21st Century Guidebook to Fungi with CD

Cover......Page 1
Title......Page 5
Copyright......Page 6
Contents......Page 7
Preface......Page 11
Part I Nature and origins of fungi......Page 15
1
21st century fungal communities......Page 17
1.1 What and where are fungi?......Page 18
1.4 The nature of soil and who made it......Page 19
1.6 Microbial diversity in soil......Page 21
1.7 Microbial diversity in general......Page 22
1.8 Geomycology......Page 23
1.9 The origins of agriculture and ourdependence on fungi......Page 24
1.10 References and further reading......Page 29
2
Evolutionary origins......Page 32
2.1 Life, the universe and everything......Page 33
2.3 The Goldilocks planet......Page 35
2.4 The tree of life has three domains......Page 37
2.5 The Kingdom Fungi......Page 43
2.6 The opisthokonts......Page 44
2.7 Fossil fungi......Page 45
2.8 The fungal phylogeny......Page 49
2.9 References and further reading......Page 52
3
Natural classification of fungi......Page 55
3.2 The chytrids......Page 56
3.3 More chytrids: the Neocallimastigomycota
......Page 59
3.4 Blastocladiomycota......Page 60
3.5 Glomeromycota......Page 64
3.6 The traditional Zygomycota......Page 66
3.7 Ascomycota......Page 69
3.8 Basidiomycota......Page 75
3.9 The species concept in fungi......Page 85
Water moulds......Page 89
3.11 Ecosystem mycology......Page 91
3.12 References and further reading......Page 93
Part II Fungal cell biology
......Page 97
4 Hyphal cell biology and growth on solid substrates
......Page 99
4.3 The fungal lifestyle: colony formation......Page 100
4.4 Mycelium growth kinetics......Page 102
4.5 Colony growth to maturity......Page 105
4.7 Duplication cycle in moulds......Page 106
4.8 Regulation of nuclear migration......Page 107
4.9 Growth kinetics......Page 108
4.10 Autotropic reactions......Page 110
4.11 Hyphal branching......Page 111
4.12 Septation......Page 113
4.13 Ecological advantage of mycelial growth in colonising solid substrates......Page 114
4.14 References and further reading......Page 115
5 Fungal cell biology
......Page 118
5.2 The fungus as a model eukaryote......Page 119
5.3 The essentials of cell structure......Page 121
5.4 Subcellular components of eukaryotic cells: the nucleus......Page 122
5.5 The nucleolus and nuclear import and export......Page 126
5.6 Nuclear genetics......Page 128
5.7 Mitotic nuclear division......Page 129
5.8 Meiotic nuclear division......Page 131
5.9 Translation of mRNA and protein sorting......Page 132
5.10 The endomembrane systems......Page 135
5.11 Cytoskeletal systems......Page 139
5.12 Molecular motors......Page 141
5.13 Plasma membrane and signalling pathways......Page 147
5.14 Fungal cell wall......Page 150
5.15 Cell biology of the hyphal apex......Page 151
5.16 Hyphal fusions and mycelial interconnections......Page 156
5.17 Cytokinesis and septation......Page 158
5.18 Yeast-mycelial dimorphism......Page 196
6.10References and further reading......Page 197
6 Structure and synthesis of fungal cell walls
......Page 202
6.2 Fundamentals of wall structure and function......Page 203
6.4 The chitin component......Page 206
6.5 The glucan component......Page 208
6.6 The glycoprotein component......Page 209
6.7 Wall synthesis and remodelling......Page 211
6.8 On the far side......Page 214
6.9 The fungal wall as a clinical target......Page 217
Part III
Fungal genetics and diversity......Page 223
7
From the haploid to the functional diploid: homokaryons, heterokaryons, dikaryons and compatibility......Page 225
7.1 Compatibility and the individualistic mycelium......Page 226
7.2 Formation of heterokaryons......Page 227
7.4 The dikaryon......Page 229
7.5 Vegetative compatibility......Page 231
7.6 Biology of incompatibility systems......Page 234
7.7 Gene segregation during the mitotic division cycle......Page 235
7.9 Cytoplasmic segregations: mitochondria, plasmids, viruses and prions......Page 240
7.10 References and further reading......Page 243

8 Sexual reproduction: the basis of diversity and taxonomy......Page 244
8.1 The process of sexual reproduction......Page 245
8.2 Mating in budding yeast......Page 246
8.3 Mating type switching in budding yeast......Page 247
8.4 Mating types of Neurospora......Page 249
8.5 Mating types in Basidiomycota......Page 251
8.6 Biology of mating type factors......Page 256
8.7
References and further reading......Page 257
