List of Soil Organisms | Soil Science

Soil organisms (Soil biota) contribute a wide range of essential services to the sustainable functioning of all ecosystems by acting as the primary driving agents of nutrient cycling; regulating the dynamics of soil organic matter, soil carbon sequestration and greenhouse gas emission; modifying soil physical structure and water regime; enhancing the amount and efficiency of nutrient acquisition by vegetation; and enhancing plant health. These services are not only essential to the functioning of natural ecosystems but also constitute an important resource for the sustainable management of agricultural systems.

The important soil organisms are as follows:

1. Bacteria:

The bacteria isolated from the soil may be placed into two broad divisions: the indigenous or autochthonous species that are true residents and the invaders or allochthonous organisms. Indigenous population may have resistant stages but at the same time, these organisms proliferate and participate in the biochemical functions of the community.

Allochthonous populations enter with precipitation, diseased tissue, animal manure, or sewage sludge and they may persist for some time but they do not contribute in a significant way to the various ecologically significant transformations or interactions. Bacteria are also been divided on a systematic or taxonomic basis by the system proposed in Sergey’s Manual of Determinative Bacteriology.

Cell structure and morphology also serves as a means of bacterial characterization and the major types are bacilli or rod shaped, which are the most numerous, the cocci or spherical shaped and the spirilla or spirals, which are not common in soil.

The prevalence of pseudomonades has been demonstrated in both cropped and un-cropped land. Strictly anaerobic bacteria classified in genus Clostridium occur in the most fertile area in spite of the apparent availability of O₂. Common to both soil and animal droppings is a group of microorganisms known as myxobacteria. The vegetative forms of these organisms are flexible rods that move gliding. Most frequently found are Chondrococcus, Archangium and Polyangium.

Various pathogens of humans, livestock, cultivated plants and other species of plants and animals is found in soil. Common species are Agrobacterium, Erivinia, and Pseudomonas causing diseases in plants. Human and animal pathogens include Clostrisium botulnium, C. tetani, Bacillus anthrasis, Listeria monocytogenes, etc.

a. Decomposers:

Bacteria play an important role in decomposition of organic materials, especially in the early stages of decomposition when moisture levels are high. In the later stages of decomposition, fungi tend to dominate. Bacillus subtilis and Pseudomonas fluorescens are examples of decomposer bacteria. Additions of these bacteria have not been proved to accelerate formation of compost or humus in soil.

b. Nitrogen Fixers:

Nitrogen-fixing bacteria form symbiotic associations with the roots of legumes like clover and lupine, and trees such as alder and locust. Visible nodules are created where bacteria infect a growing root hair. The plant supplies simple carbon compounds to the bacteria, and the bacteria convert nitrogen (N₂) from air into a form the plant host can use. When leaves or roots from the host plant decompose, soil nitrogen increases in the surrounding area.

The Nitrifying bacteria change ammonium (NH₄⁺) to nitrite (NO₂^–) then to nitrate (NO₃^–) a preferred form of nitrogen for grasses and most row crops. Nitrate is leached more easily from the soil, so some farmers use nitrification inhibitors to reduce the activity of one type of nitrifying bacteria. Nitrifying bacteria are suppressed in forest soils, so that most of the nitrogen remains as ammonium.

The Denitrifying bacteria convert nitrate to nitrogen (N₂) or nitrous oxide (N₂O) gas. Denitrifiers are anaerobic, meaning they are active where oxygen is absent, such as in saturated soils or inside soil aggregates.

Rhizobium bacteria can be inoculated onto legume seeds to fix nitrogen in the soil. These nitrogen-fixing bacteria live in special root nodules on legumes such as clover, beans, medic, wattles etc. They extract nitrogen gas from the air and convert it into forms that plants can use. This form of nitrogen fixation can add the equivalent of more than 100 kg of nitrogen per hectare per year.

Azotobacter, Azospirillum, Agrobacterium, Gluconobacter, Flavobacterium and Herbaspirillum are all examples of free-living, nitrogen-fixing bacteria, often associated with non-legumes. To date, inoculating the soil with these organisms has not proved an effective means of increasing nitrogen fixation for non-legume crops.

c. Disease Suppressors:

Bacillus megaterium is an example of a bacterium that has been used on some crops to suppress the disease- causing fungus Rhizoctonia solani. Pseudomonas fluorescence may also be useful against this disease. Bacillus subtilis has been used to suppress seedling blight of sunflowers, caused by Alternaria helianthi. A number of bacteria have been commercialized worldwide for disease suppression. However, suppression is often specific to particular diseases of particular crops and may only be effective in certain circumstances.

d. Aerobes and Anaerobes:

Aerobic bacteria are those that need oxygen, so where soil is well drained aerobes tend to dominate. Anaerobes are bacteria that do not need oxygen and may find it toxic. This group includes very ancient types of bacteria that live inside soil aggregates. Anaerobic bacteria favor wet, poorly drained soils and can produce toxic compounds that can limit root growth and predispose plants to root diseases.

e. Actinobacteria:

These soil bacteria help to slowly break down humates and humic acids in soils. Actinobacteria prefer non-acidic soils with pH higher than 5.

f. Sulfur Oxidizers:

Many soil minerals contain sulfides but this form of sulfur is largely unavailable to plants. Thiobacillus bacteria can covert sulfides into sulfates, a form of sulfur which plants can use.

2. Archaeobacteria:

The archeobacteria (Greek, archaios, ancient, and bakterion, a small rod) often live in extreme environments and have unusual metabolic processes. Important groups of these bacteria include the methanogens that produce methane gas from carbon dioxide and hydrogen in the absence of oxygen, halophiles that require high concentrations of salt to survive, and thermo-acidophiles that grow in hot and acidic places.

