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Table of Contents

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Chapter 1: 21st century fungal communities

  1. What and where are fungi?
  2. Soil, the essential terrestrial habitat
  3. How much soil is there and where is it?
  4. The nature of soil and who made it
  5. Soil biota are extremely varied and numerous
  6. Microbial diversity in soil
  7. Microbial diversity in general
  8. Geomycology
  9. The origins of agriculture and our dependence on fungi
  10. Chapter 1 References and further reading

Chapter 2: Evolutionary origins

  1. Life, the Universe and everything
  2. Planet Earth - your habitat
  3. The Goldilocks planet
  4. The tree of life has three domains
  5. The Kingdom Fungi
  6. The opisthokonts
  7. Fossil fungi
  8. The fungal phylogeny
  9. Chapter 2 References and further reading

Chapter 3: Natural classification of fungi

  1. The members of the Kingdom
  2. The Chytrids
  3. Neocallimastigomycota
  4. Blastocladiomycota
  5. The traditional zygomycetes
  6. Glomeromycotina
  7. Ascomycota
  8. Basidiomycota
  9. The species concept in fungi
  10. The untrue fungi
  11. Ecosystem mycology
  12. Chapter 3 References and further reading

Chapter 4: Hyphal cell biology and growth on solid substrates

  1. Mycelium: the hyphal mode of growth
  2. Spore germination and dormancy
  3. The fungal lifestyle: colony formation
  4. Mycelium growth kinetics
  5. Colony growth to maturity
  6. Morphological differentiation of fungal colonies
  7. Duplication cycle in moulds
  8. Regulation of nuclear migration
  9. Growth kinetics
  10. Autotropic reactions
  11. Hyphal branching
  12. Septation
  13. Ecological advantage of mycelial growth in colonising solid substrates
  14. Chapter 4 References and further reading

Chapter 5: Fungal cell biology

  1. Mechanisms of mycelial growth
  2. The fungus as a model eukaryote
  3. The essentials of cell structure
  4. Subcellular components of eukaryotic cells
  5. The nucleus
  6. The nucleolus and nuclear import and export
  7. Nuclear genetics
  8. Mitotic nuclear division
  9. Meiotic nuclear division
  10. mRNA translation and protein sorting
  11. The endomembrane systems
  12. Cytoskeletal systems
  13. Molecular motors
  14. Plasma membrane and signalling pathways
  15. Fungal cell wall
  16. Cell biology of the hyphal apex
  17. Hyphal fusions and mycelial interconnections
  18. Cytokinesis and septation
  19. Yeast-mycelial dimorphism
  20. Chapter 5 References and further reading about the cell cycle

Chapter 6: Structure and synthesis of fungal cell walls

  1. The fungal wall as a working organelle
  2. Fundamentals of wall structure and function
  3. Fundamentals of wall architecture
  4. The chitin component
  5. The glucan component
  6. The glycoprotein component
  7. Wall synthesis and remodelling
  8. On the far side
  9. The fungal wall as a clinical target
  10. Chapter 6 References and further reading

Chapter 7: From the haploid to the functional diploid; homokaryons, heterokaryons, dikaryons and compatibility

  1. Compatibility and the individualistic mycelium
  2. Formation of heterokaryons
  3. Breakdown of a heterokaryon
  4. The dikaryon
  5. Vegetative compatibility
  6. Biology of incompatibility systems
  7. Gene segregation during the mitotic division cycle
  8. Parasexual cycle
  9. Cytoplasmic segregations: mitochondria, plasmids, viruses and prions
  10. Chapter 7 References and further reading

Chapter 8: Sexual reproduction: the basis of diversity and taxonomy

  1. The process of sexual reproduction
  2. Mating in budding yeast
  3. Mating type switching in budding yeast
  4. Mating types of Neurospora
  5. Mating types in Basidiomycota
  6. Biology of mating type factors
  7. Chapter 8 References and further reading

Chapter 9: Continuing the diversity theme: cell and tissue differentiation

  1. What is diversity?
  2. Mycelial differentiation
  3. Making spores
  4. Aspergillus conidiophores
  5. Conidiation in Neurospora crassa
  6. Conidiomata
  7. Linear structures: strands, cords, rhizomorphs and stipes
  8. Globose structures: sclerotia, stromata, ascomata and basidiomata
  9. Chapter 9 References and further reading

Chapter 10: Fungi in ecosystems

  1. Contributions of fungi to ecosystems
  2. Breakdown of polysaccharide: cellulose
  3. Breakdown of polysaccharide: hemicellulose
  4. Breakdown of polysaccharide: pectins
  5. Breakdown of polysaccharide: chitin
  6. Breakdown of polysaccharide: starch and glycogen
  7. Lignin degradation
  8. Digestion of protein
  9. Lipases and esterases
  10. Phosphatases and sulfatases
  11. The flow of nutrients: transport and translocation
  12. Primary (intermediary) metabolism
  13. Secondary metabolism
  14. Chapter 10 References and further reading

Chapter 11: Exploiting fungi for food

  1. Fungi as food
  2. Fungi in food webs
  3. Wild harvests: commercial mushroom picking
  4. Cells and mycelium as human food
  5. Fermented foods
  6. Industrial cultivation methods
  7. Gardening insects and fungi
  8. Development of a fungal fruit body
  9. Chapter 11 References and further reading

