Microbiome in Plant Health and Disease: Challenges and Opportunities

541 Pages·2019·9.492 MB·English

by  Vivek Kumar, Ram Prasad, Manoj Kumar, Devendra K. Choudhary

Vivek Kumar · Ram Prasad 
Manoj Kumar · Devendra K. Choudhary
Editors
Microbiome in
Plant Health
and Disease
Challenges and Opportunities
Microbiome in Plant Health and Disease
Vivek Kumar • Ram Prasad • Manoj Kumar
Devendra K. Choudhary
Editors
Microbiome in Plant
Health and Disease
Challenges and Opportunities
Editors
Vivek Kumar Ram Prasad
Himalayan School of Biosciences School of Environmental Science & Engg
Swami Rama Himalayan University Sun Yat-sen University
Dehradun, Uttarakhand, India Guangzhou, Guangdong, China
Manoj Kumar Devendra K. Choudhary
Centre for Life Sciences Amity Institute of Microbial Technology
Central University of Jharkhand Amity University
Ranchi, Jharkhand, India Noida, Uttar Pradesh, India
ISBN 978-981-13-8494-3 ISBN 978-981-13-8495-0 (eBook)
https://doi.org/10.1007/978-981-13-8495-0
© Springer Nature Singapore Pte Ltd. 2019
This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of
the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation,
broadcasting, reproduction on microfilms or in any other physical way, and transmission or information
storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology
now known or hereafter developed.
The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication
does not imply, even in the absence of a specific statement, that such names are exempt from the relevant
protective laws and regulations and therefore free for general use.
The publisher, the authors, and the editors are safe to assume that the advice and information in this book
are believed to be true and accurate at the date of publication. Neither the publisher nor the authors or the
editors give a warranty, express or implied, with respect to the material contained herein or for any errors
or omissions that may have been made. The publisher remains neutral with regard to jurisdictional claims
in published maps and institutional affiliations.
This Springer imprint is published by the registered company Springer Nature Singapore Pte Ltd.
The registered company address is: 152 Beach Road, #21-01/04 Gateway East, Singapore 189721,
Singapore
Preface
Microbiome diversity in association with plant roots is gargantuan; the microbial
number includes tens of thousands of various species. This multifaceted plant
accompanying microbial population, also referred to as the integrated part of the
plant, is imperative for plant health. Current progresses in plant-microbe synergism
research disclosed that plants have capabilities to shape their rhizospheric microbial
community. This has been substantiated by the information that dissimilar plant
species host particular microbial populations even when grown in the same climatic
conditions and soil. Accumulation of not good or unwanted microbiome communi-
ties in host plant leads to negative effect on plant health, on the other hand, associa-
tion of beneficial and constructive microbiome community in plant leads to positive
effect on the host health.
Pathogenic microbiome could lead to adverse effects on plant health. Interactions
between pathogens and plants are regularly considered as conflict between the two
organisms, this ignores the significance of beneficial microbiome. But the preva-
lence and proliferation of virtuous microbiome can appreciably influence infection
progression. Plants survive in close connection with microbial community that
thrives the habitat in which the plants grow. The soil microbial population structure
exemplifies the largest reservoir of biodiversity known till date. The rhizospheric
zone of plant is the confined zone of soil around roots, which is manipulated by root
exudates, can harbor up to 1011 microbial cells per gram of root and numerous other
prokaryotic species. The combined genome of this microbial population is much
higher than that of host plant and is therefore also insinuated as the host plant’s
additional genome.
We understand that the human system also benefits from beneficial probiotic
bacteria. Similarly, host plants also have the dependence on specific favorable
microbiome which are also recognized as plant growth strengtheners, biostimula-
tors, phytomodulators, biofertilizers, bioinoculants, phytostimulators, biopesticides,
biocontrol agents, etc., which are eventually advantageous to plant health. The exact
mechanism through which these microbiome become associated with the plant sys-
tem is unknown. This association depends upon the type of plant species and its age,
though it also depends on diverse ecological factors.
A lot of investigation has been done in the past but not much has been achieved
to understand the mutualistic interaction between microbiome and their host plants.
