Importance of Microbiology

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IMPORTANCE OF MICRO ORGANISMS IN AGRICULTURE
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93 | Climate and Environmental changes: Impact,Challenges and Solutions
IMPORTANCE OF MICRO ORGANISMS IN

AGRICULTURE
Satybhan Singh, Virendra Singh and Krishan Pal

Department of Agricultural Sciences & Engineering, IFTM
University Moradabad, 244 102
Email - satya123216@gmail.com
ABSTRACT
The concept of “friendly microorganisms” was proposed by
Professor Teruo Higa, from the University Of Ryukyus in Okinawa,
Japan. He stated in the 1980s that a combination of approximately
80 different microorganisms was capable of positively influencing
decomposing organic matter such that it reverts into a “life promoting”
process. Professor Higa invoked a “dominance principle” to explain
the asserted effects of his “Effective Microorganisms”. He claimed
that three groups of microorganisms exist: “positive microorganisms”
(regeneration), “negative microorganisms” (decomposition,
degeneration) and “opportunist microorganisms” (regeneration or
degeneration). Higa stated that in every medium (soil, water, air, the
human intestine), the ratio of “positive” and “negative” microorganisms
was critical, since the opportunist microorganisms followed the trend
to regeneration or degeneration. Therefore, he claimed that it was
possible to positively influence the given media by supplementing
with “positive microorganisms”, Anonymous, (2010).
INTRODUCTION
Modern agricultural practices largely rely on high inputs of

mineral fertilizers to high yields and involve applications of chemical
pesticides to protect crops from diseases and pests. These practices
are now being reevaluated and are coming under scrutiny as our
awareness of potential health and environmental consequences of
excessive mineral fertilizer and chemical pesticide usage improves. It
is widely recognized that applications of mineral fertilizers (especially

nitrogen) can result in ground water contamination by nitrates
leaching through the soil profile. Under certain soil conditions, de
- nitrification of applied nitrogen fertilizer can give rise to gaseous
nitrogenous compounds that volatilize from soil into the atmosphere.
Some of them e.g. nitrous oxide are thought to contribute to the
greenhouse effect and the alteration in the ozone layer. Similarly, use of
chemical pesticides has raised concern about their possible presence
and that of their residues in the food chain and in the environment.
Concerns about the possible health and environmental

consequences of using increasing amounts of mineral fertilizers
and chemical pesticides have led to strong interest in alternative
strategies to ensure competitive yields and protection of crops. This
new approach to farming, often referred to as sustainable agriculture,
seeks to introduce agricultural practices that are more friendly to
the environment, earth and that maintain the long – term ecological
balance of the soil ecosystem.
In this article, use of microbial inoculants in agriculture

represent, an attractive eco-friendly alternative to further applications
of mineral fertilizers and chemical pesticides. A continued exploration
of the natural biodiversity of soil microorganisms and the manipulation
of microbial interactions in the rhizosphere of crops represents a
prerequisite step to develop more efficient microbial inoculants.
Global agriculture has to double food production by 2050 in

order to feed the world’s growing population and at the same time
reduce its reliance on inorganic fertilisers and pesticides. To achieve
this goal, there is an urgent need to harness the multiple beneficial
interactions that occur between plants and microorganisms. The
beneficial influences of microorganisms on plant growth include
nitrogen fixation, acquisition and uptake of major nutrients,
promotion of shoot and root growth, disease control or suppression
and improved soil structure. Some of the commonly promoted and
used beneficial microorganisms in agriculture worldwide include
Rhizobia, Mycorrhizae, Azospirillum, Bacillus, Pseudomonas,

Trichoderma, Streptomyces species and many more. Unravelling
the biota black box using modern molecular methods is helping to
find new suites of beneficial microorganisms that can help improve
agricultural production worldwide, Gupta (2012).
The rhizosphere: a site of intense interactions between plant root

and soil
The roots of plants are involved in the uptake of mineral

nutrients and water for plant growth, but they also release a wide range
of organic compounds in the surrounding soil. Consequently, the area
of soil in contact with the plant root, termed the rhizosphere, is a site
of intense microbial activity. Not surprisingly, many microorganisms
are present at higher numbers on the surface of plant roots and in the
rhizosphere than in soil not influenced by the presence of roots.
The rhizosphere is a key soil habitat, where the numerous

