Microbial Symbionts and Plant Health: Trends and Applications for Changing Climate

Preface
Contents
Editors and Contributors
Chapter 1: Global Climate Perturbations: Sustainable Microbial Mitigation Strategies
1.1 Introduction
1.2 Global Climate Change and Consequences
1.3 Current Global Climate Scenario and Status
1.4 Spatial and Temporal Changes in the Soil Microflora as Affected by Global Climate Change
1.4.1 Elevated CO2
1.4.2 Drought
1.4.3 Permafrost Thaw and Soil Microbiome
1.4.4 Effect of Temperature on Soil Microbiome
1.5 Effect of Climate Change on Plant-Microbe Interaction
1.5.1 Influence on Inter-Kingdom Interactions or Trophic-Level Interactions
1.6 Microbiome Dynamics
1.7 Metabolic Modulation in the Microbiome
1.7.1 Increased Temperatures
1.7.1.1 Incidence of Plant Diseases
1.7.1.2 Pathogen Overwintering
1.8 Microbial Strategies to Mitigate the Global Climate Change
1.9 Conclusions
References
Chapter 2: Soil Microflora and Their Interaction with Plants Under Changing Climatic Scenarios
2.1 Introduction
2.2 Soil Microflora and Their Distribution
2.2.1 Groups of Soil Microflora, Their Characteristics, and Distribution
2.2.2 Factors Affecting the Soil Microflora Distribution
2.2.2.1 Soil Moisture
2.2.2.2 Soil Reaction or Soil pH
2.2.2.3 Soil Organic Matter
2.2.2.4 Types of Vegetation
2.2.2.5 Spatial and Seasonal Variation
2.3 Impact of Climate Change on Plant Microbial Interaction
2.3.1 Elevated CO2 Impacts on Soil Microbes
2.3.2 Influence of Soil Moisture Variation on Soil Microbes
2.3.3 Influence of Temperature Variation
2.4 Climate Change Alters Plant and Microbial Distribution
2.4.1 Climate Change Vis-a-Vis Plant Distribution
2.4.2 Climate Change Vis-à-Vis Microbial Distribution
2.5 Micro-Microbe Interaction
2.5.1 Symbiotic Interaction
2.5.2 Protocooperation Interaction
2.5.3 Commensalism Interaction
2.5.4 Amensalism Interaction
2.5.5 Competition, Parasitism, and Predation
2.6 Conclusion
References
Chapter 3: Beneficial Microbial Consortia and Their Role in Sustainable Agriculture Under Climate Change Conditions
3.1 Introduction
3.2 Players in Rhizosphere Function: The Rhizosphere Microbiome
3.3 The Microbial Consortia/Microbiome
3.4 Microbial Consortia and Their Diverse Roles
3.5 Microbial Consortia and Rhizospheric Interactions
3.6 Microbial Consortia-Interaction-Establishment and Responses
3.7 Microbial Consortia and Overcoming the Host Immune Barrier
3.8 Microbial Consortia and Abiotic Rhizospheric Factors
3.9 Microbial Consortia and Diverse Mechanisms for Tolerance Against Climate Change
3.10 Conclusion and Future Perspectives
References
Chapter 4: Unfolding the Role of Beneficial Microbes and Microbial Techniques on Improvement of Sustainable Agriculture Under ...
