Climate Change and Indian Agriculture:

Challenges and Adaptation Strategies

Editors
Ch. Srinivasa Rao
Tavva Srinivas
R.V.S. Rao
N. Srinivasa Rao
S. Senthil Vinayagam
P. Krishnan

ICAR-National Academy of Agricultural Research Management

Hyderabad, Telangana, India
 Climate Change and Indian Agriculture:
Challenges and Adaptation Strategies

Editors
Ch. Srinivasa Rao
Tavva Srinivas
R.V.S. Rao
N. Srinivasa Rao
S. Senthil Vinayagam
P. Krishnan

ICAR-National Academy of Agricultural Research Management

Hyderabad, Telangana, India
Preferred Citation of Book
Srinivasarao, Ch., Srinivas, T., Rao, R.V.S., Srinivasarao, N., Vinayagam, S.S., Krishnan, P. (2020).
Climate Change and Indian Agriculture: Challenges and Adaptation Strategies,
ICAR-National Academy of Agricultural Research Management, Hyderabad,
Telangana, India. p-584.

Preferred Citation of Chapters

Kumar, K., Bhattacharjee, S., Vaikuntapu, PR., Sharma, CL., Jayaswal, D., Sharma, R.,
Sundaram, R.M. 2020. Climate Change Mitigation and Adaptation Through Biotechnological
Interventions. In: Ch. Srinivasarao et al., (Eds). Climate Change and Indian Agriculture:
Challenges and Adaptation Strategies, ICAR-National Academy of Agricultural Research
Management, Hyderabad, Telangana, India. pp-1-22.

ISBN No. : 978-81-943090-7-9

Published by
Director
ICAR-NAARM
Hyderabad - 500 030

July 2020

For Copies contact:

Director
ICAR-NAARM
Rajendranagar, Hyderabad-500 030
Telangana, India
Tel: 040-24581322/24581285
Fax: 040-24015912
Email: director@[Link]

Climate Change and Indian Agriculture: Challenges and Adaptation Strategies

 CONTENTS
[Link]. Title Page No
Foreword
Preface
1 Climate Change Mitigation and Adaptation through 1
Biotechnological Interventions
2 Exploration of CRISPR/Cas Toolbox for Developing 23
Climate-Smart Plants
3 Accelerated Crop Breeding towards Development of 49
Climate Resilient Varieties
4 Offsetting Climate Change Impact through Genetic Enhancement 71
5 Climate Change Adaptation and Mitigation through Soil Management 105
6 Resource Conservation Technologies for Climate Change Adaptation 131
and Mitigation
7 Climate Smart Soil and Water Management Strategies for 157
Sustainable Agriculture
8 Can Planting Trees Avert Climate Emergency? 183
9 Physiological Responses and Strategies for Temperature and Water Stress 199
Tolerance in Plants
10 Impact of Climate Change on the Production of Secondary 215
Metabolites in Plants
11 Relevance of Plant Associated Microorganisms in Climate 245
Smart Agriculture
12 Impact of Climate Change on Host-Pathogen Interactions and 271
its Implications on Crop Disease Management
13 Impact of Climate Change on Pests and Their Management Options 295
with Emphasis on Identi cation of Adaptation Strategies
14 Quality Seed and Climate Resilience: Challenges and Opportunities 311
15 Climate Smart Technology Based Farm Mechanization for 325
Enhanced Input Use Ef ciency
16 Climate Smart Post-Harvest Agriculture and Food Systems 359
17 Approaches for Managing Post-Harvest Handling in Climate 385
Disaster Prone Areas
18 Climate-Smart Livestock Farming in India: Addressing Issues and Challenges 397
19 Climate Change Versus Livestock Health: Impact, Mitigation and Adaptation 431
20 Hazards in the Wake of Climate Change Induced Extreme Weather 449
Events and Their Impact on Indian Fisheries
21 Role of Arti cial Intelligence (AI) and Internet of Things (IoT) in 465
Mitigating Climate Change
22 Recent Advancements in Arti cial Intelligence (AI) and 473
Internet of Things (IoT) for Ef cient Water Management in Agriculture
23 Climate Change and Agriculture: An Economic Perspective 485
24 Impact and Adaptation Strategies in Horticulture Sector in a Climate 501
Change Environment
25 Climate Change and Livestock Sector in India: Issues and Options 517
26 Role of Genomics in Agriculture in Age of Climate Change 539
27 Application of Bio-Informatics in Climate Smart Agriculture 561
28 Institutional Linkages and Community Partnerships for 569
Climate Resilient Agriculture
Authors Index
Climate Change and Indian Agriculture: Challenges and Adaptation Strategies
Climate Change and Indian Agriculture: Challenges and Adaptation Strategies
 1
Devendra Singh ,
1
Shobit Thapa , Relevance of Plant
Himanshu Mahawar1,
Saurabh Kumar1, Associated
M. Manjunath2 and
P.C. Latha
3 Microorganisms in
1
ICAR-National Academy of
Climate Smart
Agricultural Research
Management, Hyderabad,
Agriculture
Telangana
2
ICAR-Central Research
11
Institute for Dryland
Agriculture, Hyderabad,
Telangana

Abstract
3
ICAR- Indian Institute of
Rice Research, Hyderabad,
Telangana

The negative effects of climate change are occurring all over the world.
These include rising temperature and sea level, unseasonal rainfall, drought,
oods, etc. Agricultural production is also severely getting affected due to climate
change. Climate Smart Agriculture (CSA) is a sustainable approach to increase the
adaptability of agricultural production systems to improve crop production under
changing climatic conditions. CSA also draws attention to reduce greenhouse gas
(GHG) emissions and to improve carbon stability in soil. Agriculturally bene cial
microorganisms assume signi cant role in climate smart agriculture. They can help
to enhance adaptation, mitigation and build resilience to climate change effects.
Plant bene cial microorganisms are fundamental to different bio-geochemical
process in soil viz., organic matter decomposition, carbon cycle, nitrogen cycle,
phosphate solubilization and mobilization, nitrogen xation, and acquisition of
micronutrients. Microorganisms also facilitate the crop plants to withstand various
abiotic stresses viz., elevated temperature, elevated CO2, moisture stress, salinity
stress, and metal toxicity. Methanotrophs, methylotrophs and photosynthetic
microorganisms play the important role in mitigating the greenhouse gases. Soil
microorganisms also have crucial role in carbon sequestration in soil. Microbial-
based technology is low cost, eco-friendly and sustainable. Biofertilizers and
biopesticides being the major components of integrated nutrient and insect-pest
management, as well as one of the key elements of climate smart agriculture, the
application of bene cial microorganisms reduces the use of synthetic agro-
chemicals, sustains the soil health and soil biodiversity, and enhances the plant
growth.

