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Soil microorganisms and their interactions

Soil microorganisms and their interactions

The soil is considered as the land surface of the earth which provides the substratum for plant and animal life. The soil represents a favourable habitat for microorganisms and is inhabited by a wide range of microorganisms, including bacteria, fungi, algae, viruses and protozoa. The physical structure, aeration, water holding capacity and availability of nutrients are determined by the mineral constituents of soil, which are formed by the weathering of rock and the degradative metabolic activities of the soil microorganisms. Cultivated soil has relatively more population of microorganisms than the fallow land, and the soils rich in organic matter contain much more population than sandy and eroded soils. Microbes in the soil are important to us in maintaining soil fertility, cycling of nutrient elements in the biosphere and sources of industrial products such as enzymes, antibiotics, vitamins, hormones, organic acids etc. But certain microbes in the soil are the causal agents of various human and plant diseases.

       The plant and animal remains deposited in the soil contribute organic substances. Soil microorganisms breakdown a variety of organic materials and use a portion of these breakdown products to generate or synthesize a series of compounds that make up humus, a dark coloured amorphous substance composed of residual organic matter not readily decomposed by microorganisms. The three major fractions of humus are humic substances, poly-saccharides and other non-humic substances, and humin. These materials impact on the physical, chemical and bio-chemical properties of soil in many ways. Humus improves the texture and structure of the soil, contributes to its buffering capacity and increase the water holding capacity of the soil.


Microbial flora of soil

The vast differences in the composition of soils, together with differences in their physical characteristics and the agricultural practices by which they are cultivated, result in corresponding large differences in the microbial population both in total numbers and in kinds. The great diversity of the microbial flora makes it extremely difficult to determine accurately the total number of microorganisms present.

Bacterial population in soil

The bacterial population of the soil exceeds the population of all other groups of microorganisms in both number and variety. Bacterial population is one-half of the total microbial biomass in the soil ranging from 1,00000 to several hundred millions per gram of soil, depending upon the physical, chemical and biological conditions of the soil. As per the system proposed in the Bergey's Manual of Systematic Bacteriology, most of the bacteria which are predominantly encountered in soil are taxonomically included in the three orders, Pseudomonadales, Eubacteriales and Actinomycetales of the class Schizomycetes. Bacteria are also classified on the basis of physiological activity or mode of nutrition, into two groups, i.e., autotrophs and heterotrophs. Autotrophic bacteria are capable of synthesizing their food from simple inorganic nutrients. They are of two types, i.e., photoautotrophs (Chromatrum, Chlorobium), which utilize CO2 as carbon source and derive energy from sunlight and chemoautotrophs (Nitrobacter, Nitrosomonas), which utilize CO2 as carbon source and derive energy from the oxidation of simple inorganic substances present in soil. Herterotrophic bacteria derive their carbon and energy from complex organic matter, decaying roots and plant residues. Most of the bacteria present in soil are heterotrophic in nature. Both aerobic and anaerobic bacteria are present in soil. The majority of the beneficial soil-dwelling bacteria need oxygen and therefore aerobic in nature, whilst those that do not require air are referred to as anaerobic, and tend to cause putrefaction of dead organic matter.  It is generally agreed that there are many species of bacteria in soil are yet to be discovered.

Processes performed by bacteria in soil

Bacteria bring about a number of changes and biochemical transformations in the soil and thereby directly or indirectly help in the nutrition of higher plants growing in the soil. The important transformations and processes in which soil bacteria play vital role are: decomposition of cellulose and other carbohydrates, ammonification, nitrification, denitrification, biological fixation of atmospheric nitrogen, oxidation and reduction of sulphur and iron compounds. 

       The bacterial genera Nocardia, Streptomyces, and Micromonospora belong to the order actinomycetes (aerobic and heterotrophic), are capable of degrading many complex organic substances and consequently play an important role in building soil fertility. The actinomycetes are also able to synthesize and excrete antibiotics, e.g., streptomycin is produced by growing soil actinomycetes in pure culture.

