Phyto-Microbiome in Stress Regulation (Environmental and Microbial Biotechnology)

Preface
Contents
About the Editors
1: Phytostimulation and Biocontrol by the Plant-Associated Bacillus amyloliquefaciens FZB42: An Update
	1.1	 Introduction
	1.2	 Root Colonization by FZB42 and Its Impact on the Host Plant Microbiome
	1.3	 Plant Growth Promotion
	1.4	 Biocontrol
		1.4.1	 Lipopeptides, Bacillibactin, and Antifungal Activity
			1.4.1.1	 Polyketides, Bacilysin, and Bacteriocins Direct Antibacterial Activity
			1.4.1.2	 Nematicidal Activity Is Directed by Plantazolicin
	1.5	 Induced Systemic Resistance Is Triggered by Plant Growth-Promoting Bacilli
	1.6	 Conclusion
	References
2: Genetically Modified (GM) Crops Harbouring Bacillus thuringiensis (BT) Gene(S) to Combat Biotic Stress Caused by Insect Pests
	2.1	 Introduction
	2.2	 Genetic Transformation
	2.3	 Gene Transfer Method
		2.3.1	 Direct DNA Transfer Methods
		2.3.2	 Indirect DNA Transfer Method
	2.4	 Agrobacterium-Mediated Genetic Transformation
		2.4.1	 Ti Plasmid of Agrobacterium
		2.4.2	 Organization of T-DNA
		2.4.3	 Organization of vir Region
		2.4.4	 T-DNA Transfer Process
		2.4.5	 Vectors Derived from Ti Plasmids
		2.4.6	 Co-integrate Vector System
		2.4.7	 Binary Vector System
		2.4.8	 Selectable Markers
		2.4.9	 Advantages of Agrobacterium-Mediated Plant Transformation
		2.4.10	 Disadvantages of Agrobacterium-Mediated Plant Transformation
	2.5	 Factors Affecting Plant Transformation
	2.6	 Bacillus thuringiensis (Bt) Endotoxin Crystal Protein Genes for Insect Resistance
	2.7	 Mechanism of Action of Three-Domain Cry Toxins in Lepidoptera
		2.7.1	 Pore Formation Model
		2.7.2	 Signal Transduction Model
	2.8	 BT-GM Crops
	2.9	 Management of Resistance Development
	2.10	 Conclusions
	References
3: Characterization and Efficiency of Rhizobial Isolates Nodulating Cytisus monspessulanus in the Northwest of Morocco: In Relation to Environmental Stresses
	3.1	 Introduction
	3.2	 Materials and Methods
		3.2.1	 Location of Nodule Collection
			3.2.1.1	 Rhizobia Isolation and Purification
		3.2.2	 Response to Environmental Stress Factors
		3.2.3	 Utilization of Carbon and Nitrogen Sources
		3.2.4	 Heavy Metal Tolerance
		3.2.5	 Authentication of Isolates
		3.2.6	 Numerical Analysis
	3.3	 Results and Discussion
		3.3.1	 Phenotypic Evaluation
		3.3.2	 The Numbers Are the Number of Isolates Giving Positive Reaction
		3.3.3	 Plant Assay
	3.4	 Conclusion
	References
4: Isolation and Characterization of the Roots and Soil Endomycorrhizae of Hedysarum pallidum Desf. in the Northeast of Morocco
	4.1	 Introduction
	4.2	 Materials and Methods
		4.2.1	 Soil Samples and Plant Material
		4.2.2	 Methods
			4.2.2.1	 AMF Spore Extraction
			4.2.2.2	 Measuring of the Root Mycorrhization Rate
	4.3	 Results and Discussion
		4.3.1	 Richness, Diversity, and Identification of AMF Spores
		4.3.2	 Evaluation of Root Mycorrhization
	4.4	 Conclusion
	References
5: Friends and Foes: Phyto-Microbial Interactions in Molecular Perspective
	5.1	 Introduction
		5.1.1	 Friends and Foes: A Side to Pick
		5.1.2	 Microbiome Communities as a Friend for Plant
		5.1.3	 Microbial Foes: A Concern for Plant Health
	5.2	 Metagenomics Approaches for Taxonomical and Functional Classification of Microbiomes
		5.2.1	 PhyloChip and Amplicon-Based Classification of Microbiomes
		5.2.2	 Shotgun Metagenomics for Microbiome Studies
		5.2.3	 Approaches to Acquire and Analyze Metagenomics Data
	5.3	 Concluding Remarks
