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Improve the quality and productivity of your crops through selecting positive and effective interactive core-microbiomes
As microbial cells are present in overwhelming numbers in our soil, it is perhaps inevitable that microbes are found extensively in plant and animal tissue. The role of microbiomes on the regulation of physiological processes in animals has been extensively researched in recent years, but the overarching role of the plant microbiome has yet to be discovered.
Core Microbiome: Improving Crop Quality and Productivity is an attempt to remediate some of that deficit, as the first book to summarize feature of microbial communities that make up the plant microbiome. There is substantial evidence that these communities are crucial in disease control, enhanced nutrient acquisition, and stress tolerance—a feature more important than ever due to climate change. A further focus on improving how core microbiomes interact so that they are both phenotypically and genotypically very adaptive and sustainable will allow the reader to improve the quality and productivity of crops so that they may be considered sustainable agriculture.
Core Microbiome readers will also find:
- Descriptions of the basic structure of core microbiomes and their functions across various habitats
- New and cutting-edge trends and technological innovations highlighted that use core microbiomes to harness plant microbiome interaction
- The structure, classification, and biotechnological applications of aquatic core microbiomes, in addition to the material on plant microbiomes
As a broad introduction to the interaction of core microbiome and plant productivity, Core Microbiome is ideal for researchers and scientists working in the field of environmental science, environmental microbiology, and waste management. Similarly, undergraduate and graduate students in these fields, as well as in agriculture, biotechnology, biosciences, and life and environmental sciences will also benefit from this work.
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Core Microbiome
Improving Crop Quality and Productivity
Edited by
Javid A. Parray
Department of Higher Education
Government Degree College
Eidgah, Srinagar, India
Nowsheen Shameem
Cluster University Srinagar
Jammu and Kashmir, India
Elsayed Fathi Abd-Allah
King Saud University
Riyadh, Saudi Arabia
Mohammad Yaseen Mir
University of Kashmir
Srinagar, India
This edition first published 2022© 2022 John Wiley & Sons Ltd
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The right of Javid A. Parray, Nowsheen Shameem, Elsayed Fathi Abd-Allah and Mohammad Yaseen Mir to be identified as the author(s) of the editorial material in this work has been asserted in accordance with law.
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Library of Congress Cataloging-in-Publication DataNames: Parray, Javid A., author.Title: Core microbiome: improving crop quality and productivity / edited by Javid A. Parray, Govt Sheikh Ul Alam Memorial College, Jammu and Kashmir, India, Nowsheen Shameem, Cluster University Srinagar, Jammu and Kashmir, India, Elsayed Fathi Abd-Allah, King Saud University, Riyadh, Saudi Arabia, Mohammad Yaseen Mir, University of Kashmir, Srinagar, India.Description: Hoboken, NJ: John Wiley & Sons, 2022. | Includes bibliographical references and index.Identifiers: LCCN 2021053026 (print) | LCCN 2021053027 (ebook) | ISBN 9781119830764 (hardback) | ISBN 9781119830788 (pdf) | ISBN 9781119830771 (epub) | ISBN 9781119830795 (ebook) Subjects: LCSH: Soil microbiology. | Plant-microbe relationships. | Agricultural microbiology.Classification: LCC QR111. P333 2022 (print) | LCC QR111 (ebook) | DDC 579/.1757--dc23/eng/20211221LC record available at https://lccn.loc.gov/2021053026LC ebook record available at https://lccn.loc.gov/2021053027
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Contents
Cover
Title page
Copyright
List of Contributors
Preface
1 A Review of Endophytic Microbiota of Medicinal Plants and Their Antimicrobial Properties: Robeena Sarah, Nida Idrees, and Baby Tabassum
2 Plant Microbiome: A Key to Managing Plant Diseases: Dipal B. Minipara, Khushboo Pachhigar, and Himanshu R. Barot
3 Impact of Microbiomes to Counter Abiotic Stresses in Medicinal Plants- A Review: Abeer Hashem, Khaloud Mohammed Alarjani, Khalid F. Almutariri, Javid A. Parray, Sushil K. Sharma, Ashwani Kumar, Turki M. Dawoud, Khalid S. Almaary, Nosheen Shameem, and Elsayed Fathi Abd-Allah
4 Uses of Compost in Agriculture and Bioremediation – A Review: Aparna Gunjal
5 Metagenomics and Microbiome Engineering: Identification of Core Microbiome and Improvement of Rhizosphere: Bahman Fazeli-Nasab, Nafiseh Mahdinezhad, and Javid A. Parray
6 Core Microbiome: Plant Growth and Development: Thirunarayanan P, Uday Kumar Thera, Tulasi Korra, and Manoj Kumar V
7 Microbiome Engineering and Biotechnology: The Real Finenesses of a Robust Rhizosphere: Barkha Sharma, Shalini Tiwari, and Kailash Chand Kumawat
8 Role of Rhizospheric Microbiome in Enhancing Plant Attributes and Soil Health for Sustainable Agriculture: Sandeep Sharma and Kailash Chand Kumawat
9 Toxic Effects of Some Herbicides on the Fatty Acid Profile of Wheat Varieties: A Phytomicrobiome Study: Fadime Karabulut and Songul çanakcι-Gulengul
10 Microbial Prospects in Sediment Denitrification of Eutrophic Wetland Ecosystems: Rupak Kumar Sarma and Kamal Choudhury
11 Role of Plant Microbiome in Carbon Sequestration for Sustainable Agriculture: Ranjith Sellappan, Aswini Krishnan, and Kalaiselvi Thangavel
12 Functions and Emerging Trends of the Microbial Community in Heavy Metals Bioremediation: A Review: Nida Idrees, Robeena Sarah, and Baby Tabassum
13 Microbiomics and Sustainable Agriculture: New Frontiers: Shabeer Ahmad Dar, Mohammad Yaseen Mir, Azra N. Kamili, Irshad Ahmad Nawchoo, and Shabir Ahmad Bhat
14 Role of Nanotechnology in Soil Microbiome and Agricultural Development: Bisma Farooq, Shahnaz Anjum, Madiha Farooq, Gulzar Ahmed Rather, Asma Nazir, Bijaya Kumar Nayak, and Anima Nanda
15 Microbial Biofilms: Optimal Genetic Material Exchange in a Microbiome Environment: Niraj Singh and Pranjal Pratim Das
16 Rhizosphere Improvement: Role of Biotechnology and Microbioengineering: Afrozah Hassan and Irshad Ahmad Nawchoo
17 Exploring Biological Agents and Core Microbiomes as a Tool for Reclamation of Abandoned Mines: Seema B. Sharma and Rupak Dey
18 Mycorrhizal Strategy for the Management of Hazardous Chromium Contaminants: Abeer Hashem, Nowsheen Shameem, Javid A. Parray, and Elsayed Fathi Abd-Allah
Index
End User License Agreement
List of Illustrations
Chapter 1
Figure 1.1 Medicinally important parts...
