Microbial Consortia in Plant Science and Sustainable Agriculture

Ajay Tomar is an Assistant Professor at the Amity Institute of Organic Agriculture at Amity University Uttar Pradesh, India. Ajay Kumar is an Assistant Professor at the Amity Institute of Biotechnology at Amity University in Noida, India. Ramsés Ramón González Estrada is a Professor in the National Technological Institute of Mexico. Kshitij Parmar works in the Amity Institute of Organic Agriculture at Amity University Uttar Pradesh, India.

• List of Contributors xiii1 Microbial Consortia Used as Biofertilizers and Biocontrol Agents in Agriculture 1Tomás Rivas-García, Pablo Preciado-Rangel, Bernardo Murillo-Amador, Rita Schwentesius-Rindermann, Ramsés Ramón González Estrada, Benjamín Hernandez-Vazquez, and Juan Antonio Torres-Rodríguez1.1 Introduction 11.2 Microbial Consortia 21.3 Microbial Consortia for Plant Nutrition 31.4 Microbial Consortia for Plant Protection 51.5 Microbial Consortia Development and Production 71.6 Microbial Consortia’s Challenges and Limitations 81.7 Conclusions and Future Perspectives 82 Microbial Consortia to Increase Crop Resilience to Drought Stress 15Juan Antonio Torres-Rodriguez, Mercedes Susana Carranza-Patiño, Mayra Carolina Vélez Ruiz, Robinson J. Herrera-Feijoo, and Tomás Rivas-García2.1 Introduction 152.2 Selection and Design of Microbial Consortia to Increase Crop Resistance to Drought 162.3 Action Mechanisms of Microbial Consortia Against Drought Stress 182.4 Plant–Microbe Communication 192.5 Microbial Consortia Applied in Drought Stress Mitigation 202.6 Genomic and Biotechnological Advances in Microbial Consortia 242.7 Interactions Between Arthropods and Microbial Consortia in Drought Conditions 242.8 Inert Dusts and Their Synergy with Microbial Consortia in Water Retention 272.9 Leading Countries in Microbial Consortia Research 292.10 Temporal Dynamics of Keywords in Microbial Consortia Studies 302.11 Conclusions or Future Prospective 313 Impediments and Limitations in the Production and Use of Biofertilizers 43Gema Cárdenas-Flores, Ana Yareli Flores-Ramírez, Juan Edgardo Cortés-Aguilera, Martina Alejandra Chacón-López, Selene Aguilera-Aguirre, Rosa Isela Ortiz-Basurto, and Ulises Miguel López-García3.1 Introduction 433.2 Biological and Ecological Factors 443.2.1 Microbial Interactions in the Rhizosphere 443.2.2 Effect of Soil Contaminants on Biofertilizer Efficacy 463.3 Technical and Production Limitations 493.3.1 Solid Formulations 493.3.2 Liquid Formulations 503.3.3 Metabolite-based Formulations 503.3.4 Encapsulation Technology 503.4 Economic Barriers 513.5 Regulatory Challenges in Biofertilizer Commercialization 523.5.1 Regulatory Frameworks in Developed Countries 523.5.2 Global Disparities in Biofertilizer Regulations 533.5.3 The Challenge of GM Biofertilizers 533.6 Social and Cultural Acceptance 543.7 Research and Development 553.8 Conclusions 564 The Regulation of Nutrient Uptake, Transportation, and Physiological Functions of Microbial Consortia in Rice Crop Under Abiotic Stresses 65Mario Alberto Soltero-Rios4.1 Introduction 654.2 Root System in Rice and Essential Nutrients 664.2.1 Root Structure 664.2.2 Essential Nutrients 674.3 Mechanisms of Nutrient Uptake and