interactions taking place between plant root and soil microorganisms
will determine growth conditions for both the plant and the
microorganisms in the rhizosphere. Indeed, the rhizosphere
microbiota exerts an important influence on roots and on growth of
the plant. Consequently, the rhizosphere represents an important soil
habitat where introduction of beneficial microorganisms (e.g. bio-
fertilizers, phyto-stimulators and bio-pesticides) as inoculants can
results in significant improvements in crop yield and quality.
Application of microorganisms in soil stability and bioremediation:
The most fundamental and essential component of farming

systems is the soil itself: that waterlogged, compacted, desiccated,
salinised, wind and rain eroded, and generally abused habitat, which
is in fact one of our most precious resources. It is not only home to
the microorganisms with which we are presently concerned, but is
constantly modified and maintained by their activities.
Soils consist of particles of sand, silt and clay in varying

proportions, held together into aggregates of various sizes by organic

and inorganic materials. The structure of the soil profoundly affects
the infiltration, drainage and storage of water; the activity of soil biota;
crop production and the stability of the soil to erosion. Root and
microbial exudates, as well as various derivatives of organic matter
decomposition, are essential in binding micro-aggregates to maintain
a porous soil structure, although the extent to which individual species
contribute to this process is not clear Tisdal (1994).
The activities of soil organisms, in turn, depend much on

the soil in which they occur, or to which they might be introduced
and, as already suggested, soil organisms influence one another in
various ways. Studies of the possible interrelationships between
VAM fungi, associated bacteria, actinomycetes, fungi and the
stability of soil aggregates have suggested that mycorrhiza-mediated
improvements in soil aggregation can lead to increased numbers
of other microorganisms known to positively influence plant
growth (Andrade et al., 1998). The fact that greater numbers of soil
microorganisms were apparent in aggregated soils suggests that the
creation of favorable growth conditions should be a prerequisite for
introducing microorganisms to the soil.
Further evidence that VAM fungi contribute to the formation

of favorable soil conditions comes from work on pot-grown soybean
(Glycine max) in natural soil inoculated with Bradyrhizobium
japonicum. The formation of water-stable soil aggregates was positively
correlated with root and VAM mycelium development, irrespective of
N source (nitrate or ammonia) (Bethlenfalvay et al., 1999). However,
actinomycetes known to promote water stable aggregate formation,
declined with increasing pH. Soil acidification is thus an important
factor in soil aggregation and stabilization, and this in turn could be
influenced by agronomic and industrial practices.
Applications of Bacteria in Agriculture:
There are certain bacteria which contain special properties

which are beneficent for plants. These bacteria are present in soil
and they affect the crops by fighting against harmful bacteria and
they are also the source of providing nutrition to the crops. Some
bacteria like rhizobia and agro-bacteria are used to release seed
inoculants and useful for the plants. The bacteria like Azoarcus are
of much importance for the plants that it fixes the endophyte of the
grasses. This type of bacteria is mostly helpful crop of rice and they are
very much environment friendly. When the seed is sown in the soil,
bacteria play an important role in its germination. The bacteria grow
in the seed in return get food from it. Bacteria increase the fertility
of the soil and provide such nutrients to the soil which are useful for
the plant growth. They also help in softening the food in the seed and
this is the reason plants come out of the seeds. Though it is not certain
what role bacteria play when the plants grow but they are of much
importance the early stages of plant development. Certain pesticides
are developed using bacteria which give benefit to the crops. Bacillus
thurengiensis is a gram positive bacterium in agriculture.
Benefits of Mycorrhizal fungi in Agriculture:
Mycorrhizal plants show increased growth (Bloss &

Pfieffer,1984) and are generally more tolerant of adverse conditions such
as drought (Parke et al. 1983), soil pathogens (Cooper & Grandison,
1986; Dehne, 1982; Duponnois & Ba, 1998), transplantation (Scagel,
1998), poor soil nutrient status and soil pollution (Leyval et al., 1997),
compared to non-micorrhizal controls.
Improved plant growth and increased tolerance to adverse

conditions can often be attributed to enhanced water and nutrient
acquisition made possible by the extensive hyphal network which
effectively increases the absorptive area of the root. However, the
effectiveness of mycorrhizal fungi in increasing plant growth is not
always directly related to the extent of root colonization or hyphal
growth. In Eucalyptus globulus, plant dry weight was positively
correlated with the length of mycorrhiza-colonised root for some
EM species. In other cases, the benefits of EM inoculation are more
clear-cut and this approach has been used the establishment and
growth of young transplant in horticulture and forestry e.g.Eucalyptus

