Forest Microbiology: Volume 1: Tree Microbiome: Phyllosphere, Endosphere and Rhizosphere

Cover
Front matter
Copyright
Contents
Contributors
Preface
Preface_2021_Forest-Microbiology
Section A Introduction
	Chapter-1---An-introduction-to-forest-biome-and-associat_2021_Forest-Microbi
		An introduction to forest biome and associated microorganisms
			Introduction
			Forest biome
			Forest trees and their symbionts
			Microbiome: The three domain system
			Fungi: Morphological and structural features
				Classification of the fungal kingdom
			Bacteria
			Protists
			Viruses
			Ecology, biochemistry, physiology, and biotechnological features of microorganisms
			Lifestyles of microbiome
				Fungi as saprotrophs
				Fungi as endophytes
				Fungi as mutualists (mycorrhiza)
				Fungi as tree pathogens (necrotrophs, biotrophs, or hemibiotrophs)
			Lifestyles of bacteria, archaea, and protists
			Coevolution of plants (trees) and their microbial symbionts
			References
			Further reading
	Chapter-2---Wood-as-an-ecological-niche-for-microorganisms--_2021_Forest-Mic
		Wood as an ecological niche for microorganisms: Wood formation, structure, and cell wall composition
			Introduction
			Wood formation
				Cambium and wood formation
				Seasonality of wood formation
			Principles of wood anatomy
				Sectioning planes
					Transverse section (Fig. 2.5 top)
					Radial longitudinal section (Fig. 2.5 middle)
					Tangential longitudinal section (Fig. 2.5 bottom)
				Softwoods
				Hardwoods
					Vessels
					Fibers
					Axial parenchyma
				Pits
			Ultrastructure of wood cell walls
			Chemical characteristics of wood cell walls
				Major cell wall components
					Cellulose
					Hemicelluloses
					Lignin
				Molecular architecture and distribution of chemical components
			Future perspectives
			References
	Chapter-3---Methods-for-studying-the-forest-tree-micr_2021_Forest-Microbiolo
		Methods for studying the forest tree microbiome
			Introduction
			Traditional methods for studying phyllosphere and endophytic microbiota
				Culture dependent-based isolation methods
					Isolation of endophytic or phyllosphere fungi
					Cultivation of endophytes using the dilution-to-extinction method
					Isolation of endophytic bacteria
				Histological methods
			Biochemical methods (microbiota—bacteria and fungi)
				Metabolic activity
				Methods to investigate fungal secondary metabolites
				“Phenomics” methods
					Phenotype Microarrays
					Enrichment cultures
					Phospholipid fatty acid analysis
				Use of nonnucleic acid approaches (metaproteomics and metabolomics) in microbial community profiling of environmen ...
					Metaproteomics
					Metabolomics
			High-throughput or next-generation sequencing: Principles, concept, and applications
				Amplicon sequencing
				16S sequencing principle and bias
			Data analysis: Clustering, sequence identification, and operational taxonomic units
				Data quality filtering
				Chimera filtering
				Clustering
				Taxonomic identification
				Fungal guild
				Data analysis
			RNA-seq and DNA GeoChip for microbiome analyses
				RNA-seq for microbiome study
				DNA GeoChip for microbiome analysis
				GeoChip: Data generation, normalization, and analysis
			Metagenome and metagenomics
				Metagenome-wide association study
			Choice of methods for microbiome studies: Marker gene, whole metagenome, or metatranscriptomic analysis
				Marker gene analysis
				Whole metagenome analysis
				Metatranscriptome analysis
			Technical considerations and constraints
			References
	Chapter-4---Abiotic-factors-affecting-the-composition-of-_2021_Forest-Microb
		Abiotic factors affecting the composition of forest tree microbiomes
			Introduction
			The impacts of water: Flooding and drought
				Phyllosphere microbiota and drought
				Effects of flooding on the phyllosphere microbiome
				Drought tolerance requires a beneficial microbiome in the rhizosphere
				Increasing water content in the rhizosphere benefits anaerobic and copiotrophic microbes
			Impact of site factors
				Nutrient availability and pH characterize rhizosphere communities
				Site-specific environment defines phyllosphere microbiome
			The effects of pollution on a microbiome
				Air pollution
				Nitrogen and phosphorus deposition
				Particulate matter
				Soil pollution
				Combined effects of pollutants in urban areas
					Phyllosphere microbiome in urban areas
