Bacterial Endophytes for Sustainable Agriculture and Environmental Management

This book is a comprehensive account of recent advances in the endophytic research. It covers recent perspective of endophytic research, molecular diversity, bioprospecting of novel genes using high throughput molecular techniques, and most importantly application of endophytes in practicing sustainable agriculture. Endophytic micro-organisms are mysterious living component associated mutually with plant roots and soil microbes. Various endophytic bacteria have attracted considerable attention for their ability to promote plant growth through direct mechanisms or by acting as biocontrol agents. Endophytes also find use in biocontrol, medicine, agriculture and food industry. This is a useful reading for the student of agriculture, environmental microbiology and biotechnology. Contents About the Editors 1: Endophytic Bacteria: Application Against Biotic and Abiotic Stresses and Plant Health Improvements for Sustainable Agricult... 1.1 Introduction 1.2 Importance of Endophyte 1.3 Isolation of Endophytes from Plants 1.4 Application of Endophytes Microorganism in Biotic and Abiotic Stresses 1.4.1 Anti-Fungal Activity of Endophytes 1.4.2 Antibacterial Activity of Endophytes 1.4.3 Plant Growth Promoters (PGPR) 1.4.4 Applications of Endophytes in Soil pH Stress 1.4.5 Applications of Endophytes in Drought Tolerance 1.4.6 Applications of Endophytes in Soil Salinity Tolerance References 2: Endophytic Bacteria: Mitigating Abiotic Stress from Inside 2.1 Introduction 2.2 Diversity of Endophytic Bacteria and Associated Abiotic Stresses 2.3 Endophytes and the Molecular Defence Response 2.4 The Role of Multi-Omics: A Better Understanding of Molecular Interactions 2.5 Genomics and Metagenomics 2.6 Transcriptomics and Meta-transcriptomics 2.7 Proteomics and Meta-proteomics 2.8 Interactomics and Metabolomics 2.9 Integration of Multi-omics and Discovery of New Data 2.10 Conclusion References 3: Diversity and Bioactive Potential of Endophytic Bacteria from High-Value Medicinal Plants 3.1 Introduction 3.2 Diversity of Endophytic bacteria Associated to Medicinal Plants 3.2.1 Culture-Dependent Diversity 3.2.2 Diversity Based on Culture-Independent Methods 3.3 Applications of Endophytic bacteria 3.3.1 Pharmaceutical and Medical Applications 3.3.1.1 Alkaloids 3.3.1.2 Terpenoids 3.3.1.3 Flavonoids 3.3.1.4 Peptides and Their Derivatives 3.3.1.5 Quinones 3.3.1.6 Phenols 3.3.1.7 Antibiotics 3.3.2 Plant Growth Promotion Abilities 3.4 -Omics in Plant-Microbe Interactions Study 3.5 Conclusion and Prospects References 4: Plant Growth Promoting Rhizobacteria (PGPR)-Assisted Phytoremediation of Contaminated Soils 4.1 Introduction 4.2 Rhizomicrobiome 4.2.1 Plant Growth Promoting Rhizobacteria 4.3 Role of PGPRs in Phytoremediation 4.3.1 Role of Rhizobacteria in Phytoremediation of Contaminated Soil 4.3.1.1 Metal-Contaminated Soil 4.3.1.2 Petroleum-Contaminated Soil 4.4 From the Lab to the Field and Commercialization 4.5 Genetics and Genomics of Heavy-Metal Resistance in PGPRs 4.5.1 Genetically Engineered PGPRs 4.6 Conclusion References 5: Endophytic Bacteria: Role in Phosphorous Solubilization 5.1 Introduction 5.2 Colonization of Bacterial Endophytes 5.3 