Symbiotic Soil Microorganisms: Biology and Applications

Contents
Part I: Fungal Symbiosis
	Chapter 1: Current Status-Enlightens in Its Biology and Omics Approach on Arbuscular Mycorrhizal Community
		1.1 Introduction
		1.2 Goal for Studying Its Biology and Omics Approaches
		1.3 Phylogeny of New Speices of AMF
		1.4 Genomics
		1.5 Fungal Metabolism During Symbiotic Life
		1.6 Proteomics
		1.7 Symbiotic Root-Microbe Interactions
		1.8 Enzymes
		1.9 Biology of AMF on Different Crops: Insight and Impact
		1.10 AMF Applications in Different Crops Under Varied Agro-Ecology
		1.11 Opportunities and Challenges: AMF
		1.12 Conclusion
		References
	Chapter 2: An Insight through Root-Endophytic-Mutualistic Association in Improving Crop Productivity and Sustainability
		2.1 Introduction
		2.2 Endophyte Distribution Pattern, Grouping, and Transmission Mode
		2.3 The Beneficial Endophytic Secretions: Bioactive Natural Products
			2.3.1 The Antimicrobial Bioactive Metabolites
			2.3.2 Anti-Insect Bioactive Potential
		2.4 The Quadra-Brigade of Endophytic Microbes: The Components of EPH´s
			2.4.1 Rhizobiaceae
			2.4.2 Piriformaspora indica
			2.4.3 Trichodermal strains
			2.4.4 AMF: Arbuscular Mycorrhizal Fungi
		2.5 EPHs: A Mutualistic Boon for Sustainable Agriculture
			2.5.1 Promoting Plant Growth and Increasing Market Value
			2.5.2 Integrated Pest and Disease Management
		2.6 Successful Trials: Integrating Crop Management Practices with Endophytic Symbionts
			2.6.1 The SRI Trial: System of Rice Intensification
		2.7 Improved Agricultural Prospective of EPHs
			2.7.1 Developing Tolerance to Stress by Optimizing the Redox Environment
			2.7.2 Sequestering the Future Agricultural Stress
		2.8 Conclusion
		References
	Chapter 3: Interaction Between Root Endophytes and Plants: Their Bioactive Products and Significant Functions
		3.1 Introduction
		3.2 Lifestyle of Root Endophytes
		3.3 Plant-Endophyte Relationship
		3.4 Bioactive Product Synthesized by Endophytes
			3.4.1 Ambuic Acid
			3.4.2 Cryptocin
			3.4.3 Colutellin A
			3.4.4 Pesatcin
			3.4.5 Torreyanic Acid
		3.5 Influence of Endophytes on Genetic and Phenotypic Expression of Plants
		3.6 Significant Role of Root Endophytes
			3.6.1 Endophytes Are Saprobic Decomposers
			3.6.2 Endophytes as Producer of Antibiotics
			3.6.3 Antiviral Compounds
			3.6.4 Endophytic Fungal Products as Anticancer Agents
			3.6.5 Antidiabetic Agents from Endophytes
		3.7 Conclusion and Future Insights
		References
	Chapter 4: Unravelling the Role of Endophytes in Micronutrient Uptake and Enhanced Crop Productivity
		4.1 Introduction
		4.2 Major Groups of Endophytic Microbes
			4.2.1 Fungal Endophytes
			4.2.2 Class 1 Clavicipitaceous Endophytes
			4.2.3 Class 2 Endophytes
			4.2.4 Class 3 Endophytes
			4.2.5 Class 4 Endophytes
			4.2.6 Bacterial Endophytes
			4.2.7 The Ecology of Competent Endophytes
			4.2.8 Host Range
			4.2.9 Physiological Role
			4.2.10 Ecological Role
		4.3 Micronutrients and their Role in Plant Growth
			4.3.1 Boron (B)
			4.3.2 Zinc (Zn)
			4.3.3 Manganese (Mn)
			4.3.4 Iron (Fe)
			4.3.5 Copper (Cu)
			4.3.6 Molybdenum (Mo)
