Plant Pathology and Plant Diseases

Cover
Plant Pathology and Plant Diseases
Copyright
Dedication
Contents
Preface
About the Authors
Contributors
Acknowledgements
	Financial Support
Introduction
	What is plant pathology?
	The structure of the book
Part I General Plant Pathology
	1 What is a Plant Disease?
		Introduction
		The Host Plant
		The Pathogen
			Fungi and fungal-like microorganisms
			Bacteria and phytoplasma
			Nematodes
		Abiotic Stress Factors
		Koch’s Postulates
		The Disease Triangle
		Phytobiomes and Microbiomes
		Impacts of Plant Diseases
		Further Reading
	2 History of PlantPathology
		Early History of Plant Diseases
		The Modern Era: Evolution of the Germ Theory
			Fungi and fungal-like organisms
			Bacteria
			Viruses
			Nematodes
		Plant Pathology Becomes a Science
		Further Reading
	3 The Disease Cycle and Lifestyles
		Introduction
		Lifestyles in Plant–Pathogen Interactions
		The Disease Cycle
			Deposition and sources of inoculum
				Where does the inoculum come from?
				Arrival of inoculum
			Prepenetration (events before penetration)
				The pathogen adheres to the host
				Spore germination and appressorium formation
				Recognition between host and pathogen
			Penetration
				Penetrations through natural openings
				Penetrations through wounds
			Infection and colonization
				Invasion
				Haustoria
				Intracellular pathogens
				Colonization
			Reproduction of the pathogen
			Dispersal
				Dispersal by water
				Dispersal by insects, mites,nematodes and other vectors
				Dispersal by plant parts and humans
		Survival of the Pathogen
		Monocyclic and Polycyclic Pathogens
		Further Reading
Part II Plant Pathogens
	4 Plant Pathogenic Fungi
		What are Fungi?
			Characteristics of fungi
			Reproduction
				Sexual reproduction
				Asexual reproduction
			Lifestyle
		Classification of Kingdom Fungi (Eumycota)
		Phylum Chytridiomycota
		Phylum Zygomycota
		Phylum Glomeromycota
		Phylum Ascomycota (Sac Fungi)
			Sexual reproduction
				Sexual fruiting body: ascocarp
			Asexual reproduction
			Classes of Acomycota
				Taphrinomycetes
				Saccharomycetes (Yeasts)
				Leotiomycetes
				Ascomycetes with apothecia
				Ascomycetes with chasmothecia(cleistothecia)
				Sordariomycetes: Ascomycetes with perithecia
				Dothideomycetes: Ascomycetes with pseudothecia/ascostroma
		Phylum Basidiomycota(Club Fungi)
			Pucciniomycetes (rust fungi)
			Ustilaginomycetes (smut fungi)
			Agaricomycetes
		From ‘Imperfect Fungi’ to ‘One Fungus, One Name’
		Further Reading
	5 Fungal-Like Plant Pathogens
		What are Fungal-Like Plant Pathogens?
		Kingdom Chromista
		Phylum Oomycota
			Reproduction
				Sexual reproduction
				Asexual reproduction
			Lifestyle
				Classification of Oomycota
				Class Peronosporea
		Phylum Cercozoa
			Class Phytomyxea, order Plasmodiophorida
		Kingdom Protozoa
			Characteristics of Physarales
				Lifestyle
		Further Reading
	6 Bacterial Plant Pathogens
		Plant-Associated Bacteria
		Taxonomy of Plant Pathogenic Bacteria
		Symptoms Caused by Plant Pathogenic Bacteria
			Leaf lesions (or leaf spots)
			Wilts
			Cankers and diebacks
			Rots
			Galls
			Yellows, witchs’ brooms and scorch
		Dispersal of Plant Pathogenic Bacteria
			With plant material and soil
			With rain and irrigation water
			With insects, machinery and tools
		Stages of Infection
			Survival of plant pathogenic bacteria
			Survival as viable but non-culturable cells
		Infection Mechanisms and Pathogenicity Determinants
			Chemical signalling
			Biofilm and production of extracellular polysaccharides (slime)
			Secretion systems
		Lifestyles of Model Plant Pathogenic Bacteria
			Tomato speck caused by hemibiotrophic Pseudomonas syringae pv. tomato
			Soft rot caused by necrotrophic Pectobacterium and Dickeya species
			Crown gall caused by biotrophic Agrobacterium radiobacter (A. tumefaciens)
			Phloem-limited, insect-transmitted biotrophic bacteria
		Important Bacterial Diseases
			Cereals and grasses
				Halo blight of oats
				Bacterial wilt of grasses (Poaceae)
				Potato (Solanum tubersosum) Blackleg and soft rot
				Potato brown rot
				Potato ring rot
				Common scab in potato
			Woody plants
				Crown gall
				Fireblight
			Ornamentals
				Bacterial leaf spot and wilt of begonias and geranium
		Further Reading
	7 Plant Viruses
		What is a Plant Virus?
