Bacilli in Agrobiotechnology: Plant Stress Tolerance, Bioremediation, and Bioprospecting (Bacilli in Climate Resilient Agriculture and Bioprospecting)

The third volume of the series ‘Bacilli and Agrobiotechnology’ is comprised of 25 chapters that bring a unique perspective to the readers about Bacillus-mediated biotic and abiotic plant stress tolerance, bioremediation and bioprospecting. These chapters are prepared by the leading scientists of global repute. The negative impacts of agrochemicals such as chemical fertilizers and pesticides on human health and environment are paramount. Bacillus and allied genera of beneficial plant-associated microbes are presenting beacon of hope to the farmers, plant scientists and stewards of environment. Several chapters of this volume focus on the induction of various signaling pathways in plants by Bacillus spp. to alleviate biotic and abiotic stresses impacted by global climate change Agricultural lands contaminated with heavy metals affect the ecological food chain starting from crop cultivation. How the toxic effects of trace metals originating from industrial effluents and agrochemicals can be remediated? This book addresses how to overcome these issues by applying elite strains of Bacillus. Bioprospecting is a systematic and organized search for conversion of bioresources to industrially important products by utilizing microbe-derived metabolites. This volume is enriched by including the bioprospecting aspects mediated by Bacillus spp. with novel insights. Contents Chapter 1: Heavy Metal Removal by Bacillus for Sustainable Agriculture 1.1 Introduction 1.2 Heavy Metal Toxicity 1.3 Heavy Metal Stress in Agriculture 1.4 Bacillus and Bioremediation 1.5 Heavy Metal Removal by Bacillus 1.5.1 Cadmium 1.5.2 Chromium 1.5.3 Cobalt 1.5.4 Copper 1.5.5 Iron 1.5.6 Lead 1.5.7 Manganese 1.5.8 Mercury 1.5.9 Nickel 1.5.10 Other Metals 1.6 Conclusions and Future Perspectives References Chapter 2: Peptide Antibiotics Produced by Bacillus Species: First Line of Attack in the Biocontrol of Plant Diseases 2.1 Introduction 2.2 Generalities of Antagonistic Bacillus Species 2.3 Bacillus Peptide Antibiotics 2.4 Biosynthesis and Characteristics of Bacillus Peptide Antibiotics 2.4.1 Non-ribosomal Peptide Antibiotics 2.4.2 General Mechanism of Action of Bacillus Lipopeptides 2.4.3 Ribosomally Synthesized Peptide Antibiotics 2.4.3.1 General Mechanisms of Action of Bacteriocins 2.5 Engineering of Peptide Antibiotics 2.6 Conclusion References Chapter 3: Discovery of Bioactive Natural Products from Bacillus Species: Chemistry, Biosynthesis and Biological Activities 3.1 Introduction 3.2 Isolation and Taxonomic Diversity of Bacilli 3.3 Purification and Identification of Bioactive Compounds 3.4 Bioactive Compounds Isolated from Bacillus spp. 3.4.1 Lipopeptides 3.4.2 Polyketides/Lipoamides 3.4.3 Isocoumarins 3.4.4 Fatty Acids 3.4.5 Macrolactins 3.4.6 Enzymes 3.5 Detoxification of Heavy Metals 3.6 Bacillus Strains as a Source of Bioactive Compounds 3.6.1 Antimicrobial Compounds 3.6.2 Insecticidal Compounds 3.6.3 Antinematicidal Compounds 3.7 Bacillus Isolates as a Potential Source of Natural Carotenoids 3.8 Genetics and Biosynthesis Pathways 3.9 Conclusions and Future Perspectives References Chapter 4: The Industrially Important Enzymes from Bacillus Species 4.1 Introduction 4.2 Proteases 4.3 Amylases 4.4 Galactosidases 4.5 Pullulanases 4.6 β-glucanases 4.7 