Metabolomics, Proteomes and Gene Editing Approaches in Biofertilizer Industry

Preface
Acknowledgements
Contents
Editors and Contributors
1: Constraints in Biofertilizer Industry and Future Scope
	1.1 Introduction
	1.2 Biofertilizers
	1.3 Types of Biofertilizers
		1.3.1 Bacterial Biofertilizers
			1.3.1.1 Nitrogen-Fixing Bacteria
			1.3.1.2 Phosphorous-Solubilizing Bacteria
			1.3.1.3 Micronutrients Providing Bacteria
			1.3.1.4 Plant Growth-Promoting Rhizobacteria (PGPR)
		1.3.2 Fungal Biofertilizers
		1.3.3 Algal Biofertilizers
		1.3.4 Consortium or Composite Biofertilizers
	1.4 Biofertilizer: Constraints and Their Potential Solutions
		1.4.1 Carrier-Based Constraints
		1.4.2 Marketing-Based Constraints
		1.4.3 Field Application-Based Constraints
		1.4.4 Quality Control-Based Constraints
		1.4.5 Biosafety-Based Constraints
		1.4.6 Biological-Based Constraints
		1.4.7 Technical and Infrastructure-Based Constraints
		1.4.8 Regulation-Based Constraints
		1.4.9 Finance-Based Constraints
	1.5 Future Scope of the Biofertilizer Industry
	1.6 Conclusion
	References
2: Present Scenario: Status of the Biofertilizer Industry in India
	2.1 Introduction
	2.2 Biofertilizers and Their Benefits and Limitations
	2.3 Biofertilizer Market in India: Public and Private Sector
	2.4 Entrepreneurship Hurdles and Remedies
	2.5 Future Prospects
	2.6 Conclusions
	References
		Websites
3: Mode of Application of Biofertilisers in the Crop Field
	3.1 Introduction
	3.2 What Are Biofertilisers?
	3.3 Types of Biofertilisers
		3.3.1 Nitrogen-Fixing Microbes
		3.3.2 Phosphate-Solubilising Microbes
		3.3.3 Potassium-Solubilising Microbes
		3.3.4 Sulphur-Oxidising Microbes
		3.3.5 Zinc (Zn)-Solubilising Biofertilisers
		3.3.6 Plant Growth-Promoting Rhizobacteria (PGPR)
		3.3.7 Nano-Biofertilisers
	3.4 Formulation Process of Biofertilisers
	3.5 Mode of Applications of Biofertilisers
		3.5.1 Beneficial Microorganisms
		3.5.2 Nanofertilisers
	3.6 Application of Biofertilisers as Biocontrol Agents
	3.7 Potential of Biofertilisers in the Agriculture Market
	3.8 Limitations in the Production of Biofertilisers
	3.9 Future Prospects
	References
4: Carrier-Based Biofertilizers
	4.1 Introduction
	4.2 Types of Carrier-Based Materials
		4.2.1 Peat
		4.2.2 Clay
		4.2.3 Lignite
		4.2.4 Agricultural Coproducts
		4.2.5 Vermiculite
		4.2.6 Alginate
		4.2.7 Perlite
		4.2.8 Bentonite
	4.3 Process of Biofertilizer Formulation
		4.3.1 Isolation/Procurement of the Potential Microorganism
		4.3.2 Mass Culturing of Microorganisms in Fermenter
		4.3.3 Processing of the Carrier Material
		4.3.4 Mixing of Sterilized Carrier with Broth Culture
		4.3.5 Packing
	4.4 Methods of Sterilization of the Carrier Material
		4.4.1 Advantages of Steam Sterilization
		4.4.2 Disadvantages of Steam Sterilization
	4.5 Commercial Carrier Biofertilizers Available in the Market
		4.5.1 Disadvantages of Carrier-Based Biofertilizers
	4.6 Conclusion and Future Perspective
	References
5: Liquid Bio-Fertilizers: Prospects and Challenges
	5.1 Introduction of Bio-Fertilizers
