Note: Intro -- Series Preface -- Volume Preface to the Second Edition -- Volume Preface to the First Edition -- Contents -- List of Contributors -- Fungi -- 1 Saccharomycotina and Taphrinomycotina: The Yeasts and Yeastlike Fungi of the Ascomycota -- I. Introduction -- II. Occurrence, Distribution, and Ecology -- III. Importance -- A. Food, Beverage, and Industrial Uses -- B. Agriculturally Important Yeasts -- 1. Plant Pathogens -- 2. Biocontrol Yeasts -- C. Food and Beverage Spoilage -- D. Human and Animal Pathogens -- IV. Reproduction -- A. Asexual -- 1. Budding, Fission, Endospores, Chlamydospores -- 2. Pseudohyphae and True (Septate) Hyphae -- B. Sexual Reproduction -- V. Taxonomic Methods -- A. Phenotypic Characterization -- B. Genotypic Characterization -- VI. Phylogeny and Classification -- A. Phylogeny -- B. Classification -- 1. Saccharomycotina -- 2. Taphrinomycotina -- VII. Isolation, Maintenance, and Culture Availability -- A. Isolation -- B. Maintenance -- C. Culture Availability and Distribution -- VIII. Future Directions -- References -- 2 Pezizomycotina: Pezizomycetes, Orbiliomycetes -- I. Introduction -- II. Orbiliomycetes: An Overview -- III. Occurrence and Distribution -- A. Species Trapping Nematodes and Other Invertebrates -- B. Saprobic Species -- IV. Morphological Features -- A. Ascomata -- B. Asci -- C. Ascospores -- D. Paraphyses -- E. Septal Structures -- F. Nuclear Division -- G. Anamorphic States -- V. Reproduction -- VI. History of Classification and Current Hypotheses -- VII. Growth in Culture -- VIII. Pezizomycetes: An Overview -- IX. Occurrence and Distribution -- A. Parasitic Species -- B. Mycorrhizal Species -- C. Saprobic Species -- X. Morphological Features -- A. Ascomata -- B. Asci -- C. Ascospores -- D. Paraphyses -- E. Septal Structures -- F. Anamorphic States -- XI. Reproduction. , XII. History of Classification and Current Hypotheses -- A. Families of the Pezizomycetes -- 1. Ascobolaceae -- 2. Ascodesmidiaceae -- 3. Caloscyphaceae -- 4. Chorioactidaceae -- 5. Discinaceae -- 6. Glaziellaceae -- 7. Helvellaceae -- 8. Karstenellaceae -- 9. Morchellaceae -- 10. Pezizaceae -- 11. Pyronemataceae -- 12. Rhizinaceae -- 13. Sarcoscyphaceae -- 14. Sarcosomataceae -- 15. Tuberaceae -- XIII. Growth in Culture -- XIV. Conclusion -- References -- 3 Pezizomycotina: Sordariomycetes and Leotiomycetes -- I. Introduction -- II. Sordariomycetes -- A. Ecology -- B. Morphology -- 1. Ascomata -- 2. Centrum Development -- 3. Asci -- 4. Ascospores -- 5. Anamorphs -- 6. Ultrastructure -- C. Molecular Phylogeny -- D. Classification -- 1. Hypocreomycetidae -- a) Coronophorales -- b) Glomerellales -- c) Hypocreales -- d) Melanosporales -- e) Microascales -- 2. Sordariomycetidae -- a) Calosphaeriales -- b) Diaporthales -- c) Magnaporthales -- d) Ophiostomatales -- e) Boliniales -- f) Chaetosphaeriales -- g) Coniochaetales -- h) Sordariales -- 3. Xylariomycetidae -- 4. Orders Incertae Sedis -- a) Koralionastelales -- b) Lulworthiales -- c) Meliolales -- d) Phyllachorales -- e) Trichosphaeriales -- III. Leotiomycetes -- A. Classification History -- 1. History of Leotiomycetes -- 2. Current Classification of Leotiomycetes -- B. Molecular Phylogeny Update -- 1. Higher-Level Relationships of Leotiomycetes -- 2. Phylogeny Within Leotiomycetes -- C. Characters -- 1. Apothecium (Ascoma) Morphology, Anatomy, and Ultrastructure -- 2. Ecology and Biogeography -- IV. Geoglossomycetes -- V. Laboulbeniomycetes -- A. Laboulbeniales -- B. Pyxidiophorales -- VI. Problems and Perspectives -- A. Genome Project -- B. Environmental Study -- VII. Culture and Maintenance -- VIII. Conclusion -- References -- 4 Pezizomycotina: Lecanoromycetes -- I. Introduction. , II. Occurrence and Distribution -- III. Substrate Range and Ecology -- A. Substrate Range -- B. Lifestyles -- C. Mycobiont-Photobiont Associations -- IV. Mycobiont-Photobiont Cellular Contacts -- V. Morphological and Chemical Features -- A. Thalli -- B. Ascomata -- 1. Ascoma Morphology -- 2. Ascoma Development -- C. Asci -- 1. Ascus Walls -- 2. Ascus Apical Structure -- 3. Dehiscence Mechanisms -- D. Ascospores -- E. Interascal Filaments -- F. Pycnidia -- G. Asexual Propagules -- H. Secondary Compounds -- VI. Origin and Diversification -- VII. Orders and Classification -- A. Acarosporales -- B. Baeomycetales -- C. Caliciales -- D. Candelariales -- E. Lecanorales -- F. Lecideales -- G. Ostropales -- H. Peltigerales -- I. Pertusariales -- J. Rhizocarpales -- K. Sarrameanales -- L. Teloschistales -- M. Trapeliales -- N. Umbilicariales -- VIII. Conclusion -- References -- 5 Pezizomycotina: Eurotiomycetes -- I. Phylogeny and Taxonomy -- A. Eurotiomycetidae -- 1. Eurotiales -- a) Aspergillaceae -- i. Taxonomy -- ii. Asexual Morphology -- iii. Sexual Morphology and Self-Fertility -- b) Thermoascaceae -- i. Taxonomy -- ii. Asexual and Sexual Morphology -- c) Trichocomaceae -- i. Taxonomy -- ii. Asexual and Sexual Morphology -- d) Disputed Families: Monascaceae and Elaphomycetaceae -- 2. Onygenales -- a) Core Families of Onygenales -- b) Ajellomycetaceae -- 3. Arachnomycetales, Ascosphaera, and Eremascus -- 4. Coryneliales -- B. Chaetothyriomycetidae -- 1. Chaetothyriales -- 2. Verrucariales -- 3. Pyrenulales -- 4. Celotheliales ad int. (Gueidan et al. 2014) -- C. Taxa of Uncertain Placement -- 1. Mycocaliciomycetidae/Mycocaliciales -- 2. Marine Species of Dactylospora and Sclerococcum -- 3. Cirrosporium novae-zelandiae -- II. Ecology and Economic Importance -- A. Extremophilism -- B. Animal Pathogens -- 1. Onygenalean Pathogens. , a) Histoplasmosis, Blastomycosis, and Paracoccidioidomycosis -- b) Coccidioidomycosis or ``Valley Fever´´ -- c) Dermatophytes -- d) Chalkbrood of Bees -- 2. Eurotialean Pathogens -- C. Plant Pathogens -- D. Mutualistic Interactions -- 1. Ectomycorrhizae -- 2. Lichens -- 3. Myrmecophytes -- E. Food Contamination -- F. Food Production -- G. Toxic Secondary Metabolites -- H. Industrial Uses -- III. Summary -- References -- 6 Pezizomycotina: Dothideomycetes and Arthoniomycetes -- I. Introduction -- II. Character Evolution: Divergence and Convergence -- A. Morphology and Development -- B. Brief Taxonomic History -- III. Ecology and Distribution -- A. Associations with Plants and Plant Debris -- B. Aquatic Species -- C. Associations with Algae and Other Lichens -- D. Rock Environments and Oligotrophism -- IV. Modern Classification and Phylogeny -- A. Dothideomycetes -- 1. Pleosporomycetidae -- 2. Dothideomycetidae -- 3. Incertae Sedis Lineages -- B. Arthoniomycetes -- V. Maintenance and Culture -- VI. Conclusions -- References -- Nomenclature and Documentation -- 7 The Shifting Sands of Fungal Naming Under the ICN and the One Name Era for Fungi -- I. Introduction -- II. International Code of Nomenclature for Algae, Fungi, and Plants (ICN) -- A. Transition to One Name Per Fungus -- 1. History and Enactment of Rule Changes -- 2. How One Name Per Fungus Will Happen Under the New Rules -- B. Other Major and Minor Changes in the ICN -- 1. Effective Publication via Electronic Publication -- 2. Latin or English for Valid Publication of Names of New Taxa -- 3. Registration of Fungal Names -- 4. Minor Changes -- C. Practical Notes on Using the ICN -- 1. How Do I Describe New Taxa at the Rank of Species? -- a) Validation -- b) Legitimization -- 2. How Do I Describe New Taxa at the Rank of Genus? -- 3. What Is an Ex-type?. , 4. How and When Do I Designate a Lectotype for a Species? -- 5. How and When Do I Designate a Neotype for a Species? -- 6. How and When Do I Designate an Epitype for a Species? -- 7. How Do I Validly Publish New Combinations? -- 8. How Do I Validly Publish a Replacement Name Also Known as a Nomen Novum? -- 9. How Do I Correctly Give Author Citations for Taxa? -- III. Potential Changes to Nomenclatural Rules -- IV. Conspectus and the Future of Fungal Naming -- References -- 8 The Role of Herbaria and Culture Collections -- I. Introduction -- II. Best Practices for Fungal Herbaria -- A. Preparing Fungal Reference Specimens -- B. Preparing Dried Culture Specimens -- C. Numbering and Labeling Fungal Specimens -- D. Storage and Organization of Dried Specimens -- E. Requesting, Annotating, and Returning Specimens -- F. Use of Fungal Herbarium Specimens in Molecular Studies -- 1. Introduction -- 2. Contamination of Herbarium DNA Samples -- 3. Extraction of DNA from Herbarium Specimens -- 4. DNA Quality from Herbarium Specimens -- III. Maintenance of Living Cultures -- A. Introduction -- B. Metabolically Active Preservation -- 1. Storage on Agar with Periodic Transfer -- 2. Storage on Agar Under Mineral Oil and Distilled Water -- C. Metabolically Inactive Preservation -- 1. Cryopreservation (Cryogenic Storage) -- 2. Freeze Drying -- IV. Conclusions -- References -- Evolution -- 9 Subcellular Structure and Biochemical Characters in Fungal Phylogeny -- I. Introduction -- II. The Role of Subcellular Structure in Fungal Phylogeny -- III. The Role of Biochemical Characters in Fungal Phylogeny -- IV. Character and Character State Definition and Refinement -- V. Structural and Biochemical Database -- VI. Structural and Biochemical Database in Phylogenetic Analysis -- VII. Development of the Fungal Subcellular Ontology. , VIII. Specimen Preparation and Evaluation for Subcellular Structure.