The second edition of the highly popular “Westerdijk Laboratory Manual Series No. 1: Fungal Biodiversity” is now available. The volume (hard copy, full color) is extended with 150 pages. This laboratory manual focuses on techniques for isolation, cultivation, and molecular and morphological study of filamentous fungi and yeasts. It has been developed as a general text over many years, which is based on the annual mycology course given at the Westerdijk Fungal Biodiversity Institute in Utrecht, The Netherlands.

The manual provides an introductory text to systematic mycology, starting with a concise treatise of Hyphochytridiomycota and Oomycota, which have long been subject of study by mycologists, but are now classified in the Kingdom Chromista. These are followed by sections on the groups of “true fungi”: Chytridiomycota, Blastocladiomycota, “Zygomycota”, Ascomycota and Basidiomycota. This descriptive part is illustrated by numerous full-color figures of life-cycles and schematic line-drawings as well as photographic plates depicting most of the structures essential for the study and identification of these fungi. Special attention is given to basic principles of working with axenic cultures, good morphological analysis, and complicated issues for beginners such as conidiogenesis and the understanding of life-cycles. Exemplar taxa for each of these fungal groups, in total 69 mostly common species in various economically important genera, are described and illustrated in detail. In a chapter on general methods a number of basic techniques such as the preparation and choice of media, microscopic examination, the use of stains and preparation of permanent slides, and herbarium techniques are explained. Most importantly, this volume also sees the integration of asexual and sexual genera, following the abandonment of dual nomenclature for Fungi. Further chapters deal with commonly used molecular and phylogenetic methods and related identification tools such as BLAST and DNA Barcoding, fungal nomenclature, ecological groups of fungi such as soil-borne and root-inhabiting fungi, water moulds, and fungi on plants and of quarantine importance. Some topics of applied mycology are also treated, including fungi in the air- and indoor environment and fungi of medical importance. Common mycological terminology is explained in a glossary, with reference to illustrations in the book. A chapter providing more than 60 mycological media for fungal cultivation, and a comprehensive list of cited references are also provided. The book is concluded with an index, and dendrogram reflecting our current understanding of the evolutionary relationships within the Fungi.

Fungal Biodiversity, Second Edition

Introduction

What are Fungi?
How to study Fungi

The Fungal System

Introduction

Species and generic concepts
     Phenotypic species concept
     Biological species concept
     Phylogenetic species concept
     Consolidated species concept
     One fungus: one name
     One fungus: which genus?
     One fungus: which gene?
     Conclusions
General literature

Kingdom Chromista

Phylum Hyphochytriomycota
Phylum Oomycota
     Molecular phylogeny and classification
           Class Saprolegniomycetes
                 Order Saprolegniales
                 Order Leptomitales
                 Order Atkinsiellales
           Class Peronosporomycetes
                 Order Rhipidiales
                 Order Albuginales
                 Order Peronosporales
                       Family Pythiaceae
                       Family Peronosporaceae
                       Family Salisapiliaceae
           Basal clades

Kingdom Fungi

Phylum Chytridiomycota
           Class Chytridiomycetes
           Class Monoblepharidomycetes
                 Order Chytridiales
                 Order Rhizophydiales
                 Order Spizellomycetales
                 Order Cladochytriales
                 Order Polychytriales
                 Order Lobulomycetales
                 Order Monoblepharidales
Phylum Blastocladiomycota
                 Order Blastocladiales
“Zygomycota”
Phylum Zoopagomycota
     Subphylum Zoopagomycotina
     Subphylum Kickxellomycotina
     Subphylum Entomophthoromycotina
Phylum Mucoromycota
     Subphylum Mucoromycotina
     Subphylum Mortierellomycotina
     Subphylum Glomeromycotina
     Description of the order Mucorales
                       Family Mucoraceae
                       Family Rhizopodaceae
                       Family Saksenaeaceae
                       Family Pilobolaceae
                       Families Choanephoraceae, Mycotyphaceae, Cunninghamelaceae, Syncephalastraceae, and Radiomycetaceae
                       Families Phycomycetaceae (Mucorales) and Umbelopsidaceae (Umbelopsidales)
                 Genus Mucor
     Description of the order Endogonales
     Description of the order Mortierellales
                       Family Mortierellaceae
Phylum Ascomycota
     Subphylum Saccharomycotina
     Subphylum Taphrinomycotina
           Vegetative reproduction
           Sexual reproduction
           Physiological characterization
           Molecular characterization
           Data interpretation of sequencing
           Classification
           Procedure for routine identification
     Subphylum Pezizomycotina (formerly Euascomycetes)
           Recommended names for pleomorphic genera
           The principle
           Some important groups
           Lichenised ascomycetes
                 Some important groups with apothecial sporocarps
                 Some important genera of ascomycetes with hyphomycetous asexual morphs
                       The genera Aspergillus, Penicillium, Paecilomyces
                       Single name nomenclature
                       Cultivation
                       Phenotype based identification
                       Sequence based identification
                 The genus Cladosporium
                 The genera Fusarium, Calonectria and Neonectria
                 The genus Trichoderma
                 Genera with septate and pigmented poroconidia
                 The genus Alternaria
           Coelomycetes
                 Melanconiaceous coelomycetes (former “Melanconiales”)
                 Sphaeropsidaceous coelomycetes (former “Sphaeropsidales”)
            Some important genera of ascomycetes with coelomycetes asexual morphs
                 The genus Colletotrichum
                        Major species complexes
                 The Phoma generic complex
                 The Pestalotiopsis generic complex
Phylum Basidiomycota
           Taxonomy and short characterisation of the most important orders
     Subphylum Agaricomycotina
           Class Agaricomycetes (corresponding to the former Hymenomycetes)
                       Order Agaricales
                       Order Auriculariales
                       Order Boletales
                       Order Cantharellales
                       Order Gloeophyllales
                       Order Gomphales (Phallomycetidae)
                       Order Hymenochaetales
                       Order Phallales (Phallomycetidae)
                       Order Polyporales
                       Order Russulales
                       Order Thelephorales
           Class Dacrymycetes
                       Order Dacrymycetales
           Class Tremellomycetes
                       Order Filobasidiales
                       Order Tremellales
     Subphylum Pucciniomycotina
           Class Agaricostilbomycetes
           Class Atractiellomycetes
           Class Classiculomycetes
           Class Cryptomycocolacomycetes
           Class Cystobasidiomycetes
           Class Microbotryomycetes
                       Order Microbotryales
                       Order Sporidiobolales
           Class Mixiomycetes
           Class Pucciniomycetes
                       Order Pucciniales
                       Order Septobasidiales
           Class Tritirachiomycetes
     Subphylum Ustilaginomycotina
           Class Exobasidiomycetes
                       Order Ceraceosorales
                       Order Doassansiales
                       Order Entylomatales
                       Order Exobasidiales
                       Order Georgefischeriales
                       Order Golubeviales
                       Order Microstromatales
                       Order Robbauerales
                       Order Tilletiales
           Class Malasseziomycetes
                       Order Malasseziales
           Class Moniliellomycetes
                       Order Moniliales
           Class Ustilaginomycetes
                       Order Ustilaginales
                       Order Urocystidales
                       Order Violaceomycetales
     Subphylum Wallemiomycotina
           Class Wallemiomycetes
                       Order Wallemiales
                       Order Geminibasidiales

