Plant Microbiome for Plant Productivity and Sustainable Agriculture

This edited book deals with latest comprehensive information on conventional and high throughput techniques and technologies that are recently used to study plant microbial interface for agricultural research and enhancing plant productivity. Plant microbiota are important for many plant growth promotion activity and agricultural productivity and are sustainable green technology for enhancing agricultural productivity under changing environment. The book covers recent information about the plant associated microbiota and their ecology. It discusses technologies to isolate and test microbiota inhabiting in different portion of plants. The book explores the conventional methods as well as the most recently recognized high throughput technologies which are important for productive agroecosystems to feed the growing global population. This book is of interest to teachers, researchers, microbiologist, plant and environmental scientist and those interested in environment stewardship around the world. Also the book serves as additional reading material for undergraduate and graduate students of agriculture, forestry, ecology, soil science, and environmental sciences and policy makers to be a useful to read. 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