			4.3.7 Chlorine (Cl)
		4.4 Mechanism of Micronutrient Uptake by Endophytes
		4.5 Role of Endophytes in Plant Growth Promotion
			4.5.1 Phytostimulation
			4.5.2 Biofertilization
			4.5.3 Biocontrol
		4.6 Conclusion and Future Prospects
		References
	Chapter 5: Dual and Tripartite Symbiosis of Invasive Woody Plants
		5.1 Introduction
			5.1.1 Mutualistic Symbiotic Relationship of Tree Species
		5.2 Role of Mutualistic Associations in the Invasion of Alien Tree Species
		5.3 Benefits of the Dual and Tripartite Mutualistic Relationship
			5.3.1 Facultative Mutualistic Relationship
		5.4 Distribution of Invasive Tree Species in the Time of Global Climate Changes
		5.5 Conclusion
		References
	Chapter 6: Eco-friendly Association of Plants and Actinomycetes
		6.1 Introduction
		6.2 Actinomyces as Soil Dwellers
			6.2.1 Rhizospheric Actinobacteria
			6.2.2 Endophytic Actinobacteria
		6.3 Plant Growth-Promoting Rhizobacteria (PGPR)
			6.3.1 Machinery Involved in Plant-Growth Promoting Rhizobacteria
				6.3.1.1 Production of Plant Growth Regulators (PGRs)
				6.3.1.2 Production of Siderophores
				6.3.1.3 Non-Symbiotic Nitrogen Fixation
				6.3.1.4 Chitinase Production
				6.3.1.5 Antagonistic Activity Against Phytopathogenic Fungi (Franco-Correa and Chavarro-Anzola 2016)
				6.3.1.6 Mycorrhiza (MA) Helper Bacteria (Franco-Correa and Chavarro-Anzola 2016)
		6.4 Ecological Contributions of Actinomycetes
			6.4.1 Handling of Abiotic Stresses
				6.4.1.1 Salinity
				6.4.1.2 pH
			6.4.2 Auxiliary Metabolite Generation
			6.4.3 Fertility
			6.4.4 Phytoremediation
			6.4.5 Miscellaneous Contributions
		6.5 Conclusion
		References
	Chapter 7: The Arbuscular Mycorrhizal Symbiosis of Trees: Structure, Function, and Regulating Factors
		7.1 Types of Mycorrhiza
		7.2 Evolution of Mycorrhizal Symbiosis
		7.3 Classification of Arbuscular Fungi
		7.4 Structure of Arbuscular Mycorrhizae
		7.5 Global Distribution of Arbuscular Mycorrhizal Trees
		7.6 Factors Impacting Trees and Their Fungal Symbionts
		References
	Chapter 8: Effectiveness of Arbuscular Mycorrhizas in Improving Carob Culture in the Mediterranean Regions
		8.1 Introduction
		8.2 Carob Origins and Cultivation
		8.3 Economic Potential of Carob Tree
		8.4 Agroecological Potential of Carob Tree
		8.5 Importance of Mycorrhiza in Improving Carob Cultivation
			8.5.1 Occurrence of Mycorrhizal Symbiosis in Carob Tree
			8.5.2 Importance of AMF in Improving Carob Propagation
			8.5.3 Importance of AMF in Enhancing Carob Tolerance to Drought
			8.5.4 Importance of AMF in Improving Carob Tolerance to P Deficiency
			8.5.5 Importance of AMF in Improving Field Establishment of Carob Tree
		8.6 Conclusion
		References
	Chapter 9: Leaf Endophytes and Their Bioactive Compounds
		9.1 Introduction
		9.2 Leaf Endophytes
		9.3 Endophytic Secondary Metabolites and Their Biological Activities
			9.3.1 Phenolic Compounds
			9.3.2 Terpenoids and Steroids
			9.3.3 Alkaloids
			9.3.4 Lipids
		9.4 Conclusion
		References
	Chapter 10: Role of Endophytic Fungus Piriformospora indica in Nutrient Acquisition and Plant Health
		10.1 Introduction
		10.2 Role of P. indica in Plant Growth Promotion