Chapter 2
Figure 2.1 Plant–microbe...
Chapter 3
Figure 3.1 Diverse abiotic stresses...
Chapter 5
Figure 5.1 Sample of cultivated...
Figure 5.2 Clonic specimens of...
Figure 5.3 Comparison of metagenomics...
Figure 5.4 Metagenomics analysis in...
Figure 5.5 Steps involved in...
Figure 5.6 Steps involved in...
Figure 5.7 Steps involved in...
Figure 5.8 Steps involved in...
Chapter 6
Figure 6.1 Underground parts of...
Chapter 8
Figure 8.1 Role of the...
Chapter 9
Figure 9.1 Mechanisms of inorganic...
Figure 9.2 Strategy required for...
Chapter 11
Figure 11.1 Schematic diagram of...
Figure 11.2 The figure depicts...
Figure 11.2 The figure depicts...
Figure 11.3 Plant and phyllosphere...
Chapter 14
Figure 14.1 The top-down...
Figure 14.2 Different methods of...
Figure 14.3 Role of nanomaterials...
Chapter 15
Figure 15.1 Horizontal gene transfer...
Chapter 16
Figure 16.1 Plant–microbe...
Chapter 17
Figure 17.1 Bioremediation process...
Figure 17.3 Deep-sea cement...
List of Tables
Chapter 1
Table 1.1 Some Endophytic fungi obtained...
Chapter 3
Table 3.1 Plants with Medicinal Properties...
Table 3.2 Rhizosphere Microbes Interactions in...
Table 3.3 Bioactive compounds that are...
Chapter 6
Table 6.1 List of beneficial microbes...
Table 6.2 Trade names of different...
Chapter 8
Table 8.1 Role of beneficial rhizospheric...
Chapter 9
Table 9.1 Fatty acid profile effects...
Table 9.2 Fatty acid profile effects...
Table 9.3 Studies on phytoremediation of...
Chapter 12
Table 12.1 Bioremediation of heavy metals...
Table 12.2 Microorganisms as oil remediators...
Chapter 13
Table 13.1 Some representative applications of...
Chapter 15
Table 15.1 Genes involved in biofilm...
Table 15.2 Role of eDNA in...
Guide
Cover
Title page
Copyright
Table of Contents
List of Contributors
Preface
Begin Reading
Index
End User License Agreement
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List of Contributors
Elsayed Fathi Abd-AllahPlant Production Department, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
Khaloud Mohammed AlarjaniBotany and Microbiology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
Khalid S. AlmaaryBotany and Microbiology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
Khalid F. AlmutaririPlant Production Department, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
Shahnaz AnjumDepartment of Biomedical Engineering, Sathyabama Institute of Science and Technology deemed to be University, Rajiv Gandhi, Salai, Chennai, Tamil Nadu, India
Himanshu R. BarotSardarkrushinagar Dantiwada Agricultural University, Sardarkrushinagar, Banaskantha, Gujarat, India
Shabir Ahmad BhatCenter of Research for Development, University of Kashmir, Srinagar, Jammu and Kashmir, India
Songul Çanakcι-GulengulDepartment of Biology, Fırat University, Elazıg, Turkey
Kamal ChoudhuryDepartment of Botany, SBMS College, Sualkuchi, Assam, India
Shabeer Ahmad DarCenter of Research for Development, University of Kashmir, Srinagar, Jammu and Kashmir, India
Pranjal Pratim DasDepartment of Biotechnology, Darrang College, Tezpur, Assam, India
Turki M. DawoudBotany and Microbiology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
Rupak DeyDepartment of Earth and Environmental Science, KSKV Kachchh University, Mundra Road, Bhuj, Gujarat, India
Bisma FarooqDepartment of Biomedical Engineering, Sathyabama Institute of Science and Technology deemed to be University, Rajiv Gandhi, Salai, Chennai, Tamil Nadu, India
Madiha FarooqDepartment of Biomedical Engineering, Sathyabama Institute of Science and Technology deemed to be University, Rajiv Gandhi, Salai, Chennai, Tamil Nadu, India
Bahman Fazeli-NasabResearch Department of Agronomy and Plant Breeding, Agricultural Research Institute, University of Zabol, Zabol, Iran
Aparna GunjalDepartment of Microbiology, Dr D.Y. Patil, Arts, Commerce and Science College, Pimpri, Pune, Maharashtra
Abeer HashemBotany and Microbiology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
Mycology and Plant Disease Survey Department, Plant Pathology Research Institute, ARC, Giza, Egypt
Afrozah HassanDepartment of Botany, University of Kashmir, Srinagar, Jammu and Kashmir, India
Nida IdreesToxicology Laboratory, Department of Zoology, Government Raza P.G. College, Rampur, Uttar Pradesh, India
Azra N. KamiliCenter of Research for Development, University of Kashmir, Srinagar, Jammu and Kashmir, India
Fadime KarabulutDepartment of Biology, Fırat University, Elazıg, Turkey
Tulasi KorraDepartment of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India
Aswini KrishnanDivision of Microbiology, ICAR-IARI, New Delhi, India
Ashwani KumarMetagenomics and Secretomics Research Laboratory, Department of Botany, Dr. Harisingh Gour University (A Central University), Sagar, Madhya Pradesh, India
Kailash Chand KumawatDepartment of Soil Science, Punjab Agricultural University, Ludhiana, Punjab, India
Nafiseh MahdinezhadDepartment of Agronomy and Plant Breeding, Faculty of Agricultural, University of Zabol, Zabol, Iran
Manoj Kumar.VDepartment of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India
Dipal B. MiniparaAnand Agricultural University, Anand, Gujarat, India
Mohammad Yaseen MirCenter of Research for Development, University of Kashmir, Srinagar, Jammu and Kashmir, India
Anima NandaDepartment of Biomedical Engineering, Sathyabama Institute of Science and Technology deemed to be University, Rajiv Gandhi, Salai, Chennai, Tamil Nadu, India
Irshad Ahmad NawchooDepartment of Botany, University of Kashmir, Srinagar, Jammu and Kashmir, India
Bijaya Kumar NayakKanchi Mamunivar Government Institute for Post Graduate Studies and Reserach, Department of Botany, Puducherry, India
Asma NazirDepartment of Biomedical Engineering, Sathyabama Institute of Science and Technology deemed to be University, Rajiv Gandhi, Salai, Chennai Tamil Nadu, India
