Microbiomics and Sustainable Crop Production

Description

Microbiomics and Sustainable Crop Production Microbiomics and Sustainable Crop Production presents an overview of the current state of the art in microbiome research, discussing many new technologies and approaches in order to bridge knowledge gaps between field and lab experimental systems. New and emerging strategies to improve the survival and activity of microbial inoculants are covered, including the use of selected indigenous microbes, optimizing microbial delivery methods, and taking advantage of modern gene editing tools to engineer microbial inoculants. The two highly qualified authors address new molecular tools and powerful biotechnological advances, providing readers with knowledge of the complex chemical and biological interactions that occur in the rhizosphere and ensuring that strategies to engineer the rhizosphere are safe, beneficial to productivity, and result in improvements to the sustainability of agricultural systems. The relationship between phyllosphere microbial communities and functional traits of plants is also explored. Finally, approaches and priority areas for future research on phyllosphere microbiology are suggested. Topics covered in this comprehensive resource include: Transmission modes of bacteria and fungi and the nature of their interactions in the endosphere Characteristics of ‘core microbiomes’, which may be deployed to organize otherwise uncontrollable dynamics of resident microbiomes Model microbiome-plant systems, as well as the stability, resilience, and assembly of agricultural microbiomes Engineering and management of agricultural microbiomes for improving crop health, including reasons to modify plant microbiomes Microbiome research in the omics era and new efforts and challenges in assigning functions to microbes For students of plant biotechnology, agricultural sciences, and agricultural engineering, along with researchers working in related fields, Microbiomics and Sustainable Crop Production is an important resource to understand many complex modern ideas related to the subject and how they can be applied to practical applications. Cover Title Page Copyright Page Contents Preface About the Authors Chapter 1 Agricultural Microbiomes: Functional and Mechanistic Aspects 1.1 Introduction 1.2 Model Microbiome–Plant Systems 1.2.1 Plant Perception of Microbes 1.2.2 Molecular Plant 1.2.3 Bacterial Signalling: Quorum Sensing and Symbiosis Factors 1.2.4 Hormone Signalling in Microbe–Host Interactions 1.2.5 Interactome Network Analysis 1.2.6 Transcriptional Regulatory Networks 1.2.7 Metabolic Exchanges and Nutrient Competition in the Soil 1.2.8 Integrated Multi-omics Modelling 1.2.9 From Systems Biology to Crop Protection 1.3 Stability, Resilience, and Assembly of Agricultural Microbiomes 1.4 Core Plant Microbiome and Metagenome 1.5 Interactions Among the Microbes, Environment, and Management 1.5.1 Secondary Metabolism 1.5.2 Endophyte–Phytopathogen–Plant Interaction 1.5.3 Hopanoid 1.5.4 Parasitic Interaction 1.5.5 Microbial Community’s Interaction 1.5.6 Siderophore 1.5.7 Symbiotic Interaction 1.6 Microbiome Innovation in Agriculture: Insect Pest Management 1.6.1 Manipulation of Insect-Associated Microbiomes for Pest Management 1.6.2 Incompatible Insect Technique (IIT) 1.6.3 Paratransgenesis 1.6.4 Exploiting the Chemical Inventories of Microbiomes to Develop New Biopesticides 1.6.5 Microbial Insecticides and Plant-Incorporated Protectants 1.6.6 Microbial Semiochemicals 1.6.7 Combining Microbial-Based Biopesticides with Nanotechnologies 1.6.8 Microbial Interventions to Improve Fitness of Mass-Reared Insects for Autocidal Programmes References Chapter 2 Engineering and Management of Agricultural Microbiomes for Improving Crop Health 2.1 Why to Modify Plant Microbiome? 