Soil biology is the study of microbial and activity and ecology in soil.
Soil life, soil biota, soil fauna, or edaphon is a collective term that encompasses all that spend a significant portion of their life cycle within a soil profile, or at the soil-plant litter interface.
These organisms include , , protozoa, fungi, bacteria, different , as well as some reptiles (such as snakes), and species of burrowing mammals like gophers, moles and prairie dogs.
Overview
The soil is home to circa 59% of the world's
biodiversity.
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.
We know that
soil life break down
organic matter, making
available for uptake by plants and other organisms.
The nutrients stored in the bodies of soil organisms prevent nutrient loss by leaching, in particular for nitrogen and phosphorus.
Microbial exudates act to maintain
soil structure,
and
are important in
bioturbation.
However, we find that we do not understand critical aspects about how these populations function and interact. The discovery of
glomalin in 1995 indicates that we lack the knowledge to correctly answer some of the most basic questions about the
biogeochemical cycle in soils.
There is much work ahead to gain a better understanding of the
ecology of soil biological components in the
biosphere.
In balanced soil, plants grow in an active and steady environment. The nutrient content of the soil and its soil structure are important for plant well-being, but it is soil life that powers and provides soil fertility.
The soil biota includes:
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Megafauna: size range – 20 mm upward, e.g. moles, , and .
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Macrofauna: size range – 2 to 20 mm, e.g. woodlouse, , , , , , , and harvestman.
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Soil mesofauna: size range – 100 to 2 mm, e.g. , , Enchytraeidae and .
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Microfauna and Microflora: size range – 1 to 100 micrometres, e.g. , bacteria, archaea, fungus, protozoa, , and .
Of these, bacteria, archaea and fungi play key roles in maintaining a healthy soil.
Scope
Soil biology involves work in the following areas:
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Modelling of biological processes and population dynamics
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Soil biology, soil physics and chemistry: occurrence of physicochemical parameters and surface properties on biological processes and population behavior
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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
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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 structure
Complementary disciplinary approaches are necessarily utilized which involve molecular biology, genetics, ecophysiology, biogeography, ecology, soil processes, organic matter, nutrient cycling
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.
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.
Most soil bacteria live close to plant roots in the
rhizosphere and are often referred to as
rhizobacteria, helping plants to grow.
Bacteria live in
soil moisture, including the film of moisture surrounding soil particles, where some are able to swim by means of
flagellum.
The majority of the beneficial soil-dwelling bacteria need oxygen (and are thus termed
aerobic organism bacteria), whilst those that do not require air are referred to as anaerobic, and tend to cause
putrefaction of dead organic matter.
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 (
and
from organic matter) available.
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,
and those individuals with
exaptation or rapidly evolving better-adapted
Phenotypic trait may compete better in the new conditions.
Some Gram-positive bacteria (e.g.
Bacillus,
Clostridium) produce spores in order to wait for more favourable circumstances,
and Gram-negative bacteria get into a "nonculturable" resting stage.
Bacteria are colonized by persistent
virus (
) that replicate in bacterial hosts and promote
gene transfer,
a property of bacteria-virus relationships now currently used in genetic engineering.
From the organic gardener's point of view, the important roles that bacteria play are:
Nitrification
Nitrification is a vital part of the
nitrogen cycle, wherein certain chemolithotrophic nitrifying bacteria (e.g.
Nitrosomonas), called
(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
, into
, available to growing plants and once again converted to proteins.
Other nitrifying bacteria (e.g.
Arthrobacter) are able of
nitrification, a still badly known
biochemical process of soil nitrogen transformation.
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
, such as
rhizobia, or with actinorhizal plants, such as
Frankia. These form colonies in nodules they create on the roots of
,
,
Casuarina and related
. Nitrogen-fixing bacteria are able to convert nitrogen from the atmosphere into nitrogen-containing organic substances,
and thus play a decisive role in incipient soil formation.
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
, 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.
An excess of nitrogen
may cause denitrification
in addition to
nitrate loss by
percolation to the
aquifer.
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 along with the tough
chitin found in the
of
. Their various production of
volatile Metabolite is responsible for the sweet
earthy aroma associated with a good healthy soil.
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.
Fungi
A gram of garden soil can contain around one million
fungus, such as
and moulds, and around 700 km fungal
can live in 1 g of soil.