Khushboo PachhigarVeer Narmad South Gujarat University, Surat, Gujarat, India
Javid A. ParrayDepartment of Higher Education, Government Degree College, Eidgah, Srinagar, India
Gulzar Ahmed RatherDepartment of Biomedical Engineering, Sathyabama Institute of Science and Technology deemed to be University, Rajiv Gandhi Salai, Chennai, Tamil Nadu, India
Robeena SarahToxicology Laboratory, Department of Zoology, Government Raza P.G. College, Rampur, Uttar Pradesh, India
Rupak Kumar SarmaDepartment of Botany, Sadiya College, Chapakhowa, Sadiya, Assam, India
Ranjith SellappanDepartment of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
Nosheen ShameemDepartment of Environmental Science, Cluster University Srinagar, Jammu and Kashmir, India
Barkha SharmaDepartment of Microbiology, College of Basic Sciences & Humanities, G. B. Pant University of Agriculture & Technology, Pantnagar, Uttarakhand, India
Sandeep SharmaDepartment of Soil Science, Punjab Agricultural University, Ludhiana, Punjab, India
Seema B. SharmaDepartment of Earth and Environmental Science, KSKV Kachchh University, Mundra Road, Bhuj, Gujarat, India
Sushil K. SharmaICAR-National Bureau of Agriculturally Important Microorganisms, Kushmaur, Maunath Bhanjan, Uttar Pradesh, India
Niraj SinghDepartment of Microbiology, Royal Global University, Guwahati, Assam, India
Baby TabassumToxicology Laboratory, Department of Zoology, Government Raza P.G. College, Rampur, Uttar Pradesh, India
Kalaiselvi ThangavelDepartment of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
Uday Kumar TheraDepartment of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India
Thirunarayanan PDepartment of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India
Shalini TiwariDepartment of Soil Science, Punjab Agricultural University, Ludhiana, Punjab, India
Preface
An overabundance of microbial cells is present in every gram of soil, and microbes are found extensively in plant and animal tissues. The mechanisms governed by microorganisms in the regulation of physiological processes of their hosts have been extensively studied in light of recent findings on microbiomes. In plants, the components of these microbiomes may form distinct communities, such as those inhabiting the plant rhizosphere, the endosphere, and the phyllosphere. In each of these niches, the “microbial tissue” is established and responds to specific selective pressures. Although there is no clear picture of the overall role of the plant microbiome, there is substantial evidence that these communities are involved in disease control, enhance nutrient acquisition, and affect stress tolerance. This book first summarizes features of microbial communities that compose the plant microbiome and further presents a series of studies describing the underpinning factors that shape the phylogenetic and functional plant-associated communities. We advocate that understanding the mechanisms by which plants select and interact with their microbiomes may directly affect plant development and health and further lead to the establishment of novel microbes. Despite being one of the simplest metazoans, corals harbor some of the most highly diverse and abundant microbial communities. Differentiating core, symbiotic bacteria from this diverse host-associated consortium is essential for characterizing the functional contributions of bacteria but has not been possible yet. Here, we describe the coral core microbiome and demonstrate clear phylogenetic and functional divisions between the micro-scale, niche habitats within the coral host. In doing so, we discover seven distinct bacterial phylotypes that are universal to the core microbiome of coral species, separated by thousands of kilometers of oceans. The two most abundant phylotypes are co-localized specifically with the corals’ endosymbiotic algae and symbiontcontaining host cells. These bacterial symbioses likely facilitate the success of the dinoflagellate endosymbiosis with corals in diverse environmental regimes. This book primarily focuses on selecting positive and effective interactive core microbiome that are both phenotypically and genotypically very adaptive and sustainable, which further improve crop quality and productivity vis-à-vis sustainable agriculture. The bioengineering concept for rhizosphere improvement has also been discussed in one of the chapters. The book also highlights the structure, characterization, and biotechnological application of aquatic core microbiomes.
Javid A. Parray
PhD, PDF
1 A Review of Endophytic Microbiota of Medicinal Plants and Their Antimicrobial Properties
Robeena Sarah, Nida Idrees, and Baby Tabassum
Toxicology Laboratory, Department of Zoology, Govt. Raza P.G. College, Rampur 244901, India
1.1 Introduction
Medicinal plants have been used in many parts of the world for thousands of years in traditional treatments for numerous diseases. In rural areas of developing countries, they are still used as a primary source of drugs [1]. About 80% of developing countries use conventional medicines for general health care [2]. Natural products can be obtained from medicinal plants that have proven to be a rich source of biologically active compounds; many of them are used to develop novel chemicals for the pharmaceutical industry. With regard to disease-causing microorganisms, the increasing resistance to therapeutic agents currently in use, such as antibiotics and antiviral agents, has led to renewed interest in exploring novel anti-infective compounds. As approximately 450,000 plant species are available worldwide, of which only one per cent has been phytochemically analyzed, the prospects of locating new bioactive compounds are tremendously positive.
