The fungi 2nd ed m carlile (academic press, 2001)

Foreword

Fungi: 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 is "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
t o e s - 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 is 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 is produced by an Aspergillus species. Some gourmet cheeses
such as Roquefort and other blue cheeses, brie and camembert are fermented with
certain Penicillium species. Stone washed jeans are softened by Tricboderma

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 is more applicable to
human problems than is 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 Neurospora 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 Saccbaromyces cerevisiae.
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 muscae, a fungus that infects houseflies. The spores of the fungus
land on the unfortunate fly and germinate, then penetrate the exoskeleton of the
fly. The first thing the fungus does, according to reports, is 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 fly 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 fly dies. Small cracks open in the body of the fly and the
Entomopbtbora produces sporangia, each with a single spore, which are then
released in hopes of landing on another fly.
Other fungi, such as the dung fungus Pilobolus, 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 Biology
University of Wisconsin- La Crosse
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Preface to the
Second Edition

The preface to the first edition of this book, which follows, discusses the

significance of mycology 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 is emphasized. The
publication of the 8th edition of the authoritative Ainswortb ~ Bisby's
Dictionary of the Fungi has facilitated a revision of Appendix 2 to provide an upto-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 is 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

42 Durleigh Road
Bridgwater
TA6 7HU

Department of Molecular & Cell Biology
Institute of Medical Sciences
University of Aberdeen
Foresterhill
Aberdeen AB25 2ZD

Dr Sarah C. Watkinson

Department of Plant Sciences
University of Oxford
South Parks Road
Oxford OX1 3RB


Preface to the First
Edition

The study of fungi, mycology, is of importance for students of many branches of
the life sciences. Fungi are of major significance as mutualistic symbionts and
parasites of plants, so their study is an important part of courses in plant sciences,
and essential for students of plant pathology. Fungi are a major component of the
microbial world, and it is 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 is
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 is 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 is 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
Imperial College at Silwood Park
Ascot SL5 7PY

Department of Plant Sciences
University of Oxford
South Parks Road
Oxford OX1 3RA


The Fungi
A fungus familiar to almost everyone is the cultivated mushroom, Agaricus
bisporus (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

bisporus.
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



of plant diseases, such as rusts, smuts and mildews, were recognized as being
microscopic fungi (microfungi). Microfungi were also found attacking dead
organic materials. Such microfungi were termed moulds, spelt molds in the USA.
The concept developed of fungi as non-photosynthetic plants composed of
hyphae, depending for their nutrition on the absorption of organic materials and
producing a variety of spores.
Meanwhile, studies on alcoholic fermentation established that the yeast

responsible for the process was a microscopic organism reproducing by budding.
Although the cells of brewer's yeast are ellipsoidal in form and do not produce
hyphae, they were regarded as fungi on the basis of being plants that live by
absorbing organic materials rather than by photosynthesis. The discovery of
yeasts capable of producing a hyphal phase and of moulds able to produce a yeast
phase confirmed the soundness of classifying yeasts as fungi, even though some of
the best-known species did not form hyphae.
In the mid-twentieth century electron microscopy showed that all cellular
organisms, that is all organisms other than viruses, could be classified on the basis
of cell structure into two groups, the prokaryotes and the eukaryotes, as discussed
below. It was found that fungi had a cell organization that was clearly eukaryotic.
The fungi can hence be defined as non-photosynthetic hyphal eukaryotes and
related forms. Their status as one of the major groups of living organisms is
considered below.