		5.1.1 Benefits of Bio-Fertilizers
		5.1.2 Bio-Formulation
		5.1.3 Challenges in the Application of Solid Carrier-Based Bio-Fertilizers
		5.1.4 Common and Probable Causes for Withered Popularity of Bio-Fertilizers
	5.2 Liquid Bio-Fertilizers
		5.2.1 Inoculums Used in Liquid Bio-Fertilizers (LBFs)
		5.2.2 Importance and Fundamental Features of Liquid Formulation
		5.2.3 Application Methodology of Liquid Bio-Fertilizers
			5.2.3.1 Seed Treatment
			5.2.3.2 Root Dip Method/Root Dipping
			5.2.3.3 Soil/Soil Application
			5.2.3.4 Foliar Spray
		5.2.4 Type of Liquid Bio-Fertilizers and Their Characteristics
			5.2.4.1 Nitrogen-Fixing Bio-Fertilizers
				5.2.4.1.1 Rhizobium
				5.2.4.1.2 Azospirillum
				5.2.4.1.3 Azotobacter
				5.2.4.1.4 Acetobacter
			5.2.4.2 P-Solubilizing Bio-Fertilizers
			5.2.4.3 P-Mobilizing Bio-Fertilizers
			5.2.4.4 Potash-Mobilizing Bio-Fertilizers
			5.2.4.5 Bio-Fertilizers for Micronutrients
			5.2.4.6 Pink-Pigmented Facultative Methylotrophs (PPFM)
		5.2.5 Advantages of Liquid Bio-Fertilizers (LBFs)
		5.2.6 Limitations in the Application of Liquid Bio-Fertilizers (LBFs)
			5.2.6.1 Shortage of Effective Strains
			5.2.6.2 Lack of Awareness
			5.2.6.3 Technical and Infrastructure Limitations
			5.2.6.4 Environmental Factors
		5.2.7 Quality Control of Liquid Bio-Fertilizers
		5.2.8 Benefits of Liquid Bio-Fertilizer Over Traditional Carrier-Based Bio-Fertilizer
		5.2.9 Recommended Dose of Liquid Bio-Fertilizers and Their Application Method
		5.2.10 Future Perspective
	References
6: Interaction of Efficient Rhizospheric Bacteria and Responses in the Farmer´s Field
	6.1 Introduction
	6.2 Rhizosphere and Rhizobacteria
	6.3 Interactions Between Plants and Rhizobacteria: Response in the Farmer´s Field Where Theory Meets Practice
	6.4 Host Specificity
	6.5 Associations with Other Rhizosphere Inhabitant
	6.6 Associations with Organo-Mineral Amendments
	6.7 Decoding the Efficient Rhizobacteria
	6.8 Formulations and Inoculation
	6.9 Prospects of Efficient Rhizobacteria
	6.10 Constraints in the Commercialization of Efficient Rhizobacteria
	6.11 Conclusion and Future Prospects
	References
7: Enhancing Productivity Through Multiple Microbial Inoculants
	7.1 Introduction
	7.2 Microbial Inoculants
	7.3 Roles of Microbial Consortia in Nutrient Cycling for Plant Growth and Biomass Accumulation
		7.3.1 Nitrogen Fixation
		7.3.2 Phosphate and Potassium Solubilization
	7.4 Microbial Consortium Contributions to Plant Health and Plant Defensive System
		7.4.1 Support Plant Adaptation Under Abiotic Stress Conditions
		7.4.2 Enhance Plant Defense Against Invasive Pests
	7.5 Conclusion
	References
8: Challenges in the Compatibility of Microbial Inoculants with Agrochemicals
	8.1 Introduction
	8.2 Microbial Inoculants
	8.3 Agrochemicals and Their Impact
		8.3.1 Impact of Herbicides
		8.3.2 Impact of Fungicides
		8.3.3 Impact of Insecticide
	8.4 Compatibility of Microbial Inoculants with Herbicides
	8.5 Compatibility of Microbial Inoculants with Fungicides
