Freshwater Fungi (eBook)

Preface 5
List of contributing authors 17
1 Introduction 23
1.1 Origin of freshwater fungi and fungal-like organisms 26
1.2 Classification of freshwater fungi 27
1.3 Estimated number of freshwater fungi 28
1.4 World distribution 30
1.5 Endophytic fungi 30
1.6 Predacious fungi 31
1.7 Bioactive compounds 32
1.8 Barcoding of freshwater fungi 34
1.9 One name one fungus ruling 35
1.10 Role of fungi in freshwater habitats 36
1.11 Objectives and outline of the volume 37
1.12 Phylogeny of true freshwater fungi 37
1.13 Phylogeny of fungus-like organisms 37
1.14 Biodiversity of freshwater fungi and fungus-like organisms 38
1.15 Ecology 38
Acknowledgments 38
References 39
Phylogeny of freshwater fungi 45
2 Phylogeny of the Dothideomycetes and other classes of freshwater fissitunicate Ascomycota 47
2.1 Introduction 47
2.2 Geographical distribution patterns 48
2.3 Substrate distribution patterns 48
2.4 Morphological adaptations 48
2.5 Systematics 50
2.5.1 General introduction 50
2.5.2 Current phylogenetic placement based on molecular systematics 54
2.5.2.1 Dothideomycetes-Pleosporomycetidae-Pleosporales 54
2.5.2.2 Pleosporales incertae sedis 58
2.5.3 Zopfiaceae, Dothideomycetes, family incertae sedis 60
2.5.4 Dothideomycetes incertae sedis 60
2.5.4.1 Jahnulales 60
2.5.4.2 Natipusillales 61
2.5.4.3 Minutisphaera clade 61
2.5.4.4 Freshwater asexual morphs with affinities to Dothideomycetes 61
2.6 Conclusions 62
Acknowledgments 62
References 62
3 The molecular phylogeny of freshwater Sordariomycetes and discomycetes 69
3.1 Introduction 69
3.2 Materials and methods 70
3.2.1 Taxon sampling 70
3.2.2 Phylogenetic analysis 70
3.3 Discussion 70
3.3.1 Sordariomycetidae 78
3.3.1.1 Annulatascaceae 78
3.3.1.2 Magnaporthales 82
3.3.1.3 Calosphaeriales 82
3.3.1.4 Coniochaetales 83
3.3.1.5 Diaporthales 83
3.3.1.6 Sordariales 83
3.3.2 Sordariomycetidae incertae sedis 84
3.3.3 Hypocreomycetidae 84
3.3.3.1 Savoryellales 84
3.3.3.2 Microascales 85
3.3.3.3 Hypocreales 85
3.3.4 Xylariomycetidae 86
3.3.4.1 Xylariales 86
3.3.4.2 Phyllachorales 86
3.3.4.3 Trichosphaeriales 86
3.3.5 Discomycetes 86
3.3.5.1 Helotiales 86
3.3.5.2 Pezizales 87
3.3.5.3 Rhytismatales 88
3.4 Concluding remarks 88
Acknowledgments 88
References 89
4 Freshwater Basidiomycota £ 95
4.1 Group 1 freshwater yeasts 104
4.1.1 Agaricomycotina 105
4.1.1.1 Tremellomycetes 105
4.1.2 Pucciniomycotina 107
4.1.2.1 Cystobasidiomycetes 107
4.1.2.2 Microbotryomycetes 107
4.1.2.3 Microbotryomycetes Incertae sedis 108
4.1.3 Ustilaginomycotina 109
4.1.3.1 Ustilaginomycetes 109
4.2 Group 2 filamentous fungi 109
4.2.1 Agaricomycotina 109
4.2.1.1 Agaricomycetes 109
4.2.1.2 Exobasidiomycetes 114
4.2.1.3 Tremellomycetes 114
4.2.2 Pucciniomycotina 114
4.2.2.1 Atractiellomycetes 114
4.2.2.2 Classiculomycetes 115
4.2.2.3 Microbotryomycetes 116
4.2.3 Ustilaginomycotina 117
4.2.3.1 Ustilaginomycetes 117
Basidiomycota—incertae sedis 117
4.3 Group 3 endophytes 121
4.4 Adaptation to freshwater habitats 121
Acknowledgments 122
References 122
5 Taxonomy of filamentous asexual fungi from freshwater habitats, links to sexual morphs and their phylogeny 131
5.1 Introduction 131
5.2 Morphological taxonomy 132
5.2.1 Hyphomycetes 132
5.2.2 Coelomycetes 134