tereticornus (Reddy & Satyanarayana, 1998), Acacia tortilis (Munro et
al., 1999), Pinus species (Scagel & Linderman, 1998).
Interestingly, many of these beneficial effects are associated

with a range of other phenomena such as mycorrhizal IAA and
ethylene production and micorrhizal- mediated plant disease
suppression (Edwards et al., 1999; Morin et al., 1999). Black spruce
(Picea mariana), for example, is susceptible to the root rot fungus
(Cylindricocladium floridanum).When tree seedlings were inoculated
with the EM fungi Paxillus involutus and Hebeloma cylindrosporum,
50% of seedlings remained unaffected by root rot (Morin et al., 1999).
Mycorrhizal fungi and phosphorus nutrition:
A primary effect of mycorrhizal symbiosis is improved P

nutrition made possible by the extensive hyphal network. This not
only allows the plant to overcome the P depletion zone around
the root but also allows it to reach immobile P that the fungus can
solubilise. This phenomenon is most apparent in low P soils. P can
substitute the effects of mycorrhizal infection on plant survival in
non-mycorrhizal controls in many cases. However, with increasing
soil P, the benefits of mycorrhizal infection decline and mycorrhizal
infection is reduced. In general, the benefits of mycorrhizas are lost to
plants that have other means of obtaining P from the soil. The use of
fertilizers in conventional farming ignores the activity of mycorrhizal
fungi. This could have important long-term consequences for crop
production.
In examining this hypothesis, the soil bacteria Alcaligenes

eutrophus and Arthrobacter globiformis were found to differ significantly
in their preference for AM fungi associated with sorghum. Alcaligenes
eutrophus was shown to depend on the presence of G. mosseae for
survival rather than on the plant root, whereas A. globiformis persisted
equally well in both mycorrhizal and non-micorrhizal soils. This
example serves to show that understanding microbe-plant microbe
interactions in the soil will be fundamental for the management of
sustainable agro ecosystems involving intentional manipulation of the

soil biota. Again a holistic approach to research will be essential.
Effective Microorganisms:
EM is purported to support sustainable practices in farming,
improve composting operations, and to reduce environmental pollution
(Higa and James, 1994). The efficacy of EM on agricultural crops
has been studied throughout the world, while some studies stated
that Effective microorganisms (EM-A, EM-Bokashi) show no effect on
yield and soil microbiology in field experiments as bio-fertilizer in
organic farming. Observed effects relate to the effect of the nutrition
rich carrier substrate of the EM preparation, (Mayer et al. 2003-06
and Mayer et al. 2010). However, there are more studies proving the
positive effect of EM (Olle and Williams, 2013). For example, an
eleven years long application of EM compost showed effects on yield
and nutrition of the crops. Compared to the traditional compost and
control, yields and nutrition of wheat treated with EM compost was
significantly higher (Hu and Qi, 2013).
In Agriculture, the effect of long term application of EM
compost for soil fertility and crop yield improvement was investigated
at China Agricultural University from 1993 to 2013. This filed
experiment show that “The application of EM in combination with
compost significantly increased wheat straw biomass, grain yield,
straw and grain nutrition compared with traditional compost and
control treatment.” Also, the experiment indicates the significant
efficacy of EM on organic nutrition sources (Hu and Qi, 2013).
Effect of microorganisms on soil properties
1. pH value
Soil pH is an important chemical property that affects the

availability of nutrients in the soil as well as the structure and activity
of the soil microbial community. These soil microorganisms have
important functions that not only build soil structure, but also cycle
organic matters and nitrogen compounds. Most soil microorganisms
and plants prefer a neutral pH of 6 to 7 because most soil nutrient

compounds are available in this pH range. In deep layer of soil,
anaerobic microorganisms produce organic acid by anaerobic
respiration and fermentation. Furthermore, aerobic also generate
proton ions with sulfur and ammonia oxidizing, and alter the soil pH,
(Sylvia et al. 2005)
The low pH condition will suppress the availability of

phosphorus which is the important nutrient to the plants in the soil.
Besides, aluminum ions will become more available and might have
negative effects for the plants to reducing crop yields. In agricultural
fields, the addition of nitrogen fertilizers or organic nutrient sources
such as compost and manure an add lots of nitric acid and sulfuric
acid. These strong acids increase the soil acidity and reduce the pH
of the soil. Lime may be used as a management practice to control
pH. It not only increases the availability of nutrients from soil, but
it also provides extra calcium and magnesium for plants and soil
microorganisms.
2. Soil structure
“Soil structure is defined as the arrangement of particles