The archeobacteria and regular bacteria (eubacteria) appear to have separated early in the evolution of bacteria. Archaebacteria (or archaea, as they are now called) can be described as beneficial to soils which depend on microbial activity for their fertility, such as soils in organic gardens.

The types of archae found in soils are methanogens, halophiles, and thermophiles. The methanogens are anaerobic microorganisms that produce methane from carbon dioxide and hydrogen, and are also commonly found in wetlands, sewage treatment plants and intestines of ruminants. The way in which the methanogens (archaea) are beneficial in organically cultivated soils is in their relationship with anaerobic bacteria found in soils, such as the nitrogen fixing bacteria and others.

The hydrogen gas produced by these other bacteria is consumed by the methanogens for methane production. In helping to remove the hydrogen gas from the soil, the archaea are stimulating the metabolism of the anaerobic bacteria, which are essential in the anaerobic decomposition of organic materials in these soils.

Extremely Thermophilic and Hyperthermophilic S- Metabolizers:

These rods, filaments, cocci, or disk-shaped cells show no evidence of spores or resting stages. All species stain Gram negative. Motile or non-motile cells are aerobic, strictly anaerobic, or facultative anaerobic and show chemoautotrophic or chemoheterotrophic growth.

Under aerobic conditions, so is reduced to H₂S; under aerobic conditions H₂S or So is oxidized to H₂SO₄. H₂ or organic compounds serve as electron donors. The growth temperature is 45-110°C, with optimum growth at 70-105°C. No mesophilic species are known. Examples of habitats are continental solfatara fields or marine hydro thermal systems.

Extremely Halophilic, Aerobic Archaeobacteria (Halobacteria):

They are coccoid or irregular rod-shaped bacteria, 0.8-2.0 micrometers for coccoid forms, 0.3-1.2 x 1.0-15.0 micrometers for rod-shaped forms. They are motile by tufts of polar flagella, or they are nonmotile, Gram negative (rods) or Gram variable (cocci). Cocci occur singly or in pairs, tetrads, or irregular refractile clusters where the outlines of the individual cells are distinct.

The majority of rod-shaped forms has a characteristic flat cell morphology and exhibit a multitude of pleomorphic forms from regular rod or ribbon-like cells to disks, irregular triangles, or rectangles.

The cells of the rod-shaped forms lyse when suspended in distilled water and may exhibit spherical morphology in agar-grown culture or under adverse conditions. Gas vacuoles may be present. Colonies are various shades of red because of the presence of carotenoid pigments and may become pink or white if gas vacuoles are produced.

They are aerobic; some are able to grow anaerobically in the presence of nitrate. Chemoheterotrophic. Carbohydrates, alcohols, carboxylic acids, or amino acids serve as carbon and energy sources. They require at least 1.5 M NaCl for growth, most growing optimally at 2-4M NaCl. Some members are alkaliphilic, growing only at pH >8.5.

They occur in nature when the salt concentration is high (i.e. in salt lakes, soda lakes, salterns, and saline soils). One type occurs in proteinaceous products heavily salted with solar salt. The current genera are largely defined by chemotaxonomic criteria, notable polar lipid composition. The lipids of all isolates to date contain diphytanyl or phytanyl sesterpanyl derivatives of phosphatidyl glycerol and phosphatidyl glycerol phosphate.

Archaeal Sulfate Reducers:

These are irregular coccoid cells, often triangular, 0.4-0.3 micrometers in diameter, that occur singly or in pairs. Flagella may be present or absent. Cells stain Gram negative. Blue-greenish fluorescence occurs at 420 nanometers. Cells form greenish black, smooth colonies with a diameter of 1-2 millimeters. Cells are strictly anaerobic. They show chemolithotrophic, chemoorganotrophic, or chemomixotrophic growth.

Autotrophic growth occurs with thiosulfate and H₂, but with sulfate there is very little growth. Under heterotrophic conditions formate, lactate, glucose, starch, and proteins are used as electron donors and sulfate, sulfite, or thiosulfate can function as electron acceptors. H₂S is formed. So can be reduced, but no growth is obtained.

SO inhibits growth in the presence of sulfate, sulfite, and thiosulfate. The temperature range is 60-95°C, with the optimum around 83°C, and pH range is 4.5-7.5, with the optimum around 6. Salt range is 0.9-3.6%. The species are isolated from shallow (near Vulcano, Italy) and abyssal marine hydrothermal systems (Guaymas hot vent area, Gulf of California, Mexico).

Cell Wall-Less Archaeobacteria:

Pleomorphic cells range from spheres (0.1-5 micrometers in diameter) to filaments. Cells lack a cell wall and are bound by the cell membrane, approximately 7 nanometers thick. The cell membrane contains either lipids with 40-carbon isoprenoid-branched diglycerol tetraethers. Cells are Gram negative and may be motile and flagellated. Obligately thermophilic, Thermoplasma cells grow at 33-67°C; obligately acidophilic, they grow at pH 0.5-4. Cells lyse at neutral pH and grow in salt solutions up to half-strength marine water. Cells are facultatively anaerobic.

3. Actinomycetes:

Actinomycetes are numerous, widely distributed and second only to the bacteria in abundance in soil. Particularly in environments of high pH, they live as saprophytes but a few species can cause diseases of plants, animals and even humans. A variety of microscopic or plating methods have been used in ecological investigations. Particularly useful selective media for enumeration are those containing chitin. Media supplemented with antibacterial compounds are also sometimes used.

In general, the population of actinomycetes is greater in grassland and posture soils than in cultivated land and soils in warm climatic regions are more conducive for their growth. For the actinomycetes, the primary ecological influences include the organic matter status, pH, moisture and the temperature. Their numbers are especially great in land rich in organic matter.