5.2.3 Asexual-sexual connections 134
5.3 Phylogeny 135
5.3.1 Dothideomycetes 136
5.3.1.1 Capnodiales 136
5.3.1.2 Dothideales 136
5.3.1.3 Hysteriales 139
5.3.1.4 Jahnulales 139
5.3.1.5 Mytilinidiales 139
5.3.1.6 Pleosporales 139
5.3.1.7 Tubeufiales 140
5.3.2 Leotiomycetes 141
5.3.3 Orbiliomycetes 142
5.3.3.1 Orbiliales 142
5.3.4 Sordariomycetes 142
5.3.4.1 Glomerellales 145
5.3.4.2 Hypocreales 145
5.3.4.3 Sordariales 145
5.3.4.4 Savoryellales 146
5.4 Discussion 147
Acknowledgment 148
References 148
6 Phylogeny and characterization of freshwater Chytridiomycota (Chytridiomycetes and Monoblepharidomycetes) 155
6.1 Introduction 155
6.2 Chytridiomycetes 160
6.2.1 Order 1. Chytridiales (Chytridiaceae, Chytriomycetaceae) 160
6.2.2 Order 2. Spizellomycetales (Spizellomycetaceae, Powellomycetaceae) 162
6.2.3 Order 3. Rhizophlyctidiales (Rhizophlyctidaceae, Sonoraphlyctidaceae, Arizonaphlyctidaceae, Borealophlyctidaceae) 163
6.2.4 Order 4. Rhizophydiales (10 families described) 163
6.2.5 Order 5. Lobulomycetales (Lobulomycetaceae) 166
6.2.6 Order 6. Cladochytriales (Cladochytriaceae, Nowakowskiellaceae, Septochytriaceae, Endochytriaceae) 166
6.2.7 Order 7. Polychytriales (no families described) 168
6.3 Incertae sedis 169
6.4 Monoblepharidomycetes (Harpochytriales, Monoblepharidales, Hyaloraphidiales) 170
Acknowledgments 170
References 170
Phylogeny of fungus-like organisms 177
7 Microsporidia 179
7.1 Ecology 182
7.2 Classification 184
7.3 Evolutionary origins 187
7.4 Cell structure and spore significance 188
7.5 Metabolism 189
7.6 Genome structure 190
7.7 Discussion and conclusion 190
7.8 Further research avenues 192
References 193
8 Phylogenetic relationships of Pythiales and Peronosporales (Oomycetes, Straminipila) within the “peronosporalean galaxy” 199
8.1 Introduction 199
8.2 The monophyly of Chromalveolata and the relationships between heterotrophic straminipile lineages 200
8.3 Major lineages within the Oomycetes: the “galaxies” 201
8.4 The “peronosporalean galaxy”: a marine origin? 201
8.5 Ecological and economical significance 202
8.6 The phylogeny of Pythiales and Peronosporales 203
8.6.1 Clade 1: Albuginales 207
8.6.2 Clade 2: Pythiales 207
8.6.2.1 Pythiogeton 208
8.6.2.2 Pythium, Lagenidium and Phytopythium 208
8.6.3 Clade 3: Peronosporales 209
8.6.3.1 Downy mildews 210
8.6.3.2 Phytophthora and Peronophythora 210
8.6.3.3 Halophytophthora and Salisapilia 212
8.7 Conclusions and future perspectives 214
Acknowledgments 216
References 216
Biodiversity of freshwater fungi 223
9 The ecological and economic importance of zoosporic Mesomycetozoean (Dermocystida) parasites of freshwater fish 225
9.1 Phylogeny 225
9.2 Life cycles 227
9.3 The zoospore 228
9.4 Symptoms of disease 229
9.5 Ecological and economic significance 231
9.6 Discussion and conclusion 233
Acknowledgment 234
References 234
10 I nfection strategies of pathogenic oomycetes in fish 239
10.1 Introduction 239
10.2 Taxonomy of oomycetes pathogenic to fish 243
10.3 Physical adaptation and strategy for infection: macroscopic infection, the face of infection on hosts 245
10.4 Oomycete zoospores, the first line of attack 246
10.5 Triggers for zoospore formation, waking up the beast 247
10.6 Encystment and germination, one step closer to infection 247
