Freshwater Fungi: and Fungal-like Organisms

Description

The available literature on freshwater fungi is limited. Over the subsequent years a considerable volume of scientific papers have appeared scattered throughout numerous journals. There is therefore no recent synthesis of the subject and this is the objective of the proposed book. Freshwater habitats are rich in fungi with some 3,000 described species, most of papers focussing on their identification, substrata they grow on and world distribution. However, these fungi play an important role in the freshwater ecosystem, and are primarily involved in the breakdown of leaf litter contributing food for detritus feeders. Our book will bring together a wide range of acclaimed mycologists to review recent developments on the biology and ecology of freshwater fungi, particularly their molecular phylogeny, biodiversity, causative diseases of freshwater amphibians, fishes and invertebrate animals, decomposition of leaf litter, stream pollution and their potential role in bioremediation. Up-to-date overview of the morphology, molecular phylogeny and biodiversity of freshwater fungi Highlights the essential role of fungi in the freshwater ecosystem Reviews recent developments on the causative diseases of freshwater amphibians, fishes and invertebrate animals, decomposition of leaf litter, stream pollution and their potential role in bioremediation Preface List of contributing authors 1 Introduction 1.1 Origin of freshwater fungi and fungal-like organisms 1.2 Classification of freshwater fungi 1.3 Estimated number of freshwater fungi 1.4 World distribution 1.5 Endophytic fungi 1.6 Predacious fungi 1.7 Bioactive compounds 1.8 Barcoding of freshwater fungi 1.9 One name one fungus ruling 1.10 Role of fungi in freshwater habitats 1.11 Objectives and outline of the volume 1.12 Phylogeny of true freshwater fungi 1.13 Phylogeny of fungus-like organisms 1.14 Biodiversity of freshwater fungi and fungus-like organisms 1.15 Ecology Acknowledgments References Phylogeny of freshwater fungi 2 Phylogeny of the Dothideomycetes and other classes of freshwater fissitunicate Ascomycota 2.1 Introduction 2.2 Geographical distribution patterns 2.3 Substrate distribution patterns 2.4 Morphological adaptations 2.5 Systematics 2.5.1 General introduction 2.5.2 Current phylogenetic placement based on molecular systematics 2.5.2.1 Dothideomycetes-Pleosporomycetidae-Pleosporales 2.5.2.2 Pleosporales incertae sedis 2.5.3 Zopfiaceae, Dothideomycetes, family incertae sedis 2.5.4 Dothideomycetes incertae sedis 2.5.4.1 Jahnulales 2.5.4.2 Natipusillales 2.5.4.3 Minutisphaera clade 2.5.4.4 Freshwater asexual morphs with affinities to Dothideomycetes 2.6 Conclusions Acknowledgments References 3 The molecular phylogeny of freshwater Sordariomycetes and discomycetes 3.1 Introduction 3.2 Materials and methods 3.2.1 Taxon sampling 3.2.2 Phylogenetic analysis 3.3 Discussion 3.3.1 Sordariomycetidae 3.3.1.1 Annulatascaceae 3.3.1.2 Magnaporthales 3.3.1.3 Calosphaeriales 3.3.1.4 Coniochaetales 3.3.1.5 Diaporthales 3.3.1.6 Sordariales 3.3.2 Sordariomycetidae incertae sedis 3.3.3 Hypocreomycetidae 3.3.3.1 Savoryellales 3.3.3.2 Microascales 3.3.3.3 Hypocreales 3.3.4 Xylariomycetidae 3.3.4.1 Xylariales 