Plant Microbe Symbiosis

Contents
Chapter 1: The Rhizobium-Plant Symbiosis: State of the Art
	1.1 Introduction
	1.2 Legume-Rhizobium Symbiosis for Root Nodulation
	1.3 Diversity of Legumes Depending on Rhizobium
	1.4 Taxonomy and Host Specificity of Rhizobium Species
	1.5 Factors Affecting Legume-Rhizobium Symbiosis
	1.6 Mechanism Behind Root Nodulation
	1.7 Role of Nitrogen and Mechanism of Root Nodulation
	1.8 Role of Ethylene in Preinfection Events
	1.9 Organogenesis of the Nodule
	1.10 Genetic Basis of Phytohormones During Root Nodule Development
	1.11 Application of Rhizobia as Biofertilizers
	1.12 New Aspects of Plant-Rhizobia Symbiosis
	1.13 Conclusion
	References
Chapter 2: Diversity and Importance of the Relationship Between Arbuscular Mycorrhizal Fungi and Nitrogen-Fixing Bacteria in T...
	2.1 Introduction
	2.2 Agroforestry Systems in the Mexican Tropics
	2.3 Functionality of Soil Microorganisms in AFS
	2.4 Soil Microorganisms in AFS in the Tropics of Mexico
		2.4.1 Arbuscular Mycorrhizal Fungi
		2.4.2 Nitrogen-Fixing Bacteria
	2.5 Conclusion and Future Prospects
	References
Chapter 3: Nitrogen Fixation in a Legume-Rhizobium Symbiosis: The Roots of a Success Story
	3.1 Introduction
	3.2 Root Nodule
		3.2.1 Definition and Types
		3.2.2 Nodule Formation
			3.2.2.1 Preinfection Stage
			3.2.2.2 Infection Stage
			3.2.2.3 Nodule Organogenesis
	3.3 N2 Fixation in a Legume-Rhizobium Symbiosis
	3.4 Effect of Abiotic Stress on Legume-Rhizobium Symbioses and N2 Fixation
		3.4.1 Salinity Stress
		3.4.2 Drought Stress
		3.4.3 Heat Stress
		3.4.4 Soil Acidity/Low pH
		3.4.5 Soil Nutrient Deficiency
	3.5 Conclusion and Future Prospects
	References
Chapter 4: A Genome-Wide Investigation on Symbiotic Nitrogen-Fixing Bacteria in Leguminous Plants
	4.1 Introduction
	4.2 Rhizobia and Legume
	4.3 Nodulation Factors (NFs)
	4.4 Advances in Nitrogen-Fixing Root Nodule Symbiosis
	4.5 Genome-Wide Investigation of Nodule Forming Bacteria
	4.6 Conclusions and Future Prospects
	References
Chapter 5: Symbiotic Signaling: Insights from Arbuscular Mycorrhizal Symbiosis
	5.1 Introduction
		5.1.1 Types of Mycorrhiza
			5.1.1.1 Ectomycorrhizae (ECM)
			5.1.1.2 Endomycorrhizae
			5.1.1.3 Arbuscular Mycorrhiza
	5.2 Arbuscular Mycorrhizal Development
		5.2.1 Asymbiotic Stage
		5.2.2 Mutual Recognition of Symbiotic Partners
			5.2.2.1 Strigolactones
			5.2.2.2 Regulation of Strigolactone Biosynthesis
			5.2.2.3 Fungal Signaling Molecules and Plant Receptors
		5.2.3 Formation of Appresorium/Hyphopodium
		5.2.4 PPA Formation
			5.2.4.1 Plant Genes Required for PPA Formation
		5.2.5 The Common SYM Pathway
			5.2.5.1 SYMRK
			5.2.5.2 CASTOR and POLLUX
			5.2.5.3 Nucleoporins
			5.2.5.4 CCaMK
			5.2.5.5 CYCLOPS
		5.2.6 Arbuscule Development
	5.3 Diverse Roles of AM
		5.3.1 Improved Absorption of Water and Nutrients
		5.3.2 Improved Phosphorus Uptake
		5.3.3 Improvement in Nitrogen-Fixing Capacity of Nodules in Legumes
		5.3.4 Enhanced Plant Growth Hormone Production
		5.3.5 Suppression of Root Disease
		5.3.6 Improvement of Soil´s Physical Characteristics
		5.3.7 Harsh Conditions Tolerance
		5.3.8 More Survival of Seedlings
		5.3.9 Protection Against Heavy Metals
		5.3.10 Protection Against Pathogens
		5.3.11 Tool for Studying Molecular Mechanisms and Improving Productivity
	5.4 Conclusion/Future Perspectives
	References
Chapter 6: Contribution of Beneficial Fungi for Maintaining Sustainable Plant Growth and Soil Fertility
	6.1 Introduction
	6.2 Role of Mycorrhizae in Maintaining Soil Fertility
	6.3 Role of Mycorrhizae in Stress Tolerance to Plants
	6.4 Role of Mycorrhizae in Plant Disease Control
	6.5 Role of Mycorrhiza in Plant Nutrition
	6.6 Role of Mycorrhizae in Nitrogen Fixation
	6.7 Conclusion
	References
Chapter 7: Biofertilizers Toward Sustainable Agricultural Development
	7.1 Introduction
	7.2 Role of Biofertilizers in Agriculture
		7.2.1 Azotobacter
		7.2.2 Azospirillum
		7.2.3 Rhizobium
		7.2.4 Cyanobacteria
		7.2.5 Azolla
		7.2.6 Gluconacetobacter diazotrophicus
	7.3 P-Solubilization
		7.3.1 Bacteria
		7.3.2 Fungi
	7.4 P-Mobilizers
		7.4.1 Mycorrhiza
	7.5 K-Solubilizing Bacteria
	7.6 Plant Growth-Promoting Rhizobacteria (PGPR)
	7.7 Zinc Solubilizers
	7.8 Innovation Approaches of Biofertilizers for Sustainable Agriculture Production
	7.9 Conclusion and Future Prospects
