Table Of Contents:
Preface ix

PART I Nature and origins of fungi 1(82)

1 21st century fungal communities 3(15)

1.1 What and where are fungi? 4(1)

1.2 Soil, the essential terrestrial habitat 5(1)

1.3 How much soil is there and where is it? 5(1)

1.4 The nature of soil and who made it 5(2)

1.5 Soil biota are extremely varied and numerous 7(1)

1.6 Microbial diversity in soil 7(1)

1.7 Microbial diversity in general 8(1)

1.8 Geomycology 9(1)

1.9 The origins of agriculture and our dependence on fungi 10(5)

1.10 References and further reading 15(3)

2 Evolutionary origins 18(23)

2.1 Life, the universe and everything 19(2)

2.2 Planet Earth: your habitat 21(1)

2.3 The Goldilocks planet 21(2)

2.4 The tree of life has three domains 23(6)

2.5 The Kingdom Fungi 29(1)

2.6 The opisthokonts 30(1)

2.7 Fossil fungi 31(4)

2.8 The fungal phylogeny 35(3)

2.9 References and further reading 38(3)

3 Natural classification of fungi 41(42)

3.1 The members of the Kingdom Fungi 42(1)

3.2 The chytrids 42(3)

3.3 More chytrids: the Neocallimastigomycota 45(1)

3.4 Blastocladiomycota 46(4)

3.5 Glomeromycota 50(2)

3.6 The traditional Zygomycota 52(3)

3.7 Ascomycota 55(6)

3.8 Basidiomycota 61(10)

3.9 The species concept in fungi 71(4)

3.10 The untrue fungi 75(2)

3.11 Ecosystem mycology 77(2)

3.12 References and further reading 79(4)

PART II Fungal cell biology 83(94)

4 Hyphal cell biology and growth on solid substrates 85(19)

4.1 Mycelium: the hyphal mode of growth 86(1)

4.2 Spore germination and dormancy 86(1)

4.3 The fungal lifestyle: colony formation 86(2)

4.4 Mycelium growth kinetics 88(3)

4.5 Colony growth to maturity 91(1)

4.6 Morphological differentiation of fungal colonies 92(1)

4.7 Duplication cycle in moulds 92(1)

4.8 Regulation of nuclear migration 93(1)

4.9 Growth kinetics 94(2)

4.10 Autotropic reactions 96(1)

4.11 Hyphal branching 97(2)

4.12 Septation 99(1)

4.13 Ecological advantage of mycelial growth in colonising solid substrates 100(1)

4.14 References and further reading 101(3)

5 Fungal cell biology 104(52)

5.1 Mechanisms of mycelial growth 105(1)

5.2 The fungus as a model eukaryote 105(2)

5.3 The essentials of cell structure 107(1)

5.4 Subcellular components of eukaryotic cells: the nucleus 108(4)

5.5 The nucleolus and nuclear import and export 112(2)

5.6 Nuclear genetics 114(1)

5.7 Mitotic nuclear division 115(2)

5.8 Meiotic nuclear division 117(1)

5.9 Translation of mRNA and protein sorting 118(3)

5.10 The endomembrane systems 121(4)

5.11 Cytoskeletal systems 125(2)

5.12 Molecular motors 127(6)

5.13 Plasma membrane and signalling pathways 133(3)

5.14 Fungal cell wall 136(1)

5.15 Cell biology of the hyphal apex 137(5)

5.16 Hyphal fusions and mycelial interconnections 142(2)

5.17 Cytokinesis and septation 144(6)

5.18 Yeast-mycelial dimorphism 150(1)

5.19 References and further reading 151(5)

6 Structure and synthesis of fungal cell walls 156(21)

6.1 The fungal wall as a working organelle 157(1)

6.2 Fundamentals of wall structure and function 157(3)

6.3 Fundamentals of wall architecture 160(1)

6.4 The chitin component 160(2)

6.5 The glucan component 162(1)

6.6 The glycoprotein component 163(2)

6.7 Wall synthesis and remodelling 165(3)

6.8 On the far side 168(3)

6.9 The fungal wall as a clinical target 171(1)

6.10 References and further reading 172(5)

PART III Fungal genetics and diversity 177(58)

