Plant Microbiome for Plant Productivity and Sustainable Agriculture

Preface
Contents
Editors and Contributors
Chapter 1: Fungal Microbiomes: The Functional Potential for Plant Growth Promotion and Opportunities for Agriculture
1.1 Introduction
1.2 The Fungal Microbiome (Mycobiomes)
1.2.1 Molecular Markers and Fungal Metagenomics in Agriculture
1.2.2 Core Mycobiomes and Plant Health
1.3 The Mycobiome and Sustainable Agriculture
1.3.1 Mycobiomes Boost Plant Growth
1.3.2 Plant Growth-Promoting Fungal Microbiomes in Disease Management
1.4 Agroecology, Sustainable Agriculture, and Fungal Microbiomes
1.5 Opportunities for New Applications of Beneficial Fungal Communities to Improve Soils, Plant Growth, and Plant Health
1.5.1 Soil Management and Fertilization
1.5.2 Crop Diversity at Local Scale
1.5.3 The Agronomic Dark Triad: Weeds, Pests, and Diseases
1.6 Conclusion
References
Chapter 2: Unearthing the Modern Trends and Concepts of Rhizosphere Microbiome in Relation to Plant Productivity
2.1 Introduction
2.2 Composition, Abundance, and Diversity of Rhizosphere Microbiome
2.3 Types of Interactions Between Microbes and Plants
2.3.1 Negative Interactions in the Rhizosphere
2.3.2 Positive Interactions in the Rhizosphere
2.4 Evolution of Plant-Microbe Interaction
2.5 Rhizosphere Microbiome Assembly
2.5.1 Factors Affecting the Assembly of Microbial Community in the Rhizosphere
2.5.1.1 Plant Growth Changes Root Metabolite and Assembly of the Rhizosphere Microbiome
2.5.1.2 Abiotic and Biotic Stresses Modulate Root Exudation and Recruit the Rhizosphere Microbiome
2.6 Impact of Rhizosphere Communities on Plant Growth and Diseases Resistance
2.6.1 Rhizosphere Engineering
2.6.2 Plant-Mediated Engineering
2.6.3 Microbiome-Mediated Engineering
2.6.4 Engineering the Interactions Between Plants and Microbes
2.7 Techniques Associated with Rhizosphere Microbiome in Relation to Plant Productivity
2.7.1 Genomics
2.7.1.1 Polymerase Chain Reaction
2.7.2 Restriction Fragment Length Polymorphism
2.7.3 DNA Sequencing
2.7.4 Rhizospheric Microbiome Characterization by Next-Generation Sequencing
2.7.5 DNA Cloning
2.7.6 Blending Strategies
2.8 Metagenomics
2.8.1 Integrated Metagenomics Methods
2.9 Bioinformatics Tools
2.9.1 Metagenome Analysis Software
2.9.2 Transcriptomics
2.9.3 Proteomics Methods
2.9.4 Metaproteomics Methods
2.9.5 Metabolomics
2.9.6 Phenomics
2.10 The Role of CRISPR for Plant Development
2.11 Basics of CRISPR-Mediated Plant-Microbial Interactions in Agriculture
2.12 Conclusion
References
Chapter 3: The Role of the Root Microbiome in the Utilization of Functional Traits for Increasing Plant Productivity
3.1 Introduction
3.2 Overview of the Root Microbiome
3.3 Functional Traits to Enhance Plant Productivity
3.3.1 Biofertilizers that Impact Mineral Nutrient Availability and Acquisition by Roots
3.3.1.1 Nitrogen Fixation
3.3.1.2 Phosphorus Bioavailability and Uptake
3.3.1.3 Increasing Soil Iron Bioavailability via Bacterial Siderophores
3.3.2 Drought Tolerance
3.3.3 Biocontrol of Plant Diseases
3.3.4 Plant Hormone-Producing Bacteria
3.3.4.1 Indole-3-Acetic Acid (IAA)
3.3.4.2 Cytokinin
3.3.4.3 ACC Deaminase Activity and Ethylene
3.4 Conclusions
3.4.1 Genome-Level Investigations of the Root Microbiome and Holo-Omics Are Required to Fully Exploit Microbiome Functional Tr...
