Table of Contents
Cover image
Title page
Copyright
Contributors
Preface
Section A: Introduction
Chapter 1: An introduction to forest biome and associated microorganisms
Abstract
1: Introduction
2: Forest biome
3: Forest trees and their symbionts
4: Microbiome: The three domain system
5: Fungi: Morphological and structural features
6: Bacteria
7: Protists
8: Viruses
9: Ecology, biochemistry, physiology, and biotechnological features of microorganisms
10: Lifestyles of microbiome
11: Lifestyles of bacteria, archaea, and protists
12: Coevolution of plants (trees) and their microbial symbionts
Chapter 2: Wood as an ecological niche for microorganisms: Wood formation, structure, and cell wall composition
Abstract
1: Introduction
2: Wood formation
3: Principles of wood anatomy
4: Ultrastructure of wood cell walls
5: Chemical characteristics of wood cell walls
6: Future perspectives
Chapter 3: Methods for studying the forest tree microbiome
Abstract
1: Introduction
2: Traditional methods for studying phyllosphere and endophytic microbiota
3: Biochemical methods (microbiota—bacteria and fungi)
4: High-throughput or next-generation sequencing: Principles, concept, and applications
5: Data analysis: Clustering, sequence identification, and operational taxonomic units
6: RNA-seq and DNA GeoChip for microbiome analyses
7: Metagenome and metagenomics
8: Choice of methods for microbiome studies: Marker gene, whole metagenome, or metatranscriptomic analysis
9: Technical considerations and constraints
Chapter 4: Abiotic factors affecting the composition of forest tree microbiomes
Abstract
1: Introduction
2: The impacts of water: Flooding and drought
3: Impact of site factors
4: The effects of pollution on a microbiome
5: Global warming and elevated CO2
6: Effects of genetic modification of trees
7: The effects of forest management on a tree microbiome
8: Concluding remarks
Chapter 5: Interspecific interactions within fungal communities associated with wood decay and forest trees
Abstract
1: Introduction
2: Wood decay, colonization, and methods for classifying interspecific fungal interaction
3: Mechanisms of combative interactions (mycoparasitism, competition, hyphal interference, antibiosis)
4: Types of response to competitive or combative interactions
5: Interaction outcome: Replacement, deadlock, metabiosis/antibiosis
6: Impact of biotic and abiotic factors on the outcome of interspecific fungal interactions
7: Fungal succession as an interaction outcome
8: Challenges and constraints in interspecific interaction
Section B: Phyllosphere microbiome
Chapter 6: The phyllosphere mycobiome of woody plants
Abstract Acknowledgments
1: Introduction
2: Epiphytic fungi
3: Pathogenic and endophytic fungi
4: “Domestication” of endophytic fungi
Chapter 7: Tree leaves as a habitat for phyllobacteria
Abstract
1: Introduction
2: Leaf surface as an extreme environment
3: Phyllobacterial community composition
4: Role of the phyllobacterial community
5: Conclusions and future perspectives
Chapter 8: Microbiome of reproductive organs of trees
Abstract
1: Composition of the microbiome of reproductive organs
2: Vertical transmission of the microbiome of reproductive organs and microbiome maternal effects on trees
3: Microorganisms of seed from soils
4: The relationship between the flower microbiome of trees, insect vectors, pollinators, and other factors
5: Microbial evolutionary and ecological functional impacts
6: Conclusions and future study
Section C: Endosphere microbiome
Chapter 9: Bacterial biota of forest trees
Abstract
1: Introduction
2: Composition and function of bacterial biota of the above- and below-ground compartments of forest tree species
3: Comparing bacterial biota composition across tree species and forest biomes
4: Conclusions and future research priorities
Chapter 10: Fungi inhabiting woody tree tissues
Abstract
1: Introduction
2: Endophytes
3: Fungi inhabiting living woody tissues: Are Basidiomycetes underrepresented or not yet discovered?