					Urban areas share similarities with forest rhizospheres
				Bidirectional effects of plant or microbiota VOCs
			Global warming and elevated CO 2
				Rhizosphere
				Phyllosphere
			Effects of genetic modification of trees
			The effects of forest management on a tree microbiome
				Case studies of the effect of forest management on microbiomes
					Case: Effects of drainage on microbiomes of boreal peatland
					Case: Effects of stump treatment for the control of forest disease on the wood microbiome
			Concluding remarks
			References
	Chapter-5---Interspecific-interactions-within-fungal-communi_2021_Forest-Mic
		Interspecific interactions within fungal communities associated with wood decay and forest trees
			Introduction
				Fungal community species assemblage, diversity, and abundance
				Ecological aspects of fungal interactions in dead wood
				Cofungal interactions within living trees
			Wood decay, colonization, and methods for classifying interspecific fungal interaction
			Mechanisms of combative interactions (mycoparasitism, competition, hyphal interference, antibiosis)
			Types of response to competitive or combative interactions
				Morphological responses to competitive interactions
				Physicochemical responses including the production of volatile organic compounds (VOCs)
				Biochemical responses
				Transcriptional responses
			Interaction outcome: Replacement, deadlock, metabiosis/antibiosis
			Impact of biotic and abiotic factors on the outcome of interspecific fungal interactions
			Fungal succession as an interaction outcome
			Challenges and constraints in interspecific interaction
			References
Section B Phyllosphere microbiome
	Chapter-6---The-phyllosphere-mycobiome-of-woody-plan_2021_Forest-Microbiolog
		The phyllosphere mycobiome of woody plants
			Introduction
			Epiphytic fungi
			Pathogenic and endophytic fungi
				Pathogenic fungi
				Endophytic fungi
					Factors influencing the abundance of endophytic fungi and the diversity of endophyte communities
						Detection of endophytes: Cultivation versus DNA barcoding
						Climate
							Latitude
							Altitude
							Precipitation
						Host specificity
						Site specificity
						Native versus nonnative hosts
						Leaf tissue specificity
						Tree age, age of the leaf tissue, and season
						Herbivores and pathogens
						Air pollution—Urbanization
						Leaf physiology
					The role of leaf endophytes in plant defense—Endophyte-mediated resistance
					Production of secondary metabolites by leaf endophytes
					Endophytism as “pole position”
			“Domestication” of endophytic fungi
			Acknowledgments
			References
	Chapter-7---Tree-leaves-as-a-habitat-for-phyllobacter_2021_Forest-Microbiolo
		Tree leaves as a habitat for phyllobacteria
			Introduction
			Leaf surface as an extreme environment
			Phyllobacterial community composition
			Role of the phyllobacterial community
			Conclusions and future perspectives
			References
	Chapter-8---Microbiome-of-reproductive-organs-of-tre_2021_Forest-Microbiolog
		Microbiome of reproductive organs of trees
			Composition of the microbiome of reproductive organs
			Vertical transmission of the microbiome of reproductive organs and microbiome maternal effects on trees
				Vertical transfer through seeds and pollen
				Microbiome between parent and offspring trees—Maternal effects on trees
			Microorganisms of seed from soils
			The relationship between the flower microbiome of trees, insect vectors, pollinators, and other factors
				Floral microbiome
				Microbiome and plant-feeding insects
			Microbial evolutionary and ecological functional impacts
				Microbial evolution and ecology of the reproductive microbiome
			Conclusions and future study
			References
Section C Endosphere microbiome
	Chapter-9---Bacterial-biota-of-forest-trees_2021_Forest-Microbiology
		Bacterial biota of forest trees
			Introduction
				Aims
			Composition and function of bacterial biota of the above- and below-ground compartments of forest tree species
				Foliage
				Stem
				Root, rhizosphere, soil, and litter
			Comparing bacterial biota composition across tree species and forest biomes
			Conclusions and future research priorities
			References
	Chapter-10---Fungi-inhabiting-woody-tree-tissues_2021_Forest-Microbiology
		Fungi inhabiting woody tree tissues
			Introduction
			Endophytes
			Fungi inhabiting living woody tissues: Are Basidiomycetes underrepresented or not yet discovered?
