Original Research Article………..

International Journal of Agricultural Invention

(online available at www.agriinventionjournal.com)

International Journal of Agricultural Invention 1(2): 232-240: December, 2016 ISSN: 2456 – 1797 (P)

Plant microbiome in agro-ecosystem: A sustainable approach

Manoj Kumar, *Vivek Kumar, Narendra Tuteja, Ajit Varma
Amity Institute of Microbial Technology, Amity University, Gautam Budh Nagar, U.P., India
*Corresponding email: vivekbps@gmail.com

ARTICLE INFO ABSTRACT

Original Research Article
Received on October 20, 2016
Accepted on November 24, 2016
Article Authors
Manoj Kumar, Vivek Kumar,
Narendra Tuteja, Ajit Varma
Corresponding Author Email
vivekbps@gmail.com
PUBLICATION INFO
International Journal of Agricultural
Invention (IJAI)
RNI: UPENG/2016/70091
ISSN: 2456-1797 (P)
Vol.: 1, Issue: 2, Pages: 232-240
Journal Homepage URL
http://agriinventionjournal.com/
DOI: 10.46492/IJAI/2016.1.2.19
Kumar, M., Kumar, V., Tuteja, N., Varma, A. (2016) Plant microbiome in agro-ecosystem: A sustainable approach, International
Journal of Agricultural Invention, 1(2): 232-240. DOI: 10.46492/IJAI/2016.1.2.19
Endophytic microbiome have been found in almost every plant studied, where they
colonize the interior tissues of their host plant and may form a range of diverse associations
including interdependent, synergistic, mutualistic, commensalistic and trophobiotic. Most
endophytic microbes appear to originate from the rhizosphere or phyllosphere; however,
some may be transmitted through the seed. Potential endophytic microbiome can encourage
and stimulate plant growth and produce and can also act as biocontrol agents. On the other
hand, these endophytes can also be valuable to their host plant by producing a wide range
of natural products that could be utilized for possible use in medication, agronomy or
commerce. Furthermore, it has been revealed that they too have the potential to remove soil
contaminants by enhancing phytoremediation process and could play a significant role in
soil fertility improvement through nitrogen fixation and phosphate solubilization. There is
an increasing interest in developing the biotechnological applications of potential
endophytes for improving crop growth, phytoremediation and the sustainable production of
food crops for biomass and biofuel production, which is a viable step towards sustainable
agriculture.
KEYWORDS
Endophytes, Microbiome, Plant, Sustainable Agriculture
HOW TO CITE THIS ARTICLE

