Table Of ContentForeword
:ignuF The threads that keep ecosystems together
When people ask what I do for a living, and I tell them I'm a mycologist, they
usually react with surprise. Often they don't know what a mycologist is, but when
I tell them, the next question si "why?" Why study fungi?
When someone mentions "fungi" you may think immediately of mushrooms
on pizza or maybe moldy food in your refrigerator or the fungus growing on your
toes- But in fact fungi are everywhere and affect our lives every day, from
mushrooms to industrially important products to plant helpers to plant
pathogens to human diseases.
Fungi affect human lives in many and varied ways, so it is important to know
something about fungal biology in order to be able to control or exploit them for
our own purposes. The study of fungi has increased exponentially in the past 100
years, but they are still being ignored or neglected in many fields of study. For
example, more than 90% of fungal species have never been screened for
antibiotics or other useful compounds. Many ecologists do not even think about
fungi when doing their experiments or observations. However fungi play very
important roles in the ecosystem. They are a vital part of the links in the food web
as decomposers and pathogens and are important in grassland and forest
ecosystems alike. Fungi have many different kinds of associations with other
organisms, both living and dead. Since all fungi are heterotrophic, they rely on
organic material, either living or dead, as a source of energy. Thus, many are
excellent scavengers in nature, breaking down dead animal and vegetable
material into simpler compounds that become available to other members of the
ecosystem. Fungi are also important mutualists; over 90% of plants in nature
have mycorrhizae, associations of their roots with fungi, which help to scavenge
essential minerals from nutrient poor soils. Fungi also form mutualistic
associations with algae and cyanobacteria in the dual organisms known as
lichens.
On the other hand, many fungi are detrimental, inciting a large number of plant
diseases, resulting in the loss of billions of dollars worth of economic crops each
year, and an increasing number of animal diseases, including many human
maladies. Fungi can cause human disease, either directly or through their toxins,
including mycotoxins and mushroom poisons. They often cause rot and
contamination of foods - you probably have something green and moldy in the
back of your refrigerator right now. They can destroy almost every kind of
manufactured good- with the exception of some plastics and some pesticides. In
this age of immunosuppression, previously innocuous fungi are causing more and
more human disease.
There are many ways in which people have learned to exploit fungi. Of course,
there are many edible mushrooms, both cultivated and collected from the wild.
Yeasts have been used for baking and brewing for many millennia. Antibiotics
such as penicillin and cephalosporin are produced by fungi. The
immunosuppressive anti-rejection transplant drug cyclosporin si produced by the
mitosporic fungus Tolypocladium inflatum. Steroids and hormones- and even
birth control pills - are commercially produced by various fungi. Many organic
acids are commercially produced with fungi- e.g. citric acid in cola and other
soda pop products si produced by an sulligrepsA species. Some gourmet cheeses
such as Roquefort and other blue cheeses, brie and camembert are fermented with
certain muillicineP species. Stone washed jeans are softened by amredobcirT
species. There are likely many potential uses that have not yet been explored.
Fungi are also important experimental organisms. They are easily cultured,
occupy little space, multiply rapidly, and have a short life cycle. Since they are
eukaryotes and more closely related to animals, their study si more applicable to
human problems than si the study of bacteria. Fungi are used to study metabolite
pathways, for studying growth, development, and differentiation, for determining
mechanisms of cell division and development, and for microbial assays of
vitamins and amino acids. Fungi are also important genetic tools, e.g. the "one
gene one enzyme" theory in aropsorueN won Beadle and Tatum the Nobel prize
for Physiology or Medicine in 1958. The first eukaryote to have its entire DNA
genome sequenced was the bakers' and brewers' yeast secymorabccaS .eaisiverec
Mycologists study many aspects of the biology of fungi, usually starting with
their systematics, taxonomy, and classification (you have to know "what it is"
before you can work effectively with it), and continuing on to their physiology,
ecology, pathology, evolution, genetics, and molecular biology. There are quite a
few disciplines of applied mycology, such as plant pathology, human pathology,
fermentation technology, mushroom cultivation and many other fields.
Fungi never fail to fascinate me. They have interesting life cycles and occupy
many strange, even bizarre, niches in the environment. Take for example
Entomopbtbora ,eacsum a fungus that infects houseflies. The spores of the fungus
land on the unfortunate ylf and germinate, then penetrate the exoskeleton of the
fly. The first thing the fungus does, according to reports, si grow into the brain of
the fly, in order to control its activities. The mycelium of the fungus grows into
the particular area of the brain that controls the crawling behavior of the fly,
forcing the ylf to land on a nearby surface and crawl up as high as possible.