4: Fungi causing tree diseases
5: Fungi in woody tissues of conifers
6: Fungi inhabiting woody tissues of deciduous trees
7: Fungal vascular wilt pathogens
8: Wood-decay fungi
9: Conclusion
Chapter 11: Dark septate endophytes of forest trees
Abstract
1: Historical perspectives on dark septate endophytes
2: Endophytes and forest trees
3: Ecology of DSE
4: Beneficial effects of DSE on their hosts
5: Phialocephala fortinii s.l.-Acephala applanata species complex
6: Changes in PAC/DSE communities
7: DSE and host interactions in harsh environments
8: DSE-tree host interactions
9: DSE-mycorrhiza-host interactions
10: DSE and metabolites
11: DSE-tree interaction under changing environment
12: Future studies needed
Section D: Rhizosphere microbiome
Chapter 12: Nature and characteristics of forest soils and peat soils as niches for microorganisms
Abstract
1: Forest soils and peat soils defined
2: Characteristics of forest soils
3: Physicochemical properties of forest soils
4: Mire and peat formation
5: Peat types and decomposition
6: Drained peatlands and peat
Chapter 13: Fungal community of forest soil: Diversity, functions, and services
Abstract
1: Introduction
2: Fungal community structure
3: Roles of soil fungi in forest ecosystems
4: Changing roles of soil fungi in different biomes
5: Soil fungi and forest management in a changing world
Chapter 14: The influence of mycorrhizal fungi on rhizosphere bacterial communities in forests
Abstract
1: Forest soil as a microbial landscape
2: Interactions between mycorrhizal fungi and rhizosphere bacteria
3: Conclusions
Chapter 15: Pathobiome and microbial communities associated with forest tree root diseases
Abstract
1: Diverse drivers of microbial change in plants
2: Pathobiome
3: Soil microbiomes
4: Plant-pathogen-microbe interactions in disease-suppressive soils
5: Role of metabolites from bacteria-fungal interactions on plant disease development
6: Plant infections by fungal pathogens result in changes in beneficial taxa
7: Changes in fungal diversity as a response to root pathogens
8: Changes in bacterial diversity as a response to root pathogens
9: Microbiomes linked taxa to the pathobiome
10: Impact of natural secondary metabolites on pathobiome composition
11: Microbial changes in other anatomic regions of trees
12: Considerations
Chapter 16: Microbiome of forest soil
Abstract
1: Introduction
2: Microbiome in a tropical peatland forest
3: Microbiome in a boreal peatland forest
Section E: Archaea and viruses in forest ecosystem and
microbiota of forest nurseries and tree pests
Chapter 17: Mycobiome of forest tree nurseries
Abstract
1: Introduction
2: Bare root and container seedling production
3: Mycobiome as disease agents of forest nursery
4: Mycobiota of forest nursery
5: Control approaches to minimize pathogenic infections in forest nursery
6: Impact of pesticides (fungicides) on mycobiota of forest nursery
7: Concluding remarks
Chapter 18: Microbiome of forest tree insects
Abstract
1: Introduction
2: Insects as vital components of forest ecosystems
3: Ecological roles of insects in forest ecosystems
4: Classification of forest insects
5: Microbiome of diverse forest insect orders
6: Functional roles of insect symbionts
7: Transmission route in insects
8: Interactions of insect microbiomes with forest trees and their environment
9: Challenges and constraints in the study of the insect microbiome
Chapter 19: Archaea as components of forest microbiome
Abstract
1: What are Archaea
2: Archaea in boreal forests
3: Evolving taxonomy of methanogens and Crenarchaeota
4: Archaea in alpine forests
5: Archaea in tropical forests
6: Archaea adapting to environments causing energy stress
7: Conclusions
Chapter 20: Viruses as components of forest microbiome
Abstract
1: Introduction
2: Plant viruses
3: Entomopathogenic viruses
4: Fungal viruses
5: Bacterial viruses
6: Viruses of oomycetes: Examples from the genus Phytophthora
7: Complex host interactions shape the ecology of forest viruses
Section F: Challenges and potentials
Chapter 21: Translational research on the endophytic microbiome of forest trees
Abstract
Acknowledgments
1: Introduction
2: Translational research of forest tree microbiomes
3: Concluding remarks
Chapter 22: Forest microbiome: Challenges and future perspectives
Abstract
Index of Microorganisms
Index of Plants and Trees
Index of Insects
Index
Copyright
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Contributors
Numbers in parentheses indicate the pages on which the authors’ contributions begin.
