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Chapter: Microbiology

Microbiology of soil

The term soil refers to the outer, loose materials of earth surface. Agriculturally, it is the region supporting plant life and from which plants obtain their mechanical support and required nutrients.



The term soil refers to the outer, loose materials of earth surface. Agriculturally, it is the region supporting plant life and from which plants obtain their mechanical support and required nutrients. The soil con-tains multitude of organic substances. The soil environment is unique in several ways: it contains bacteria, fungi, actinomycetes, algae and pro-tozoa. It is one of the most dynamic sites of biological interactions in nature. Soil is the region in which occur many of the biochemical reac-tions concerned in the destruction of organic matter, in the weathering of rocks and in the nutrition’s of crops.

The soil is composed of five major components: mineral matter, water, air, organic matter and living organisms. The quantity of these constituents is not the same in all soils but varies with the locality. The inorganic portion of the soil, because its influence on nutrient availabil-ity, aeration, and water retention has a marked effect on the microbial inhabitants. The soil is not a dead inert material. Actually it is full of life. One gram of soil contains approximately one million microorganisms. Man depends upon the soil for his food. The soil depends upon the microorganisms for its fertility. The soil is not a static medium. The soil is a tremendous growth medium. The soil has organic matter soil solu-tion and soil air. All these components are affected by the activities of microorganisms. So the soil is constantly changing medium. The soil solution in agricultural soil has ions like K+, Na+, Mg++, Ca++, Fe+, S-, No3- So4-, Po4 and others. These ions are very essential in culture media. In a fertile soil, these elements in mineral form are supple-mented by organic compounds derived from the decomposition of ani-mal and plant residues. Thus the soil is an excellent natural medium for microorganisms.


Distribution of different types of soil microorganisms

Soils contain five major groups of microorganisms. They are bacteria, actinomycetes, fungi, algae and protozoa. Among the soil microorganisms, bacteria are most dominant group of organisms. All kinds of bacteria are found in the soil. This is because all kinds of organic refuse are disposed off on the soil. Many of the soil bacteria perform useful functions like decomposition of organic matter, conver-sion of soil constituents into useful materials, production of antibiotics in the soil, and biogeochemical cycling of elements like carbon, nitro-gen, phosphorus, iron, sulfur and manganese.

The bacterial population of the soil exceeds the population of all other groups of microorganisms in both number and variety. Direct microscopic counts as high as several billions bacteria per a gram of soil have been reported.

The actinomycetes population as many as millions per gram of soil is present. The most predominant genera present in the soil are Nocardia, Streptomyces and Micromonospora. These organisms areresponsible for the characteristic musty or earthy odour soon after the rainfall. This is due to sporulation of actinomycetes. Actinomycetes are capable of degrading many complex organic substances and con-sequently play an important role in building soil fertility. The actino-mycetes have ability to synthesize and excrete antibiotics. Most of the antibiotics are produced by actinomycetes. The presence of antibiotic substances in soil can be detected with great difficulty.

The fungal population ranging from thousands to hundred thou-sands per gram of soil has been reported. They are aerobic in nature and found more numbers near the earth surface. They exist in the atmosphere as mycelial and spore stage. Fungi are active in decom-posing the major constituents of plant tissues, namely, cellulose, hemi-cellulose, lignin and pectin.

The population of algae in soil is very smaller than that of either bacteria or fungi. The major types present in the soil are the greenalgae and diatoms. Their photosynthetic nature accounts for their pre-dominance on the surface or just below the surface layer of soil. In a fertile soil biochemical activities of algae are masked by bacteria and fungi. In certain conditions, algae perform prominent and beneficial changes. For example, on barren and eroded lands they may initiate the accumulation of organic matter because of their ability to carry out photosynthesis and other metabolic activities.

Many soil protozoa are flagellates or amoebas; the population per gram soil ranges from a few hundred to several thousand in moist soils rich in organic matter. Protozoa are of significance since their dominant mode of nutrition involves ingestion of bacteria.

Factors that influencing microbial population

Factors that influencing microbial population include 1) Soil mois-ture, 2) Aeration, 3) Temperature, 4) pH and 5) Organic and inor-ganic nutrient supply. In addition to this, cultivation, ploughing, season and depth of soil also influence microbial population in soil.

