Plant-Microbe Interaction: An Approach to Sustainable Agriculture

515 Pages·2016·10.51 MB·English

by  Devendra K. Choudhary

Devendra K. Choudhary · Ajit Varma
Narendra Tuteja Editors
Plant-Microbe
Interaction:
An Approach
to Sustainable
Agriculture
Plant-Microbe Interaction: An Approach
to Sustainable Agriculture
Devendra K. Choudhary
Ajit Varma • Narendra Tuteja
Editors
Plant-Microbe Interaction:
An Approach to
Sustainable Agriculture
Editors
Devendra K. Choudhary Ajit Varma
Amity Institute of Microbial Amity Institute of Microbial
Technology (AIMT) Technology (AIMT)
Amity University Uttar Pradesh Amity University Uttar Pradesh
Noida, UP, India Noida, UP, India
Narendra Tuteja
Amity Institute of Microbial
Technology (AIMT)
Amity University Uttar Pradesh
Noida, UP, India
ISBN 978-981-10-2853-3 ISBN 978-981-10-2854-0 (eBook)
DOI 10.1007/978-981-10-2854-0
Library of Congress Control Number: 2016963687
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Preface
Sustainable agriculture involves designing a farm system employing nature as a
model. In most natural ecosystems, the greater the diversity, the more resistant an
ecosystem is to change and better able to recover from disturbances. In an agricul-
tural ecosystem or the so-called agroecosystems (AESs), disturbance is much more
frequent, regular, and intense. The ecological concepts of disturbance and their
recovery through succession play an important role in AES management. AESs are
undergoing disturbances in the form of cultivation, soil preparation, sowing, plant-
ing, irrigation, fertilizer application, pest management, pruning, harvesting, and
burning. The diversity and intensity of AESs in developing and developed countries
have been changing over time in response to a number of interacting biophysical
and social factors at the local, regional, and global levels. The impact of increased
spatiotemporal climate variability on AESs is likely to be intensified by climate
change, which will disrupt many ecosystem functions, altering their capacity to
provide goods and services and rendering them more susceptible to degradation. In
addition, the security of food supply to an increasing world population has turned
into a pressing issue worldwide. Sustainable food production can be achieved by
avoiding excessive disturbance and allowing successional processes to generate
greater AES stability. One can enhance the ability of AESs to maintain both fertility
and productivity through appropriate management of disturbance and recovery.
Plant productivity is often limited by soil nutrient availability and the interface
between living roots and soils, i.e., rhizosphere, which is a central commodity of
exchange where organic C flux from root fuels and microbial decomposers can
provide nutrients available to roots. It is virtually impossible to investigate the intri-
cacies of potential rhizosphere interaction in every environmental condition by vir-
tue of tremendous diversity of soil microbes, soil fauna, and plants. In addition, the
physicochemical and structural properties of soils including development have been
strongly affected by the action of rhizosphere over consecutive evolutionary time
frame, and the evolution of true plant roots along with their extension deep into
substrate is considerably hypothesized to have led to a revolution in planetary C and
water cycling that reflects on the biogeochemical functions of the rhizosphere on
Earth today. Understanding the complex microbial community in the rhizosphere
environment has proven to be a challenging task because of the vast diversity and
the enormity of the population inhabiting this unique habitat. Extensive studies have
investigated perturbation of microbial community equilibrium population by
v
vi Preface
changes in environmental conditions and soil management practices. It has long
been recognized that the activity of soil microorganisms plays an intrinsic role in
residue decomposition, nutrient cycling, and crop production. Any shift in micro-
bial community structure can be reflected in the implementation of various land use
and management systems that lead to development of best management practices
for an AES.
