Plant Growth-Promoting Microorganisms:

Interaction with Plants and Soil

Vankayalapati Vijaya Kumar

Contents
1 Introduction 2
2 Plant Growth-Promoting Microorganisms (PGPM) 3
2.1 Plant Growth-Promoting Rhizobacteria (PGPR) 3
2.1.1 Nitrogen Fixation 4
2.1.2 Phytohormones Production 5
2.1.3 Siderophore Production 6
2.1.4 Phosphate Solubilization 7
2.2 Plant Growth-Promoting Fungi (PGPF) 8
2.2.1 Arbuscular Mycorrhizal Fungi (AMF) 8
2.2.2 Trichoderma 10
3 Bioremediation 11
4 Interaction of PGPM with Plants and Soil 12
5 Conclusions and Future Prospects 13
References 13

Abstract Soil acts as a medium for a wide variety of microorganisms such as

bacteria, fungi, actinomycetes, algae, and protozoa. Soil also gives the necessary
support for anchorage to plant roots. The complex interactions between soil, plants,
and microorganisms lead to different associations in the rhizosphere. These interac-
tions are useful in (a) more nutrient recycling by nitrogen fixation, phosphate and
potash solubilization; (b) disease suppression in crop plants; and (c) bioremediation
in contaminated soils. Plant roots secrete different inorganic and organic compounds
which encourage the growth of microorganisms; in turn the chemicals secreted by

V.V. Kumar (*)

Core Green Sugar and Fuels Private Limited,
Tumkur Village, Shahapur Taluk, Yadgir District 585355, Karnataka, India
e-mail: vijayakumarv@coregreen.in; vankayalapati99@hotmail.com

© Springer International Publishing Switzerland 2016 1

K.R. Hakeem et al. (eds.), Plant, Soil and Microbes,
DOI 10.1007/978-3-319-27455-3_1
2 V.V. Kumar

microorganisms release the bound minerals from the organic materials in the soil,
which are absorbed by plant roots. This chapter reviews bacteria, fungi and their
associations and interactions with plants and soil for beneficial effects on crop
plants such as mineral nutrition, disease suppression, bioremediation, etc.

Keywords Bacteria • Bioremediation • Fungi • Nutrient recycling • Disease

suppression

1 Introduction

Microorganisms in the rhizosphere soil play a key role in maintaining the soil
fertility (Yadav et al. 2015), which is key for successful crop production to meet
the increasing global food demand. Soil is a mixture of minerals, organic matter,
gases, liquids, and many other organisms that are supporting the plant life. Soil
acts as a reservoir of air, water, and nutrients that is essential for plant growth.
Only a few grams of soil contain hundred millions to billion microorganisms.
Bacteria are the most abundant microbes in soil followed by fungi; however, the
actinomycetes are ranges in between bacteria and fungi. The fungi and actinomy-
cetes degrade various plants and animal residues that reach soil, such as complex
carbohydrates, simple sugars, starch, cellulose, hemicelluloses, pectins, lignins,
proteins, fats, oils, waxes, resins, and other products. Bacteria finish the degrada-
tion by eating the digestible materials. Other microbes that are found in smaller
numbers are algae, cyanobacteria, protozoa, and nematodes. Soil gives the neces-
sary support for anchorage to plant roots (Yadav et al. 2012; Bhaduri et al. 2015).
The metabolism of microorganisms and root growth in the soil add to texture and
fertility. The association of microorganisms with plants leads to different associa-
tions such as mutualism (both plants and microorganisms are benefited), com-
mensalism (one partner is benefited and others remain unaffected), and parasitism
(one partner benefited and the other harmed).
The microorganisms present in the rhizosphere that colonize plant roots are
termed as plant growth-promoting microorganisms. The roots provide anchorage
to plant, increase the uptake of water and mineral nutrients, and secrete a variety
of compounds as root exudates. The secretion of the chemical compounds alters
the physical and chemical properties of soil, and also regulates the microbial com-
munity in the vicinity of the rhizosphere (Yadav et al. 2012). This may help in
attracting active microorganisms to metabolize the secreted compounds in the
rhizosphere. Some of the root exudates attract microorganisms, while others act
as repellents against a wide range of microorganisms. This chapter highlights the
plant growth-promoting microorganism types, their associations and interactions
with plants and soil.
Plant Growth-Promoting Microorganisms: Interaction with Plants and Soil 3