3.3.4.2 Phyllachorales 3.3.4.3 Trichosphaeriales 3.3.5 Discomycetes 3.3.5.1 Helotiales 3.3.5.2 Pezizales 3.3.5.3 Rhytismatales 3.4 Concluding remarks Acknowledgments References 4 Freshwater Basidiomycota £ 4.1 Group 1 freshwater yeasts 4.1.1 Agaricomycotina 4.1.1.1 Tremellomycetes 4.1.2 Pucciniomycotina 4.1.2.1 Cystobasidiomycetes 4.1.2.2 Microbotryomycetes 4.1.2.3 Microbotryomycetes Incertae sedis 4.1.3 Ustilaginomycotina 4.1.3.1 Ustilaginomycetes 4.2 Group 2 filamentous fungi 4.2.1 Agaricomycotina 4.2.1.1 Agaricomycetes 4.2.1.2 Exobasidiomycetes 4.2.1.3 Tremellomycetes 4.2.2 Pucciniomycotina 4.2.2.1 Atractiellomycetes 4.2.2.2 Classiculomycetes 4.2.2.3 Microbotryomycetes 4.2.3 Ustilaginomycotina 4.2.3.1 Ustilaginomycetes Basidiomycota—incertae sedis 4.3 Group 3 endophytes 4.4 Adaptation to freshwater habitats Acknowledgments References 5 Taxonomy of filamentous asexual fungi from freshwater habitats, links to sexual morphs and their phylogeny 5.1 Introduction 5.2 Morphological taxonomy 5.2.1 Hyphomycetes 5.2.2 Coelomycetes 5.2.3 Asexual-sexual connections 5.3 Phylogeny 5.3.1 Dothideomycetes 5.3.1.1 Capnodiales 5.3.1.2 Dothideales 5.3.1.3 Hysteriales 5.3.1.4 Jahnulales 5.3.1.5 Mytilinidiales 5.3.1.6 Pleosporales 5.3.1.7 Tubeufiales 5.3.2 Leotiomycetes 5.3.3 Orbiliomycetes 5.3.3.1 Orbiliales 5.3.4 Sordariomycetes 5.3.4.1 Glomerellales 5.3.4.2 Hypocreales 5.3.4.3 Sordariales 5.3.4.4 Savoryellales 5.4 Discussion Acknowledgment References 6 Phylogeny and characterization of freshwater Chytridiomycota (Chytridiomycetes and Monoblepharidomycetes) 6.1 Introduction 6.2 Chytridiomycetes 6.2.1 Order 1. Chytridiales (Chytridiaceae, Chytriomycetaceae) 6.2.2 Order 2. Spizellomycetales (Spizellomycetaceae, Powellomycetaceae) 6.2.3 Order 3. Rhizophlyctidiales (Rhizophlyctidaceae, Sonoraphlyctidaceae, Arizonaphlyctidaceae, Borealophlyctidaceae) 6.2.4 Order 4. Rhizophydiales (10 families described) 6.2.5 Order 5. Lobulomycetales (Lobulomycetaceae) 6.2.6 Order 6. Cladochytriales (Cladochytriaceae, Nowakowskiellaceae, Septochytriaceae, Endochytriaceae) 6.2.7 Order 7. Polychytriales (no families described) 6.3 Incertae sedis 6.4 Monoblepharidomycetes (Harpochytriales, Monoblepharidales, Hyaloraphidiales) Acknowledgments References Phylogeny of fungus-like organisms 7 Microsporidia 7.1 Ecology 7.2 Classification 7.3 Evolutionary origins 7.4 Cell structure and spore significance 7.5 Metabolism 7.6 Genome structure 7.7 Discussion and conclusion 7.8 Further research avenues References 8 Phylogenetic relationships of Pythiales and Peronosporales (Oomycetes, Straminipila) within the “peronosporalean galaxy” 8.1 Introduction 8.2 The monophyly of Chromalveolata and the relationships between heterotrophic straminipile lineages 8.3 Major lineages within the Oomycetes: the “galaxies” 8.4 The “peronosporalean galaxy”: a marine origin? 