Advances in Agricultural and Industrial Microbiology: Volume-2: Applications of Microbes for Sustainable Agriculture and in-silico Strategies

This book is developed in a lucid manner for readers to grasp information about the role and potential of microbes in sustainable agriculture & computational strategies associated with it. Present volume focuses on advancements of microbial research in increasing agricultural productivity and sustainability viz. plant growth promotion by rhizobacterial biostimulants, endophytes, actinobacteria, arbuscularmycorrhizal fungi and biocontrol. Present day research is focused on role of soil microbe’s in agriculture, diazotropic & azotobacterial N2 fixation, PGPR etc. However, there is dearth of information on bioremediation of agrochemicals, biocontrol etc. This book is a compilation of research advances in both the aspect from eminent experts around the globe. In addition, in-silico mediated understandings of plant pathology, use of artificial neural networks in phytopathogen prediction, computational approaches in enhancing secondary metabolites production will be beneficial to professionals and academicians for sustainable agriculture. This volume will be very helpful for the students, teachers, professionals, and scientists concerned in agricultural production, food security, soil microbiology, agricultural biotechnology, and computational techniques. Contents About the Editors 1: Plant Growth-Promoting Rhizobacteria for Sustainable Agriculture 1.1 Introduction 1.1.1 Plant Growth-Promoting Rhizobacteria (PGPR) 1.1.2 Diversity of the PGPR 1.2 Mechanism of Actions of PGPR for Plant Growth Promotion and Disease Suppression 1.2.1 Root Colonization and Competition 1.2.2 Nitrogen Fixation 1.2.3 Phosphate Solubilization 1.3 Phytohormone Synthesis 1.3.1 Indole Acetic Acid (IAA) 1.3.2 Cytokinins 1.3.3 Gibberellins (GAs) 1.3.4 Abscisic Acid (ABA) 1.3.5 Xanthoxin 1.3.6 Ethylene 1.3.7 Production of 1-Aminocyclopropane-1-Carboxylate Deaminase 1.3.8 Siderophore 1.4 Secondary Metabolite Production 1.4.1 Production of Hydrolytic Enzymes 1.5 Future Prospective and Conclusion References 2: Plant-Microbe Interactions and Its Effect on Crop Productivity 2.1 Introduction 2.2 Different Types of Plant-Microbe Interactions 2.2.1 Mutualism 2.2.2 Commensalism 2.2.3 Amensalism 2.2.4 Symbiosis 2.2.5 Pathogenic Interaction 2.3 Mechanismsof Plant-Microbe Interaction 2.3.1 Through Root Exudates 2.3.1.1 Positive Plant-Microbe Interaction Mediated by Root Exudates 2.3.1.2 Negative Plant-Microbe Interaction Mediated by Root Exudates 2.3.2 Siderophores 2.4 Beneficial/Positive Interactions to Increase Plant Productivity 2.4.1 Nitrogen Fixation 2.4.2 Phosphate Solubilization 2.4.3 Biofertilizers 2.4.3.1 Production of Biofertilizer 2.4.3.2 Different Types of Biofertilizers 2.4.3.3 Advantages of Biofertilizers 2.4.4 Biopesticides 2.4.4.1 Classification of Biopesticides 2.4.5 Phytostimulants 2.4.5.1 Advantages of Phytostimulants 2.5 Plant-Microbe Interactions in Protecting Against Biotic Stresses 2.5.1 Plant Defence Mechanism Against Herbivore 2.6 Plant-Microbe Interactions in Protecting AgainstAbiotic Stress 2.6.1 Water 2.6.2 Temperature 2.6.3 Heavy Metal 2.7 Conclusion References 3: Rhizobacterial Biostimulants: Efficacy in Enhanced Productivity and Sustainable Agriculture 3.1 Introduction 3.2 Rhizosphere 3.3 Plant Growth-Promoting Rhizobacteria (PGPR) 3.4 PGPR Growth-Promoting Mechanisms 3.4.1 Phytohormone Production 3.4.2 Utilization of 1-Aminocyclopropane-1-Carboxylate 3.4.3 Exopolysaccharide (EPS) Production 3.4.4 Phosphate Solubilization 3.4.5 Potassium Solubilization 3.4.6 Production of Enzymes 3.5 PGPR for Disease Management 3.5.1 Biocontrol 3.5.2 Mechanisms of Biological Control 3.5.2.1 Antibiosis 3.5.2.2 Competition 3.5.2.3 Siderophore Production 3.5.2.4 Production of Hydrogen Cyanide 3.6 Rhizobacterium-Mediated Induced Systemic Resistance 3.6.1 Production of Enzymes 3.6.2 Production of Volatile Organic Compounds (VOCs) 3.7 Commercialization