Chapter 1 Aquatic hyphomycete spores: What do we know, where do we go from here? 1 Introduction 2 Rethinking aquatic hyphomycete spores: Going beyond its discovery 3 Spore biodiversity research gaps besets potential large scale patterns and processes 4 Environmental cues for aquatic hyphomycetes sporulation are ambiguous 5 Mechanisms governing aquatic hyphomycete spore production, germination and viability require further attention 6 Aquatic hyphomycete spores may be conveyors of essential molecules in food webs 7 Conclusion Appendix: Supplementary material Acknowledgments References Chapter 2 Diversity of freshwater ascomycetes in the Western Ghats of India 1 Introduction 2 Habitats and substrates 3 Species richness and diversity 3.1 Ascomycetes in Karnataka 4 Occurrence in marine habitats 5 Conclusions Acknowledgments References Chapter 3 Diversity of freshwater fungi in polar and alpine lakes 1 Polar and alpine regions 2 Characteristics of polar and alpine lakes 3 Fungi in Arctic lakes 4 Fungi in Antarctic lakes 5 Fungi in alpine lakes 6 Conclusions Acknowledgments References Chapter 4 Fungal diversity in drinking water distribution systems 1 Introduction 2 Ecology of fungi in water 2.1 Water temperature 2.2 Nutrient concentration 2.3 Pipe material 2.4 Particle accumulation 2.5 Regulations 3 Maintenance methods 3.1 Water treatment and disinfection 3.2 Removal of fungi 3.3 Inactivation of fungi 4 Biotic variables and their effects on the ecology of aquatic fungal taxa 4.1 Interactions with bacteria 4.2 Interactions with protozoa 4.3 Interactions with viruses 4.4 Interactions with algae 5 Ways of exposure 5.1 Sources of pathogenic or allergenic fungi 6 Pathways of exposure 7 Impacts on human health 7.1 Direct health effects of fungal infections 7.2 Fungal metabolites 7.3 Management of adverse health effects 7.4 Indirect health effects 7.4.1 Biocorrosion 7.4.2 Taste and odor issues 7.4.3 Fungal compounds responsible for taste and odor issues 8 Conclusions References Chapter 5 Phyllosphere of submerged plants: A reservoir of mycobiota 1 Introduction 2 Isolation of phyllosphere fungi 3 Factors affecting phyllosphere mycobiota 4 The roles of phyllosphere fungi 4.1 Effect of phyllosphere fungi on plant growth 4.2 Phyllosphere fungi as biocontrol agents 4.3 Phyllosphere fungi in bioremediation 4.4 Phyllosphere fungi as pathogens 5 The most common fungi isolated from the phyllosphere of submerged plants References Chapter 6 Fungal organisms: A check for harmful algal blooms 1 Introduction 2 Harmful algal bloom 2.1 Route of exposure 2.1.1 Direct exposure 2.1.2 Indirect exposure 2.2 Impact 2.2.1 Acute 2.2.2 Chronic 2.2.3 Organism and habitat affected 2.3 Ecological impacts of freshwater algal blooms on 2.3.1 Water quality 2.3.2 Plankton biodiversity 2.3.3 Effect on food chains and food webs 2.3.4 Ecosystem functioning 3 Types of biotoxins produced by harmful algal blooms 3.1 Saxitoxins 3.2 Brevetoxins 3.3 Domoic acid 3.4 Ciguatoxins 4 Techniques applied to control the harmful algal blooms and their toxins 4.1 Microorganisms-based methods for HABs control 4.1.1 Single-species microorganisms based methods Rapid decrease of algal cells density Bacterial bioflocculation 4.1.2 Methods for inhibition of harmful algal growth 4.1.3 Methods for the lysis or killing of harmful algal growth Algicidal bacteria-based methods Algicidal actinomycete based methods 4.1.4 Microbial aggregates-based methods for HABs control Periphyton based methods Biofilm based methods 4.2 Zooplanktons used to mitigate