Chapter 12: Development and morphogenesis

  1. Development and morphogenesis
  2. The formal terminology of developmental biology
  3. The observational and experimental basis of fungal developmental biology
  4. Ten ways to make a mushroom
  5. Competence and regional patterning
  6. The Coprinopsis fruit body: making hymenia
  7. Coprinopsis and Volvariella making gills (not forgetting how polypores make tubes)
  8. The Coprinopsis fruit body: making stems
  9. Co-ordination of cell inflation throughout the maturing fruit body
  10. Mushroom mechanics
  11. Metabolic regulation in relation to morphogenesis
  12. Developmental commitment
  13. Comparisons with other tissues and other organisms
  14. Genetic approaches to study development: through the classic to genomic systems analysis
  15. Senescence and death
  16. Basic principles of fungal developmental biology
  17. Relevance to commercially cultivated fungi
  18. Chapter 12 References and further reading

Chapter 13: Ecosystem mycology: saprotrophs, and mutualisms between plants and fungi

  1. Ecosystem mycology
  2. Fungi as recyclers and saprotrophs
  3. Make the earth move
  4. Fungal toxins: food contamination and deterioration
  5. Decay of structural timber in dwellings
  6. Using fungi to remediate toxic and recalcitrant wastes
  7. Release of chlorohydrocarbons to the atmosphere by wood decay fungi
  8. Introduction to mycorrhizas
  9. Types of mycorrhiza
  10. Arbuscular (AM) endomycorrhizas
  11. Ericoid endomycorrhizas
  12. Arbutoid endomycorrhizas
  13. Monotropoid endomycorrhizas
  14. Orchidaceous endomycorrhizas
  15. Ectomycorrhizas
  16. Ectendomycorrhizas
  17. The effects of mycorrhizas and their commercial applications, and the impact of environmental and climate changes
  18. Introduction to lichens
  19. Introduction to endophytes
  20. Epiphytes
  21. Chapter 13 References and further reading

Chapter 14: Fungi as pathogens of plants

  1. Fungal diseases and loss of world agricultural production
  2. A few examples of headline crop diseases
  3. The Rice Blast fungus Magnaporthe grisea (Ascomycota)
  4. Armillaria (Basidiomycota)
  5. Pathogens that produce haustoria (Ascomycota and Basidiomycota)
  6. Cercospora (Ascomycota)
  7. Ophiostoma (Ceratocystis) novo-ulmi (Dutch Elm disease or DED) (Ascomycota)
  8. Black stem rust (Puccinia graminis f. sp. tritici) threatens global wheat harvest
  9. Plant disease basics: the disease triangle
  10. Necrotrophic and biotrophic pathogens of plants
  11. The effects of pathogens on their hosts
  12. How pathogens attack plants
  13. Host penetration through stomatal openings
  14. Direct penetration of the host cell wall
  15. Enzymatic penetration of the host
  16. Pre-formed and induced defence mechanisms in plants
  17. Genetic variation in pathogens and their hosts: co-evolution of disease systems
  18. Chapter 14 References and further reading

Chapter 15: Fungi as symbionts and predators of animals

  1. Fungal co-operative ventures
  2. Ant agriculture
  3. Termite gardeners of Africa
  4. Agriculture in beetles
  5. Anaerobic fungi and the rise of the ruminants
  6. Nematode-trapping fungi
  7. Chapter 15 References and further reading

Chapter 16: Fungi as pathogens of animals, including man

  1. Pathogens of insects
  2. Microsporidia
  3. Trichomycetes
  4. Laboulbeniales
  5. Entomogenous fungi
  6. Biological control of arthropod pests
  7. Cutaneous chytridiomycosis: an emerging disease of amphibians
  8. Aspergillosis disease of coral
  9. Snake fungal disease
  10. White-nose syndrome of bats
  11. Mycoses: the fungus diseases of humans
  12. Clinical groupings for human fungal infections
  13. Fungi within the home and their effects on health: allergens and toxins
  14. Comparison of animal and plant pathogens and the essentials of epidemiology
  15. Mycoparasitic and fungicolous fungi
  16. Chapter 16 References and further reading

Chapter 17: Whole organism biotechnology

  1. Fungal fermentations in submerged liquid cultures
  2. Culturing fungi
  3. Oxygen demand and supply
  4. Fermenter engineering
  5. Fungal growth in liquid cultures
  6. Fermenter growth kinetics
  7. Growth yield
  8. Stationary phase
  9. Growth as pellets
  10. Beyond the batch culture
  11. Chemostats and turbidostats
  12. Uses of submerged fermentations
  13. Alcoholic fermentations
  14. Citric acid biotechnology
  15. Penicillin and other pharmaceuticals
  16. Enzymes for fabric conditioning and processing, and food processing
  17. Steroids and use of fungi to make chemical transformations
  18. The Quorn fermentation and evolution in fermenters
  19. Production of spores and other inocula
  20. Natural digestive fermentations in herbivores
  21. Solid state fermentations
  22. Digestion of lignocellulosic residues
  23. Bread; the other side of the alcoholic fermentation equation
  24. Cheese and salami manufacture
  25. Soy sauce, tempeh and other food products
  26. Chapter 17 References and further reading

Chapter 18: Molecular biotechnology

  1. Antifungal agents that target the membrane
  2. Antifungal agents that target the wall
  3. Clinical control of systemic mycoses for the 21st century
  4. Agricultural mycocides for the 21st century: strobilurins
  5. Understanding fungal genetic structure
  6. Introns
  7. Alternative splicing
  8. Transposons
  9. Ploidy and genomic variation
  10. Sequencing fungal genomes
  11. Annotating the genome
  12. Fungal genomes and their comparison
  13. Manipulating genomes: gene editing
  14. Fungi as cell factories
  15. Chapter 18 References and further reading

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Except where otherwise indicated, all content copyright © David Moore, Geoffrey D. Robson, Anthony P. J. Trinci 2021

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Updated September, 2021