In subsistence AESs, crop yields are directly dependent on the inherent soil fer-
tility and on microbial processes that govern the mineralization and mobilization of
nutrients required for plant growth. In addition, the impact of different crop species
that are used in various combinations is likely to be an important factor in determin-
ing the structure of plant-beneficial microbial communities that function in nutrient
cycling, the production of plant growth hormones, and the suppression of root dis-
eases. Microorganisms represent a substantial portion of the standing biomass in
terrestrial ecosystem and contribute in regulation of C sequestration, N availability
and losses, and P dynamics. The size and physiological state of the standing micro-
bial biomass are influenced by management practices including rotational diversity,
tillage, and the quality and quantity of C inputs to the soils. In AES, sustainability is
dependent on the biological balance in the soils that is governed by the activity of
microbial communities. Soil microbial populations are immersed in a framework of
interactions known to affect plant fitness and soil quality; thereby, the stability and
productivity of both AES and natural ecosystem are enhanced. The global necessity
to increase agricultural productivity from steadily decreasing and degrading land
resource base has placed significant strain on the fragile agroecosystems. Therefore,
it is necessary to adopt strategies to maintain and improve agricultural productivity
employing high-input practices. Improvement in agricultural sustainability requires
the optimal use and management of soil fertility and soil physical properties and
relies on soil biological processes and soil biodiversity. It is necessary to understand
the perspectives of microbial diversity in agricultural context that is important and
useful to arrive at measures that can act as indicators of soil quality and plant
productivity.
Sustainable agriculture has currently to cope with serious threats that compro-
mise the food security for a human population under continuous growth, all these
exacerbated by climate change. Some of these include the loss of usable land
through overuse, deforestation, and poor irrigation practices, which have led to
desertification and salinization of soils, especially in dry lands. Approaches cur-
rently being taken to face this situation come from the development of stress-t olerant
crops, e.g., by genetic modification or breeding traits from wild plants. Genetic
engineering has been proposed as the solution to these problems through a rapid
improvement of crops. Crop genetic modification has generated a great public con-
cern regarding their potential threats to the environmental and public health. As a
consequence, legislation of several countries has restricted their use in agriculture.
On the other hand, exotic libraries from wild plants for clever plant breeding could
overcome the problem of narrowed genetic variability of today’s high-yield crops.
Plant breeding driven by selection marker has also been a major breakthrough.
However, these approaches have met limited success, probably because stress
Preface vii
tolerance involves genetically complex processes and the ecological and evolution-
ary mechanisms responsible for stress tolerance in plants are poorly defined.
Heavy metal contamination in soils is one of the world’s major environmental
problems, posing significant risks to public health and ecosystems. Therefore, the
development of a remediation strategy for metal-contaminated soils is urgent for
environmental conservation and human health. Phytoremediation offers signifi-
cantly more benefits than conventional technology to accumulate heavy metals from
the soil due to it being less expensive and safer for humans and the environment. But
slow growth and low biomass of plants in heavy metal-contaminated soil may limit
the efficiency of phytoremediation. This has prompted us to explore the possibilities
of enhancing the biomass of metal accumulators using bacteria as plant growth-
promoting bioinoculants. Bacteria that can produce IAA, siderophores, and ACC-
deaminase are capable of stimulating plant growth; lowering the level of ethylene
by consuming ACC, the immediate precursor of ethylene in plants growing in the
presence of heavy metals; and helping plants acquire sufficient iron for optimal
growth. Most of the heavy metals have low mobility in soil and are not easily
absorbed by plant roots. Plant roots and soil microbes and their interaction can
improve metal bioavailability in rhizosphere and lead to host adaptation to a chang-
ing environment.
Pathogen suppression by antagonistic microorganisms can result from one or
more mechanisms depending on the antagonist involved. Direct effects on the
pathogen include competition for colonization or infection sites, competition for
carbon and nitrogen sources as nutrients and signals, competition for iron through
the production of iron-chelating compounds or siderophores, inhibition of the
pathogen by antimicrobial compounds such as antibiotics and HCN, degradation of
pathogen germination factors or pathogenicity factors, and parasitism. These effects
can be accompanied by indirect mechanisms, including improvement of plant nutri-
tion and damage compensation, changes in root system anatomy, microbial changes
in the rhizosphere, and activation of plant defense mechanisms, leading to enhanced
plant resistance. Nowadays, it is well known that some soils are naturally suppres-
sive to some soilborne plant pathogens including Fusarium, Gaeumannomyces,
Rhizoctonia, Pythium, and Phytophthora. Although this suppression relates to both
physicochemical and microbiological features of the soil, in most systems, the bio-
logical elements are the primary factors in disease suppression, and the topic of
“biological control of plant pathogens” gained feasibility in the context of sustain-
able issues. The groups of microorganisms with antagonistic properties toward
plant pathogens are diverse, including plant-associated prokaryotes and eukaryotes.