       Ammonification is a process where amino acids are subject to a variety of pathways for microbial decomposition. The production of ammonia is referred to as ammonification. The soil bacteria belong to the genera Bacillus and Pseudomonas carry out the process of ammonification. Nitrification is a process where microorganisms convert ammonia to nitrate. This process happens in two steps and each step is performed by a different group of bacteria. The first step is oxidation of ammonia to nitrite which is performed by ammonia-oxidizing bacteria (genera include Nitrosomonas, Nitrosococcus, Nitrosovibrio), and the second step is the oxidation of nitrite to nitrate which is performed by nitrite-oxidizing bacteria (genera include Nitrobacter and Nitrospina).

       Dentrification is a process where the transformation of nitrates to gaseous nitrogen is accomplished by a series of biochemical reactions. Species of several genera of bacteria are capable of transforming NO3- to N2, e.g., Agrobacterium, Bacillus, Chromobacterium, Flavobacterium, Achromobacter, Hyphomicrobium, Pseudomonas, Alcaligenes, Thiobacillus and Vibrio.

       Many microorganisms are capable of using molecular nitrogen in the atmosphere as their nitrogen source. The conversion of molecular nitrogen into ammonia by soil microorganisms is known as nitrogen fixation. The process is carried out by both non-symbiotic and symbiotic microorganisms. Non-symbiotic microorganisms live freely and independently in the soil whereas symbiotic microorganisms live in roots of plants. The bacterial genera Clostridium and Azotobacter carry out non-symbiotic nitrogen fixation whereas symbiotic nitrogen fixation is carried out by the genus Rhizobium. Rhizobium accomplishes the process in association with the plants belong to the family leguminoceae. It is a process where both the plant and the bacteria benefit by the association. The bacteria convert atmospheric nitrogen into fixed nitrogen, which is available to the plant, and in turn, the bacteria derive nutrients from plant tissues. 

       Some bacteria are capable of synthesizing organic matter from inorganic carbon. The organic carbon compound that eventually are deposited in the soil are degraded by microbial activity. Carbon dioxide is released as the end product into the air and soil. Cellulose is the most abundant organic material in plants which is readily attacked by many species of bacteria and fungi. 

       Some bacterial species oxidize and others reduce various sulphur compounds. Sulphur in its elemental form cannot be utilized by plants or animals. The bacterium Thiobacillus thiooxidans oxidize sulphur into sulphates. Sulphates may also be reduced to hydrogen sulphide by soil microorganisms.  Certain pigmented sulphur bacteria oxidize hydrogen sulphide to elemental sulphur.

Soil fungi

More than hundreds of different species of fungi inhabit the soil. They prefer to live in the soil in an aerobic condition. Fungi perform important functions within the soil in relation to nutrient cycling, disease suppression and water dynamics, all of which help plants become healthier and more  vigorous. Fungi exist in both the mycelial and spore stage. Soil fungi are microscopic plant-like cells that grow in long threadlike structures or hyphae that make a mass called mycelium. The mycelium absorbs nutrients from the roots it has colonised, surface organic matter or the soil. From the mycelia the fungi is able to throw up its fruiting bodies, the visible part above the soil (e.g., mushrooms), which may contain millions of spores. When the fruiting body bursts, these spores are dispersed through the air to settle in fresh environments, and are able to lie dormant for up to years until the right conditions for their activation arise. The physical structure of soil is improved by the accumulation of mold mycelium within it.

       Fungi are active in decomposing the major constituents of plant tissues namely cellulose, lignin and pectin. Saprophytic fungi convert dead organic matter into fungal biomass, carbon dioxide and organic acids. These fungi have enzymes that work to "rot" or "digest" the cellulose and lignin found in the organic matter, with the lignin being an important source of carbon for many organisms. Without their digestive activities, organic material would continue to accumulate until the forest became a huge rubbish dump of dead leaves and trees.  By consuming the organic matter fungi play an important role in immobilising and retaining nutrients in the soil.