Key words: Abiotic Stresses, Climate Change, Carbon Stability, Climate Smart
Agriculture (CSA), Greenhouse Gas, Nutrient Management.

Climate Change and Indian Agriculture: Challenges and Adaptation Strategies 245
Relevance of Plant Associated Microorganisms in Climate Smart Agriculture

responsible for both production and

I. Introduction consumption of greenhouse gases
Climate change refers to any such as carbon dioxide, methane and
signi cant statistical change in the nitrous oxide. The large diversity of
distribution of weather patterns over microbes provides an opportunity to
an extensive period of time which can explore and exploit untapped
range from decades to millions of microbial resources for improving the
years (Enete and Amusa, 2010). It can ef ciency of agricultural production
be due to a number of factors like systems by enhancing the adaptation
oceanic circulation, variations in solar and mitigation options to overcome
radiation, plate tectonics, volcanic the negative effects of climate
eruptions, and anthropogenic change so as to achieve the goal of
interventions. Rise in atmospheric climate-smart agriculture. A thorough
concentrations of greenhouse gases understanding of microbial ecology
(GHGs), e.g., CO2, CH4 and N2O, is the and soil-plant-microbe interaction in
principal cause of global climate a changing climate scenario is
change (IPCC, 2013). essential to make best use of
microbial technology for climate
Changes in the climatic conditions are
change adaptation and mitigation.
directly or indirectly affecting the life
on earth by signi cantly impacting
not only human or animal life but II. Role of Agriculturally
also that of plants and Important Plant
microorganisms. Extensive melting of
polar ice, accelerated rise in sea level, Associated
more intense heat waves, longer
periods of drought and increase in
Microorganisms
the number, and duration and Microbial inoculants are an
intensity of tropical storms are due to attractive eco-friendly alternative to
global climate change. These extreme chemical fertilizers and pesticides.
conditions are signi cantly affecting They exert bene cial effects on soil
plants and microorganisms. Climate and plant health by different
change affects agriculture in a mechanisms highlighted below.
number of ways which include
II.1 Nutrient Management and
changes in average temperature,
Biofertilizers
rainfall, growing season, pests and
diseases incidence, nutritional quality The ef cient crop production
of some foods, and soil erosion due to depends on the nutrient status of the
intermittent oods and drought soil that is vital for sustainable
(World Bank, 2008). agriculture. Chemical fertilizers are
primarily used to increase the crop
Microorganisms are the most
yield. However, their indiscriminate
important components of agricultural
use has led to serious environmental
ecosystem (Mohanty and Swain,
consequences. Nowadays, more
2018). They perform essential
emphasis is being given to
functions in biogeochemical cycling of
biofertilizers and other organic
nutrients such as carbon, nitrogen,
sources of nutrients. Biofertilizers are
phosphorus, and sulphur. They are

246 Climate Change and Indian Agriculture: Challenges and Adaptation Strategies
 Relevance of Plant Associated Microorganisms in Climate Smart Agriculture

the preparations consisting of Rhizobium, Azotobacter,

bene cial microorganisms, either live Azospirillum, etc. x atmospheric
or latent cells that when applied nitrogen (N2) to plant available form
improve the nutrient status of the soil through the process of nitrogen
and facilitate their accessibility to xation (Shabbir et al., 2019).
crops by various mechanisms (Fu et Symbiotic associations involving
al., 2017). The rise in the awareness of Rhizobia-legume is the most
people about the adverse effects of important N- xation system
chemical fertilizers has led to contributing up to 230 kg N/ha
increased use of microbial inoculants annually, and non-symbiotic
as biofertilizers in organic farming associations also contribute to the
and integrated farming systems. tune of 13-22 kg N/ha (Bargaz et al.,
Regular application of organic and 2018). Similarly, phosphorus is an
inorganic fertilizers in a balanced important nutrient for plant growth;
proportion would help to enhance but majority of the applied
soil organic carbon and soil microbial phosphatic fertilizers immediately
activity (Vineela et al., 2008; gets xed in the soil and becomes
Srinivasarao et al., 2018). Long-term unavailable to plants. Phosphorus
(18-21 years) studies conducted in two solubilization by synthesis of organic
cropping systems viz., upland rice- acids by the microbes is an important
lentil sequence and pearlmillet- part of nutrient management as they
clusterbean-castor rotation in improve the soluble or plant available
Inceptisols of sub-humid region of forms of phosphorus. Microorganisms
Varanasi and Entisols of the semi-arid such as Bacillus, Pseudomonas,
region of Gujarat, respectively Penicillium, Flavobacterium,
revealed that use of 50 per cent Aspergillus, and Micrococcus have
reduced dose of chemical fertilizers in been reported to carry out the
combination with FYM enhanced the process of phosphate solubilization
soil microbial activities in both that adds up to 30-35 kg P2O5/ha
Inceptisols and Entisols (Srinivasarao (Gaur et al., 2004). The process such as
et al., 2018). Combination of organic assimilation and dissimilation of
nutrients such as poultry manure @ nitrogen, phosphorus, magnesium,
2.5 t/ha + vermicompost @ 3.5 t/ha iron, etc. plays signi cant role in
stimulated the metabolically active effective management of these
soil microbial communities in nutrients and their availability to
vegetable cropping system of the plants (Lalitha, 2017). In recent
Indo-Gangetic plains (Manjunath et studies, siderophore producing
al., 2018). (Arthrobacter sulfonivorans DS-68
and Enterococcus hirae DS-163) and
Nitrogen, being the major component
Zn solubilizing (Bacillus subtilis DS-178
of chlorophyll, is vital for plant
and Arthrobacter sp. DS-179) bacteria
growth and development besides
played signi cant role in
being conspicuous in plant
micronutrients acquisition in wheat
metabolism. Therefore, nitrogen
grains besides enhancing the plant
availability and management is the
biomass and yield (Singh et al., 2017a,
key factor in governing the plant
2017c, 2018, 2020).
growth. Microorganisms like

