Plant Mycobiome: Diversity, Interactions and Uses

Description

Plant mycobiome represents a diverse array of plant-associated communities of endophytic and epiphytic fungi. These communities fundamentally affect plant health, development, adaptation, and communication with the surrounding ecosystem. Furthermore, they have key roles in the establishment, diversification, productivity, and sustainability of different natural ecosystems. However, some of these communities are pathogenic for the plant itself or dangerous for the consumers, due to the production of mycotoxins. In other words, plant mycobiome represents two faces of a coin. This book aimed to explore contributions of the plant mycobiome in plant-environment interactions from different perspectives. Chapters of this book address numerous themes covering the recent advances in roles, diversity, and dynamics of these fungi as biocontrol agents, biofertilizers, growth promoters, and their secondary metabolites in the area of crop improvement for sustainability and biotechnology, as well as the plant pathogenic and toxigenic fungi. This book will be useful to postgraduate students, botanists, mycologists, ecologists, plant pathologists, and physiologists. Preface Introduction Contents Mycotoxins and Their Producers: Diversity, Side Effects and Control 1 Introduction 2 Economic Importance of Mycotoxins 2.1 Market Losses 2.2 Health Influences of Mycotoxins on Humans and Animals 3 The Major Families of Mycotoxins 3.1 Aflatoxins 3.2 Ochratoxins 3.3 Zearalenone 3.4 Fumonisins 3.5 Trichothecenes 3.6 Patulin 3.7 Ergot Alkaloids 4 Mycotoxins-Producing Fungi 4.1 Aspergillus spp. 4.2 Penicillium spp. 4.3 Fusarium spp. 4.4 Claviceps spp. 5 Occurrence in Foodstuffs 5.1 Cereals and Cereal Based-Products 5.2 Meat and Processed Meat Products 5.3 Milk and Dairy Products 5.4 Fruits and Fruit-Based Products 6 Factors Affecting Mycotoxin Production and Occurrence in Foodstuffs 6.1 Pre-harvest Conditions 6.2 Harvest and Post-harvest Conditions 7 Control Strategies of Mycotoxins 7.1 Pre-harvest Strategies 7.2 Post-harvest Strategies 7.2.1 Physical Methods 7.2.2 Chemical Methods 7.2.3 Biological Methods 8 Future Perspectives 9 Conclusions References Seed-Borne Mycoflora and Their Management 1 Introduction 2 Detection of Seed-Borne Mycoflora 3 Effect of Mycoflora on Seed Health and Viability, Plant Growth, and Yield 4 Management of Seed-Borne Mycoflora 5 Biological Seed Enhancement Treatment to Control Seed-Borne Mycoflora and Improve Seed Quality, Plant Growth, and Yield 6 Concluding Remarks and Future Research References Rhizosphere Mycobiome: Roles, Diversity, and Dynamics 1 Introduction 2 Neutral Processes 3 Selective Processes 3.1 The Biotic Effects Among Microbes 3.1.1 Interaction with Other Microorganisms 3.1.2 Plant Type Effect on Rhizosphere Community 3.2 The Abiotic Effects Among Microbes 3.2.1 Temperature, pH, and Moisture Effect on Mycobiome Diversity 3.2.2 Soil Type as a Factor Affecting the Mycobiome Diversity 4 Inferences in Microbial Community Assembly 4.1 Community Assembly in Host-Associated Systems 4.2 Host Development 4.2.1 Metabolites Phytohormone Production Phosphate Solubilization ACC Deaminase Production by Rhizospheric Fungi 5 Geographic Distribution References Phyllosphere Mycobiome: Diversity and Function 1 Introduction 2 High Diversity of the Phyllosphere Mycobiome 2.1 Natural Ecosystems 2.2 Agroecosystems 2.3 Urban Ecosystems 3 Fungal Biogeographic Patterns in Phyllosphere 3.1 Fine and Local Scales 3.2 Regional Scales 3.3 Continental and Global Scales 4 Fungal Temporal Dynamics in Phyllosphere 4.1 Temporal Factors Shaping Phyllosphere Mycobiome Assembly 4.2 Temporal Patterns of Fungal Diversity, Composition, and Networks 5 Fungal Community Assembly in Phyllosphere 5.1 Community Assembly Processes 5.1.1 Selection 5.1.2 Dispersal 5.1.3 Diversification and Drift 5.2 Co-occurrence Networks 5.3 Source Analyses of Phyllosphere Fungi 6 Fungal Functions in Phyllosphere 6.1 Functional Traits 6.2 Functional Genes 6.3 