4.1 Introduction
4.2 Plant Growth-Promoting Rhizobacteria
4.2.1 Nitrogen Fixation
4.2.2 Phosphorus Solubilizing Bacteria
4.2.3 Plant Growth-Promoting Mycorrhizal Bacteria
4.3 Effect of Climate Change on Agriculture
4.3.1 Drought
4.3.2 Heat Stress
4.3.3 Cold Stress
4.3.4 Soil Properties
4.3.4.1 Soil Salinity and Acidity Stress
4.3.4.2 Over Usage of Chemical Fertilizers Causes Loss of Soil Fertility Resulting in Crop Yield Loss
4.4 Plant Growth-Promoting Microorganisms (PGPMs)
4.4.1 Plant Growth-Promoting Rhizobacteria (PGPR)
4.4.2 Plant Growth-Promoting Fungus (PGPF)
4.4.3 Plant Growth-Promoting Endophytes (PGPE)
4.5 Formulation of Plant Growth-Promoting Microorganisms (PGPMs)
4.5.1 Ingredients Used in the Formulation
4.5.2 Types of Formulation
4.5.2.1 Liquid-Based Formulation
4.5.2.2 Talc-Based Formulation
4.5.2.3 Sawdust-Based Formulation
4.5.2.4 Fly Ash-Based Formulation
4.5.2.5 Encapsulation-Based Formulation
4.5.2.6 Peat-Based Formulation
4.6 Survival of PGPMs in Formulation
4.7 Interaction of Beneficial Microbes with Crops
4.7.1 Endophytic Microbiomes
4.7.1.1 Applications
4.7.1.2 Mechanism
4.7.2 Phyllospheric Microbiome
4.7.2.1 Mechanism
4.7.3 Rhizospheric Microbiome
4.7.3.1 Mechanism
4.8 Microbial Tools
4.9 Future Perspectives and Conclusion
References
Chapter 5: Microbes and Their Role in Alleviation of Abiotic and Biotic Stress Tolerance in Crop Plants
5.1 Introduction
5.2 Types of Stress
5.2.1 Biotic Stress and Crop Plants
5.2.2 Abiotic Stress and Crop Plants
5.2.2.1 Cold
5.2.2.2 Salt/Salinity
5.2.2.3 Drought
5.2.2.4 Heat or Temperature
5.2.2.5 Toxin
5.3 Role of Microbes in Stress Tolerance in Crop Plants
5.4 Soil Microorganisms and their Role in Abiotic Stress Management
5.5 Microbes as Stress-Alleviating Agents under Various Stress Situation
5.5.1 Drought Stress
5.5.2 High/Low Temperature Stress
5.5.3 Soil/Salinity
5.5.4 Heavy Metals
5.5.5 Nutrient Deficiency-Associated Stresses
5.6 Regulatory Mechanism in Plants in Response to Stress
5.6.1 Plant Hormones and Transcription Factors
5.6.2 Transcription Factors
5.6.3 Heat Shock Proteins
5.6.4 Receptor Proteins
5.6.5 Epigenetic Changes
5.7 Microbial Application in Agricultural Sustainability
5.7.1 Microbes and Drought Stress Tolerance
5.7.2 Microbes and Salinity Stress Tolerance
5.7.3 Microbes and Heavy Metal Stress Tolerance
5.7.4 Microbes and Temperature Stress Tolerance
5.8 Microbes and Biotic Stress
5.9 Conclusion
References
Chapter 6: Plant-Microbe Interaction and Their Role in Mitigation of Heat Stress
6.1 Introduction
6.2 Plant and Soil Microbiome Interaction
6.3 Effect of Elevated Temperature on Plant-Microbe Interactions
6.4 Microbes as a Stress Ameliorating Agent under Temperature Stress
6.4.1 PGPR
6.4.2 Arbuscular Mycorrhizal Fungi (AMF)
6.4.3 Endophytes
6.5 Genetic Perspectives of Plant-Microbe Interaction
6.6 Conclusion and Future Aspects
References
Chapter 7: Role of Soil Microbes against Abiotic Stresses Induced Oxidative Stresses in Plants
7.1 Introduction
7.2 Adverse Effects of Major Abiotic Stress on Plants
7.2.1 Drought
7.2.2 High Temperature
7.2.3 Low Temperature
7.2.4 Salt
7.2.5 Heavy Metals
7.3 Beneficial Microorganisms Save Plants from Abiotic Stress-Induced Oxidative Stress
7.3.1 Plant Growth-Promoting Bacteria
7.3.2 Mycorrhizal Fungi
7.3.3 Cyanobacteria
7.3.4 Actinomycetes
7.4 Mechanisms of Stress Alleviation by Microbes
7.4.1 Hormones
7.4.2 Protective Metabolites
7.4.3 Ion Homeostasis
7.4.4 Nutrient Uptake Enhancement
7.4.5 Antioxidant Mechanisms
7.5 Conclusion
References
Chapter 8: An Overview of the Multifaceted Role of Plant Growth-Promoting Microorganisms and Endophytes in Sustainable Agricul...