10.7 Repeated zoospore emergence, the back-up plan 249
10.8 Chemotactic response of zoospores, the specialization 250
10.9 Proteins and amino acids as substrates for growth 251
10.10 Sexual reproduction, seeing through the bad times 253
10.11 Molecular adaptation and strategy in setting infection: microscopic infection 253
10.12 Host responses to oomycete infections 255
10.13 The animal trade is responsible for the spread of pathogens into novel and wild ecosystems 256
10.14 Future perspectives 257
Acknowledgments 258
References 258
11 Zoosporic parasites of amphibians 267
11.1 Chytridiomycota 267
11.2 Mesomycetozoea 269
11.3 Oomycota (oomycetes or water moulds) 272
11.4 Perkinsozoa 273
11.5 The Fisher concept of emerging infectious diseases (EIDs) 274
11.6 Host switching by parasites 274
11.7 Genetic variation in parasite populations 276
11.8 Proteases 277
11.9 International animal trade 277
11.10 Discussion and conclusion 278
Acknowledgments 279
References 279
12 Pythiosis 285
12.1 History 285
12.2 Biology 285
12.3 Molecular typing 287
12.4 Epidemiology 288
12.5 Pathogenesis 288
12.6 Clinical features 289
12.6.1 Human pythiosis 289
12.6.2 Animal pythiosis 291
12.7 Diagnosis 291
12.8 Management 293
12.9 Research direction 294
Acknowledgment 295
References 296
13 Zoosporic parasites of phytoplankton 301
13.1 The main groups of zoosporic parasites and parasitoids of phytoplankton 302
13.1.1 Aphelidea 302
13.1.2 Chytridiomycota 305
13.1.3 Blastocladiomycota 315
13.2 Ancient interactions 316
13.3 Novel food webs 317
13.3.1 Vorticella communities attached to cyanobacterial filaments 317
13.3.2 Communities involving other protists 317
13.4 Host parasite dynamics 318
13.5 Conclusion 320
Acknowlegments 321
References 322
14 Zoosporic parasites of freshwater invertebrates 327
14.1 Parasites in the Blastocladiomycota and Chytridiomycota 328
14.2 Parasites in the Oomycota 329
14.3 Parasites in the Mesomycetozoea 333
14.4 Parasites of crayfish 334
14.4.1 Crayfish plague 334
14.4.2 Psorospermium haekeli 335
14.5 Parasites of mosquitoes, blackflies and midges 335
14.5.1 Coelomomyces 336
14.5.2 Lagenidium giganteum 337
14.5.3 Pythium 338
14.5.4 Leptolegnia 338
14.5.5 Crypticola 338
14.5.6 Amoebidium and Paramoebidium 339
14.6 Parasites of Daphnia 339
14.7 Parasites of rotifers and nematodes 340
14.7.1 Sommerstorffia spinosa 342
14.7.2 Aquastella 343
14.8 Parasites of protozoans 343
14.9 Discussion 343
Acknowledgments 346
References 346
Ecology 353
15 Freshwater lichens 355
15.1 Ecology 358
15.1.1 Habitats and diversity of freshwater lichens 358
15.1.2 Collecting and identifying freshwater lichens 360
15.2 Physiological challenges for freshwater lichens 361
15.2.1 Water saturation and diffusion resistance 361
15.3 Freshwater lichens as a food source for other organisms 365
15.4 Biogeography of freshwater lichens 366
15.5 Zonation 367
15.6 Lichen trimlines 370
15.7 Freshwater lichen communities 371
15.8 Freshwater lichens as bioindicators 372
15.9 Water quality 373
15.10 Conservation 374
Acknowledgments 375
References 375
16 Aquatic Trichomycetes 381
16.1 Trichomycetes, an ecological group 381
16.2 Phylogenetic considerations 381
16.3 Distribution and success of Trichomycetes 386