			Constituents
				Nucleic acids
				Coat protein
				Lipids
				Other constituents
			Satellites and viroids
			Nomenclature and taxonomy
			Viruses as molecular tools
			Viruses as plant pathogens
		Plant Virus Genera and Families
			Viruses with spherical particles
			Viruses with elongated virus particles
			Virus with other shapes
		The Virus Infection
			Virus replication
			Translation of virus genesin to proteins
			Cell-to-cell spread
			Long-distance spread in the plant
			Effect on plant structure and physiology at the cellular and tissue level
		Symptoms in Plants
			Colour changes and necrosis
				Mosaic (ring spots, veinclearing, etc.)
				Yellowing/reddening
			Growth reduction and disorders
				Deviating growth
			Damage and economic losses
		Detection and Identification
			Symptoms in the original host
			Test plants
			Electron microscopy
			Serology
			Nucleic acid techniques
			The choice of method and Koch’s postulates
		Virus Transmission and Epidemiology
			Vegetative propagation
			Grafting
			Seed
			Pollen
			Mechanical
			Vectors
				Insects as viral vectors
				Mites as viral vectors
				Nematodes as viral vectors
				Fungi and Cercozoa as viral vectors
			Infection sources for plant viruses
		Control of Plant Viruses
			Exclusion
			Healthy planting material
			Removal of sources of infection
			Preventing spread
			Vector control
			Resistance
			Cross-protection and induced resistance
			Transgenic plants
		Further Reading
	8 Nematodes as Plant Pathogens
		General Characteristics of Nematodes
			Two sides of the coin
			Nematode extraction
			Systematics of Plant-Parasitic Nematodes
		Morphology of a Plant-Parasitic Nematode
		Feeding Groups of Plant-Parasitic Nematodes
			Bionomics of ectoparasitic nematodes
				Life cycle
				Stunt nematodes
				Spiral nematodes
				Pin nematodes
				Ring nematodes
				Stubby-root nematodes
				Needle nematodes
				Dagger nematodes
				Virus transmission
			Bionomics of migratory endoparasitic nematodes
				Life cycle
				Bud and leaf nematodes
				Stem and bulb nematodes
				Root-lesion nematodes
				Burrowing nematodes
				Rice root nematodes
				Wood nematodes
				Root gall nematodes
			Bionomics of sedentary endoparasitic nematodes
				Root-knot nematodes
				Cyst nematodes
				Sedentary semi-endoparasites
			Host status and reproductive rates
			Damage thresholds
		Plant-Parasitic Nematodes as Plant Pathogens
		Field Symptoms of Nematodes
			Symptoms on plants aboveground and on tubers
			Symptoms on roots
		Nematodes as Parts of Disease Complexes
		Plant Resistance
			Resistance mechanisms
		Nematode Management
		Further Reading
	9 Diagnosis of Plant Diseases
		Introduction
			Symptoms and signs
		Abiotic Causes of Disorders
		Koch’s Postulates
		Classical Procedures for Diagnosis
		Detection of Seedborne Pathogens
		Molecular Diagnosis Using Laboratory Facilities
			DNA-based diagnostic methods
				Multiplex PCR
				Loop-mediated isothermal amplification
			Serological analyses
		In-field Diagnostic Tests
			Image analysis
			Lateral flow devices
			PCR-based techniques
			Diagnostic Laboratories and Plant Clinics
		Further Reading
Part III Plant–Pathogen Interactions from Genes to Populations
	10 Mechanisms of Pathogenicity
		Why Study Pathogenicity?