Transport in Rice 674.3.1 Nutrient Uptake 674.3.2 Nutrient Transport 694.4 Microbial Consortia and Their Role in Rice Nutrition 704.4.1 Rhizosphere Microbes 704.4.2 Phyllosphere Microbes 704.4.3 Endosphere Microbes 714.5 Abiotic Stress in Rice Crops: Effects and Physiological Responses 724.5.1 Drought Stress 724.5.2 Salinity Stress 724.5.3 Flooding Stress 724.5.4 Heat Stress 724.5.5 Cold Stress 734.5.6 Nutrient Deficiency Stress 734.6 Response of Microbial Consortia to Abiotic Stress Conditions 734.6.1 Drought Stress 744.6.2 Salinity Stress 744.6.3 Flooding Stress 754.6.4 Heat and Cold Stress 754.7 Microbial Mechanisms for Enhancing Nutrient Availability Under Abiotic Stress 774.8 Perspectives and Challenges in the Research of Microbial Consortia and Their Regulation Under Stress Conditions 794.9 Conclusions 805 Plant Pathogen-specific PR Proteins Produced in Response to PGPR 89Selene Aguilera-Aguirre, María Fernanda Olmedo-Díaz, Miriam del Carmen Bañuelos-González, Gema Cárdenas-Flores, Ulises Miguel López-García, Rosa Isela Ortiz-Basurto, and Martina Alejandra Chacón-López5.1 Introduction 895.2 Recognition Systems in Plant Immunity 905.3 PR Proteins 915.3.1 PR Protein Classification 925.3.2 Factors That Promote PR Protein Production 935.4 Plant Growth-promoting Rhizobacteria 955.4.1 Mechanism of the Production of PR Proteins by PGPRs 955.4.2 PGPR Inducers of PR Proteins in Plants 965.4.3 PGPR Consortia in the Induction of the Defense System 975.4.4 Application of PGPR Bacteria in Plants and Their Beneficial Effect Against Phytopathogens 985.5 Conclusion 1016 Current and Emerging Molecular Techniques for Microbial Consortia to Diagnose Plant Diseases 111Dalpat Lal, Aparna, Sunidhi Tiwari, Nidhi Bhatt, and Durga Prasad6.1 Introduction 1116.2 Molecular Techniques 1126.2.1 PCR and Its Modification 1126.2.2 DNA Microarray 1146.2.3 DNA Macroarrays 1156.2.4 Fluorescence In Situ Hybridization 1156.2.5 Next-generation Sequencing 1166.2.6 RNA Interference 1166.2.7 CRISPR/Cas Technology 1176.3 Immunological Methods 1186.3.1 Enzyme-linked Immunosorbent Assay 1186.3.2 Lateral Flow Immunoassay 1226.3.3 Aptamers Binding Assay 1246.4 Biochemical Methods 1246.4.1 Flow Cytometry 1246.4.2 Gas Chromatography–Mass Spectroscopy 1256.5 Biosensors 1266.5.1 Classification of Biosensors 1267 Microbes: A New Approach Towards Sustainable Environment 141Abha Sharma, Abhay Sharma, Agrim Rattan, Guneshori Maisnam, and Devashish7.1 Introduction 1417.1.1 Microbial Diversity and Ecosystem Functioning 1437.2 Regulating Services 1507.2.1 Climate Regulation 1507.2.2 Microbial Communities and the Carbon Cycle 1507.2.3 Water Regulation and Purification 1517.2.4 Disease and Pest Regulation 1517.2.5 Biodegradation of Organic Waste and Xenobiotics 1527.2.6 Metal Detoxification 1537.3 Supporting Services 1537.3.1 Microbial Interactions in Soil Formation 1547.3.2 Nutrient Cycling 1547.3.3 Organic Matter Transformation 1557.3.4 Role of Microbes in Plant Growth Promotion 1567.3.5 Soil Microorganisms as Indicators 1567.4 Provisioning Services 1577.4.1 Importance of Microorganisms in Food Processing 1587.4.2 Importance of Microorganisms in Food Production 1587.4.3 Use of Microorganisms in Pharmaceuticals 1597.5 Cultural