Xylanases 4.8 Cellulases 4.9 Chitinases 4.10 Esterases and Lipases 4.11 Levansucroses 4.12 Keratinases 4.13 Conclusions and Perspectives References Chapter 5: Bacillus Species and Their Invaluable Roles in Petroleum Hydrocarbon Bioremediation 5.1 Introduction 5.2 The Chemistry of Hydrocarbons in Petroleum Crude Oil 5.2.1 Toxicity and Fate of Petroleum Hydrocarbons in the Environment 5.3 Bioremediation 5.3.1 Biostimulation and Bioaugmentation Methods for Bioremediation 5.3.2 The Potential of Microorganisms for Hydrocarbon Bioremediation 5.3.3 The Mechanisms Employed by Bacillus spp. for Bioremediation of Hydrocarbons 5.3.3.1 Surfactants and Biosurfactants for Bioavailability of Pollutants 5.3.3.2 Bacterial Chemotaxis, Flagellar Motility and Biofilm Formation 5.3.3.3 Uptake and Trans-membrane Transport of Hydrocarbons 5.3.4 Enzymatic Approach for Bioremediation of Hydrocarbons 5.3.4.1 Enzymatic Degradation of Aliphatic Hydrocarbons 5.3.4.2 Enzymatic Degradation of Aromatic Hydrocarbons 5.4 Conclusion References Chapter 6: Current Understanding and Future Directions of Biocontrol of Plant Diseases by Bacillus spp., with Special Reference to Induced Systemic Resistance 6.1 Introduction 6.2 Bacillus Diversity and Antagonism 6.3 Mechanism of Induction of Resistance Against Plant Disease by Bacillus spp. 6.3.1 Competition for Nutrients 6.3.2 Synthesis and Excretion of Lytic Enzymes 6.3.3 Production of Lipopeptides and Antibiotics 6.4 Induction of Resistance in Plants 6.4.1 Bacillus Against Fungi 6.4.2 Bacillus Against Nematodes 6.4.3 Bacillus Against Bacterial Pathogens 6.4.4 Bacillus Against Viral Phytopathogens 6.5 Genomics and Molecular Basis of Induction Resistance by Bacillus on Plant 6.6 Commercial Applications of Bacillus Species 6.7 Mode of Application of Bacillus Species 6.8 Conclusion References Chapter 7: Enhanced Root Morphogenesis in Non-legumes as Induced by Rhizobacteria Bacillus spp. 7.1 Introduction 7.2 Mode and Mechanism of Beneficial Effects 7.2.1 Colonization of Bacteria 7.2.2 Enhanced Root Growth and Development 7.2.3 Root Hair 7.2.4 Lateral Roots Formation 7.2.5 Role of Auxin in Lateral Root Initiation 7.2.6 Secretion of Hormone and Translocation Through Root System 7.2.7 Translocation of Phytohormone Through Root System 7.3 Conclusions and Future Perspective References Chapter 8: Mechanisms Involved with Bacilli-Mediated Biotic and Abiotic Stress Tolerance in Plants 8.1 Introduction 8.2 Major Abiotic Stresses and Their Impacts on Crop Growth and Yield 8.2.1 Mechanisms of Abiotic Stress Alleviation 8.2.1.1 Mechanisms to Mitigate Drought Stress on Plants 8.2.1.2 Bacillus-Mediated Mechanisms of Mitigating Drought Stress 8.2.1.3 Extent and Impact of salinity Stress on Plants 8.2.1.4 Bacillus-Based Mechanism of Salinity Stress Tolerance 8.2.1.5 Impact of Heavy Metal Stress on Plants 8.2.1.6 Bacillus-Based Heavy Metal Stress Alleviation in Plants 8.2.1.6.1 Adsorption and Absorption of Heavy Metal by Bacillus 8.2.1.6.2 Bioleaching 8.2.1.6.3 Other Mechanisms of Bacillus-Based Heavy Metal Remediation 8.2.1.7 Mechanism of Nutrient Stress Alleviation by Bacillus 8.3 Biotic Stress Mitigation in Plants by Bacillus spp. 8.3.1 Extent and Impact of Biotic Stress on Crop Growth and Productivity 8.3.2 Mechanism of Biotic stress Mitigation in Plants by Bacilli 8.3.2.1 Depriving Biotic Agents by Outcompeting them for Nutrients and Space 8.3.2.2 Production of Inhibitory