		Pathogenicity Genes and their Products
		The Pathogenicity Factors
			Hydrolytic enzymes
			Toxins: Phytotoxins
			Mycotoxins
			Hormones (Phytohormones)
				The unusual case of Agrobacterium tumefaciens
			Effector proteins
			miRNA – microbial regulators of host defences
			Evolution of pathogenicity genes:Mobile genes
		Further Reading
	11 Plant Defence Against Pathogens
		Disease Resistance and Defence Against Pathogens
		Physical Barriers
		The Hypersensitive Response: Programmed Cell Death
		Antimicrobial Metabolites: Phytoalexins and Phytoanticipins
		Antimicrobial Proteins
		Genes/Proteins of Unknown Function
		Further Reading
	12 Race Specificity and Plant Immunity
		The Regulation and Inheritance of Plant Defences
		Plant Immunity
			MAMP and PRR receptors
			Effector-triggered immunity
			Disease resistance – or immunity
				Race specificity
				HRP-dependent activation of the hypersensitive response (HR) in bacteria
		Cloning of Resistance Genes
			The NBS-LRR R-gene family
			Mode of action
			The receptor–ligand, guardand decoy hypotheses
				How do the different R genesevolve in specificity?
				The tomato–Pto system
			AvrPto and Pto protein interactions
			Downstream of Pto: signal transduction
				The systemic inductionof resistance
		Mutation as a Tool for Studying Disease Resistance
		Further Reading
	13 Population Genetics in Plant–Pathogen Interactions
		Introduction
		Definitions
		Population Biology of Plant Pathogens
		Genetic Structure of a Pathogen Population
		Measurement of Genetic Variation in Pathogen Populations
		The Five Evolutionary Forces
		Population Genetics of Phytophthora infestans
		Population Genetics of Rusts
		Further Reading
	14 Epidemiology: Disease in Plant Populations
		What is Epidemiology?
			Processes and sub-processes
			Monocyclic and polycyclic processes
			Quantification of disease
		Monocyclic Processes
			Simple interest disease
			Differences in terminology
			Estimating the rate of disease increase, rs
		Polycyclic Processes
			Compound interest disease
			Unrestricted growth
			Logistic growth
			The size of r and how to estimate it
		Modifications of the Logistic Equation: Back to Biology
			Paralogistic growth
			SIR models
		Applications
			The continuation of an epidemic
			The basic reproductive number
			The three phases of an epidemic
			Epidemiological aspects of plant disease management
		Further Reading
Part IV Disease Management
	15 Cultural Practices for Disease Management
		What are Cultural Practices?
		Pathogen-free Propagation Material
			Removing pathogen contamination from seeds and propagation material
			Pathogen-free material of clonally propagated crops
		Removal of Infected Plants or Infested Plant Debris
		Removal of Alternative and Alternate Hosts
		Soil Treatment
		Hygiene: Tools and Machinery
		Crop Rotation
		Soil and Water Management
		Fertilization
		Sowing, Planting, Weeding, Planting Site
		Quarantine
		Further Reading
	16 Chemical Plant Disease Control
		The Role of Fungicides in Plant Disease Management
		Fungicide History
		How are Fungicides Used?
		Classification of Fungicides
		Fungicide Resistance
			What is fungicide resistance?
			Development of fungicide resistance
			Determining fungicide resistance
			Fungicide resistance risk reduction
		Further Reading
	17 Biological Control of Plant Diseases
		Introduction and Definition of Biological Control
		How to Select a Good Biological Control Agent?
		Mechanisms of Biological Control
		Direct Biological Control Interactions
			Exploitation competition
			Interference competition
			Hyperparasitism
		Indirect Control of Plant Diseases
			Induced resistance
			Plant growth promotion
			The tolerance of BCAs to hars henvironments experienced under biological control interactions
		Importance of Understanding the Plant Host/Disease Cycle for Optimal Biological Control
		Production, Formulation and Delivery
			Is it possible to improve or even create better BCAs?