2.2 Methods for Detecting Endophytes Within the Plant 2.2.1 Media for Isolation of Fungal Endophytes 2.2.2 Media for Isolation of Bacterial Endophytes 2.2.3 Identification of Endophytes 2.2.4 Molecular Tools to Identify Endophytes 2.2.5 Markers and Primers for Endophyte Identification 2.2.6 Techniques to Evaluate Endophyte Distribution in Plants 2.2.6.1 Hood and Shew Staining Protocol 2.2.6.2 Fluorescent Probes for Localization of Bacterial and Fungal Endophytes 2.2.6.3 ROS Staining to Study Bacterial Endophytes 2.2.7 Analysis of Endophyte Diversity 2.2.8 Non-Culture Methods 2.2.9 Metagenomics and Pyrosequencing 2.2.10 Microarray: Gene Chips to Study the Expression and Mechanisms of Interaction 2.3 Engineering of the Plant Microbiome 2.3.1 Host-Mediated and Multi-Generation Microbiome Selection 2.3.2 Inoculation into the Soil and Rhizosphere 2.3.3 Inoculation into Seeds or Seedlings 2.3.4 Tissue Atomization 2.3.5 Direct Injection into Tissues or Wounds 2.4 In Situ Harnessing of Agricultural Microbiome 2.4.1 Recent Advancement in Plant Microbiome Studies 2.4.2 Microbial-Based Strategies 2.4.3 Biochemical Strategies 2.4.4 Molecular Strategies 2.5 Future Perspective of Agricultural Microbiome Engineering References Chapter 3 Approaches and Challenges in Agricultural Microbiome Research 3.1 Microbiome Research in the Omics Era 3.2 New Efforts and Challenges in Assigning Function to Microbes 3.3 Characterization of Complex Microbial Communities 3.4 Advanced Fundamental Research on Microbe–Microbe and Plant–Microbe Interactions : Bridging the Lab–Field Gap 3.4.1 Bridging the Lab–Field Gap 3.4.1.1 Limitations on the Experiments Performed in Controlled Conditions: The Lack of Context References Chapter 4 Perceptive of Rhizosphere Microbiome 4.1 Introduction 4.2 Multiple Levels of Selection in the Plant Rhizosphere 4.2.1 Microbial Experimental Systems and Network Analysis 4.2.2 Observing Microbiome Controls over Observed Phenotypes of the Plant Using -Omics Techniques 4.2.3 Genome-Editing Techniques to Uncover Plant Host Controls over Microbiome Composition and Function 4.2.4 Rhizosphere Engineering and Sustainable Agriculture 4.2.5 Engineering Plants 4.2.6 Case Study 1: Manipulating Rhizosphere pH 4.2.7 Case Study 2: Enhancing Organic Anion Efflux from Roots 4.2.8 Approach 1: Engineering Metabolic Pathways for Greater Organic Anion Efflux 4.2.9 Approach 2: Engineering Transport Proteins for Greater Organic Anion Efflux 4.2.9.1 ALMT Family 4.2.9.2 MATE Family 4.2.10 Engineering Microbes 4.2.11 Strategic Issues for Strain Development 4.2.12 PGPR Activity Is Enhanced in Engineered Strains 4.2.13 Recombinant Strains and Rhizosphere Competence 4.2.14 Non-Target Effects of Wild-Type and Genetically Engineered PGPR 4.3 Engineering Microbial Populations and Plant–Microbe Interactions 4.4 Emerging Approaches in Rhizoremediation 4.4.1 Impact of Rhizosphere Microbiome on Rhizoremediation 4.4.2 Current Approaches to Understand the Role of the Microbiome in Rhizoremediation 4.4.3 Metagenomics 4.4.4 Metatranscriptomics 4.4.5 Metaproteomics 4.4.6 Genomics 4.5 Heritability of Rhizosphere Microbiome 4.6 Future Course of Orientations References Chapter 5 Microbial Communities in Phyllosphere 5.1 Introduction 5.2 Diversity of Microbes in Phyllospheric Environment 5.2.1 Sources of Microbes Colonizing the Phyllosphere 5.2.2 Leaf Characteristics and Environmental Factors Controlling Phyllosphere Microbiology 5.3 Microbial Adaptation to the Phyllosphere 5.3.1 Plant Genotype and Phyllosphere Microbiology 