These filamentous organisms are present in the ‘A’ horizon as well as considerable depths below the surface, but the cell density. Most actinomycetes are mesophyles with an optimum temperature in the range of 25 to 30° C. Thermophilic actinomycetes are common in soil, manure and compost heaps.

Thirty nine genera of Actinomycetes have been described in Bergey’s Manual.

The important one are:

i. Nocardia (Nocardioforms -11 Genera):

Filaments unstable, fragmenting easily; 0.5-1.2 micro-meters in diameter. Chains of conidia on aerial or both aerial and substrate hyphae. No sporangia produced. Aerobic and mesophilic. Mycobacterium, Corynebacterium, and Arthrobacter are now classified in this group of Actinomycetes.

ii. Frankia (Multiloculars -3 Genera):

Filaments 0.5-2.0 micrometers in diameter; no aerial mycelium. Multilocular sporangia formed by hyphal septation in three planes; sporangiospores nonmotile. Mutualistic or symbiotic diazotrophs, forming root nodules on nonleguminous plants.

iii. Micromonospora (Actinoplanetes -5 Genera):

Branched septate mycelium. 0.5 micrometers in diameter. Aerial mycelium absent. Spores formed singly on substrate mycelium. Growth between 20° and 40°, not above 50°C.

iv. Streptomyces (Streptomycetes -4 Genera):

Filaments 0.5-2.0 micrometers in diameter; extensively branched. Chains of three to many spores, usually aerial. Optimal growth 25°-35°C. Production of pigments or antibiotics or both.

v. Streptosporangium (Maduromycetes -7 Genera):

Stable, branched mycelium producing globose sporangia on aerial hyphae. Sporangiospores formed on a coiled, unbranched hypha. Hyphal hydrolysates contain madurose, a methylated galactose.

vi. Thermonospora (Thermomonosporas -4 Genera):

Branched, nonfragmenting filaments forming leathery colonies. Spores formed in clusters at tips of branched sporophores. Optimal growth 40°-48°C. Common in manures, composts, and rotting hay.

vii. Thermoactinomycetes (Thermoactinomycetes -1 Genus):

Substrate mycelium well developed, branched, septate; 0.4-0.8 micrometers in diameter. Forms endospores, suggesting classification should be with the Bacillaceae rather than with the Actinomycetales. Optimal growth 35°-58°C. Common in composts.

viii. Glycomyces (Others -4 Genera):

Branching vegetative hyphae, 0.4 micrometers in diameter. Forms short chains of aerial, square-ended conidia. Mycelium contains no nitrogenous phospholipids and no mycolic acid, but does contain glycolipids.

Other taxonomically valuable properties are the morphology and color of mycelia and sporangia, the surface features and arrangement of conidiospores, the per cent G + C in DNA, the phospholipid composition of cell membranes, and spore heat resistance. Recently, newer techniques are being applied to actinomycete taxonomy. Comparison of 16S rRNA sequences has proven valuable. Another useful technique is the production of large DNA fragments by restriction enzyme digestion and their separation and comparison using pulsed field ectrophoresis.

Actinomycetes: Practical Significance:

1. They are primarily soil inhabitants and are very widely distributed.

2. They can degrade an enormous number and variety of organic compounds and are extremely important in the mineralization of organic matter.

3. They produce most of the medically useful natural antibiotics. Although most actinomycetes are free-living microorganisms, a few are pathogens of humans, other animals and some plants.

4. Actinoplanetes:

Actinoplanetes (Greek actinos, a ray or beam, and planes, a wanderer). It is described in the section 28 of Bergey’s Manual. They grow in almost all soil habitats, ranging from forest litter to beach sand.

They also flourish in fresh water, particularly in streams and rivers (probably because of abundant oxygen and plant debris). Some have been isolated from the ocean. The soil-dwelling species may have an animal material. Pilimelia grows in association with keratin. Micromonospora actively degrades chitin and cellulose, and it can produce antibiotics such as gentamicin.

1. They have an extensive substrate mycelium.

2. The hyphae are highly coloured and produce diffusible pigments. Usually, an aerial mycelium is absent or rudimentary.

3. Condiospores are usually formed within a sporangium raised above the surface of the substratum at the end of a special hypha called a sporangiophore.

4. The spores can be either motile or non-motile. These bacteria vary in the arrangement and development of their spores. Some genera (Actinoplanes, Ampullariella, Pillimelia) have spherical, cylindrical, or irregular sporangia with a few to several thousand spores per sporangium.

The sporangium develops above the substratum at the tip of a sporangiophore; the spores are arranged in coiled or parallel chains. Dactylosporangium forms club-shaped, fingerlike, or pyriform sporangia with one to six spores. Micromonospora bears single spores, which often occur in branched clesters of sporophores. The section presently contains five genera.

Streptomyces and Related Genera:

Streptomyces is an enormous genus; 378 species are given in the approved lists of bacterial names. Streptomycetes play a major role in mineralization. They are flexible nutritionally and can aerobically degrade resistant substances such as pectin, lignin, chitin, keratin, latex, and aromatic compounds.

Streptomycetes are best known for their synthesis of a vast array of antibiotics, some of which are useful in medicine and biological research. Examples include amphotericin B, chloramphenicol, erythromycin, neomycin, nystatin, streptomycin, and tetracycline, etc.

1. Members of the section as a whole are often called streptomycetes [Greek streptos, bent or twisted, and myces, fungus]. Currently there are five genera of streptomycetes and their relatives.

2. They have aerial hyphae divided in a single plane to form chains of 5 to 50 or more non-motile conidiospores with surface texture ranging from smooth to spiny.

3. All have a type I cell wall and a G + C content of around 69 to 78%. Members of the genus are strict aerobes, are wall type I, and form chains of non-motile spores within a thin, fibrous sheath.