and associated pores in soils across the size range from nanometres
to centimetres.” (Oades, 1993) It is important for providing flow
pathways for water and nutrients. Aggregation of soil particles
determinants the soil structure, and microorganisms play important
role for soil aggregation. Microorganisms can promote aggregation
by extracellular polysaccharides, glomalin and hyphae. Soil microbes
also can bind soil particles to contribute to the formation of soil
structure. Furthermore, the products of soil microorganisms, organic
matters, are central factors for soil aggregation, (Sylvia et al. 2005).
In agricultural fields, soil structure is disturbed by tillage,

liming, crop rotation, and other human activities. Thus, while the role
of microorganisms in soil structure stabilization is important, there
are many disturbances to the soil in agricultural land, and this reduces
the influence of microbes in the process of soil aggregation in all but
the deeper soil layers.
Factors Affecting Microbial Communities in Agriculture:
1. Crop Rotation
Crop rotation is a method that utilizes different type of crops

in the same field in different time periods. It is one of the oldest
agricultural methods, and it is beneficial for pest and pathogen
control. Rotation also can help increase biodiversity and soil nutrients
by using dissimilar crops with differing essential nutrient demands.
2. Fertilization
Nitrogen (N) and Phosphorus (P) are the essential elements

for all organisms. Crop fertilization is an important factor of the soil
nutrient pools, (Stevenson & Cole 1999). The availability of nutrients
has also been reported to influence soil microbial growth and
activity, (Broeckling et al. 2008). Recent studies have indicated that
high concentrations of NH4+ can inhibit NO3- uptake by fungi (Wang
et al. 2007).Additionally, high soil phosphorus concentrations have
been reported to impact the diversity of soil bacteria, and saprophytic
and arbuscular mycorrhizal (AM) fungi. Soil fertility has also been
shown to affect microbial activities, (Wei et al. 2008).
3. Tillage
Tillage is a mechanical stirring of soil surface to provide a

suitable environment for seed germination and root growth (Sylvia
et al. 2005).Tillage overturns the soil and affect soil microbial
communities in several aspects, including N transformation rates and
the build-up of soil organic matter (SOM), (Muruganandam et al.
2010).
Microorganisms for Agricultural use:
I. Bacteria
A. Non symbiotic nitrogen fixating bacteria:

Azotobacter chroocochum: Azotobacter species are free-living, nitrogen-
fixing bacteria; in contrast to Rhizobium species, they normally fix
molecular nitrogen from the atmosphere without symbiotic relations
with plants, although some Azotobacter species are associated with
plants, (Kasset al. 1971). Nitrogen fixation is inhibited in the presence
of available nitrogen sources, such as ammonium ions and nitrates,
(Burgmann et al. 2003).
Azotobacter vinelandii: Azotobacter vinelandii is Gram-
negative diazotroph that can fix nitrogen while grown aerobically. It
is a genetically tractable system that is used to study nitrogen fixation.
These bacteria are easily cultured and grown .A. vinelandii is a free-living
N2 fixer known to produce many phytohormones and vitamins in
soils. It produces fluorescent pyoverdine pigments, (Menhart et al.
1991).
Glucanobacter diazotrophicus: Glucanobacter is nitrogen fixing
bio inoculants exclusively meant for sugarcane. G. diazotrophicus
was described as a species associated with sugar rich plants, it has
been found naturally associated with other types of plants, and can
be recovered from inoculated, non-sugar rich plants (Sevilla and
Kennedy, 2000).
Acetobacter xylinum: Acetobacter is a genus of acetic acid
bacteria. Acetic acid bacteria are characterized by the ability
to convert ethanol to acetic acid in the presence of oxygen.
Of these, the genus Acetobacter is distinguished by the ability
to oxidize lactate and acetate into carbon dioxide and water,
(Cleenwerck et al. 2002). Bacteria of the genus Acetobacter have
been isolated from industrial vinegar fermentation processes and are
frequently used as fermentation starter cultures, (Sokollek et al. 1998).
Azospirillum lipoferum: Azospirillum lipoferum, is a free living,
gram positive, plant-growth-promoting a-proteobacteria,
capable of affecting the growth and yield of numerous plant
species, many of agronomic and ecological significance.

