Soil life or
soil biota is a collective term for all the organisms living within the soil.
Overview
In a balanced soil, plants grow in an active and vibrant environment. The
mineralA mineral is a naturally occurring solid chemical substance that is formed through geological processes and that has a characteristic chemical composition, a highly ordered atomic structure, and specific physical properties. By comparison, a rock is an aggregate of minerals and/or mineraloids and...
content of the soil and its physical structure are important for their well-being, but it is the life in the earth that powers its cycles and provides its fertility. Without the activities of soil organisms, organic materials would accumulate and litter the soil surface, and there would be no food for plants.
The soil biota includes:
- Megafauna: size range 20 mm upwards, e.g. mole
Moles are the majority of the members of the mammal family Talpidae in the order Soricomorpha. Although moles burrow, some species are semi-aquatic. Moles have cylindrical bodies covered in fur while the ears are generally not visible. They have small or covered eyes and can probably still tell...
s, rabbitRabbits are small mammals in the family Leporidae of the order Lagomorpha, found in several parts of the world. There are seven different genera in the family classified as rabbits, including the European rabbit , Cottontail rabbit , and the Amami rabbit...
s, and rodentRodentia is an order of mammals also known as rodents, characterised by two continuously growing incisors in the upper and lower jaws which must be kept short by gnawing....
s.
- Macrofauna: size range 2-20 mm, e.g. woodlice
A woodlouse is a crustacean with a rigid, segmented, long exoskeleton and fourteen jointed limbs...
, earthwormEarthworm is the common name for the largest members of Oligochaeta in the phylum Annelida. In classical systems they were placed in the order Opisthopora, on the basis of the male pores opening posterior to the female pores, even though the internal male segments are anterior to the female...
s, beetleBeetles are the group of insects with the largest number of known species. They are classified in the order Coleoptera , which contains more described species than in any other order in the animal kingdom, constituting about 25% of all known life-forms...
s, centipedeCentipedes are arthropods belonging to the class Chilopoda and the Subphylum Myriapoda. They are elongated metameric animals with one pair of legs per body segment. Despite the name, centipedes can have a varying number of legs from under 20 to over 300...
s, slugSlug is a common name that is normally applied to any gastropod mollusc that lacks a shell, has a very reduced shell, or has a small internal shell. This is in contrast to the common name snail, which is applied to gastropods that have coiled shells that are big enough to retract into.All slugs are...
s, snailSnail is a common name for almost all members of the molluscan class Gastropoda that have coiled shells in the adult stage. When the word is used in a general sense, it includes sea snails, land snails and freshwater snails. Otherwise snail-like creatures that lack a shell are called slugs...
s, antAnts are social insects of the family Formicidae and, along with the related wasps and bees, belong to the order Hymenoptera. Ants evolved from wasp-like ancestors in the mid-Cretaceous period between 110 and 130 million years ago and diversified after the rise of flowering plants. More than...
s, and harvestmen.
- Mesofauna: size range 100 micrometre
A micrometre is one millionth of a metre, or equivalently one thousandth of a millimetre or one thousand nanometres. It can also be written in scientific notation as 1×10
−6 m, meaning m.A strand of human hair is about 100 μm wide. Red blood cells are approx...
-2 mm, e.g. tardigradeTardigrades form the phylum Tardigrada, part of the superphylum Ecdysozoa. They are microscopic, water-dwelling, segmented animals with eight legs. Tardigrades were first described by Johann August Ephraim Goeze in 1773...
s, miteMites, along with ticks, belong to the subclass Acari and the class Arachnida. The scientific discipline devoted to the study of ticks and mites is called acarology.-Diversity and systematics:...
s and springtailSpringtails form the largest of the three lineages of modern hexapods that are no longer considered insects...
s.
- Microfauna and Microflora: size range 1-100 micrometres, e.g. yeast
Yeasts are eukaryotic micro-organisms classified in the kingdom Fungi, with the 1,500 species currently described estimated to be only 1% of all yeast species. Most reproduce asexually by budding, although a few do so by binary fission...
s, bacteria (commonly actinobacteriaActinobacteria are a group of Gram-positive bacteria with high G+C ratio. They can be terrestrial or aquatic.Use of the ferric uptake regulator has been suggested for classification...