4. The substrate mycelium, when present, does not undergo fragmentation.

5. The three too many conidia in each chain are often pigmented and can be smooth, hairy, or spiny in texture.

6. Streptomyces species are determined by means of a mixture of morphological and physiological characteristics, including the following- the color of the aerial and substrate mycelia, spore arrangement, surface features of individual spores, carbohydrate use, antibiotic production, melanin synthesis, nitrate reduction, and the hydrolysis of urea and hippuric acid.

Actinobacteria:

In earlier time the Actinomycetes were designated as fungi because of their morphological appearance and the development like fungi of true mycelium. Therefore, they were at first called “ray fungi”. However, recent exhaustive studies give support to the opinion that the Actinomycetes are more closely related to bacteria than to fungi.

They include some of the most common soil life, playing an important role in decomposition of organic materials, such as cellulose and chitin and thereby playing a vital part in organic matter turnover and carbon cycle. This replenishes the supply of nutrients in the soil and is an important part of humus formation. Other Actinobacteria inhabit plants and animals, including a few pathogens, such as Mycobacterium, Corynebacterium, Nocardia, Rhodococcus and a few species of Streptomyces.

Actinomycets are widely distributed in nature, having been found in soil, water, in living tissues of men and animals, and in the atmosphere. In general, but with exceptions, we can state that most of the Actinomycetes are soil organisms.

The number of Streptomyces spp. in the soil very widely, absolutely as well as relatively. Depth, moisture content, soil reaction, soil type, and soil vegetation influence the occurrence and growth of Streptomyces in soil at least to the same extent as with other microorganisms.

The proportion of Streptomyces in the total number of microorganisms ranges between 10 and 70%. The absolute numbers of Actinomycetes decreases with the depth of soil, but they increase in proportion to the bacteria by from 10 to 65%. Also the number of different species in deeper layers is much reduced. Szabo confirmed this observation and found that sterile types dominate in deeper layers (B- horizon), while sporulating types more frequently occur in the A- horizon. They explain this by the better aeration and dryness of the upper layers in comparison with the wet B-horizon.

Streptomyces is higher in grassland because it is richer in plant roots. A considerable number of chromogenous, i.e., peptone-browning strains in grassland have been reported. This fact may probably also be related to the so-called soil fertility, as found earlier when comparing manured and unmanured soils.

Thermophilic Actinomycetes occur primarily in manure, compost, and mouldy hay, but also in nearly all kinds of soil. The geographical distribution of Streptomyces is worldwide. Their occurrence is not limited to any particular climate, although they are more abundant in the warmer zones. Streptomyces have been found even under the most extreme conditions in deserts.

Actinobacteria are well known as secondary metabolite producers and hence of high pharmacological and commercial interest. In 1940 Selman Waksman discovered that the soil bacteria he was studying made actinomycin, a discovery which granted him a Nobel Prize. Since then hundreds of naturally occurring antibiotics have been discovered in these terrestrial microorganisms, especially from the genus Streptomyces.

Some Actinobacteria form branching filaments, which somewhat resemble the mycelia of the unrelated fungi, among which they were originally classified under the older name Actinomycetes. Most members are aerobic, but a few, such as Actinomyces Israeli, can grow under anaerobic conditions. Unlike the Firmicutes, the other main group of Gram-positive bacteria, they have DNA with a high GC-content and some Actinomycetes species produce external spores.

Some types of Actinobacteria are responsible for the peculiar odor emanating from the soil after rain, mainly on warmer climates. Actinobacteria are critical in the decomposition of organic matter and in humus formation, and their presence is responsible for the sweet “earthy” aroma which is 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.

5. Algae:

Microalgae are tiny plants which are active converters of solar energy, carbon dioxide, and other nutrients into sugars, proteins, and other complex organic compounds beneficial to the nutrient cycling and soil structure of croplands. Some species are able to fix atmospheric nitrogen; others form compounds conducive to the growth of associated plants. In the natural world, they are important foundations of both terrestrial and aquatic ecosystems. The algae are the simplest members of the plant kingdom, and the blue-green algae are the simplest of the algae.

Algae are found in soils everywhere and are usually most abundant at or close to the surface but may also be found in the lower horizons of the soil. Sometimes the largest population is found a few centimeters below the surface where there will be insufficient light for photosynthesis. It may be, therefore, that these aggregations are produced by the action of rain on superficial growths, but there is still some uncertainty about the amount of growth possible in the dark under natural conditions. Found nearly 700 species at 15 to 20 cm below the surface of soils from many parts of the word.

Rain and earthworms are believed to be the chief agents in the vertical transport of algae. Many soil algae are able to return to the surface if they are not buried too deeply. Nearly all the diatoms and Cyanophyta are motile forms, and many Chlorophyta and Xanthophyta produce zoospore, especially when they are wetted after a dry period.

Among pigmented flagellates, the commonest are species of Chlamydomonas and Euglena. Though motility may be of biological advantage over small distances and in relation to the microclimate, distribution over greater distances seems to be in wind-borne dust.

In the temperate region blue-greens are especially common in calcareous and alkaline soils. Certain species, Nostoc commune, are often conspicuous on the soil surface. Acid soils, however, lack blue-green element and are usually dominated by diatoms and green algae.

Same species may be found throughout the year and from one year to another. In temperate lands they are least numerous in winter and multiply spasmodically at other times in relation to the weather conditions and to the growth of higher plants (e.g., in deciduous woodlands). In arid or tropical regions rainfall seems to be the major factor determining their periodicity.

Benefits of Soil Algae:

Some blue-green algae, along with a few other species are rather unique in their ability to perform the nitrogen-fixing function in the presence of oxygen at the soil/air interface, and excrete substances which further serve to glue soil particles into aggregates. This provides more aerated soil area for further growth of these and associated beneficial microorganisms.