Role of Bacterial Endophytes in Phosphorous Solubilization 5.4 Mechanism of Soil P-Solubilization 5.4.1 Mechanism of Organic P-Solubilization 5.4.1.1 Phosphatases 5.4.1.2 Phytases 5.4.1.3 C-P Lyases and Phosphonatases 5.4.2 Inorganic P Solubilization 5.4.2.1 Role of Proton Liberation P- Solubilization 5.4.2.2 Role of Siderophores in Mineral P- Solubilization 5.4.2.3 Role of Exopolysaccharides in Phosphate Solubilization 5.4.3 Plant Growth Promoting Attributes of P-Solubilizing Endophytic bacteria 5.4.4 Genetics of Phosphate Solubilization 5.4.4.1 Genetics of Inorganic Phosphate Solubilization 5.4.4.2 Genetics of Organic P Mineralization 5.4.5 Bacterial Endophytes as Crop Bio-Inoculant 5.4.6 Conclusions References 6: Endophytes of Medicinal Plants: Diversity and Bioactivity 6.1 Introduction 6.2 Entry and Colonization of Endophytes 6.3 Movement and Localization of Endophytes 6.4 Medicinal Plants 6.5 Endophytic Diversity in Medicinal Plants 6.6 Endophytic Microbes in Metabolites Production 6.7 Conclusion and Future Prospects References 7: Biotechnological Applications of Bacterial Endophytes 7.1 Introduction 7.2 History of Endophytes 7.3 Endophytes and Their Mode of Association with Host 7.3.1 Symbiotic Association of Fungi with Host 7.3.2 Symbiotic Association of Endophytic Bacteria with Host 7.3.3 Cyanobacterial Association with Host 7.3.4 Interaction of Endophytes to Increase Resistance to Biotic and Abiotic Stress 7.4 Host Associated Biotic Factors and Endophyte Ecology 7.4.1 Endophytes Attracted by the Host Plants 7.4.2 Entry of Endophytic Microbes Through Root Into the Plants 7.4.3 Colonization of Endophytes by Roots of the Plant 7.4.4 Entry and Colonization of Endophytes by Aerial Parts of the Plants 7.5 Physiology and System Diversity in Association 7.5.1 Crucial Changes in Plant Physiology Due to Bacterial Endophytes 7.5.2 Diversity of Endophytic Bacteria and Their Association with Host 7.5.3 Factors Affecting the Diversity in Host Plants 7.5.3.1 Endophytic Species and Strains 7.5.3.2 Host Plant 7.5.3.3 Environmental Conditions 7.6 Molecular Events During the Endophytes Association 7.6.1 Molecular CounterAction Upon Endophytic Association in Plants 7.6.1.1 Defensive Response of Host Plant 7.6.1.2 Activation of Plants Immune System 7.6.1.3 Biotic and Abiotic Stress Remediator 7.6.1.4 Protection from Reactive Oxygen Species 7.6.1.5 Modulation of Protein Secretion Systems 7.6.1.6 Phytoremediation Mediated by Endophytic Microbes in Association with Host Plant 7.7 Application of Endophytes 7.7.1 Endophytes in Agriculture 7.7.2 Endophytes in Industry 7.7.3 Endophytes in Nanobiotechnology 7.7.4 Endophytes in Pharmaceutical 7.7.4.1 Antimicrobial Compounds 7.7.4.2 Anti-Cancerous Compounds 7.7.4.3 Antibiotics 7.8 Conclusion References 8: Genetic Basis of Fungal Endophytic Bioactive Compounds Synthesis, Modulation, and Their Biotechnological Application 8.1 Introduction 8.2 The Genetic Basis of Secondary Metabolites Production 8.2.1 Important Biosynthetic Gene Clusters in Endophytes 8.2.1.1 NRPS Gene Clusters 8.2.1.2 Polyketide Synthases Gene Clusters for Maklamicin Biosynthesis 8.2.1.3 Indole-Diterpenes Gene Cluster 8.2.1.4 Loline Biosynthetic Gene Cluster 8.3 Potential of Endophytic Bioactive Compounds 