9 Continuing the diversity theme: cell and tissue differentiation
......Page 259
9.2 Mycelial differentiation......Page 260
9.3 Making spores......Page 262
9.4 Aspergillus conidiophores......Page 266
9.6 Conidiomata......Page 269
9.7 Linear structures: strands, cords, rhizomorphs and stipes......Page 271
9.8 Globose structures: sclerotia, stromata, ascomata and basidiomata......Page 273
12.17 References and further reading......Page 310
Part IV Biochemistry and developmental biology of fungi
......Page 281
10
Fungi in ecosystems......Page 283
10.1 Contributions of fungi to ecosystems......Page 284
10.2 Breakdown of polysaccharide: cellulose......Page 285
10.3 Breakdown of polysaccharide: hemicellulose......Page 286
10.6 Breakdown of polysaccharide: starch and glycogen......Page 287
10.7 Lignin degradation......Page 288
10.8 Digestion of protein......Page 292
10.11 The flow of nutrients: transport and translocation......Page 293
10.12 Primary (intermediary) metabolism......Page 297
10.13 Secondary metabolites, including commercial products like statins and strobilurins......Page 303
11 Exploiting fungi for food
......Page 312
11.2 Fungi in food webs......Page 313
11.3 Wild harvests: commercial mushroom picking......Page 318
11.5 Fermented foods......Page 320
11.6 Industrial cultivation methods......Page 321
11.7 Gardening insects and fungi......Page 325
11.9 References and further reading......Page 326
12 Development and morphogenesis
......Page 328
12.2 The formal terminology of developmental biology......Page 329
12.3 The observational and experimental basis of fungal developmental biology......Page 331
12.4 Ten ways to make a mushroom......Page 332
12.5 Competence and regional patterning......Page 335
12.6 The Coprinopsis fruit body: making hymenia......Page 337
12.7 Coprinopsis and Volvariella making gills (not forgetting how polypores make tubes)......Page 341
12.8 The Coprinopsis fruit body: making stems......Page 347
12.9 Coordination of cell inflation throughout the maturing fruit body......Page 350
12.11 Metabolic regulation in relation to morphogenesis......Page 351
12.12 Developmental commitment......Page 354
12.13 Comparisons with other tissues and other organisms......Page 356
12.14 Classic genetic approaches to study development and the impact of genomic data mining......Page 357
12.15 Degeneration, senescence and death......Page 361
12.16 Basic principles of fungal developmental biology......Page 362
Part V Fungi as saprotrophs, symbionts and pathogens
......Page 369

13 Ecosystem mycology: saprotrophs, and mutualisms between plants and fungi......Page 371
13.2 Fungi as recyclers and saprotrophs......Page 372
13.4 Fungal toxins: food contamination and deterioration (including mention of statins and strobilurins)......Page 374
13.5 Decay of structural timber in dwellings......Page 377
13.6 Using fungi to remediate toxic and recalcitrant wastes......Page 380
13.8 Introduction to mycorrhizas......Page 382
13.9 Types of mycorrhiza......Page 383
13.10 Arbuscular (AM) endomycorrhizas......Page 384
13.11 Ericoid endomycorrhizas......Page 419
13.13 Monotropoid endomycorrhizas......Page 421
13.14 Orchidaceous endomycorrhizas......Page 422
13.15 Ectomycorrhizas......Page 424
13.17 The effects of mycorrhizas and their commercial applications and the impact of environmental and climate changes......Page 429
Structure and change of natural communities......Page 431
The impact of climate change......Page 432
Commercial applications of mycorrhizas......Page 433
13.18 Introduction to lichens......Page 434
13.19 Introduction to endophytes......Page 438
13.21
References and further reading......Page 439
14 Fungi as pathogens of plants
......Page 445
14.1 Fungal diseases and loss of world agricultural production......Page 446
14.4 Armillaria (Basidiomycota)......Page 448
14.5 Pathogens that produce haustoria (Ascomycota and Basidiomycota)......Page 449
14.7 Ophiostoma (Ceratocystis) novo-ulmi (Dutch elm disease or DED) (Ascomycota)......Page 450
14.8 Black stem rust (Puccinia graminis f. sp. tritici) threatens global wheat harvest......Page 451
14.9 Plant disease basics: the disease triangle......Page 452
14.11 The effects of pathogens on their hosts......Page 454
14.13 Host penetration through stomatal openings......Page 457
14.15 Enzymatic penetration of the host......Page 460
14.16 Preformed and induced defence mechanisms in plants......Page 463