General methods

Aseptic working
Safety in working with fungi
Single-spore cultures
Preparation of media

General procedure
Choice of media, incubation

Microscopic examination (light microscopy)

Optical equipment
     The Dissecting Microscope
     The Compound Microscope
Measurement of fungal structures
Mounting fluids
Preparations
Permanent mounts
Drawing tube and illustrations
Inking
Stains
     Common stains
     Fluorescence microscopy
     Staining of nuclei
Electron microscopy
Growth studies
Induction of sporulation
     Effect of nutrition
     Effect of light
     Effect of aeration and the concentration of other gases
     Effect of temperature

Preservation of living cultures
Fungarium techniques
Collections and the CBD

Molecular and phylogenetic methods

Introduction
Isolation of genomic DNA
Westerdijk Institute DNA Bank
Polymerase chain reaction

Protocol standard PCR procedure

Agarose gel electrophoresis
Automated sequencing
Nucleotide BLAST search
Phylogenetic analysis

Character matrix
Analysis of character matrix
Presentation and interpretation of the tree

DNA barcoding
Recommended further reading
MALDI-TOF MS and other protein-based methods

Standardised growth conditions
Sample preparation method
Target plate
Score values and data interpretation
Databases
Challenges for further optimization

Nomenclature

The most important rules

Rules for valid publication of new taxa
Typification

Recent and proposed changes
Name changes

Rules for determining legitimate names
     Priority
     Synonyms and homonyms
     Starting point

MycoBank

Ecological groups of fungi

Introduction
Symbionts and endophytes
Soil fungi

Direct observation
Isolation techniques
     Direct isolation techniques
           The dilution plate technique
           Surface culture on agar media
           Warcup’s soil plates
           Soil washing techniques
     Selective techniques
           Bait technique
           Ascospore activation using heat or chemical agents
                 Ascospore activation using chemical agents
                 Ascospore activation using heat

Aquatic fungi

Freshwater fungi
Marine fungi

Fungi and plants

Plant-pathogenic fungi
Soil-borne, root-inhabiting fungi
Above-ground plant-pathogenic fungi
Preventing the spread of plant pathogens
Fungi on seeds
     Agar plate method
     Blotting paper method
     Seed washing method
Fungi on decaying wood
Fungi on dung (Coprophilous fungi)
Fungicolous fungi
Entomogenous fungi
Rock-inhabiting fungi
Thermophilic and thermotolerant fungi
Pyrophilous fungi
Psychrotolerant and psychrophilic fungi
Osmophilic and xerophilic fungi
Acidophilic and alkalophilic fungi
Halophilic fungi
Oligotrophic fungi

Applied mycology

Food-borne fungi

General-purpose methods and media
     Direct examination and direct plating
     Dilution plating
General methods for the enumeration of yeasts
Enumeration of heat-resistant fungi

Biodeterioration
Mycotoxins
Fungi in the air and indoors
Fungi of medical importance

Pathogenic fungi: evolutionary advantage of animal-association
Opportunistic fungi: coincidental agents of human disease
Commensals and superficial pathogens: single-factor association and mild pathogenicity
Endosaprobes: delicate balance with the immune system
Host responses: recognition of pathogens and saprobes

Glossary and descriptive terms

Mycological media

References

Arrangement of the major fungal taxa

Reference taxa

Publish Date: 2019
Format: 9" x 12" hardcover
Pages: 425
Publication Weight: 5 lbs