortex without entering its cells (forming theHartig 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 thecarbohydrates that it requires from the root,[53] in return providing the plant with nutrients, including nitrogen[54] and phosphorus,[55] and with moisture.[56] Later the plant roots will also absorb the mycelium into its own tissues.[57] 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).[58] Mycorrhizae can also benefit nutrients (other thansugar carbon) and moisture from the host,[59][60] and exchange nutrients (including carbon) and moisture between plants through commonmycorrhizal networks.[61][62][63]Chemical signalling between plants through commonmycorrhizal networks, although a beautiful concept, is still a matter of conjecture, more research being needed.[64][65]
Beneficial mycorrhizal associations (eitherectomycorrhizae orarbuscular mycorrhizae) are to be found in many of our edible and flowering crops, to the exception ofBrassicaceae (e.g.cabbage,turnip) as well as in the majority oftree species, especially inforests andwoodlands, withEricaceae (e.g.bracken,bilberry) harbouring a special type, calledericoid mycorrhizae.[66] 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.[67] 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 theforest floor, a youngseedling cannot obtain sufficient light tophotosynthesise for itself and will not grow properly, causing a deficit of regeneration.[68] 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.[69]
David Attenborough points out the plant, fungi, animal relationship that creates a "three way harmonious trio" to be found in forestecosystems, 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.[70] A greater understanding of the complex relationships that pervade natural systems is one of the major justifications of theorganic gardener, in refraining from the use of artificial chemicals and the damage these might cause.[71]
Recent research has shown thatarbuscular mycorrhizal fungi produceglomalin, a protein that binds soil particles and stores both carbon and nitrogen. These glomalin-related soil proteins are an important part ofsoil organic matter.[72]
Soil fauna affectsoil formation and soil organic matter dynamically on many spatiotemporal scales.[73]Earthworms,ants andtermites, known asecosystem engineers, mix the soil as they burrow, significantly affecting soil formation and organic matter dynamics.[74] Earthworms ingest soil particles and organic residues, enhancing the availability of plant nutrients in the material that passes through and out of their bodies.[75] By aerating and stirring the soil, and by increasing the stability of soil aggregates, these organisms help to assure the ready infiltration of water.[76] These organisms in the soil also help improvepH levels, bybuffering them around neutrality, an equilibrating process (negative feedback loop) by which fungal activity is favoured inalkaline soils[77] while bacterial activity is favoured inacid soils.[78]
Ants and termites are also often referred to assoil engineers because, when they create their nests, there are several chemical and physical changes made to the soil.[79] Among these changes are increasing presence of the most essential elements like carbon, nitrogen, and phosphorus, elements needed for plant growth.[80] 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.[81][82]
The soil is also important to many mammals.Gophers,moles,prairie dogs, and other burrowing animals rely on this soil for protection and food.[83] 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 decreasingrunoff along slopes.[84]
^Stockdale, Elizabeth A.; Goulding, Keith W. T.; George, Timothy S.; Murphy, Deniel V. (9 January 2013)."Soil fertility". In Gregory, Peter J.; Nortcliff, Stephen (eds.).Soil conditions and plant growth. Oxford, United Kingdom:Wiley-Blackwell. pp. 49–85.doi:10.1002/9781118337295.ch3.ISBN978-1-118-33729-5. Retrieved17 July 2025.
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. Definingsoil 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.
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