Climate Change and Indian Agriculture: Challenges and Adaptation Strategies 247
Relevance of Plant Associated Microorganisms in Climate Smart Agriculture

a. Organic Matter Decomposition Verticillium. Lignin is degraded

primarily by white rot fungi
Soil Organic Matter (SOM)
(Phanerochaete chrysosporium,
decomposition is the biological
Coriolus versicolor and Trametes
transformation of complex organic
versicolor), brown rot fungi
matter into simple inorganic
(Fomitopsis palustris) and ascomycetes
compounds. Decomposition of SOM
(Trichoderma reesei) (Dashtban et al.,
results in stabilized organic matter
2010). The organic wastes are
which is further resistant to microbial
converted into valuable resources like
decomposition and termed as humus.
plant nutrients, thus maintaining the
This humus plays crucial role in soil
ow of nutrients from one system to
aggregates formation and improving
the other. The composting process
water and nutrient holding capacity
takes place in three phases, and uses
of soil. Soil organic matter is mainly
diverse micro- ora such as bacteria,
derived from the plant residues. The
fungi, and mesophilic (Streptomyces
SOM decomposition is carried out by
rectus) and thermophilic
heterotrophic microorganisms
actinomycetes
comprising soil bacteria, fungi,
[Actinobi dachromogena
protozoa, and actinomycetes.
(Thermomonosporafusca)
Cellulose, hemicelluloses and lignin
Microbisporabispora,
are the major components of soil
Therinomnonosporacurvata, and
organic matter which are degraded
Thermoactinomyces sp.] eventually
comparatively slower than the other
converting organic waste to humus
components like sugars, amino acids
(Pan et al., 2012). Compost prepared
and lipids (Pérez et al., 2002).
from bixa capsule shells by
Earthworms also play an important
inoculating Trichoderma +
role in the initial breakdown of
Phanerochaete and effective
organic residues.
microorganisms led to the
Cellulose degrading fungi include enhancement of nutrient content i.e.,
Trichoderma, Phanerochaete, total N (47.5% to 161%),
Penicillium, and Aspergillus. exchangeable K (25% to 88%),
Cellulomonas, Clostridium available P (36% to 150%) and
thermocellum, Streptomyces, and calcium (19.4% to 94.4%) (Pratibha et
Pseudomonas are the bacteria al., 2013). The microorganisms also
involved in cellulose degradation represent an important renewable
(Beaton et al., 2019). Hemicellulose is source of energy. They play an
degraded into monomeric sugars and important role in the conversion of
acetic acid by: fungi like Aspergillus, organic waste to humus-like
Polyporus, Trichoderma reesei, and substances which improves soil
Phanerochaete chrysosporium; and structure and health, in a process
bacteria like Thermomonospora, called composting.
Actinomadura, Thermotoga, Bacillus,
Streptomyces, and Butyrivibrio b. Nitrogen Fixation
brisolvens (López-Mondéjar et al., Biological Nitrogen Fixation (BNF)
2016). Decomposition of soil chitin is is the xation of atmospheric
carried out by Streptomyces, nitrogen into ammonia. After
Nocardia, Trichoderma, and photosynthesis, nitrogen xation is

248 Climate Change and Indian Agriculture: Challenges and Adaptation Strategies
 Relevance of Plant Associated Microorganisms in Climate Smart Agriculture

the second most crucial process Rhizobium leguminosarum biovar

in uencing plant growth and trifolii nodulating in Trifolium
development. Only some prokaryotes, (clovers); R. leguminosarum biovar
known as diazotrophs, have the leguminosarum in peas and lentils; R.
ability to x stable atmospheric leguminosarum biovar phaseoli in
nitrogen into reactive nitrogen which beans; Sinorhizobium meliloti in
can be easily taken up by plants. Medicago and Melilotus;
These diazotrhophs are distributed in Bradyrhizobium japonicum, B. elkanii,
38 genera of bacteria, 2 genera of and B. liaonginense in soybean;
archaea and 20 genera of Mesorhizobium loti in Trefoil; M.
cyanobacteria (Harwani et al., 2009). ciceri in chickpeas; and stem
Hellriegel and Wilfarth (1886) for the nodulating Azorhizobium
rst time reported biological nitrogen caulinodans in Sesbania rostrata.
xation in the year 1886 and Moreover, Parasponia is the only non-
discovered that legumes bearing root legume that can establish nitrogen-
nodules could use gaseous nitrogen. xing symbiosis with Rhizobia (Behm
The BNF contributes around 110 and et al., 2014). Actinomycete Frankia
140 Tg per year of xed nitrogen on establishes nitrogen xing symbiosis
land and ocean, respectively (Pajares with actinorhizal plants such as Alder
and Ramos, 2019). Overall estimates (Alnus spp.), Sea buckthorn
suggest that, a total of 50-70 Tg (Hippophae rhamnoides) and
nitrogen is biologically xed annually Casuarina (Benson and Silvester,
in agricultural systems (Herridge et 1993). Anabaena-Azolla symbiosis is a
al., 2008). classic example where cyanobacteria
Anabaena azollae xes atmospheric
Microorganisms can x nitrogen as
nitrogen symbiotically with Azolla
free living organism, maintaining
(aquatic fern). In an earlier study,
association with grasses or by
Azospirillum spp. a nitrogen xing
establishing symbiotic relationship
endophytic bacteria was isolated from
with legumes, actinorhizal plants and
wheat which signi cantly enhanced
termites gut. Free living diazotrophs
the plant growth and biomass (Singh
include: Azotobacter, Beijerinckia,
et al., 2017b).
Bacillus, Clostridium, and Klebsiella;
and most nitrogen xing c. Phosphorus Solubilization and
cyanobacteria like Gloeothece, Mobilization
Cyanothece, Lyngbya, Trichodesmium,
Phosphorus (P) is one of the most
Katagnymene, Nostoc, Calothrix,
essential and limiting mineral
Tolypotkrix, Hassalia, and Gloeotrichia
nutrients after nitrogen. It is a
(Issa et al., 2014). Azospirillum spp.
component of nucleic acids, enzymes,
are able to form close associations
coenzymes, nucleotides, and
with several members of the grasses,
phospholipids. It constitutes about 0.2
including agriculturally important
- 0.8 per cent of plant's dry weight
cereal crops. Root legume symbiosis is
(Sharma et al., 2013). Availability of
the most effective nitrogen xing
phosphorus for plants is limited
process wherein Rhizobia x nitrogen
mainly because of the presence of P
in symbiotic association with legumes.
in insoluble form (about 95 to 99%).
Examples of Rhizobia include:
Plant growth promoting rhizobacteria