8.1 Introduction
8.2 PGPM Vs. Endophytes
8.3 Colonization and Rhizospheric Competence
8.3.1 Mechanism of and Factors Controlling PGPR Colonization
8.3.2 Mechanism of and Factors Controlling Endophytes Colonization
8.4 Role of PGPR and Endophytes toward Plant Physiology
8.4.1 Nutrient Assimilation
8.4.2 Phytohormone Production
8.4.3 Abiotic Stress Tolerance
8.4.4 Biotic Stress Tolerance and Biocontrol
8.4.5 Impact on Plant Transcriptome
8.4.6 PGPR and Endophytes-Mediated Phytoremediation
8.4.7 Biotechnological and Industrial Applications of PGPR and Endophytes
8.5 Strategies and Applications of PGPR and Endophytes
8.5.1 Strategies for Improving Rhizosphere Colonization
8.5.2 Applications
8.5.3 Applications of PGPR and Endophytes in Sustainable Agriculture under Climate Change
8.5.4 Formulation and Commercialization of the Products
8.5.5 Challenges
8.6 Conclusion
References
Chapter 9: Plant Growth-Promoting Rhizobacteria (PGPR): An Indispensable Tool for Climate-Resilient Crop Production
9.1 Introduction
9.2 Rhizosphere and Plant Growth-Promoting Rhizobacteria (PGPR)
9.3 PGPR-A Sustainable Approach against Climate Change
9.4 PGPR-Mediated Plant Tolerance against Abiotic Stresses
9.5 Broad Mechanisms of PGPR to Overcome Stress
9.5.1 PGPR Undertakes a Couple of Strategic Mechanisms to Overcome Stress
9.5.1.1 Production of Biologically Active Metabolites
9.5.1.2 Production of Special Enzymes
9.5.1.3 Production of Volatile Organic Compounds
9.5.1.4 Production of Biofilms and Exopolysaccharides
9.5.1.5 Production of Bacterial Secondary Metabolites
9.5.1.6 Supply of Essential Plant Nutrients
9.5.1.7 Changing the Redox and Acidity/Basicity Status of the System
9.5.2 Abiotic Stresses and their Alleviation
9.5.2.1 Drought Stress
9.5.2.2 Salinity Stress
9.5.2.3 Nutrient Stress
9.5.2.4 Acidity Stress
9.5.3 Biotic Stress Management by PGPR
9.5.3.1 Production of Protective Enzymes
9.5.3.2 Development of Induced Systemic Resistance
9.5.3.3 Production of Siderophores
9.5.3.4 Production of Antibiotics and Volatile Organic Compounds
9.6 Challenges and Prospects
9.7 Conclusion
References
Chapter 10: Plant-Endophyte Interactions: A Driving Phenomenon for Boosting Plant Health under Climate Change Conditions
10.1 Introduction
10.2 Host-Endophyte Interactions and Molecular Signaling: Molecular and Chemical Signals for Successful Colonization
10.3 Endophytes and their Beneficial Plant Growth-Promoting Attributes
10.3.1 Direct Mechanisms of Plant Growth Promotion
10.3.1.1 Biological Fixation of the Atmospheric Nitrogen
10.3.1.2 Phosphate Solubilization
10.3.1.3 Production of Phytohormones
10.3.1.4 ACC Deaminase Activity
10.3.1.5 Production of Siderophores
10.3.2 Indirect Mechanisms of Plant Growth Promotion
10.4 Endophytes Modulate Host Defense Mechanisms under Biotic Stress Conditions
10.4.1 Role of Quorum Sensing in Modulation of Host Defense Mechanisms
10.4.2 Host Defense-Related Transcriptional Alterations Brought on by Interactions Between Plants and Microbes in Plant Cells
10.5 Endophytes as a Tool to Combat Climate Change
10.6 Conclusion
References