Soil moisture :Soil moisture governs microbial activity in two ways.Since water is the major component of protoplasm, an adequate sup-ply must be available for vegetative growth and multiplication. But, where moisture becomes excessive, microbial proliferation is suppressed because the over supply of water limits gaseous exchange and lowers the available oxygen supply, creating an anaerobic environment. Moisture is present in the form of film in soil pores. The amount of water in-creases with increase in porosity of soil. Soil moisture is affected through irrigation, drainage or management practices.

Aeration : The air is essential for the growth of the aerobic organisms.The water logging condition brings about a decrease in the abundance of aerobic organisms. The change from an aerobic to a largely anaero-bic flora is effected by the disappearance of free oxygen as a result of its utilization by oxygen-requiring microorganisms, so that only micro-organisms tolerant of low oxygen levels complete anaerobiosis are ca-pable of proliferation.

Temperature :Temperature governs all biological processes and it isthus prime factor of concern to the microorganisms. Each microorgan-ism has an optimum temperature for growth. Most microorganisms are mesophilic that can able to grow between 25-35oC. Certain spe-cies develop best at temperature below 20oC and they are termed as psychrophiles. Thermophilic microorganisms that grow readily at tem-peratures of 45oC to 65oC.

pH :The neutral pH is favourable for many types of microorganisms.Highly acidic or alkaline conditions tend to inhibit many common mi-crobes. The greater hydrogen ion concentration, the smaller is the size of the microbial community. Soil-borne fungi are sensitive to high pH.

Organic and inorganic nutrients :These organic and inorganicnutrients are very important for microorganisms a s these provide nutrition for growth, activity and survival of microorganisms in soil. The chemical factors are gases, acids, micro and macro elements and clay minerals etc. In the soilsolution, gases and microorganisms are dissolved. However, the dissolved components are in constantly shifting equilibrium with the solid phase. The dead organic materials of plant and animal origin serve as total organic matter, which later is subjected to microbial colonization and decomposition. However, due to incorporation of green manures , crop residues etc., in soil, the community size of microorganisms gets increased. At the same time application of these organic matter alters the composition of soil microflora, microfauna and relative dominance of antagonistic micro-organisms. The types of vegetation and its growth stages of plant domi-nate one or more groups of soil microorganisms. Increased population of microorganisms can be found in the rhizosphere region according to season, growth stages and abundant availability of nutrients.

Harmful microbial interactions

Harmful microbial interaction is otherwise described as negative interaction or antagonistic interaction. The composition of the microf-lora microfauna of any habitat is governed by the biological balance created through interactions and associations of all individuals present present in a community. Any inhibitory effect of an organism created by any means to the other organisms is known as harmful interactions or antagonistic interaction and the phenomenon of this activity is called antagonism. Harmful interactions have three types. They are amensalism, competition and parasitism.


Amensalism is the phenomenon where one microbial species is affected by the other species, where as other species is unaffected by first one. Amensalism is accomplished by secretion of inhibitory sub-stances such as antibiotics. Certain organisms may be of great practical importance, since they often produce antibiotics or other inhibitory sub-stances, which affect the normal growth of other organisms. Antago-nistic relationships are quite common in nature. For example,

Pseudomonas aeruginosa is antagonistic towards Aspergillus terreus.


A negative association may result from competition among spe-cies for essential nutrients. In such situations the best adapted micro-bial species will predominate or eliminate other species which are de-pendent upon the same limited nutrient substance.


Parasitism is defined as a relationship between organisms in which one organism lives in or on another organism. The parasites feed on the cells, tissues or fluids of another organisms, the host, which is harmed in this process. The parasite depends on the host and lives in intimate physical and metabolic contact with the host. All types of plants and animals are susceptible to attack by microbial parasites.

Beneficial Interactions

The beneficial interactions such as symbiosis (mutualism), proto cooperation, and commensalism are found to operate among the soil inhabitants.