16.4 Variations in symbiotic associations 387
16.5 Medical implications 389
Acknowledgments 390
References 390
17 Tropical peat swamp fungi with special reference to palms 393
17.1 Material and methods 395
17.1.1 Sample collection 395
17.2 Results 395
17.2.1 Abundance of fungi on four palms (Eleiodoxa conferta, Licuala longicalycata, Metroxylon sagu and Nenga pumila) 395
17.2.1.1 Eleiodoxa conferta 401
17.2.1.2 Licuala longicalycata 402
17.2.1.3 Metroxylon sagu 402
17.2.1.4 Nenga pumila 402
17.2.2 Fungal diversity 403
17.2.3 Percentages overlap in fungal diversity between the four palms 404
17.3 Conclusion 405
Acknowledgments 407
References 408
18 Stream pollution and fungi 411
18.1 The importance of aquatic hyphomycetes in woodland streams 411
18.2 Effects of nutrient enrichment on stream fungi 413
18.3 Effects of heavy metals and acidification on stream fungi 416
18.4 Ecological and toxicological effects of engineered nanoparticles on stream fungi 417
18.5 Effects of organic xenobiotics on stream fungi 419
18.6 Effects of thermal pollution on stream fungi 420
18.7 Effects of the interaction among factors on stream fungi 425
18.8 Conclusions 426
Acknowledgments 426
References 427
19 Association of animals and fungi in leaf decomposition £ 435
19.1 History 435
19.2 Effects of the leaf-fungus complex on invertebrate consumers 438
19.2.1 Nutritional value of mycelium vs. leaf substrate 438
19.2.2 Modifications of leaf substrate 439
19.2.3 Do invertebrates differ in their feeding strategies? 442
19.2.4 What factors ultimately determine food choice and feeding selectivity? 443
19.2.5 Stoichiometric considerations 445
19.2.6 Stimulation of fungi by invertebrate feeding 446
19.2.7 Anthropogenic changes 446
19.2.8 Research outside temperate regions 448
19.3 Effects of invertebrate consumers on the leaf-fungus complex 450
19.3.1 Invertebrate ingestion of conidia 451
19.3.2 Invertebrate ingestion of the leaf-fungus complex 451
19.4 Conclusions 453
Acknowledgments 454
References 454
20 Yeasts from extreme aquatic environments: hyperacidic freshwaters 465
20.1 Introduction 465
20.2 The River Agrio-Lake Caviahue acidic aquatic system 466
20.2.1 Yeast occurrence 467
20.2.2 Yeast diversity 468
20.3 Comparative yeast diversity study between RAC and the acidic environments of the Iberian Pyrite Belt (IPB) 473
20.4 Acidic rock drainage (ARD) yeasts ecoclade 476
20.5 Physiological aspects of acidophilic yeasts 478
20.6 Possible ecological roles of yeasts in acidic aquatic environments 479
20.7 Final remarks 480
Acknowledgments 481
References 482
21 Decomposition of wood in tropical habitats 487
21.1 Review of fungal diversity on wood in freshwater streams 488
21.2 Colonization of 15 timbers exposed at two locations in Thailand 489
21.2.1 Materials and methods 489
21.2.2 Results 490
21.2.3 Rate of decay of selected timbers at two contrasting freshwater ecosystems in Thailand 494
21.2.4 Discussion 495
21.2.4.1 Fungal community 495
21.2.4.2 Decay of wood in freshwater habitats 496
Acknowledgments 498
References 499
22 Epliogue 503
22.1 Introduction 503
22.2 Freshwater fungi 503
22.3 Freshwater fungus-like organisms 504
22.4 Knowledge gaps and future work in freshwater mycology 504
22.5 Conclusions 508
References 508
Index 511