	References
Chapter 8: Plant Microbiome: Trends and Prospects for Sustainable Agriculture
	8.1 Introduction
	8.2 Plant Microbiome Concept
		8.2.1 Evolution of Microbial Interaction: The Hologenome Concept
		8.2.2 Composition of Plant-Associated Microflora
		8.2.3 Impact of Anthropogenic Interventions on Plant Microbiome Composition
		8.2.4 Taking the Plant Microbiome Association to the Next Level: Genomic Level
	8.3 Plant Associative Microbiota Leases Each Other Services for Survival
	8.4 Approaches to Study Plant Microbiome
		8.4.1 Metagenomics in Plant Microbiome Studies
		8.4.2 Metatranscriptomics in Plant Microbiome Studies
		8.4.3 Metaproteomics in Plant Microbiome Studies
		8.4.4 Metabolomics in Plant Microbiome Studies
	8.5 Microbiome and Crop Production
		8.5.1 Phytohormone Production
		8.5.2 Nutrient Acquisition in Plants
		8.5.3 Alleviation of Abiotic Stress
		8.5.4 Biocontrol
	8.6 Future Prospects
	References
Chapter 9: Plants and Microbes: Bioresources for Sustainable Development and Biocontrol
	9.1 Introduction
	9.2 Biocontrol for Sustainable Development
	9.3 Bioresources
		9.3.1 Need for Sustainable Development
		9.3.2 Plants as Bioresources
			9.3.2.1 Source of Lignocellulosic Biomass Wastes
			9.3.2.2 Microbes as a Bioresource
	9.4 Plants and Microbial Interactions
	9.5 Beneficial Interaction of Plants and Microbes for Bioresource Production
	9.6 What is Biocontrol?
		9.6.1 Need of Biocontrol
		9.6.2 Major Factors for the Success of Biocontrol
		9.6.3 Role of Cyanobacteria for Biotechnology: Environment and Sustainability
			9.6.3.1 Cyanobacterial Bioactive Compounds
			9.6.3.2 Cyanobacterial Bioplastics
			9.6.3.3 Cyanobacterial Consortia for Bioremediation Purposes
	9.7 Integrated Resource Management
	9.8 Applications of Plants and Microbially Derived Biomass in Sustainable Development
		9.8.1 Agriculture Application
		9.8.2 Composting
		9.8.3 Wastewater Treatment
	9.9 Conclusion
	References
Chapter 10: Plant-Microbiome Interactions in Hydrocarbon-Contaminated Soils
	10.1 Introduction
	10.2 The Active Role of Plants in the Metabolism of Hydrocarbons and How They Are Assisted by Microorganisms
		10.2.1 Uptake and Degradation of Hydrocarbons by Plants
		10.2.2 Phytotoxicity of Hydrocarbons
		10.2.3 The Role of Bacteria to Assist Plants in Hydrocarbon-Contaminated Soils
		10.2.4 The Role of Fungi to Assist Plants in Hydrocarbon-Contaminated Soils
	10.3 The Active Role of Microorganisms in the Metabolism of Hydrocarbons and How They Are Assisted by Plants
		10.3.1 Uptake and Degradation of Hydrocarbons by Bacteria
		10.3.2 Degradation of Hydrocarbons by Fungi
		10.3.3 The Role of Plants in Assisting Hydrocarbon Uptake/Degradation by Microorganisms
	10.4 The Construction of the Holobiont Concept Through Omics Approaches
	10.5 Conclusion and Future Prospects
	References
Chapter 11: Rhizoremediation: A Unique Plant Microbiome Association of Biodegradation
	11.1 Introduction
	11.2 Bioremediation Approaches
	11.3 Bioaugmentation Approaches
	11.4 Phytoremediation Approaches
	11.5 Rhizoremediation Approaches
	11.6 Factor Influencing PAH Degradation
	11.7 Bioavailability Approaches
	11.8 Biodegradation of PAH
	11.9 The Rate of PAH Biodegradation
	11.10 Microbial Enzymes Involved in PAH Degradation Process
	11.11 Improvement in Rhizoremediation
	11.12 Conclusion
	References
Chapter 12: Pesticide Tolerant Rhizobacteria: Paradigm of Disease Management and Plant Growth Promotion
	12.1 Introduction
	12.2 Mechanism of Plant Growth Promotion
		12.2.1 Direct Mechanism of Plant Growth Promotion
			12.2.1.1 N2 Fixation
			12.2.1.2 Plant Hormones
			12.2.1.3 Phosphate Solubilization
			12.2.1.4 ACC Deaminase (EC 4.1.99.4)
		12.2.2 Indirect Mechanism of Plant Growth Promotion
			12.2.2.1 Induced Systemic Resistance (ISR)
			12.2.2.2 Antibiosis
	12.3 Pesticide Degradation/Toleration by Soil Bacteria
	12.4 Plant Growth-Promoting Activities of Pesticide-Degrading/Tolerating Strains
	12.5 Conclusion
	References
Chapter 13: Structure and Function of Rhizobiome
	13.1 Introduction
	13.2 Structure of Rhizobiome
	13.3 Functions of Rhizobiome
		13.3.1 Rhizobiome Contributes to Plant Nutrition by Increasing Availability of the Limiting Nutrients
		13.3.2 Rhizobiome Contributes to Plant Growth by Producing Plant Growth Hormones, ACC Deaminase, and/or Volatile Organic Compo...