		10.3 Role of P. indica in Nutrient Transport
		10.4 Role of P. indica in Phytohormones Regulation
		10.5 P. indica as a Biocontrol Agent in Disease Resistance
		10.6 Role of P. indica in Stress Response
		10.7 Interaction of P. indica with Model Plants Arabidopsis thaliana and Nicotiana attenuate
		10.8 Effect of P. indica on Transgenic Plants
		10.9 Conclusion and Discussion
		References
	Chapter 11: The Role of Symbiotic Fungi in Nutri-Farms
		11.1 Introduction
		11.2 AMF as Bio-Fertilizer
		11.3 AMF and Mineral Nutrition
		11.4 AMF and Anti-Nutrients
		11.5 AMF and Abiotic Stresses
			11.5.1 Heavy Metals
			11.5.2 Drought
			11.5.3 Salinity
			11.5.4 Temperature
			11.5.5 Biotic Stress
		11.6 AMF and Secondary Metabolites
		11.7 Conclusion and Future Prospects
		References
Part II: Bacterial Symbiosis
	Chapter 12: Understanding the Evolution of Plant Growth-Promoting Rhizobacteria
		12.1 Introduction
		12.2 Biology of PGPR
			12.2.1 Symbiosis
			12.2.2 Growth Promotion
		12.3 Role of PGPR as Biocontrol Agents
		12.4 Application of PGPR in Agriculture
		12.5 Commercialization
		12.6 Conclusion
		References
	Chapter 13: Rhizobia-Legume Symbiosis During Environmental Stress
		13.1 Introduction
		13.2 Diversity of Rhizobia in Soil
		13.3 Interaction Between Legume and Rhizobia
		13.4 Role of Exopolysaccharides in Legume-Rhizobia Interaction
		13.5 Role of ROS in Nodulation
		13.6 Environmental Stresses and Their Regulation
			13.6.1 Temperature Stress
			13.6.2 Salt Stress
			13.6.3 Drought Stress
			13.6.4 Agrochemical Based Stress
			13.6.5 pH Stress
			13.6.6 Waterlogging Stress
		13.7 Conclusion
		References
	Chapter 14: Archaeal Symbiosis for Plant Health and Soil Fertility
		14.1 Introduction
		14.2 Distribution of Archaea in Soil
		14.3 Plant Archaeal Microbiome
		14.4 Role of Archaea in Biogeochemical Cycling
			14.4.1 Carbon Cycling
			14.4.2 Nitrogen Cycle
			14.4.3 Sulphur Cycle
			14.4.4 Phosphorous Cycle
		14.5 Archaea in Plant Health Improvement
		14.6 Conclusion
		References
	Chapter 15: Microbial Symbionts of Aquatic Plants
		15.1 Introduction
		15.2 Uses of Aquatic Plants
		15.3 Microbial Symbionts
		15.4 Benefits of Microbial Symbiosis in Aquatic Plants
			15.4.1 Biofiltration
				15.4.1.1 Removal of Nutrients from Eutrophic Wastewater
				15.4.1.2 Removal of Heavy Metals
				15.4.1.3 Removal of Organic Xenobiotic
			15.4.2 Nitrogen Fixation
			15.4.3 Production of Phytohormones
			15.4.4 Bioenergy Production
		15.5 Conclusion
		References
	Chapter 16: Rhizobium Presence and Functions in Microbiomes of Non-leguminous Plants
		16.1 The Genus Rhizobium at a Glance
		16.2 The Study of Rhizobium in the Era of the Omics
			16.2.1 Classical Techniques: Culturomics
			16.2.2 Genomics
			16.2.3 Proteomics
			16.2.4 Metabolomics
		16.3 Rhizobium and co.: Interactions with Non-leguminous Plants
		16.4 Finding Rhizobium in the Microbiomes associated with nonlegumes
		16.5 Concluding Remarks
		References
Part III: Insect-Fungus Mutualism
	Chapter 17: Symbiotic Harmony Between Insects and Fungi: A Mutualistic Approach
		17.1 Introduction
