New and Future Developments in Microbial Biotechnology and Bioengineering: Sustainable Agriculture: Advances in Microbe-based Biostimulants

Front cover
	Half title
	Full title
	Copyright
Contents
Contributors
About the Editors
Preface
1 - Plant growth promoting rhizobacteria - Advances and future prospects
	1.1 Introduction
	1.2 Review literature & recent developments
		1.2.1 Sustainable agriculture
		1.2.2 Biofertilizers
		1.2.3 Vesicular arbuscular mycorrhizal root inoculant (VAMRI)
		1.2.4 Mycorrhiza
		1.2.5 Mycorrhiza as a biocontrol agent
		1.2.6 Mycorrhiza as a bioremediation agent
		1.2.7 Arbuscular mycorrhizal fungi
		1.2.8 AMF shape the bacterial community in the mycorrhizosphere
		1.2.9 Mechanisms employed by plant growth-promoting bacteria
		1.2.10 Nitrogen fixation
		1.2.11 Indole-3-Acetic acid production
		1.2.12 Biocontrol activity
		1.2.13 Siderophore production
		1.2.14 Chitinase production
		1.2.15 Zinc solubilizing microorganism
		1.2.16 Potassium solubilizing microorganism
		1.2.17 Phosphate solubilizing microorganism
	1.3 Conclusion
	References
2 - Prospects of beneficial microbes as a natural resource for sustainable legumes production under changing climate
	2.1 Introduction
	2.2 Potential of symbiotic nitrogen fixation (SNF)
	2.3 Factors affecting nodule formation and biological nitrogen fixation (BNF)
		2.3.1 Environmental factors
			2.3.1.1 High temperature
			2.3.1.2 Cold stress
			2.3.1.3 Moisture stress
			2.3.1.4 Soil pH
			2.3.1.5 Salinity
			2.3.1.6 Drought
		2.3.2 Nutritional factors
			2.3.2.1 Nitrogen (N) level
			2.3.2.2 Phosphorus (P) level
			2.3.2.3 Other soil nutrients
				2.3.2.3.1 Potassium (K)
				2.3.2.3.2 Calcium (Ca)
				2.3.2.3.3 Sulfur (S)
				2.3.2.3.4 Molybdenum (Mo)
				2.3.2.3.5 Boron (B)
				2.3.2.3.6 Iron (Fe)
				2.3.2.3.7 Cobalt (Co)
				2.3.2.3.8 Nickel (Ni)
			2.3.2.4 Organic matter
		2.3.3 Biological factors
	2.4 Conclusion
	2.5 Future prospective
	Acknowledgments
	References
3 - Trichoderma as biostimulant - a plausible approach to alleviate abiotic stress for intensive production practices
	3.1 Introduction
	3.2 Review of literature
		3.2.1 Trichoderma: habitation and growth
		3.2.2 Trichoderma—Plant – pathogen interactions
			3.2.2.1 Trichoderma—Plant Interactions
			3.2.2.2 Effects on plant morphology
			3.2.2.3 Effects on plant defense mechanism and physiology
			3.2.2.4 Interaction between Trichoderma-pathogen
		3.2.3 Induction of disease resistance through biostimulation
		3.2.4 Trichoderma—a versatile biostimulant on abiotic stress tolerance, nutrient uptake capacity and growth of crops
		3.2.5 Bioactive metabolites from Trichoderma as a tool to overcome abiotic stresses
		3.2.6 Antioxidant mechanisms implicated in biostimulatory effects of trichoderma
		3.2.7 Uses of Trichoderma in growth, yield and mass propagation of horticultural crops
		3.2.8 Concept of bioformulation and composition
		3.2.9 Expression of genes associated with biocontrol mechanism
		3.2.10 Current scenario for production/market constraints
		3.2.11 Guideline frame work and bio-commercial aspects for sustainable agriculture and horticultural applications
	3.3 Conclusion
	References
4 - Mode of action of different microbial products in plant growth promotion
	4.1 Introduction
	4.2 Major microbial genera and their products
		4.2.1 Bacteria
		4.2.2 Fungi
		4.2.3 Mycorrhizae
	4.3 Mode of action(s) of microbes and their products
		4.3.1 Through Microbially produced phytohormones