The plant microbiome are one of the most significant reasons for plant health, its
v
vi Preface
sustainability and productivity, furthermore, this research area has grasped wide
attention and consideration, in recent years. Microbiome associated with host plants
also play a decisive and essential role in general biogeochemical cycles. Plant-
associated beneficial microbiome also help hosts to surmount pathogenic microbes,
encourage growth, and inhabit space that would otherwise be reachable to host
pathogens. Besides these beneficial aspects, good microbiome also stimulate vari-
ous stress resistance, and ultimately persuade plant growth promotion through
nutrients mobilization, uptake, and transport. Consequently, the plant microbiome
proves to be a noteworthy and substantial determinant for host health and
production.
To understand complex communication pathways regulation within the plant and
their associated microbiome involves manifold functions of microbiome and plant
root excretions and their influences on genome expression and translation. The uni-
versal and all-inclusive approach to understanding any organismic structure and
function is to apprehend the organism in its entireness. The root associated or the
endophytic microbiome and their functional inputs are undoubtedly essential for all
plants on the sphere. It should be apparent that how the associated microbiome
influence or are being influenced by host plant will definitely vary across species, as
well as by several genetic and environmental factors. Studies on the plant microbi-
ome need to authenticate the microbial population, this will help us in understand
the change or fluctuations in microbiome community correlated with environmental
habitats. Further development is required for functional examination that exploits
metagenomics and metatranscriptomics techniques. This screening will be a front
runner for us to understand plant attributes and behaviors based on microbiome
knowledge. This will help us comprehend when, where, and how this “additional
genome” also functions as an intact organ system of the host plant.
In this book, we discuss evidences related to associated plant microbiome,
whether rhizospheric, phyllospheric, or endophytic, playing a significant role in
plant health or disease formation. Microbiome in Plant Health and Disease:
Challenges and Opportunities is focused on, but not limited to: microbiome coloni-
zation, their role in plant growth, development, nutrient recycling, mycorrhizae, and
an overview of phytospheric microbiome in sustainable agro-eco-system.
It is believed that the enthusiasm, eagerness, and remarkable opportunities pre-
sented in this work about our latest perception of the challenges and relationships
that bring about learning plant microbiome mutualistic approach will encourage and
inspire readers to push the field forward to new frontiers.
Dehradun, Uttarakhand, India Vivek Kumar
Guangzhou, Guangdong, China Ram Prasad
Ranchi, Jharkhand, India Manoj Kumar
Noida, Uttar Pradesh, India Devendra K. Choudhary
Contents
1 Applications of Plant–Microbe Interactions
in Agro-Ecosystems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
Rasheed A. Adeleke, Bhavna Nunthkumar, Ashira Roopnarain,
and Linda Obi
2 Exploring the Phyllosphere Bacterial Community
for Improving Tree Crop Protection . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
Diogo Mina, José Alberto Pereira, Teresa Lino-Neto,
and Paula Baptista
3 Microbes: An Important Resource for Sustainable Agriculture . . . . 53
Kalaivani K. Nadarajah
4 Bacteria-Inducing Legume Nodules Involved
in the Improvement of Plant Growth, Health and Nutrition . . . . . . . 79
Encarna Velázquez, Lorena Carro, José David Flores-Félix,
Esther Menéndez, Martha-Helena Ramírez-Bahena, and Alvaro Peix
5 Applications of Beneficial Microbe in Arid
and Semiarid Agroecosystem: IAA-Producing Bacteria . . . . . . . . . . . 105
Mohammad Javad Zarea
6 Role of Endophytes in Plant Health and Abiotic
Stress Management . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119
Ahmed Mohamed Eid, Salim S. Salim, Saad El-Din Hassan,
Mohamed A. Ismail, and Amr Fouda
7 Affirmative Plant-Microbe Interfaces Toward
Agroecosystem Sustainability . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145
Qasim Ali, Sana Ashraf, Muhammad Kamran, and Muhammad Ijaz
8 Emerging Insights on Rhizobacterial Functions . . . . . . . . . . . . . . . . . 171