Symbiosis (Mutualism)

Mutualism is an example of symbiotic relationship in which each organism benefits from the association. One type of mutualistic asso-ciation is that involving the exchange of nutrients, between two species, a phenomenon called syntrophisms. Many microorganisms synthesis vitamins and aminoacids in excess of their nutritional requirements. Others have a requirement for one or more of these nutrients.

Symbiosis is an obligatory relationship between two populations that benefit both the populations. Both populations are living together for mutual benefit. The relationship between algae and fungi that result in the formation of lichens is a classical example of mutualistic intermicrobial relationship. Lichens are composed of primary producer, the phycosymbiont (algae) and a consumer the mycosymbiont (fungus).


It is an association of mutual benefit between two populations, but not obligatory and only complementary. Both population are capable of surviving in their natural environment on their own, although when offered, the association offers some mutual advantages.

For an example, the mixed culture of Proteus vulgaris (pro-duce biotin/requiring nicotinic acid) and Bacillus polymyxa (produce nicotinic acid/ requiring biotin). Both grow as partner bacterium syn-thesizes the missing vitamin.


In a commercial relationship between two microbial populations, one population is benefited and other population remains unaffected. Commensalism is a unidirectional relationship between two popula-tions. The unaffected population does not benefit by the action of sec-ond population. For receiving population, the benefit provided may be essential.

In commensalism, the unaffected population modifies the habitat in such a way that another population benefits. For example, a popu-lation of facultative anaerobes utilizes oxygen and creates a habitat suit-able for the growth of anaerobes. In soil, vitamin and growth factors producing organisms benefit vitamin and growth factors requiring organisms.


The region which is adjacent to the root system is called rhizosphere. The microbial population on and around roots system considerably higher than that of root-free soil or non-rhizosphere soil. This may be due to the availability of nutrients from plant roots in the form of root nodules, secretions, lysates mucigel and sloughed off cells. Plant roots provide shelter to soil microbes in the rhizoplane (root surface) and endorhizosphere (inside root).

Rhizosphere effect

Bacteria predominate in rhizosphere soil and their growth is in-fluenced by nutritional substances released from the plant tissues eg. aminoacids, vitamins and other nutrients; the growth of the plant is in-fluenced by the products of microbial metabolism that are released into the soil. It has been reported that aminoacid - requiring bacteria exist in the rhizosphere in larger numbers than in the root-free soil. It has been demonstrated that the microflora of the rhizosphere is more active physiologically than that of non-rhizosphere soil. The rhizosphere effect improves the physiological conditions of the plant and ultimately result in higher yield. Greater rhizosphere effect is seen with bacteria (R:S ratio ranging from 10-20 times more) than with actinomycetes or fungi.


The Dutch Microbiologist Ruinen coined the term phyllosphere. The leaf surface has been termed as phylloplane and the zone on leaves inhabited by the microorganisms as phyllosphere. In forest vegetation, thick microbial epiphytic associations exist on leaves. The dominant and useful microorganisms on the leaf surfaces in the forest, vegetation happened to be nitrogen fixing bacteria such as Beijerinckia and Azotobacter. Apart from these nitrogen fixing bacteria, other generasuch as PseudomonasPseudobacteriumPhytomonoas are also encountered on the leaf surface. The quantity and quality of phyllosphere organisms vary with the plant species and its morphological, physiological and environmental factors. The age of plant, its leaf spread, morphology and maturity level and the atmospheric factors greatly influence the phyllosphere microflora.


The region, which is adjacent to the seed surface is termed as spermosphere. Healthy seeds carry specific bacterial flora in respect of number and species. There are several reports in the litera-ture on the quantity and quality of microorganisms carried by the seeds of different plant species both externally and internally. Many of the organisms are harmless some may be positively beneficial and very few may be pathogenic under certain favourable conditions. It has been shown that some organisms have beneficial effects on the germinating seed through some biological products, such as growth hormones. It has been reported that the germinating seed excretes some chemicals, which influence the quality and quantity of the microorganisms on the seed. Picci defined the region of such influence around the seed as spermosphere and the phenomenon as spermosphere effect. When the seed is sown in soil, certain interactions between the seed-borne microflora and the soil microorganisms take place, under the influence of chemicals exuded by the germinating seed.

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