Biochemicals by Bacillus 8.3.2.2.1 Specific Mechanism Associated with Activity of Cyclic Peptides 8.3.2.3 Induction of Host Defense against Biotic Stress 8.3.3 Mechanism of Bacterial Disease Prevention by Bacillus Spp. 8.3.4 Mechanism of Fungal Disease Control 8.3.5 Mechanism of Nematode and Virus Disease Control by Bacillus 8.4 Mechanism of Insect Stress Alleviation in Plants by Bacillus 8.5 Conclusion and Future Perspectives References Chapter 9: Amelioration of Salinity Stress by Bacillus Species as Promoters of Plant Growth in Saline Soil 9.1 Introduction 9.2 Diversity of Salt-Tolerant PGPR Bacteria 9.3 The Genus Bacillus Is a Good Source for Making a Green Revolution in the Saline Area 9.4 Induction of Salt Tolerance in Plant by the Bacillus Species 9.5 Conclusion and Future Trends References Chapter 10: Bacillus spp. of Ruminant Origin as Major Sources of Potential Industrial Amylases 10.1 Introduction 10.2 Mechanism of Action and Structure Variation of Amylases 10.2.1 Endoamylases 10.2.2 Exoamylases 10.2.3 Debranching Enzymes 10.2.4 Glucotransferases 10.3 Source of Microbial Amylases 10.4 Amylase Enzyme Production by Bacillus spp. in the Ruminant’s GIT 10.5 Industrial Application of Amylases 10.5.1 Biofuel Production 10.5.2 Therapeutic 10.5.3 Brewing 10.5.4 Paper and Pulp 10.5.5 Textile 10.5.6 Bioremediation 10.5.7 Detergent 10.5.8 Medicine and Analytical 10.5.9 Baking 10.5.10 Other Applications 10.6 Future Research Outlooks 10.7 Concluding Remarks References Chapter 11: Bacilli and Sustainable Jhum Agrobiotechnology 11.1 Introduction 11.1.1 Bacillus and Its Distribution in Soil 11.2 Bacillus as a Potential PGPR for Agriculture: Roles and Reports 11.2.1 Bacillus, a PGPR 11.2.1.1 Bacillus as a P Solubiliser 11.2.1.2 Role in IAA 11.2.1.3 Bacillus in the Indirect Mechanism of Plant Growth Promotion 11.2.2 Bacillus in Agricultural Use 11.3 Bacillus Diversity in a Jhum System of Farming 11.4 Bacillus and Their PGP Role in Jhum Agroecosystem 11.5 Bacillus Bioinoculants in Jhum Fields: In Vitro and In Situ Applications 11.6 Conclusion References Chapter 12: Bacillus Species of Ruminant Origin as a Major Potential Sources of Diverse Lipolytic Enzymes for Industrial and Therapeutic Applications 12.1 Introduction 12.2 Rumen Microbiota as a Bacillus Habitat 12.3 Lipolytic Enzymes 12.3.1 Esterases 12.3.2 Phospholipases 12.3.3 Lipases 12.3.3.1 Lipase-Catalyzed Reaction 12.3.3.2 Lipase Structure and Mechanism of Action 12.3.3.2.1 Lipase Structure 12.3.3.2.2 Mechanism of Action 12.3.3.3 Properties of Lipases 12.3.3.3.1 Stability in Organic Solvents 12.3.3.3.2 Tolerance to High and Low Temperatures 12.3.3.3.3 Tolerance to Alkaline and Acidic pHs 12.3.3.4 Classification of Lipases Based on Substrate and Region-Specificity 12.4 Sources of Lipase 12.4.1 Plant Lipase 12.4.2 Animal Lipase 12.4.3 Microbial Lipase 12.4.3.1 Fungal Lipase 12.4.3.2 Bacterial Lipase 12.5 Mining of Bacterial Lipase 12.5.1 Conventional Method 12.5.2 Metagenomic Approach 12.5.2.1 Sequence-Based Metagenomic Approach 12.5.2.2 Function-Driven Metagenomic Approach 12.6 Application of Lipases 12.6.1 Industrial Applications 12.6.1.1 Food Industry 12.6.1.1.1 Fat and Oil Industry 12.6.1.1.2 Dairy Industry 12.6.1.1.3 Meat Processing Industry 12.6.1.1.4 Bakery Industry 12.6.1.2 Detergent Industry 12.6.1.3 Pulp and Paper Industry 12.6.1.4 Leather Industry 12.6.1.5 Textile Industry 12.6.1.6 Cosmetics 12.6.1.7 Agrochemical