The Classification of Organisms into Major Groups
Man, faced with the diversity of living things, has classified them in a variety of
ways on the basis of their more striking features. Traditionally, the most
fundamental distinction is between animals, motile and food-ingesting, and
plants, static and apparently drawing their nourishment from the soil or in some

Figure 1.1 The mushroom. A, Fruit bodies of Agaricus bitorquis, a close relative of the
cultivated mushroom. On the left note the stalk and the gills below the cap. At the right is
a fruit body inverted to show the gill pattern more clearly (T. J. Elliott). B-G, The
cultivated mushroom, Agaricus bisporus. B, Scanning electron micrograph of the surface of
a gill, showing basidia each bearing two spores, interspersed with sterile spacer cells,
paraphyses (P. T. Atkey). C, Light micrograph of a basidium bearing two spores (T. J.
Elliott). D, Spore print, made by slicing off the stalk of a fruit body, and laying the cap with
gills facing downwards on a surface. The discharged spores reproduce the pattern of the
gills (M. P. Challen). E, Germ-tubes emerging from spores (From Elliott, T. J. (1985). The

general biology of the mushroom. In Flegg, P. B., Spencer, D. M. & Wood, D. A., eds., The
Biology and Technology of the Cultivated Mushroom, pp. 9-22. Reprinted by permission
of John Wiley & Sons Ltd, Chichester.) F, Branching hyphae at the edge of a colony on
agar medium (T. J. Elliott). G, A colony covering a Petri dish. Prominent multihyphal
strands, radiating from the centre, are developing (Reproduced with permission from
Challen, M. P. & Elliott, T. J. (1987). Production and evaluation of fungicide resistant
mutants in the cultivated mushroom, Agaricus bisporus. Transactions of the British
Mycological Society 88, 433-439. (A-G reproduced by permission of Horticulture
Research International.)


instances from other plants. This concept of two kingdoms, animals and plants,
has dominated scientific classification from ancient times until quite recently.
At first it seemed that the fungi could be assigned without question to the plant
kingdom, since they are non-motile and draw their nourishment from the
substratum. During the nineteenth century it was realized, however, that the most
fundamental features of green plants are that they are phototrophs, utilizing
energy from light, and autotrophs, synthesizing their organic components from
atmospheric carbon dioxide. Animals on the other hand are chemotrophs,
obtaining energy from organic materials, and heterotrophs, utilizing the same
materials as the source of carbon for the synthesis of their own organic
components. On these fundamental metabolic criteria it is clear that fungi,
although non-motile, resemble animals rather than plants. Further problems were
created by studies on unicellular organisms, which revealed the existence of
numerous photosynthetic but motile forms, and of species which were obviously
closely related but differed from each other in that some ingested food and some
were photosynthetic. These and other problems led to criticism of the two
kingdom scheme and to various proposed alternatives, but a deep attachment to
the traditional idea of living organisms being divisible into plants and animals
dominated biology until a couple of decades ago.

A willingness to consider alternative schemes can be traced to progress in
knowledge of cell structure that resulted from electron microscopy in the period
1945-1960. It became clear that at the most fundamental level there are two
types of organism- not animals and plants, but those with cells that have a true
nucleus (eukaryotes) and those with cells that do not (prokaryotes). Differences in
cellular organization are so profound as to indicate a very early evolutionary
divergence of cellular organisms into prokaryotes and eukaryotes. Fungi, in their
cellular organization, are clearly eukaryotes.
Whittaker in 1969 proposed a five kingdom classification of organisms. The
prokaryotes were accepted as constituting one kingdom, the Monera, but the
eukaryotes, within which there is a far greater number of species and structural
diversity, were divided into four groups on nutritional and structural criteria.
Unicellular eukaryotes (protozoa and unicellular algae) were considered as a
single kingdom, the Protista. The multicellular eukaryotes, however, were
subdivided on the basis of nutrition into three kingdoms, the photosynthetic
plants (Plantae), the absorptive fungi (Fungi) and the ingestive animals
(Animalia).
This classification of fungi as one of five kingdoms of living organisms, all
with equal taxonomic status, was until recently a useful one. However, new
molecular and cladistic approaches (pages 281-286) have yielded a wealth of new
information about fundamental similarities and differences between organisms,
and these new approaches have been recognized as providing valid evidence for
interpreting evolutionary relationships. This has led to the discovery that at the
molecular level, life on earth can be classified into three groups, called domains,
of which two are prokaryotic and the third eukaryotic (Fig. 1.2). Fungi are now
recognized as one of five eukaryotic kingdoms, the others being Animalia
(animals), Plantae (plants), Chromista (corresponding roughly to the algae and
also known as Stramenopila) and Protozoa, which contains a wide variety of
mainly phagotrophic unicellular organisms.