Medicinal plants are essentially considered complex and dynamic when used in systems for remedial therapy. Hence, their chemical composition depends upon several factors, such as botanical species, genetically determined chemotypes, anatomically a part of the plant (e.g., seed, flower, root, and leaf), storage, sun exposure, humidity, kind of ground, time of harvesting, and ecological area. Moreover, biogenic factors, such as the fungal and bacterial endophytes related to diverse parts of the plant, can influence their chemical composition. In recent years, the research and study of the multiple interactions occurring between endophytes and medicinal plants have modernized our knowledge of plant biology, with entirely unexpected and remarkable application perspectives: the probability of modulating, amplifying, or interfering within the biosynthesis of phytoconstituents (e.g., terpenes, polyphenols, and alkamides), but also to engineer the synthesis of latest molecules directly, for instance with antibiotic activity.
1.2 Antimicrobial Properties of Medicinal Plants with Particular Reference to Neem (Azadirachtaindica)
There are many reports on conventional medicinal plants and natural products to treat several diseases. Many plant-based medicines utilized in traditional therapeutic systems as agents in the treatment of infectious diseases are recorded in pharmacopoeia, a variety of which have been investigated recently for their efficiency against disease-causing microorganisms. The general antimicrobial activities of medicinal plants and their products, such as essential oils, were analyzed earlier [3,4].
Moreover, medicinal plants also can play an elementary function against rising antibiotic resistance both directly for their antimicrobial activities (e.g., antibacterial, antiviral, antifungal, and antiparasitic ones) and indirectly by reducing resistance against antibiotics.
There are numerous medicinal plants with well-known antimicrobial activity, including traditional Chinese or Ayurvedic medicine. Among medicinal plants adopted in experimental studies, a classic example is the Azadirachta indica (Figure 1.1) commonly known as neem, an evergreen tree of the sub-tropics and tropics, indigenous to the Indian subcontinent, with a recognized ethnomedicinal value and significance in agriculture and also in the pharmaceutical industry [5]. Every part of the neem plant, such as leaves, fruits, seeds, bark, and roots, contains compounds with proven antioxidant, anti-inflammatory [6], antidiabetic, antibacterial, antigingivitic, antifungal, anticancer, antiviral, antiulcer, neuroprotective, antipyretic, hepatoprotective, nephroprotective, and wound-healing properties. It possesses incredible potential within the field of medicine, pest management, and environmental protection. Neem may be a natural source of eco-friendly herbal pesticides, insecticides, and agro-based chemicals [7]. The impact of mouthwash containing neem on plaque and gingivitis was analyzed in a clinical study, indicating that it may help maintain mouth hygiene and suggest an enhanced effect on preventing oral diseases since it is both cost-effective and easily accessible [8]. Approximately 400 compounds are isolated from various parts of neem until now, and significant bioactive secondary metabolites and relatively 30 compounds are isolated from endophytes of neem [5]. Endophytic fungi of neem produce a wide range of secondary bioactive metabolites with potential compounds, namely, melanin, antimicrobial, antioxidant, anti-inflammatory, insecticides, nematicides, etc. [5].
Figure 1.1 Medicinally important parts of the Azadirachta indica (neem) tree showing flowers; fruits; twigs; bark and leaves.
Neem imposes a check on microbial growth and, in the breakdown of cell membrane capability, exhibits antimicrobial properties [9]. Neem nanoemulsion displayed antibacterial activity by disturbing the integrity of the bacterial cell membrane against strains of a bacterial pathogen. Different parts of the plant reveal antimicrobial properties against a wide range of pathogenic microbes [10]. Neem extract has shown antimicrobial effects against Streptococcus mutans and S. faecalis [11]. A new vaginal contraceptive, NIM-76, obtained from neem oil, has shown an inhibitory effect on the growth of various pathogenic microorganisms, including fungi, bacteria, and viruses [12]. The antibacterial property of neem seed oil in vitro against 14 strains of pathogenic bacteria has been recently assessed [13].
1.3 Current Trends on Bioactive Metabolites from Endophytic Microbiota of Medicinal Plants
A significant development in the understanding of plant-associated microbiota has been prompted by massive DNA sequencing technology in the past decade. Such close connection of microorganisms with plants has a broad contribution to plant nutrient absorption, growth, stress tolerance, and health status, and secondary metabolite production [14]. Metal hyper-accumulating plants are known to shelter a co-evolved microbiota [15,16], and an essential role has been recognized in microbial-assisted phytoremediation [17]. Medicinal plants are well-known to shelter endophytes that are potentially concerned with the biosynthesis of phytoconstituents and can synthesize bioactive compounds.
The composition of biologically active components of medicinal plants differs broadly depending on their soil type, plant species, and their association with microorganisms [18,19]. These plant-linked microbial communities and their physiological functions are also strongly influenced by bioactive secondary metabolites synthesized by medicinal plants [20–22]. Moreover, for specific character and activities, including growth, nutrient acquirement, induced systemic resistance, and tolerance to abiotic stress factors, plants depend on their microbiome [23–27]. Although many medicinal plants are well-studied with relation to their microbiome, phytochemical constituents, and pharmacological properties, the physiological interactions between host and microorganisms remain inadequately understood [28]. The plant-linked microbiome consists of different microbial communities existing within the endosphere, shoots, and roots [27,29]. The rhizosphere of many plants is known to be a potential source for selecting good microorganisms that may affect plant health and is well-studied [21,30,31]. Hence, a valuable understanding of the microbial ecology of plant-associated bacteria may provide by considering the response of microbial communities to adaptation within the physiochemical atmosphere of the rhizosphere. The abundance of antagonistic bacteria within the rhizosphere of medicinal plants like sweet false chamomile (Matricaria chamomilla), Solanum distichum, and common marigold (Calendula officinalis) was observed [32]. The root-linked bacteria of Ajuga bracteosa displayed a broad range of plant growth-promoting activities by producing siderophores (iron-chelating compounds) and indole ethanoic acid and reveal antioxidant activity [33]. The vast and considerable collection of endophytic fungi from neem may represent a distinct source of the useful bioactive antimicrobial and insecticidal compounds [table 1.1] associated with Azadirachta indica such as the azadirachtins and related tetranortriterpenoids [50]. Recently, endophytic microbes have been on the verge of increased investigation due to their close interaction with the host [34]; it is assumed that the phytochemical constituents of plants are related, however, directly or indirectly, to endophytic microorganisms and their associations with host plants [20,35].