Eventually the hyphae of the fungus grow throughout the body of the fly,
digesting its guts, and the ylf dies. Small cracks open in the body of the ylf and the
Entomopbtbora produces sporangia, each with a single spore, which are then
released in hopes of landing on another .ylf
Other fungi, such as the dung fungus ,suloboliP produce spore "capsules" that
are shot off with great force, up to 3 meters away from their 1 cm sporulating
structure. Some fungi are "farmed" by Attine ants and by termites. Some fungi
can actually trap and eat small worms called nematodes. Known for their diverse
and amazing physiology, fungi can grow through solid wood, and in lichen
associations can even break down rocks. Fungi have intriguing and captivating
sex lives, some species with thousands of different sexes. Tetrad analysis in the
Ascomycetes has helped to solve some fundamental mysteries about genetics in
eukaryotic organisms.
I am pleased to introduce you to THE book for teaching and for learning fungal
biology. Michael Carlile, Sarah Watkinson, and Graham Gooday have produced
an eminently readable book to introduce students to all aspects of the biology of
fungi, including physiology and growth of hyphae and spores, fungal genetics,
fungal ecology and how these aspects of the fungi can be exploited in
biotechnology. The authors cover many of the topics I have alluded to above in
great depth, as well as thoroughly explaining the mostly hidden lives of fungi.
For new students of the fungi, I know you will enjoy learning about these
amazing organisms. For those of you who are already mycophiles, this book will
serve as a handy reference to fungi and their activities.
Thomas J. Volk
Department of ygoloiB
ytisrevinU of Wisconsin- aL essorC
http://www.wisc.edu/botany/fungi/volkmyco.html
Preface ot the
Second Edition
The preface to the first edition of this book, which follows, discusses the
significance ofm ycology for various branches of science and its value for students
of different biological disciplines, and explains the approach used and rationale
behind the arrangement of chapters and the selection of topics. All the principles
there discussed apply to the second edition, but the passage of six years has
inevitably led to changes in the material presented. Many of these changes result
from progress in molecular biology and its application to the fungi. When the
writing of the first edition was completed in 1993, it was clear that molecular
methods, which were already having revolutionary consequences for bacterial
classification, identification and ecology, would have equally profound effects in
mycology. However, at that time, apart from the use of molecular methods in
biotechnology (such as yeast as a host for cloned genes) and population genetics
of plant pathogens, rather little had been published. We therefore had to limit
ourselves very largely to outlining molecular methods and stating their potential
for mycology. The situation had changed sufficiently by the time of publication
for some otherwise enthusiastic reviewers to regret the paucity of molecular
material. We are now able to make proper use of molecular insights in discussing
fungal development, classification, ecology and pathogenicity, as indicated below
in a consideration of changes in each chapter.
Chapter I now has an improved presentation of the place of fungi in the major
groups of organisms, made possible by progress in molecular phylogeny. This
applies also to the consideration of the major groups of fungi in Chapter 2,
although the terminology used by practising mycologists si emphasized. The
publication of the 8th edition of the authoritative Ainswortb ~ Bisby's
yranoitciD of eht ignuF has facilitated a revision of Appendix 2 to provide an up-
to-date classification. Chapter 3 includes new material on the way in which
hyphae and yeast cells grow, and Chapter 4 on mating in fungi, much of which
results from the application of molecular methods. Whereas in 1993 there had
been a very limited application of molecular cladistics to fungi, now every issue of
leading mycological journals has phylogenetic trees for further fungal groups.
Molecular methods are also giving an increased insight into the extent of genetic
recombination in nature, especially among apparently asexual fungi. These
developments have necessitated considerable revision of Chapter 5. A major
problem in fungal ecology has been a very limited ability to identify fungi in
nature unless they are sporulating, a problem that si diminishing through the
application of molecular methods, as described in Chapter 6, which also includes
an account of the recently established threat to fungal biodiversity along with
approaches to fungal conservation. Chapter 7 includes new material on the
molecular basis of fungal pathogenicity, and has more material on medical
mycology than did the first edition. A major recent development in medicine has
been the rise of immunosuppressive and cholesterol-lowering drugs of fungal
origin into the category of best-selling pharmaceuticals. These and other new
products of fungal origin are considered in Chapter .8 Chapters now end with
questions, with answers at the end of the book.
We wish to renew our thanks to our friends who read or commented upon
chapters or sections and provided illustrations for the first edition of the book.