       Some fungi live in a mutually beneficial relationship with plants. Mycorrhizal fungi are perhaps the best known of the mutualists. Mycorrhizal fungi form a partnership mainly with trees but also with some plants, but rather then harming the tree, their presence significantly increases the roots' effectiveness. In a mycorrhizal association, the fungus colonizes the host plant's roots, either intracellularly as in arbuscular mycorrhizal fungi (AMF), or extracellularly as in ectomycorrhizal fungi. Arbuscular mycorrhiza (VAM) are the most common form of mycorrhiza, especially in agricultural plant associations. This mutualistic association provides the fungus with relatively constant and direct access to carbohydrates, such as glucose and sucrose. The carbohydrates are translocated from the leaves to root tissue and on to the plant's fungal partners.  Plant roots alone may be incapable of taking up phosphate ions that are demineralized in soils with a basic pH. The mycelium of the mycorrhizal fungus can, however, access these phosphorus sources, and make them available to the plants they colonize.

       Another group of fungi also known as pathogenic fungi (parasitic fungi), the second largest group present in the soil. This group includes the fungi genera Verticillium, Phytophthora, Rhizoctonia and Pythium. These group of fungi being parasitic on plants, draw all the nutrients from the plant and ultimately cause its death.

       Fungi tend to dominate over bacteria and actinomycetes in acid soils as they can tolerate a wide pH range. Fungi can survive in the soil for long periods even through periods of water deficit by living in dead plant roots and as spores or fragments of hyphae.

Soil algae

Algae population in soil is generally smaller than that of either bacteria or fungi. Their number in soil usually ranges from 100 to 10,000 per gram of soil. They are photoautotrophic, aerobic organisms and obtain CO2 from atmosphere and energy from sunlight and synthesize their own food. Their photosynthetic nature accounts for their predominance on the surface or just below the surface layer of soil. On bare and fretted land, algae initiate the accumulation of organic matter because of their ability to carry out photosynthesis and other metabolic activities. The major types of algae are present in the soil are green algae and diatoms.

       Soil algae are divided into four major classes, i.e., cyanophyta (blue-green algae), chlorophyta (grass-green algae), xanthophyta (Yellow-green algae), and bacillariophyta (diatoms). Out of these four classes, class cyanophyta (blue-green algae) and chlorophyta (grass-green algae) are more abundant in soil. Algae of the class chlorophyta and bacillariophyta are dominant in the soils of temperate region while blue-green algae are dominant in tropical soils. Chlorella, Chlamydomonas, Chlorococcum are some of the common genera of grass-green algae (chlorophyta) present in the soil whereas Navicula, Pinnularia are some of the genera of diatoms present in the soil.

       Cyanobacteria, also known as blue green algae are the unicellular, oxygenic photosynthetic prokaryotes grow on the surface of freshly exposed rocks where the accumulation of their cells result in simultaneous deposition of organic matter. This gives a nutrient base that will support growth of other bacterial species. Unlike bacteria, which are heterotrophic decomposers of the wastes and bodies of other organisms, cyanobacteria contain the green pigment chlorophyll (as well as other pigments), which traps the energy of sunlight and enables these organisms to carry on photosynthesis. Cyanobacteria are thus autotrophic producers of their own food from simple raw materials. The dominant genera of blue green algae in soil are: Chrococcus, Phormidium, Anabaena, Aphanocapra, Oscillatoria etc. Some blue green algae help in nitrogen fixation. Cyanobacteria are common in neutral to alkaline soil. They secrete a substance known as mucilage, which helps in increasing water retention capacity of the soil. The cyanobacteria play a key role in the transformation of rock to soil, a first step in rock-plant succession.

       Most of the soil algae, specially blue-green algae act as cementing agent in binding soil particles and thereby prevent soil erosion. In un-cropped soil, soil algae check the loss of nitrates through leaching and drainage. They liberate large quantity of oxygen through photosynthesis in the soil environment and thus facilitate the aeration in submerged soils. In tropical soils, soil algae  maintain soil fertility.