Among the prokaryotes, a wide range of bacteria such as Agrobacterium, Bacillus
spp. (e.g., B. cereus, B. pumilus, and B. subtilis), Streptomyces, and Burkholderia
have been shown to be effective antagonists of soilborne pathogens. The most
widely studied bacteria by far in relation to biocontrol are Bacillus spp. and
Pseudomonas spp., viz., P. aeruginosa and P. fluorescens, which are probably
among the most effective root-colonizing bacteria.
Sustainable agriculture has a long history of research targeted at understanding
how to improve the effectiveness of root symbionts, viz., rhizobia and mycorrhiza.
viii Preface
A promising approach has been employed to understand how natural selection regu-
lates changes in mutualistic interactions. A descriptive knowledge of basic evolu-
tionary processes can be employed to develop agricultural management practices
that favor the most effective symbionts. Mutually beneficial interactions between
plant and associated rhizospheric microorganisms are ubiquitous which is important
for ecosystem functioning. Symbiotic nitrogen fixation by bacteria, e.g., Rhizobium,
Bradyrhizobium, Mesorhizobium, Sinorhizobium, and Azorhizobium spp., that are
collectively known as rhizobia or by Frankia spp. is the major N input to many natu-
ral and agricultural ecosystems in the root nodules of legumes or actinorhizal plants,
respectively. In addition, mycorrhizal fungi supply their host plants with mineral
nutrients, viz., P, and other benefits. Several rhizospheric microorganisms cause
severe infection to roots, and these so-called root pathogens can be suppressed by
Pseudomonas fluorescens after colonization of the roots thereby improving plant
health.
The exploitation of plant–fungal symbiosis appears as a smart alternative for
plant adaptation due to their great quantity, ubiquity, diversity, and broad range of
ecological functions they play in the natural ecosystem. Recent studies have shown
that symbiotic microbes are of crucial importance in the distribution of plant com-
munities worldwide and are responsible of their adaptation to environments under
highly selective pressure. These indicate that some microbes confer tolerance to
specific stresses and are responsible of the survival of plants to environments sub-
mitted to these particular conditions. The stress tolerance conferred by the symbio-
sis is a habitat-specific phenomenon, which has been defined as habitat-adapted
symbiosis that confers tolerance to heat but not salt and coastal symbiotic microbes
conferring tolerance to salt but not to heat. The same fungal species isolated from
plants in habitats devoid of salt or heat stress did not appear to confer tolerance to
these stresses. It is currently thought that each plant in natural ecosystems com-
prises a community of organisms, including mycorrhizae and bacteria. The ability
of the symbiotic fungi to confer tolerance to stress may provide a new strategy to
mitigate the impacts of global climate change on agriculture and natural plant com-
munities. Such symbiotic lifestyles suppose a potential source for the improvement
of food crops through adapting them to situations of increasing desertification and
drought on global crop lands. It appears therefore as a sustainable alternative to the
use of genetically modified organisms, which on the other hand did not yield the
expected results.
Finally, plant-associated microorganisms can play an important role in confer-
ring resistance to abiotic stresses. These organisms could include rhizoplane and
symbiotic bacteria and fungi that operate through a variety of mechanisms like trig-
gering osmotic response and induction of novel genes in plants. The development of
stress-tolerant crop varieties through genetic engineering and plant breeding is an
essential but a long-drawn process, whereas microbial inoculation to alleviate
stresses in plants could be a more cost-effective environmental friendly option
which could be available in a shorter time frame. Taking the current leads available,
concerted future research is needed in this area, particularly on field evaluation and
application of potential organisms. It is our contention that native plants survive and
Preface ix
flourish in stressed ecosystems because of endosymbiotic organisms that have
coevolved and were essential for their adaptation to changing environments. Plant
growth and development cannot be adequately described without acknowledging
microbial interactions. We need to determine the extent of microbial associations in
the plant kingdom. This question will only be answered as technology is developed
to detect their presence in plant tissues. What we have learned is that there is a need
to understand how plant and microbes communicate in these endosymbiotic rela-
tionships and how they regulate basic genetic and physiological functions.