2 Plant Growth-Promoting Microorganisms (PGPM)

Plant growth-promoting microorganisms are defined by three intrinsic characteristics:

(1) they must be able to colonize the root/rhizosphere, (2) they must survive and
multiply in micro-habitats associated with the root surface, in competition with
other microbiota, at least for the time needed to express their plant promotion/pro-
tection activities, and (3) they must promote plant growth. The PGPM are either
bacteria or fungi that are living in the soil. The bacteria are either free living or pos-
sess a symbiotic association with plant roots. Plant growth-promoting bacteria
enhance the growth of plants by their microbial processes such as nitrogen fixation,
phosphate solubilization, potash mobilization, zinc solubilization, micronutrient
mobilization, and also phytohormone secretion (auxin, cytokinin, gibberellins like
substances), desirable for the growth and development of crop plants (Akhtar and
Siddiqui 2010; Akhtar et al. 2010). Similarly, arbuscular mycorrhizal fungi (AMF)
increase P nutrition, micronutrient mobilization (Akhtar and Siddiqui 2008; Akhtar
and Panwar 2011). The AM fungal hypae extend into the soil beyond roots and
transport nutrients to the plant and increase the surface area of roots (Akhtar et al.
2011). This may help mycorrhizal plants to withstand several abiotic and biotic
stresses. However, the secretion of glomalin by AM fungi increases soil quality and
porosity, which may assist plant roots in aeration.

2.1 Plant Growth-Promoting Rhizobacteria (PGPR)

The term PGPR was first coined by Kloepper and Schroth (1978) to describe the
beneficial rhizospheric bacterial populations that may colonize plant roots and
exhibit growth promotion attributes. In general, the PGPR are free-living bacteria,
colonize roots, and promote plant growth directly by nitrogen fixation, phosphate
solubilization, production of phytohormones and siderophores or indirectly by their
biocontrol properties such as antibiotic production, production of lytic enzymes,
competition with phytopathogens for nutrients and colonizing sites, and induced
systemic resistance (Akhtar et al. 2011).
The application of a mixture of PGPRs (Azospirillum lipoferum, Azotobacter
chroococcum, Pseudomonas fluorescens, and Bacillus megaterium) has increased
germination rate, shoot and root length and dry weight, chlorophyll and nutrient
(NPK) content compared to control or individual application in Catharanthus
roseus (Lenin and Jayanthi 2012). Similarly, improvement in growth parameters
(fresh and dry weight, stem diameter, seedling height, chlorophyll content, and leaf
area) was reported in cabbage seedlings by the application of PGPR strains (B.
megaterium, B. subtilis and Pantoea agglomerans) compared to control (Turan et al.
2014). Sen and Chandrasekhar (2014) reported the significant increase in plant
height, and dry weight by the inoculation of P. fluorescens in rice seedlings under
salt stress conditions. Furthermore, the application of different PGPR (Bacillus,
4 V.V. Kumar