		4.3.2 Through Microbially produced enzymes
		4.3.3 Through microbially produced secondary metabolites
		4.3.4 Through microbially produced antipathogenic products and antibiotics
	4.4 Direct benefits to the plant
	4.5 Indirect benefits to the plant
	4.6 Challenges in understanding the mode of action
	4.7 Future perspectives and conclusion
	References
5 - Role of AM fungi in growth promotion of high-value crops
	5.1 Introduction
	5.2 Arbuscular mycorrhizal fungi
	5.3 AMF mediated benefits to high-value crops
		5.3.1 Plant growth promotion
		5.3.2 Biotic stress tolerance
		5.3.3 Abiotic stress tolerance
		5.3.4 Improvement in nutraceutical value
	5.4 AMF application in micro propagation programme
	5.5 Commercialization of AM fungi
	5.6 Challenges of AMF technology
	5.7 Conclusion and future prospects
	References
6 - Pseudomonas and Bacillus: A biological tool for crop protection
	6.1 Introduction
	6.2 Pseudomonas
		6.2.1 Mechanism of action
			6.2.1.1 Biological nitrogen fixation
			6.2.1.2 Production of HCN or volatile organic compounds (VOCs)
			6.2.1.3 Production of hormones
				6.2.1.3.1 IAA
				6.2.1.3.2 GA
				6.2.1.3.3 Ethylene
			6.2.1.4 Production of siderophore
			6.2.1.5 Phosphates solubilization
	6.3 Bio-control activity of Pseudomonas against plant pathogens
		6.3.1 Bacillus
			6.3.1.1 Plant growth promotion
			6.3.1.2 Lipopeptide
			6.3.1.3 Systemically induced disease resistance
	6.4 Bio-control activity of Bacillus spp. against plant pathogens
	References
7 - Underlying forces of plant microbiome and their effect on plant development
	7.1 Introduction
	7.2 Plant microbiome diversity
		7.2.1 Microbiota diversity belowground
		7.2.2 Microbiota above the ground
	7.3 Dynamic of plant microbes in plants
	7.4 Plant microbe’s adaptability
	7.5 Microbiome functions
		7.5.1 Application of microbes in sustainable agriculture
		7.5.2 Farm microbiome preparation
		7.5.3 Plant hormone analogue biosynthesis through plant microbiome
		7.5.4 Nitrogen fixation through plant-microbiome
		7.5.5 Effect of microbiome-based hormones in plant stresses
	7.6 Conclusions and future prospects
	References
8 - Plant viruses as biopesticides
	8.1 Introduction
	8.2 Research methodology
	8.3 Categories of pesticides
	8.4 Major viral biopesticides
	8.5 Mode of action
	8.6 Formulation / synthesis of viral biopesticides
	8.7 Biopesticides manufacturing companies
	8.8 Governing authorities / policies
	8.9 RNAi viral biopesticides with nanotech approach
	8.10 Recombinant viral biopesticides
	8.11 A case study
	8.12 Challenges and drawbacks
	8.13 Major advantages
	8.14 Conclusion, future prospects and take away
	Acknowledgment
	Authors contribution
	Declaration of competing interest
	References
9 - Microalgal based biostimulants as alleviator of biotic and abiotic stresses in crop plants
	9.1 Introduction
	9.2 Positive effects of microalgal extract on plant growth and productivity
	9.3 Microalgal biostimulants for managements of biotic and abiotic stress
	9.4 Microalgal biostimulants emphasized under abiotic stress
	9.5 Effects of microalgae biostimulants on biotic stress
	9.6 Microalgal extract: a mixture with multifaceted mechanisms
		9.6.1 The mechanism under the action of abiotic stress
		9.6.2 Mechanism of action under biotic stress
	9.7 Concluding remarks and future prospects
	References
10 - Utilization of omics approaches for underpinning plant-microbe interaction
	10.1 Introduction
	10.2 Plant- microbial communications
	10.3 Rhizospheric root microbial interaction