References
Chapter 4: Crop Microbiome for Sustainable Agriculture in Special Reference to Nanobiology
4.1 Introduction
4.2 Nanotechnology in Sustainable Agriculture
4.2.1 Nano-Agrochemicals
4.3 Nanoparticles and Plant Microbiomes
4.3.1 Positive Impact
4.3.2 Negative Impact
4.3.3 Nanomaterial´s Role in Crop Abiotic Stress
4.4 Future Trends and Challenges
4.5 Conclusion
References
Chapter 5: Changes in Plant Microbiome in Response to Abiotic Stress
5.1 Introduction
5.2 Abiotic Stresses and Plants
5.2.1 Consequences of Drought
5.2.2 Consequences of Flooding
5.2.3 Consequences of Salinity
5.2.4 Consequences of Extreme Temperature
5.2.5 Consequences of Heavy Metals
5.2.6 Consequences of Nutrition Deficiency
5.3 Microbiome
5.3.1 Role of Microbiome in Relieving Drought
5.3.2 Role of the Microbiome in Relieving Flooding
5.3.3 Role of the Microbiome in Relieving Salinity
5.3.4 Role of the Microbiome in Relieving Extreme Temperatures
5.3.5 Role of the Microbiome in Relieving Heavy Metals
5.3.6 Role of the Microbiome in Relieving Nutrient Deficiency
5.4 Current Insights and Future Prospectives of Research
5.5 Conclusion
References
Chapter 6: Functional Potential of Plant Microbiome for Sustainable Agriculture in Conditions of Abiotic Stresses
6.1 Introduction
6.2 Role of Plant Microbiome in Metal(loid) Stress Tolerance
6.3 Role of Plant Microbiome in Drought Stress Tolerance
6.4 Role of Plant Microbiome in Salinity Stress Tolerance
6.5 Sustainable Agriculture in the Future Scenarios
References
Chapter 7: The Beneficial Plant Microbial Association for Sustainable Agriculture
7.1 Introduction
7.2 Beneficial Microbial Interactions in Plants
7.3 Rhizosphere Microbiome Interaction
7.3.1 Rhizobium Nodulation: A Beneficial Microbe-Plant Interaction
7.3.2 Azotobacter
7.3.3 Azospirillum
7.3.4 Actinorhizal (Frankia-Plants) Interaction
7.3.5 Mycorrhizal Interaction
7.3.5.1 Ectomycorrhizae
7.3.5.2 Endomycorrhizae
7.3.5.3 Fungal Endophytes
7.3.6 Benefits of Fungal-Plant Interactions
7.3.6.1 Soil Health
7.3.6.2 Nitrogen Uptake
7.3.6.3 Phosphate Transfer
7.3.6.4 Other Soil Nutrients Transport
7.3.6.5 Mutual Exchange of Minerals
7.3.6.6 Drought Resistance
7.3.6.7 Salinity Stress Tolerance
7.3.6.8 Heavy Metal(s) Tolerance
7.3.6.9 Adaptation Under High and Low Temperature
7.4 Beneficial Microbial Association on Phyllosphere
7.4.1 Phyllosphere Microbiome
7.4.1.1 Phyllosphere Bacteria
7.4.1.2 Phyllosphere Fungi
7.4.1.3 Phyllosphere Actinomycetes
7.4.2 Functions of Phyllosphere Microorganism for Sustainable Agriculture
7.4.2.1 Plant Nutrition Acquisition and Growth
7.4.2.2 Biological Control
7.4.2.3 Anti-insect Activity
7.4.2.4 Host Stress Tolerance
7.5 PGBs Bioinoculant Formulation for Sustainable Agriculture
7.5.1 Microbial Consortium as Bioinoculum
7.6 Engineering Host Microbiome for Sustainable Agriculture
7.6.1 Rhizosphere Microbiome Engineering
7.7 Conclusion
References
Chapter 8: Microbiome of Plants: The Diversity, Distribution, and Their Potential for Sustainable Agriculture
8.1 Introduction
8.2 Plant Microbiome: Diversity, Composition, and Distribution
8.3 Approaches for Studying Plant Microbiome Diversity
8.4 Factors Affecting Plant Microbiome Diversity
8.4.1 Impact of Genomic Organization
8.4.2 Impact of Agricultural Activities
8.4.3 Impact of Bioinoculants
8.4.4 Impact of Pathogens
8.4.5 Impacts of Abiotic Factors
8.5 Role of Plant Microbiome in Sustainable Agriculture
8.6 Current Trends and Future Perspectives
References