Omics 6.3.1 Metagenomics 6.3.2 Metatranscriptomics 6.3.3 Metabolomics and Metaprotemics 7 Interactions of Phyllosphere Mycobiome with Plants 7.1 Roles in Plant Health 7.1.1 Phyllosphere Fungi as Pathogens that Inhibit Plant Health 7.1.2 Phyllosphere Fungi as Bio-control Agents that against Pathogens and Herbivores 7.2 Effects on Plant Growth and Biomass 7.2.1 Phyllosphere Fungi Promote Plant Growth and Biomass through Producing Phytohormones 7.2.2 Phyllosphere Fungi Promote Plant Growth and Biomass through Increasing Nutrient Uptake 7.2.3 Phyllosphere Fungi Increase Plant Tolerance to Environmental Stresses 7.3 Effects on Plant Population and Community 8 Interactions of Phyllosphere Mycobiome with Global Change Factors 8.1 Warming, Precipitation, and Drought 8.2 Fertilization, Nitrogen Deposition, Acid Rain, and Urbanization 9 Future Prospects References Plant Mycobiome in Sustainable Agriculture 1 Introduction 2 Mycobiota Diversity and Composition Differ Among Plant Compartments 2.1 Rhizosphere Mycobiota 2.2 Phyllosphere Mycobiota 2.3 Endosphere Mycobiota 3 Management of Native Mycobiota for Sustainable Agriculture 3.1 Crop Rotation 3.2 Organic Amendments Application 3.3 Arbuscular Mycorrhizal Fungi (AMF) 4 Conclusions & Perspectives References Plant-Fungus Interactions in Rust Diseases 1 Introduction 2 ATPase Activity at the Host-Pathogen Interfaces of Rust Infection 2.1 Spermognial-Aecial Stages 2.2 Uredinial Stages 3 Infection of Vascular Tissues in Host-Rust Interaction 3.1 Puccinia Punctiformis 3.2 Puccinia lagenophorae 4 Cytochemical Aspects of the Interaction Between the Rust Fungus Melampsora euphorbiae and Its Host, Euphorbia peplus 5 Conclusion References Rust Haustoria 1 Introduction 2 Rust Haustorium 2.1 Monokaryotic and Dikaryotic Haustoria 2.2 Case Study: Haustoria of Puccinia punctiformis 2.2.1 Filamentous Haustoria (M-haustoria) 2.2.2 Clavate Haustoria (D-haustoria) 2.2.3 Development of D-haustorium of Melampsora euphorbiae 2.2.4 The Function of Rust Haustorium References Recent Advancement in Fungal Biocontrol Agents 1 Introduction 2 Fungal Biocontrol Agents (FBCAs) 3 Modes of Action of Fungal Biocontrol Agents (FBCAs) 4 Modern Biotechnological Approaches 5 Microbial Consortia 6 Myconanotechnology 6.1 Filamentous Fungi 6.2 Mushrooms 7 Arbuscular Mycorrhizal Fungi (AMF) 8 Rust Fungi 9 Recent Molecular Approaches References New Perspectives on Fungal Siderophores 1 Introduction 2 Structure and Biosynthesis of Siderophores 3 The Function of Siderophores 4 Mechanism of Siderophores-Mediated Iron Uptake 5 Role of Siderophores 5.1 Siderophore and Microbial Community 5.2 Siderophores Promotes Plant Growth 5.3 Siderophores and Fungal Virulence 5.4 Siderophores and Plant Immune Responses References Biogenic Synthesis of Nanoparticles Mediated by Fungi 1 Introduction 2 Nanoparticles 3 Biosynthesis of NPs 3.1 Myconanotechnology 3.2 Strategies Used for the Fungal Biosynthesis of Nanoparticles 3.2.1 Top Down 3.2.2 Bottom Up 3.3 Mechanism of Myco-synthesis of Nanoparticles 3.4 Different Metallic Nanoparticles Are Produced During Myco-synthesis 3.4.1 Silver Nanoparticle Production (AgNP) 3.4.2 Gold Nanoparticle Production (AuNP) 3.4.3 Miscellaneous Nanoparticle Production 3.5 Potential Uses for Mycogenic Nanoparticles References Plant Growth-Promoting Fungi for Growth Improvement and Resistance Induction 1 Introduction 2 Impact of PGPF on Plant Growth Promotion 3 Impact of PGPF on Plant Resistance Induction 4 Conclusions References An Insight into Fungi in Forest Ecosystems 1 Introduction 2 Mycorrhizal Fungi 2.1 Ectomycorrhizal Fungi (EMF) 2.2 Endomycorrhizal Fungi (EF) 2.3 Arbuscular Mycorrhizal Fungi (AMF) 2.4 Ericoid Mycorrhizal Fungi (ERM) 2.5 Orchid Mycorrhizal Fungi (OMF) 3 Role of Mycorrhizal Fungi 4 Phyllosphere Epiphytic and Endophytic Fungi 5 Fungal Endophytes 6 Role of Endophytic Fungi 7 Pathogenic Fungi 8 Emerging Forest Pathogenic Fungi 9 Major Plant Diseases 9.1 Dutch Elm Disease 9.2 Canker 9.3 Ash Dieback 9.4 Red Needle Cast Disease 9.5 Foliar Rust Disease 9.6 Oak Decline 9.7 Cypress Canker 9.8 Shoot Blight 10 Mushrooms and Wood Decay Fungi References Recent Progress on Fungal Enzymes 1 Introduction 2 Production of Fungal Enzymes 2.1 Optimization of Medium 2.2 Genetic Approaches 3 Purification of Fungal Enzymes 4 Recent Applications of Fungal Enzymes 4.1 Industrial Applications 4.2 Biomedical Applications 4.3 Environmental Applications 5 Conclusion References Endophytic Fungi as Sources of Novel Natural Compounds 1 Introduction 2 What Are Endophytes? 