	8.6 Compatibility of Microbial Inoculants with Insecticides
	8.7 Alternative Technologies and Conclusion
	References
9: Microbial Metabolite-Based Product for Plant Growth Promotion
	9.1 Introduction
	9.2 Function of Endophytic Bacteria That Colonize Plant Roots
		9.2.1 Role of Endophytes in Plant Growth Promotion
		9.2.2 Synthesis of Plant Root Endophytes and Bioinoculants
		9.2.3 Genomics of Root-Endophytic Bacterial Population
	9.3 Development of Rhizosphere Competency
		9.3.1 Chemical Responses
		9.3.2 Chemotactic Actions
		9.3.3 Plant Proliferation and Pathogen Resistance
		9.3.4 PGPR Traits and the Role of Pseudomonas in Plant Growth Promotion
		9.3.5 Plant Disease Management with Pseudomonas
	9.4 Conclusion
	References
10: Microbes from Wild Plants
	10.1 Introduction
	10.2 Plant Microbiome and Its Importance
	10.3 Domestication/Breeding and Its Effect on Composition of Plant Microbiome
	10.4 Importance of Wild Variety Microbiota
	10.5 Conclusions
	References
11: Fungal Biofertilizers: Present Trends and Future Prospects
	11.1 Introduction
	11.2 Fungi Employed in the Production of Biofertilizers
		11.2.1 Mycorrhiza
		11.2.2 Trichoderma Species
		11.2.3 Chaetomium Species
		11.2.4 Penicillium Species
		11.2.5 Aspergillus Species
		11.2.6 Gliocladium Species
	11.3 Formulation of Fungal Biofertilizers
	11.4 Current Status and the Global Trend of Fungal Biofertilizers
	11.5 Challenges Associated with Fungal Biofertilizers and Future Perspective
	11.6 Conclusions
	References
12: Endophytes as Plant Growth Inducers: A New Arena in the Bio-inoculant Industry
	12.1 Introduction
	12.2 Role of Endophytes in Nutrient Uptake and Phytohormone Regulation
		12.2.1 Phosphate Solubilization
		12.2.2 Zinc Solubilization
		12.2.3 Potassium Solubilization
	12.3 Role of Endophytes in Biotic and Abiotic Stress Management
	12.4 Are Endophytes More Than Biocontrol Agents?
	12.5 Endophytes as a Treasure House of Bioactive Compounds
	12.6 Problems and Prospects in Mainstreaming Endophytes as a Novel Source for the Bio-inoculant Industry
	12.7 Interventions Needed for Farmers and Industry for Fast Commercialization and Adoption
	12.8 Conclusion and Future Prospects
	References
13: Immobilization and Co-mobilization: An Unexploited Biotechnological Tool for Enhancing Efficiency of Biofertilizers
	13.1 Introduction
	13.2 Biofertilizer Formulation
		13.2.1 Bioformulation Steps
			13.2.1.1 Selection of Strain
			13.2.1.2 Selection of Carrier Material
			13.2.1.3 Stickers and Additives
	13.3 Role of Biofertilizers in Crop Production
		13.3.1 Commercially Available Biofertilizers
	13.4 Method to Improve Production of Biofertilizer
	13.5 Microbial Fortification
	13.6 Immobilization and Co-immobilization
	13.7 Application
	13.8 Conclusion
	References
14: Microbial Biostimulants: Bioformulations for Enhanced Biofertilizer Efficacy and Sustainable Crop Management
	14.1 Introduction
	14.2 Plant Biostimulants of Microbial Origin
		14.2.1 Biostimulatory Potential of Plant Growth-Promoting Bacteria