Pseudomonas, and Serratia) species has improved germination percentage, seedling

height, root length, chlorophyll content, dry weight of maize seedlings (Almaghrabi
et al. 2014). Moreover, Elekhtyar (2015) reported that P. fluorescens has increased
plant growth attributes (seedling germination, seed vigor index, shoot and root ratio,
fresh and dry weight, leaf area), chlorophyll concentration in leaves, and nutrient
uptake in rice.
PGPR are also advantageous in bioremediation of contaminated sites with
pollutants like hydrocarbons, chloralkali, effluents from the distillery and textiles,
heavy metals, etc. Among the rhizosphere bacteria Azospirillum, Azotobacter, and
Rhizobium are the major N2-fixing bacteria, while the Bacillus spp. (B. megaterium
and B. subtilis) and Pseudomonas spp. are P solubilizers and are used as both bio-
fertilizers and PGPR. Moreover, some other bacteria (Burkholderia, Enterobacter,
Erwinia, and Mycobacterium) could also be recognized as PGPR. The continuous
application of NPK nutrients for crop plants leads to changes in soil pH, soil fertil-
ity, and soil microbial communities, leading to decreased yields. The PGPR
enhances the growth directly by increasing the nutrient acquisition by nitrogen fixa-
tion, phosphate solubilization, potassium mobilization, and zinc solubilization.
Bacillus isolated from different agroclimatic zones has shown good phosphate-
solubilizing ability, and are positive for gelatin liquefaction, catalase test, indole
production test (Patil et al. 2013). Akram et al. (2013) reported that B. subtilis and
B. fortis effectively controlled Fusarium wilt in a split root experiment on tomato
under greenhouse condition and increased the level of phenolics (55.45–67.15 %),
peroxidase (56.70 %), polyphenol oxidase (41.56 %), and phenyl ammonia lyase
(57.57 %). Apart form this, they also secrete vitamins, amino acids, hormones (IAA
and gibberellic acid), and are now widely used in the biocontrol of a wide range of
phytopathogenic fungi. Similarly, Pseudomonas is a good P solubilizer, and also
produced significant levels of plant IAA and showed increased HCN production,
siderophore production compared to control (Deshwal and Kumar 2013). The high
level of chitinase activity is responsible for the degradation of the fungal cell walls
of pathogenic fungi such as Colletotrichum gloeosporioides (58.3 %), Alternaria
brassicola (50 %), A. brassicae (12.5 %), A. alternata (16.66 %), Fusarium oxyspo-
rum (14.28 %), Rhizoctonia solani (50 %), and Phytophthora (15 %) (Ramyasmruthi
et al. 2012). Burkholderia sp. isolated from the rhizosphere of Rhododendron
arboreum has shown good P solubilization, and IAA and siderophore production.
Burkholderia sp. isolated from the rhizosphere of Rhododendron arboretum has
shown good P solubilization, IAA and siderophore production. The germination
percentage of treated seed was high (54.18 %) compared to control (38.12 %)
(Nailwal et al. 2014).

2.1.1 Nitrogen Fixation

Azospirillum is an associative symbiotic nitrogen-fixing bacterium found in many

grasses and cereals. It lives either on the root surface or inside roots. It fixes the
atmospheric nitrogen by the enzyme nitrogenase in nonleguminous crops. It could
Plant Growth-Promoting Microorganisms: Interaction with Plants and Soil 5

also be used as a biofertilizer because of its ability to produce plant growth-

promoting substances. Inoculation of different isolates of Azospirillum in tomato
has increased the yield from 34.9–92.4 % compared to control. Apart from yield
improvement in growth parameters such as plant height, root length, and fresh
weight, number of fruits/plant, fruit diameter, fruit weight, yield per plant were also
recorded. Tripathi et al. (2013) reported that the leaf nitrogen content was signifi-
cantly improved in Azospirillum-treated plots. The study conducted by Faruq et al.
(2015) on maize with Azospirillum in the presence and absence of nitrogen has
improved all test parameters such as shoot length, root length, root number, and
biomass compared to control. The Azospirillum-treated seedlings have shown
higher numbers of lateral and tertiary roots in the presence and absence of nitrogen
compared to control. However, inoculation of Azospirillum has increased leaf area,
shoot dry matter, and yield compared to control plots in maize (Marini et al. 2015).
Similarly, Azotobacter is an aerobic, free-living, heterotrophic nitrogen fixing
soil bacterium. It fixes atmospheric nitrogen through the enzyme nitrogenase in
nonleguminous crops. It secretes hormones such as IAA, gibberellins and vitamins,
and also produces antifungal metabolites. Azotobacter evolved a special defensive
mechanism for nitrogen fixation, which may reduce the concentration of oxygen in
cells. It is found beneficial in a wide range of crops covering cereals, millets, vege-
tables, cotton, and sugarcane (Tabar 2013). Inoculation of Azotobacter in Ocimum
increased plant growth, number of leaves (Shanmugapriya et al. 2013) in the potted
plant in pot experiment, and grain yield of wheat (Soleimanzadeh and Gooshchi
2013) compared control treatments. Rhizobium is a symbiotic bacterium associated
with leguminous crops and fixes atmospheric nitrogen. Trabelsi et al. (2011)
reported that inoculation of R. gallicum and Ensifer meliloti increased nodule num-
ber, shoot dry weight, and grain yield in Phaseolus vulgaris compared to the unin-
oculated controls. The inoculation of Rhizobia in Vigna radiata has increased plant
length and dry weight compared to control plants under pot experiments and an
increase in IAA, HCN, ammonia, siderophore, and phosphate solubilization activity
has also been observed (Rajpoot and Panwar 2013). In another study, Patra et al.
(2012) concluded that inoculation of different strains of Rhizobia increased the
growth and yield of soybean under field condition.