The leading theory concerning its growth promotion capacity lies
in its ability to produce various phyto-hormones that improve root
growth, adsorption of water and minerals that eventually yield larger,
and in many cases more productive plants (Dobbelaere et al. 2001)
B. Symbiotic nitrogen fixating bacteria:
a. Rhizobium leguminosarum: Rhizobium leguminosarum is a

bacterium which lives in a mutualistic symbiotic relationship
with legumes, and has the ability to fix free nitrogen from the air,
(Young et al. 2006). This is used in Peas, Lathyrus, Vicia, Lentil.
b. Rhizobium Tripoli: Used in berseem.
c. Rhizobium phaseoli: Used in kidney beans.
d. Rhizobium lupine: Used in lupinus, ornithopus.
e. Rhizobium japonicum: Used in soybean.
f. Rhizobium meliloti: Used in melilotus, lucerne, fenugreek.
C. Phosphorus solubilising bacteria:
a. Bacillus megaterium: Bacillus megaterium is a cytokinin

promoting bacterium used to promote plant root overgrowth. The
possible applications of Bacillus megaterium is being examined in
the deserts of Egypt for the promotion of desert agriculture by
(Koberl et al. 2011). It is a gram-positive, rod shaped, spore
forming bacteria. It is used in the biocontrol of plant diseases and
nitrogen fixation has been demonstrated in some strains.
b. Pseudomonas putida: Pseudomonas putida is also important in

maintaining plant health. It lives in most soils and associated
with plant roots, where it frequently improves plant health. The
organism also produces molecules that sequester iron from the
area around the plant. This deprives fungi and other bacteria of a
necessary nutrient, limiting their growth. By doing so, it can affect

the biological control of some plant pathogens.
D. Potash mobilize bacteria:

Frateuria aurentia: Frateuria aurantia is a species of Proteobacteria,
(Johansen et al. 2005). The microbe, Frateuria aurentia is a
beneficial bacterium capable of mobilizing available Potash
into near the roots of the plants. It works well in all types of soil
especially, low K content soil. Use of such bacteria in powder
form can increase the availability of more potash in usable form
to the plants.
E. Plant growth promoting rhizobacteria (PGPR):-
a. Bacillus subtilis: Bacillus subtilis is spore forming bacteria which,

when applied to the seeds or plants, it colonize the developing
root system of the plants. The bacteria compete with and thereby
suppress plant disease fungal organisms such as Rhizoctonia,
Fusarium, Aspergillus, and others. Bacillus subtilis continue to live
on the root system and provide protection throughout the growing
season. Therefore, even if treated seeds are stored for prolonged
periods, the bacteria stay alive, and then grow and multiply after
the seeds are planted.
Bacillus polymyxa: Bacillus polymyxa is used as inoculants in
agriculture and horticulture.Biofilms of B. polymyxa growing on plant
roots have been shown to produce exopolysaccharides which protect
the plants from pathogens. The interactions between this bacterial
species and plant roots also cause the root hairs to undergo physical
changes, (Yegorenkova 2013).
Pseudomonas fluorescens: This is non-pathogenic saprophytes that
colonize soil, water and plant surface environments. Pseudomonas
fluorescens suppress plant diseases by production of number of
secondary metabolites including antibiotics, siderophores and
hydrogen cyanide. This microbe has the unique ability to enter the
plant vascular system, reach the various parts of the plant system and
act as a systemic bio-control agent against various fungal and bacterial
diseases. Competitive exclusion of pathogens as the result of rapid

colonization of the rhizosphere by Pseudomonas fluorescens may also
be an important factor in disease control.
Pseudomonas putida: Pseudomonas putida also interacts with other
organisms in the soil. One such interaction with Saccharomyces
cerevisiae in the rhizosphere led to beneficial effects on the state of
the Pseudomonas putida. Fungi Saccharomyces cerevisiae produced
the necessary glucose and also maintained the pH which was
both favourable to the bacteria Pseudomonas putida, (Romano
and Kolter 2005). The complex interaction of Pseudomonas
putida and Saccaromyces cerevisiae together regulate plant health.
Moreover, the bacteria itself is a great maintainer of abundant plant
life. The production of the siderophores, such as pyoverdine and
pyochelin, protect the plants from fungal pathogens. The mutual
relationship benefits both partners. While Pseudomonas putida is
able to reside in the plant seed and rhizosphere, the plant is, in turn,
protected from plant pathogens and able to obtain vital nutrients from
the bacteria, (Espinosa et al. 2000).
II. Fungus
A. Insecticide fungus
a. Metarhizium anisopliae: Metarhizium anisopliae is being

