Introduction and Importance of Soil Microbiology

Soil represents a medium or substrate in which numerous microorganisms live and bring
about a great variety of processes which are responsible for continuation of the cycle of life in
nature. The numerous living forms which spend all or part of their life in soil ranging from sub
microscopic forms to the lower animal forms. With the growing recognition of the numerous
processes carried out by the microorganisms in the soil there gradually emerged a branch of
microbiology, which came to known as soil microbiology. It is a branch of soil science concerned
with soil inhabiting microorganisms and their functions and activities.
Since soil microbiology concerns with soil microorganisms and their processes it is
closely associated with soil biochemistry. Medical bacteriologists were interested in the soil as a
medium for the growth and survival of disease producing organisms. Agricultural chemists are
also interested in the soil processes that result from the activities of microorganisms. General
bacteriologist, zoologist, botanist were interested in certain special group of organisms found in
soil. Recently, soil microbiology has expanded to include the study of the role of soil
microorganisms in genetic engineering, in the biological control of pests and diseases, the
degradation of pollutants, production and destruction of radioactive gases and its transfer. Thus
microbial participation in several important processes emphasizes that soil microbiology has
become a global science.
Soil microbiology
• Deals with the microscopic organisms of the soil
• Their population and activities
• Role in various transformations taking place in the soil and
• Their importance in plant nutrition and crop production
Distribution, importance of microorganisms and factors influencing the activities of
microorganisms
Soil contains five major groups of microorganisms - bacteria, actinomycetes,
fungi, algae and protozoa. The soil ecosystem includes these microbial groups as well as the
inorganic and organic constituents of a given site. The collections of cells represented in the
community are considered as distinct populations.
All the inhabitants of the particular locality make up the community.
I. Bacteria
Bacteria are the most dominant group of M.O in soil and more numerous than the other four
combined. They present in all types of soil but their population decreases as the depth of soil
increases (Horizon A > B > C). The number of cells of bacteria in the soil is always great, but the
individuals are small, (µm in length). Because of the minute size of the bacteria and large cells or
filaments of the other 4 groups, the bacteria probably account for appreciably less than halt of
the total microbial cell mass. In aerated soil, B, will be dominating, alone are responsible for all
the activities in environment lacking O2 or little O2. In transformation process Bacteria stand
first, due to their rapid growth and capacity of vigorous decomposition of variety of substrates.
Soil microbiological population has been divided into two broad groups - autochthonous
and zymogenous (Allochthonous).
a. Autochthonous or native microbes; Indigenous, which are characteristic of the
particular soil and which many be expected always to be found there. eg. Arthrobacter
b. Zymogenous, or fermentative organisms require an external source of and their
normal population in soil is low (Pseudomonas, Bacillus). When specific substrates are added to
soil, the population is increased. Then gradually declines when the added substrate is
exhausted. eg.cellulose decomposers. N utilizing bacteria, nitrifiers etc.,
c. Transient microbes - comprising organisms that are introduced into the soil by
legume inoculation unintentially as in the case of agents producing animal and plant diseases.
Bergey's Manual of Determinative Bacteriology is universally used for the classification
of Bacteria.
a) Based on nutrition
1. Autotrophs: synthesize their own food derive energy from light or chemicals.
2. Heterotrophs: depends on preformed food for nutrition, derive energy and C from
organic compounds.
Photoautotrophs: energy from slight, C from CO2
Chemoautotrophs: energy from oxidation of inorganic chemicals, C from CO2.
Several reactions in N transformation of soil depend on the chemoautotrophic
organisms viz., Nitrobacter and Nitrosomonas and hence Chemoautotrphy of bacteria in soil is
intimately related to crop production.
b) Based on the O2 requirement
Aerobes: need O2 for growth
 Anaerobes: does not require O2 for growth
Facultative anaerobes: live in the presence or absence of O2.
c) Based on structure
Bacilli - Rod shaped
Cocci - Spherical shaped
Spirillum - Spiral shaped
Abundance of Bacteria
In Arctic regions, frozen 9-10 m / year bacterial counts of 106 / g are observed even
when temperature remains below freezing point. Such organisms are in a state of dormancy
awaiting the spring to recover.
Desert soil is another extreme. Bacteria exist even in oven dry state. Spore forming
bacilli are often predominant.
Importance
 In transformation process bacteria stands first, due to their rapid growth and capacity of
vigorous decomposition of variety of substrate.
 Involved in N 2 fixation P soluilization, CO2 fixation, S & Fe transformation, Si
solubilization etc.,
 Molecular vectors
II. Actinomycetes
A transitional group between the simple Bacteria and Fungi are the actinomycetes.
These are microorganisms producing slender, branded filaments that develop into a
mycelium in all soil. They are classified under bacteria, but resembles fungi in some aspects.
o produces mycelium with extensive branching
o Like Fungi many actinomycetes form aerial mycelium and conidia
o Growth in liquid medium do not resemble (which bacteria is turbid), but form clumps and
pellets like Fungi.
Certain actinomycetes resemble mycobacterium and Corynebacterium in all respects
both morphologically and physiologically including susceptibility to virus attack.
Actinomycetes differ from fungi that they do not have chitin and cellulose which are
commonly found in the cell walls of fungi.
The colony characters are not similar to bacteria.
Some species have flagella that resemble those of true Bacteria.
 Similarities in cell wall composition and sensitivity to antibacterial compounds.
Common genera in soils
Streptomyces (70%) , Nocardia, Micromonaspora, Frankia.
Actinomycetes are sensitive to antibacterial compounds and not antifungal compounds.
Streptomycetes
Musty odour they elaborate; an odour reminiscent of freshly turned soil, the metabolite
of Streptomyces formed geosmin and other volatile products elaborated by Streptomyces are
responsible for the characteristic earth odor/ smell.
Distribution
Actinomycetes are numerous and widely distributed not only in soil but in a variety of
other habitats including composts, river muds and lake bottoms. Present in surface soil and also
in lower horizons to considerable depth. In abundance they are second only to the Bacteria and
the viable counts almost equal to both. Saprophytic existence, but a few species can cause
diseases of plants, domestic animals and even humans.
Isolation
Population is 105 to 108 / g in temperate zone, but lower counts in waterlogged soils,
acid peat, arctic, Tundra regions. In alkaline areas, especially when dry, the relative abundance is
high.
Importance
 Decomposition of resistant components of plant and animal tissue.
 Transformations at high temperature particularly in the manure and compost pits –
thermophiles are dominant.
 Cause certain soil borne diseases of plants, potato scab of apple, sweet potato pox.
 Cause infection to humans, animals.
 Importance in microbial antagonism by production of antibiotics and production of
enzymes.
 Antibiotic Industry