Table 1.1 Some Endophytic fungi obtained from different parts of neem tree. [54]
Genus (former name) of Endophytic fungi
Parts of neem tree
References
Trichoderma
Root, seed, leaf, bark, flower
[
51
,
53
]
Verticillium
Root
[
51
,
53
]
Humicola
Flower
[
51
,
53
]
Chloridium
Root
[
51
]
Nigrospora
Root, seed, leaf, bark
[
50
,
51
,
53
]
Scytalidium
,
Penicillium
Root
[
51
]
Aspergillus
Root, seed, leaf, bark, flower
[
52
]
Alternaria
,
Drechslera
Flower
[
50
,
51
]
Phoma
Leaf
[
53
]
Periconia
Bark
[
50
,
53
]
Stenella
Bark
[
50
]
Cercinella
Root
[
51
]
1.4 Plant Growth-Promoting Rhizobacteria (PGPR): Biological Management of Plant Pathogens
In plant pathology, “biocontrol” is often considered weapon to manage plant diseases. It is the use of antimicrobial compounds produced by microbial antagonists. Microorganisms that control the causative agents of plant diseases are collectively known as “biological control agents” (BCA) [36] with microorganisms, chemical mediators, and natural substances [37]. Endophytes are the microbial antagonists, mainly fungal and bacterial, that play an essential role in controlling disease. Both of them act differently to effect biological control, from the struggle at the niche level (colonization) during the making of antimicrobial compounds to bringing on the host resistance response [38–42], thus aiding in enhancing plant development along with health.
The constricted zone of soil particularly inclined by the root system is the rhizosphere [43]. This zone is loaded with nutrients due to the abundance of plant secretions, like amino acids and sugars, compared with most of the earth, providing a good source of energy and nutrients for bacteria [44]. Various microorganisms colonize the rhizosphere, and therefore, the bacteria settling in this environment are called rhizobacteria [45]. Plant-linked bacteria are often categorized within three groups, i.e. beneficial, harmful, and neutral groups, based on their effects on plant growth [43]. Beneficial free-living soil bacteria are usually characterized as PGPR [46]. Bacteria of various genera are identified as PGPR, of which the most important groups are Bacillus and Pseudomonas spp. [47]. PGPR affects plant growth directly or indirectly. The direct promotion of plant growth by PGPR involves providing the plant with a compound synthesized by the bacterium, for example, plant hormones, or promoting the uptake of certain nutrients from the environment [48]. The indirect progress of plant growth happens when PGPR prevents or reduces the harmful effects of one or more phytopathogenic organisms. This can be done by inducing resistance to pathogens or producing antagonistic substances [49].
1.5 Conclusion
The rhizosphere of many plants is known to be a potential source for selecting good microorganisms that may affect plant health. PGPR offer an excellent substitute for environmental-friendly biological control of plant-pathogen and amelioration of the cropping systems into which they can be most beneficially applied. The role of medicinal plants and their endophytic microbiota in producing plant antimicrobial compounds is concerned with plant health and remedial applications. The production of antimicrobial bioactive compounds by endophytes is currently receiving urgent concern due to the emergence of multidrug-resistant pathogens. Indeed, the study of medicinal plants especially neem and their endophyte interaction is a flourishing prospect to develop sustainable methods to restrain human and plant pathogens. Therefore, more work on endophytes of medicinal plants for their antioxidant activities can impose a strong effect on the search for novel bioactive compounds.
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2 Plant Microbiome A Key to Managing Plant Diseases
Dipal B. Minipara1, Khushboo Pachhigar2, and Himanshu R. Barot3
1Anand Agricultural University, Anand, Gujarat, India
2Veer Narmad South Gujarat University, Surat, Gujarat, India
3Sardarkrushinagar Dantiwada Agricultural University, Sardarkrushinagar, Banaskantha, Gujarat, India
2.1 Introduction
Microbes are fundamental for a balanced life on Earth, and understanding their function is crucial. Culture-based microbial techniques and next-generation sequencing have added benefits. Metagenomics studies have allowed studying the microbial genome and its function, which are not culturable but have an essential role in the ecosystem. Microbiome study enables the exploration of the genome of all microorganisms, including symbiont and pathogens. The microbial community varies with host health and environmental factors that shape the microbiome. The concept of association of microbiome with plant health and disease state received focus over the past decades. However, it is critical to identify prominent microbiota associated with biotic stress in variable environmental conditions on the field, as most studies were conducted under greenhouse conditions. Core microbiota, a host-associated persistence microbial community carrying functional genes, are critically important for plant health. Therefore, identifying host-associated core microbiota and their response toward biotic stress is essential to understanding disease management and improving productivity.
Plant microbiome can be categorized at the interface where plant and microbes can communicate, which include plant–microbe interaction at rhizosphere, phyllosphere, and endosphere (Figure 2.1) [1]. Plant microbiome alters as plant species or cultivar changes; it also depends on plant developmental stages, disease conditions, and geographical locations [2].
Figure 2.1 Plant–microbe interaction in rhizosphere, endosphere, and phyllosphere and biocontrol mechanism acquired by beneficial microorganism.
2.2 Plant–Microbe Interaction in the Rhizosphere
“Rhizosphere” is derived from “rhiza” or root and “sphere” or the field of influence in ancient Greek. The rhizosphere is the soil environment surrounding plant roots, and it is a crucial underground region for plant–microbe interaction. The rhizosphere comprises 10-fold microbes more than that in the surrounding soil, and the rhizosphere microbiome may consist of fungi, bacteria, archaea, actinomycetes, and viruses [3]. Roots utilize photosynthates to produce exudates used by rhizosphere microbiota to exchange nutrients and water [4]. Root exudates also function as signaling molecules, attractants, stimulants, or repellents to rhizosphere microbes. Bioactive compounds of exudates vary with plant species that define microbial community [5]. Root secretion influences soil pH, soil structure, oxygen obtainability, and influences plant–microbe interaction. A study on secondary metabolite benzoxazinoids showed it’s defensive role in cereals, alters rhizosphere fungal and bacterial microbiota, and influences plant growth [6]. Bacteria produce protein and polysaccharides, which allow them to attach with roots as biofilm aggregates [7]. Symbiotic association evolved millions of years ago, and most living plants form a symbiotic relationship with arbuscular mycorrhizal fungi (AMF) [8]. Upon sensation of strigolactone from plant roots, AMF initiates hyphal branching to colonize roots and releases lipochito oligosaccharides, promoting plant growth by increasing root surface area [1]. Almost all soilborne fungi are necrotrophic, and they do not require the living cell to acquire nutrients.