A primary benefit of soil algae, other than the nitrogen-fixing abilities of a few species, is the production of external polysaccharide sheaths. These polysaccharides bind together soil particles, forming porous aggregates. This is particularly beneficial where repeated tillage has degraded soil structure.

As a result, erosion is reduced, aeration and water absorbing power increased, the soil has better insulative properties, and organic matter as well as amino acids and vitamins are added. After two or more years of application, farmers are finding that tillage requires less energy in the algae-conditioned soils and less irrigation water is needed, while crop production is increased.

They play major role in the flooded paddy fields by helping in nitrogen fixation in such an inhospitable habitat. One of the significance is its photo autotrophic nutrition, i.e. the generation of organic matter from inorganic substances. This is particularly important in creating organic carbon de novo by colonising barren/eroded areas.

They contribute significantly to the soil structure and erosion control by binding together soil particles (due to the production of the hygroscopic exopolysaccharide on their outer cell surface). Some BGA can fix atmospheric nitrogen and thus have assisted in replacing nitrogen fertilizers to a great extent, e.g. Nostoc, Anabaena, Tolypothrix, Chroococcus, Calothrix, etc.

Green Algae:

The “green algae” is the most diverse group of algae, with more than 7000 species growing in a variety of habitats. The “green algae” is a paraphyletic group because it excludes the Plantae. In soil, green algae are found ubiquitously, entirely dominating the algal flora in acid soils.

Some common species are Arkistrodesmus characium, Chlamydomonas, Chlorella, Chlorococcum, Dactylococcus, Hormidium, Protococcus, Patosiphon, Scenedesmus, Spongiochloris, Srichococcus, and Ulothrix. The yellow-green algae classified as Xanthophyta; are relatively rare. Some widespread genera are Botrydiopsis, Bumilleria, Bumilleriopsis, Heterococcus and Heterothrix.

Blue Green Algae:

Blue-green algae can be considered as simple aquatic plants that occur naturally in habitats such as rivers, lakes, damp soil, tree trunks, hot springs and snow. They can vary considerably in shape, colour and size.

i. Nostoc:

It is a filamentous, heterocyst-forming cyanobacterium capable of nitrogen fixation. They are found in gelatinous colonies, composed of filaments called trichomes surrounded by a thin sheath. They are common in both aquatic and terrestrial habitats. These organisms are known for their unusual ability to lie dormant for long periods of time and abruptly recover metabolic activity when rehydrated with liquid water. Nostoc environments are diverse and widespread over the globe; isolates have been found in fresh water, soils, and both extremely cold and extremely arid habitats.

It may also grow symbiotically within the tissues of plants, such as the aquatic fern Azolla (mosquito fern) or hornworts, providing nitrogen to its host. These cyanobacteria are photosynthetic prokaryotes that carry out an oxygen-evolving photosynthesis virtually identical to that of higher plants.

Some cyanobacteria are also capable of nitrogen fixation. Because the enzyme that performs nitrogen fixation is extremely sensitive to oxygen, nitrogen fixation must occur in an anaerobic environment, this creates a special problem for cyanobacteria since oxygen is generated as a by-product of photosynthesis and yet photosynthesis is required to produce the energy for nitrogen fixation.

ii. Anabaena:

It is a filamentous blue green alga. The cells are ovoid or barrel-shaped, often giving the filaments (trichomes) the appearance of a string of beads. Anabaena possesses heterocysts and can also develop akinetes (thick walled resting cells that can survive in sediments for many years). Sometimes the trichomes are set in mucilage, but it does not form the clearly defined mucilaginous colonies seen in its close relative, Nostoc.

It has the ability to fix nitrogen and is widespread in freshwater and also in damp soil. Certain species are symbionts in higher plants, e.g. Anabaena azollae in species of Water Fern (Azolla). Some species have been used successfully to provide nitrogen to rice crops in flooded paddy fields, adding up to 40 kg bound nitrogen per hectare per year.

Use of Azolla gives even higher levels of nitrogen fixation, reported as 120 – 310 kg per hectare per year. Anabaena has been shown to help release soil-bound phosphorus, although the exact ways in which this happens are not known at this time.

iii. Tolypothrix:

The uniseriate trichomes of Tolypothrix are composed of cells that are long and cylindrical or short and barrel- shaped. The filaments are covered by mucilage that varies in thickness and form wooly mats or tufts of filaments that are grayish blue- green, yellowish, or brownish in color.

Young filaments are long with heterocysts at the base and free apical ends. The heterocysts are spherical, cylindrical, or discoid in shape, and have 1-2 pores at their base. Akinetes are rarely observed. Tolypothrix forms single false branches when the filament on one side of the heterocyst continues to grow but the other side does not. The frequent false branching makes the clumps of filaments look like wooly hair.

Double false branching occasionally forms if both ends of the interrupted filament continue to grow. These forms are very similar to Scytonema, so some researchers think that the two genera should in fact be merged.

iv. Scytonema:

The genus is considered to be one of the most primitive autotrophic organisms on the planet, they are credited with converting earth’s atmosphere from an oxygen-free to an oxygen-rich environment, and thus setting the stage for the evolution of aerobic organisms. Scytonema filaments form dark mats or tufts amongst other algae or submerged vegetation in lakes or on terrestrial stones, wood, or soil. The trichomes are cylindrical and isopolar, and are usually colored pale blue-green, olive green, brownish, or even violet.

Heterocytous cyanophytes can flourish in environments limited in nitrogenous compounds in that they can supply their own fixed nitrogen. It has been demonstrated that nitrogen fixed by free-living, heterocystous cyanobacteria bacteria is transferred to higher plants.

Cyanobacteria (Scytonema hofmanni) produce bioactive compounds including plant growth regulators. Naphthalene acetic acid (NAA), a toxic substance, is a synthetic plant regulator used in micro-propagation.

