Microbiomics and Sustainable Crop Production

Preface xi

About the Authors xii

1 Agricultural Microbiomes: Functional and Mechanistic Aspects 1

1.1 Introduction 2

1.2 Model Microbiome--Plant Systems 2

1.3 Stability, Resilience, and Assembly of Agricultural Microbiomes 11

1.4 Core Plant Microbiome and Metagenome 13

1.5 Interactions Among the Microbes, Environment, and Management 14

1.6 Microbiome Innovation in Agriculture: Insect Pest Management 21

2 Engineering and Management of Agricultural Microbiomes for Improving Crop Health 66

2.1 Why to Modify Plant Microbiome? 67

2.2 Methods for Detecting Endophytes Within the Plant 69

2.3 Engineering of the Plant Microbiome 79

2.4 In Situ Harnessing of Agricultural Microbiome 82

2.5 Future Perspective of Agricultural Microbiome Engineering 86

3 Approaches and Challenges in Agricultural Microbiome Research 97

3.1 Microbiome Research in the Omics Era 97

3.2 New Efforts and Challenges in Assigning Function to Microbes 99

3.3 Characterization of Complex Microbial Communities 101

3.4 AdvancedFundamental Research on Microbe--Microbe and Plant--Microbe Interactions : Bridging the Lab--Field Gap 102

4 Perceptive of Rhizosphere Microbiome 111

4.1 Introduction 112

4.2 Multiple Levels of Selection in the Plant Rhizosphere 113

4.3 Engineering Microbial Populations and Plant--Microbe Interactions 127

4.4 Emerging Approaches in Rhizoremediation 128

4.5 Heritability of Rhizosphere Microbiome 137

4.6 Future Course of Orientations 139

5 Microbial Communities in Phyllosphere 154

5.1 Introduction 154

5.2 Diversity of Microbes in Phyllospheric Environment 156

5.3 Microbial Adaptation to the Phyllosphere 160

5.4 Relationship between Phyllosphere Microbial Communities and Functional Traits of Plants 163

5.5 Metabolic Dynamics of Phyllosphere Microbiota 166

5.6 Impact of Phyllospheric Microorganisms on Plant--Plant, Plant--Insect, and Plant Atmosphere Chemical Exchanges 167

5.7 Quorum Sensing in Phyllosphere 169

5.8 Applications for Phyllosphere Microbiology 171

6 Endosphere and Endophyte Communities 193

6.1 Reproduction and Transmission Modes of Microbes 194

6.2 Vertical Transmission 196

6.3 Endophyte Genomes and Metagenomes 207

6.4 Bacteria and Fungi in Mixed Biofilms in Plants 213

6.5 Conclusion and Future Perspectives 216

7 Core Microbiomes: For Sustainable Agroecosystems 240

7.1 Core Microbiome for Agriculture: A Taxonomic and Functional Aspect 241

7.2 Core Microorganisms and Priority Effects in Initial Assembly 249

7.3 Informatics of Microbial Networks 255

7.4 Designing Core Microbiomes 257

7.5 Management of Agroecosystems with Core Microbiomes 260

8 Microbiome Mediated: Stress Alleviation in Agroecosystems 272

8.1 Effect of Biotic and Abiotic Stresses on Plants 273

8.2 Molecular and Physiological Responses of Plants Against Stresses 285

8.3 Microbiome Mediated Mitigation of Stress Conditions 288

8.4 Multi-Omics Strategies to Address Stress Alleviation 293

References 303

Index 320