2.2.1 Microbial Population in the Rhizosphere
The most enriched microbiota in the rhizosphere are bacteria, which influence the plant rhizosphere significantly. Next-generation sequencing (NGS) has provided insight into microbial diversity and composition. Internal transcribed spacer (ITS), 16s rRNA sequencing of fungi and bacteria, respectively [9,10] and shotgun metagenomic sequencing [11] have unravelled root-associated microbiome. The relative abundance of taxonomic marker genes has provided more information on phyla Proteobacteria, Bacteroidetes, and Actinobacteria, which were augmented in the rhizosphere [12]. Predominant genera in the rhizosphere are Pseudomonas, Bacillus, Rhizobia, Azotobacter, Mycobacterium, Flavobacter, Cellulomonas, Agrobacterium, and Micrococcus [13]. So far, various gram-positive and aerobic spore-forming bacteria are inferior because of the low availability of oxygen [14]. For fungal communities, phyla Ascomycota, Basidiomycota followed by Zygomycota, Glomeromycota dominate in the rhizosphere of Arabidopsis thaliana. Plant-friendly microorganisms comprise nitrogen-fixing bacteria viz., Azotobacter, cyanobacteria, clostridium, plant growth-promoting rhizobacteria, fungi, and endo ectomycorrhizal fungi [13].
2.2.2 Biocontrol Mechanism in the Rhizosphere
To grow a healthy plant, it is necessary to examine soil niches surrounding the root area to detect pathogens and enhance advantageous microorganisms. The rhizosphere is the battlefield where phytopathogens acquire parasitic relations with the plant. Biocontrol agents have a mechanism that includes rivalry for space and nutrients, antagonistic activity, and hyperparasitism. The level of decomposition of organic matter influences microbial communities and biocontrol activities [14]. The introduction of beneficial microorganisms can also change microbial community structure in the rhizosphere.
2.2.2.1 Competition
Some strains of Pseudomonas fluorescens act as biocontrol by competing for nutrients and root surface colonization aggressively. Pseudomonas sp. RU47 colonizes the rhizosphere with sufficient density and compete with Rhizoctonia solani and minimizes the severity of black potato scurf and lettuce bottom rot in diluvial sand, alluvial loam, and loess loam soils [15]. The competition can also be for micro-nutrients, specifically iron, associated with high-affinity chelators called siderophores secreted by microorganisms. An experiment with transgenic tobacco overexpressing ferritin showed that fluorescent Pseudomonads could survive in a less iron-containing environment and have an antagonistic activity to the pathogen [16].
2.2.2.2 Parasitism
Parasitism as a biocontrol mechanism is mainly associated with fungal biocontrol agents. Biocontrol agents parasitize the pathogen by looping around fungal hyphae and derive nutrition from the pathogen. Some beneficial microorganism secretes hydrolytic enzymes such as chitinase and cellulase [17]. Trichoderma and Gliocladium parasitize on Rhizoctonia, Sclerotinia, Verticillium, and Gaeumannomyces and cause cell damage to the pathogen [18]. Firmicute bacteria Pasteuria penetrans also control Meloidogyne nematode, and its activity is stimulated by two beneficial rhizospheric bacteria [19].
2.2.2.3 Antagonism
Antagonism is mediated by antibiosis in which antimicrobial compounds, lytic enzymes, or effector molecules are produced by biocontrol agents toxic to pathogens. Antibiotics compounds, viz., phenazines, pyrrolnitrin, lipopeptides, hydrogen cyanide, and 2,4-diacetylphloroglucinol, produced by specific biocontrol agents are well characterized [20]. Certain Bacillus species make antifungal lipopeptide iturin A [21], antimicrobial and antiviral cyclic lipodecapeptide fengycin [22], and various biosurfactants [23]. Bacillus subtilis RB14 produces antibiotic iturin, and surfactant was found to control Rhizoctonia solani, which causes damping-off disease of tomato seedlings [24]. Several strains can also induce plant defense-related genes by biocontrol metabolites or lipopolysaccharides and flagella and can control phytopathogen [25]. Streptomyces pactum, a biocontrol agent, increases the indigenous P. koreensis GS population in ginseng rhizoplane by expressing chemotaxis and flagellar biosynthesis-related genes and antagonizes soilborne pathogens [26].
Extracellular lytic enzymes such as cellulase, protease, and chitinase produced by certain antagonistic microorganisms are common. Other lytic enzymes target phytotoxins like fusaric acid produced by Fusarium oxysporum [23]. Another mechanism acquired by Pseudomonas is the type III secretion system that targets oomycetes [27]. According to Vacheron et al. [28] plant roots preferentially shaped Pseudomonads had one to five plant-beneficial properties [28].
2.2.2.4 Induced Systemic Resistance (ISR)
In the theory of plant immune system, the initial defense system activated by plants is pathogen-associated molecular patterns (PAMP), PAMP-triggered immunity (PTI), in which pattern recognition receptors (PRRs) recognize bacterial flagella or fungal chitin. The subsequent defense after initial defense is effector-triggered immunity (ETI), in which the nucleotide binding leucine-rich repeat (NB-LRR) receptor recognizes effector molecules of a pathogen. These two lines of defense often trigger induced resistance in unexposed parts of the plant by pathogens, and the mechanism is termed “systemic acquired resistance” (SAR) [29].