5.4 Relationship between Phyllosphere Microbial Communities and Functional Traits of Plants 5.5 Metabolic Dynamics of Phyllosphere Microbiota 5.6 Impact of Phyllospheric Microorganisms on Plant–Plant, Plant–Insect, and Plant Atmosphere Chemical Exchanges 5.7 Quorum Sensing in Phyllosphere 5.8 Applications for Phyllosphere Microbiology 5.8.1 Biocontrol Agents 5.8.2 Plant Growth-Promoting Compounds 5.8.3 Biopharmaceutical Importance 5.8.4 Other Applications 5.8.5 Conclusion and Future Prospects References Chapter 6 Endosphere and Endophyte Communities 6.1 Reproduction and Transmission Modes of Microbes 6.2 Vertical Transmission 6.2.1 Vertical Transfer via Seeds 6.2.2 Vertical Transfer via Pollen 6.2.3 Horizontal Transmission 6.2.3.1 Colonization of Seed and Root via Soil 6.2.4 Endophytic Colonization of the Spermosphere 6.2.5 Colonization of the Root Endosphere via the Rhizosphere 6.2.6 Entry into Aerial Tissues 6.2.7 Aerial Dispersal of the Plant Microbiome 6.2.8 Endophytic Leaf Colonization via Stomata 6.2.9 Floral Transmission of Bacterial Endophytes 6.2.10 Endophyte Transmission by Plant-Feeding Insects 6.3 Endophyte Genomes and Metagenomes 6.3.1 Genome Analysis 6.3.2 Multigenome Analysis 6.3.3 Metagenomics 6.3.4 Advanced Fundamental Research on Microbe Interactions in the Endosphere 6.3.5 Fungal Hyphae as Vehicles for Bacterial Colonization of the Endosphere 6.3.6 Bacterial Intrahyphal Colonization 6.4 Bacteria and Fungi in Mixed Biofilms in Plants 6.5 Conclusion and Future Perspectives References Chapter 7 Core Microbiomes: For Sustainable Agroecosystems 7.1 Core Microbiome for Agriculture: A Taxonomic and Functional Aspect 7.1.1 Core Microbiome Identification 7.1.2 Functional Core Microbiome 7.1.3 Conservative Approaches to Core Plant Microbiomes 7.2 Core Microorganisms and Priority Effects in Initial Assembly 7.2.1 Microbiome Types 7.2.2 Priority Effects in Initial Assembly 7.2.3 Deploying Core Microorganisms 7.2.4 Prioritizing a Core Microbiome over Space 7.2.5 Prioritizing a Core Microbiome over Time 7.2.6 Neutral Model to Inform Core Taxa That Are Deterministically Assembled 7.3 Informatics of Microbial Networks 7.3.1 Microbial Networks 7.4 Designing Core Microbiomes 7.4.1 Criterion for Nominating Core Microorganisms 7.4.1.1 Functional Species Recruitment 7.4.1.2 Pathogen/Pest Blocking 7.4.1.3 Core Reinforcement 7.5 Management of Agroecosystems with Core Microbiomes 7.5.1 Logistics of Core Microbiomes 7.5.2 Portfolios with Multiple Cores 7.5.3 Smart Farming with AI and Robots References Further Reading Chapter 8 Microbiome Mediated: Stress Alleviation in Agroecosystems 8.1 Effect of Biotic and Abiotic Stresses on Plants 8.1.1 Biotic and Abiotic Stresses 8.1.2 Biotic Stress 8.1.3 Abiotic Stress 8.1.4 Water Stress 8.1.5 Transpiration 8.1.6 Water Loss 8.1.7 Temperature Stress 8.1.7.1 Chilling Stress 8.1.7.2 Freezing Stress 8.1.7.3 Heat Stress 8.1.7.4 Low-Oxygen Atmosphere and High-Carbon-Dioxide Atmosphere 8.1.7.5 Low-Oxygen Atmosphere 8.1.7.6 High-Carbon-Dioxide Atmosphere 8.1.7.7 Ethylene and Nonethylene Volatiles 8.1.7.8 Light 8.1.7.9 Mechanical Stress 8.1.7.10 Oxidative Stress 8.1.7.11 Mineral Stress 8.2 Molecular and Physiological Responses of Plants Against Stresses 8.2.1 Morpho-Physiological Responses 8.2.2 Molecular Responses 8.3 Microbiome Mediated Mitigation of Stress Conditions 8.3.1 Improved Understanding of a Microbiome Role in Plant Defence and Immune Systems 8.3.2 Cry for Help’ Strategy for the Applied Plant Stress Probiotics 8.4 Multi-Omics Strategies to Address Stress Alleviation 8.4.1 Genomics 8.4.2 Metagenomics 8.4.3 Transcriptomics 8.4.4 Proteomics 8.4.5 Metabolomics References Index EULA