Industry 12.6.1.8 Waste Management 12.6.2 Therapeutic Applications 12.6.3 Biodiesel Production 12.7 Conclusion and Future Prospects References Chapter 13: Bacillus spp. Facilitated Abiotic Stress Mitigation in Rice 13.1 Introduction 13.2 Abiotic Stresses 13.2.1 Drought 13.2.2 Effect of Drought Stress in Rice Crop 13.3 Salt Stress 13.3.1 Effect of Salt Stress in Rice Crop 13.4 Heavy Metal Stress 13.4.1 Effect of Heavy Metal Stress in Rice Crop 13.5 Temperature Stress 13.5.1 Effect of Temperature (Heat and Cold) Stress in Rice Crop 13.6 Plant-Microbe Interaction Assisting Stress Tolerance 13.7 Bacillus spp.: A Multifunctional Toolbox 13.8 Bacillus spp. Mediated Alleviation of Abiotic Stress in Rice 13.8.1 Drought Tolerance by Bacillus spp. 13.8.2 Salinity Tolerance by Bacillus spp. 13.8.3 Heavy Metal Tolerance by Bacillus spp. 13.8.4 Temperature Tolerance by Bacillus spp. 13.9 Conclusion References Chapter 14: Growth Enhancement and Bioremediation of Heavy Metal in Crop Plants Through Bacillus Species Application 14.1 Introduction 14.2 Production of Plant Growth Promoting (PGP) Substances by Bacillus Species 14.2.1 Production of PGP Substances by Individual Bacillus Species Under Culture Conditions Supplemented with Heavy Metal 14.2.2 Production of PGP Substances by Bacillus Species in Association with Plants 14.2.3 Role of Phytohormone (IAA) and Enzyme (ACC Deaminase) in Mitigating the Heavy Metal Stress in Plants 14.3 Bacillus Species and Heavy Metal Transformation, Detoxification, and Mobilization 14.4 Physiological and Biochemical Mechanisms of Heavy Metal Tolerance of Bacillus 14.5 Molecular and Genetic Basis for Plant Growth Promotion and Heavy Metal Tolerance Ability of Bacillus Species 14.6 Enhancement of Plant Growth and Heavy Metal Tolerance of Plants in Association with Different Species of Bacillus 14.7 Conclusions and Future Perspective References Chapter 15: Bacillus Probiotics and Bioremediation: An Aquaculture Perspective 15.1 Introduction 15.2 The Concept of “Water Probiotic” and Microbial Community Manipulation 15.3 Application of Bacillus as Bioremediator in Aquaculture 15.4 Mechanism of Bioremediation by Bacillus spp. 15.5 Conclusions References Chapter 16: Enhanced Nutrient Accumulation in Non-leguminous Crop Plants by the Application of Endophytic Bacteria Bacillus Species 16.1 Introduction 16.2 Beneficial Effects of Endophytes on Accumulation of Nutrients in Non-legumes 16.2.1 Mechanism of Beneficial Effects of Bacillus Spp. on Plants 16.2.2 Phytohormone Production in Relation to More Root Growth for Higher Nutrient Uptake 16.2.3 Atmospheric Nitrogen (N2) Fixation 16.2.4 Transfer of Fixed N2 to Host Cell 16.2.5 Solubilisation of Soil Insoluble Phosphates 16.2.6 Enhancement of K Uptake by Plants 16.2.7 Improvement of Ca Uptake and Absorption by Plants 16.2.8 Influence of Endophytic Bacilli on Uptake and Absorption of Mg by Plants 16.2.9 Influence of Bacillus Spp. on Siderophores Production and Iron Uptake 16.3 Conclusion and Future Perspectives References Chapter 17: Role of Bacillus Species in Alleviating Biotic Stress in Crops 17.1 Introduction 17.2 Alleviation of Biotic Stress in Plants by the Bacillus Species 17.2.1 Molecular Mechanisms Behind Inducible Resistance (SAR and ISR) 17.2.2 Crop Protection from Pathogenic Fungi by the Application of Bacillus spp. 17.2.3 Bacillus spp. in Prevention of Bacterial Diseases 17.2.4 Bacillus in Pest/Insect/Nematode