			Fungi causing tree diseases
				Lifestyle switch from endophytic to pathogenic
					Sphaeropsis sapinea –emerging endophyte switching to pathogenic lifestyle
			Fungi in woody tissues of conifers
			Fungi inhabiting woody tissues of deciduous trees
				Fungal species in Quercus tissues
				Fungal species in Fagus tissues
				Fungal species in Alnus tissues
				Fungal species in Betula tissues
				Fungal species in Populus tissues
				Fungal species in Eucalyptus tissues
			Fungal vascular wilt pathogens
				Ceratocystis vascular wilt
				Fusarium vascular wilt
				Ophiostoma vascular wilt
				Verticillium vascular wilt
			Wood-decay fungi
				White rot fungi
				Brown rot fungi
				Soft rot fungi
			Conclusion
			References
	Chapter-11---Dark-septate-endophytes-of-forest-trees_2021_Forest-Microbiolog
		Dark septate endophytes of forest trees
			Historical perspectives on dark septate endophytes
			Endophytes and forest trees
			Ecology of DSE
			Beneficial effects of DSE on their hosts
			Phialocephala fortinii s.l.- Acephala applanata species complex
			Changes in PAC/DSE communities
			DSE and host interactions in harsh environments
			DSE-tree host interactions
			DSE-mycorrhiza-host interactions
			DSE and metabolites
			DSE-tree interaction under changing environment
			Future studies needed
			References
Section D Rhizosphere microbiome
	Chapter-12---Nature-and-characteristics-of-forest-soils-and_2021_Forest-Micr
		Nature and characteristics of forest soils and peat soils as niches for microorgan isms
			Forest soils and peat soils defined
			Characteristics of forest soils
			Physicochemical properties of forest soils
			Mire and peat formation
			Peat types and decomposition
			Drained peatlands and peat
			References
	Chapter-13---Fungal-community-of-forest-soil--Diversity--_2021_Forest-Microb
		Fungal community of forest soil: Diversity, functions, and services
			Introduction
			Fungal community structure
				Biotic and abiotic drivers of soil fungal communities
				Impact of disturbances on soil fungal communities
				Biogeography and spatial distribution across different scales
			Roles of soil fungi in forest ecosystems
				Soil fungi and drought
				Soil fungi and decomposition
				Soil fungi and nutrient cycling
			Changing roles of soil fungi in different biomes
			Soil fungi and forest management in a changing world
				Restoration activities, plantation, and fungal inoculation in response to global change
				Nitrogen deposition, liming, and other fertilization impact
				Thinning, harvesting, and residues removal
			References
	Chapter-14---The-influence-of-mycorrhizal-fungi-on-rhizosph_2021_Forest-Micr
		The influence of mycorrhizal fungi on rhizosphere bacterial communities in forests
			Forest soil as a microbial landscape
				Fungal influences on nutrient and carbon availability through decomposition
				Mycorrhizal fungal influences on rhizodeposition
				Other chemical and physical changes in the rhizosphere influenced by mycorrhizal fungi
			Interactions between mycorrhizal fungi and rhizosphere bacteria
				Community structure of rhizosphere bacteria associated with ectomycorrhizal fungi
				General effects of fungi on bacterial functional groups
			Conclusions
			References
	Chapter-15---Pathobiome-and-microbial-communities-associat_2021_Forest-Micro
		Pathobiome and microbial communities associated with forest tree root diseases
			Diverse drivers of microbial change in plants
			Pathobiome
			Soil microbiomes
			Plant-pathogen-microbe interactions in disease-suppressive soils
			Role of metabolites from bacteria-fungal interactions on plant disease development
			Plant infections by fungal pathogens result in changes in beneficial taxa
			Changes in fungal diversity as a response to root pathogens
			Changes in bacterial diversity as a response to root pathogens
			Microbiomes linked taxa to the pathobiome
			Impact of natural secondary metabolites on pathobiome composition
			Microbial changes in other anatomic regions of trees
			Considerations
			References
	Chapter-16---Microbiome-of-forest-soil_2021_Forest-Microbiology
		Microbiome of forest soil
			Introduction
			Microbiome in a tropical peatland forest
				Bacterial diversity in a tropical peatland forest
				Bacterial composition in a tropical peatland forest
				Fungal diversity in a tropical peatland forest
				Fungal composition in a tropical peatland forest
			Microbiome in a boreal peatland forest
				Bacterial diversity in a boreal peatland forest
				Bacterial composition in a boreal peatland forest
				Fungal diversity in a boreal peatland forest
				Fungal composition in a boreal peatland forest
			References
Section E Archaea and viruses in forest ecosystem and microbiota of forest nurseries and tree pests
	Chapter-17---Mycobiome-of-forest-tree-nurseries_2021_Forest-Microbiology
		Mycobiome of forest tree nurseries
			Introduction
			Bare root and container seedling production
				Techniques in container seedling production
					Growth substrates
					Manipulation of growth rhythm
					Winter storage
				Disease pressure in nurseries
			Mycobiome as disease agents of forest nursery
				Seed pathogens and damping-off
				Root dieback
				Gray mold
				Phytophthora spp.