HABs 4.3 Algae used to mitigate HABs 4.4 Fungi used to mitigate HABs 4.5 Cyanophage used to mitigate HABs 4.6 Fish species used to mitigate HABs 5 Fungi used to mitigate HABs 6 Detection methods and mechanism of action of controlling the harmful algal bloom by fungi 7 Swotting socio-economic impacts of harmful algal blooms and their control by fungi 8 Conclusions References Chapter 7 Mycoloop: Role in shaping aquatic ecosystems 1 Introduction 2 The concept of mycoloop 3 The role of fungi in aquatic environment 3.1 Physico-chemical properties of aquatic environment 3.2 Role of fungi as decomposers, predators, endophytes, parasites, and disease-causing organisms in the aquatic milieu 3.2.1 Fungi as decomposers 3.2.2 Fungi as predators 3.2.3 Fungi as endophytes 3.2.4 Fungi as parasites 3.2.5 Fungi as disease-causing agents 3.2.6 Fungi as organic matter producers 3.2.7 Role of fungi in stabilization of ecosystems 3.3 Biogeochemical functions of planktonic fungi 3.3.1 Nutrient cycling 3.4 Fungi in hypoxic and anoxic habitats 3.4.1 Ecological significance of fungi in hypoxic and anoxic environments 3.5 Diversity of fungi in hypoxic and anoxic aquatic environments 3.6 Molecular methods for fungal identification and metagenomics 3.6.1 Extraction of DNA 3.6.2 PCR method for amplifying the genes of interest 3.6.3 Sequencing of the amplified gene 3.6.4 Phylogenetic analysis References Chapter 8 Biochemical and industrial potential of aquatic fungi 1 Introduction 2 Aquatic fungi 3 Biodiversity of aquatic fungi 4 Industrial applications of aquatic fungi 5 Aquatic fungi: Sources of various enzymes and their potential applications 5.1 Amylases 5.2 Lipases 5.3 Esterases 5.4 Lignocellulases 5.5 Xylanases 5.6 Other enzymes 6 Biosurfactants and other polysaccharides from aquatic fungi 7 Secondary metabolites from aquatic fungi: Potential producers of pharmaceutical biomolecules 8 Use of fungi derived bioactive compounds in cosmetics 9 Aquatic fungi in bioremediation 9.1 Hydrocarbons 9.2 Heavy metals 10 Conclusions References Chapter 9 Bioprospecting, biotransformation and bioremediation potential of fungi in freshwater ecosystems 1 Introduction 2 Aquatic habitat and ecological features 3 Aquatic fungi 3.1 Aquatic ascomycetes 3.1.1 Aquatic dothideomycetes 3.1.2 Aquatic sordariyomycetes 3.1.3 Aquatic ascomycetous yeast 3.2 Aquatic basidiomycetes 3.3 Aquatic chytridiomycetes 3.4 Aquatic blastiocladiomycota 3.5 Aquatic rozellomyceta 3.6 Aquatic aphelidiomycota 4 Decomposition and food web 5 Organic matter producers 6 Fresh water fungi-bioprospecting 6.1 Dibenzo[ b, e ]oxepinones 6.2 Methyl gallate 7 Bioremediation using aquatic fungi 7.1 Organic agrochemical bioremediation using fungi 7.2 White rot fungi and bioremediation of pesticides 7.3 Bioremediation of dyes 7.4 Bioremediation of heavy metals using fungi 7.4.1 Bioremediation of chromium [Cr(VI)] 7.4.2 Bioremediation of selenium 7.5 Bioremediation of pharmaceutical contaminants 8 Biotransformation using aquatic fungi 8.1 Biotransformation of 1-Naphthol 8.2 Biotransformation of lignin 8.3 Biotransformation of diterpenoids 9 Conclusions References Chapter 10 Fungicide and pesticide fallout on aquatic fungi 1 Introduction 2 Pesticides in aquatic ecosystems 2.1 Fungicides and water resources contamination 2.2 Fungicide effects on aquatic microorganisms and animals 3 Reducing the adverse impacts of fungicides 3.1 Continuous and regular monitoring of water and soil resources 3.2 Bio-fungicides and reduction of chemical fungicides consumption 3.3 