		14.2.2 Biostimulatory Potential of Plant Growth-Promoting Fungus
	14.3 Beneficial Effects and Mechanisms of Action of Microbial Biostimulants on Crop Health
		14.3.1 Promotion of Plant Growth Through Hormonal Regulation and Effective Nutrient Usage
		14.3.2 Abiotic Stress Tolerance Mediated by Microbial Biostimulants
			14.3.2.1 Salinity and Drought Stress
			14.3.2.2 Temperature Stress
		14.3.3 Enhanced Quality Attributes of the Plant Produce
	14.4 Bioformulations
	14.5 Market Trends and Regulatory Framework
	14.6 Conclusion and Future Prospects
	References
15: Futuristic Approaches in Biofertilizer Industry Through Metabolomics, Proteomes, and Gene Editing
	15.1 Introduction
	15.2 The Use of Synthetic Biology to Modify Microbes
	15.3 Plant-Rhizosphere Interaction
	15.4 Microbiome of the Rhizosphere: Complexity, Relationships, and Functions of Microbes
	15.5 Approaches for Microbiome Engineering
	15.6 Metabolite Engineering
	15.7 Quorum Sensing
	15.8 R&D Architecture and ÓMICS
	15.9 Applications of Omics Technology
		15.9.1 Enhancement of Antioxidants in Tomato
		15.9.2 Omics Approaches for Enhancement of Antioxidants in Tomatoes
		15.9.3 Plant Biomarkers Characterization with Omics
		15.9.4 Extremophiles and Their Metagenomics as a Source of Biofertilizers
		15.9.5 For Biofertilizers Selection of Strains with Approach of Integrated Omics
		15.9.6 Identification of Potential Microbes with Metagenomics as Biofertilizer
		15.9.7 Identification of Various Inoculants for Biofertilizers
			15.9.7.1 Capturing of Potential Microbes for Biofertilizers with Sequence-Based Metagenomics
			15.9.7.2 Identification of Rhizosphere as Biofertilizers
		15.9.8 Metaproteomic and Metabolite Profiling Approach
		15.9.9 Shotgun Metagenomics Approach and Strain Selection Strategies with Whole Genome Sequencing
	15.10 Other Applications
	15.11 Rhizosphere Microbiome Engineering
	15.12 Conclusion
	References
16: Metabolomics and Proteomics Behind Plant Growth-Promoting Potential of Rhizobacteria
	16.1 Introduction
	16.2 Plant Growth-Promoting Rhizobacteria (PGPRs)
		16.2.1 Direct PGPR Traits
			16.2.1.1 Nitrogen Fixation
			16.2.1.2 Phosphate Solubilization
			16.2.1.3 Siderophore Production
			16.2.1.4 Zinc Solubilization
			16.2.1.5 Phytohormone Production
				16.2.1.5.1 Auxin
				16.2.1.5.2 Cytokinin
			16.2.1.6 Ethylene
			16.2.1.7 Potassium Solubilization
		16.2.2 Indirect PGPR Traits
			16.2.2.1 Induced Systemic Resistance
			16.2.2.2 Antibiotic Production
			16.2.2.3 Hydrolytic Enzymes
			16.2.2.4 Volatile Organic Compounds
	16.3 Omics
		16.3.1 Metabolomics to Explore Plant Growth Promotion by Associated PGPR
		16.3.2 Proteomics to Explore Plant Growth Promotion by Associated PGPR
	16.4 Analytical Techniques
		16.4.1 Nuclear Magnetic Resonance (NMR)
			16.4.1.1 Advantages and Disadvantages of NMR
			16.4.1.2 Applications of NMR
		16.4.2 Gas Chromatography Mass Spectrometry (GC-MS)
			16.4.2.1 Advantages and Disadvantages of GC-MS
			16.4.2.2 Application of GC-MS
		16.4.3 Fourier Transform Infrared (FTIR) Spectroscopy