2.1.2 Phytohormones Production

Indole acetic acid (IAA) is the most common natural auxin having a positive effect
on root growth. Most of the rhizobacteria colonizing the seed coat or root surface is
proposed to act in conjunction with endogenous IAA in stimulating cell prolifera-
tion and uptake of minerals and nutrients from the soil (Akhtar and Siddiqui 2009).
IAA affects plant cell division, extension, and differentiation; stimulates seed and
tuber germination; increases the rate of xylem and root development; controls
processes of vegetative growth; initiates lateral and adventitious root formation;
mediates responses to light, gravity, and florescence; affects photosynthesis, pigment
formation, biosynthesis of various metabolites, and resistance to stressful
6 V.V. Kumar

conditions. Tryptophan commonly found in root exudates is identified as the precur-

sor for the production of IAA by the rhizobacteria.
Several PGPR (Azotobacter sp., B. subtilis, Pantoea agglomerans, Paenibacillus
polymyxa, P. fluorescens, Rhizobium sp., and Rhodospirillum rubrum) have the abil-
ity to produce cytokinins or gibberellins during growth and development events.
Similarly, ethylene can also affect plant growth and development in a number of
ways, including root initiation, inhibiting root elongation, fruit ripening, lowering
wilt, stimulating seed germination, promoting leaf abscission, and activating the
synthesis of other plant hormones.
Due to the secretion of auxins under the root exudate deficit conditions, plant
roots sense the auxin molecules and lateral roots, root hairs are emitted which are
the sources of root exudates to maintain the bacterial population in the root zone.
Most of the P. fluorescens species isolated from paddy soils produced IAA (Noori
and Saud 2012). However, IAA production was also reported by Azotobacter sp., in
wheat. The IAA-producing PGPR strains lead to vigorous root growth resulting in
more surface area and thus enabling access to more nutrients in the soil (Singh et al.
2013). Moreover, the production of IAA by bacteria and fungi on Pikovskaya broth
under in vitro condition was reported by Priya et al. (2013). They reported that out
of 28 isolates, only 18 produced IAA by using tryptophan in the growth medium.
However, the IAA production was achieved in JNFb liquid medium at 100 μg/ml
tryptophan concentration (Srivatsava 2013).

2.1.3 Siderophore Production

Iron is one of the most important essential nutrients for growth of microorganisms
in diverse environments. It is required for various cellular, metabolic, and biosyn-
thetic processes, including DNA synthesis, electron transport system, formation of
heme, cofactor for enzymes, oxygen transport, synthesis of ATP, and nitrite reduc-
tion in the nitrogen cycle. Although it is abundant in nature, it is not easily available
in the preferred state. In the presence of oxygen and neutral pH it undergoes rapid
oxidation from Fe2+ to Fe3+ and finally forms insoluble ferric-oxyhydroxide, which
is almost unavailable for acquisition by microbes. The siderophores are relatively
low molecular weight (400–1500 Da) iron-chelating compounds produced by many
bacteria and fungi under iron-starved conditions. Generally, siderophores can be
classified into three categories depending upon the moiety that donates oxygen
ligands for Fe3+ coordination: (a) catecholates (or phenolates) (b) hydroxymates (or
carboxylate), and (c) mixed types. Siderophores mainly scavenge iron and also form
complexes with other elements (i.e., Mo, Mn, Co, and Ni) from the surrounding
environment and make them available to host microbial cells. They promote plant
growth by creating an antagonistic impact on phytopathogens. In soya bean, seed
germination, shoot and root length were increased by the application of siderophore-
producing Bacillus spp. GN-01 isolated from groundnut soil (Afreen and Chavan
2014). Siderophore production was observed in iron-limited King’s B medium by P.
fluorescens isolated from the rhizosphere soil of faba bean (Alemu 2013).
Plant Growth-Promoting Microorganisms: Interaction with Plants and Soil 7

Siderophore-producing Bacillus spp., isolated from rice, chili, ragi, and beans con-
trolled Fusarium oxysporum. Maximum siderophore secretion was recorded on sec-
ond and third day, and thereafter a decline was observed.
Siderophores directly stimulate the synthesis of antimicrobial compounds by
increasing the availability of minerals and suppressing the growth of pathogenic
organisms (Sobha and Kumudini 2012). Siderophores produced by Arthrobacter
luteolus isolated from the rare earth environment from Kerala, India reported the
accumulation of rare earth metals Samarium and Scandium (Emmanuel et al. 2012).
The nodule-forming bacteria isolated from the root nodules of leguminous plants
such as Rhizobium spp., Bradyrhizobium spp. and Sinorhizobium spp. also produced
siderophores (Deshwal et al. 2013). Verma et al. (2012) reported that R. meliloti has
the ability to produce siderophores.