7 From the haploid to the functional diploid: homokaryons, heterokaryons, dikaryons and compatibility 179(19)

7.1 Compatibility and the individualistic mycelium 180(1)

7.2 Formation of heterokaryons 181(2)

7.3 Breakdown of a heterokaryon 183(1)

7.4 The dikaryon 183(2)

7.5 Vegetative compatibility 185(3)

7.6 Biology of incompatibility systems 188(1)

7.7 Gene segregation during the mitotic division cycle 189(5)

7.8 Parasexual cycle 194(1)

7.9 Cytoplasmic segregations: mitochondria, plasmids, viruses and prions 194(3)

7.10 References and further reading 197(1)

8 Sexual reproduction: the basis of diversity and taxonomy 198(15)

8.1 The process of sexual reproduction 199(1)

8.2 Mating in budding yeast 200(1)

8.3 Mating type switching in budding yeast 201(2)

8.4 Mating types of Neurospora 203(2)

8.5 Mating types in Basidiomycota 205(5)

8.6 Biology of mating type factors 210(1)

8.7 References and further reading 211(2)

9 Continuing the diversity theme: cell and tissue differentiation 213(22)

9.1 What is diversity? 214(1)

9.2 Mycelial differentiation 214(2)

9.3 Making spores 216(4)

9.4 Aspergillus conidiophores 220(3)

9.5 Conidiation in Neurospora crassa 223(1)

9.6 Conidiomata 223(2)

9.7 Linear structures: strands, cords, rhizomorphs and stipes 225(2)

9.8 Globose structures: sclerotia, stromata, ascomata and basidiomata 227(4)

9.9 References and further reading 231(4)

PART IV Biochemistry and developmental biology of fungi 235(88)

10 Fungi in ecosystems 237(29)

10.1 Contributions of fungi to ecosystems 238(1)

10.2 Breakdown of polysaccharide: cellulose 239(1)

10.3 Breakdown of polysaccharide: hemicellulose 240(1)

10.4 Breakdown of polysaccharide: pectins 241(1)

10.5 Breakdown of polysaccharide: chitin 241(1)

10.6 Breakdown of polysaccharide: starch and glycogen 241(1)

10.7 Lignin degradation 242(4)

10.8 Digestion of protein 246(1)

10.9 Lipases and esterases 247(1)

10.10 Phosphatases and sulfatases 247(1)

10.11 The flow of nutrients: transport and translocation 247(4)

10.12 Primary (intermediary) metabolism 251(6)

10.13 Secondary metabolites, including commercial products like statins and strobilurins 257(7)

10.14 References and further reading 264(2)

11 Exploiting fungi for food 266(16)

11.1 Fungi as food 267(1)

11.2 Fungi in food webs 267(5)

11.3 Wild harvests: commercial mushroom picking 272(2)

11.4 Cells and mycelium as human food 274(1)

11.5 Fermented foods 274(1)

11.6 Industrial cultivation methods 275(4)

11.7 Gardening insects and fungi 279(1)

11.8 Development of a fungal fruit body 280(1)

11.9 References and further reading 280(2)

12 Development and morphogenesis 282(41)

12.1 Development and morphogenesis 283(1)

12.2 The formal terminology of developmental biology 283(2)

12.3 The observational and experimental basis of fungal developmental biology 285(1)

12.4 Ten ways to make a mushroom 286(3)

12.5 Competence and regional patterning 289(2)

12.6 The Coprinopsis fruit body: making hymenia 291(4)

12.7 Coprinopsis and Volvariella making gills (not forgetting how polypores make tubes) 295(6)

12.8 The Coprinopsis fruit body: making stems 301(3)

12.9 Coordination of cell inflation throughout the maturing fruit body 304(1)

12.10 Mushroom mechanics 305(1)

12.11 Metabolic regulation in relation to morphogenesis 305(3)

12.12 Developmental commitment 308(2)

12.13 Comparisons with other tissues and other organisms 310(1)

12.14 Classic genetic approaches to study development and the impact of genomic data mining 311(4)

12.15 Degeneration, senescence and death 315(1)

12.16 Basic principles of fungal developmental biology 316(1)

12.17 References and further reading 316(7)

Part V Fungi as saprotrophs, symbionts and pathogens 323(126)

13 Ecosystem mycology: saprotrophs, and mutualisms between plants and fungi 325(42)

13.1 Ecosystem mycology 326(1)

13.2 Fungi as recyclers and saprotrophs 326(2)

13.3 Make the earth move 328(1)

13.4 Fungal toxins: food contamination and deterioration (including mention of statins and strobilurins) 328(3)

13.5 Decay of structural timber in dwellings 331(3)

13.6 Using fungi to remediate toxic and recalcitrant wastes 334(2)

13.7 Release of chlorohydrocarbons into the atmosphere by wood-decay fungi 336(1)

13.8 Introduction to mycorrhizas 336(1)

13.9 Types of mycorrhiza 337(1)

13.10 Arbuscular (AM) endomycorrhizas 338(3)

13.11 Ericoid endomycorrhizas 341(2)

13.12 Arbutoid endomycorrhizas 343(1)

13.13 Monotropoid endomycorrhizas 343(1)

13.14 Orchidaceous endomycorrhizas 344(2)

13.15 Ectomycorrhizas 346(5)

13.16 Ectendomycorrhizas 351(1)

13.17 The effects of mycorrhizas and their commercial applications and the impact of environmental and climate changes 351(5)