Chapter 11: Deciphering the Role of Growth-Promoting Bacterial Endophytes in Harmonizing Plant Health
11.1 Introduction
11.2 Culture-Dependent Techniques
11.3 Culture-Independent Techniques
11.4 Plant Growth-Promoting Traits (PGPs)
11.4.1 Phytohormone Regulation
11.4.2 Antibiotic Synthesis
11.4.3 Siderophores
11.4.4 Phosphate Solubilization
11.4.5 Induced Systemic Resistance
11.5 Functional Role in Biocontrol
11.5.1 Endophytic Bacteria in Disease Management
11.5.2 Endophytes in Insect Pest Management
11.6 Mechanism of Biocontrol
11.6.1 Growth Promotion Activity
11.6.2 Induced Systemic Resistance (ISR)
11.6.3 Peroxidase (PO)
11.6.4 Polyphenol Oxidase (PPO)
11.6.5 Phenylalanine Ammonia Lyase (PAL)
11.6.6 Scavengers of Active Oxygen Species (AOS)
11.6.7 Pathogenesis-Related Proteins (PRs)
11.6.8 Interactions between Signaling Molecules Involved in Plant Defense
11.7 Role of Omics in Biocontrol
11.7.1 Metagenomics
11.7.2 Plant-Endophyte Interactions in Genomic and Post-Genomic Era
11.7.3 Proteomics and Metaproteomics Study
11.7.4 Volatilomics in Plant Growth Regulation
11.7.5 Practical Applications
11.8 Conclusion and Future Thrusts
References
Chapter 12: Endophytic Microbes and Their Role in Plant Health
12.1 Introduction
12.2 History
12.3 Methods to Detect and Identify Endophytes in Plant Tissues
12.4 Diversity of Endophytes
12.5 Nature of an Endophyte
12.6 Differences Between an Endophyte and Pathogen Colonization of a Plant
12.7 Endophyte Biodiversity
12.8 Fungal Endophytes
12.9 Bacterial Endophytes
12.10 Endophytes and Plant Growth Promotion
12.10.1 Underlying Mechanisms in Plant Growth Promotion
12.10.1.1 Phytostimulation
12.10.1.2 Biofertilization
12.10.1.3 Nitrogen Fixation
12.10.1.4 Phosphorus Solubilization
12.10.1.5 Siderophore Production
12.10.2 Defense Mechanism
12.10.2.1 Direct Mechanism
Antibiosis
Hyper-parasitism
Competition
12.10.2.2 Indirect Mechanism
12.11 Conclusion
References
Chapter 13: Multitrophic Reciprocity of AMF with Plants and Other Soil Microbes in Relation to Biotic Stress
13.1 Paleobiology of Glomerales
13.2 Metabolic Pathways Involved in Symbiotic Association with Plants
13.2.1 Pre-symbiosis
13.2.2 Symbiosis
13.2.3 Post-symbiosis
13.3 Interaction Between Mycorrhizae with Other Beneficial Microbes
13.3.1 AMF with Nitrogen-Fixing Rhizobium
13.3.2 AMF with Mycorrhiza Helper Bacteria (MHB)
13.4 Increased Fitness of Plants Colonized with AMF Against Biotic Stress
13.4.1 Effect on Plant Pathogens
13.4.1.1 Altered Nutrient Uptake
13.4.1.2 Competition for Niche and Photosynthates
13.4.1.3 Alteration of Root Morphology and Physiology
13.4.1.4 Alteration of Plant Defense
13.4.1.5 Alteration of Rhizosphere
13.4.2 Effects of AMF Against Herbivorous Insects
13.4.2.1 AMF-Induced Plant Resistance Against Herbivores
13.4.2.2 AMF-Induced Plant Tolerance Against Herbivores
13.4.3 Effect of AMF on Plant Parasitic Nematodes
13.4.4 Effect of AMF on Parasitic Plants
13.5 Conclusion
References
Chapter 14: Effect of Temperature and Defense Response on the Severity of Dry Root Rot Disease in Chickpea Caused by Macrophom...