	10.4 Endosphere and microbial communication
	10.5 Plant microbial interaction and quorum sensing
	10.6 Fungal-plant interaction
	10.7 Plant-microbe signaling
	10.8 Agrobacterium – crown gall disease
	10.9 Different perspectives of bioinformatics to apprehend soil microorganisms
	10.10 Plant-microbe interactions promote plant growth
	10.11 Omics approaches for plant-microbe interaction
	10.12 Transcriptomics
	10.13 Next generation sequencing
	10.14 Amplicon sequencing
	10.15 Reverse transcription polymerase chain reaction (RT-PCR) and real-time polymerase chain reaction (qPCR)
	10.16 TRAC anaylsis
	10.17 Biochemical methods
	10.18 Laser microdisinfection
	10.19 CRISPR
	10.20 Proteomics
	10.21 Two- dimensional gel electrophoresis (2-DE)
	10.22 Fluorescence 2-D difference gel electrophoresis (DIGE)
	10.23 Isotope-Coded affinity tag (ICAT)
	10.24 Mass spectrometry
	10.25 Secretome
	10.26 Metagenomics
	10.27 Conclusion and future prospect
	References
11 - Extremophiles for sustainable agriculture
	11.1 Introduction
	11.2 Temperature
	11.3 Thermophiles in agriculture
	11.4 Psychrophiles in agriculture
	11.5 Ice-binding proteins
	11.6 Anti-freeze proteins (AFPs)
	11.7 pH tolerants in agriculture
	11.8 Alkalophiles and acidophiles in relation to soil pH
	11.9 Managing high and low pH stressors in plants
	11.10 PGPM enhanced tolerance to soil acidity
	11.11 PGPM enhanced tolerance to soil alkalinity
	11.12 Drought resistance
	11.13 Halophiles in agriculture
	11.14 Radiations
	11.15 Managing toxins and chemicals in soil
	11.16 Biosurfactants
	11.17 Future perspectives
	References
12 - Seed biopriming with biopesticide: A key to sustainability of agriculture
	12.1 Introduction
	12.2 Agricultural sustainability
	12.3 Biopesticides
	12.4 Biopriming with beneficial microbes
	12.5 Seed priming and its mechanism of action
	12.6 Biopriming and induced systemic resistance
	12.7 Biopriming and sustainable agriculture
	12.8 Conclusion
	References
13 - Insights into novel cell immobilized microbial inoculants
	13.1 Introduction
	13.2 Bio-inoculant formulations and challenges
	13.3 Contemporary vs advanced formulations
	13.4 Microbial immobilization
		13.4.1 Flocculation
		13.4.2 Adsorption to surface
		13.4.3 Covalent bonding with carrier
		13.4.4 Matrix entrapment
		13.4.5 Encapsulation in polymer gel
	13.5 Advanced bio-encapsulation
		13.5.1 Macro-encapsulation
		13.5.2 Micro-encapsulation
			13.5.2.1 Co-acervation
			13.5.2.2 Extrusion
			13.5.2.3 Spray drying
			13.5.2.4 Solvent evaporation
			13.5.2.5 Emulsion
			13.5.2.6 Interfacial polymerization
			13.5.2.7 Gelation
			13.5.2.8 Pre-gel dissolution
	13.6 Carriers used in bio-encapsulation
	13.7 Additives in immobilization matrix
		13.7.1 Chitin and derivatives
		13.7.2 Skim milk
		13.7.3 Starch
		13.7.4 Sugars
		13.7.5 Clay
		13.7.6 Humic acid
		13.7.7 Protein hydrolysates
		13.7.8 Miscellaneous materials
	13.8 Microbial exo-polysaccharides- the miracle molecules
	13.9 Cell immobilization, microbial biomass and physiology
	13.10 Microbial resilience in immobilized cells
		13.10.1 Environmental stress alleviation
		13.10.2 Toxicity resistance
		13.10.3 Resistance to predation
	13.11 Immobilized microbial cells in agriculture
	13.12 Immobilized microbes as bio-remediators
	13.13 Conclusion and future prospective
	References
14 - Role of mycorrhizosphere as a biostimulant and its impact on plant growth, nutrient uptake and stress management
	14.1 Introduction
	14.2 Plant growth promoting rhizobacteria (PGPR)