Protozoa in soil

Most soil protozoa are flagellates or amoebas; the number per gram of soil ranges from a few hundred to several hundred thousand in moist soils rich in organic matter. They are larger than bacteria and are abundant in surface soil. Their dominant mode of nutrition involves ingestion of bacteria. They can withstand adverse soil conditions as they are characterized by "cyst stage" in their life cycle. Most of them reproduce asexually by binary fission. Most of the soil protozoa possess flagella, cillia or pseudopodia as their locomotive organ. Depending upon the type of locomotion, protozoa can be classified as four different classes: rhizopoda, mastigophora, ciliophora, and sporophora.

       Class rhizopoda includes protozoa without appendages, having naked protoplasm without cell-wall. Amoeba, Biomyxa, Euglypha, etc. are some of the important genera belong to class rhizopoda. Flagellated protozoa which are predominant in soil belong to class mastigophora. Some of the important genera belong to class mastigophora include  Allention, Bodo, Cercobodo, Cercomonas etc. Some of the members of this class are saprophytic whereas some are autotrophic in nature. The class ciliophora, according to the name possess members which have the presence of cilia around their body. Cilia are short, hair like appendages which help in locomotion. The important genera present in soil belong to class ciliophora include Balantiophorus, Colpidium, Uroleptus, Vortiicella etc.

       As the dominant mode of nutrition in protozoa, involves ingestion of bacteria, they play an important role in maintaining bacterial equlibrium in soil. The soil bacterial genera upon  which they depend include Agrobacterium, Bacillus, Enterobacter, Escherichia, Micrococcus, and Pseudomonas. Some protozoa can be used as biological control agents against phytopathogens.


Bacterial viruses as well as plant and animal viruses present in soils through additions of plant and animal wastes. Soil viruses are of great importance as they may influence the ecology of soil biological communities through both an ability to transfer genes from host to host and as a potential cause of microbial mortality. Soils probably harbour many absolutely novel viral species that together may represent a large reservoir of genetic diversity.  Different virus morphotypes including tailed, spherical, rod-shaped, filamentous and bacilliform particles were detected in the soil samples.

       Soil-borne wheat mosaic virus (SBWMV) can cause severe stunting and mosaic in susceptible wheat, barley and rye cultivars. Soil-borne wheat mosaic (SBWM) affects autumn-sown small grains.  Irregular, chlorotic patches in the field suggest soil-borne viral infection, although similar symptoms may be caused by a number of other viruses or other biotic or abiotic factors.


Interactions among soil microorganisms

The microbial ecosystem is the sum of the biotic and abiotic components of soil. It includes the total microbial flora together with the physical composition and physical characteristics of the soil. The microorganisms that inhabit the soil exhibit many different types of interactions or associations. Some interactions are indifferent or neutral; while some are positive and some are negative in nature. The associations existing between different soil microorganisms, whether of a symbiotic or antagonistic nature, influence the activities of microorganisms in the soil.

Neutral associations

Neutral association or neutralism is the association between microorganisms, where two different species of microorganisms occupy the same environment without affecting each other. Such an association might be transitory; as conditions change in the environment, like nutrients availability, there might be a change in the relationship.

Positive associations

There are three types of positive associations exist between microorganisms, which are given below.


Mutualism is an example of a symbiotic relationship in which each organism benefits from the association. The way in which benefit is derived depends on the type of interactions. Syntrophism is a type of mutualistic association, which involves the exchange of nutrition between two species. The association between blue green algae and a fungus (lichen) is known as syntrophism.

       The fungus surrounds the algal cells, often enclosing them within complex fungal tissues unique to lichen associations. In this type of association, algae benefits by protection afforded to it by the fungal hyphae from environmental stresses, while the fungus obtain and use CO2 released by the algae during photosynthesis. The algal or cyanobacterial cells are photosynthetic, and as in plants they reduce atmospheric carbon dioxide into organic carbon sugars to feed both symbionts. Both partners gain water and mineral nutrients mainly from the atmosphere, through rain and dust. The lichen association is a close symbiosis. It extends the ecological range of both partners but is not always obligatory for their growth and reproduction in natural environments, since many of the algal symbionts can live independently.