		13.3.3 Rhizobiome Directly Contributes to Plant Health by Controlling the Pathogens
		13.3.4 Rhizobiome Indirectly Contributes to Plant Health by Stimulating the Plant Resistance
		13.3.5 Functional Genomics of Barley Rhizobiome
	13.4 Factors That Affect Structure of Rhizobiome
		13.4.1 Root Exudates Determine the Structure of Rhizobiome
			13.4.1.1 Root Exudates
			13.4.1.2 Root Exudates Recruit Certain Microbial Species into Rhizocompartments
			13.4.1.3 Root Exudates Defend Plant Roots from Natural Enemies, Thereby Indirectly Altering Rhizobiome
		13.4.2 Plant Immune System Also Shapes Rhizobiome
	13.5 Methods for Studying Rhizobiome Structure and Function
	13.6 Summary
	References
Chapter 14: Soil Microbes-Medicinal Plants Interactions: Ecological Diversity and Future Prospect
	14.1 Introduction
	14.2 Diversity of Rhizospheric Bacteria Associated with Medicinal Plant
	14.3 Diversity of Rhizosphere Fungi Associated with Medicinal Plant
	14.4 Effect of Rhizospheric Microbiome on Medicinal Plant Growth and Nutrient Uptake
	14.5 Effect of Rhizospheric Microbiome on Biotic and Abiotic Stress Tolerance
	14.6 Conclusions
	References
Chapter 15: Insight to Biotechnological Advances in the Study of Beneficial Plant-Microbe Interaction with Special Reference t...
	15.1 Introduction
	15.2 Agrobacterium tumefaciens: Natural Plant Genetic Engineer
	15.3 Signal Transduction and Host Immune Response
	15.4 Quorum Sensing and Quenching
	15.5 Plant Genes Involved in Susceptibility/Resistance to Agrobacterium Transformation
		15.5.1 Factor Affecting Agrobacterium Plant Transformation
	15.6 Recent Advances/Application in Plant Biology Research
	15.7 Omics Approaches for Understanding Plant-Microbe Interaction Complexity
	15.8 Conclusion
	References
Chapter 16: Amelioration of Salt Stress Tolerance in Plants by Plant Growth-Promoting Rhizobacteria: Insights from ``Omics´´ A...
	16.1 Introduction
	16.2 Physiological and Molecular Responses of Plants to Salinity Stress
	16.3 Rhizospheric Bacteria to Mitigate Salt Stress in Plants
	16.4 Role of PGPR in Salinity Stress Tolerance and Plant Growth Promotion
	16.5 Omics Approaches to Address the Alleviation of Salt Stress by PGPR: Transcriptome, Proteome and Metabolome Analyses
	16.6 Future Perspectives
	References
Chapter 17: Plant Microbial Ecology as a Potential Option for Stress Management in Plants
	17.1 Introduction
	17.2 What is Stress?
	17.3 Stress in Plants
	17.4 Types of Plant Stresses
	17.5 Abiotic and Biotic Plant Stresses
	17.6 Different Phases Induced by Stress
		17.6.1 Response Phase
		17.6.2 Restitution Phase
		17.6.3 End Phase
		17.6.4 Regeneration Phase
	17.7 Plant-Microbe Interactions for Stress Management in Plants
	17.8 Mechanisms of Plant-Microbe Interactions in Rhizosphere
	17.9 Plant-Microbe Interactions for Alleviation of Abiotic Stresses
		17.9.1 Drought as Stress
		17.9.2 Salinity as Stress
		17.9.3 Heavy Metal Toxicity as Stress
		17.9.4 Cold Stress in Plants
		17.9.5 Heat Stress of Plants
		17.9.6 Osmotic Stress to Plants
		17.9.7 Alleviation of Biotic Stresses
	17.10 OMICS Approach of Stress Management in Fields
	17.11 Conclusion
	References