III. Fungi
As the important constituent group of the soil population, they are widely distributed in
most well cultivated soils. Fungi account for a large part of the total microbial population.
Though they are not the major inhabitants, they do in fact makeup the significant part of the
biomass because of the large diameter and extensive network of the filaments. Fungi exist in soil
in the form of vegetative mycelium and spores. Characteristically the fungi possess a
filamentous mycelium network of individual hyphal strands. The hypha itself is rather broad and
has a diameter appreciably greater than that found in the common actinomycetes. In nature
consider or asexual spores are abundant and widespread, the sexual spores relatively
uncommon. In contrast with bacteria the high can be effectively differentiated into Genera and
species on the basis of morphology.

Distribution and Abundance

Several techniques have been developed for the study of the fungal flora. Plate count
and burial slide techniques are used for estimation. Slight alteration of pH and addition of
Novobiocin and streptomycin inhibit bacteria and actinomycets.
Estimates of microbial density reveal the presence in soil is ranging a few as 20,000 to as
many as 1,000,000 fungal propagules per gram, the propagule being considered as any spare, or
hyphal filament that is capable at giving rise to a colony. The length of the fungal mycelium has
been reported to range from 10 to 100m per g surface soil, but various up to 500 and
sometimes in excess of 1000mt have also been obtained. Assuming the filament has an average
diameter of 5µm and a specific gravity of 1.2 and taking the range of 10 to 100 m per gram. It
would appear that the weight of fungi ranges from 500 to 5000 kg per ha of surface soil. Thus
the filaments make up a significant part of the soil mass.
Individual species and genus have been recorded in diverse and highly dissimilar habits.
They are the inhabitants of peats, flooded soils planted to rice, regions with low and extremely
high salt contents, locations in many deserts, ice in Antartica, as well as in the tundra.
Importance:
 Degrade complex molecules - cellulose, hemicellulose, pectin, starch, lignin
 Improve soil structure-aggregate formation
 Pathogenecity in plants, animals and humans
 Predator against soil protozoa- Hyphal penetration reduces mobility, total cessation of
movement
 Trapping nematodes-Arthrobotrys, Dacylaria, Dactylella, Harposporium
 Beneficial association with plants-Mycorrhizal fungi.
IV. Yeast