8.3.1 Antioxidant Activity 8.3.2 Antimicrobial Activity 8.3.3 Antiviral Activity 8.3.4 Anticancer Activity 8.3.5 Antidiabetic Activity 8.3.6 Insecticidal Activity 8.4 Strategy for Production of Endophytic Secondary Metabolites 8.5 Major Obstacles to the Production of Bioactive Compounds from Endophytes 8.6 Conclusion and Future Prospects References 9: Endophytic Bacteria for Plant Growth Promotion 9.1 Introduction 9.2 Ecology and Diversity 9.3 Mechanism of Plant Growth Promotion 9.3.1 Direct Mechanism 9.3.1.1 Nutrient Acquisition 9.3.1.2 Phytohormone Production 9.3.1.3 Ethylene Level Maintenance and Role of 1-Aminocyclopropane-1-Carboxylase (ACC) Deaminase 9.3.2 Indirect Mechanism 9.4 Gene Responsible for Plant Growth 9.5 Agricultural Application of Bacterial Endophytes 9.5.1 Growth Promotion 9.5.2 Phytoremediation 9.6 Conclusion References 10: Bacterial Endophytes and Bio-nanotechnology 10.1 Introduction 10.2 Applications of Bacterial Endophytes 10.3 Biosynthesis of Nanoparticles Using Endophytic Bacteria 10.3.1 Isolation of Endophytic Bacteria from Plant Leaves 10.3.2 Biosynthesis of Nanoparticles Using Endophytic Bacterial Culture 10.4 Advantages Over Conventional Nanoparticles 10.5 Discussion 10.6 Future Prospects References 11: Role of Endophyte Metabolites in Plant Protection and Other Metabolic Activities 11.1 Introduction 11.2 Endophytic Bacteria 11.3 Plant Colonization by Endophytic Bacteria 11.4 Endophytic Bacteria Diversity 11.5 Bioactive Compounds synthesized by Bacterial Endophytes 11.6 Modulation of Plant ́s Defence by Endophytes 11.7 Endophytic Metabolites in Plant Protection 11.7.1 Direct Mechanism 11.7.1.1 Antibiosis 11.7.1.2 Synthesis of Lytic Enzymes 11.7.1.3 Essential Nutrients: Availability and Competition 11.7.2 Indirect Mechanism 11.7.2.1 Phytohormone Modulation 11.7.2.2 Stress Tolerance 11.7.2.3 Bioremediation 11.8 Conclusion References 12: Role of Bacterial Endophytes in the Promotion of Plant Growth 12.1 Introduction 12.2 Endophytes Biodiversity 12.3 Isolation, Identification and Colonization of Endophytes 12.4 Strategies Employed by Endophytes for Plant Growth Promotion 12.5 Applications of Bacterial Endophytes 12.5.1 Bacterial Endophytes in Plant Growth Promotion 12.5.2 Endophytes-Mediated Biodegradation of Soil Contaminants 12.5.3 The Bacterial Endophytes Towards Inhibition of Plant Pathogens 12.5.4 Endophytes Maintain the Free Radicals in the Plant Tissue 12.6 Concluding Remarks and Future Perspectives References 13: Bacterial Endophytes and Abiotic Stress Mitigation 13.1 Introduction 13.2 International and Indian Scenario of Various Abiotic Stress 13.3 Plant Responses to Abiotic Stress 13.3.1 Drought and Heat Stress 13.3.2 Salt Stress 13.3.3 Cold Stress 13.3.4 Heavy Metal Stress 13.3.5 Other Abiotic Stresses 13.4 Diversity and Colonization of Bacterial Endophytes 13.5 Endophytic Bacteria as Mitigants for Various Abiotic Stress 13.5.1 Production of Phytohormones 13.5.2 Production of Exopolysaccharides (EPS) 13.5.3 1-aminocyclopropane-1-carboxylate (ACC) Deaminase Production 13.5.4 ROS Production 13.6 Role of Endophytic Bacteria in Mitigation of Heavy Metal Stress 13.7 Gene Expression Under Abiotic Stress in Plants Inhabited with Endophytes 13.8 Conclusion References