Climate Change and Indian Agriculture: Challenges and Adaptation Strategies 249
Relevance of Plant Associated Microorganisms in Climate Smart Agriculture

(PGPR) are capable of solubilizing and solubilization (Richardson et al., 2009;

mineralizing insoluble soil Bhattacharyya and Jha, 2012; Singh et
phosphorus and thereby, enhances its al., 2018). Fungi involved in
availability for plant use (Alaylar et solubilization and mineralization of
al., 2019; Islam et al., 2019; Remy et phosphorus include strains of
al., 1994). Alternaria, Achrothcium, Aspergillus,
Phosphorus solubilization is a process Arthrobotrys, Curvularia,
wherein microorganisms convert Cephalosporium, Fusarium,
insoluble inorganic phosphorus into Chaetomium, Micromonospora,
plant available phosphorus. They Glomus, Oidiodendron, Mortierella,
solubilize P mainly by the production Phoma, Penicillium, Pichiafermentans,
of organic acids (citric acid, malic acid, Trichoderma, Rhizopus, Populospora,
oxalic acid, and gluconic acid), and Yarrowia (Alori et al., 2017).
inorganic acids and phosphatase Extensive utilization of phosphorus
enzymes (phosphor-mono-esterase, solubilizing microorganisms in
phosphor-di-esterase) (Hayat et al., agriculture is a promising strategy to
2010; Glick, 2012; Singh et al., 2018). enhance plant uptake and reduce the
On the other hand, phosphorus use of chemical fertilizers that have
mineralization refers to the negative impacts on the environment.
solubilization of organic phosphorus d. Potassium Solubilization
into plant available phosphorus
Potassium (K) is the third major
through microbial activity. Several
essential nutrient for plant growth
bacteria and fungi are reported to
after nitrogen and phosphorus. It
solubilize insoluble inorganic
plays vital role in protein synthesis,
phosphorus and mineralize insoluble
enzyme activity and photosynthesis
organic phosphorus in soil
(Hasanuzzaman et al., 2018).
ecosystems. Moreover, arbuscular
De ciency of K in soil results in
mycorrhizal symbiosis between soil
decreased crop yield and disease
fungi and approximately 80 per cent
resistance. Although the potassium
of all vascular plant species scavenge
reserves in the earth crust account for
phosphorus from soil and provide to
2.1 to 2.3 per cent, majority of it
root cortical cells while bypassing the
(about 90%) are insoluble silicate
direct uptake (Kobae, 2019).
minerals which are unavailable for
Phosphorus solubilization and plants use (Xiao et al., 2017). In soil, K
mineralization bacteria include is present as mineral K, non-
Agrobacterium spp., Azotobacter exchangeable K, exchangeable K, and
spp., Bacillus spp., Bradyrhizobium dissolved or solution K (K+ ions) forms;
spp., Pseudomonas spp., Beijerinckia, but plants have the ability to uptake
Arthrobacter spp., Burkholderia spp., only water-soluble and exchangeable
Enterobacter spp., Paenibacillus spp., forms.
Ralstonia spp., Rhizobium spp.,
Microorganisms such as bacteria,
Serratia spp., Sinomonas spp., and
fungi and actinomycetes have
Thiobacillus spp.; and Actinomycetes
remarkable ability to dissolve
mainly from the genus Actinomyces,
potassium from its mineral forms.
Micromonospora and Streptomyces
Similar to P solubilizing bacteria, K
are also involved in phosphorus

250 Climate Change and Indian Agriculture: Challenges and Adaptation Strategies
 Relevance of Plant Associated Microorganisms in Climate Smart Agriculture

solubilizing bacteria also produce various metabolically active

organic and inorganic acids which substances which regulate plant
solubilize potassium minerals either physiological and morphological
directly or indirectly by chelating properties. Auxins are produced by
mineral silicon ions to release K into Agrobacterium spp., Pseudomonas
solution. The prominent K solubilizing spp., Rhizobium spp., Bradyrhizobium
microbes include; Arthrobacter spp., spp., and Bacillus spp. GA was rst
Aminobacter spp., Acidithiobacillus reported in Rhizobium meliloti, and is
ferrooxidans, Bacillus mucilaginosus, also produced by Acetobacter
B. circulanscan, B. edaphicus, diazotrophicus, Bacillus spp., and
Enterobacter hormaechei, Pseudomonas spp. Cytokinin
Paenibacillus mucilaginosus, production is reported in
Aminobacter, Sphingomonas, Agrobacterium spp., Azotobacter
Burkholderia, Paenibacillus spp., Rhizobium spp., Pseudomonas
glucanolyticus, Aspergillus terreus, spp., Bacillus spp., Pantoea spp.,
Aspergillus niger, Cladosporium and Methylobacterium spp., and
Pencillium spp. (Shanware et al., Xanthomonas spp. ABA production is
2014). Rajawat et al. (2019a, 2019b, well documented in Bradyrhizobium
2020) also isolated K solubilizing japonicum and Azospirillum
bacteria from rhizosphere of different brasilense. Therefore, phytohormones
crops and screened for K of microbial origin provide abiotic
solubilization in different and biotic stress tolerance to plants
temperature ranges. The amount of K under changing environmental
solubilized by different isolates in conditions. The bacterial IAA plays an
liquid medium ranged from 10.6±0.92 important role in lateral roots
to 50.80±2.43 μg/mL. Use of K formation and increase in root length
solubilizing bacteria in wheat, and surface area, so that plants can
sorghum, maize, peanut, potato, pea, access more soil nutrients. Likewise,
and cotton resulted in improved plant rhizobacterial IAA relaxes plant cell
growth and yield (Meena et al., 2014). walls and therefore, stimulates root
Therefore, use of KSB as biofertilizer exudation that gives extra nutrients
in agriculture is a promising for the development of rhizospheric
alternative to synthetic K fertilizers. microbes (Glick, 2012). Inoculation of
IAA producing Providencia spp. and
e. Phytohormone Production
Alcaligenes spp. enhanced the plant
Phytohormones such as auxins, growth and yield of wheat
gibberellins (GA), cytokinins, and (Manjunath et al., 2011). Application
abscisic acid (ABA) regulate plant of Azotobacter spp., Anabaena spp. -
growth and development at various Providencia spp., and Anabaena spp. -
stages (Egamberdieva et al., 2017). Azotobacter spp. had signi cant
Microorganisms are also known to effect on root weight and yield of
produce these phytohormones to okra (Manjunath et al., 2016).
improve plant growth and enhance Gibberellins producing bacterial
tolerance to several abiotic stresses strains increase the shoot length (Jha
(Santner et al., 2009; Glick, 2014; and Saraf, 2015). Vacheron et al.
Vejan et al., 2016). Rhizobacteria (2013) found that a combination of
colonize the root surface and produce