used as a biological insecticideto control a number of pests
such as Grasshoppers, Termites, Thrips, Catterpillers,
Aphids etc.and its use in the control of malaria-transmitting
mosquitos is under investigation. Metarhizium anisopliae is
an entomopathogenic fungus that infects insects that come in
contact with it. Once the fungus spores attach to the surface of
the insect, germinate and begin to grow, they then penetrate
the exoskeleton of the insect and grow very rapidly inside the
insect causing the insect to die. Other insects that come in
contact with infected insects also become infected with the
fungus.
Beauveria bassiana: Beauveria bassiana can be used as a
biological insecticide to control a number of pests such

as termites, whiteflies, and many other insects. Its use in the control
of malaria-transmitting mosquitos is under investigation, (Donald
and McNeil 2005). As an insecticide, the spores are sprayed on
affected crops as an emulsified suspension or wettable powder or
applied to mosquito nets as a mosquito control agent.
Beauveria bassiana is a naturally occurring entomopathogenic

fungus in most part of the world. The spore of this fungus when
comes in contact with the cuticle (skin) of the target insect
pest they germinate and grow directly through the cuticle to the inner
body of the host. The fungus proliferates throughout the insect’s
body, draining the insect of nutrients, eventually killing it in about
48-72 hours after spray.
Verticillium lecanii: Verticillium lecanii is an entomopathogenic

fungus. The mycelium of this fungus produces a cyclodepsipeptide
toxin called bassianolide and other insecticidal toxins such as
dipicolinic acid, which infect aphids, whiteflies, rust fungi, scale
insects and lead to death the host. This fungus was first described in
1861 and has a worldwide distribution. Insects are infected when they
come into contact with the sticky fungal spores which then grow and
invade the body, thus the internal organs are consumed, leading to
their death. In horticulture and agriculture L. lecanii is sometimes
used as a biological pesticide for controlling insect pests such as
whitefly, thrips and aphids.
B. Nematicide fungus
Paecilomyces lilacinus: Plant-parasitic nematodes cause significant
economic losses to a wide variety of crops. Chemical control is
a widely used option for plant-parasitic nematode management.
However, chemical nematicides are now being reappraised in respect
of environmental hazard, high costs, limited availability in many
developing countries or their diminished effectiveness following
repeated applications. Paecilomyces lilacinus is a naturally occurring
fungus found in many kinds of soils throughout the world. As a
pesticide active ingredient, Paecilomyces lilacinus is applied to soil

to control nematodes that attack plant roots. It acts against plant root
nematodes by infecting eggs, juveniles, and adult females.
Arthrobotrys spp.: The fungus is a biological indicator of nematodes,
(Niu and Zhang, 2011). The annual global cost of plant-parasitic
nematodes is approximately 100 billion USD, (Degenkolb and
Vilcinskas 2016). Nematode capturing fungi such as the A.
oligospora can be used to control growth of nematodes, (Zhang et al.
2014, Domsch et al. 1980). This means that they can be potentially used
as a bio-control agent to protect crops against nematode infestations,
(Niu and Zhang, 2011). This may not be feasible since the nematodes
occasionally eat the fungi, (Domsch et al. 1980).
C. Fungicide fungus
a. Trichoderma viride: Trichoderma viride is the potential

antagonistic fungus which prevents the crops from diseases
viz. Root rots, wilts, brown rot, damping off, charcoal
rot and other soil borne diseases in c r o p s .
Trichoderma is able to suppress more than 60 species of
pathogens (Pythium, Botritis, Phoma, Sclerotinia, Fusarium,
Ascochyta, Alternaria and others) on different plants (cucumbers,
tomatoes, cabbages, peppers, various ornamentals, cereals and
grain legume crops).
How to apply microorganisms
A) Seed inoculation: On the basis ofefficiency Azotobacter,

other micro-organisms present in the soil benefits obtained from
microorganisms and expenditure it has been fixed to use Azotobacter
microorganism at the rate of 250 g microorganism for 10-15 kg seed.
If one knows this proportion then take a definite quantity of seed to be
inoculated. The required quantity of fresh microorganism is secured
and slurry is made by adding adequate, quantity of water. This slurry
is uniformly applied to seed; seed is then dried in shed and sown.
Some stickers are used in order to adher microorganism to seed, viz.
Jaggery or gum arebia.
B) Seedling inoculation: This method of inoculation is used where