Non filamentous fungi, their presence maybe demonstrated in most soils. Soil yeasts
are – Candida, Debaryomyces, Rhodotorula, Torulopsis. Yeasts have been found in comparable
numbers in soils of Antarctica, grasslands, cultivated fields, and forests.

Function and activity

 Involved in the degradation of complex molecules. They can utilize and degrade the
major plant constituents – cellulose, hazicellulose, pertins, starch and lignin.
 Participate in humus formation from fresh organic residues.
 Carry out inorganic transformations and influences the formation of stable aggregates
by means of hyphal penetration and the mechanical binding of the particles.
 Pathogenecity is common character associated with several soil borne Fungi Fusarium,
Helminthosporium.
 Cause disease among humans, animals
 Predator against protozoa. The hyphae penetrate the protozoan with a resulting
decrease in motility of the animal and an eventual total cessation of movement. The F
slowly digests the cellular components and assimilates the substances released.
 Nematodes are also trapped by fungi by hyphal extensions. Eg: Arthropotrys, Dactylaria,
Dactylella, Harposporium
 Has beneficial association with higher plants eg. Mycorrhiza – nutrient mobilisation.
IV. Algae
They occur in small numbers in soil. They are photosynthetic organism. Abundant in
habitats in which moisture is adequate and light accessible. Isolation can be done in liquid media
and by planting with agar media. Because of their similarities to bacteria, the BGA are
sometimes classified together i the bacteria.
Photoautotrophic nutrition
In the absence of light heterotrophy occur in some species of chlorophyta, cyanophyta
and diatoms. These species use the oxidation of organic carbon to replace the light in supplying
energy for anabolic process (called facultative photoautotrophs). Occurrence of this photo
synthetic microorganism has been recorded in soils throughout the world. Algae are moderately
adaptable to environmental changes, persist in unfavourable circumstances such as in alkaline
and desert soils.
 Some species colonise the zone under the surface crusts of limestone and sandstone
rocks in the desert, most likely at sites where the nutrient is retained and has sufficient light.
• Enumeration by MPN
• 100 to 50,000 / g soil
• biomass – 7 to 300 kg / ha (Chlorophyll ext).
• flooded paddy field is the environment algae could have a great agronomic
significance. The microbial action may be associated with the utilization of N, the release of O2 or
the excretion of products stimulating plant developments. Under water logged rill soils, an algal
film farms at the liquid surface, make up an appreciable mass.
Common inhabitants: Anabaena, Calothrix, Nostoc, Oscillatoria.
Importance
 Involved in CO2 fixation
 Colonizes the barren surface and corrode and weather rocks-Contribute to soil formation
 Algal layer covers the rocks ,on death it favors secondary colonizers
 Surface bloom reduces erosion losses probably by binding together with soil particles
 Improve soil structure, texture and add fertility to soil after decay
 Photosynthesis liberates 02, provides 02 to the roots and other microorganisms.
 N2 fixation and ammonia excretion
 N2 is released after decomposing of algal biomass
 Production of metabolites
 SCP Production, β-carotene
V. Protozoa
The subterranean soil contains protozoa, earthworms, nematodes, insects. Most abundant
one is protozoa, the simple from of animal life which are primitive and unicellular. Majority of
protozoans are dependent on preformed organic matter as saprobic feeder obtaining their nutrition
from soluble organic and inorganic substances, or by phagotrophic nutrition (direct feeding upon
microbial cells). They maintain the equilibrium by engulfing.
• Regulate the bacterial community
• Maintain the biological equilibrium in soil
• Participate in the decomposition of plant remains
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