8.5 Ecological and economical significance 8.6 The phylogeny of Pythiales and Peronosporales 8.6.1 Clade 1: Albuginales 8.6.2 Clade 2: Pythiales 8.6.2.1 Pythiogeton 8.6.2.2 Pythium, Lagenidium and Phytopythium 8.6.3 Clade 3: Peronosporales 8.6.3.1 Downy mildews 8.6.3.2 Phytophthora and Peronophythora 8.6.3.3 Halophytophthora and Salisapilia 8.7 Conclusions and future perspectives Acknowledgments References Biodiversity of freshwater fungi 9 The ecological and economic importance of zoosporic Mesomycetozoean (Dermocystida) parasites of freshwater fish 9.1 Phylogeny 9.2 Life cycles 9.3 The zoospore 9.4 Symptoms of disease 9.5 Ecological and economic significance 9.6 Discussion and conclusion Acknowledgment References 10 I nfection strategies of pathogenic oomycetes in fish 10.1 Introduction 10.2 Taxonomy of oomycetes pathogenic to fish 10.3 Physical adaptation and strategy for infection: macroscopic infection, the face of infection on hosts 10.4 Oomycete zoospores, the first line of attack 10.5 Triggers for zoospore formation, waking up the beast 10.6 Encystment and germination, one step closer to infection 10.7 Repeated zoospore emergence, the back-up plan 10.8 Chemotactic response of zoospores, the specialization 10.9 Proteins and amino acids as substrates for growth 10.10 Sexual reproduction, seeing through the bad times 10.11 Molecular adaptation and strategy in setting infection: microscopic infection 10.12 Host responses to oomycete infections 10.13 The animal trade is responsible for the spread of pathogens into novel and wild ecosystems 10.14 Future perspectives Acknowledgments References 11 Zoosporic parasites of amphibians 11.1 Chytridiomycota 11.2 Mesomycetozoea 11.3 Oomycota (oomycetes or water moulds) 11.4 Perkinsozoa 11.5 The Fisher concept of emerging infectious diseases (EIDs) 11.6 Host switching by parasites 11.7 Genetic variation in parasite populations 11.8 Proteases 11.9 International animal trade 11.10 Discussion and conclusion Acknowledgments References 12 Pythiosis 12.1 History 12.2 Biology 12.3 Molecular typing 12.4 Epidemiology 12.5 Pathogenesis 12.6 Clinical features 12.6.1 Human pythiosis 12.6.2 Animal pythiosis 12.7 Diagnosis 12.8 Management 12.9 Research direction Acknowledgment References 13 Zoosporic parasites of phytoplankton 13.1 The main groups of zoosporic parasites and parasitoids of phytoplankton 13.1.1 Aphelidea 13.1.2 Chytridiomycota 13.1.3 Blastocladiomycota 13.2 Ancient interactions 13.3 Novel food webs 13.3.1 Vorticella communities attached to cyanobacterial filaments 13.3.2 Communities involving other protists 13.4 Host parasite dynamics 13.5 Conclusion Acknowlegments References 14 Zoosporic parasites of freshwater invertebrates 14.1 Parasites in the Blastocladiomycota and Chytridiomycota 14.2 Parasites in the Oomycota 14.3 Parasites in the Mesomycetozoea 14.4 Parasites of crayfish 14.4.1 Crayfish plague 14.4.2 Psorospermium haekeli 14.5 Parasites of mosquitoes, blackflies and midges 14.5.1 Coelomomyces 14.5.2 Lagenidium giganteum 14.5.3 Pythium 14.5.4 Leptolegnia 14.5.5 Crypticola 14.5.6 Amoebidium and Paramoebidium 14.6 Parasites of Daphnia 14.7 Parasites of rotifers and nematodes 14.7.1 Sommerstorffia spinosa 14.7.2 Aquastella 14.8 Parasites of protozoans 14.9 Discussion Acknowledgments References Ecology 15 Freshwater lichens 15.1 Ecology 15.1.1 Habitats and diversity of freshwater lichens 15.1.2 Collecting and identifying freshwater lichens 15.2 Physiological challenges for freshwater lichens 15.2.1 Water saturation and diffusion resistance 15.3 Freshwater lichens as a food source for other organisms 15.4 Biogeography of freshwater lichens 15.5 Zonation 15.6 