Plant-microorganism are evolved to gather according to different taxa and soil types but nowadays focus has been on functional microbiota, which provides fitness to halobiont. Induced systematic resistance (ISR) is a well-studied mechanism and first described for Pseudomonas in which certain beneficial bacteria, viz., Pseudomonas, Bacillus, and Serratia strains, and nonpathogenic fungi, viz., Trichoderma, F. oxysporum, and Piriformospora isolated strains, and the symbiotic mycorrhiza species in the rhizosphere prime immune system in the unexposed parts of plants to fight against infectious agents [30]. Seed-grown maize plant exposed to Trichoderma harzianum strain T22 had minimized symptoms of anthracnose, which was explained by root colonization by Trichoderma strain-ISR [31].
2.2.3 Plant Disease Management
Every natural soil can suppress pathogens to a certain level; this phenomenon is called general disease suppression, and it depends on the total microbial biomass. Specific suppression comes into the picture when an individual or group of microorganisms causes soil to suppress disease [32]. Some soil can retain its condition by suppressing activity for a long time, while some could develop after several years of monoculture. Moreover, the establishment of disease suppression in soil was described for several diseases. In an experiment conducted on a tomato plant, a susceptible cultivar was treated with rhizosphere microbiota of resistant cultivar, which suppressed disease symptoms.
Further analysis showed that flavobacterium TRM1 could antagonize R. solanacearum and inhibited the progress of bacterial wilt in tomatoes [33]. A root disease termed as “take-all” of Triticum aestivum caused by Gaeumannomyces graminis var. tritici was suppressed through several years of monoculture in soil by disease-suppressive microorganisms. This phenomenon is called “take-all decline,” which is associated with the antagonistic activity of fluorescent Pseudomonas spp. by the antifungal compound 2,4-diacetylphloroglucinol (DAPG) [32]. Soil metagenomics study of potato plants associated with potato common scab disease revealed a positive correlation between pathogenic Streptomyces and scab severity but negative correlation with Geobacillus, Curtobacterium unclassified Geodermatophilaceae [34]. Some commercial products such as “Mycostop,” containing Streptomyces griseoviridis strain, which can suppress root rot and wilt diseases by occupying the rhizosphere are also available [35], “BlightBan A506” containing P. Fluorescens can control fire blight frost damage in fruits caused by Erwinia amylovora and “Epic Kodiak” to target Rhizoctonia solani by Bacillus subtilis [36]. A microbial consortium containing four isolates, Serratia marcescens isolate 59, Pseudomonas fluorescens 57, Rahnella aquatilis 36, and Bacillus amyloliquefaciens 63 was able to increase soil disease suppression ability against Fusarium spp. in chickpea rhizosphere, which causes wilt and root rot [37].
Various management practices in combination or isolation are being used to suppress diseases, including intercropping, organic amendments, crop rotation, and tillage management. Several years of monoculture of one variety in the same field causes replanting disease. Intercropping changes root exudates that alter the rhizospheric microbiome. An experiment with intraspecific intercropping on Radix pseudostellariae plant increased beneficial Nitrosomonadales, Nitrospirales, Pseudomonadales, and decreased pathogenic Aspergillus and Talaromyces [38]. Atractylodes lancea, a medicinal plant, suppressed Fusarium oxysporum mediated root rot disease in peanut while used as inter-crop [39] and while intercropping with aerobic rice, conquered Fusarium oxysporum mediated watermelon wilt [40]. Intercropping between maize and soybean can cause phenolic acid-mediated inhibition of Phytophthora sojae, responsible for Phytophthora blight of soybean [41]. Reduced conventional tillage practices increase organic matter, which prevents C. sativus from germinating and changes nutrient availability, which influences pathogen survival. Crop rotation changes root exudates and compounds released from crop residue decomposition, which affects the rhizosphere microbial community. Fungicide compounds released from canola residues breakdown procedure can diminish the extremity of common root rot in cereals [42]. Animal manures and organic composts also influence plant pathogens. Providing beneficial microbiota from compost to conductive soil remains the critical strategy for increasing suppression against soilborne pathogens. Five compost–peat mixtures were used to control Pythium ultimum, Rhizoctonia solani, and Sclerotinia minor – Lepidium sativum to manage dumping off diseases [43]. Combining effort with selective biological control agents, organic amendments, and suppressive disease compost can achieve natural disease control against soilborne pathogens. A positive balance is obligatory between phytopathogens and beneficial microorganisms to obtain optimal plant growth and health.
2.3 Plant–Microbe Interaction in the Endosphere
Plants develop an association with their surrounding ecosystem to thrive in their natural environment. The most common type of association is the plant–microbe association, where the indigenous microbes help plant survival in biotic and abiotic stress. The plant endosphere consists of complex microbial communities whose function ranges from mutualism to pathogenicity. These microorganisms colonize at least a part of their life inside the plant interior and are termed “endophytes” [44]. While living near plant hosts, endophytic bacteria exchange for a consistent nutrient supply exerts a beneficial effect [45]. For establishing an asymptomatic association with the host plant, the endophyte must avoid triggering the plant’s defense system, which is achieved by maintaining low cell densities. Colonization of endophytes involves competition in the plant rhizosphere for space and nutrients, which is assisted by the production of polysaccharides and motility. Once they are established in the rhizosphere and rhizoplane, they make their way in by producing adhesion molecules and ultimately gain entry into the root by an active (low levels of cell-wall degrading enzymes) or passive (through cracks in roots) process [46]. After entering the roots, they migrate to above-ground plant tissue through the plant transpiration stream. Movement through intercellular spaces requires cell-wall degrading enzymes. However, migration through the xylem element occurs through perforated plates [47].
2.3.1 Microbial Population in the Endosphere
Numerous studies have already characterized endophytes from a plethora of plant hosts and different plant compartments above and below the ground. Endophytes are present ubiquitously in most of the plant, either actively or latently colonizing the plant tissue. Generally, the plant endosphere is enriched with members of Proteobacteria [48] and to a lesser amount with Actinobacteria, Firmicutes, and Bacteroidetes [49]. Other classes that are less commonly found include Acidobacteria, Chloroflexi, Verrucomicrobia, and Planctomycetes [48]. Endophytic genera of bacteria commonly found to belong to Microbacterium, Burkholderia, Micrococcus, Bacillus, Pseudomonas, and Pantoea, where Bacillus and Pseudomonas spp. dominate [50]. Fungal endophytes commonly found belong to Ascomycota, and a few belong to Basidiomycota, Zygomycota, and Oomycota. Common genera that are reported are Trichoderma, Fusarium, and Aureobasidium [51]. However, the dominance of the phyla varies depending on the plant host species.