	14.3 Plant health promoting fungi (PGPF)
	14.4 Biostimulant phenomenon of mycorrhizosphere for sustainable agriculture
	14.5 Efficiency of nutrient uptake
	14.6 Mycorrhizospheric effect on stress management
	14.7 Symbiotic effect of arbuscular mycorrhizae
	14.8 Effect of AM fungi on mycorrhizosphere bacteria and vice versa
	14.9 Significance of AM fungi on enhancing sustainable plant growth
		14.9.1 Cellular level interactions
		14.9.2 Effect of soil microbial communities on the influence of agricultural management
		14.9.3 Molecular tools for functional analysis of mycorrhizosphere
	14.10 Conclusion
	14.11 Future prospects
	References
15 - Trichoderma spp. as bio-stimulant: Molecular insights
	15.1 Introduction
	15.2 Hormones
	15.3 Volatile organic compounds
	15.4 Other secondary metabolites
	15.5 Bioaugmentation and biostimulation of problem soils
	15.6 Efficacy of microbial bio-stimulation
	15.7 Synergistic actions
	15.8 Formulations
	15.9 Conclusions and future prospects
	References
16 - Enhancing the growth and disease suppression ability of Pseudomonas fluorescens
	16.1 Introduction
	16.2 Mechanism of biocontrol by Pseudomonas
		16.2.1 Antibiosis
		16.2.2 Hydrogen cyanide production
		16.2.3 Siderophores production
	16.3 Plant growth promotions
		16.3.1 Phytohormone production
			16.3.1.1 Indole-3-acetic acid
			16.3.1.2 Cytokinins
			16.3.1.3 1-Aminocyclopropane-1-Carboxylate (ACC) deaminase
	16.4 Molecular confirmations of Pseudomonas fluorescens by 16S ribosomal RNA sequencing
	16.5 Control of plant diseases in crops
		16.5.1 Agronomical crops
		16.5.2 Fruits and vegetables
	16.6 Future prospects and conclusion
	References
17 - Synthetic biology tools: Engineering microbes for biotechnological applications
	17.1 Introduction
	17.2 History of synthetic biology
	17.3 Engineering central dogma of life
		17.3.1 Optimization central dogma’s processes
			17.3.1.1 DNA engineering
			17.3.1.2 Transcriptional engineering
			17.3.1.3 Translational engineering
		17.3.2 Engineering intrinsic regulatory mechanism
			17.3.2.1 Control over transcription
			17.3.2.2 Control of translation
			17.3.2.3 Regulation over protein modification
		17.3.3 Engineering extrinsic environment of cell
			17.3.3.1 Genetic circuit with signal receptors
	17.4 Designing of synthetic biology tools
		17.4.1 Designing predictable tools
			17.4.1.1 Chassis selection
			17.4.1.2 Designing and engineering of biological parts
			17.4.1.3 Characterization of biological parts
		17.4.2 Types of designs and bio-engineering’s of synthetic tools
			17.4.2.1 Automated biological tools
			17.4.2.2 Phenotypic engineering
			17.4.2.3 Metabolic engineering
			17.4.2.4 Horizontal transfer and transmissibility
			17.4.2.5 Xenobiology
			17.4.2.6. Modulation of human physiology
	17.5 Build-up of synthetic biology tools
		17.5.1 DNA construction
		17.5.2 Genome editing
		17.5.3 Construction libraries
		17.5.4 Booting of constructs
		17.5.5 Strategies for DNA assemblage
	17.6 Testing of DNA constructs
		17.6.1 High throughput screening (HTS)
		17.6.2 Directed evolution
	17.7 Application of synthetic biological tools
		17.7.1 Pharmaceutical application
		17.7.2 Application in food, dairy and beverage
		17.7.3 Agricultural application
			17.7.3.1 Enhancement of nutritional contents like carotenoids, fatty acids, natural sweetener and steroids
			17.7.3.2 Denovo pathways for greater improvement in growth and prognosticating the functions in silico and to attain therm ...