Climate Change and Indian Agriculture: Challenges and Adaptation Strategies 251
Relevance of Plant Associated Microorganisms in Climate Smart Agriculture

auxin and gibberellins can modulate inducing resistance or priming plants

the root design. Ruzzi and Aroca against pathogen infection by
(2015) found that cytokinin producing systemic acquired resistance (SAR) and
PGPR increases the permeability of induced systemic resistance (ISR),
cell membrane and therefore, change competing for limiting nutrients and
the root exudation pattern of plant directly killing the pathogen by
species. Xie et al. (2009) reported that hyperparasitism (Kohl et al., 2019).
the soil bacterium Bacillus subtilis
Different species of bacteria, fungi,
GB03 could enhance Fe acquisition of
yeast, and viruses act as BCAs. Some
Arabidopsis plants by activating the
popular examples include
Fe-de ciency-inducible responses,
Agrobactarium radiobacter strain 84,
suggesting that soil microorganisms
Bacillus subtilis, Pseudomonas
could regulate plant Fe acquisition via
uorescens, Streptomyces griseoviridi,
signalling processes.
Gliocladium spp., Metarrhizium
II.2 Biopesticides anisopliae, Ampelomyces quisqualis,
Beauvaria bassiana, Trichoderma spp.,
Indiscriminate application of Verticillum lecanii, Verticillium
chemical pesticides to tackle plant chlamydosporium, Chaetomium
diseases has affected the soil health, globosum, Burkholderia cepacia, VAM
besides causing deleterious effect on fungi, and Nuclear Polyhedrosis
non-target organisms and the Viruses (NPV) (Singh, 2014). Fungicide
environment. Microbial pesticides are compatible biocontrol agent
promising options to avoid the Trichoderma asperellum effectively
deleterious effects of chemical inhibited the mycelia growth of
pesticides and are gaining importance Sclerotium rolfsii Sr3, Pythium
among the farmers and researchers. aphanidermatum, Sclerotium rolfsii
Biocontrol is de ned as the Sr1 and P. debaryanum by 54.87,
application of a living organism to 43.57, 42.56 and 38.16 per cent,
control other plant detrimental respectively (Manjunath et al., 2017).
organisms (Sporleder and Lacey, Biopesticides have the potential for
2013). Microorganisms having the development of integrated pest
potential for disease suppression are management strategies.
referred to as the microbial biological
control agents (BCA) which includes II.3 Bioremediation
most likely bacteria (Pseudomonas
Bioremediation is a
spp. and Bacillus spp.) and fungi
transformation or degradation of
(Trichoderma spp. and Gliocladium
contaminants into non-hazardous or
spp.). These biocontrol agents provide
less-hazardous substances by
low-cost, environmental-friendly and
microorganisms and plants. Synthetic
sustainable alternative for hazardous
chemicals like industrial solvents,
synthetic chemical pesticides used in
agricultural pesticides, poisons, and
agriculture. Microbial biological
heavy metals are recalcitrant in
control agents provide plant
nature and cause environmental
protection by producing
pollution. Microorganisms carry out
allelochemicals such as antibiotics,
bioremediation by producing various
biocidal volatiles and siderophores,
enzymes like mono-oxygenase, di-

252 Climate Change and Indian Agriculture: Challenges and Adaptation Strategies
 Relevance of Plant Associated Microorganisms in Climate Smart Agriculture

oxygenases, laccases, peroxidases, and and future generations. Microbes are

hydrolytic enzymes that attack the the major component of biological
pollutants and convert them into diversity and are crucial for sustaining
nonhazardous substances (Karigar environmental quality. They play
and Rao, 2011). main role in regulation of
biogeochemical cycles, soil formation
Acinetobacter spp., Pseudomonas
and climate regulation (Byarugaba,
spp., Ralstonia spp., Microbacterium
2004). Organic matter decomposition
spp., Alcaligenes odorans, Bacillus
and regulation of essential elements
subtilis, Corynebacterium
have been the key components that
propinquum, Aspergillus niger, A.
involve microbial activity which in
fumigatus, and Penicillium
turn, are vital for the maintenance of
chrysogenum are reported in
soil fertility and structure. Improving
bioremediation of monocyclic
the organic matter content is very
aromatic hydrocarbons, e.g. benzene
critical to sustain rainfed
and xylene (Singh and Fulekar, 2009;
agroecosystems. Incorporation of
Wolicka et al., 2009; Di Martino et al.,
fresh horse gram biomass at 3.03-4.28
2012). Bacillus cereus strain XMCr-6,
t/ha/year for 10 years signi cantly
Pseudomonas putida, Enterobacter
improved the soil fertility. It had
cloacae B2-DHA, Bacillus subtilis,
improved microbial biomass carbon
Gloeophyllum sepiarium and
and organic carbon by 28 and 24 per
Rhizopus oryzae can carry out
cent, respectively. There was also an
bioremediation of chromium, while
increase in grain yield of sun ower
Sporosarcina ginsengisoli is reported
and sorghum by 18 and 28 per cent,
for arsenic, Pseudomonas veronii and
respectively (Venkateswarlu et al.,
Saccharomyces cerevisiae for
2007). The microbial extracellular
cadmium, Aspergillus fumigates for
polysaccharide has been reported to
lead, and Aspergillus versicolor for
restore the soil structure by acting as
nickel bioremediation. In pesticides
cementing material and thus,
bioremediation, Bacillus and
reducing the soil erosion (Costa et al.,
Staphylococcus are reported for
2018). In earlier studies,
endosulfan, Enterobacter spp.,
exopolysaccharide (EPS) producing
Chlorpyrifos spp., Acenetobactor spp.,
Pseudomonas spp. and rhizobacteria viz., Bacillus cereus,
Photobacterium spp. for methyl Microbacterium resistens and
parathion, and Phanerochaete Pseudomonas sp. were isolated and
chrysosporium for biphenyl and evaluated for moisture stress
triphenyl methane bioremediation alleviation. These EPS producing
(Abatenh et al., 2017). bacteria signi cantly increased the
water stable aggregates, mean
II.4 Preservation of Natural weight diameter and root adhering
Resources and Environment soil (Singh et al., 2014, 2015a, 2015b,
2015c). The microbes also act as sink
Natural resources include land, and source of several nutrients
soil, water, plants, and animals. required for plant growth.
Preservation or management of
natural resources is important for
keeping the quality of life for current