		17.2 Fungi and the Ecosystem
		17.3 The Evolutionary Antiquity of Fungus-Farming Insects
		17.4 Mutualism Between Leaf-Cutter Ants and Fungi
		17.5 Adaptation of the Ant Genome
		17.6 Fungus Cultivating Termite Species
		17.7 Mutualistic Association of Beetle With Fungi
		17.8 Fungi and Insect Mutualistic Association
		17.9 Services Offered and Benefits Gained
		17.10 Conclusion
		References
	Chapter 18: Panorama of Metarhizium: Host Interaction and Its Uses in Biocontrol and Plant Growth Promotion
		18.1 Introduction
		18.2 Hosts
		18.3 Structure and Mechanism
			18.3.1 Host Structure
				18.3.1.1 Hemolymph
				18.3.1.2 Hemocoel
				18.3.1.3 Hemocytes
				18.3.1.4 Fat Bodies
			18.3.2 Fungal Spores
				18.3.2.1 Appressorium as a Structure
			18.3.3 Pathogenesis
				18.3.3.1 Adhesion
				18.3.3.2 Germination
				18.3.3.3 Formation of Appressorium
				18.3.3.4 Penetration
				18.3.3.5 Colonization
				18.3.3.6 Sporulation
		18.4 Metarhizium Application Methods in Vector Control: A Superfluity
			18.4.1 Experimental Huts
			18.4.2 Using Paper Substrates as a Resting Material for Fungal Spores
			18.4.3 Water Storage Pots as a Carrier Material for Metarhizium
			18.4.4 Combination of Metarhizium with Insecticide-Treated Nets
			18.4.5 Metarhizium in Odor Bait Stations (OBS)
			18.4.6 Oil as a Carrier Material
				18.4.6.1 Mineral Oil
				18.4.6.2 Vegetable Oil
			18.4.7 Mosquito Landing Boxes (MLBs) for Metarhizium
			18.4.8 Metarhizium in Combination with Phytochemicals
			18.4.9 Metarhizium for Chemical Resistant Vector Hosts
			18.4.10 Delivery System in Agriculture Fields
				18.4.10.1 Kaolin Based
				18.4.10.2 Patty Blend Formulation
			18.4.11 Molecular Approaches
		18.5 Plant Growth Promotion
			18.5.1 Exchange of Nutrients and Endophytic Nature
			18.5.2 Improved Iron Absorption on Calcareous Substrates
			18.5.3 Auxin Formation for Plant Growth
			18.5.4 Proliferation of Plant Cells and Disease Suppression
		18.6 Conclusion: In the Light of Recent Advances
		References
	Chapter 19: Arbuscular Mycorrhizal Fungi: Potential Plant Protective Agent Against Herbivorous Insect and Its Importance in Su...
		19.1 Introduction
		19.2 AMF Primed Plant Defense
		19.3 AMF-Mediated Direct and Indirect Defense Mechanisms of Plants Against Herbivorous Insect
		19.4 Direct Defense
			19.4.1 AMF Induced Changes in Morphological Characteristics of Plant Against Herbivorous Insect
			19.4.2 AMF-Induced Plant Defense by Improving the Nutrient Content
			19.4.3 The Antioxidant Activity of Plants Infested with AMF and Herbivore
			19.4.4 AMF Alters Primary Metabolite Production and Allocation of It as Defense Response Against Insect Damage
			19.4.5 Herbivore Induced Synthesis of Secondary Metabolites in AMF Associated Plants
			19.4.6 The AMF Associated Plant Produced Anti-Nutritional/Digestive Proteins Involved in Defense Against Herbivore Performance
		19.5 Indirect Plant Defense Against herbivorous Insect Modulated by AM Fungi Association
		19.6 Conclusion and Future Thrust
		References
	Chapter 20: Eradication of Malaria by the Mutualistic Interaction Between Wickerhamomyces anomalus and Anopheles sp.