			Formulation and application of BCAs
		Legislation and Risk Assessment
			Perspectives
		Further Reading
	18 Disease Management Strategies Using Host Resistance
		Host Resistance Based on Resistance Genes
			Sources of host resistance
			Race-specific resistance
				Directional selection
			Race-non-specific resistance
			Race-specific and race-non-specific resistance in the same host
			Durable disease resistance
			Fitness cost of resistance
			Induced resistance
		Disease Management Strategies Using Host Resistance
			Genotype mixtures
				Which mechanisms are operating in mixtures?
				Directional selection in mixtures
				Why grow variety mixtures?
			Pyramiding resistance genes
			Deployment in time and space
			Intercropping
		Further Reading
	19 Biotechnology for Plant Disease Control
		Application of Biotechnological Tools for Plant Disease Control
		Antimicrobial Metabolites
		Regulating Plant Immunity
			Do all transgenic plants need to make new proteins?
				Viruses
				Host-induced gene silencing
		Tools for Plant Breeding, Biological and Chemical Control
		Mutational Approaches
		Summary and Some Predictions
		Further Reading
	20 From Disease Assessment to Decision Support Systems
		Disease Assessment
			Which assessment method should be chosen?
				The purpose of the diseaseassessment
				Type of plant disease
				Growth stage of the crop
		Disease Forecasting
			Selected examples of forecasting systems
				Downy mildew of lettuce
				Stem rot of oilseed rape
				Potato late blight
				Septoria tritici blotch
		Decision Support Systems
			Selected examples of decision support systems
				EPIPRE
				Crop Protection Online (CPO)
				DSSs in potato
				DSSs in fruit production
		Thresholds (Action Before Damage)
		Yield and Yield Loss
			Yield
			Yield loss
			Types of yield loss
				Chronic, acute and emerging losses
				Quantitative and qualitative losses
				Potential and actual losses
			Yield loss assessment
			Different types of yield loss models
				Single point models
				Multiple point models
				AUDPC models
				Multiple pest models
				Loss models based on the crop plant
				Simulation models
		Further Reading
	21 Integrated Pest Management
		Introduction
		Background
		Steps of Integrated Pest Management
			Step 1: Preparation
			Step 2: Inspection
			Step 3: Identification
			Step 4: Biology
			Step 5: Action thresholds
			Step 6: Management tools
			Step 7: Evaluation
		General Principles of Integrated Pest Management
		Integrated Pest Management Guidelines
		Evaluation of the Impact of Integrated Pest Management
			EU and national level
			Farm level
		Further Reading
	22 Plant Health Legislation
		Why do we Have a Chapter on Law and Regulations in a Book on Plant Pathology?
		Background of International Plant Health Regulations
		International Conventions and Organizations
			The International Plant Protection Convention
			World Trade Organization and the SPS agreement
			International Standards for Phytosanitary Measures
		Regional Plant Protection Regulations and Bodiesin Europe
			The European and Mediterranean Plant Protection Organization
			The European Union
			The European Food Safety Authority
				Risk assessments at a national level
		Quarantine Pests
		Pest Risk Analysis and Risk Assessment
			What initiates a pest risk analysis?
				PRA initiated by the identification of a pathway
				PRA initiated by the identification of a pest
				PRA initiated by the review or revision of a policy
				Pest risk assessment (for quarantine pests)
				Pest risk management (for quarantine pests)
				Risk communication
		Further Reading
Part V Perspectives
	23 Plant Pathology in a Changing World
		Introduction
		Agriculture in the Future
		Challenges for Future Food Security
		Future Plant Disease Challenges
		Future Disease Management –Educated Guesses
			Actions focused on the pathogen
			Actions focused on the plant
			Integrated actions focused on the holobiome
		Closing Words
Appendix 1 Glossary
Appendix 2 Molecular Methods and Terms  Relevant for Plant Pathology
Taxonomic Index of Pathogens, Vectors and Biocontrol Agents
General Index
Back Cover