			16.4.3.1 Advantages and Disadvantages of FTIR
			16.4.3.2 Applications of FTIR
		16.4.4 High-Performance Liquid Chromatography Mass Spectrometry (HPLC-MS)
			16.4.4.1 Advantages and Disadvantages of HPLC-MS
			16.4.4.2 Application of HPLC-MS
		16.4.5 Liquid Chromatography Mass Spectrometry (LC-MS)
			16.4.5.1 Advantages and Disadvantages of LC-MS
			16.4.5.2 Application of LC-MS
		16.4.6 Ionization Techniques
		16.4.7 Free Online Tools
	16.5 Conclusion
	References
17: Proteomics in Shaping the Future of Biofertiliser Delivery Technique
	17.1 Introduction
	17.2 Techniques Involved in Proteomic Analysis
	17.3 Study of Plant-Microbe Interaction Using Proteomics
	17.4 Use of Proteomics for the Study of PGPR
	17.5 Proteomics in the Study of PGPR Potential of Rhizobacteria
	17.6 Future Perspectives
	References
18: Application of Nanosilica for Plant Growth Promotion and Crop Improvement
	18.1 Introduction
	18.2 Role of Silica in Plant Growth
	18.3 Silica Nanoparticles as a Source of Silica for Plant Growth
	18.4 Application of SiNPs in Agriculture
		18.4.1 SiNP as Pesticides
		18.4.2 SiNP as a Delivery Agent for Fertilizers
		18.4.3 SiNP for Improving Water-Holding Capacity
		18.4.4 SiNP for Overcoming Different Abiotic Stresses
			18.4.4.1 Physical Stress
			18.4.4.2 Chemical Stress
		18.4.5 SiNP for Overcoming Biotic Stress
		18.4.6 SiNP as Nano-Sensors
	18.5 Limitation and Research Prospects of SiNP-Based Nano-Biofertilizer
	18.6 Conclusion and Future Prospects
	References
19: Industrial Sustainability: Economics, Cost, and Bioavailability of Biofertilizers
	19.1 Introduction
	19.2 Biofertilizer: The Way Forward
		19.2.1 Various Uses of Biofertilizers
	19.3 Recent Progress in Phosphate Biofertilizers
	19.4 Development of Phosphate Biofertilizers
	19.5 Mechanisms of Action of Beneficial Microbes
		19.5.1 Microbes for Nitrogen Fixation
			19.5.1.1 Phosphorus-Solubilizing Microbes
		19.5.2 Mycorrhizal Biofertilizers
		19.5.3 Growth-Promoting Microbes in Plants
	19.6 Types of Biofertilizers
		19.6.1 Rhizobium Biofertilizer
		19.6.2 Azotobacter Biofertilizer
		19.6.3 Azospirillum Biofertilizer
		19.6.4 Azolla and Blue-Green Algae Biofertilizer
		19.6.5 Phosphate-Solubilizing Biofertilizer
		19.6.6 Silicon-Solubilizing Biofertilizer
		19.6.7 Arbuscular Mycorrhizal (AM) Biofertilizer
	19.7 Biofertilizers: A Bon or a Ban for the Society
	19.8 Market Potential for Agricultural Biofertilizers
	19.9 Conclusive Outlook
	References
20: Phyllosphere Engineering: Tailoring Leaf Surface Microbes for Boosting Plant Tolerance
	20.1 Introduction
	20.2 Phyllosphere Microbiome
		20.2.1 Factors Affecting Phyllosphere Microbiome Composition
			20.2.1.1 Environmental Factors
			20.2.1.2 Leaf Anatomy, Physiology and Chemistry
			20.2.1.3 Plant Immunity
	20.3 The Strategies for Manipulation: Microbiome Analysis Based on High-Throughput Multi-Omics Data
		20.3.1 Phyllosphere Microbiome Engineering
		20.3.2 Strategies of Phyllosphere Microbiome Engineering
	20.4 Conclusion
	References