			17.7.3.3 Engineering with photoautotrophs for productions of biofuels, antibodies, vaccines, biopharmaceuticals
			17.7.3.4 Engineering microbes take the edge off chemical fertilizers and pesticides
		17.7.4 Other industrial application
	17.8 Challenges in the way of synthetic biology tools
		17.8.1 Designing of proper chassis
		17.8.2 Enhancing host repertory
		17.8.3 Development of universal system of production
		17.8.4 Constructing cell- free environment
		17.8.5 System for standardizing, modeling and metrology
	17.9 Conclusion
	References
18 - Role of microbial consortia in remediation of soil, water and environmental pollution caused by indiscriminate use of ...
	18.1 Introduction
	18.2 Microbial consortia
		18.2.1 Naturally occurring strategies of microbial consortium
		18.2.2 Types of consortium
			18.2.2.1 Artificial consortium
			18.2.2.2 Synthetic consortium
			18.2.2.3 Natural consortia
	18.3 Soil, water and environmental pollution and bioremediation by microbial consortia
		18.3.1 Degradation of soil by the indiscriminate use of chemicals and remedial measures
			18.3.1.1 Herbicides
				18.3.1.1.1 Important herbicides, their toxicity and bioremediation measures
			18.3.1.2 Fungicides
			18.3.1.3 Insecticides and acaricides
				18.3.1.3.1 Important insecticides/acaricides, their toxicity and bioremediation measures
		18.3.2 Contamination of water bodies by harmful chemicals and remedial measures
		18.3.3 Other environmental pollution and remedial measures
	18.4 Future opportunities and challenges
	18.5 Concluding remarks
	References
19 - Sustainable agriculture and viral diseases of plants: An overview
	19.1 Introduction
	19.2 Plant stress and immune response
		19.2.1 Host and pathogen interaction
		19.2.2 Biotic stress and plant immune response
	19.3 Biostimulants
		19.3.1 Microbe-based biostimulants
		19.3.2 Microbial biostimulants as a source of sustainable agricultural practice in viral disease resistance/management
	19.4 Sustainable agriculture, biotechnology and plant viruses
	19.5 Conclusion
	Conflict of interest
	References
20 - Enhancement of plant nutrient uptake by bacterial biostimulants
	20.1 Introduction
	20.2 Plant nutrient uptake mechanisms
	20.3 Biostimulants
	20.4 Categories of biostimulants and their effect on plant growth and productivity
		20.4.1 Vegetal and animal protein hydrolysates
		20.4.2 Humic and fulvic acid
		20.4.3 Macroalgae seaweeds extracts
		20.4.4 Silicon
		20.4.5 Arbuscular mycorrhizal fungi
		20.4.6 Bacterial biostimulants
	20.5 Indirect mechanism of bacterial biostimulants to enhance nutrient uptake
	20.6 Direct mechanism of bacterial biostimulants to enhance plant nutrient uptake
	20.7 Bacterial biostimulants to enhance the growth and stress tolerance
	20.8 Bacterial biostimulants as biocontrol agents
	20.9 Conclusion and prospects
	References
Index
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