Lichen trimlines 15.7 Freshwater lichen communities 15.8 Freshwater lichens as bioindicators 15.9 Water quality 15.10 Conservation Acknowledgments References 16 Aquatic Trichomycetes 16.1 Trichomycetes, an ecological group 16.2 Phylogenetic considerations 16.3 Distribution and success of Trichomycetes 16.4 Variations in symbiotic associations 16.5 Medical implications Acknowledgments References 17 Tropical peat swamp fungi with special reference to palms 17.1 Material and methods 17.1.1 Sample collection 17.2 Results 17.2.1 Abundance of fungi on four palms (Eleiodoxa conferta, Licuala longicalycata, Metroxylon sagu and Nenga pumila) 17.2.1.1 Eleiodoxa conferta 17.2.1.2 Licuala longicalycata 17.2.1.3 Metroxylon sagu 17.2.1.4 Nenga pumila 17.2.2 Fungal diversity 17.2.3 Percentages overlap in fungal diversity between the four palms 17.3 Conclusion Acknowledgments References 18 Stream pollution and fungi 18.1 The importance of aquatic hyphomycetes in woodland streams 18.2 Effects of nutrient enrichment on stream fungi 18.3 Effects of heavy metals and acidification on stream fungi 18.4 Ecological and toxicological effects of engineered nanoparticles on stream fungi 18.5 Effects of organic xenobiotics on stream fungi 18.6 Effects of thermal pollution on stream fungi 18.7 Effects of the interaction among factors on stream fungi 18.8 Conclusions Acknowledgments References 19 Association of animals and fungi in leaf decomposition £ 19.1 History 19.2 Effects of the leaf-fungus complex on invertebrate consumers 19.2.1 Nutritional value of mycelium vs. leaf substrate 19.2.2 Modifications of leaf substrate 19.2.3 Do invertebrates differ in their feeding strategies? 19.2.4 What factors ultimately determine food choice and feeding selectivity? 19.2.5 Stoichiometric considerations 19.2.6 Stimulation of fungi by invertebrate feeding 19.2.7 Anthropogenic changes 19.2.8 Research outside temperate regions 19.3 Effects of invertebrate consumers on the leaf-fungus complex 19.3.1 Invertebrate ingestion of conidia 19.3.2 Invertebrate ingestion of the leaf-fungus complex 19.4 Conclusions Acknowledgments References 20 Yeasts from extreme aquatic environments: hyperacidic freshwaters 20.1 Introduction 20.2 The River Agrio-Lake Caviahue acidic aquatic system 20.2.1 Yeast occurrence 20.2.2 Yeast diversity 20.3 Comparative yeast diversity study between RAC and the acidic environments of the Iberian Pyrite Belt (IPB) 20.4 Acidic rock drainage (ARD) yeasts ecoclade 20.5 Physiological aspects of acidophilic yeasts 20.6 Possible ecological roles of yeasts in acidic aquatic environments 20.7 Final remarks Acknowledgments References 21 Decomposition of wood in tropical habitats 21.1 Review of fungal diversity on wood in freshwater streams 21.2 Colonization of 15 timbers exposed at two locations in Thailand 21.2.1 Materials and methods 21.2.2 Results 21.2.3 Rate of decay of selected timbers at two contrasting freshwater ecosystems in Thailand 21.2.4 Discussion 21.2.4.1 Fungal community 21.2.4.2 Decay of wood in freshwater habitats Acknowledgments References 22 Epliogue 22.1 Introduction 22.2 Freshwater fungi 22.3 Freshwater fungus-like organisms 22.4 Knowledge gaps and future work in freshwater mycology 22.5 Conclusions References Index