14.17 Genetic variation in pathogens and their hosts: co-evolution of disease systems......Page 465
14.18References and further reading......Page 467
15 Fungi as symbionts and predators of animals
......Page 470
15.2 Ant agriculture......Page 471
15.3 Termite gardeners of Africa......Page 476
15.4 Agriculture in beetles......Page 477
15.5 Anaerobic fungi and the rise of the ruminants......Page 478
15.6 Nematode-trapping fungi......Page 483
References......Page 486
16 Fungi as pathogens of animals, including humans
......Page 489
16.2 Microsporidia......Page 490
16.3 Trichomycetes......Page 492
16.4 Laboulbeniales......Page 494
16.5 Entomogenous fungi......Page 495
16.6 Biological control of arthropod pests......Page 499
16.7 Cutaneous chytridiomycosis: an emerging infectious disease of amphibians......Page 500
16.9 Mycoses: the fungus diseases of humans......Page 502
16.10 Clinical groupings for human fungal infections......Page 504
16.11 Fungi within the home and their effects on health: allergens and toxins......Page 510
16.12 Comparison of animal and plant pathogens and the essentials of epidemiology......Page 514
16.13 Mycoparasitic and fungicolous fungi......Page 517
16.14
References and further reading......Page 522
Part VI Fungal biotechnology and bioinformatics
......Page 527
17 Whole organism biotechnology
......Page 529
17.2 Culturing fungi......Page 530
17.3 Oxygen demand and supply......Page 534
17.4 Fermenter engineering......Page 536
17.5 Fungal growth in liquid cultures......Page 538
17.6 Fermenter growth kinetics......Page 540
17.7 Growth yield......Page 542
17.8 Stationary phase......Page 543
17.9 Growth as pellets......Page 544
17.10 Beyond the batch culture......Page 547
17.11 Chemostats and turbidostats......Page 548
17.12 Uses of submerged fermentations......Page 551
17.13 Alcoholic fermentations......Page 552
17.14 Citric acid biotechnology......Page 555
17.15 Penicillin and other pharmaceuticals......Page 556
17.16 Enzymes for fabric conditioning and processing, and food processing......Page 561
17.17 Steroids and use of fungi to make chemical transformations......Page 564
17.18 The QuornTM
fermentation and evolution in fermenters......Page 565
17.19 Production of spores and other inocula......Page 570
17.20 Natural digestive fermentations in herbivores......Page 571
17.21 Solid state fermentations......Page 572
17.22 Digestion of lignocellulosic residues......Page 575
17.23 Bread: the other side of the alcoholic fermentation equation......Page 577
17.24 Cheese and salami manufacture......Page 579
17.25 Soy sauce, tempeh and other food products......Page 582
17.26
References and further reading......Page 584
18 Molecular biotechnology
......Page 589
18.1 Antifungal agents that target the membrane......Page 590
18.2 Antifungal agents that target the wall......Page 599
18.3 Clinical control of systemic mycoses at the start of the 21st century: azoles, polyenes and combinatorial therapy......Page 600
18.4 Agricultural mycocides at the start of the twenty-first century: strobilurins......Page 604
18.5 Understanding fungal genetic structure......Page 607
18.6 Sequencing fungal genomes......Page 609
18.7 Annotating the genome......Page 613
18.8 Fungal genomes and their comparison......Page 618
18.9 Manipulating genomes: targeted gene disruption, transformation and vectors......Page 625
18.10 Fungi as cell factories producing heterologous proteins......Page 630
18.11 Recombinant protein production by filamentous fungi......Page 632
18.12 Bioinformatics in mycology: manipulating very large data sets......Page 635
18.13 Genomic data mining supports the notion that there are different developmental control mechanisms in fungi, animals and plants......Page 638
18.14 Effects of climate change on fungi revealed by analysis of large survey data sets......Page 640
18.15 Cyber fungi: mathematical modelling and computer simulation of hyphal growth......Page 641
18.16 References and further reading......Page 645
Part VII
Appendices......Page 651
Appendix1
Outline classification of fungi......Page 653
Critical appraisal......Page 664
References......Page 665
Websites to visit......Page 666
Mycelial differentiation......Page 667
Conidia and conidiogenesis......Page 668
Differentiation in ascomata......Page 671
Differentiation in basidiomata......Page 673
Index......Page 683