Blue-green algae have great agronomic significance, especially in flooded paddy fields. During the extended periods in which rice soils are water logged, an algal film forms. The common inhabitant are Anabaena, Calothrix, Nostoc, Oscillatoria and Tolypothrix. These microorganisms make significant contribution to the nitrogen and oxygen status of the paddy fields.

Diatoms:

Diatoms are unicellular, microscopic algae of the class Bacillariophyceae. They have an intricate siliceous frustule (valve or shell), the morphology of which is the basis for their taxonomy. They satisfy all the conditions to qualify as suitable indicators in that they are simple. Diatom species are cosmopolitan. They have a consistent tolerance of a wide range of environmental parameters such as light, moisture, current velocity, pH, salinity, oxygen and inorganic and organic nutrients.

Diatoms are generally less frequent in acid soils and more prevalent in natural or slightly alkaline soils; even in culture a number of species are limited to pH values greater than 6.0. The prominent genera in soil include Achnanthes, Cymbella, Fragilaria, Hantzchia, Navicula, Nitzschia, Pinnularia, Surirella and Synedra.

6. Fungi:

Soil is an oligotrophic medium for the growth of fungi. Readily available nutrients are present for short periods of time in a limited zone. For the remainder of the time, fungi metabolize and grow very slowly utilizing a range of organic molecules, or the fungi are dormant. In general, the concentration of microbes is greatest close to the surface of roots where exudates from the root supply an extraordinarily important source of organic energy to the soil (rhizosphere).

Away from the root, the remains of plants and microbes are the primary source of energy. These become composted and degraded, usually very rapidly, leaving behind modified waxes, lignin, melanin and other complex molecules of plant and microbial origin.

The recalcitrant remains are known as humus. Humus consists of a mixture of aromatic compounds that are resistant to enzymatic degradation. Humus forms an important part of the carbon stored in soil. The loss of humus to the atmosphere because of human activities is an important contribution to the increasing carbon dioxide in the atmosphere.

Human degradation of ecosystems may be responsible for some 20% of the greenhouse gases, and this carbon comes from soil. If mycologists are to be part of the scientific response to global climate change, efforts to better understand carbon cycling in soil would be a useful place to start.

7. Soil Fauna:

Soil fauna (or zoo) are found in soil.

They are following types:

i. Microfauna:

Protozoa are important in mineralization and immobilization of N, P, and S. They are the most numerous soil fauna and prey on microbes (especially bacteria). They help enhance nitrification rates while suppressing bacterial and fungal pathogens but can be agents of plant diseases.

ii. Mesofauna:

Nematodes, arthropods (mites, centipedes, and springtails), molluscs microscopic un-segmented worms. They are ecologically diverse and found in all habitats. They population range from 10-20 million/m-sq. They are the major consumer group. They include both free-living and parasitic groups.

iii. Soil Macrofauna:

Earthworms and other worms; Ants, beetles, termites, spiders and vertebrates like rodents. They are important in mixing and redistributing organic matter. They contribute to soil physical properties. They neutralize soil pH and increase the availability of many nutrients. They stimulate microbial populations while reducing levels of harmful nematodes.

Soil Microfauna:

Protozoa:

Phylum-protozoa are a highly successful and diverse group of organisms, there are about 50,000 known species of protozoa. The phylum “Protozoa” (Gr. Prozos = first; Zoon = animal) comprise microscopic animals in which single cell perform all vital activities for this reason protozoan. Protozoology is the science of protozoa.

As members of the soil population, protozoa hold an intermediate place between the bacteria on the one hand and the higher plants and animals on the other. Most protozoa feed chiefly on bacteria preferring some species to others and thereby influence both bacterial numbers and bacterial activity. In their turn they are consumed either by other protozoa or microscopic carnivores or else upon their death they become fresh centres of bacterial activity.

All this contributes to the turnover of organic matter in the soil and as such the protozoa play their part in the soil organic cycle. Soil protozoa are the drivers of microbial interactions in the rhizosphere of plants. Although protozoa are the primary consumers of bacteria in soil, the consequences of protozoan predation for the composition and functioning of bacterial communities are poorly understood.

Protozoa need water in which they move and that plays a big role in determining which types of protozoa will be present. Protozoa are particularly active next to roots. Fungal-infested soils, like forests, tend to have more testate amoebae and ciliates. In bacterial-infested soils, flagellates and naked amoebae dominate. High clay soils contain a higher number of flagellates and naked Amoeba.

Many types of Protozoa are found in the soil, but flagellates and amoebae usually outnumber the ciliates. Their total numbers may range from a few hundred to several thousands. Depending upon the conditions of the soil the Protozoa may exist as vegetative or cyst forms.

Ciliates are found in both soil and fresh water but there are only a few species common to both habitats. Species of ciliates are known from soil and fresh water but only five of these occur in both habitats. In cases where a genus of ciliates is common to both environments the soil species are usually distinct from the freshwater species.

The soil species are smaller than freshwater species and their small size is doubtless related to the restricted space in which most soil protozoa live. The different species of soil protozoa occur in characteristic groupings which can be correlated with soil type.

Such a correlation excludes the possibility of explaining the distribution by random scattering. In soils of closely related types the species of the different systematic groups; amoebae, testaceans, holotrichous and spirotrichous ciliates show a common pattern or ratio although the actual species involved are not necessarily the same.

Related soil types under different conditions of vegetation, weathering and podzolization can also be compared, and the effect of the soil processes upon the character of the fauna can be judged. With increased leaching and podzolization for example the total number of species in the soil tends to fall but this reduction appears to affect the ciliate fraction less than the rhizopod fraction. Again, wherever there is accumulation of litter or plant matter associated with acidity, rhizopods, especially testaceans, occur in large numbers.