), fungiA fungus is a member of a large group of eukaryotic organisms that includes microorganisms such as yeasts and molds, as well as the more familiar mushrooms. The Fungi are classified as a kingdom that is separate from plants, animals and bacteria...
, protozoaProtozoa is a subkingdom of microorganisms that are generally classified as unicellular non-fungal eukaryotes. Protozoans play a key role in maintaining the balance of the ecosystem.The word protozoan is originally an adjective and is used as a noun...
, roundworms, and rotiferThe rotifers make up a phylum of microscopic and near-microscopic pseudocoelomate animals. They were first described by Rev. John Harris in 1696, and other forms were described by Anton van Leeuwenhoek in 1703...
s.
Of these, bacteria and fungi play key roles in maintaining a healthy soil. They act as decomposers that break down organic materials to produce
detritusIn biology, detritus is non-living particulate organic material . It typically includes the bodies or fragments of dead organisms as well as fecal material. Detritus is typically colonized by communities of microorganisms which act to decompose the material...
and other breakdown products. Soil
detritivoreDetritivores, also known as detritus feeders or saprophages, are heterotrophs that obtain nutrients by consuming detritus . By doing so, they contribute to decomposition and the nutrient cycles....
s, like earthworms, ingest detritus and decompose it. Saprotrophs, well represented by fungi and bacteria, extract soluble nutrients from delitro.
Bacteria
Bacteria are single-celled organisms, and are the most numerous denizens of agriculture, with populations ranging from 100 million to 3 billion in a gram. They are
capable of very rapid reproduction by binary fission (dividing into two) in favourable conditions. One bacterium is capable of producing 16 million more in just 24 hours. Most soil bacteria live in close proximity to plant roots and are often referred to as rhizobacteria. Bacteria live in soil water, including the film of moisture surrounding soil particles, and some are able to swim by means of
flagellaA flagellum is a tail-like projection that protrudes from the cell body of certain prokaryotic and eukaryotic cells, and functions in locomotion. There are some notable differences between prokaryotic and eukaryotic flagella, such as protein composition, structure, and mechanism of propulsion...
. The majority of the beneficial soil-dwelling bacteria need oxygen (and are thus termed
aerobicAn aerobic organism or aerobe is an organism that can survive and grow in an oxygenated environment. -Types:*Obligate aerobes require oxygen for aerobic cellular respiration...
bacteria), whilst those that do not require air are referred to as
anaerobicAn anaerobic organism or anaerobe is any organism that does not require oxygen for growth, could possibly react negatively and may even die in its presence...
, and tend to cause
putrefactionPutrefaction is the decomposition of animal proteins, especially by anaerobic microorganisms, described as putrefying bacteria. Decomposition is a more general process. Putrefaction usually results in amines such as putrescine and cadaverine, which have a putrid odor...
of dead organic matter. Aerobic bacteria are most active in a
soilSoil is a natural body consisting of layers of mineral constituents of variable thicknesses, which differ from the parent materials in their morphological, physical, chemical, and mineralogical characteristics....
that is moist (but
not saturated, as this will deprive aerobic bacteria of the air that they require), and neutral
soil pHSoil pH is a measure of the soil acidity or soil alkalinity. An acid solution has a pH value less than 7. While a basic solution always has a pH larger than 7, an alkaline solution , can also be defined as the negative logarithm of hydroxide ions in the soil. It therefore does not necessarily have...
, and where there is plenty of food (
carbohydrateA carbohydrate is an organic compound with the general formula C
mn, that is, consists only of carbon, hydrogen and oxygen, with the last two in the 2:1 atom ratio. Carbohydrates can be viewed as hydrates of carbon, hence their name.The term is most common in biochemistry,...
s and
micronutrientMicronutrients are nutrients needed throughout life in small quantities. They are dietary minerals needed by the human body in very small quantities as opposed to macrominerals which are required in larger quantities...
s from organic matter) available. Hostile conditions will not completely kill bacteria; rather, the bacteria will stop growing and get into a dormant stage, and those individuals with pro-adaptive
mutationMutations are changes in the DNA sequence of a cell's genome and are caused by radiation, viruses, transposons and mutagenic chemicals, as well as errors that occur during meiosis or DNA replication...
s may compete better in the new conditions. Gram positive bacteria produce spores in order to wait for more favourable circumstances, and Gram negative bacteria gets into a "nonculturable" stage.