Hence, in the present book, editors compiled researches carried out by research-
ers in three sections with elaborate description related to “plant–microbe interaction
for sustainable agriculture.”
Part I: An Introduction to Plant-Microbe Interaction
Chapter 1 summarizes an exposition of plant–microbe and microbe–plant interac-
tions describing the interplay of chemicals and signals that participate in the com-
plex domain of the rhizosphere. The information derived from the current studies
and the utilization of current technological platforms will enable researchers to
explore and garner more information at the plant–microbe and plant–microbiome
levels.
Chapter 2 briefly describes the various physical and chemical processes occur-
ring in the rhizosphere, how the change in environment hampers these factors, and
how that affects the rhizospheric diversity in modifying the microbial ecology and
root architecture.
Chapter 3 emphasizes the insight of the rhizosphere and plant growth-promoting
rhizobacteria under the current viewpoints. Conclusively, the applicability of these
favorable rhizobacteria in different agroecosystems has been offered systematically
under both normal and stress circumstances to focus the recent trends with the
objective to improve upcoming visions.
Chapter 4 describes a holistic perception of rhizosphere functioning with a high-
light on the ecological drivers that promote colonization of coherent functional
groups of microorganisms influencing plant life through several direct and indirect
mechanisms.
Chapter 5 describes the concept of rhizosphere, hyphosphere, and mycorrhizo-
sphere and the various activities involved in understanding the functional diversity
of microorganisms inhabiting the mycorrhizosphere necessary to optimize soil
microbial technology for the benefit of plant growth and health.
Chapter 6 highlights the importance of mycorrhizae with beneficial microbes in
plant growth promotion, nutrient uptake, and stress tolerance either biotic or abi-
otic. The presence of bacteria in the rhizosphere synchronizes with mycorrhizae
termed as “mycorrhizae helper bacteria” that increase plant growth by focusing on
N and P in particular while micronutrients in general.
x Preface
Part II: Plant-Microbe Interaction Under Abiotic and Biotic
Stress
Chapter 7 describes deployment of microbe–plant interactions that results in the
promotion of plant health in arid and semiarid regions with reference to India under
abiotic stress.
Chapter 8 briefly describes an attempt to explore current knowledge of bacterial
ACC-deaminase-mediated physiological and molecular changes in the plants under
diverse environmental conditions (drought and high salinity), mode of ACC-
deaminase enzyme action, and drastic effects of salinity and drought on plant growth
with a special reference to ethylene evolution.
Chapter 9 highlights the success and efficiency of phytoremediation with asso-
ciation of heavy metal-resistant plant growth-promoting rhizobacteria.
Chapter 10 briefly describes the importance of microbe–plant interaction under
salt stress. It describes strategies that plants adapt to deal with salinity, and current
biotechnological efforts toward producing salt-tolerant crops are summarized.
Chapter 11 summarizes the comprehensive understanding that required learning
the mechanisms and critical factors influencing the plant–microbe–toxicant interac-
tion in soils for success of phytoremediation.
Chapter 12 elaborately describes priming of benign microbes especially bacteria
for plant growth promotion under biotic stresses to unravel the mystification of
mechanisms involved in plant defense including ISR and SAR using sustainable
development of plants.
Chapter 13 discusses on the susceptibility of most important bacterial and fungal
plant pathogens toward different essential oils and their constituents responsible for
biological activities such as antibacterial and antifungal. In addition, the potential
effectiveness of herb essential oils against different plant pathogenic fungi and bac-
teria has been verified.
Chapter 14 elaborately describes the use of halophilic bacteria in agriculture
system toward producing salt stress-tolerant crops and understanding the mecha-
nisms of plant and halophilic bacterial interaction.
Chapter 15 describes that PGPR has the ability to mitigate most effectively the
impact of abiotic stresses on plants through degradation of the ethylene precursor
ACC by bacterial ACC-deaminase and through biofilm and exopolysaccharide
production.
Part III: Plant-Microbe Interaction and Plant Productivity
Chapter 16 presents an overview of the importance of the microbiome to the plant
growth promotion, focusing on the diversity, functional and taxonomic, of the
microbiota associated to maize, and the desirable characteristics of microorgan-
ism’s candidates to the use in PGP formulations.