Fungi have no
chlorophyll, and are not able to
. They cannot use atmospheric carbon dioxide as a source of carbon, therefore they are chemo-heterotrophic, meaning that, like
, 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).
Many fungi are Parasitism, 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 and , which are succeeded by those that are able to break down cellulose and .
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., , , and ), which may contain millions of . When the fruiting body bursts, these spores are dispersed through the air to settle in fresh environments, and are able to lie dormancy for up to years until the right conditions for their activation arise or the right food is made available.
Mycorrhizae
Those fungi that are able to live
Symbiosis with living plants, creating a relationship that is beneficial to both, are known as
(from
myco meaning
fungus and
rhiza meaning
root). In mycorrhizae plant roots are invaded by the
Mycelium 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 (
) or be present in cortical cells in the form of arbuscules (arbuscular mycorrhizae). The mycorrhizal fungus obtains the
that it requires from the root,
in return providing the plant with nutrients, including nitrogen
and phosphorus,
and with moisture.
Later the plant roots will also absorb the mycelium into its own tissues.
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).
Mycorrhizae can also benefit nutrients (other than
sugar carbon) and moisture from the host,
and exchange nutrients (including carbon) and moisture between plants through common mycorrhizal networks.
Chemical signalling between plants through common mycorrhizal networks, although a beautiful concept, is still a matter of conjecture, more research being needed.
Beneficial mycorrhizal associations (either 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 and , with Ericaceae (e.g. bracken, bilberry) harbouring a special type, called ericoid mycorrhizae.
David Attenborough points out the plant, fungi, animal relationship that creates a "three way harmonious trio" to be found in forest , 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 ( Private Life Of Plants, 1995). 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.
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.
Invertebrates
Soil fauna affect
soil formation and soil organic matter dynamically on many spatiotemporal scales.
,
ants and
termites mix the soil as they burrow, significantly affecting soil formation. Earthworms ingest soil particles and organic residues, enhancing the availability of plant nutrients in the material that passes through and out of their bodies. By aerating and stirring the soil, and by increasing the stability of soil aggregates, these organisms help to assure the ready infiltration of water. These organisms in the soil also help improve pH levels.
Ants and termites are often referred to as "Soil engineers" because, when they create their nests, there are several chemical and physical changes made to the soil. Among these changes are increasing the presence of the most essential elements like carbon, nitrogen, and phosphorus—elements needed for plant growth.
Vertebrates
The soil is also important to many mammals.
Gophers, moles, prairie dogs, and other burrowing animals rely on this soil for protection and food. The animals even give back to the soil as their burrowing allows more rain, snow and water from ice to enter the soil instead of creating erosion.
Table of soil life
This table includes some familiar types of soil life,
[ , Les Bases de la Production Végetal, tome I: Le Sol et son amélioration, Collection Sciences et Téchniques Agricoles, 2003] coherent with prevalent taxonomy as used in the linked Wikipedia articles.
See also
Notes
Bibliography
-
Alexander, 1977, Introduction to Soil Microbiology, 2nd edition, John Wiley
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Alexander, 1994, Biodegradation and Bioremediation, Academic Press
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Bardgett, R.D., 2005, The Biology of Soil: A Community and Ecosystem Approach, Oxford University Press
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Burges, A., and Raw, F., 1967, Soil Biology: Academic Press
-
Coleman D.C. et al., 2004, Fundamentals of Soil Ecology, 2nd edition, Academic Press
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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.
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Paul, P.A. and F.E. Clark. 1996, Soil Microbiology and Biochemistry, 2nd edition, Academic Press
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Richards, 1987, The Microbiology of Terrestrial Ecosystems, Longman Scientific & Technical
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Sylvia et al., 1998, Principles and Applications of Soil Microbiology, Prentice Hall
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Soil and Water Conservation Society, 2000, Soil Biology Primer.
-
Tate, 2000, Soil Microbiology, 2nd edition, John Wiley
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van Elsas et al., 1997, Modern Soil Microbiology, Marcel Dekker
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Wood, 1995, Environmental Soil Biology, 2nd edition, Blackie A & P
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Vats, Rajeev & Sanjeev, Aggarwal. (2019). Impact of termite activity and its effect on soil composition.
External links