From the organic gardener's point of view, the important roles that bacteria play are:
Nitrification
NitrificationNitrification is the biological oxidation of ammonia with oxygen into nitrite followed by the oxidation of these nitrites into nitrates. Degradation of ammonia to nitrite is usually the rate limiting step of nitrification. Nitrification is an important step in the nitrogen cycle in soil...
is a vital part of the
nitrogen cycleThe nitrogen cycle is the process by which nitrogen is converted between its various chemical forms. This transformation can be carried out via both biological and non-biological processes. Important processes in the nitrogen cycle include fixation, mineralization, nitrification, and denitrification...
wherein certain bacteria (which manufacture their own
carbohydrateA carbohydrate is an organic compound with the general formula C
mn, that is, consists only of carbon, hydrogen and oxygen, with the last two in the 2:1 atom ratio. Carbohydrates can be viewed as hydrates of carbon, hence their name.The term is most common in biochemistry,...
supply without using the process of photosynthesis) are able to transform
nitrogenNitrogen is a chemical element that has the symbol N, atomic number of 7 and atomic mass 14.00674 u. Elemental nitrogen is a colorless, odorless, tasteless and mostly inert diatomic gas at standard conditions, constituting 78.08% by volume of Earth's atmosphere.Many industrially important...
in the form of ammonium, which is produced by the decomposition of proteins, into nitrates, which are available to growing plants, and once again converted to proteins.
Nitrogen fixation
In another part of the cycle, the process of
nitrogen fixationNitrogen fixation generally refers to the natural process, either biological or abiotic, by which nitrogen in the atmosphere is converted into ammonia. This process is essential for life because fixed nitrogen is required to biosynthesize the basic building blocks of life, e.g. nucleotides for DNA...
constantly puts additional nitrogen into biological circulation. This is carried out by free-living nitrogen-fixing bacteria in the soil or water such as
AzotobacterAzotobacter is a genus of usually motile, oval or spherical bacteria that form thick-walled cysts, and may produce large quantities of capsular slime. Azotobacter is an aerobic, free-living soil microbe which fixes nitrogen from the atmosphere. Beyond Azotobacter’s use as a model organism it has...
, or by those that live in close symbiosis with
leguminousA legume in botanical writing is a plant in the family Fabaceae , or a fruit of these specific plants. Alegume fruit is a simple dry fruit that develops from a simple carpel and usually dehisces on two sides. A common name for this type of fruit is a pod, although "pod" is also applied to a few...
plants, such as
rhizobiaRhizobia are soil bacteria that fix nitrogen after becoming established inside root nodules of legumes . Rhizobia require a plant host; they cannot independently fix nitrogen. Morphologically, they are generally gram negative, motile, non-sporulating rods.- History :The first species of rhizobia, R...
. These bacteria form colonies in nodules they create on the roots of
peaA pea is most commonly the small spherical seed or the seed-pod of the legume Pisum sativum. Each pod contains several peas. Peapods are botanically a fruit, since they contain seeds developed from the ovary of a flower. However, peas are considered to be a vegetable in cooking...
s,
beanBean is a common name for large plant seeds of several genera of the family Fabaceae used for human food or animal feed....
s, and related species. These are able to convert nitrogen from
the atmosphere into nitrogen-containing organic substances.
Denitrification
While nitrogen fixation converts nitrogen from the
atmosphereThe atmosphere of Earth is a layer of gases surrounding the planet Earth that is retained by Earth's gravity. The atmosphere protects life on Earth by absorbing ultraviolet solar radiation, warming the surface through heat retention , and reducing temperature extremes between day and night...
into organic compounds, a series of processes called denitrification returns an approximately equal 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
AchromobacterThe Achromobacter are a genus of bacteria, included in the order Burkholderiales....
and
PseudomonasPseudomonas is a genus of gamma proteobacteria, belonging to the larger family of pseudomonads.Recently, 16S rRNA sequence analysis has redefined the taxonomy of many bacterial species. As a result the genus Pseudomonas includes strains formerly classified in the genera Chryseomonas and Flavimonas...
