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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