2.1.4 Phosphate Solubilization

Phosphorus (P) is the most important element in the nutrition of plants, next to nitro-
gen (N). It plays a key role in all major metabolic process, including photosynthesis,
energy transfer, signal transduction, macromolecular biosynthesis, respiration, and
nitrogen fixation. Phosphorus is abundant in soils in both inorganic and organic
forms. Inorganic phosphorus occurs in soil mostly in insoluble complexes, some of
them appearing after frequent application of chemical fertilizers. Organic matter is
also an important reservoir of immobilized P in soils. It has been suggested that the
accumulated P in agricultural soils would be sufficient to sustain maximum crop
yields worldwide for more than 100 years. Several bacterial and fungal species have
been described for their phosphate-solubilizing abilities. Bacillus and Pseudomonas
are the predominant bacteria, while Aspergillus and Penicillium are the predominant
fungi. The other important P-solubilizing bacteria include Rhodococcus, Arthrobacter,
Serratia, Chryseobacterium, Gordonia, Phyllobacterium, Azotobacter, Xanthomonas,
Enterobacter, Pantoea, Klebsiella, Vibrio, and Xanthobacter. Nodule-forming
Rhizobium has also shown P-solubilizing activity. Moreover, some species of
Trichoderma and Rhizoctonia also have P-solubilizing potential. Apart from bacteria
and fungi, actinomycete genera Streptomyces and Micromonospora, algae such as
cyanobacteria, and arbuscular mycorrhizal fungi and Entrophospora colombiana
have shown P-solubilizing ability. Azotobacter spp. isolated from slightly alkaline
soils have shown a good P-solubilizing ability along with nitrogen fixation under
in vitro conditions (Nosrati et al. 2014). Garg and Sharma (2013) reported that 16
rhizobial isolates from root nodules Trigonella and Tephrosia were found positive for
P solubilization and 14 isolates were found positive for IAA production. Klebsiella
oxytoca isolated from heavy metal contaminated soil has shown P solubilizing
activity in the presence of various C & N sources. Highest P solubilization was
recorded with glucose (460 μg/ml) followed by fructose (444 μg/ml) and galactose
(435 μg/ml) in the medium. Very poor P solubilization was recorded when lactose
(141 μg/ml) was used as C source. Among different N sources (NH4)2SO4 (460 μg/
ml)was best for growth and P solubilization of K. oxytoca, where as yeast resulted in
8 V.V. Kumar

poor growth and P solubilization (215 μg/ml) (Walpola et al. 2014). Co-inoculation
of tomato plants with P. agglomerans and Burkholderia anthina has shown P solubi-
lization under lab conditions and increase in plant growth parameters under field
conditions (Walpola and Yoon 2013).

2.2 Plant Growth-Promoting Fungi (PGPF)

The arbuscular mycorrhizal fungi (AMF) and Trichoderma spp. are well recognized
as plant growth-promoting fungi. AMF promote growth of crop plants by supplying
various nutrients (mainly phosphorus). Through its hyphae nutrients are released
into plant roots through arbuscules. The vesicles formed in the cortical region store
the excess phosphorus in the form of polyphosphate, and this polyphosphate is
again converted into phosphate through enzymatic action and utilized by the plant
under phosphate-deficient condition, whereas Trichoderma promotes growth of
crop plants by controlling the disease-causing fungi and also through biofertiliza-
tion potential. Trichoderma decomposes the organic materials through the secretion
of enzymes, cellulases, hemicellulases, etc., thus releasing the nutrients that are
readily available to plants.