Climate Change and Indian Agriculture: Challenges and Adaptation Strategies 253
Relevance of Plant Associated Microorganisms in Climate Smart Agriculture

belonging to the class Beta-

III. Microbial Contribution proteobacteria (Teske et al., 1994). In
to Climate Change contrast, denitri cation is a multistep
process in which each step is
Microorganisms act as both mediated by a speci c group of
source and sink of greenhouse gases microorganisms having the enzymes
(GHGs) (Kolb and Horn, 2012). They necessary to catalyze a particular step
are vital components of C-N cycle in (Arrigo and Kevin, 2005). The
soil. Through various biochemical production of N2O is typically the
processes such as decomposition and result of incomplete denitri cation
heterotrophic respiration, they (Conthe et al., 2019). Nitri cation is
release GHGs viz., carbon dioxide the main source of N2O under aerobic
(CO2), methane (CH4) and nitrous conditions, while denitri cation
oxide (N2O) into the atmosphere. dominates in anoxic environment.
Methanogens produce methane in Anaerobic ammonium oxidation
natural and arti cial anaerobic (ANAMMOX) is an alternate
environments, mainly sediments, microbial-mediated pathway
water-saturated soils such as paddy responsible for nitrogen loss in the
elds, gastrointestinal tracts of form of N2 and N2O in aquatic system
animals (particularly ruminants), (Dalsgaard et al., 2005).
wastewater facilities, and biogas
facilities. It is carried out by a group
of anaerobic archaea in wetlands,
IV. Effect of Climate
oceans, rumens and termite guts, in Change on Microbes
addition to the anthropogenic
methane production (Cappenberg, Variations in the climatic
1974; Gambrell and Patrick, 1978; conditions in uence the diversity and
Jakobsen et al.,1981; Loveley and structure of various microbial
Phillips, 1987; De Groot et al.,1994; communities (Castro et al., 2010;
Kolb and Horn, 2012). Global Brockett et al., 2012; Kembel et al.,
emissions of CH4 are possibly even 2012). Microbial community
more directly controlled by composition, abundance and function
microorganisms than emissions of CO2 are altered when microbes are
(IPCC, 2007). exposed to new extremes in
environmental condition. Moreover,
Similar to global CO2 and CH4 signi cant changes also happen over
emissions, microbial nitri cation and time in their functional genes and
denitri cation processes release N2O traits. This kind of effect happens
(IPCC, 2007). It has been reported over each biogeochemical cycle (Sayer
that, for every ton of nitrogen et al., 2017). The main direct effects
deposited on the earth's surface, of climate change on soil
either naturally or arti cially as microorganisms are likely to be
fertilizer, 10-50 kg N2O is released caused by changes in temperature
(Crutzen et al., 2016). Most of the N2O and moisture content. These factors
is produced by nitri cation as a result can affect processes such as
of the activity of autotrophic greenhouse gas ux in two ways: by
ammonia (NH3)-oxidizing bacteria modifying the physiology of existing

254 Climate Change and Indian Agriculture: Challenges and Adaptation Strategies
 Relevance of Plant Associated Microorganisms in Climate Smart Agriculture

microbial populations and/or by diminish their biomass, which will

changing the structure of the subsequently reduce primary
microbial community. For example, at production and CO2 uptake
higher temperatures, most (Behrenfeld et al., 2013). Climate
microorganisms grow and use change facilitates a shift in microbial-
substrates at faster rates, so that the community structure, the process
rate at which processes such as rates and the mechanism of control
respiration occur may change; might change, because the new
however, the control mechanism microbial community will have
remains the same (von Lutzow and different physiologies (Schimel and
Kogel-Knabner, 2009; Conant et al., Gulledge, 1998).
2011). Temperature directly affects
enzyme activity and microbial V. Role of Microbes in
physiological property. Soil microbial
diversity plays an important role for Climate Smart
different ecosystem functions and can Agriculture
in uence plant diversity through the
cycling of various nutrients in nature Effect of climate change on
(Delgado-Baquerizo and Singh, 2016). agriculture is evident now. The rising
The direct effect of climate change is temperature, elevated CO2,
rising temperature whereas, indirectly unseasonal rainfall, ood, cyclone,
it can affect the plant composition, and drought have led to the idea of
root exudate pattern or even litter climate smart agriculture (CSA) so as
decomposition (Singh et al., 2010). to make agriculture more resilient to
changing climatic conditions.
The effects of increased CO2 levels on
Economically improving pro ciency,
microbial communities are often
adjustment to and relief of
indirect, as they are mediated by
environmental change are three
cascading effects on plant
mainstays of CSA (Lipper et al., 2014;
metabolism, growth and diversity,
Paustian et al., 2016). Microorganisms
and the associated changes in soil
are indispensable to various biological
physicochemical properties such as
activities in agro-ecosystems.
soil moisture and resource quality
Application of bene cial
(carbon to nitrogen ratio) (Bardgett
microorganisms such as biofertilizers
and Wardle, 2010). Global climate
and biopesticides besides improving
change could increase the
soil health and productivity, they also
heterotrophic microbial activity,
help in reducing the use of
which will ultimately increase the net
agrochemicals which in turn, may
carbon ef ux into the atmosphere as
help to decrease the use of fossil fuels
the rate of soil respiration is
in manufacturing agrochemicals and
extremely sensitive to increase in
subsequent release of GHGs into the
temperature (Bardgett et al., 2008).
atmosphere (Wagg et al., 2014). They
Diatoms perform 25-45 per cent of play crucial role in plant nutrient
total primary production in the cycling. They are both source and
oceans (Malviya et al., 2016). sink of carbon dioxide, methane and
Anthropogenic climate change will nitrous oxide (Kolb and Horn, 2012).
directly affect timing of blooms and