Estimates of numbers per unit area involve assumptions such as the population being uniformly distributed and concentrated largely in the organic horizons and in the topsoil (say the top 10 cm). These may be invalid, so estimates to field populations and biomass based on them must be treated with caution.

Nevertheless, it is probable that population have been under-estimated rather than overestimated. In estimating biomass it is important to remember that the commonest species are generally the smallest and that protozoa in soil are often smaller than in culture.

In three types of forest soil, a calcareous mull and a more under beech (Fagus sylvaticus), Stout found that the ciliate fauna differed less than the ciliate fauna differed less than the rhizopod fauna. The main difference lay between the more restricted testacean fauna of the calcareous mull, which resembled a grassland fauna. There appeared to be no difference in the amoeba fauna of the three soils.

Although their pattern of distribution differs in many respects, the ciliate and testacean faunas of soil have much in common. Both are closely related to the fauna of mosses and Sphagnum and both reflect the moisture regime and base status of the habitat.

Functions of Protozoa:

i.. Protozoa help mineralize nutrients, which make them available for use by plants and other soil organisms.

ii. Protozoa regulate bacteria populations as they graze on bacteria and it seems to stimulate growth of that bacterial population. Suppress bacterial and fungal pathogens

iii. Protozoa is a food source for other soil organisms.

iv. They help to suppress disease by feeding on pathogens.

v. Protozoa release excess nitrogen as they eat bacteria that will then be used by plants and other members of the food web.

vi. Enhance nitrification rates.

vii. Can be agents of plant disease.

It is now recognized that the effect of steaming soil is more extensive than its biological effects and that physical and chemical characteristics of the soil are also affected. These include water-holding capacity, capillary properties, destruction of the colloidal film surrounding soil particles, increased concentration of the soil solution, and increased solubility of soil constituents, e.g. Ca, Mg, Mn, and phosphate and also to a lesser extent K, Si, and Al.

The biological effects are an initial inhibition both of bacterial activity and seed germination followed by greatly stimulated bacterial and plant growth. The present view of sterilization is that the destruction of organisms removes possible disease-causing or antibiotic organisms and releases plant nutrients both by the autolysis of microbial protoplasm and by reducing microbial competition for nutrients.

Deficiencies of trace elements can be removed by partial sterilization. The whole phenomenon may be viewed as a gross reorganization of the soil equilibrium and the stimulated bacterial, protozoan, and plant activity as resultants of the new equilibrium reached.

Their resistance to unfavourable conditions depends largely upon their ability to encyst. In the ciliate genus Colpoda, one of the most common and characteristic soil protozoa, there are basically two types of cyst. In the complete absence of oxygen some free-living protozoa die within an hour or two, e.g. the fresh-water ciliate Stylonychia mytilus. Some survive for a time but do not feed, e.g. the normally sessile Vorticella microstoma which becomes free-swimming.

Soil Mesofauna:

1. Nematode:

Nematodes are an attractive system for evolutionary developmental biology. Nematodes are known as thread worms because the word nematode is derived from the Greek word Nemata, meaning thread. They are also known as eel worms due to their resemblance to eel fish and as round worms because of their round transverse section.

A typical nematode may be defined as a microscopic, ventrally arcuate animal which is pseudocoelomte, triploblastic, metamerically unsegmented, bilaterally symmetrical, protostomiate and which does not possess respiratory and circulatory systems and cilia. Further, they are soft-bodied, heterotrophic and dioeceous in nature. They exhibit a serpentine motion through the lateral side (creeping side).

Nematodes are the most numerous multicellular animals on earth. A handful of soil will contain thousands of the microscopic worms, many of them parasites of insects, plants or animals. Free-living species are abundant, including nematodes that feed on bacteria, fungi, and other nematodes, yet the vast majority of species encountered are poorly understood biologically. There are nearly 20,000 described species classified in the phylum Nemata. Nematodes are non-segmented worms typically 1/500 of an inch (50μm) in diameter and 1/20 of an inch (1 mm) in length.

Distribution:

Nematodes are found everywhere. Some live in the soil, some in the water, and some even live as parasites inside other animals but are often overlooked because most of them are microscopic in size. For instance, a square yard of woodland or agricultural habitat may contain several million nematodes.

Many species are highly specialized parasites of vertebrates, including humans, or of insects and other invertebrates. Other kinds are plant parasites, some of which can cause economic damage to cultivated plants. Nematodes are particularly abundant in marine, freshwater, and soil habitats.

About 100 cc of soil may contain several thousand of them. Agricultural soils generally support less than 100 nematodes in each teaspoon (dry gram) of soil. Grasslands may contain 50 to 500 nematodes, and forest soils generally hold several hundred per teaspoon.

The less disturbed soils contain more predatory nematodes, suggesting that predatory nematodes are highly sensitive to a wide range of disturbances. Because of their importance to agriculture, much more is known about plant-parasitic nematodes than about the other kinds of nematodes which are preset in soil.

Most kinds of soil nematodes do not parasitize plants, but are beneficial in the decomposition of organic matter. These nematodes are often referred to as free-living nematodes. The rhizosphere soil around small plant roots and root hairs is a particularly rich habitat for many kinds of nematodes.

Nematodes are concentrated near their prey groups. Bacterial- feeders abound near roots where bacteria congregate; fungal-feeders are near fungal biomass; root-feeders are concentrated around roots of stressed or susceptible plants. Predatory nematodes are more likely to be abundant in soils with high numbers of nematodes.

Those few species responsible for plant diseases have received a lot of attention, but far less is known about the majority of the nematode community that plays beneficial roles in soil.

The soil nematodes can facilitate the symbiotic relationship between legume plants and nitrogen-fixing bacteria. Some alfalfa plants are able to bring symbiotic bacteria into areas of soil that previously lacked this bacteria; one of the ways they apparently accomplish this is by attracting certain larger organisms, such as soil- dwelling nematodes, which carry the beneficial bacteria on their bodies and in their feces.