P. Jishma and E. K. Radhakrishnan
9 Microbiome in Plant Health and Disease:
Challenges and Opportunities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 191
Ranjini Ramesh
vii
viii Contents
10 Influence of the Rhizospheric Microbiome
in Plant Health Management . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 215
Vankayalapati Vijaya Kumar
11 Role of Microbes in Plant Health, Disease Management,
and Abiotic Stress Management . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 231
Zabta Khan Shinwari, Faouzia Tanveer, and Irum Iqrar
12 Plant-Microbiome Interactions in Agroecosystem:
An Application . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 251
Maqshoof Ahmad, Sajid Mahmood Nadeem,
and Zahir Ahmad Zahir
13 Biodiversity and Biotechnological Applications
of Microorganisms Associated with Tropical Plants . . . . . . . . . . . . . . 293
João Lúcio Azevedo and Maria Carolina Quecine
14 Rhizobia for Biological Control of Plant Diseases . . . . . . . . . . . . . . . . 315
Camila Gazolla Volpiano, Bruno Brito Lisboa,
Camille Eichelberger Granada, Jackson Freitas Brilhante São José,
Andreia Mara Rotta de Oliveira, Anelise Beneduzi,
Yelena Perevalova, Luciane Maria Pereira Passaglia,
and Luciano Kayser Vargas
15 Bioactive Compounds Produced by Biocontrol
Agents Driving Plant Health . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 337
Miguel O. P. Navarro, Amanda C. M. Piva, Ane S. Simionato,
Flávia R. Spago, Fluvio Modolon, Janaina Emiliano,
Anabela Marisa Azul, Andreas Lazaros Chryssafidis,
and Galdino Andrade
16 The Continuous Story of Truffle-Plant Interaction . . . . . . . . . . . . . . . 375
Ghoson Mosbah Daba, Waill Ahmed Elkhateeb, Ting- Chi Wen,
and Paul William Thomas
17 Can Soil Microorganisms Reduce Broomrape
(Orobanche spp.) Infestation in Cropping Systems? . . . . . . . . . . . . . . 385
Gholamreza Mohammadi
18 Environmental Perspectives of Plant- Microbe Nexus
for Soil and Water Remediation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 403
Mahmoud Nasr
19 Development of Future Bioformulations
for Sustainable Agriculture . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 421
Muhammad Ijaz, Qasim Ali, Sana Ashraf, Muhammad Kamran,
and Abdul Rehman
Contents ix
20 Exploring Diversity of Bacterial Endophyte Communities
Using Advanced Sequencing Technology . . . . . . . . . . . . . . . . . . . . . . . 447
Inga Tamošiūnė, Elena Andriūnaitė, Vidmantas Stanys,
and Danas Baniulis
21 Perceptions of Microbe–Microbe and Plant–Microbiome
Interfaces: The Metagenomic Maneuver . . . . . . . . . . . . . . . . . . . . . . . 483
Nikhi Verma and Vivek Kumar
22 Metagenomic Approach in Relation to Microbe–Microbe
and Plant–Microbiome Interactions . . . . . . . . . . . . . . . . . . . . . . . . . . . 507
Abdul Rehman, Muhammad Ijaz, Komal Mazhar, Sami Ul-Allah,
and Qasim Ali
Editors and Contributors
About the Editors
Vivek Kumar is working as an Associate Professor at
the Himalayan School of Biosciences, Swami Rama
Himalayan University, Jolly Grant, Dehradun, India,
and is leading plant-microbe interaction, bioremedia-
tion, and microbial ecology research group. He has
obtained his masters and doctoral degrees from CCS
Haryana Agricultural University, Hisar, India. Serving
as Editor and Reviewer of several reputed international
journals, he has more than hundred publications to his
credit. He has authored a practical manual book and
edited several books with Springer Nature. He had also
served as Microbiologist in Public Authority of
Agricultural Affairs and Fish Resources, Kuwait, and
has been credited with first time reporting of Pink Rot
inflorescence disease of Date palm in Kuwait caused
by Serratia marcescens.
Ram Prasad is associated with Amity Institute of
Microbial Technology, Amity University, Uttar
Pradesh, India, since 2005. His research interests
include applied microbiology, plant-microbe interac-
tion, sustainable agriculture, and nanobiotechnology.
Dr. Prasad has more than 150 publications to his credit,
including research papers, review articles, book chap-
ters, 5 patents issued or pending, and several edited or
authored books. He has been awarded the Young
Scientist Award and Prof. J.S. Datta Munshi Gold
Medal by the International Society for Ecological
Communications; FSAB fellowship by the Society for
Applied Biotechnology; the American Cancer Society
xi