Climate Change and Indian Agriculture: Challenges and Adaptation Strategies 255
Relevance of Plant Associated Microorganisms in Climate Smart Agriculture

Methanotrophic bacteria serve as a 2007). The huge diversity of microbes

critical buffer to the huge amounts of gives an opportunity to explore and
CH4. The enzyme N2O reductase in exploit them for improving
rhizobacteria (in root nodules) and pro ciency of crop production,
other soil microorganisms can also adjusting to and alleviating
convert N2O to N2 (not a greenhouse environmental change impacts to soil
gas) (Sameshima-Saito et al., 2006; and plant health. Climate resilient
Zumft and Kroneck, 2006; Thomson et village (CRV) modules have been
al., 2012). Plant associated developed in the National
microorganisms help to improve Innovations in Climate Resilient
adaptation of crops to climate change Agriculture (NICRA) project to
by imparting resistance to biotic and manage the climate vulnerabilities at
abiotic stresses. Novel biocontrol village level to improve crop
agents can be utilized to contain the productivity and livelihood of farmers
destructive effect of emerging insect- and also to mitigate GHG emissions
pests under changing climatic (Srinivasarao et al., 2016). Microbial
conditions. Joshi et al. (2010) reported based technologies can be integrated
that Neozygites fresenii and into CRV modules to reap more
Maravalia cryptostegiae had been bene ts. Overall, microorganisms play
used to control of cotton aphid Aphis important role in climate smart
gossypii and weed rubber vine, agriculture through climate change
respectively. adaptation, GHG mitigation, and soil
carbon storage (Mohanty and Swain,
Bacillus thuringiensis (Bt) has been
2018; Das et al., 2019).
commercialized to control of
Lepidoptera and Diptera larvae. Bt V.1 Climate Change or Greenhouse
produces crystalline like pro-toxin,
Gas (GHG) Mitigation
which enters inside the mid gut of
larvae through feeding of plant Soil microorganisms through
leaves. Proteolysis occurs inside the their metabolic activities affect soil-air
alkaline mid gut of larvae and carbon exchanges. Methanotrophs
produces toxic peptides, consequently are speci c group of microorganisms
rupturing of epithelial cell of larvae which oxidize methane or other C1
causing the death of larvae (Estela et carbon compounds like formate,
al., 2004; Roh et al., 2007). methyl amine, dimethyl amine,
Bioaugmentation and biostimulation methanol to carbon dioxide and
are the two basic principles of release it to the environment (Kolb
biological control of soil-borne and Stacheter, 2013). Methanotrophs
phytopathogens, which can help to represent about~5 per cent of the
enhance adaptation to climate worldwide sink of atmospheric CH4
change. Recently identi ed Rhizobia (Hanson and Hanson, 1996) whereas,
species related with Medicago sativa it is up to 90 per cent for CH4 in the
can possibly work under different soil (Oremland, 1992). Many strains of
abiotic conditions, for example, low methylotrophic microbes are being
or high temperature, pH or low used for plant growth promotion
degrees of organic matter in the soil (Yim et al., 2012; Agafonova et al.,
(Ahmad et al., 1997; Bertrand et al., 2013; Jeyajothi et al., 2014). A

256 Climate Change and Indian Agriculture: Challenges and Adaptation Strategies
 Relevance of Plant Associated Microorganisms in Climate Smart Agriculture

recently discovered methanotrophic increase the soil biodiversity (Malik et

bacteria- Methylokorus infernorum al., 2017; Singh et al., 2019).
can utilize CH4 gas about 11 kg per Expanded biodiversity gives expanded
year. Another bacteria biological system exibility, which can
Methylobacterium extorquens also support and settle environmental
consumes many C1 carbon change impacts. Microorganisms
compounds like methane, methanol increase the ecosystem stability, and
and methylated amines and converts likewise can assume a key role in
them into CO2 (Jhala et al., 2014) and climate change buffering. For
make it available for autotrophic instance, bio-control agents can settle
microbes (Large, 1983). Zuniga et al. population levels of plants and
(2011) found that Methylobacterium herbivores, making them stronger to
organophilum CZ, Methylobacterium environmental change (Hoover and
organophilum CZ‐2 and Methylosinus Newman, 2004).
trichosporium OB3b transformed
Microorganisms have immense
methane gas into poly-β-
potential in synthesizing bioethanol,
hydroxybutyrate with limited CO2 biodiesel and methane utilizing
emission. Thus, renewable raw materials such as
methanotrophs/methylotrophs play molasses, cellulose, and other
the signi cant role in mitigation of biomass. The Saccharomyces
GHG emission. cerevisiae is being used to convert
Some denitrifying microorganisms are molasses and cellulose to bioethanol.
known to change nitrous oxide into Similarly, Green algae are used to
nitrogen gas (Itakura et al., 2013; produce biodiesel by utilizing sunlight
Nishizawa et al., 2014; Akiyama et al., (Scott et al., 2010; Krohn et al., 2011;
2016; Gao et al., 2016). Nishizawa et Patil et al., 2011; Pfromm et al., 2011).
al. (2014) reported that inoculation of Upscaling of its production and
pelleted poultry manure with utilization will go a long way in
Burkholderia spp., Azoarcus and drastically reducing the use of fossil
Niastella and their application as fuels and GHG emissions by way of
biofertilizers signi cantly decreased manufacturing of petroleum
the N2O emission by 40-60 per cent as products, power generation, etc.
compared to control. Gao et al. (2016)
also reported that in a greenhouse V.2 Soil Carbon Storage
study, association of Azospirillum and Soil health and crop productivity
Herbaspirillum with red clover are largely dependent on soil organic
signi cantly decreased the N2O carbon. Degraded soils, long periods
emissions. These organisms can of drought, low soil organic carbon
possibly alleviate GHG emissions. content, and low productivity are
Around the world, an expected 70- important characteristics of dryland
140 million tons of nitrogen are xed agroecosystems. Soil organic carbon
by nitrogen xing microbes content of Indian soils is very low, and
(Brockwell et al., 1995). Soil it follows in the following decreasing
microorganisms decrease the order: Vertisols > Inceptisols > Al sols
utilization of agrochemicals which are > Aridisols. These soils have potential
responsible for climate change and to sequester carbon provided that