2.3.2 Biocontrol Mechanism in the Endosphere
Endophytes produce various substances that directly help enhance the growth of the host plant and discourage phytopathogens and plant pests’ survival. These metabolites could be antibiotics, siderophores, hydrolytic enzymes, volatile organic compounds (VOCs), and toxins [52]. Antimicrobial activity has been reported for endophytic Pseudomonas putida (PpBP25) in black pepper with aggressive action against plant pathogen Phytophthora capsici and Radopholus similis [52]. The most common genera with antagonistic activity against phytopathogens include Bacillus, Enterobacter, Actinobacteria, Pseudomonas, Serratia, and Paenibacillus [53,54].
2.3.2.1 Competition
There is a race between endophytes and phytopathogens to prevent host tissue colonization [55]. They colonize either systemically or locally and act by inhabiting locations available for the pathogens and lurking for nutrients that are available for the proper functioning of the plant [56]. There are not many reports on how nutrient management/uptake by beneficial microbiomes is related. Still, some reports confirm the crosstalk between Fe-deficient/nutrient starvation and resistance elicited by microorganisms. For instance, Herbaspirillum seropedicae Z67, a nitrogen-fixing endophyte, is dependent on iron for its vital cellular processes and produces serobactins (siderophores) to fulfill its iron requirement [57]. Some studies have provided valuable insights into the iron competition between endophyte Streptomyces sporocinereus OsiSh-2 and a pathogen of rice Magnaporthe oryzae [58]. The study indicated that M. oryzae is dependent more on iron supplementation than OsiSh-2 for growth and follows different strategies to acquire iron. Many genes involved in siderophore synthesis and iron uptake were present in endophytes than in pathogens, and OsiSh-2 has an added advantage for capturing iron over M. oryzae [58].
2.3.2.2 Parasitism
Parasitism is another mechanism that the endophytes use to defend their plant host. Generally, it is observed when there is an interaction between bacteria and fungi or fungi and fungi. Endophytes fight the pathogens directly and produce lyase that helps in destroying the pathogen’s cell wall. For instance, out of all the endophytes isolated from poplar, the Burkholderia cepacia complex could efficiently control Cytospora chrysosperma, Phomopsis macrospora, and Fusicoccum aesculi causative agent of poplar canker. The interaction of endophytic cotton bacteria Bacillus halotolerans (Y6) hinders spore germination in vitro along with mycelial growth of Verticillium dahlia pathogen. Mousa et al. (2016) observed that the endophyte swarmed toward the root-invading pathogen and completely covered F. graminearum hyphae by forming a biofilm that acts as a physical barrier that obstructs the passage and entraps the pathogen and is eliminated then. Thus, the bacteria construct a microhabitat of their own to invade the pathogen. Furthermore, the isolated strain can increase root hair proliferation and create a barrier to block and destroy the invaders [59].
2.3.2.3 Antagonism
Endophytes and phytopathogens live in a similar niche; they release a range of bioactive compounds to suppress or impede pathogens’ average growth and activity. Production of antibiotics, metabolites with antifungal properties, and production of volatile compounds such as hydrogen cyanide (HCN) by endophytes are directed mainly toward inhibiting plant pathogens [60]. Several compounds with antimicrobial properties have been purified and identified from endophytes, including peptides, terpenoids, steroids, alkaloids, phenols, quinones, flavonoids, and polyketides [61]. When different microbial species are near each other, endophytes or the host plants obstruct the growth of invading microbes, which is evident from the secretion of bioactive metabolites [62]. Phomopsis cassia, an endophyte from Cassia spectabilis, synthesized compounds similar to cadinene sesquiterpenes and 3,11,12-trihydroxycadalene, which showed activity against fungi like Cladosporium cladsporioides and C. sphaerospermum [63]. Similarly, the antagonistic potential of five endophytic Bacillus sp. isolated from Solanum sp. was screened against Fusarium oxysporum.
It was reported that the endophyte was capable of limiting pathogen sporulation and mycelial growth by the production of extracellular metabolites such as chitinases and lipopeptide antibiotics [64]. Effective inhibition of phytopathogenic nematodes [65,66], oomycetes, and fungi [67–71] by bacterial species have been reported through the production of VOCs. Thus, VOCs have been shown to have enormous potential in biocontrol.
2.3.2.4 Induced Systemic Resistance
The ISR and SAR primes plant defense against pathogenic microbes and herbivore insects by protecting plants from future attacks. Plants exhibit resistance by several molecular defense mechanisms such as ethylene/jasmonic/salicylic acid (ET/JA/SA) signaling pathway, callose deposition, regulation of polyamines uptake, accumulation of phytoalexins, producing reactive oxygen species, and gene expression that codes for pathogenesis-related (PR) proteins [46,69]. Defense-related genes were expressed in Arabidopsis, which simultaneously activated both defense pathways triggered by Bacillus cereus AR156 [70]. This increased biomass of plants and a simultaneous reduction in pathogen density and disease severity was observed. Moreover, an up-regulation of both of the defense pathways in Arabidopsis thaliana was observed by Conn et al. [71]. Inoculation of Actinobacteria protected against infection from both fungus Fusarium oxysporum and bacteria Erwinia carotovora. However, the defense pathways primed were different for both types of pathogens. The resistance to F. oxysporum involved the SA pathway, while the jasmonic acid pathway provided resistance to E. carotovora. Thus, the bacteria used two different ways, which helped in conferring resistance to two different pathogens [71].
2.3.3 Plant Disease Management
Disease management involves strategies and methods for manipulating the antagonistic populations to hinder pathogen survival and plant growth promotion. Endophytes are environmentally benign agents and thus are ideal candidates for efficiently promoting plant growth and act as bioactive candidates against parasitic nematodes. Bogner et al. (2016) showed that Fusarium solani and F. oxysporum