of Rhizobacteria 3.8 Future Trends and Prospects References 4: The Role of Arbuscular Mycorrhiza in Sustainable Agriculture 4.1 Introduction 4.2 The Range of Symbiotic Plants 4.3 Taxonomy of Arbuscular Mycorrhizal Fungi 4.4 The Role of AM Fungi in the Management of Plant Diseases 4.4.1 Impact on Fungal and Fungal-Like Diseases 4.4.2 Impact on Plant Parasitic Nematodes 4.4.3 Impact on Plant Bacterial Diseases 4.4.4 Impact on Phytoplasmas 4.4.5 Impact on Plants ́ Physiological Disorders 4.5 Arbuscular Mycorrhizal Fungi ́s Mode of Action 4.5.1 Greater Water and Nutrient Uptake, and Minimizing Environmental Stresses 4.5.2 Changes in Plant Tissue Chemicals 4.5.3 Compete with Pathogens for Location and Nutrients 4.5.4 Structural Changes in Roots 4.5.5 Increasing the Population of Beneficial Soil Bacteria 4.6 AM Fungi ́s Importance in Phytoremediation of Polluted Soils 4.7 Conclusion References 5: Biocontrol Efficacy of Biomass and Secondary Metabolites of P. fluorescens Against Predominant Pest Affecting Agricultural ... 5.1 Introduction 5.2 Fluorescent Pseudomonas 5.3 Mode of Action of Fluorescent Pseudomonas 5.3.1 Biofertilizers 5.3.2 Biocontrol Agents 5.3.3 Microbial Activity of Secondary Metabolites 5.4 Conclusion References 6: Exopolysaccharide-Producing Azotobacter for Bioremediation of Heavy Metal-Contaminated Soil 6.1 Introduction 6.2 Source of Heavy Metal Contamination in Agricultural Soil 6.3 Heavy Metal Toxicity to Plants 6.4 Composition of Exopolysaccharide of Azotobacter 6.5 Azotobacter Resistance to Heavy Metal 6.6 Azotobacter Mechanisms for Metal Bioremediation 6.7 Conclusion References 7: Utilization of Arbuscular Mycorrhizal Fungi to Boom the Efficiency and Product Nature of Horticultural Crops 7.1 Introduction 7.2 Arbuscular Mycorrhizal Fungi 7.2.1 Taxonomy 7.2.2 Life Cycle and Arrangement of the Beneficial Interaction of AMF 7.2.3 Creation of Inocula and Quality Viewpoints 7.3 Benefits of AMF Inoculants for Creation of Green Harvest 7.4 Effect of AMF on Harvest Resistance to Abiotic Stresses 7.5 Effect of AMF on Yield Resistance to Biotic Anxieties 7.6 Impact of AMF on Horticultural Crops 7.7 Environmental and Management Impact on the Effects of AMF for the Host Crop 7.8 The Role of Mycorrhizae in Sustainable and Regenerative Agriculture 7.9 Conclusions and Possibilities References 8: Microbial Remediation of Persistent Agrochemicals 8.1 Introduction 8.2 Persistent Agrochemicals 8.2.1 Impact of Persistent Agrochemicals on Agriculture and Environment 8.3 Mechanism of Microbial Bioremediation of Persistent Agrochemicals 8.3.1 Bioadsorption 8.3.2 Bioaccumulation 8.3.3 Biodegradation 8.4 Persistent Agrochemical-Degrading Microbes 8.4.1 Bacteria as PA-Degrading Agents 8.4.1.1 Mechanism and Pathways of Remediation Process 8.4.1.2 Bacterial Enzymes/Genes Involved in PA Degradation 8.4.2 Cyanobacteria as PA-Degrading Agents 8.4.2.1 Mechanism and Pathways of Remediation Process 8.4.2.2 Cyanobacterial Genes Involved in PA Degradation 8.4.3 Fungus as PA-Degrading Agents 8.4.3.1 Mechanism and Pathways of Remediation Process 8.4.3.2 Fungal Genes/Enzymes Involved in PA Degradation 8.5 Factors Affecting Biodegradation of PA 8.5.1 Chemical Structure and Concentration of PA 8.5.2 pH 8.5.3 Temperature 8.5.4 Moisture and Water Availability 8.5.5 Salinity 8.5.6 Nutrients 8.6 Advantages and Limitations of Bioremediation 8.7 Strategies to Enhance the Efficacy of PA Degradation 8.7.1 Immobilization 8.7.2 Acclimation 8.7.3 Co-cultivation 8.7.4 Genetic Modification and Enzyme Application 8.8 Conclusion References 9: Microbe-Based Pesticides for Insect Pest Control and Their Management 9.1 Introduction 9.2 Types of Microbiological Insecticides 9.2.1 Bacteria 9.2.2 Fungi 9.2.3 Virus 9.3 Protozoan as Microbial Insecticides 9.4 Present Prospectus of Microbial Pesticides in Global Context 9.5 Present Prospectus of Microbial Insecticides in India 9.6 Conclusion References 10: In Silico Tools and Approach of CRISPR Application in Agriculture 10.1 Introduction 10.2 Mechanism