Control and Bacillus-Based Commercial Products 17.3 A Comparison of Biopesticides and Synthetic Pesticides 17.4 Future Perspective 17.5 Conclusion References Chapter 18: Bacilli and Polyhydroxyalkanoates: An Intracellular Granule Having Promising Feature as a Resource for Production of Bioplastics 18.1 Introduction 18.2 Biodegradable Biopolymer: Polyhydroxyalkanoates 18.2.1 Monomeric PHA and Its Derivatives 18.2.2 PHA as Carbon and Energy Reserves for Prokaryotes 18.2.3 Structure of PHA 18.2.4 Comparative Aspects of Plastics and PHA 18.3 Bacilli and PHA 18.3.1 Diversity of PHA-Producing Bacillus Species 18.3.2 Nutrients Essential for PHA Production by Bacilli 18.3.3 Metabolic Overview for PHA Production in Bacilli 18.3.4 Molecular Evidences for PHA Production by Bacilli 18.3.5 Strategy for PHA Accumulation and Recovery 18.3.6 Techniques Involved in Characterization of PHA 18.3.7 Challenges for Bacilli to Produce PHA 18.3.8 Approaches for Improving Properties of PHA for Industrial Application 18.3.9 Commercial Applications of PHA Obtained from Bacilli 18.3.10 PHA Depolymerase of Bacilli and Biodegradation 18.4 Future Prospects 18.5 Conclusions References Chapter 19: Bacillus as a Versatile Tool for Crop Improvement and Agro-Industry 19.1 Introduction 19.2 Functions of Bacillus Various Metabolites 19.2.1 Enzymes 19.2.2 Biopolymer 19.2.3 Protein Crystal 19.2.4 Antimicrobial Agents 19.2.4.1 Bacteriocin 19.2.4.2 Lipopeptides 19.2.4.3 Polyketides 19.2.4.4 Zwittermicin A 19.2.4.5 Terpenoids 19.2.5 Insecticides and Pesticides 19.2.6 Nematocides 19.3 Stress Tolerance 19.3.1 Water Stress 19.3.2 Salt Stress 19.3.3 Heavy Metal Stress 19.3.4 Temperature Stress 19.3.5 Radiation Stress 19.4 Plant Growth Promotion 19.4.1 Plant Growth Promotion Hormone 19.4.2 Siderophore 19.5 Conclusion References Chapter 20: Mechanisms of the Beneficial Effects of Probiotic Bacillus spp. in Aquaculture 20.1 Introduction 20.2 Bacillus in Aquaculture 20.3 Competition for Nutrients and Energy 20.4 Exo-enzymes Produced by Bacillus 20.5 Production of Organic Acids 20.6 Production of Antioxidant Enzymes by the Bacillus spp. 20.7 Mechanisms of Suppression of Fish Pathogens by the Probiotic Bacillus spp. 20.7.1 Production of Bacteriocins 20.7.2 Quorum Quenching 20.7.3 Suppression of Fish Pathogens by the Production of Lytic Enzymes by Probiotic Bacillus spp. 20.7.4 Production of Antibiotics 20.7.5 Enhancement of Immune Response in Fish 20.7.5.1 Nonspecific Immunity 20.7.5.2 Immune Gene Expression in Host 20.8 Enhancement of Abiotic Stress Tolerance 20.9 Repair Tissue Damage in Farmed Fishes 20.10 Water Quality Enhancement 20.11 Conclusions References Chapter 21: Bacillus spp.-Mediated Drought Stress Tolerance in Plants: Current and Future Prospects 21.1 Introduction 21.2 Impact of Drought on Crop Productivity 21.3 Bacillus spp. Root Colonization and its Role in Plant Growth Improvement 21.3.1 Nutrient Acquisition and Phytohormones Production by Bacillus spp. in Plants 21.3.2 Indirect Plant Growth Promotion by Suppressing Phytopathogens 21.4 Bacillus spp. for Mitigating the Impact of Drought Stress 21.4.1 Antioxidant Defenses and ROS 21.4.2 Modification of Phytohormonal Activities to Impart Drought Tolerance in Plants 21.4.3 Control of ET Levels by ACC Deaminase 21.4.4 ROS-Scavenging Antioxidant Enzymes 21.4.5 Drought Stress Tolerance Induced by the Accumulation of Osmolytes, Soluble Sugars, Exopolysaccharides (EPS), and Bacterium-Derived Volatiles 21.5 Mechanisms of Bacillus spp.