The important soil nematodes are- Pellioditis sp., Pristionchus lheritieri, Acrobeloides sp., Panagrolaimus sp., Panagrolaimus sp., Aporcelaimellus obtusicaudatus, Panagrolaimus sp., Cephalobus, Acrobeloides sp., etc.

Types of Nematodes:

i. Herbivores:

These are the plant parasites, which are relatively well known. This group includes many members of the order Tylenchida, as well as a few genera in the orders Aphelenchida and Dorylaimida. The mouthpart is a needlelike stylet which is used to puncture cells during feeding. Ectoparasites remain in the soil and feed at the root surface. Endoparasites enter roots and can live and feed within the root.

ii. Bacterivores:

Bacterial-feeders consume bacteria. Many kinds of free-living nematodes feed only on bacteria, which are always extremely abundant in soil. In these nematodes, the “mouth”, or stoma, is a hollow tube for ingestion of bacteria. This group includes many members of the order Rhabditida as well as several other orders which are encountered less often. These nematodes are beneficial in the decomposition of organic matter.

iii. Fungivores:

Fungal-feeders feed by puncturing the cell wall of fungi and sucking out the internal contents. This group of nematodes feeds on fungi and uses a stylet to puncture fungal hyphae. Many members of the order Aphelenchida are in this group. Like the bacterivores, fungivores are very important in decomposition.

iv. Predators:

Predatory nematodes eat all types of nematodes and protozoa. They eat smaller organisms’ whole, or attach themselves to the cuticle of larger nematodes, scraping away until the prey’s internal body parts can be extracted. They feed indiscriminately on both plant parasitic and free-living nematodes.

One order of nematodes, the Mononchida, is exclusively predacious, although a few predators are also found in the Dorylaimida and some other orders. Compared to the other groups of nematodes, predators are not common, but some of them can be found in most soils.

v. Omnivores:

Omnivores eat a variety of organisms or may have a different diet at each life stage. The food habits of most nematodes in soil are relatively specific. For example, bacterivores feed only on bacteria and never on plant roots, and the opposite is true for plant parasites. A few kinds of nematodes may feed on more than one type of food material, and therefore are considered omnivores.

For example, some nematodes may ingest fungal spores as well as bacteria. Some members of the order Dorylaimida may feed on fungi, algae, and other animals. Root-feeders are plant parasites, and thus are not free-living in the soil.

vi. Unknown:

Since free-living nematodes have not been studied very much, the food habits of some of them are unknown. The microscopic size of these animals presents additional difficulties. For example, it can be very difficult to distinguish whether a nematode is feeding on dead cells from a plant root or on fungi growing on the cell surface. Sometimes a nematode showing this feeding behavior may be classified simply as a root or plant associate.

Functions of Nematodes:

(a) Decomposition and Nutrient cycling,

(b) Grazing,

(c) Dispersal of microbes,

(d) Food source,

(e) Disease suppression and development.

2. Arthropods:

Soil arthropods range in size from microscopic to several inches in length. They include insects, such as springtails, beetles, ants’ crustaceans and such as sowbugs; arachnids such as spiders and mites; myriapods, such as centipedes and millipedes; and scorpions. Soil arthropods can be grouped as shredders, predators, herbivores, and fungal-feeders.

Following are the function of soil arthropods in soil community:

i. Shredders:

Arthropods increase the surface area accessible to microbial attack by shredding dead plant residue and greatly increase the rate of decomposition. Arthropods ingest decaying plant material to eat the bacteria and fungi on the surface of the organic material. As arthropods graze on bacteria and fungi, they stimulate the growth of mycorrhizae and other fungi, and the decomposition of organic matter. Predatory arthropods are important to keep grazer populations under control and to prevent them from over-grazing microbes.

They help out by distributing nutrients through the soil, and by carrying bacteria on their exoskeleton and through their digestive system. By more thoroughly mixing microbes with their food, they enhance organic matter decomposition. As they graze, arthropods mineralize some of the nutrients in bacteria and fungi, and excrete nutrients in plant-available forms.

In most forest and grassland soils, every particle in the upper several inches of soil has been through the gut of numerous soil fauna. Each time soil passes through another arthropod or earthworm; it is thoroughly mixed with organic matter and mucus and deposited as fecal pellets. Fecal pellets are a highly concentrated nutrient resource, and are a mixture of the organic and inorganic substances required for growth of bacteria and fungi.

In many soils, aggregates between 1/10,000 and 1/10 of an inch (0.0025 mm and 2.5 mm) are actually fecal pellets. Relatively very arthropod species burrow through the soil. Yet, within any soil community, burrowing arthropods and earthworms exert an enormous influence on the composition of the total fauna by shaping habitat. Burrowing changes the physical properties of soil, including porosity, water-infiltration rate, and bulk density.

Complete digestion requires a series of many types of bacteria, fungi, and other organisms with different enzymes. At any time, only small subsets of species is metabolically active – and are the only capable species for available resources currently available. Soil arthropods consume the dominant organisms and permit other species to move in and take their place, thus facilitating the progressive breakdown of soil organic matter.

ii. Predators:

Some arthropods can be damaging to crop yields, but many others that are present in all soils eat or compete with various root- and foliage-feeders. Some (the specialists) feed on only a single type of prey species. Other arthropods (the generalists), such as many species of centipedes, spiders, ground-beetles, rove-beetles, and gamasid mites, feed on a broad range of prey.

Where a healthy population of generalist predators is present, they will be “available to deal with a variety of pest outbreaks”. A population of predators can only be maintained between pest outbreaks if there is a constant source of non- pest prey to eat. That is, there must be a healthy and diverse food web.