Fred O. Asiegbu (3, 35, 75, 305, 327, 395), Department of Forest Sciences, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland
H. Umair Masood Awan (75), Department of Forest Sciences, Faculty of Agriculture and Forestry, University of Helsinki Helclean Consultancy Services, Helsinki, Finland
Kathrin Blumenstein (35, 175), Forest Pathology Research Group, Department of Forest Botany and Tree Physiology, Faculty of Forest Sciences and Forest Ecology, University of Gö ingen, Gö ingen, Germany
Khumbuzile N. Bophela (133), Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics/Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
Marc Buée (231), French National Research Institute for Agriculture, Food and the Environment (INRAE), Lorraine University, Department of “Tree-Microbe Interactions”, Champenoux, France
David J. Burke (257), The Holden Arboretum, Kirtland, OH, United States
Johanna Bußkamp (175), Section Mycology and Complex Diseases, Department of Forest Protection, Northwest German
Forest Research Institute (NW-FVA), Gö ingen, Germany
Sarah R. Carrino-Kyker (257), The Holden Arboretum, Kirtland, OH, United States
Teresa A. Coutinho (133), Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics/Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
Wei Dong (145), China Electric Power Research Institute, Beijing, China
Jarkko Hantula (371), Natural Resources Institute Finland (Luke), Helsinki, Finland
Risto Kasanen (59, 305), Department of Forest Sciences, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland
Mee-Sook Kim (277), USDA Forest Service, Pacific Northwest Research Station, Corvallis, OR, United States
Yoon Soo Kim (17), Department of Wood Science and Engineering, Chonnam National University, Gwangju, South Korea
Ned B. Klopfenstein (277), USDA Forest Service, Rocky Mountain Research Station, Moscow, ID, United States
Andriy Kovalchuk (3), Department of Forest Sciences, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki Industrial Biotechnology and Food Solutions, VTT Technical Research Centre of Finland, Espoo, Finland
Bradley Lalande (277), USDA Forest Service, Forest Health Protection, Gunnison, CO, United States
Gi a Ju a Langer (175), Section Mycology and Complex Diseases, Department of Forest Protection, Northwest German Forest Research Institute (NW-FVA), Gö ingen, Germany
Björn D. Lindahl (231), Department of Soil and Environment, SLU, Uppsala, Sweden
Riikka Linnakoski (327), Natural Resources Institute Finland (Luke), Helsinki, Finland
Eglantina Lopez-Echartea (357), University of Chemistry and Technology, Prague, Czech Republic
Juan A. Martín (385), School of Forest Engineering and Natural Resources, Technical University of Madrid (UPM), Madrid, Spain
James E. McDonald (161), School of Natural Sciences, Bangor University, Bangor, Gwynedd, United Kingdom
Leticia Pérez-Izquierdo (231), Department of Soil and Environment, SLU, Uppsala, Sweden
Bethany J. Pe ifor (161), School of Natural Sciences, Bangor University, Bangor, Gwynedd, United Kingdom
Marja Poteri (305), Natural Resources Institute Finland (Luke), Helsinki, Finland
Zhao-lei Qu (293), Department of Forest Protection, College of Forestry, Nanjing Forestry University, Nanjing, China
Fei Ren (145), Forestry Experiment Center in North China, Chinese Academy of Forestry, Beijing, China
Ana Rincón (231), Institute of Agricultural Sciences (ICA), Spanish National Research Council (CSIC), Madrid, Spain
Carmen Romeralo (385), Swedish University of Agricultural Sciences, Southern Swedish Forest Research Centre, Alnarp, Sweden
Uwe Schmi (17), Thünen Institute of Wood Research, Hamburg, Germany
Thomas Niklaus Sieber (111), ETH Zurich, Department of Environmental Systems Science, Forest Pathology and Dendrology, Zurich, Swi erland
Adya P. Singh (17), Scion, Rotorua, New Zealand
Mike Starr (223), Department of Forest Sciences, University of Helsinki, Helsinki, Finland
Jane E. Stewart (277), Department of Agricultural Biology, Colorado State University, Fort Collins, CO, United States
Hui Sun (35, 293), Department of Forest Protection, College of Forestry, Nanjing Forestry University, Nanjing, China
Eeva Terhonen (35, 175, 207), Forest Pathology Research Group, Department of Forest Botany and Tree Physiology, Faculty of Forest Sciences and Forest Ecology, University of Gö ingen, Gö ingen, Germany
Juliana A. Ugwu (327), Forestry Research Institute of Nigeria, Ibadan, Nigeria Department of Forest Sciences, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland
Eeva J. Vainio (371), Natural Resources Institute Finland (Luke), Helsinki, Finland
Harri Vasander (223), Department of Forest Sciences, University of Helsinki, Helsinki, Finland
Johanna Wi ell (385), Swedish University of Agricultural Sciences, Southern Swedish Forest Research Centre, Alnarp, Sweden