Chapter 9: Decoding Beneficial Plant Microbe Association with Latest Techniques for Sustainable Agriculture
9.1 Introduction
9.1.1 Microbiomes and Potential
9.2 Abiotic and Biotic Stress Tolerance
9.2.1 Abiotic Stress and Microbial Potential
9.2.2 Salt Stress and Heavy Metal Stress
9.2.3 Thermal and Radiation Stress
9.2.4 Drought Stress
9.3 Biotic Stress and Microbial Potential
9.4 Modern Approaches for Sustainable Agriculture
9.4.1 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas System
9.4.2 Gene Editing
9.4.3 Transcription Activator like Effector Nucleases (TALEN)
9.5 Analytical Tools and Techniques
9.5.1 Gas Chromatography-Mass Spectrometry (GC-MS)
9.5.2 Capillary Electrophoresis-Mass Spectrometry
9.5.3 Fourier Transform Ion Cyclotron Resonance-Mass Spectrometry (FTICR-MS)
9.5.4 Matrix-Assisted Laser Desorption/Ionization (MALDI)
9.5.5 Nuclear Magnetic Resonance (NMR)
9.6 OMICS Approaches
9.6.1 Genomics
9.6.2 Transcriptomics
9.6.3 Proteomics
9.6.4 Metabolomics
9.7 Conclusion
References
Chapter 10: Phosphate Solubilizing Microorganisms: Multifarious Applications
10.1 Introduction
10.2 Phosphorus in Soil
10.3 Phosphate Solubilizing Microorganisms
10.4 Need of Phosphate Solubilizing Microorganism
10.5 Mechanisms of Phosphate Solubilization
10.5.1 Inorganic Phosphate Solubilization
10.5.2 Organic Phosphate Solubilization
10.5.3 Phosphatase
10.5.4 Phytase
10.5.5 Phosphonatases
10.6 Application of Phosphate Solubilizing Microorganisms
10.6.1 Phosphate Solubilizing Microorganisms as Plant Growth Promoters
10.6.2 Phosphate Solubilizing Microorganisms in Ecological Restoration and Phosphorus Cycling
10.6.3 Phosphate Solubilizing Microorganisms in Sustainable Agriculture
10.6.4 Phosphate Solubilizing Microorganisms in Immobilization of Heavy Metals
10.7 Conclusion
References
Chapter 11: Bacillus and Streptomyces for Management of Biotic Stresses in Plants for Sustainable Agriculture
11.1 Introduction
11.1.1 General
11.2 Biotic Stress
11.3 Bacillus and Streptomyces
11.4 Antibiotics from Bacillus and Streptomyces
11.5 Volatile Organic Compounds (VOCs)
11.6 Plant Growth-Promoting (PGP) Traits
11.6.1 Indole Acetic Acid (IAA)
11.6.2 1-Aminocyclopropane-1-Carboxylic Acid Deaminase (ACCd) Activity
11.6.3 Siderophore Production
11.6.4 Induced Systematic Resistance (ISR)
11.7 Mutation
11.8 Formulations
11.9 Prospects and Conclusions
References
Chapter 12: Omic Route to Utilize Endophytes and Their Functional Potentials in Plant Growth Advancement
12.1 Introduction
12.2 Role of Endophytes in Combating Abiotic Stress
12.3 Phytohormones Production by Endophytes
12.3.1 Auxin
12.3.2 Gibberellin
12.3.3 Cytokinin
12.3.4 Endophytic ACC Deaminase Production
12.4 Plant Growth Promotion and Stress Management by Endophytes
12.5 `Ome´ Approach of Plant-Endophyte Communications Under Abiotic Strain
12.5.1 Metaproteogenomics
12.5.2 Microarray-Based Techniques
12.6 Conclusions and Future Perspectives
References
Chapter 13: Siderophore Production in Iron Uptake and Plant Biofortification
13.1 Introduction
13.2 Micronutrient Deficiency and Strategies for Control of Micronutrient Malnutrition
13.3 Need for Biofortification
13.4 Strategies for Biofortification
13.4.1 Agronomic Interventions
13.4.2 Genetic Approaches
13.4.3 Microorganisms and Plant-Based Strategies
13.5 Production of Siderophore and Other Chelating Substances
13.5.1 Siderophores Secreted by Mycorrhizal Fungi
13.5.2 Siderophores Produced by Dark Septate Fungi and Root Endophytic Fungi