	References
6: Isolation and Screening of Inorganic Phosphate Solubilizing Pseudomonas Strains from the Lotus creticus Rhizosphere Soil from the Northwest of Morocco
	6.1	 Introduction
	6.2	 Materials and Methods
		6.2.1	 Isolation of Pseudomonas from Lotus creticus Rhizosphere
		6.2.2	 Phosphate Solubilization
		6.2.3	 Production of Hydrogen Cyanide (HCN)
		6.2.4	 Determination of Indole Acetic Acid (IAA) Production
		6.2.5	 Production of Siderophores
		6.2.6	 Production of Hydrolytic Enzymes
			6.2.6.1	 Cellulase
			6.2.6.2	 Chitinase
			6.2.6.3	 Protease
			6.2.6.4	 Amylase
			6.2.6.5	 Urease
		6.2.7	 Production of Ammonia
		6.2.8	 Qualitative Phosphate Solubilization Assay
		6.2.9	 Antifungal Activity
		6.2.10	 Statistical Analysis
	6.3	 Results and Discussion
		6.3.1	 Isolation and Selection of Phosphate Solubilizing Bacteria (PSB)
		6.3.2	 Screening of PGP Activities of Isolated Pseudomonas
		6.3.3	 Production of Lytic Enzymes
		6.3.4	 Ammonia Production
		6.3.5	 Quantitative Test of Phosphate Solubilization in Liquid Medium
		6.3.6	 Antagonism Test
	6.4	 Conclusion
	References
7: Screening and Characterization of Phosphate-Solubilizing Rhizobia Isolated from Hedysarum pallidum in the Northeast of Morocco
	7.1	 Introduction
	7.2	 Materials and Methods
		7.2.1	 Bacterial Isolates
		7.2.2	 Inorganic Phosphate Solubilization
		7.2.3	 Hydrogen Cyanide (HCN) Production
		7.2.4	 Siderophores Production
		7.2.5	 Quantitative Assay of Indole Acetic Acid (IAA) Production
		7.2.6	 Cellulase Production
		7.2.7	 Urease Production
		7.2.8	 Amylase Production
		7.2.9	 Protease Production
		7.2.10	 Chitinase Production
		7.2.11	 Quantitative Assay of P Solubilization
		7.2.12	 Statistical Analysis
	7.3	 Results and Discussion
		7.3.1	 Selection of PSB
		7.3.2	 In Vitro Screening of Isolates for Multiple PGP Activities
			7.3.2.1	 Hydrogen Cyanide (HCN) Production
			7.3.2.2	 Siderophore Production
			7.3.2.3	 Quantification of Phytohormone (IAA)
		7.3.3	 Characterization for Extracellular Hydrolytic Enzyme Production
		7.3.4	 Quantitative Assay of P Solubilization
	7.4	 Conclusion
	References
8: Development of Abiotic Stress Tolerance in Crops by Plant Growth-Promoting Rhizobacteria (PGPR)
	8.1	 Introduction
	8.2	 Tolerance to Drought Stress
	8.3	 Protection Against Salt Stress
	8.4	 Protection Against Heavy Metal Stress
	8.5	 Harmful Aspects of PGPR
	8.6	 Concluding Perspectives
	References
9: Plant Growth-Promoting Rhizobacteria (PGPR) and Their Action Mechanisms in Availability of Nutrients to Plants
	9.1	 Introduction
	9.2	 Action Mechanisms of PGPR of Providing Nutrients for Plants
		9.2.1	 Increasing Nutrient Supply of Plants
		9.2.2	 Increasing Nutrient Availability to Plants
		9.2.3	 Enhancing Plant’s Greater Access to Soil Nutrients
	9.3	 Essential Plant Nutrients
		9.3.1	 Nitrogen (N)
			9.3.1.1	 N2-Fixing Bacteria (NFB)
			9.3.1.2	 Action Mechanisms of Bacteria in Providing N for Plant
				Biological N2 Fixation (BNF)
				Mineralization of Organic Nitrogenous Compounds
				Immobilization of Soluble Inorganic N
				Increased Root System of Plant
				IAA Production
				ACC Deaminase Activity
		9.3.2	 Phosphorus (P)
			9.3.2.1	 Phosphate-Solubilizing Bacteria (PSB)
			9.3.2.2	 Action Mechanisms of P Solubilization by PSB
				Production of Organic Acids
				Production of Inorganic Acids
				Production of IAA and ACC Deaminase
				Production of Siderophores
				Production of Exopolysaccharides (EPS)
				Mineralization of Organic P