13.18 Introduction to lichens 356(4)

13.19 Introduction to endophytes 360(1)

13.20 Epiphytes 361(1)

13.21 References and further reading 361(6)

14 Fungi as pathogens of plants 367(25)

14.1 Fungal diseases and loss of world agricultural production 368(2)

14.2 A few examples of headline crop diseases 370(1)

14.3 The rice blast fungus Magnaporthe grisea (Ascomycota) 370(1)

14.4 Armillaria (Basidiomycota) 370(1)

14.5 Pathogens that produce haustoria (Ascomycota and Basidiomycota) 371(1)

14.6 Cercospora (Ascomycota) 372(1)

14.7 Ophiostoma (Ceratocystis) novo-ulmi (Dutch elm disease or DED) (Ascomycota) 372(1)

14.8 Black stem rust (Puccinia graminis f. sp. tritici) threatens global wheat harvest 373(1)

14.9 Plant disease basics: the disease triangle 374(2)

14.10 Necrotrophic and biotrophic pathogens of plants 376(1)

14.11 The effects of pathogens on their hosts 376(3)

14.12 How pathogens attack plants 379(1)

14.13 Host penetration through stomatal openings 379(3)

14.14 Direct penetration of the host cell wall 382(1)

14.15 Enzymatic penetration of the host 382(3)

14.16 Preformed and induced defence mechanisms in plants 385(2)

14.17 Genetic variation in pathogens and their hosts: co-evolution of disease systems 387(2)

14.18 References and further reading 389(3)

15 Fungi as symbionts and predators of animals 392(19)

15.1 Fungal co-operative ventures 393(1)

15.2 Ant agriculture 393(5)

15.3 Termite gardeners of Africa 398(1)

15.4 Agriculture in beetles 399(1)

15.5 Anaerobic fungi and the rise of the ruminants 400(5)

15.6 Nematode-trapping fungi 405(3)

15.7 References and further reading 408(3)

16 Fungi as pathogens of animals, including humans 411(38)

16.1 Pathogens of insects 412(1)

16.2 Microsporidia 412(2)

16.3 Trichomycetes 414(2)

16.4 Laboulbeniales 416(1)

16.5 Entomogenous fungi 417(4)

16.6 Biological control of arthropod pests 421(1)

16.7 Cutaneous chytridiomycosis: an emerging infectious disease of amphibians 422(2)

16.8 Aspergillosis disease of coral 424(1)

16.9 Mycoses; the fungus diseases of humans 424(2)

16.10 Clinical groupings for human fungal infections 426(6)

16.11 Fungi within the home and their effects on health: allergens and toxins 432(4)

16.12 Comparison of animal and plant pathogens and the essentials of epidemiology 436(3)

16.13 Mycoparasitic and fungicolous fungi 439(5)

16.14 References and further reading 444(5)

PART VI Fungal biotechnology and bioinformatics 449(124)

17 Whole organism biotechnology 451(60)

17.1 Fungal fermentations in submerged liquid cultures 452(1)

17.2 Culturing fungi 452(4)

17.3 Oxygen demand and supply 456(2)

17.4 Fermenter engineering 458(2)

17.5 Fungal growth in liquid cultures 460(2)

17.6 Fermenter growth kinetics 462(2)

17.7 Growth yield 464(1)

17.8 Stationary phase 465(1)

17.9 Growth as pellets 466(3)

17.10 Beyond the batch culture 469(1)

17.11 Chemostats and turbidostats 470(3)

17.12 Uses of submerged fermentations 473(1)

17.13 Alcoholic fermentations 474(3)

17.14 Citric acid biotechnology 477(1)

17.15 Penicillin and other pharmaceuticals 478(5)

17.16 Enzymes for fabric conditioning and processing, and food processing 483(3)

17.17 Steroids and use of fungi to make chemical transformations 486(1)

17.18 The Quorn™ fermentation and evolution in fermenters 487(5)

17.19 Production of spores and other inocula 492(1)

17.20 Natural digestive fermentations in herbivores 493(1)

17.21 Solid state fermentations 494(3)

17.22 Digestion of lignocellulosic residues 497(2)

17.23 Bread: the other side of the alcoholic fermentation equation 499(2)

17.24 Cheese and salami manufacture 501(3)

17.25 Soy sauce, tempeh and other food products 504(2)

17.26 References and further reading 506(5)

18 Molecular biotechnology 511(62)

18.1 Antifungal agents that target the membrane 512(9)

18.2 Antifungal agents that target the wall 521(1)

18.3 Clinical control of systemic mycoses at the start of the 21st century: azoles, polyenes and combinatorial therapy 522(4)

18.4 Agricultural mycocides at the start of the twenty-first century: strobilurins 526(3)

18.5 Understanding fungal genetic structure 529(2)

18.6 Sequencing fungal genomes 531(4)

18.7 Annotating the genome 535(5)

18.8 Fungal genomes and their comparison 540(7)

18.9 Manipulating genomes: targeted gene disruption, transformation and vectors 547(5)

18.10 Fungi as cell factories producing heterologous proteins 552(2)

18.11 Recombinant protein production by filamentous fungi 554(3)

18.12 Bioinformatics in mycology: manipulating very large data sets 557(3)

18.13 Genomic data mining supports the notion that there are different developmental control mechanisms in fungi, animals and plants 560(2)

18.14 Effects of climate change on fungi revealed by analysis of large survey data sets 562(1)

18.15 Cyber fungi: mathematical modelling and computer simulation of hyphal growth 563(4)

18.16 References and further reading 567(6)

PART VII Appendices 573(32)

Appendix 1 Outline classification of fungi 575(14)

Appendix 2 Mycelial and hyphal differentiation 589(16)
Index 605