3 Isolation of the Fungal Endophytes 4 Benefits of the Plant’s Endofungi 5 Bioactive Metabolites Produced by the Endophytic Fungi 5.1 Indole Alkaloids 5.2 Polyketides 5.3 Alkaloids 5.4 Phenolic Compounds 5.5 Lipids 5.6 Terpenoids and Steroids 5.7 Vinblastine 5.8 Paclitaxel 5.9 Camptothecin (CPT) 5.10 Podophyllotoxin (PDT) 6 Bio-applications of the Endofungal Metabolites 6.1 Antibacterial Potential 6.2 Antifungal Efficacy 6.3 Antiviral Potency 6.4 Anti-Cancerous Activity 6.5 Cerebral Stimulant and Vasodilator 6.6 Endophytes as Promoters of Plant Growth 7 Approach’s Employed to Enhance the Production of Endofungal Secondary Metabolites 8 Conclusion References Symbiotic Relationships with Fungi: From Mutualism to Parasitism 1 Introduction 2 Mutualism in Plant Fungi Symbiosis 2.1 Plant–Endophyte Association 3 Commensalism in Plant Fungi Symbiosis 4 Parasitism in Plant Fungi Symbiosis 4.1 Hyperparasitism 4.2 Types of Parasitism 4.2.1 Obligatory 4.2.2 Nonobligatory (Facultative) 4.3 Factors Affecting Parasitism 5 Signaling and Quorum Sensing in Plant Symbiotic Relationships with Fungi 5.1 Endophytism Interactions References Roles and Benefits of Mycorrhiza 1 Introduction 2 Roles and Mechanisms of AMF in Water and Nutrients Acquisition 2.1 Water Acquisition 2.2 AMF-Mediated Induction of Tolerance Responses to Drought 2.2.1 Induction of Phytohormones 2.2.2 Improving Plant Water Uptake 2.2.3 Enhancing the Hydraulic Conductivity 2.2.4 Osmoprotectants Production 2.2.5 Induction of Antioxidant Activity 2.2.6 Improvement of the Photosynthesis Efficiency 2.3 Nutrients Acquisition 2.3.1 Nitrogen 2.3.2 Phosphorus 2.3.3 Potassium 3 Roles and Mechanisms of AMF in Plant Growth 4 Roles and Mechanisms of AMF in Plant Protection 5 Role and Mechanism of Arbuscular Mycorrhizal Fungi in Plant Tolerance to Salinity 6 Role and Mechanism of Arbuscular Mycorrhizal Fungi in Plant Tolerance to Drought 7 Role and Mechanism of Arbuscular Mycorrhizal Fungi in Plant Tolerance to Heavy Metal Toxicity 8 Role and Mechanism of Common Mycorrhizal Networks References Mycorrhizal Networks: A Secret Interplant Communication System 1 Introduction 2 Mycorrhiza in Rhizosphere 3 Taxonomy of Mycorrhizal Fungi 4 Plant-Mycorrhizal Association 5 How Plants Recognize the Mycorrhizal Fungi as Friends 6 Role of Mycorrhiza in Exchange of Info-Chemical Molecules 7 Role of Mycorrhiza in Exchange of Allelo-Chemical and Toxic Molecules 8 Resource Exchange in the Plant-Mycorrhizal Association 9 Models That Mycorrhiza Follow for Transfer of Nutrients Between Plants 10 Impact of Mycorrhizas on Plant Immunity 11 Application of Mycorrhizas in Agriculture, Horticulture and Forestry 11.1 Arbuscular Mycorrhizas in Agriculture and Horticulture 11.2 Ectomycorrhizas and Forest Production 12 Mycorrhiza Restore Human Activity and Climate Disturbance 13 Conclusion References Impacts of Climate Change on Plant Mycobiome 1 Introduction 2 Effect of Climate Change on Plants and Mycobiota 2.1 Ultraviolet Radiations 2.1.1 Nature of Light 2.2 Electromagnetic Spectrum 2.3 Photobiology: Interaction of Light with Living Organisms 3 Climate Warming 3.1 Plant Responses to Climate Warming 3.2 Climate Affects Symbiotic Fungal Endophyte Diversity and Performance 3.3 Climate Change and Fungal Pathogens 3.4 Climate Affects Symbiotic Fungal Endophyte Diversity and Performance 3.5 Effect of Climate Change on Fodder and Forage Availability and Livestock 3.5.1 Nutritional Factors 3.5.2 Effect of Climate on Fodder 3.5.3 Effect of Climate on Livestock References