Figure 1.2 A phylogenetic tree showing the relationships between the two Prokaryote
and five Eukaryote kingdoms. The kingdom Fungi consists solely of organisms regarded as
fungi, but there are phyla within the Chromista and Protozoa that either resemble fungi
(such as the Oomycota) or have been studied by mycologists (such as the Myxomycota).
The tree is an unrooted one (page 282), involving no assumptions about the point where
the common ancestor is situated, but indicating the amount of evolutionary change and
pattern of divergence. It is based on the extent of differences between the small sub-unit
ribosomal RNA sequences (page 326) for over 70 species. Note that the Fungi, Animals
(Animalia), Plants (Plantae) and Chromista form compact groups indicating relatively
close relationships compared with much greater evolutionary distances in the protozoa.
After Hawksworth, D. L. et al. (1995) Ainsworth & Bisby's Dictionary of the Fungi, 8th
edn. CAB International, Wallingford.

The Study of Fungi
Mycology, the study of fungi, arose as a branch of botany. As indicated earlier,
fungi were at one time considered to be members of the plant kingdom, and their
structure, life cycles and dispersal have received a great deal of attention from
scientists initially trained as botanists.
The microfungi are, however, microorganisms (microbes). Colonies of
microfungi in nature are usually of microscopic dimensions, and such organisms
can only be studied in detail by the methods of microbiology, separating them
from all other organisms and growing them in pure culture. The techniques
necessary for achieving and maintaining pure culture were developed by Robert
Koch in the late nineteenth century for the study of pathogenic bacteria, but were
soon applied to both micro- and macrofungi and were indeed essential for the
further development of mycology. Like most bacteria, the nutrition of fungi is


heterotrophic and absorptive, and in many environments microfungi and yeasts

are closely associated with bacteria and compete with them. Hence in many
investigations in microbial ecology it is essential for the activities of bacteria and
of fungi to receive equal attention. The similarities between bacteria and fungi as
regards the techniques needed for their study, their physiology and their ecology
are such that mycology can be considered as a branch of microbiology, and major
contributions to the study of fungi are now being made by microbiologists.
The fungi are relatively simple eukaryotes, and many species can be grown
easily in pure culture, with high growth rates and if necessary in large amounts.
These features have made them attractive research material for scientists whose
interest lies not in any specific group of organisms but in fundamental biological
processes such as the generation of energy, the control of metabolism and the
mechanisms of inheritance. Fungi have been the material with which many
fundamental biological discoveries have been made. For example, at the end of
the nineteenth century Buchner showed that yeast extracts could perform the
conversion of sugar into alcohol, a process previously known only as an activity
of the intact cell. The elucidation of the pathways involved was a major activity
of biochemistry during the first quarter of the twentieth century. During the
1940s studies on nutritional mutants of the mould Neurospora crassa by Beadle
and Tatum established the concept that an enzyme is specified by a gene, and
founded biochemical genetics. In the 1950s work by Pontecorvo on Aspergillus
nidulans, another mould, showed that genetic analysis could be carried out in the
absence of the sexual process, and the methods of genetic analysis developed with
this organism have subsequently been of great value in mapping human
chromosomes. Currently fungi are used as model organisms to study the structure
and function of genes. The sequencing of the genome of the yeast Saccbaromyces
cerevisiae, completed in 1996, contributed to a recognition that not only many
genes, but also their cellular functions, were common to animals and fungi. The
application of recombinant DNA technology to fungi, and their commonly
haploid state, in which a change in a gene is not concealed by the activity of a
dominant allele, increases the value of fungi for the analysis of fundamental