2.2.1 Arbuscular Mycorrhizal Fungi (AMF)

Arbuscular mycorrhizal fungi have unique characteristic structures known as

“arbuscules” formed in the cortical region. The arbuscules are dichotomously
branched structures and are the main sites for nutrient exchange between plant roots
and the fungus (Akhtar et al. 2011). The host plant absorbs nutrients through the
hyphae and in return the fungus obtains sugars and other essential nutrients from the
plant (Akhtar and Siddiqui 2008). In the intercellular spaces the hyphae forms oval
to globose structures called vesicles. These vesicles store P in the form of polyphos-
phate granules. Under phosphate-deficient conditions the polyphosphate from the
vesicles is released by enzymatic action into the roots. Some species of AM fungi
form spores within the roots known as intraradical spores (Fig. 2). The hyphae
inside and outside the roots form abundant spores. AM fungi stimulate plant growth
by nutrient acquisition and P uptake. AM fungi take up P from the same pool of
soluble ions and act as an extension of the root system. There is also evidence that
phosphatase activity is higher in mycorrhizal roots compared to non-mycorrhizal
roots. AM fungi also improves the uptake of zinc, iron, calcium, copper, magne-
sium, and manganese and the hyphae travels beyond the nutrient depletion zone and
transport nutrients to roots (Fig. 1).
AM colonization on roots increases the root surface area of the host plant.
Mycorrhizal plants will withstand biotic and abiotic stresses such as heavy metal
toxicity, salinity, alkalinity, pathogens and pests, etc. Mechanisms of heavy metal
tolerance in fungi include reduction of metal uptake and/or increased efflux, metal
Plant Growth-Promoting Microorganisms: Interaction with Plants and Soil 9

Fig. 1 Diagrammatic
representation of
mycorrhizal associations in
plants

Plant roots

Mycorrhizal Hyphae Mycorrhizal spores

immobilization (e.g., cell-wall adsorption), extracellular metal sequestration, e.g.,

exo-polysaccharides or other extracellular metabolites, intracellular chelation, e.g.,
metallothioneins or phytochelatins, and metal localization/sequestration within vacu-
oles. Accumulation of metal ions on the cell wall has been shown to be an important
mechanism leading to metal immobilization by AM fungi. AM fungi produce gloma-
lin, a strong and irreversible sequester of Cu, Cd, and Zn. When it is applied to the
plants growing in nursery in pots and polybags, the seedling survival improved on
transplantation. This is due to the faster generation of new roots in nursery plants on
transplantation. Mycorrhiza secrete a substance called glomalin, a glycoprotein which
binds the soil particles together forming aggregates, giving way for good aeration and
water-holding capacity, organic matter accumulation, and root penetration.
Significant growth enhancement was observed in bamboo seedlings inoculated
with four AM fungi strains (G. intraradices, BEG 193 and 141; G. mosseae, BEG
167; and G. etunicatum, BEG 168). The results showed that the bamboo seedlings
inoculated with all the strains of AM fungi significantly increased shoot number
and diameter, leaf number, leaf area in different growth stages compared to control
(Jiang et al. 2013). Similarly, Abohatem et al. (2011) reported that application of
AM fungal consortium (Acaulospora sp., Glomus sp., Sclerocystis sp., and
Scutellospora sp.) improved growth of seedlings in date palm and also reduced the
incidence of pathogens by the stimulation of the secretion of defense-related
enzymes. Najjar et al. (2012) found that use of Glomus sp. and P. fluorescens along
with rock phosphate increased dry matter yield and nutrient uptake (NPK and Mg)
in maize and faba bean.
10 V.V. Kumar

Fig. 2 Microscopic view of root showing intraradical mycorrhizal spores and hyphae

2.2.2 Trichoderma

Trichoderma is a filamentous fungus isolated from soil, dead wood, and organic
materials. Currently, different species of Trichoderma such as T. harzianum, T.
viride, and T. virens have proven their worth to be used as biocontrol agent against
a wide range of pathogenic fungi (Rhizoctonia spp., Pythium spp., Botrytis cinerea,
and Fusarium spp. Phytophthora palmivora). Trichoderma also has a unique ability
to produce siderophores. The production of siderophores chelate the available iron
from the environment and this iron starvation causes the death of phytopathogens.
Srivastava et al. (2013) reported that all the three tested Trichoderma strains
(MPPLUNS1, MPPLUNS2, and MPPLUNS3) had the ability to produce sidero-
phores, but MPPLUNS1 was found best among all the tested strains. Likewise,
antibiosis is another mechanism of disease protection, where the metabolites are
secreted by underground parts of plants, soil microorganisms, plant residues, etc.
Plant Growth-Promoting Microorganisms: Interaction with Plants and Soil 11