		20.1 Introduction
		20.2 Malaria and Its Mechanisms
			20.2.1 The Causative Agent: Plasmodium
			20.2.2 Lifecycle of Plasmodium
			20.2.3 The Vector: Anopheles Mosquito
		20.3 Wickerhamomyces anomalus
			20.3.1 Basic Characteristics and Morphology
				20.3.1.1 Niche
				20.3.1.2 Abiding Environment
				20.3.1.3 Compounds Secreted and Its Uses
			20.3.2 Killer Toxin
				20.3.2.1 Conditions for Secretion
				20.3.2.2 Mechanism of Action
				20.3.2.3 Validation of the Mechanism of Action
			20.3.3 The Mutualism of W. anomalus and Anopheles Mosquito
			20.3.4 Competition
				20.3.4.1 In Vivo
				20.3.4.2 In Vitro
				20.3.4.3 Impact
		20.4 Malaria Eradication
			20.4.1 Symbiotic Control of Malaria by Mutualism Between W. anomalus and Anopheles sp.
			20.4.2 Symbiotic Control of Malaria by Other Mutualistic Examples
		20.5 Conclusion
		References
Part IV: Microbial Symbiosis in Disease and Stress Management
	Chapter 21: Halophyte-Endophyte Interactions: Linking Microbiome Community Distribution and Functionality to Salinity
		21.1 Introduction
		21.2 Salicornia a Potential Halophytic Crop Plant
		21.3 Biodiversity of Endophytic Microbiome in S. europaea
			21.3.1 Salicornia Bacterial Diversity
			21.3.2 Salicornia Fungal Diversity
		21.4 Factors Shaping S. europaea-Endophyte Association
		21.5 S. europaea as a Reservoir of Specialized Endophytic Diversity
		21.6 Conclusions
		References
	Chapter 22: Root Endophytic Microbes and Their Potential Applications in Crop Disease Management
		22.1 Introduction
		22.2 Concerns of Economically Important Plants
		22.3 Crop Pathogens
		22.4 Endophytes and Their Mechanism of Action
			22.4.1 Phytohormone Production
			22.4.2 Nitrogen Fixation
			22.4.3 Phosphate Solubilization
			22.4.4 Siderophore Production
			22.4.5 ACC Deaminase Production
		22.5 Importance in Sustainable Agriculture
			22.5.1 Cereals
			22.5.2 Pulses
			22.5.3 Vegetables
			22.5.4 Fruits
			22.5.5 Sugar and Starches
			22.5.6 Spices and Condiments
		22.6 Conclusion
		References
	Chapter 23: Do Mycorrhizal Fungi Enable Plants to Cope with Abiotic Stresses by Overcoming the Detrimental Effects of Salinity...
		23.1 Introduction
		23.2 Effects of Mycorrhizal Inoculation on Salt and Drought Tolerance
		23.3 Effects of Salinity and Water Stress on Soil Properties and Plant Growth
			23.3.1 Mycorrhizal Fungi: Role in Soil Property  Improvement Under Stress Conditions
			23.3.2 Effects of Salt and Drought Condition on Arbuscular Mycorrhiza Development
			23.3.3 Mycorrhizal Fungi for Salinity Stress Remediation
		23.4 Mycorrhizal Inoculation: Effects on Plant Shoot and Root Growth Under Salt Conditions
		23.5 Mycorrhizal Symbiosis and Mineral Uptake Under Salt and Drought Stress Factors
			23.5.1 Phosphate Uptake Assisted by the AM Symbiosis Under Salt Stress Conditions
			23.5.2 Nitrogen Uptake and Transfer at the Mycorrhizal Interface Under Salt Stress Conditions
			23.5.3 Water and Potassium Relationship in AM Colonized Plant Under Salt and Drought Conditions
			23.5.4 Mycorrhizal Fungi: Effects on Macro and Micronutrients Uptake Under Salt and Drought Stress Conditions
		23.6 Effects of Mycorrhizal Inoculation and Biochar Application to Reduce the Salt Effects on Nutrient Uptake and Plant Growth
		23.7 Effects of Mycorrhizal Inoculation on Water Uptake
		23.8 Mechanisms of Mycorrhizae on Salt Tolerance in Soil and Inside the Host Plant
			23.8.1 Mycorrhizal Effectiveness for Hormonal Process and Signaling Under Salt Stress
		23.9 Alleviation of Salt and Drought Stresses by Arbuscular Mycorrhizal (AM) Fungi
			23.9.1 Arbuscular Mycorrhizal Fungi Increase Tolerance to Salinity in Plant Species
			23.9.2 Crop Tolerance to Salinity and Drought and Relation with Mycorrhizal Dependency
				23.9.2.1 Selective Interactions Between Different Species of Mycorrhizal Fungi and Plant for Salt and Drought Tolerance
			23.9.3 Effects of AMF-Colonization on Survival Rate of Horticultural Plants After Transplantation to the Field Conditions
			23.9.4 Effect of Biochar and Mycorrhizae on Alleviation of Salt and Drought
		23.10 Conclusion
		References
	Chapter 24: Combined Use of Beneficial Bacteria and Arbuscular Mycorrhizal Fungi for the Biocontrol of Plant Cryptogamic Disea...