Dong-Hui Yan (145), Research Institute of Forest Ecology, Environment and Protection, Key Laboratory of Biodiversity Conservation of National Forestry and Grassland Administration, Chinese Academy of Forestry, Beijing, China
Kim Yrjälä (357), Zhejiang A & F University, Hangzhou, China
Preface
Fred O. Asiegbu; Andriy Kovalchuk, University of Helsinki, Finland
Microorganisms constitute an integral component of all terrestrial and aquatic ecosystems. They are indispensable for the global nutrient cycling and for the existence of higher multicellular forms of life. In fact, all macroorganisms (e.g., plants and animals) live in close association with a diverse range of microbial symbionts. The ecological community of bacteria, archaea, fungi, and protists associated with a given organism, its organs and tissues is referred to as microbiota. Microbiome by definition refers to the entire assemblage of all microbial genomes of the microbial community (microbiota) associated with certain environment or organism (human, animal, or plant including forest trees). Research on microbiome of forest biomes has a racted much a ention in recent years but still lags far behind comparable knowledge on human and agricultural crop microbiomes. Our interest in compiling the volume 1 of this Forest Microbiology book stems from the paucity and great disparity of information on forest tree microbiome, including phyllosphere, rhizosphere, and endosphere. Our understanding and perception of forest tree microbiome have recently been facilitated due to novel technological advances using metabarcoding, metagenomics, and metatranscriptomics approaches. In this book, recent advances in the study of tree microbiome were highlighted. An overview of our current understanding of taxonomic and functional diversity of microorganisms (fungi, bacteria, archaea, and viruses) associated with tissues of various broad-leaf and conifer trees was provided. Microbial communities associated with various forest insects, host trees, and different tree organs were compared,
and generalists and specialists among tree-associated microbes were identified. Biotic and abiotic factors determining the composition and the structure of forest tree microbial communities were presented. However, despite significant progress so far achieved in our understanding of the factors affecting the composition of microbial communities associated with plants, very li le is known about the effect of plant pathogens (pathobiomes) on their structure, particularly the least studied forest trees. In several chapters of this book, studies that unravel the potential functional roles of these microbes and their impact on forest tree health were uncovered.
The research on the integration of beneficial microbiomes into forest production is increasingly a racting a ention. The rational engineering of microbial communities of forest trees is expected to be of great significance for the sustainable wood and timber production, for the improved tolerance of forest ecosystems against environmental stressors, and for the management of forest tree diseases and pests. New insights on how to harness and link the acquired knowledge on microbiomes of forest biomes for translational forest management were highlighted and discussed in this book. Translational aspects of forest microbiome study are however not without challenges. Despite the challenges, one of the emerging research directions in microbiome study is represented by metagenome-wide association studies (MWAS). In this approach, a relative abundance of a certain gene in the metagenome is used to establish an association with an occurrence of a disease of interest. The success of MWAS in human and animal models suggests that its applications can be extended to analyze associations between tree microbiome and diseases. Network modeling also represents an alternative approach to establish a link between microbiome composition and its function.
In this book, our wish was to highlight the microbiota inhabiting forest trees and their potential impact on the health and fitness of, and disease progression in, forest biomes. Additionally, to uncover the nature and structure of niches occupied by forest microbes together with their functional roles in the decomposition of wood debris and forest li er, uptake and nutrient cycling in forest
p y g ecosystems, mutualistic symbiosis and microbial parasitic interactions with trees. The book also addressed current advances in these fields of study, made possible by use of novel and modern biological techniques. We hope that this book will fill a major knowledge gap, serve as a single information source as well as prove valuable for students of biology and forest sciences, forest pathologists, other practitioners in specific areas of forestry, and everyone interested in the microbiota of forest biomes.