and resulted in the production of lytic enzymes, volatile and toxic compounds.
A wide range of antibiotics such as tropolone, gliotoxin, gliovirin, viridin, viridol,
trichodermin, trichozianin, pyrones, and terpenes is produced by Trichoderma sp.
These antibiotics may play a significant role in the biocontrol of plant pathogens.
Qualhato et al. (2013) concluded that the Trichoderma species grown in liquid
cultures challenged with fungal pathogens secreted various cell wall-degrading
enzymes, viz., β-1,3-glucanase, N-acetyl-b-d-glucosaminidase, chitinase, acid
phosphatase, acid proteases, and alginate lyase.
Mycoparasitism involves sequential events such as recognition of host, attack
and subsequent penetration, and subsequent killing of pathogens. The cell wall sur-
face of the host and non-hosts contains d-galactose and N-acetyl d-glucosamine
residues as lectin binding sites. With the help of lectins present on cell wall,
Trichoderma recognizes the suitable sites (residues of lectins) and binds the hyphae.
After attachment with pathogens, it makes a coil around the pathogens and secretes
the cell wall-degrading enzymes to digest the cell wall and enters into the lumen of
the host. Akrami et al. (2012) reported that use of T. harzianum and T. asperellum
alone or in combination reduced Fusarium rot on Phaseolus vulgaris by the action
of mycoparasitism. Similarly, Gajera et al. (2012) found that different species of
Trichoderma controlled the growth of Macrophomina phaseolina by the action of
cell wall-degrading enzymes (chitinase, β-1,3-glucanase, protease, and cellulase)
under in vitro conditions. Muriungi et al. (2013) reported that the inoculation of
T. viride and T. koningii effectively controlled the growth of F. oxysporum under
in vitro conditions. Leelavathi et al. (2014) concluded that the extract of T. harzia-
num at a concentration of 100–150 μl/ml controlled growth of Aspergillus,
Cladosporium, Rhizopus, and Fusarium. Moreover, root colonization of Trichoderma
sp. directly influenced plant growth and productivity, production of growth regula-
tors like zeatin and gibberellin. It may also increase the uptake of nutrients and
resistance against abiotic stresses.

3 Bioremediation

Bioremediation is a waste management technique that uses the organisms to remove

or neutralize pollutants from contaminated sites. Bioremediation is defined as the
process whereby organic wastes are biologically degraded under controlled condi-
tions to an innocuous state, or the levels below concentration limits established by
regulatory authorities. By definition, bioremediation is the use of living organisms,
primarily microorganisms, to degrade the environmental contaminants into less
toxic forms. It uses naturally occurring bacteria and fungi or plants to degrade or
detoxify substances hazardous to human health and/or the environment.
Bioremediation may occur on its own (natural attenuation or intrinsic bioremedia-
tion) or may only effectively occur through the addition of fertilizers, oxygen, etc.,
that help encourage the growth of the pollution-eating microbes within the medium
(biostimulation). Bioremediation is classified as in situ when the pollutant is treated
12 V.V. Kumar

at the site or ex situ when the pollutant is taken elsewhere and treated. Some examples
of bioremediation are bioventing, bioleaching, landfarming, bioreactor, compost-
ing, bioaugmentation, and rhizofiltration. Bioremediation is becoming a very useful
tool in many industries to prevent environmental pollution. The microorganisms
applied to the contaminated sites secrete enzymes that degrade various chemical
pollutants. Many microorganisms have been isolated from the polluted site, indicat-
ing that they have the ability to tolerate pollutants (Akhtar et al. 2013).
Bioremediation has been demonstrated and is being used as an effective means
of mitigating hydrocarbons, halogenated organic solvents and compounds, non-
chlorinated pesticides and herbicides, nitrogen compounds, metals, and radionu-
clides. P. aeruginosa, isolated from the crude oil contaminated sites in the Mangala
oil field, Barmer district, Rajasthan, could be used for the bioremediation of oil
spills because it has the potential to utilize crude oil as a sole carbon source (Prakash
and Irfan 2011).
In an interesting experiment Ajao et al. (2011) found that the inoculation of
immobilized culture of P. aeruginosa and B. subtilis into a bioreactor fitted with air
sparger containing textile effluent reduced COD from 1200 to 200 mg/l, BOD from
750 to 23 mg/l in 15 days. The other parameters in textile effluent such as total sol-
ids, suspended solids, dissolved solids, heavy metals, nitrate, sulfate, phosphate also
have been reduced significantly and copper disappeared within this period from the
textile effluent. Similarly, use of Trichoderma species culture based on diffusible
and volatile metabolites under in vitro conditions reduced the growth of Pythium in
tomato Patil et al. 2012). The volatile metabolites exhibited broad-spectrum inhibi-
tion of Pythium compared to diffusible metabolites.