14.1 Introduction
14.2 Historical Backgrounds
14.2.1 Host-Pathogen Interaction
14.2.1.1 Systemic Acquired Resistance
14.2.1.2 Salicylic Acid
14.2.2 Elicitors and Their Functions
14.2.3 Mechanism to Defense Responses
14.2.4 Hypersensitive Responses
14.2.5 Phytoalexin
14.2.6 Phenylalanine Ammonia Lyase
14.2.7 Oxidative Burst
14.2.8 Peroxidase
14.2.9 Polyphenols
14.2.10 Toxins of M. phaseolina
14.2.11 Pathogenic-Related Protein
14.2.12 Chitinase and Function in the Plant
14.3 Conclusion
References
Chapter 15: Emerging Roles of Plant Growth Promoting Rhizobacteria in Salt Stress Alleviation: Applications in Sustainable Agr...
15.1 Introduction
15.2 Halotolerant PGPR
15.3 Plant Growth Promoting Traits
15.4 Halotolerant PGPR-Mediated Salinity Stress Tolerance
15.5 Effects of Inoculation of Halotolerant PGPR on Plants Under Salinity Stress
15.6 Interaction of Halotolerant PGPR with the Surrounding Microbial Community
15.7 Gene Expression Profiles in Plants Inoculated with Halotolerant PGPR
15.8 Methods for PGPR Inoculation
15.9 Increasing the Efficiency of Halotolerant PGPR
15.10 Conclusions and Future Prospects
References
Chapter 16: Studies on Orchidoid Mycorrhizae and Mycobionts, Associated with Orchid Plants as Plant Growth Promoters and Stimu...
16.1 Introduction
16.2 Historical Background of Orchids
16.2.1 Pre-linnaean
16.2.2 Linnaean and Post-linnaean
16.3 Morphology of Orchids
16.4 Mycorrhiza: Mycorrhiza and Its Types
16.5 Protocorms
16.6 Orchid Fungi
16.6.1 Phenology
16.6.2 Entry and Colonization of Fungi in Orchids
16.7 Role of Mycorrhiza
16.7.1 Nutrient Transfer by Orchid Mycorrhizal Fungi (OMF)
16.7.2 Carbon Transfer
16.7.3 Nitrogen Transfer
16.7.4 Phosphorous Transfer
16.7.5 Plant Growth Stimulation by OMF
16.7.6 Phytohormone Production by OMF
16.7.7 Role of OMF in Disease Resistance
16.8 Micro Seeds and Strategies Adopted for Germination
16.9 Role of Mycorrhiza Against Plant Stress
16.10 Possibility of Mycorrhizal Fungal Diversity in Orchids and Role in Seed Germination
16.11 Conclusion
References
Chapter 17: Current Status of Mycorrhizal Biofertilizer in Crop Improvement and Its Future Prospects
17.1 Introduction
17.2 Current Agroecosystem Perspective
17.2.1 Heavy Metal Contamination
17.2.2 Pollution by Fertilizer
17.2.3 Nutrient Leaching and Availability
17.2.4 Drought Stress
17.2.5 Soil Salinity Stress
17.2.6 Oxidative Stress
17.2.7 Air Pollution
17.2.8 Agricultural Practices
17.2.9 Nanoparticle Pollution
17.2.10 Pollution by Radioactive Material
17.3 Current Perspective of Mycorrhizal Research
17.4 Mitigation of Challenged Agroecosystems with AM Fungi
17.4.1 Nutrient Uptake
17.4.2 Water Uptake
17.4.3 Abiotic Stress Tolerance
17.4.4 Modulation of Plant Physiology
17.4.5 Nutrient Recycling and Leaching
17.4.6 Soil Health and Plant-Soil Feedback (PSF)
17.4.7 Agricultural Costs and Pollution
17.4.8 Mycoremediation
17.5 Conclusion and Future Perspectives
References
Chapter 18: New Developments in Techniques Like Metagenomics and Metaproteomics for Isolation, Identification, and Characteriz...