Services 1607.6 Conclusion 1618 Identification of Plant-derived Microbial Consortium Resistant to Biotic Stress 171Ashwini Ananda, Aditya Kumar, Abha Sharma, Victor Thingujam, and Aashita Shree8.1 Introduction 1718.2 Microbial Diversity in Plant Systems 1728.2.1 Types of Beneficial Plant-associated Microbes 1728.2.2 Common Microbial Genera Associated with Plant Protection 1728.2.3 Role of Microbial Consortia in Plant–Microbe Interactions 1738.3 Mechanisms of Biotic Stress Resistance Mediated by Microbial Consortia 1748.3.1 Direct Mechanisms 1748.3.2 Indirect Mechanisms 1748.4 Methods for Identification and Characterization of Microbial Consortia 1768.4.1 Culture-dependent Approaches 1768.4.2 Culture-independent Molecular Tools 1768.4.3 Biochemical and Physiological Screening 1778.5 Plant-associated Factors Influencing Microbial Consortia Selection 1778.6 Application of Microbial Consortia in Biotic Stress Management 1788.6.1 Development of Bioinoculants and Biopesticides 1788.6.2 Field Application Strategies (Seed Treatment, Foliar Spray, Soil Drenching) and Compatibility with Integrated Pest and Disease Management Programs 1798.6.3 Case Studies of Successful Microbial Consortia in Disease Suppression 1798.7 Conclusion 1819 Support of Microbial Formulations to Achieve the Sustainable Development Goal 2 (SDGs) 189Monika Singh, R.S. Sengar, Karuna Singh, Rakesh, Aastha, Shivani Pal, and Rocky Kumar9.1 Introduction 1899.2 Bioformulation as Plant Growth-promoting Bacteria 1919.2.1 Molecular Approaches in Plant–Microbe Interaction 1959.3 Biofertilizers and Biopesticides as Microbial Bioformulation 1979.4 Bioplastics 1979.4.1 Polyhydroxybutyrates as a Promising Approach to Achieve Zero Hunger 1989.5 Microbial Biochar 2009.6 Bioaugmentation Support to Crop Productivity 2019.7 Microbial Formulations as Bio-control Agents 2029.7.1 Molecular Mechanism of Microbial Cells: As Biocontrol Agents Against Plant Pathogens 2029.8 Microbial Enzymes Promoting Nutrient Uptake 2049.8.1 Soil Enzymes’ Role in Agriculture 2059.8.2 Enzymes Promoting Plant Growth 2059.9 Challenges and Future Prospects 2069.10 Conclusion 20610 The Synergism of Microbial Interactions Impacting Health and the Environment 215Meenakshi Sharma, Raj Kishor Kapardar, and Rajpal Srivastav10.1 Introduction 21510.2 Microbial Synergistic Activities and Antimicrobial Resistance 21610.3 Microbes Alter Metabolism 21710.4 Microbial Synergism, Biofilms, and Plastisphere 21810.5 Conclusive Remarks 219Acknowledgment 21911 Encouraging Probiotics as Plant Stimulants for Sustainable Agriculture Through Microbial Consortium 223Deepika Sharma and Sakshi Singh11.1 Introduction 22311.2 Plant Stimulants as Probiotics 22511.2.1 Different Biostimulants with Different Modes of Action 22711.2.2 Organic Extracts 22711.2.3 Microbial Endophytes 22711.2.4 Role of PGPRs 22811.3 Role of Biostimulants 22911.4 Microbial Consortium-mediated Protection 23111.5 Conclusion 23112 Commercialization Aspects of Microbial Biocontrol Agents 239Saurabh Sharma, Justine Sanasam, Umalaxmi Thingujam, Krishnakumari Yendrembam, and Guneshori Maisnam12.1 Introduction 23912.1.1 History of BCAs 24012.1.2 Mechanisms of Action 24012.1.3 Indirect Mechanisms 24012.1.4 