4 Interaction of PGPM with Plants and Soil

Plant roots under nutrient-deficient condition releases certain nutrients like carbo-
hydrates, amino acids, and vitamins into the soil to attract microorganisms. The
microorganisms utilize the root exudates for their growth and multiplication. The
microbes produce hormones like auxins (IAA, IBA), cytokinins, GA3, abscisic acid
(ABA). The plant roots sense these auxins and start emitting lateral roots and root
hairs which absorb water, minerals from the rhizosphere. The uptake of minerals is
increased due to the increased surface area of the roots. Some microorganisms may
colonize in the rhizosphere soil (e.g., Azotobacter, and phosphate-solubilizing bac-
teria (PSB), some (e.g., Rhizobium, Azospirillum, and AM fungi) colonize either on
the surface or inside the roots.
The interaction of microorganisms with plants and soil helps in the improvement
of nutrient (NPK) uptake by various mechanisms. The combined application of
Azospirillum and Azotobacter in maize has resulted in the increase in plant growth,
yield, and hormone (IAA, GA3, cytokinin) production (Naseri et al. 2013). Mehran
et al. (2011) reported that increase in yield was not significant between treated (bac-
teria inoculated) and control plots, whereas a significant increase in yield was
Plant Growth-Promoting Microorganisms: Interaction with Plants and Soil 13

observed in manure applied treatment. Rafi et al. (2012) found that the co-inoculation
of Azospirillum and PSB together resulted in increased shoot and root dry weight,
panicle weight, and 1000 seed weight compared to control or individual inoculation
in foxtail millet. It has been also reported that inoculation of Azotobacter and
Rhizobium together resulted in increase water and nutrient uptake in faba bean
(Dashadi et al. 2011). However, inoculation of Rhizobium with PGPR alone or in
combination significantly increased the nodule number, nodule fresh and dry
weights, grain yield compared to control under salt stress conditions in mung bean
and also improved K/Na ratio in grains by decreasing the Na content compared to
control (Aamir et al. 2013). Similarly, inoculation of Azotobacter and Azospirillum
in maize significantly increased grains weight and yield when bacteria was rapped
with seeds before sowing compared to control (Amiri and Rafiee 2013).

5 Conclusions and Future Prospects

The interaction of PGPM with plants and soil is very important in improving crop
productivity. Soil is fortified with various root exudates of plants attracting microor-
ganisms, which in turn help plants through nitrogen fixation, phosphate solubiliza-
tion, and nutrient mobilization. Different bacteria and fungi are used as biofertilizers
due to their ability in producing phytohormones, siderophores, antimicrobial com-
pounds, developing induced systemic resistance and bioremediation. Microorganisms
could be applied alone or in combination in various crops, but it is advisable to
apply nitrogen-fixing bacteria along with phosphate-solubilizing bacteria because
P requirement during nitrogen fixation is met by phosphate-solubilizing bacteria.
The selection of microorganisms is crucial for a field application for maintaining the
quality of crops. By adopting the biofertilizer strategies in sustainable agriculture
practices the adverse effects of chemical fertilizers and pesticides could be easily
nullified. Moreover, the isolation of microorganisms from the contaminated sites
and their potential application in bioremediation is quite a permissible approach.
The future research will be more focussed on the revolutionization of a consortium
of microorganisms for agricultural inputs and bioremediation of contaminated sites
by the efficient application of microorganisms and their interaction with the plant
and soil in various ecological niches.

Acknowledgement The author is thankful to the Management of Core Green Sugar and Fuels for
giving an opportunity and encouragement in preparation of this chapter.

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