Advantageous and positive plantmicrobe
interactions that encourage plant health and
development have been the subject of substantial
study. Most of these studies have focused on
bacteria from the rhizosphere of plants (Adachi et
al. 2002; Ali and Hasnain, 2007 and Andreote et
al., 2010). Endophytic microbiome can be defined
as those microbes that colonize the internal tissue
of the plant showing no external sign of infection
or negative, bad or undesirable effect on their host
(Sturz, 1995; Holliday, 1989; Zinnielet et al.
2002), and of the nearly 300,000 plant species that
exist on the earth, each individual plant is host to
one or more endophytes (Thomas and Soly, 2009;
Lopez et al. 2011). Only a limited of these plants
have ever been wholly studied relative to their
endophytic biology. Subsequently, the prospects
to find new fangled and beneficial endophytes
colonize an ecological niche similar to that of
phytopathogens, which makes them suitable as
biocontrol agents (Sturz et al., 1997; Backman
International Journal of Agricultural Invention, 1(2): 232-240, December, 2016
andSikora, 2008 and Larrana et al. 2016).
Certainly, plentiful reports have revealed that
endophytic microorganisms can have the capacity
to control plant pathogens (Sturzand Matheson,
1996 and Duijff et al., 1997), insects (Azevedo et
al., 2000) and nematodes (Hallmann et al., 1997,
1998 and Schouten 2016). In some cases, they can
also accelerate seedling emergence, promote plant
establishment under adverse conditions (Chanway,
1997 and Ryan et al. 2008) and enhance plant
growth (Bent and Chanway, 1998). Bacterial
endophytes have been shown to prevent disease
development through endophyte-mediated de novo
synthesis of novel compounds and antifungal
metabolites. Investigation of the biodiversity of
endophytic strains for novel metabolites may
identity new drugs for effective treatment of
diseases in humans, plants and animals (Strobel
and Daisy 2003). Along with the production of
novel chemicals, many endophytes have shown a
natural capacity for xenobiotic degradation or may
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 Manoj Kumar, Vivek Kumar, Narendra Tuteja, Ajit Varma
act as vectors to introduce degradative traits (Kang
et al. 2012). The ability of some endophytes to
show resistance to heavy metals/antimicrobials
and degrade organic compounds probably stems
from their exposure to diversecompounds in the
plant/soil niche (Ruppel et al. 1992 and Varsha et
al. 2011). This intrinsic and natural ability
todegrade these xenobiotic compounds has been
investigated with regardto improving
phytoremediation (Germaine et al., 2006;
Porteous-Mooreet et al., 2006). This article intent
to providean impression about the potential use of
microbial endophytes predominantly in the area of
sustainable agriculture.
Mechanisms of Plant Growth Promotion
The mechanisms and procedures by which
endophytic microbes can influence plant growth
differ among species and strains, so typically there
is no single mechanism for promoting plant
growth. Studies have been conducted regarding
the abilities of various endophytic microbiotas to
promote plant growth, among them the endophytic
bacteria predominate (Hallmann et al. 1997,
Strobel 2003 and Hardoim et al. 2008).
Endophytes are conventionally defined as bacteria
or fungi that colonize internal plant tissues, can be
isolated from the plant after surface disinfection
and cause no negative effects on plant growth
(Fisher et al. 1992; Kuklinsky-Sobral et al. 2004
and Gaiero et al., 2013). Many endophytic
microbes promote plant growth at various stages
of the host plant life cycle by means of various
mechanisms.
Endophytes as Biocontrol Agent
Endophytic microbes are able to reduceor
prevent the deleterious effects of certain
pathogenic organisms. The beneficial effects of
bacterial endophytes on their host plant appear to
occur through similar mechanisms as described for
rhizosphere associated bacteria. These
mechanisms have been reviewed in great detail by
Larran et al. (2016) oralso by Backman and Sikora
(2008) and Compant et al. (2005). Diseases of
fungal, bacterial, viral origin and insome instances
even damage caused by insects and nematodes can
International Journal of Agricultural Invention 1(2):2016
be reduced following prior inoculation with
endophytes (Hallmann et al. 1998; Azevedo, 2000
and Schouten, 2016). It is thought that some
endophyte bacteria activate a phenomenon known
as induced systemic resistance (ISR), which is
phenotypically similar to systemic acquired
resistance (SAR). SAR develops when plants
successfully activate their defense mechanism in
response to primary infection by a pathogen,
notably when the latter induces a hypersensitive
reaction through which it becomes limited in a
local necrotic lesion of brown desiccated tissue
(Van Loon et al., 1998 and Melnick et al. 2011).
ISR is effective against different types of
pathogens but differs from SAR in that the
inducing bacterium does not cause visible
symptoms on the host plant (Yi et al. 2103).
Bacterial endophytes and their role in ISR have
been reviewed recently by Kloepperand Ryu
(2006).
Biological Nitrogen Fixation
Among the leguminous plants of the
Fabaceae family, the soil bacteria of the
Rhizobiaceae (rhizobia) family are confined to the
root nodules (Olivares et al. 1013). Within these
nodules, rhizobia effectively perform BNF
through the adequate control of the presence of
oxygen, an inhibitor of nitrogenase activity
(Galloway et al. 2004 and Bru et al. 2011). Many
species of microorganisms are used in the