				Immobilization of Inorganic P
			9.3.2.3	 Promotion of Plant Growth by PSB
		9.3.3	 Potassium (K)
			9.3.3.1	 KSB (Potassium-Solubilizing Bacteria)
			9.3.3.2	 Action Mechanisms of KSB in the Availability of K
				Acidolysis
				Chelation Process
				Oxidation
				Production of CO2
			9.3.3.3	 KSB and Increased Availability of K and Other Nutrients
		9.3.4	 Sulfur (S)
			9.3.4.1	 Action Mechanisms of Sulfur (S) Availability by PGPR
				Mineralization of Sulfur (S)
				Immobilization of Sulfur (S)
				Oxidation of Sulfur (S)
				Reduction of Sulfur (S)
	9.4	 Action Mechanisms of PGPR in Availability of Micronutrients
		9.4.1	 Production of Organic and Inorganic Acids
		9.4.2	 Production of Chelating Agents
		9.4.3	 Production of IAA
	9.5	 Iron (Fe)
		9.5.1	 Fe Acquisition Strategies by Plants
		9.5.2	 Action Mechanisms of PGPR in Fe Availability
			9.5.2.1	 Production of Siderophores
			9.5.2.2	 Production of IAA
	9.6	 Manganese (Mn)
	9.7	 Concluding Remarks and Future Perspectives
	References
10: Plant Growth and Development Under Suboptimal Light Conditions
	10.1	 Introduction
		10.1.1	 Light Quantity, Quality, and Duration
		10.1.2	 Phytohormones
	10.2	 Seed Germination
		10.2.1	 Phytochromes and Their Role in Seed Germination
		10.2.2	 Photoreversibility
		10.2.3	 Gene Signaling Mechanism During Seed Germination
	10.3	 Seedling Growth and Development
		10.3.1	 Skotomorphogenesis
		10.3.2	 Photomorphogenesis
	10.4	 Shade Avoidance
	10.5	 Role of Light in Plant Defense
	10.6	 Light-Mediated Floral Induction
		10.6.1	 Photoperiodism
		10.6.2	 Photoreceptor Proteins Regulating Floral Formation
		10.6.3	 Genes Involved in Floral Formation
	10.7	 Summary
	References
11: Microbial Biotechnology: A Key to Sustainable Agriculture
	11.1	 Introduction
	11.2	 Role of Microbes in Sustainable Agriculture
	11.3	 Role of Biotechnology in Sustainable Agriculture
	11.4	 Microbial Biotechnology and Agriculture
	11.5	 Molecular Tools for Manipulation of Microorganisms
	11.6	 Applications of Genetically Modified Microbes in Agriculture
		11.6.1	 Improvement in Phytostimulation Activity
		11.6.2	 Enhanced Biofertilization Capability
		11.6.3	 Improvement in Stress Tolerance Activity
			11.6.3.1	 Abiotic Stress Tolerance
			11.6.3.2	 Biotic Stress Tolerance
		11.6.4	 Genetic Engineering to Improve Bioremediation Potential of Microbes
	11.7	 Achievements
	11.8	 Future
	11.9	 Conclusion
	References
12: Stress Signalling in the Phytomicrobiome: Breadth and Potential
	12.1	 Introduction: Phytomicrobiome
	12.2	 Different Types of Plant-Microbe Interactions
		12.2.1	 Mycorrhizal Symbiosis
			12.2.1.1	 Endomycorrhizal Fungi
			12.2.1.2	 Ectomycorrhizal Fungi
		12.2.2	 Nitrogen-Fixing Microorganisms
		12.2.3	 Cycad-Cyanobacterial Symbiosis
	12.3	 Molecular Signalling in Phytomicrobiome
		12.3.1	 Signalling in the Legume-Rhizobia and Mycorrhizal Symbioses: The Common Symbiotic Pathway
		12.3.2	 Communication Among Bacterial Community
	12.4	 Phytomicrobiome Signalling and Plant Growth
		12.4.1	 Biofertilization
		12.4.2	 Phytohormone Production
		12.4.3	 Biocontrol for Disease Suppression
			12.4.3.1	 Production of Broad-Spectrum Antibiotics
			12.4.3.2	 Production of Narrow-Spectrum Bacteriocins
			12.4.3.3	 Production of Extracellular Lytic Enzymes
		12.4.4	 Volatile Signal Compound Production for Disease Control
		12.4.5	 Induction of Plant Disease Resistance to Phytopathogens
			12.4.5.1	 Systemic Acquired Resistance