      Another mutalistic association is characterized by different metabolic products from the association as compared with the sum of the products of the separate species. A mutualism between Thiobacillus ferrooxidans and Beijerinckia lacticogenes helps in ore leaching. Both of these species when grown in a medium free of added carbon and nitrogen sources and with a sterile ore concentrate, the growth of the two species in association and the resulting effect on the rate of leaching copper from the ore concentrate is observed. Leaching is process of recovery of metal from the ore, where microorganisms play the important role of oxidizing insoluble metal sulphides to soluble sulphates.

       Microorganisms may also form mutualistic relationships with plants in soil, an example of which is nitrogen fixing bacteria i.e. Rhizobium growing in the roots of legumes (Plants of the family leguminoceae). In this Rhizobium-legume association, Rhizobium bacteria are benefited by protection from the environmental stresses while in turn plant is benefited by getting readily available nitrate nitrogen released by the bacterial partner.


Commensalism refers to a relationship between organisms, in which one species of a pair benefits whereas the other is not affected. This happens commonly in soil with respect to degradation of complex molecules like cellulose and lignin. For example, many fungi can degrade cellulose to glucose, which is utilized by many bacteria. Many bacteria are unable to utilize cellulose, but they can utilise the fungal breakdown products of cellulose, e.g., glucose and organic acids.

       Another example of commensalism is that of a change in the substrate produced by a combination of species and not by individual species. For example, lignin which is major constituent of woody plants and is usually resistant to degradation by most of the microorganisms. But in forest soils, lignin is readily degraded by a group of Basidiomycetous fungi and the degraded products are used by several other fungi and bacteria which can not utilize lignin directly.


It is a mutually beneficial association between two species. Protocooperation is a form of mutualism, but they do not depend on each other for survival. An example of protocooperation happens between soil bacteria or fungi, and the plants that occur growing in the soil. None of the species rely on the relationship for survival, but all of the fungi, bacteria and higher plants take part in shaping soil composition and fertility. Soil bacteria and fungi interrelate with each other, forming nutrients essential to the plants survival. Plants utilize these microorganism synthesized nutrients through root nodules thereby decomposing organic substances. Soil bacteria and fungi help in improving the fertility of the soil and shaping of soil. Plants get essential carbon dioxide and nutrients. Nutritional proto-cooperation between bacteria and fungi has been reported for various vitamins, amino and purines in terrestrial ecosystem and are very useful in agriculture.


Negative associations


It is the relationship in which one species of an organism is inhibited or adversely affected by another species in the same environment. The relationship is also known as antagonism. The species which adversely affects the other is said to be antagonistic. Such organisms may be of great practical importance, since they often produce antibiotics or other inhibitory substances which affect the normal growth processes or survival of other organisms.

       Antagonistic relations are most common in nature. One example of which is the antagonistic nature of both Staphylococcus aureus and Pseudomonas aeruginosa towards the fungus Aspergillus terreus. Certain Pseudomonas pigments inhibit germination of Aspergillus spores. Staphylococcus aureus produces a diffusable antifungal material that causes distortions and hyphal swellings in Aspergillus terreus.

       An antibiotic is a microbial inhibitor of biological origin. Soil microorganisms are the most common producers of antibiotics. Production of antibiotics in soil may enable the antibiotic producing organism to thrive successfully in a competitive environment. One example of which is the presence of large populations of actinomycetes in the chitinaceous shells of dead crustaceans in the sea. Their existence, in the environment free of other microorganisms, is may be due to the production of antibodies by them. Several species of Streptomyces from soil produces antibacterial and antifungal antibiotics. Most of the commercial antibiotics such as streptomycin, chloramphenicol, Terramycin and cyclohexamide have been produced from the mass culture of Streptomyces. Thus, species of Streptomyces are the largest group of antibiotic producer’s in soil. The bacterial genus Bacillus  produces an antifungal agent which inhibits growth of several soil fungi.