				Scleroderris canker
				Sirococcus blight
				Sphaeropsis blight (Diplodia blight)
				Dothistroma needle blight
				Snow blight Phacidium infestans and brown felt blight (black snow mold) Herpotrichia juniperi
				Needle diseases
				Powdery mildews and leaf spots
				Rust diseases
			Mycobiota of forest nursery
				Endophytic and saprotrophic mycobiota
				Potentials of mycorrhizas in nursery production
				Saprotroph communities pose a risk in nurseries
				Endophytes in rhizosphere and phyllosphere may promote seedling health
					Root endophytes and dark septate endophyte (DSE)
					Endophytes of phyllosphere
			Control approaches to minimize pathogenic infections in forest nursery
				Alternatives for pesticides are needed
				Reduction of natural inoculum sources
				Seedling management and biostimulants
				Hygiene
				Chemical control of diseases
			Impact of pesticides (fungicides) on mycobiota of forest nursery
			Concluding remarks
			References
	Chapter-18---Microbiome-of-forest-tree-insects_2021_Forest-Microbiology
		Microbiome of forest tree insects
			Introduction
			Insects as vital components of forest ecosystems
			Ecological roles of insects in forest ecosystems
				Ecosystem cycling and herbivory
				Pollination
				Predation/parasitism
				Decomposition: Organic waste
				Seed dispersal
				Insects as a key link in the food chain in the forest
				The detrimental roles of insects in the forest
			Classification of forest insects
			Microbiome of diverse forest insect orders
				Microbiome of Hemiptera (bugs)
				Microbiome of Lepidoptera (moth and butterflies)
				Microbiomes of Coleoptera (beetles)
				Microbiome of Isopteran (termites)
				Microbiome of Diptera
			Functional roles of insect symbionts
				Functional roles of bacterial symbionts of insects
				Functional roles of fungi associated with insects
				Functional roles of viruses associated with insects
			Transmission route in insects
				Fungal transmission route in insects
				Bacterial symbionts and transmission routes in insects
				Viral transmission route in insects
			Interactions of insect microbiomes with forest trees and their environment
			Challenges and constraints in the study of the insect microbiome
			References
			Further reading
	Chapter-19---Archaea-as-components-of-forest-microbio_2021_Forest-Microbiolo
		Archaea as components of forest microbiome
			What are Archaea
				The three domains of life
			Archaea in boreal forests
				Methanogens in boreal peatlands
				Crenarchaeota and methanogens in rhizospheres
			Evolving taxonomy of methanogens and Crenarchaeota
				From Crenarchaea to Thaumarchaeota
				The TACK superphylum
			Archaea in alpine forests
			Archaea in tropical forests
			Archaea adapting to environments causing energy stress
				Ammonium oxidizers in forests
				Methane oxidizers in forests
					Methane metabolism from an evolutionary perspective
			Conclusions
			References
			Further reading
	Chapter-20---Viruses-as-components-of-forest-microbio_2021_Forest-Microbiolo
		Viruses as components of forest microbiome
			Introduction
			Plant viruses
				Introduction to plant viruses
				Taxonomic diversity
				Host ranges
				Economic importance of viruses in forest trees
				Case example: Birch leaf roll disease—New culprit revealed by HTS
				Viroids: Subviral agents smaller than any known viruses
			Entomopathogenic viruses
				Low impact on insect populations, but still useful
				Nuclear polyhedrosis viruses as biological control agents
			Fungal viruses
				Fungi are hosting a diverse group of viruses
				Intracellular lifestyle has consequences
				Case example: Effects of viruses on Dutch elm disease
				Case example: Control of a fungal disease by viruses
				Viruses of root rot pathogens
				Viruses of mycorrhizal (mutualistic) fungi
			Bacterial viruses
				The most common biological entities
				Phage taxonomy
				Surface-bound microbial communities
				Case example: Interactions of bacteria and phages on horse chestnut
				Case example: Biological control of Xylella fastidiosa by bacteriophages
			Viruses of oomycetes: Examples from the genus Phytophthora
			Complex host interactions shape the ecology of forest viruses
			References
			Further reading
Section F Challenges and potentials
	Chapter-21---Translational-research-on-the-endophytic-mic_2021_Forest-Microb
		Translational research on the endophytic microbiome of forest trees
			Introduction
			Translational research of forest tree microbiomes
				Gap 1. From knowledge generation to interpretation
				Gap 2. From interpretation to implementation
				Gap 3. From implementation to impacts
			Concluding remarks
			Acknowledgments
			References
	Chapter-22---Forest-microbiome--Challenges-and-future-p_2021_Forest-Microbio
		Forest microbiome: Challenges and future perspectives
			References
Index of Microorganisms
	A
	B
	C
	D
	E
	F
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	Z
Index of Plants and Trees
	A
	B
	C
	D
	E
	F
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Index of Insects
	A
	B
	C
	D
	E
	G
	H
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	T
Index
	A
	B
	C
	D
	E
	F
	G
	H
	I
	J
	L
	M
	N
	O
	P
	Q
	R
	S
	T
	U
	V
	W
	X