. The putrefaction process caused by oxygen-free conditions converts nitrates and nitrites in soil into nitrogen gas or into gaseous compounds such as
nitrous oxideNitrous oxide, commonly known as laughing gas, is a chemical compound with the formula . It is an oxide of nitrogen. At room temperature, it is a colorless non-flammable gas, with a pleasant, slightly sweet odor and taste. It is used in surgery and dentistry for its anesthetic and analgesic effects...
or
nitric oxideNitric oxide or nitrogen monoxide is a chemical compound with chemical formula NO. This gas is an important signaling molecule in the body of mammals, including humans, and is an extremely important intermediate in the chemical industry...
. In excess, denitrification can
lead to overall losses of available soil nitrogen and subsequent loss of soil fertility. However, fixed nitrogen may circulate many times between organisms and the soil
before denitrification returns it to the atmosphere. The diagram above illustrates the nitrogen cycle.
Actinobacteria
ActinobacteriaActinobacteria are a group of Gram-positive bacteria with high G+C ratio. They can be terrestrial or aquatic.Use of the ferric uptake regulator has been suggested for classification...
are critical in the decomposition of organic matter and in
humusIn soil science, humus refers to any organic matter that has reached a point of stability, where it will break down no further and might, if conditions do not change, remain essentially as it is for centuries, if not millennia....
formation, and their presence 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
fungiA fungus is a member of a large group of eukaryotic organisms that includes microorganisms such as yeasts and molds, as well as the more familiar mushrooms. The Fungi are classified as a kingdom that is separate from plants, animals and bacteria...
, such as
yeastYeasts are eukaryotic micro-organisms classified in the kingdom Fungi, with the 1,500 species currently described estimated to be only 1% of all yeast species. Most reproduce asexually by budding, although a few do so by binary fission...
s and moulds. Fungi have no
chlorophyllChlorophyll is a green pigment found in all plants, algae, and cyanobacteria. Its name is derived from the Greek χλωρός and φύλλον . Chlorophyll absorbs light most strongly in the blue portion of the electromagnetic spectrum, followed by the red portion...
, and are not able to
photosynthesisPhotosynthesis is a process that converts carbon dioxide into organic compounds, especially sugars, using the energy from sunlight. Photosynthesis occurs in plants, algae, and many species of bacteria, but not in archaea...
e; besides, they can't use atmospheric carbon dioxide as a source of carbon, therefore they are
chemo-heterotrophicA chemoorganoheterotrophic organism is one that requires organic substrates to get its carbon for growth and development, and that produces its energy from oxido-reduction of an organic compound. This group of organisms may be further subdivided according to what kind of organic substrate and...
, meaning that, like
animalAnimals are a major group of mostly multicellular, eukaryotic organisms of the kingdom Animalia or Metazoa. Their body plan eventually becomes fixed as they develop, although some undergo a process of metamorphosis later on in their life. Most animals are motile, meaning they can move spontaneously...
s, 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.
Many fungi are parasitic, often causing disease to their living host plant, although some have beneficial relationships with living plants as we shall see 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 forms 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
celluloseCellulose is an organic compound with the formula , a polysaccharide consisting of a linear chain of several hundred to over ten thousand β linked D-glucose units....
and
ligninLignin or lignen is a complex chemical compound most commonly derived from wood, and an integral part of the secondary cell walls of plants and some algae. The term was introduced in 1819 by de Candolle and is derived from the Latin word lignum, meaning wood...
s.
Fungi spread underground by sending long thin threads known as
myceliumthumb|right|Fungal myceliaMycelium is the vegetative part of a fungus, consisting of a mass of branching, thread-like hyphae. The mass of hyphae is sometimes called shiro, especially within the fairy ring fungi. Fungal colonies composed of mycelia are found in soil and on or within many other...
throughout the soil; these threads can be
observed throughout many soils and
compostCompost is composed of organic materials derived from plants and animal that has been decomposed largely through aerobic decomposition. The process of composting is simple and practiced by individuals in their homes, farmers on their land, and industrially by industries and cities.Compost is rich...
heaps. From the mycelia the fungi is able to throw up its fruiting bodies, the visible part above the soil (e.g.,
mushroomA mushroom is the fleshy, spore-bearing fruiting body of a fungus, typically produced above ground on soil or on its food source. The standard for the name "mushroom" is the cultivated white button mushroom, Agaricus bisporus, hence the word mushroom is most often applied to those fungi that have...
s, toadstools and
puffballA puffball is a member of any of a number of groups of fungus in the division Basidiomycota. The puffballs were previously treated as a taxonomic group called the Gasteromycetes or Gasteromycetidae, but they are now known to be a polyphyletic assemblage...
s), which may contain millions of
sporeIn biology, a spore is a reproductive structure that is adapted for dispersal and surviving for extended periods of time in unfavorable conditions...
s. 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.