cultivation of plants of economic interest,
facilitating the host plant growth without the use
of nitrogenous fertilizers. For instance, the
production of soybean (Glycine max L.) in Brazil
is an excellent example of the efficiency of BNF
through the use of different strains of Brady
rhizobium sp., such as B. japonicum and B. elkanii
(Bohrer et al. 1998 and Alves et al., 2004). The
importance of endophytic Nitrogen fixing bacteria
has also been the object of studies in non-
leguminous plants such as sugarcane (Saccharum
officinarum L. and Thaweenut et al., 2011). Other
studies have suggested that bradyrhizobia colonize
and express nifH not only in the root nodules of
leguminous plants but also in the roots of sweet
potatoes (Ipomoea batatas L.), acting as
diazotrophic endophytes (Torreset et al. 2008).
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 Plant microbiome in agro-ecosystem: A sustainable approach
Indolic Compounds Production
The influence of endophytic microbes of
host plant is largely due to the production of auxin
phytohormones (Celloto et al. 2012 and Uma
Maheswari et al., 2013). Several bacterial species
can produce indolic compounds (ICs) such as the
auxin phytohormone indole-3-acetic acid (IAA),
which present great physiological relevance for
bacteria-plant interactions, varying from
pathogenesis to phytostimulation (Jha and Kumar,
2007 and Uma Maheswari et al., 2013). The
ability to produce ICs is widely distributed among
plant-associated bacteria. Sturz et al. (2000)
demonstrated that approximately 80% of bacteria
isolated from the rhizosphere of rice produce ICs.
Other studies have shown that rhizosphere bacteria
produce more ICs than bulk soil bacteria (Thuler
et al., 2003), and in a recent study (Costa et al.
2014) showed that this effect was also observed in
endophytic bacteria, demonstrating high IC
production in the Enterobacteriaceae. The
synthesis of ICs in bacteria depends on the
presence of precursors in root exudates. Among
the various exudates, L-tryptophan has been
identified as the main precursor for the route of IC
biosynthesis in bacteria (Stijn, 2003). The
characterization of intermediate compounds has
led to the identification of different pathways that
use L-tryptophan as the main precursor. The
different pathways of IAA synthesis in bacteria
show a high degree of similarity with the IAA
biosynthesis pathways in plants (Spaepen et al.,
2007). Beneficial bacteria predominantly
synthesize IAA via the indole-3-pyruvic acid
pathway, an alternative pathway dependent on L-
tryptophan (Bianco et al. 2006 and Govindarajan
et al. 2007).
Siderophore Production
Iron (Fe) is an essential micronutrient for
plants and microorganisms, as it is involved in
numerous significant biological processes, such as
photosynthesis, respiration, chlorophyll
biosynthesis (Costa and Loper 1994 and Rout et
al. 2013), and BNF (Thaweenut et al. 2011). In
anaerobic and acidic soils, such as flooded soils,
International Journal of Agricultural Invention 1(2):2016
high concentrations of ferrous (Fe2+) ions
generated through the reduction of ferric (Fe3+)
ions might lead to iron toxicity due to excessive
Fe uptake (Bohrer et al., 1998). Under aerobic
conditions, iron solubility is low, reflecting the
predominance of Fe3+ typically observed as
oxyhydroxide polymers, thereby limiting the Fe
supply for different forms of life, particularly in
calcareous soils (Abdallah 1991 and Andrews et
al., 2003). Microorganisms have developed active
strategies for Fe uptake. Bacteria can overcome
the nutritional Fe limitation by using chelator
agents called siderophores. Siderophores are
defined as low-molecular-mass molecules (< 1000
Da) with high specificity and affinity for chelating
or binding Fe3+, followed by the transportation
and deposition of Fe within bacterial cells (Liaqat
and Eltem, 2016). The excretion of siderophores
by endophytic microbes might stimulate plant
growth, thereby improving nutrition (direct effect)
or inhibiting the establishment of phytopathogens
(indirect effect) through the sequestration of Fe
from the environment (Leong, 1986). Unlike
microbial pathogens, plants are not affected by
microbial mediated iron depletion, and some
plants can even capture and utilize
+++
Fe siderophore bacterial complexes (Dimkpa, et
al., 2009). The role of endophytic
siderophoreproducing bacteria has been rarely
studied; however, the ability to produce
siderophores confers competitive advantages to
endophytic bacteria for the colonization of plant
tissues and the exclusion of other microorganisms
from the same ecological niche (Loaces et al.,
2011). These authors observed that the community
of endophytic siderophore-producing bacteria
associated to rice roots is richer than those from
the soil at the tillering and grain-filling stages.
Endophytic bacterial strains belonging to genus
Burkholderia showed preferential localization
inside rice plants, and their role may be relevant to
prevent the infection of young plants by
Sclerotium oryzae and Rhizoctonia oryzae.
Acc Deaminase Activity
Ethylene is an endogenously produced
gaseous phytohormone that acts at low
concentrations, participating in the regulation of
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 Manoj Kumar, Vivek Kumar, Narendra Tuteja, Ajit Varma
all processes of plant growth, development and
senescence (Nonaka et al. 2008 and Sun et al.,
2009). In addition to acting as a plant growth
regulator, ethylene has also been identified as a
stress phytohormone. Under abiotic and biotic
stresses (including pathogen damage, flooding,
drought, salt, and organic and inorganic