cellular processes. Fungi have hence been of great value to biochemists and
geneticists, who have in turn made important contributions to the study of fungi.
In addition to having a role in fundamental biological research, fungi are of
great practical importance. In most natural ecosystems there are fungi associated
with the roots of plants which help to take up nutrients from soil, and the
decomposition of plant litter by fungi is an essential part of the global carbon
cycle. Fungi cause some of the most important plant diseases, and hence receive
much attention from plant pathologists. Some cause disease in man and domestic
animals, so there are specialists in medical and veterinary mycology. Many cause
spoilage of food, damage manufactured goods or cause decay of timber. These
attract the attention of food microbiologists, experts in biodeterioration, and
timber technologists, respectively. Fungi also fulfil many roles beneficial to
humans. The larger fungi have been gathered for food from ancient times, but
now Agaricus bisporus and a variety of other species are cultivated, and a branch
of mycology termed mushroom science is seeking to improve the strains and
methods used. Yeasts have been used for thousands of years in brewing and
baking and the preparation of a variety of foods, and their study is a major aspect


of research in brewing science and in food technology. The metabolic versatility
of fungi is exploited by the fermentation industry, to make antibiotics and other
high value substances of interest to medicine, agriculture and the chemical
industry, to produce enzymes and to carry out specific steps in chemical processes.
Recent developments in recombinant DNA technology (genetic manipulation or
gene cloning) have led to fungi being used to produce hormones and vaccines
hitherto available only from mammalian sources. Fungi are likely to remain of
great practical as well as academic interest, and to attract the attention of
scientists trained in a variety of disciplines.

Further Reading and Reference

General Works on Fungi
Alexopoulos, C. J., Mims, C. W. & Blackwell, M. (1996). Introductory Mycology, 4th
edn. Wiley, Chichester.
Deacon, J. W. (1997). Introduction to Modern Mycology, 4th edn. Blackwell, Oxford.
Esser, K. & Lemke, P. (1993-). The Mycota. Springer-Verlag, Berlin.
Gow, N. A. R. & Gadd, G. M., eds. (1994). The Growing Fungus. Chapman & Hall,
London.
Gravesen, S., Frisvad, J. C. & Samson, R. A. (1994). Microfungi. Munksgaard,
Copenhagen.
Griffin, D. H (1994). Fungal Physiology, 2nd edn. Wiley-Liss, New York.
Hawksworth, D. L., ed. (1990). Frontiers in Mycology. CAB International, Wallingford.
Hawksworth, D. L., Kirk, P. M., Pegler, D. N. & Sutton, B. C. (1995). Ainsworth &
Bisby's Dictionary of the Fungi, 8th edn. CAB International, Wallingford.
Hudson, H. J. (1986). Fungal Biology. Arnold, London.
Ingold, C. T. & Hudson, H. J. (1993). The Biology of the Fungi, 6th edn. Chapman &
Hall, London.
Jennings, D. H. & Lysek, G. (1999). Fungal Biology: Understanding the Fungal Lifestyle,
2nd edn. Bios, Oxford.
Moore, D. (1998). Fungal Morphogenesis. Cambridge University Press, Cambridge.
Moore-Landecker, E. (1996). Fundamentals of the Fungi, 4th edn. Prentice-Hall, New
Jersey.
Oliver, R. P. & Schweizer, M., eds. (1999). Molecular Fungal Biology. Cambridge
University Press, Cambridge.
Webster, J. (1980). Introduction to Fungi, 2nd edn. Cambridge University Press,
Cambridge.

Prokaryotes, Eukaryotes and Major Groups of Microorganisms
Barr, D. J. S. (1992). Evolution and kingdoms of organisms from the perspective of a
mycologist. Mycologia 84, 1-11.
Carlile, M. (1982). Prokaryotes and eukaryotes: strategies and successes. Trends in

Biochemical Sciences 7, 128-130.
Gooday, G. W., Lloyd, D. & Trinci, A. P. J., eds. (1980). The Eukaryotic Microbial Cell.
Symposium of the Society for General Microbiology, Vol. 30. Cambridge University
Press, Cambridge.