-Mediated Drought Tolerance 21.6 Molecular Mechanisms in Alleviating Drought Stress by Bacillus spp. 21.7 Mass Production, Formulation, and Applications of Bacillus spp. 21.8 Conclusion and Future Prospects References Chapter 22: Unveiling the Potential of Bacillus sp. in Bioremediation and Biocontrol 22.1 Introduction 22.2 Role of Bacillus sp. in Bioremediation Process 22.2.1 Mechanism of Microbial Bioremediation 22.2.1.1 Mobilization 22.2.1.2 Enzymatic Oxidation 22.2.1.3 Enzymatic Reduction 22.2.1.4 Complexation 22.2.1.5 Siderophores Production 22.2.1.6 Immobilization 22.2.1.7 Precipitation or Solidification 22.3 Factors Affecting Bioremediation Process 22.4 Role of Bacillus sp. in Remediating Different Contaminants 22.4.1 Volatile Organic Compounds 22.4.2 Heavy Metal Remediation by Bacillus sp. 22.5 Production of Bioactive Compounds as Tools for Biocontrol of Phytopathogens 22.5.1 Polypeptides 22.5.2 Lipopeptides 22.5.3 Fatty Acids 22.5.4 Macrolactins 22.5.5 Induced Systemic Resistance as a Mode of Biocontrol by Bacillus 22.6 Conclusions and Prospects References Chapter 23: Impacts of Bt Brinjal on Economic Benefit of Farmers and Environmental Sustainability in Bangladesh 23.1 Introduction 23.2 The Developmental Concept of Bt Brinjal in Bangladesh 23.2.1 History of Bt Brinjal 23.3 Structure and Mode of Action of Cry1Ac Protein 23.4 The Economic Benefit Incurred by the Bt Brinjal Growers 23.4.1 Rapid Adoption 23.4.2 Cost of Production 23.4.3 Net Return from Brinjal Production 23.4.4 Higher Market Price of Bt Brinjal 23.5 The Economic Impact of Bt Technology Worldwide 23.6 The Maintenance of Environmental Sustainability by the Cultivation of Bt Brinjal 23.6.1 Reduction of Pesticide Use Ensures Toxic-Free Environment 23.6.2 The Effect of Bt Crops on Nontarget Organism (NTO) 23.6.2.1 Effect on Soil Arthropods 23.6.2.2 Effect on Pollinators 23.6.2.3 Effect on Biological Control Agents 23.6.3 Establishment and Persistence of Cry1Ac-Expressing Plants in the Environment 23.7 Conclusions References Chapter 24: Bacillus subtilis: A Multifarious Plant Growth Promoter, Biocontrol Agent, and Bioalleviator of Abiotic Stress 24.1 Introduction 24.2 Bacillus subtilis as Plant Growth-Promoting Bacterium (PGPB) 24.2.1 Influence of B. subtilis on Physiological Parameters of Vegetables, Cereals, and Other Plants 24.3 Biocontrol Potential of B. subtilis 24.3.1 Mechanisms Involved in Biocontrol 24.3.1.1 Induction of Host Enzymes Such as Peroxidase, Polyphenol Oxidase, Superoxide Dismutase 24.3.2 B. subtilis as a Biocontrol Representative in Different Crops 24.4 Alleviation of Abiotic Stress by B. subtilis 24.4.1 Antioxidant Enzymes in Stress Management 24.5 Conclusion References Chapter 25: Bacillus thuringiensis Proteins: Structure, Mechanism and Biological Control of Insect Pests 25.1 Introduction 25.2 Bt Toxin Diversity 25.3 Structure and Specificity of Bt Proteins 25.3.1 Cry Toxins 25.3.2 Cyt Toxins 25.3.3 Vip Toxins 25.4 Mechanism of Action of Bt Proteins 25.4.1 Mechanism of Action of Cry Proteins 25.4.2 Mechanism of Action of Cyt Proteins 25.4.3 Mechanism of Action of Vip Proteins 25.5 Bt Products for Biological Control of Insect Pests 25.5.1 Bt Biopesticides 25.5.2 Bt Crops 25.5.2.1 Bt Maize 25.5.2.2 Bt Cotton 25.5.2.3 Bt Soybean 25.5.2.4 Bt Rice 25.5.2.5 Bt Eggplant 25.6 Conclusion References Index