contaminants), endogenous ethylene production is
substantially accelerated and adversely affects the
growth of the roots and thus the growth of the
plant as a whole (Grincko and Glick, 2001). A
number of mechanisms have been investigated
aiming to reduce the levels of ethylene in plants.
One of these mechanisms involves the activity of
the bacterial enzyme 1-aminocyclopropane-1-
carboxylate (ACC) deaminase (Glick et al. 2007).
ACC deaminase regulates the production of plant
ethylene by metabolizing ACC (the immediate
precursor of ethylene biosynthesis in higher
plants) into α-ketobutyric acid and ammonia
(Onofre-Lemus et al. 2009). A significant amount
of plant ACC might be excreted from the plant
roots and subsequently taken up by soil
microorganisms and hydrolyzed by the enzyme
ACC deaminase, thus decreasing the amount of
ACC in the environment. When associated with
plant roots, soil microbial communities with ACC
deaminase activity might have a better growth
than other free microorganisms, as these
organisms use ACC as a source of nitrogen (Ali et
al. 2014).
Phosphate Solubilization
Phosphorus (P) is an essential nutrient for
plants, participating as a structural component of
nucleic acids, phospholipids and adenosine
triphosphate (ATP), as a key element of metabolic
and biochemical pathways, important particularly
for BNF and photosynthesis (Goldstein, 1986).
Plants absorb P in two soluble forms: the
monobasic (H2PO4) and the dibasic (HPO 4 2−)
(Glass, 1989). However, a large proportion of P is
present in insoluble forms and is consequently not
available for plant nutrition. Low levels of P
reflect the high reactivity of phosphate with other
soluble components (Valverde, 2006), such as
aluminum in acid soils (pH < 5) and calcium in
alkaline soils (pH > 7) (Chen et al. 2006). Organic
International Journal of Agricultural Invention 1(2):2016
(incorporated into biomass or soil organic matter)
and inorganic compounds, primarily in the form of
insoluble mineral complexes, are major sources of
available P in the soil (Oteino et al. 2015).
Therefore, the availability of P depends on the
solubility of this element, which could be
influenced by the activity of plant roots and
microorganisms in the soil. Phosphatesolubilizing
bacteria and fungi constitute approximately 1-50%
and 0.1-0.5%, respectively, of the total population
of cultivable microorganisms in the soil (Illmerand
Schinner, 1992). Among the different sources of P
in the soil (as previously mentioned), the
solubilization of inorganic phosphates has been
the main focus of research studies.
Phosphatesolubilizing bacteria solubilize
inorganic soil phosphates, such as Ca3 (PO4)2,
FePO4, and AlPO4, through the production of
organic acids, siderophores, and hydroxyl ions
(Chen et al., 2006; Taurian et al. 2010). Some
bacteria only solubilize calcium phosphate, while
other microorganisms are capable of solubilizing
other forms of inorganic phosphates at different
intensities. Bacterial isolates belonging to genera
Enterobacter, Pantoea and Klebsiella solubilize
Ca3 (PO4)2 to a greater extent than FePO4 and
AlPO4 (Chen et al., 2014). The production of
organic acids, particularly gluconic and
carboxylic, is one of the well-studied mechanisms
utilized by microorganisms to solubilize inorganic
phosphates (Kim et al. 2003).
CONCLUSION AND FUTURE ASPECTS
All over the globe, effects of incessant
agricultural practices such as chemical fertilization
could lead tograve and stern damage to the
ecosystem. Inoculation of plants or seeds with
potential endophytic microbes is one of the utmost
significant to maintainable agricultural practices,
sinceendophytic microbes establish associations
with plants and encourage plant growth by ways
of numerous valuable and positive characteristics.
Endophytic microbes are appropriate for plant
inoculation, reflecting the ability of these micro-
organisms for plant colonization. Numerous
studies have established that the precise and basic
interaction among endophytic bacteria and host
plants of different species and genotypes.
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 Plant microbiome in agro-ecosystem: A sustainable approach
Combination of dissimilar techniques and
methodologies with these endophytic microbes,
such as detection of plant growthpromoting
properties, the identification of potential
endophytic strains, in addition to the seed
inoculation assays under laboratory conditions.
After selecting prospective endophytes they are
tested for cultivation experiments in the field,
which is a part of the search for novel
technologies for agricultural crop enhancement.
Therefore, after this research shows a possible
endophytic bacterial inoculant, acceptable for
reintroduction into the ecosystem, many
endophytic genera such as Pseudomonas, Bacillus,
Rhizobium, Fusarium, Alternaria could be the
crucial candidates. Lastly, the hunt for beneficial
endophytic microbiome is an important aspect for
development of innovative, competent and
effectual inoculants for agriculture. Also other
significant aspects could be investments in new
technologies that can contribute to upsurge the
inoculum efficiency and survival rate of
endophytic microbes adherent to the plants and
seeds. Consequently, introduction of beneficial
endophytes in the ecosystem tends to be less
aggressive, more beneficial and cause less impact
to the environment compared to chemical
fertilization, which makes it a popular sustainable
agriculture practice and a way of reducing the
production costs.
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