of Action 10.3 CRISPR Role in Agriculture Advancement 10.3.1 Overview of CRISPR Application in Agriculture 10.3.2 In Silico-Assisted Gene Editing Using CRISPR/Cas 10.4 Applications of CRISPR in Agriculture 10.5 Future Prospects References 11: Application of Bioinformatics in the Plant Pathology Research 11.1 Introduction 11.2 Applications of Bioinformatics in the Plant Pathological Study 11.2.1 Plant-Pathogen Interaction Study 11.2.2 Gene Expression, Structural and Comparative Genomics Study 11.2.3 Molecular Modelling Study 11.2.4 GWAS Study in Plant Pathology 11.3 Future Aspects 11.4 Conclusion References 12: New-Age Genomic Measures for Uncovering Plant-Microbiome Interactions: Tools, Pipelines and Guidance Map for Genomic Data ... 12.1 Introduction 12.2 OMICS, System Biology and PGPR 12.3 Genomics: Sequencing the Organism ́s Genetic Code 12.3.1 Sequencing Platforms and Processes 12.3.2 Sequence Data Assembly, Correctness and Interpretation 12.3.3 Gene Function Assignments: Annotation and Genetic Analyses 12.3.3.1 RAST 12.3.3.2 IMG-ER 12.3.3.3 Microscope-Genoscope (MaGe) 12.3.3.4 MetaCyc-BioCyc 12.3.3.5 Pseudomonas Genome Database 12.3.4 Functional and Comparative Genomic Analyses of PGP Taxa 12.3.4.1 CARD (Antibiotic Resistance) 12.3.4.2 VFDB (Virulence Factors/Pathogenic Markers) 12.3.4.3 antiSMASH 5.0 (Secondary Metabolites) 12.3.5 Mobile Genomics: Regions of Genomic Plasticity 12.3.5.1 ICEberg 2.0 12.3.5.2 IslandViewer 4.0 (for Larger Scale Datasets) 12.4 Conclusion and Future Prospects References 13: Bioinformatics: A Tool for Sustainable Agriculture 13.1 Introduction 13.2 Role of Bioinformatics 13.2.1 Web Tools and Resources 13.3 Agriculture and India: A Brief History 13.3.1 Postindependence Agricultural Scenario in India 13.4 The Need for Sustainable Agriculture 13.4.1 Positive Impacts of Sustainable Agriculture 13.4.1.1 Towards a Healthier Ecosystem by Employing Natural Resources 13.4.1.2 Reduces Pollution and Adverse Effects on the Land Resources 13.5 Bioinformatics as a Tool for Sustainable Agriculture 13.5.1 Genomics, Metabolomics, and Interactomics for Sustainable Agricultural Development 13.5.2 Impact of Genome Sequencing in Agriculture 13.5.3 Applications of Agricultural Bioinformatics 13.5.4 Molecular Plant Breeding 13.6 Conclusion References 14: Recent Advances in Deep Learning CNN Models for Plant Disease Detection 14.1 Introduction 14.2 Various Plant Diseases 14.2.1 Caused by Fungus 14.2.2 Caused by Bacteria 14.2.3 Caused by Virus 14.3 Different Deep CNN Models 14.3.1 AlexNet 14.3.2 VGGNet 14.4 ResNet 14.5 Various Materials Available Related to Plant Diseases 14.6 Related Work 14.6.1 Application 14.6.2 Comparison Accuracies with Training Samples 14.7 Conclusion References This book, the second volume of Advances in Agricultural and Industrial Microbiology is the compilation of modern technologies with scientific advancement in promoting plant growth by rhizobacterial biostimulants, endophytic microbes, and arbuscular mycorrhizal fungi. The volume also highlights the critical roles of soil microbes in the biocontrol of plant pathogens/diseases, bioremediation of toxic agrochemicals, and nitrogen fixation. Agricultural sustainability and environmental management strongly depend on microbial communities. Management of soil fertility is the key aspect that is facilitated by soil microbes and their interactions. The book also has a section focuses on the in-silico approaches and techniques involved in agriculture which enhances the readers understandings of plant-pathogen interactions, prediction of pathogenicity, improving variety through CRISPER, and its role in the agroindustry. Additionally, the interventions of ICTs (Information and Communication Technologies) have benefited agricultural stakeholders, i.e., farmers to policymakers, in predicting and combating them. The covered topics of the microbial domain and computational tools have high implications for the researchers, students, faculty, and scientists working on these areas