Mycorrhizae
Those fungi that are able to live symbiotically with living plants, creating a relationship that is beneficial to both, are known as
MycorrhizaA mycorrhiza is a symbiotic association between a fungus and the roots of a vascular plant....
e (from
myco meaning fungal and
rhiza meaning root). Plant root hairs are invaded by the mycelia of the mycorrhiza, which lives partly in the soil and partly in the root, and may either cover the length of the root hair as a sheath or be concentrated around its tip. The mycorrhiza obtains the carbohydrates that it requires from the root, in return providing
the plant with nutrients including nitrogen and moisture. Later the plant roots will also absorb the mycelium into its own tissues.
Beneficial mycorrhizal associations are to be found in many of our edible and flowering crops.
Shewell CooperDr. Wilfred Edward Shewell-Cooper was a British organic gardener and pioneer of no dig gardening. He was the author of Soil, Humus and Health , The Royal Gardeners , Grow your own food supply , The ABC of Vegetable Gardening and many other books on gardening...
suggests that these include at least 80% of the
brassicaBrassica is a genus of plants in the mustard family . The members of the genus may be collectively known either as cabbages, or as mustards...
and
solanumSolanum, the nightshades, horsenettles and relatives, is a large and diverse genus of annual and perennial plants. They grow as forbs, vines, subshrubs, shrubs, and small trees, and often have attractive fruit and flowers. Many formerly independent genera like Lycopersicon or Cyphomandra are...
families (including
tomatoThe tomato , also called the love apple, is a herbaceous, usually sprawling plant in the nightshade family widely cultivated for its edible fruit. Savory in flavor, the fruit of most varieties ripens to a distinctive red color. Tomato plants typically reach to in height and have a weak, woody stem...
es and
potatoThe potato is a starchy, tuberous crop from the perennial Solanum tuberosum of the Solanaceae family . The word potato may refer to the plant itself as well as the edible tuber. In the region of the Andes, there are some other closely related cultivated potato species...
es), as well as the majority of
treeA tree is a perennial woody plant. It is most often defined as a woody plant that has many secondary branches supported clear of the ground on a single main stem or trunk with clear apical dominance. A minimum height specification at maturity is cited by some authors, varying from 3 m to...
species, especially in
forestA forest is an area with a high density of trees. There are many definitions of a forest, based on the various criteria...
and woodlands. Here the 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. 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, such as the North American pine forests, a young seedling cannot obtain sufficient light to photosynthesise for itself and will not grow properly in a sterile soil. 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, often indirectly obtained from its parents or neighbouring trees.
David AttenboroughSir David Frederick Attenborough OM, CH, CVO, CBE, FRS, FZS, FSA is a broadcaster and naturalist. His career as the respected face and voice of natural history programmes has endured for more than 50 years...
points out the plant/fungi/animal relationship that creates a "Three way harmonious trio" to be found in forest
ecosystemAn ecosystem consists of all the organisms living in a particular area, as well as all the nonliving, physical components of the environment with which the organisms interact, such as air, soil, water, and sunlight. It is all the organisms in a given area, along with the nonliving factors with...
s 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.
See also
- Agroecology
The term agroecology can be used in multiple ways, as a science, as a movement and as a practice. Broadly stated, it is the study of the role of agriculture in the world. Agroecology provides an interdisciplinary framework with which to study the activity of agriculture. In this framework,...
- Biogeochemical cycle
In ecology and Earth science, a biogeochemical cycle or nutrient cycle is a pathway by which a chemical element or molecule moves through both biotic and abiotic compartments of Earth...
- Soil biology
Soil biology is the study of microbial and faunal activity and ecology in soil. These organisms include earthworms, nematodes, protozoa, fungi, bacteria and different arthropods...
- Soil zoology
Soil zoology is the study of animals living fully or partially in the soil . The term was apparently first used for a Conference attended by a large number of soil zoologists, to present their research dealing with the subject at the University of Nottingham, UK, whose proceedings were published in...
- Soil food web
The soil food web is the community of organisms living all or part of their lives in the soil. It describes a complex living system in the soil and how it interacts with the environment, plants, and animals....
External links