Biocontrol Microorganisms 24212.1.5 Types of Biocontrol Microorganisms 24212.1.6 Applications in Agriculture 24312.1.7 Success Stories in Biocontrol 24412.1.8 Challenges and Future Directions 24412.1.9 Advantages and Disadvantages of BCAs 24412.1.10 Challenges in Adopting BCAs 24612.1.11 Government Regulations on BCAs 24812.1.12 Case Studies of Biocontrol Regulation 24812.1.13 Biocontrol Industries 24912.1.14 Types of BCAs 24912.1.15 Evolution and Development of Biocontrol Industries 25012.1.16 Key Players and Market Dynamics 25012.1.17 Production and Formulation Challenges in the Commercialization of MBAs 25112.1.18 Regulatory and Market Barriers in the Commercialization of MBAs 25212.1.19 Regulatory Barriers 25212.1.20 Market Barriers 25312.1.21 Addressing Regulatory and Market Barriers 25312.1.22 Strategies for Successful Commercialization of MBAs 25412.1.23 Commercialization of BCAs 25612.1.24 Challenges in Commercialization of BCAs 25612.2 Future Prospects 25712.3 Conclusion 25712.3.1 The Future of the Commercialization of BCAs: Opportunities, Challenges, and Pathways Forward 25812.4 Conclusion 25813 Management of Soil-borne Diseases with Trichoderma spp. 263Manoj Kumar Maurya, Vivek Singh, and Ajay Tomar13.1 Introduction 26313.2 Soilborne Pathogens and Their Impact 26413.2.1 Economic Consequences 26413.3 Trichoderma spp. 26513.3.1 Taxonomy of Trichoderma 26513.3.2 Biology of Trichoderma 26513.3.3 Morphology of Trichoderma 26613.3.4 Trichoderma spp. as Biocontrol Agents 26713.3.5 Major Trichoderma spp. 26713.4 Mode of Action/Mechanisms of Trichoderma spp. 26713.4.1 Mycoparasitism 26713.4.2 Antibiosis 26813.4.3 Competition 26813.4.4 Induced Systemic Resistance 26913.5 Effect of Trichoderma spp. Against Soil-borne Phytopathogens 26913.6 Formulation and Application Techniques 27013.6.1 Formulation Types 27013.7 Application Methods of Trichoderma spp. 27013.8 Merit and Demerit of Trichoderma spp. as Biocontrol Agents 27213.8.1 Merit (Advantages) 27213.8.2 Demerit (Limitations) 27213.9 Challenges and Future Prospects of Trichoderma spp. 27213.10 Conclusion 27314 Significance of Microbial Genome Protective Enzymes in Tolerating Synthetic Dyes 279Riya Raghav, Raj Kishor Kapardar, and Rajpal Srivastav14.1 Introduction 27914.2 Variation in Chemical Nature 28014.3 Microbial Pigments 28214.4 Environmental Toxicity 28314.5 Role of Microbes and Genome Protection 28514.6 Control of DNA Damage 28814.7 Conclusive Remarks 289Acknowledgment 29015 Microbial Consortia: Enhanced Availability of Micronutrients and Elimination of Biotic Stresses in Plants 295Vikash Kumar, Lucky Gupta, Saurabh Singh, Nikhil Raghuvanshi, and Lokesh Sisodiya15.1 Introduction 29515.2 Source of Microbial Consortia 29615.2.1 Bacteria 29715.2.2 Fungus 29815.2.3 Actinomycetes 30015.2.4 Viruses 30115.2.5 Algae 30115.3 Microbial Consortia for Biotic Stress 30215.3.1 Microbial Consortia for Plant Diseases 30315.3.2 Microbial Consortia for Pest 30915.4 Microbial Consortia for Micronutrient Availability 31015.4.1 Siderophore Production and Micronutrient Availability 31015.4.2 Zinc-solubilizing Bacteria for Zinc Solubilization and Micronutrient Availability in Crops 31215.4.3 Other Micronutrients 313Acknowledgment 315Index 325