Climate Change and Indian Agriculture: Challenges and Adaptation Strategies 257
Relevance of Plant Associated Microorganisms in Climate Smart Agriculture

there are suitable crop productions carbon in SOM and also discharging
and management practices. carbon as CO2 from the degradation
Enhancing the soil organic matter of SOM. Climate change modi es soil
content is an important strategy to carbon stockpiling through organic
improve soil health and crop matter decomposition or
productivity. To achieve this, the role mineralization, altering the
of soil microorganisms is very aggregation and accumulation of soil
important for SOM decomposition organic matter, and affecting soil
and nutrient cycling (Srinivasarao et erosion and respiration (Song et al.,
al., 2009; Srinivasarao et al., 2013). 2012; Brevik, 2013).
Microorganisms can have a crucial Soil microorganisms are imperative in
role in alleviating climate change. For the carbon cycle, assuming a crucial
instance, agriculture itself brings role in the sequestration of carbon in
about environmental change, soil organic matter (SOM) and
indirectly by way of using petroleum furthermore, the release of carbon as
products and land use, and directly carbon dioxide (CO2) from the
through GHGs emergence from degradation of SOM. Soil
farming practices. Greenhouse gas microorganisms assume a vital role in
out ows are particularly identi ed the carbon stabilization process by
with methane discharges from changing the dead organic matter
ruminant domesticated animals and into simple carbon molecules that are
rice eld in addition to nitrous oxide bound to be ensured and sequestered
discharges from fertilizers application, (Six et al., 2006). At each point on this
which represents 80 per cent of decay pathway, various kinds of
overall nitrous oxide emanations. carbon of contrasting size and
Expanded land use for agriculture synthetic intricacy are created that
brings about CO2 emissions connected can be incorporated with sediment
to deforestation and because of the and soil particles or fused into soil
expanded utilization of soil. It aggregates (Six et al., 2006; Grandy
additionally prompts enhanced CO2 and Wickings, 2010).
concentration in the atmosphere
Fungi assume a signi cant role in soil
because of decreased carbon re-take-
carbon stabilization or sequestration
up, and increased greenhouse gas
by amplifying the amount of carbon
discharge. The carbon sink limit of the
assigned to the soil and delivering
soil, which is interceded by
exacerbates that improve soil
microorganisms, has signi cant
aggregates stability. Arbuscular
rami cations for climatic change. Soil
Mycorrhizal Fungi (AMF) show
is both source and sink of global
symbiotic relationship with plant
carbon. It is the second largest
roots by giving plants soil
reservoir of carbon followed by
supplements while plants giving AMF
atmosphere which is more dynamic
basic sugars (Govindarajulu et al.,
(Baldini et al., 2018). Accumulation of
2005). As plants feed AMF, their
carbon in soil is a major approach for
biomass enhances by adequately
climate change alleviation (Schils,
expanding the amount of carbon in
2008). One of the signi cant roles of
soil (Rillig et al., 2001). Besides, AMF
soil microbes is sequestration of
also produce a sticky protein called

258 Climate Change and Indian Agriculture: Challenges and Adaptation Strategies
 Relevance of Plant Associated Microorganisms in Climate Smart Agriculture

glomalin that holds the soil particles control various pests and diseases. In
together, helping to conserve soil both ways, they reduce the
carbon (Rillig, 2004). Wilson et al. overexploitation of fertilizers and
(2009) reported that AMF are pesticides which are detrimental to
positively correlated with soil both soil and the environment. The
aggregation and carbon PGPR (Plant Growth Promoting
sequestration. Besides soil fungi, soil Rhizobacteria) forms an attractive
bacteria also assume a signi cant role group of bene cial micro- ora which
in organic matter decomposition. is being used worldwide and are
Nitrifying microorganisms convert gaining acceptance in climate stressed
complex nitrogen mixes from dead agriculture management or in
organic matter into simple forms that restoring degraded lands. The
are easily accessible for plants, while application of such microorganisms
Actinomycetes are liable for the not only helps in improving the soil
disintegration of more complex health, but also improves the plant
organic substrate (lignin, cellulose or growth through production of
hydrocarbon). These degradation various metabolites under different
processes are fundamental for stress conditions. It also becomes
microbial biomass creation and imperative to develop a
carbon sequestration into stable comprehensive knowledge of microbe
structures in soil. Overseeing soils for mediated reduction of greenhouse
soil microorganisms by giving gas emissions and the interaction
adequate and different plant inputs between different biotic and abiotic
and by decreasing tillage can improve components regulating it. This will
the carbon sequestration (Six et al., ultimately help in enhancing the
2006). predictions of various feedback
responses of microbes to climate
VI. Future Prospects and change, that can be incorporated into
future models of terrestrial feedback
Challenges loop and climate change. Novel
With the changing climatic biofertilizer strains could be
conditions, there have been changing developed having multifarious role in
rainfall patterns, rising average mean improving crop productivity and soil
temperature along with increasing health that can be better suited
incidence of extreme climatic events under changing environmental
like oods, droughts, and cyclone conditions. Crop yields could also be
which are directly affecting improved by developing new
agriculture. Therefore, it becomes strategies based on a better
extremely important to transform and understanding of various plant-
reorient agriculture making it more microbe and microbe-microbe
resilient to climate change. interactions. These crops could work
Microorganisms form an important well under different climatic
component of sustainable agriculture conditions and are economically
system where they can be used as viable to the farmers. Microorganisms
biofertilizers to promote plant may be out of sight, but we cannot
growth, or as biocontrol agents to afford for them to be out of mind.

Climate Change and Indian Agriculture: Challenges and Adaptation Strategies 259
Relevance of Plant Associated Microorganisms in Climate Smart Agriculture

and PCBs”. International

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270 Climate Change and Indian Agriculture: Challenges and Adaptation Strategies