Determination/detection of pesticides residues in water resources 4 Future perspectives 5 Conclusions Acknowledgments References Chapter 11 Heavy metal accumulation potential of aquatic fungi 1 Introduction 2 Worldwide contamination of air, water and soils by heavy metals 2.1 Air contamination by heavy metals 2.2 Water contamination by heavy metal 2.3 Soil contamination by heavy metals 3 Direct and indirect effect of ecotoxic heavy metals on life 4 Effective microbial processes for heavy metal transformation 5 Genetically engineered microorganisms for heavy metal removal 6 Importance of fungi in heavy metals degradation and processing 7 Mechanism of action to remove heavy metal by fungal strains 8 Conclusion References Chapter 12 Diseases and infections due to freshwater fungi 1 Introduction 1.1 Non-infectious diseases 1.2 Infectious diseases 2 Potential causes of infections and diseases in freshwater 3 Fungal infection in freshwater 4 The life style of fungal pathogens 5 Pathogenic Fungi derived from different sources of freshwater 5.1 Opportunistic Fungi from groundwater 5.2 Opportunistic Fungi from surface water 5.3 Opportunistic Fungi from Tapwater 6 Common fungal infections and diseases 6.1 Fungal keratitis 6.2 Fungal Keratoconjunctivitis 6.3 Fungal acute otitis externa 6.4 Saprolegniosis 6.5 Ichthyophoniasis 6.6 Branchiomyces 6.7 Black gill disease (fusarium disease) 6.8 Aflatoxicosis (red disease) 6.9 Other fungal infections 7 Detection techniques for identification of the freshwater derived fungal pathogens 8 Treatment and preventive measures against freshwater derived fungal infections 9 Conclusions References Chapter 13 An insight into the study methods of aquatic fungi 1 Introduction 2 A little about the classic studies 3 Studies using molecular techniques 3.1 Essential elements for molecular techniques 3.1.1 DNA as a tool for the study of fungi 3.1.2 The fungi DNA barcoding 3.2 Techniques that made molecular analyses possible 3.2.1 RFLP—Restriction fragment length polymorphism 3.2.2 T-RFLP—Terminal restriction fragment length polymorphism 3.2.3 Amplified fragment length polymorphism 3.2.4 DGGE—Denaturing gradient gel electrophoresis 3.2.5 FISH—Fluorescent in situ hybridization 3.2.6 Next-generation sequencing and the metagenomics 4 What do the current studies show and where are we going now? Acknowledgments References Chapter 14 Metagenomic insights into the fungal assemblages of freshwater ecosystems 1 Introduction 2 Role of Fungi in freshwater ecosystems 3 Linking metagenomics to aquatic microbial ecology 3.1 PCR amplification of internal transcribed spacer (ITS) regions/use of specific marker genes 3.2 Shotgun metagenomics 4 Diversity, spatial distribution, and activity of freshwater fungi 5 Freshwater fungal biodiversity is controlled by the environment and governs ecological functions 6 Conclusions References Chapter 15 Freshwater fungi in the Amazon as a potential source of antimicrobials 1 Introduction 2 Aquatic ecosystems in the Amazon 3 Freshwater fungi 4 Aquatic fungi as a source of antimicrobials 5 Conclusions Financing information Conflict of interest References Chapter 16 Fungi: The indicators of pollution 1 Introduction 2 Classification of pollution indicators 2.1 Physical indicators 2.2 Chemical indicators 2.3 Biological indicators 3 Significance of biological indicators 4 Fungi as an indicator of air pollution 5 Fungi as an indicator of water pollution 6 Fungi as an indicator of soil pollution 7 Fungi as an indicator of radioactive contamination 8 Conclusions