We now add our gratitude to those who have provided similar help in the
preparation of the second edition, including Professor Joan Bennett, Professor
Tom Bruns, Professor Mark Seaward, Professor Nick Talbot, Professor Tom
Volk, those whose names appear in the legends to the Figures that they provided,
and Lilian Leung of Academic Press. Finally, as before, we thank members of our
families, Elizabeth Carlile, Margaret Gooday and Anthony, Charles and Ruth
Watkinson, for their help.
Dr Michael J. Carlile Professor Graham W. Gooday
24 Durleigh Road Department of & Molecular Cell Biology
retawgdirB Institute of Medical secneicS
TA6 7HU ytisrevinU of Aberdeen
llihretseroF
Dr Sarah C. Watkinson Aberdeen AB25 2ZD
Department of Plant secneicS
ytisrevinU of Oxford
South Parks Road
Oxford OX1 3RB
Preface to the First
Edition
The study of fungi, mycology, si of importance for students of many branches of
the life sciences. Fungi are of major significance as mutualistic symbionts and
parasites opfl ants, so their study si an important part of courses in plant ,secneics
and essential for students of plant pathology. Fungi are a major component of the
microbial world, and it si increasingly being recognized that they should receive
proper consideration in microbiology courses. Yeasts, filamentous fungi or both
are important in brewing, in the preparation of many foods, in biodeterioration
and in the fermentation industry, and hence need consideration in the context of
biotechnology. Yeasts have also had a major role in the development of
biochemistry, and filamentous fungi in that of genetics, especially biochemical
genetics, and both are now of major importance in molecular biology as hosts for
gene cloning. Fungi are of crucial importance in the breakdown of the vast
amounts of organic carbon produced annually by photosynthesis, and thus are
important in ecology and environmental science. Like bacteria, plants and
animals, the fungi are one of the great groups of living organisms, whether
considered in terms of numbers of species, biomass or role in the environment.
Fungi therefore deserve a place in the curriculum for degrees in biology, and in
introductory courses for any branch of the life sciences. The present book si
intended to provide an account of the fungi useful for students of all the above
mentioned disciplines, as well as to others who need information about the fungi.
The present authors have taught general courses in mycology to first and
second year undergraduates, and more specialized fungal topics to senior students
including those on MSc courses. The students were specializing in varied aspects
of biology, including biochemistry, biotechnology, microbiology, plant sciences
and plant pathology. Most students, prior to taking a course in mycology, had
acquired some knowledge of biochemistry, genetics, microbiology and molecular
biology and were interested in these subjects. Their knowledge of the structure
and classification of organisms, and of the procedures involved in identification
and morphology was however limited, and they needed to be convinced of the
importance of these topics and the extent to which they had been revitalized by
new, often molecular, methods. Colleagues teaching mycology in other
universities in both the United Kingdom and overseas report similar situations.
They agree that a book that covered aspects of the fungi of importance in a wide
range of disciplines, and which took into account the strengths and limitations of
present day students, would be a useful one. We have aimed to produce such a
book.
The perspective that we have adopted si a microbiological one. Most students
now come to mycology with some microbiological knowledge and, without the
application of the microbiological techniques of isolation and growth in pure
culture, most of our present understanding of the fungi could never have been
gained. We hence concentrate attention on fungi that can be grown in pure
culture, while maintaining an interest in their performance in nature. The opening
chapter introduces the fungi by reference to the cultivated mushroom, considers
their status as one of the major groups of organisms, and indicates the ways in
which varied disciplines have contributed to knowledge of the fungi, and the
study of fungi to fundamental biological discoveries. The second chapter surveys
fungal biodiversity, describing in some detail a well-studied representative of each
major group before discussing variety within the group, a didactic approach
pioneered by the great nineteenth century biologist and educationalist Thomas
Henry Huxley. A practical attitude is adopted with respect to classification and
nomenclature, with the terms and groupings used by mycologists in their work
and conversation, rather than in their taxonomic papers. There are sections on
yeasts and lichens, since books, journals, conferences and scientific societies are
devoted to them even though, on the basis of phylogeny, they should be
distributed among other groups of fungi. A formal classification and
nomenclature is provided in Appendix 2. High growth rates and yields are
essential for success in the fermentation industry, and valuable for the microbial
biochemist. Chapter 3 hence deals in some detail with the growth of fungi in pure
culture and the conditions that influence growth. Spores - which seem to be able
to get nearly everywhere and to survive almost everything- are crucial to the
success of most fungi. Their formation, in both yeasts and filamentous fungi, also
provides promising systems for fundamental studies on the control of
developmental processes- fungi develop rapidly, are amenable to genetic
manipulation, and have some of the smallest genomes among eukaryotes.