       Antibiosis may result from a variety of other conditions operative in mixed populations. Certain fungi produce cyanide in concentrations toxic to other microorganisms and the algae elaborate fatty acids which exhibit a marked antibacterial activity. Many soil microorganisms, for example the myxobacteria and streptomycetes are antagonistic because they secret potent lytic enzymes which destroy other cells by digesting their cell wall or other protective surface layers. It appears that in the natural environment producers of lytic substances are often found in close proximity with sensitive organisms and do not predominate over them.

    Ammensalism is the interaction between two species, where one species suppresses the growth of other by producing toxins like antibiotics or harmful gases like methane, ethylene, nitrite, or HCN or sulphides and other volatile sulphur compounds.


Soil is inhabited by different kinds of microorganisms, and  therefore they exhibit competition among themselves for nutrients and space. In this kind of situation, the best adapted microorganism will predominate or eliminate the others which are dependent upon the same limited nutrient substance. The organisms with inherent ability to grow fast are better competitors.

       Exogeneous nutrients are required for the germination of chlamydospores of Fusarium, Oospores of Aphanomyces and conidia of Verticillium dahlae in soil. But other fungi and soil bacteria deplete these critical nutrients required for spore germination and thereby hinder the spore germination resulting into the decrease in population. Soil bacteria compete for space and suppress the growth of the fungal population.


Parasitism is the relationship between two organisms, in which one organism lives in or  on another organism. The parasite is dependent upon the host and feeds on the cells, tissues or fluids of the host organism. The parasite lives in intimate physical contact with the host and forms metabolic association with the host. All major groups of plants, animals, and microorganisms are susceptible to attack by microbial parasites.

       The bacterial parasite of Gram-negative bacteria Bdellovibrio bacteriovorus which is widespread in soil and sewage attaches to a host cell at a special region and eventually causes the lysis of that cell. As a consequence, plaque like areas of lysis appear when these parasites are plated along with their host bacteria. Parasitism is widely spread in soil communities. Viruses which attack bacteria (bacteriophages), fungi, and algae are strict intracellular parasites since they cannot be cultivated as free-living forms. There are also many strains of fungi which are parasitic on algae and other fungi by penetration into the host. Fungi with antagonistic activity toward plant pathogens have an essential role in plant growth and health.  Mycoparasites and presumptive mycoparasites have biocontrol potential, some are responsible for natural suppressiveness of soils to certain plant pathogens. Several species of Trichoderma were used successfully against certain pathogenic fungi. Trichoderma sp. was used as commercial bio-fungicides to control a range of economically important soil-borne fungal plant pathogens. Soils contain a large number and great diversity of oospore parasites, which may have the potential to reduce populations of plant pathogenic Phycomycetes in soil.  


Predation is an association in which predator organism directly feed on and kills the pray organism. Predators may or may not kill their prey prior to feeding on them, but the act of predation often results in the death of its prey and the eventual absorption of the prey's tissue through consumption.

       Many species of the soil-dwelling myxobacteria are predators of other microbes.  Many myxobacteria, e.g.,  Myxococcus xanthus, exhibit several complex social traits, including fruiting body formation and spore formation cooperative swarming with two motility systems, and group  predation on both bacteria and fungi. Myxobacteria use gliding motility to search the soil matrix for prey and produce a wide range of antibiotics and lytic compounds that kill and decompose prey cells and break down complex polymers, thereby releasing substrates for growth.  The nematophagous fungi are the best predatory soil fungi. Species of Arthrobotrytis and Dactylella are known as nematode trapping fungi.



1. Alexander, M. Introduction to soil Microbiology, Wiley, New York, 1977.

2. Pelczar,  Michael J., Chan, E.C.S., Krieg, Noel R.(2003). Microbiology of soil.  Microbiology, 5th Edn. Tata McGraw-Hill Publishing Company Limited, New Delhi.


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