		24.1 Introduction
		24.2 Beneficial Microorganisms in Plant Health
			24.2.1 Arbuscular Mycorrhizal Fungi (AMF)
				24.2.1.1 Main Beneficial Effects of AMF on Plants
				24.2.1.2 Underlying Mechanisms in Plant Protection by AMF
					24.2.1.2.1 Direct Modes of Action Involved in Reducing Pathogen Development
					24.2.1.2.2 Indirect Modes of Action Involved in Reducing Pathogen Development
			24.2.2 Beneficial Bacteria: Definition Boundaries and Modes of Action
				24.2.2.1 How to Define a Beneficial Bacteria?
				24.2.2.2 Underlying Mechanisms in Plant Protection by Beneficial Bacteria
					24.2.2.2.1 Direct Modes of Action Involved in Reducing Pathogen Development
					24.2.2.2.2 Indirect Modes of Action Involved in Reducing Pathogen Development
		24.3 Plant Protection Against Fungal Diseases Using AMF and Bacteria Co-Inoculation: Several Scenarios and Possible Mechanisms
			24.3.1 Common Base Grounds Between Studies
			24.3.2 ``Full-Gain´´ Scenario
				24.3.2.1 Evidence for Protection Gain with a Dual Inoculation
				24.3.2.2 Possible Mechanisms Explaining a ``Full-Gain´´ Scenario
			24.3.3 ``Partial-Loss´´ Scenario
				24.3.3.1 Evidence for a Partial Protection Loss with a Dual Inoculation
				24.3.3.2 Possible Mechanisms Explaining a ``Partial-Loss´´ Scenario
			24.3.4 ``No-Gain, No-Loss´´ Scenario
				24.3.4.1 Evidence for No Protection Gain with a Dual Inoculation
				24.3.4.2 Possible Mechanisms Explaining a ``No-Gain, No-Loss´´ Scenario
		24.4 Methodological Guide: How to Start Working on Tripartite Interactions ?
			24.4.1 Microbial Inoculation Methods
			24.4.2 Choosing the ``Mock-Inoculum´´
			24.4.3 Colonization or Bacterial Viability Assessment Methods
		24.5 Future Challenges Regarding Current Limits for Practical Use
		References
	Chapter 25: Remediation of Toxic Metal-Contaminated Soil and Its Revitalisation with Arbuscular Mycorrhizal Fungi
		25.1 Introduction
		25.2 Soil Remediation Using EDTA (Ethylenediamine Tetraacetate) Soil Washing
		25.3 Arbuscular Mycorrhizal Fungi in Metal Contaminated Soil
			25.3.1 Arbuscular Mycorrhiza
			25.3.2 Use of Molecular Methods in Community Ecology of Arbuscular Mycorrhizal Fungi
			25.3.3 Arbuscular Mycorrhizal Fungal Diversity in Toxic Metal Contaminated Soil
		25.4 Microbial Communities in Soils After Soil Remediation with EDTA
			25.4.1 Importance of Soil Biodiversity for Ecosystem Stability
			25.4.2 Diversity of Arbuscular Mycorrhizal Fungal Communities in Remediated Soil
		25.5 Future Prospects
		25.6 Conclusion
		References