seedlings are used to grow the crop. In this method, seedlings required
for one acre are inoculated using 4-5 packets (2-2.5 kg). For this in a
bucket adequate quantity of water is taken and microorganisms from
these packets is added to bucket and mixed properly. Roots seedlings
are then dipped in this mixture so as to enable roots to get inoculums.
These seedlings are then transplanted e.g. Tomato, Rice, Onion, Cole
crops, flowers.
C) Self inoculation or tuber inoculation: in this method50 litres of

water is taken in a drum and 4-5 kg of microorganism is added and
mixed properly. Sets are required for one acre of land is dipped in this
mixture. Potato tubers are dipped in the mixture of microorganism
and planting is done.
D) Soil application: This method is mostly used for fruit crops,

sugarcane and trees. At the time of planting fruit trees 20 g of
microorganism mixed with compost is to be added per sapling, when
trees becomes matured the same quantity of microorganism is applied.
Current Research
Soil microbial communities are important and are directly

involved in the functions of soil. Before high throughput DNA
fingerprinting identification, it was very difficult to identify the soil
microbial diversity. In a previous study, Dr. Bornman and Dr. Triplett
investigated soil microbial community in the Amazonia forest and
pasture soil, (Borneman & Triplett 1997). The results indicated that
microbial communities are significantly different in these two soils,
and this might be related to the pH and other factors such as high soil
nutrients due to deforestation, (Piccolo et al. 1994).In a recent study,
pyrosequencing, a high throughput DNA sequencing technology,
was used to identify soil microbial diversity in forest and agricultural
soils, (Roesch et al. 2007). The results demonstrated that the richness
of soil microbes is immense and the most abundant bacterial groups
in three agricultural soils were Bacteroidetes, Betaproteobacteria and
Alphaproteobacteria. Some bacteria in these three classes are linked
with Nitrogen cycle.
Current research is not only focused on the soil microbial

diversity. Soil organic matter (SOM) is also an important factor for crop
yield and soil structure in agricultural fields. The Ultuna Long-Term
Soil Organic Matter Experiment is located at Ultuna, Uppsala and was
established in 1956 to study the effects of fertilizing and other factors
in the agricultural systems. In 2005, Dr. Enwall’s group published a
paper report about relationship between soil nutrient content and
different kinds of organic and inorganic fertilizers. The report showed
that the addition of fertilizers can affect the microbial activity and the
composition of the denitrifying communities. Different molecular
fingerprinting technologies such as ribosomal intergenic spacer
analysis (RISA), denaturing gradient gel electrophoresis (DGGE)
and restriction fragment length polymorphism (RFLP) were used
in this article for identifying the denitrifying bacterial communities.
The results showed that it is not only the well-known bacterial class
Alphaproteobacteria that is involved in the denitrifying process, but
some actinomycetes belonging to Actinobacteria also take part in this
process in agricultural fields, (Enwall et al. 2010). Land usage is
another disturbance that can influence soil microbial community and
functions. In 2009, Dr. Jesus’s group reported the relationship between
land usage use systems and bacterial community composition,(Jesus
et al. 2009). The results showed that the bacterial community structure
is correlated with the soil attributes, and the bacterial communities
are very different between crops and the forest soil.
Future prospects of microorganisms in agriculture:
Agronomic practices have a profound effect on soil organisms.

Intervention with essential microorganism inoculants should not be
regarded as a single solution to the problems caused by damaging
agricultural operations. Firstly, agricultural management practices
should at least be designed to minimize undesirable impacts on the
soil environment. At least they should be designed to work in harmony
with biological process in order to support sustainable agricultural
system.
Different terms related to microorganisms
Psychrophiles:- microorganism which requirements of temperature

< 10˚C is known as psychrophiles.
Mesophiles:- microorganism which requirements of temperature 20

to 40˚C is known as mesophiles.
Thermophiles:- microorganism which requirements of temperature

> 40˚C is known as thermophiles.
Saprophytes:- microorganisms that are capable of decomposing

organic matter at a faster rate can be used as a fertilizer for quick
release of nutrients. Aspergillus, Penicillium, Trichoderma are
celluloytic fungi which break down cellulose of plant material. The
composting time is reduced by 4 to 6 weeks by the use of inoculants
of these organisms.
Symbiotic bacteria: Bacteria belong to the genus Rizobium are

capable of fixing atmospheric nitrogen in associated with leguminous
crops.
Free living organisms: The importantfree living organisms that

can fix atmospheric nitrogen are blue green algae (BGA), Azolla,
Azotobacter and Rhizospirillum. Among them BGA and Azolla can
survive only lowland conditions.
Blue green algae:- The most importantspecies of BGA are Anabaena