			12.4.5.2	 Induced Systemic Resistance
	12.5	 Plant-Microbe Interaction for Improving the Efficiency of Ecosystem
		12.5.1	 Drought
		12.5.2	 Extreme Temperatures
		12.5.3	 Salinity
		12.5.4	 Soil Acidity
		12.5.5	 Heavy Metals
		12.5.6	 Pesticides
	12.6	 Conclusion
	References
13: A Simple Procedure for Isolation, Culture of Protoplast, and Plant Regeneration
	13.1	 Introduction
	13.2	 Sources of Explant for Protoplast Isolation
	13.3	 Techniques of Isolation, Culture and Regeneration of Protoplast
		13.3.1	 Mechanical Method
			13.3.1.1	 Limitation of Mechanical Method
		13.3.2	 Enzymatic Method
			13.3.2.1	 Enzymes for Protoplast Isolation
			13.3.2.2	 The One-Step Method
			13.3.2.3	 The Two-Step Method
	13.4	 Advantages of Enzymatic Method
	13.5	 Purification of Protoplasts
	13.6	 Viability of Protoplasts
		13.6.1	 There Are Several Methods to Assess the Protoplast Viability
	13.7	 Protoplast Culture and Regeneration
		13.7.1	 Formation of Cell Wall
		13.7.2	 Development of Callus/Whole Plant
			13.7.2.1	 Culture Media
			13.7.2.2	 Nutritional Components
		13.7.3	 Osmoticum
			13.7.3.1	 Nonionic Osmotica
			13.7.3.2	 Ionic Osmotica
	13.8	 Culture and Regeneration of Protoplast
	13.9	 Conclusions
	References
14: Plant Antimicrobial Peptides: Next-Generation Bioactive Molecules for Plant Protection
	14.1	 Introduction
	14.2	 Antimicrobial Microbial Peptides (AMPs) from Plants
		14.2.1	 Thionins
		14.2.2	 Defensins
		14.2.3	 Lipid Transfer Proteins (LTP)
		14.2.4	 Knottin-Type Peptides
		14.2.5	 Hevein-Like Peptides
		14.2.6	 Snakins
		14.2.7	 Mode of Action of Plant AMPs
		14.2.8	 Plant AMPs as Plant Protection Agents: A Plausible Application in Agriculture
	14.3	 Conclusion
	References
15: Nitrogen Stress in Plants and the Role of Phytomicrobiome
	15.1	 Introduction
		15.1.1	 Biological Nitrogen Fixation (BNF)
		15.1.2	 Phytomicrobiome and Its Role in N Fixation
			15.1.2.1	 Nonsymbiotic N Fixation
			15.1.2.2	 Symbiotic N Fixation
		15.1.3	 N Uptake and Its Regulation in N-Deficit Conditions
			15.1.3.1	 Root Architecture
			15.1.3.2	 Nitrate Transporters
			15.1.3.3	 Ammonium Transporters
		15.1.4	 Nitrate Sensing and Signaling
			15.1.4.1	 How Plants Perceive N Stress
			15.1.4.2	 Candidates in Nitrate Sensing and Signaling
		15.1.5	 Epigenetic Regulation in N Homeostasis
		15.1.6	 Cross Talk Between Nitrate and Other Mineral Nutrients
		15.1.7	 Use of Microbiome as Bioinoculants or Biofertilizers
	15.2	 Conclusion
	References
16: Halotolerant Microbes for Amelioration of Salt-Affected Soils for Sustainable Agriculture
	16.1	 Introduction
	16.2	 Reclamation and Management of Salt-Affected Soils
	16.3	 The Effect of Salinity on the Soil Microorganisms
		16.3.1	 Salinity Impacts on Rhizosphere Microbes
	16.4	 Soil Salinity Effects on Plant Growth and Development
	16.5	 Halotolerant Microbes
		16.5.1	 Mechanisms for Halotolerance
		16.5.2	 Vesicular Arbuscular Mycorrhiza (VAM)
	16.6	 Applications of Halophilic Bacteria
	16.7	 Microbial Bioremediation
		16.7.1	 Plant Growth-Promoting Rhizobacteria (PGPR) for Bioremediation
	16.8	 Plant-Microbiome Interactions for Salt Stress Alleviation
	16.9	 Isolation of Halophilic Microbes from Rhizospheric Soils of Halophytes
		16.9.1	 Isolation of Halophilic Rhizobia spp.
		16.9.2	 Isolation of Halophilic Endophytic Bacteria
	16.10	 Liquid Bioformulations Developed for Enhancing Crop Production in Salt-Affected Soils
	16.11	 Ameliorative Potential of Halophilic Microbes
	References