Chapter 4 hence includes both classical material on the production, dispersal,
survival and germination of fungi spores and an introduction to some recent
approaches to the control of sporulation. Variability within fungal species is an
important topic. For example, variability in culture concerns fermentation
technologists, interested in the stability or improvement of their strains, and
variability in nature, plant pathologists assessing whether plants may succumb to
more virulent strains. Chapter 5 deals with this topic, as well as the principles
involved in classification and in understanding fungal evolution. Fungi are the
organisms mainly responsible for the breakdown of the most abundant form of
organic carbon, lignocellulose, and so have a crucial role in the ecosystem. This,
and other saprotrophic activities, are dealt with in Chapter 6. Since conclusions
about the presence and activities of microbes in the environment are highly
dependent upon which of a range of techniques are employed, this chapter has a
substantial section on methods, some of which are revolutionizing microbial
ecology as well as other aspects of mycology. Chapter 7 concentrates on the
relationships, mutualistic and parasitic, between fungi and plants, which have
interacted with each other throughout their evolution, although the relations
between fungi and other groups of organisms are also considered. The final
chapter on fungal biotechnology si concerned with both traditional and novel
ways in which fungi are exploited by man. Fundamental principles are stressed
throughout, rather than details likely to be modified by future research, or
matters best taught by observation and experiment in the laboratory.
We wish to thank friends who have read and commented upon chapters or
sections. These include Dr Ken Alvin, Dr Simon Archer, Mr Paul Browning,
Professor Ken Buck, Professor Keith Clay, Dr Molly Dewey, Dr John Gay,
Professor Graham Gooday (who read the whole book), Dr Paul Kirk, Dr Bernard
Lamb, Dr Peter Newell, Dr Nick Read, Dr Tim Taylor and Professor Tony Trinci.
We are also grateful to Dr Maureen Lacey, who drew Fig. 4.11 illustrating the air
spora especially for the book, Dr Jeff Smith and Professor David Wood who
helped obtain mushroom photographs for Chapters 1 and 8, Mr Frank Wright
who prepared many of the prints, John Baker who took the cover photograph,
those who are named in the legends to the Figures that they provided and finally,
the many colleagues who in conversation have corrected errors or introduced us
to new developments. Finally, we thank members of our families, Elizabeth
Carlile and Anthony and Charles Watkinson, who helped in many ways.
Dr Michael J. Carlile Dr Sarah C. Watkinson
Department of Biology Department of Plant secneicS
Imperial egelloC at Silwood Park ytisrevinU of Oxford
Ascot SL5 7PY South RoaPda rks
Oxford OX1 3RA
The ignuF
A fungus familiar to almost everyone is the cultivated mushroom, suciragA
suropsib (Fig. 1.1), which is grown commercially on a very large scale, and also
survives in nature. The role of the edible fruit bodies (or fruiting bodies) is the
production of large numbers of spores by means of which dispersal occurs. The
spores are borne on the gills below the cap, and a stalk raises the fruit body above
the ground to facilitate spore dispersal by air currents.
Examination of the stalk, cap and gills with a microscope shows that the fruit
body is composed of long, cylindrical branching threads known as hyphae (sing.,
hypha). The hyphae are divided by cross-walls into compartments which typically
contain several nuclei. Such compartments, together with their walls, are
equivalent to the cells of other organisms. The spores are borne on specialized
cells termed basidia (sing., basidium). In most mushrooms each basidium bears
four spores, but in Agaricus bisporus only two - hence the specific epithet
.suropsib
If a spore of a cultivated mushroom is placed on a suitable substratum, such
as a nutrient agar medium, it may germinate, a slender hypha or germ-tube
emerging from the spore. Hyphal growth is apical, wall extension being limited to
the roughly hemispherical apex of the hypha. Nutrients are absorbed from the
substratum, and growth, nuclear division and hyphal branching occur to give an
approximately circular colony which increases in diameter at a uniform rate.
Similar colonies can be established by excising tissue from the fruiting body and
placing on a suitable medium. The hyphae of a growing colony are termed a
mycelium (pl., mycelia). Although the fruiting body is the spectacular feature of
the cultivated mushroom and related fungi, it is entirely dependent for its
nutrition on an extensive mycelium penetrating the substratum.
Different kinds of large fungi or macrofungi have been recognized for
thousands of years. In current English edible ones are often called mushrooms
and poisonous ones toadstools. During the eighteenth century, botanists made
considerable progress in the recognition and classification of the fungi, and early
microscopists observed and described hyphae and spores. In the early nineteenth
century it was established that many serious plant diseases were caused by
infection of the plant by minute living organisms. These organisms were found to
be composed of hyphae and to produce spores, so many of the causal organisms