and Nostoc. The amount of nitrogen fixed by BGA ranges from 15 to
45 kg ha-1. Standing water of 2 to 10 cm in the field is a prerequisite
for the growth of BGA. It can grow at a temperature range 25 to
45˚C and pH range of 7.0 to 8.0 and in soil with higher organic matter.
Azolla:- Azolla is a free floating fresh water fern. Azolla pinnata is

the most common species occurring in India. A thick mate of Azolla
supplies 30 to 40 kg N ha-1. Normal growth of Azolla occurs in

temperature range of 20 to 30˚C and pH range of 5.5 to 7.0.
Azotobacter and Azospirillum:- Azotobacter chroccum is capable of

fixing 20 to 30 kg ha-1 N. It can be applied by seed inoculation,
seedling dip or by soil application. Azotobacter can be used for rice,
cotton and sugarcane. Azospirillum inoculum is used for sorghum.
Mycorrhiza and phospho-microorganisms:- Phosphorus availability

and phosphorus use efficiency can be increased with mycorrhiza,
phosphate solubilising bacteria and fungi. Micorrhiza inhabits
roots of several crops and solubilises soil phosphates. Inoculation
of mycorrhiza increases the pod yield of groungnut. Some
microorganisms like Psuedomonasstriate, Aspergillus awaneorii and
Bacillus polymyxa are capable of solubilising phosphates.
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IMPORTANCE OF MICRO ORGANISMS IN AGRICULTURE

Chapter · February 2017

Satybhan Singh Virendra Singh

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IMPORTANCE OF MICRO ORGANISMS IN

Satybhan Singh, Virendra Singh and Krishan Pal

Modern agricultural practices largely rely on high inputs of

is widely recognized that applications of mineral fertilizers (especially

Concerns about the possible health and environmental

In this article, use of microbial inoculants in agriculture

Global agriculture has to double food production by 2050 in

Rhizobia, Mycorrhizae, Azospirillum, Bacillus, Pseudomonas,

The rhizosphere: a site of intense interactions between plant root

The roots of plants are involved in the uptake of mineral

The rhizosphere is a key soil habitat, where the numerous

Application of microorganisms in soil stability and bioremediation:

The most fundamental and essential component of farming

Soils consist of particles of sand, silt and clay in varying

proportions, held together into aggregates of various sizes by organic

The activities of soil organisms, in turn, depend much on

Further evidence that VAM fungi contribute to the formation

Applications of Bacteria in Agriculture:

There are certain bacteria which contain special properties

Benefits of Mycorrhizal fungi in Agriculture:

Mycorrhizal plants show increased growth (Bloss &

Improved plant growth and increased tolerance to adverse

growth of young transplant in horticulture and forestry e.g.Eucalyptus

Interestingly, many of these beneficial effects are associated

Mycorrhizal fungi and phosphorus nutrition:

A primary effect of mycorrhizal symbiosis is improved P

In examining this hypothesis, the soil bacteria Alcaligenes

sustainable agro ecosystems involving intentional manipulation of the

Effect of microorganisms on soil properties

Soil pH is an important chemical property that affects the

and plants prefer a neutral pH of 6 to 7 because most soil nutrient

The low pH condition will suppress the availability of

“Soil structure is defined as the arrangement of particles

In agricultural fields, soil structure is disturbed by tillage,

the deeper soil layers.

Factors Affecting Microbial Communities in Agriculture:

Crop rotation is a method that utilizes different type of crops

Nitrogen (N) and Phosphorus (P) are the essential elements

Tillage is a mechanical stirring of soil surface to provide a

Microorganisms for Agricultural use:

A. Non symbiotic nitrogen fixating bacteria:

species, many of agronomic and ecological significance.

B. Symbiotic nitrogen fixating bacteria:

a. Rhizobium leguminosarum: Rhizobium leguminosarum is a

b. Rhizobium Tripoli: Used in berseem.

c. Rhizobium phaseoli: Used in kidney beans.

d. Rhizobium lupine: Used in lupinus, ornithopus.

e. Rhizobium japonicum: Used in soybean.

f. Rhizobium meliloti: Used in melilotus, lucerne, fenugreek.

C. Phosphorus solubilising bacteria:

a. Bacillus megaterium: Bacillus megaterium is a cytokinin

b. Pseudomonas putida: Pseudomonas putida is also important in

necessary nutrient, limiting their growth. By doing so, it can affect

D. Potash mobilize bacteria:

E. Plant growth promoting rhizobacteria (PGPR):-