13.5.3 Siderophores Produced from PGPR
13.6 Effects of Siderophores Secreted by Beneficial Microorganisms on Cellular Structures and Iron Distribution in Host Plants
13.7 Conclusion
References
Chapter 14: Plant Microbiome Diversity and Potential for Crops and Sustainable Agriculture
14.1 Introduction
14.2 Plant Microbiome Diversity
14.2.1 Rhizosphere Microbiome
14.2.2 Phyllosphere Microbiome
14.2.3 Endosphere Microbiome
14.3 Plant and Soil Microbiome Interaction
14.4 Microbiomes and Secreted Metabolites in Plant Growth Promotion
14.4.1 Phosphate Solubilization and Mobilization
14.4.2 Nitrogen Fixation
14.4.3 Potassium Solubilization and Mobilization
14.4.4 Microbial ACC Deaminase
14.4.5 Siderophores
14.4.6 Phytohormones
14.4.7 Volatile Compounds
14.4.8 Other Secondary Metabolites
14.5 Endophytes Contribute to Plant Stress Adaptation
14.5.1 Hypersaline Habitat Adaptability
14.5.2 Alleviating Temperature Stress
14.5.3 Drought Stress Reduction
14.6 Applications of Microbiome Engineering
14.7 Application of Endophytes as Potential Biofertilizer and Biocontrol
14.8 Conclusion and Future Prospects
References
Chapter 15: Endophytic Phytohormone Production and Utilization of Functional Traits in Plant Growth Promotion
15.1 Introduction
15.2 Endophytic Phytohormones
15.2.1 Auxin
15.2.2 Gibberellic Acid
15.2.3 Cytokinin
15.2.4 Ethylene
15.2.5 Abscisic Acid
15.2.6 Salicylic Acid
15.2.7 Jasmonic Acid
15.3 Endophytic Fungi
15.4 Conclusion
References
Chapter 16: Role of Endophytic Microorganisms in Phosphate Solubilization and Phytoremediation of Degraded Soils
16.1 Introduction
16.2 Role of Endophytes for Mine Spoil Reclamation
16.2.1 Phytostimulation and Nutrient Cycling
16.2.2 Enzyme Production, Antimicrobial Activity and Source of Bioactive
16.2.3 Bioremediation
16.3 Role of Endophytes for Phosphate Solubilization
16.4 Role of Endophytes for Phytoremediation
16.5 Case Studies
16.5.1 Fungal Root Endophytes in Metal-Polluted Tailings
16.5.2 Root Colonizing Endophytes for Succession in a Mine Degraded Land
16.6 Conclusion
References
Chapter 17: Techniques to Study Plant-Microbe Interactions that Lead to Efficient Sustainable Agriculture
17.1 Introduction
17.2 Agroecosystems and the Importance of Plants and Microorganisms and Their Interactions
17.3 Methods to Study Plant-Microbe Interaction
17.3.1 Conventional Techniques
17.3.1.1 Microscopy
17.3.2 Biochemical Techniques
17.3.2.1 Immunoassays
Labeled Immunoassays
Direct Immunoassays
17.3.3 Molecular Techniques for Detection of Plant-Microbe Interaction
17.3.3.1 Polymerase Chain Reaction (PCR) Technique
17.3.3.2 16S rRNA Gene Sequencing for Bacterial Identification
17.3.3.3 Next-Generation Sequencing (NGS)
17.3.3.4 CRISPR/Cas9
17.3.3.5 Other Approaches to Study the Plant-Microbe Interface
17.4 Conclusion
17.5 Future Perspective
References
Chapter 18: Plant Microbiome in Agroecosystems for Sustainable Agriculture and Environments
18.1 Introduction
18.2 Microbiomes and Sustainability Concepts
18.3 Agriculture Productivity and the Constituent of Soil Microbiome
18.3.1 Specialization of Microbes in Soil Fertility and Improving Agricultural Productivity
18.3.2 Role of Microbes in Greenhouse Gas Reduction
18.3.3 Impact of Microbes in Biotic and Abiotic Stress Reduction in Plant
18.4 Plant Microbial Associations for Sustainable Agroecosystems and Productivity
18.4.1 Seed Microbiomes
18.4.2 Rhizosphere Microbiomes
18.4.3 Phyllosphere Microbiomes
18.5 The Current Approaches and Prospects of Microbiomes
References