Gouy, M. & Wen-Hsiung Li (1989). Molecular phylogeny of the kingdoms Animalia,
Plantae and Fungi. Molecular Biology and Evolution 6(2), 109-122.
Lederberg, J., ed. (2000). Encyclopedia of Microbiology, 2nd edn. Academic Press,
London.
Madigan, M. T., Martinko, J. M. & Parker, J. (2000). Brock's Biology of Microorganisms,
9th edn. Prentice-Hall, New Jersey.
Margulis, L. & Schwartz, K. V. (1998) Five Kingdoms: an Illustrated Guide to the Phyla
of Life on Earth, 3rd edn. Freeman, New York.
Margulis, L., Corliss, J. O., Melkonian, M. & Chapman, D. J., eds. (1989). Handbook of
Protoctista: the Structure, Cultivation, Habitats and Life Cycles of Eukaryotic
Microorganisms and their Descendants. Jones & Bartlett, Boston.
Postgate, J. (2000). Microbes and Man, 4th edn. Cambridge University Press, Cambridge.
Roberts, D. Mc. L., Sharp, P., Alderson, G. & Collins, M., eds. (1996). Evolution of
Microbial Life. Cambridge University Press, Cambridge.
Tudge, C. (2000). The Variety of Life. Oxford University Press, Oxford.
Whittaker, R. H. (1969). New concepts of kingdoms of organisms. Science 163, 150-160.

The Study of Fungi: Methodology
Hawksworth, D. L. & Kirsop, B. E., eds. (1988). Living Resources for Biotechnology:
Filamentous Fungi. Cambridge University Press, Cambridge.
Kirsop, B. E. & Doyle, A., eds. (1991). Maintenance of Microorganisms and Cultured
Cells, 2nd edn. Academic Press, London.
Kirsop, B. E. & Kurtzman, C. P., eds. (1994). Living Resources for Biotechnology: Yeasts,
2nd edn. Cambridge University Press, Cambridge.

Paterson, R. R. M. & Bridge, P. D., eds. (1994). Biochemical Techniques for Filamentous
Fungi. IMI Technical Handbooks 1. CAB International, Wallingford.
Smith, D. & Onions, A. H. S. (1994). The Preservation and Maintenance of Living Fungi,
2nd edn. Commonwealth Mycological Institute, Kew.
Stamets, P. (1993). Growing Gourmet and Medicinal Mushrooms. Ten Speed Press,
Berkeley.

The Study of Fungi: History
Ainsworth, G. C. (1976). Introduction to the History of Mycology. Cambridge University
Press, Cambridge.
Ainsworth, G. C. (1981). Introduction to the History of Plant Pathology. Cambridge
University Press, Cambridge.
Ainsworth, G. C. (1986). Introduction to the History of Medical and Veterinary
Mycology. Cambridge University Press, Cambridge.
Sutton, B. C., ed. (1996) A Century of Mycology. Cambridge University Press, Cambridge.

Journals and Serial Publications on Fungi and other Microbes
Advances in Microbial Ecology
Advances in Microbial Physiology
Annual Review of Microbiology
Annual Review of Phytopathology
Applied and Environmental Microbiology
Archives of Microbiology


Current Opinion in Microbiology
FEMS Microbiology Ecology
FEMS Microbiology Letters
FEMS Microbiology Reviews
Fungal Genetics and Biology

Journal of Bacteriology
Medical Mycology
Microbiological Reviews
Microbiology
Mycologia
Mycological Research
Mycologist
Mycorrhiza
Mycoses
Phytopathology
Studies in Mycology
Symposia of the British Mycological Society
Symposia of the Society for General Microbiology
Trends in Biochemical Sciences
Trends in Ecology and Evolution
Trends in Microbiology

Web sites
/>This site maintained at the University of Arizona incorporates molecular data as they
become available to present a continually developing phylogenetic tree for the
diversification of life throughout evolution. The Ascomycete and Basidiomycete branches
of the tree are illustrated by pictures of fungi in different groups, and references are given
to the scientific literature supporting the divergences within the tree.
/>This site at Cornell University provides an enormous collection of mycological links.
/>This is maintained by T. Volk of the University of Wisconsin and contains pictures of
hundreds of different fungal fruiting bodies with accompanying details of special points of
interest and biological significance of each.
www.THEFUNGI.com
A website maintained in connection with this book. Contains mycological links, images
and list of book contents.