18.1 Introduction
18.2 DNA Sequencing Methods
18.2.1 Illumina Sequencing
18.2.2 Pacific Biosciences SMRT
18.2.3 Nanopore Sequencing
18.2.3.1 Nanopore Sequencing Methodology
18.3 MAGs: Metagenome-Assembled Genomes and Reference Databases
18.4 Metaproteomics
18.4.1 Mass Spectrometry
18.4.2 Metaproteome Bioinformatics
18.5 Conclusion
References
Chapter 19: Mushroom Metagenome: Tool to Unravel Interaction Network of Plant, Mycorrhiza, and Bacteria
19.1 Introduction
19.2 Mushroom Taxonomy and Ecology
19.3 Mushroom Biology and Their Potential Roles for Sustainable Agriculture
19.4 Cataloguing Rhizospheric Bacterial Consortium in the Active Zone of the Mushroom
19.4.1 Bacterial Population in the Gleba, Peridium, and Fruit Bodies of the Mushroom
19.5 Mushroom Metagenomics Cloud-Based Pipeline
19.5.1 Community Profiling by Alpha Diversity: A Measure of Within-Sample
19.5.2 Community Profiling by Beta Diversity: A Measure of Similarity Between Samples
19.6 Microbial Ecology and Roles of Bacteria as Ecosystem Engineer
19.6.1 Insights into Bacterial Ecology
19.6.2 Bacteria as Ecosystem Engineer
19.7 Functional Annotation of Mushroom Rhizospheric Bacteria Consortium
19.7.1 KEGG Metabolism, Pathway, and Module
19.7.2 Cluster of Orthologous Groups of Protein
19.8 Cross Talk and Fungi-Bacteria Interaction
19.9 Conclusion
References
Chapter 20: Extremophile Bacterial and Archaebacterial Population: Metagenomics and Novel Enzyme Reserve
20.1 Introduction
20.2 Bacteria and Archaea in Extreme Environments
20.2.1 Bacteria and Archaea of Saline to Hypersaline Environment
20.2.2 Thermophilic Bacterial Diversity and Enzymatic Potential
20.2.3 Psychrophilic Bacterial Diversity and Enzymatic Potential
20.2.4 Polyextremophiles and Other Realms of Extreme Conditions
20.3 Enzymatic Potential of Extremophiles
20.4 Metagenomics of Extremophiles
20.5 Limitations of Metagenomics
20.6 Conclusion
References
Chapter 21: Microbial Nanotechnology: A Biocompatible Technology for Sustainable and Green Agriculture Practice
21.1 Introduction
21.2 Synthesis of Nanomaterials by Microorganism
21.3 Microorganism-Assisted Nanomaterials in Plant Growth
21.3.1 Amplification of Adhesion of Beneficial Bacteria by Nanoparticle
21.3.2 Advantages of Nanosilica over Sodium Silicate as Fertilizer
21.3.3 Uses of Nano-hydroxyapatite to Increase Soil Quality Along with Microbial Growth
21.4 Toxic Metal Removal by Microbial Nanotechnology
21.4.1 Metal-Removing Microbes
21.4.2 Conversion to Nanostructure of Toxic Metal by Microbes
21.5 Environmental Issues and Optimal Use of Nanoparticles in Microbial Nanotechnology
21.6 Conclusion
References
Chapter 22: Bacteriophage-Assisted Diagnostics and Management of Plant Diseases
22.1 Introduction
22.2 Historical Background
22.3 Types of Bacteriophages
22.4 Role of Bacteriophages in Plant Disease Diagnostics
22.4.1 Phage Typing
22.4.2 Reporter Phages
22.4.3 Phage Progeny-Based Detection
22.5 Successful Detection and Diagnosis of Plant Diseases Using Bacteriophages
22.5.1 Fire Blight (Erwinia amylovora)
22.5.2 Bacterial Blight of Crucifers (Pseudomonas cannabina pv. alisalensis)
22.5.3 Bacterial Wilt (Ralstonia solanacearum)
22.6 Advantages of Bacteriophage-Mediated Diagnostics
22.7 Disadvantages of Bacteriophage-Mediated Diagnostics
22.8 Role of Bacteriophages in Plant Disease Management
22.8.1 Xanthomonas
22.8.2 Ralstonia solanacearum
22.8.3 Dickeya and Pectobacterium
22.8.4 Xylella fastidiosa
22.8.5 Erwinia amylovora
22.8.6 Pseudomonas Phages
22.9 Advantages of Using Bacteriophage Over Other Biocontrol Agents
22.10 Disadvantages of Using Bacteriophage Over Other Biocontrol Agents
22.11 Conclusion
References