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- Herausgeber: John Wiley & Sons
- Kategorie: Wissenschaft und neue Technologien
- Sprache: Englisch
Visit the accompanying website from the author at www.blackwellpublishing.com/deacon.
Fungal Biology is the fully updated new edition of this undergraduate text, covering all major areas of fungal biology and providing insights into many topical areas.
- Provides insights into many topical areas such as fungal ultrastructure and the mechanisms of fungal growth, important fungal metabolites and the molecular techniques used to study fungal populations.
- Focuses on the interactions of fungi that form the basis for developing biological control agents, with several commercial examples of the control of insect pests and plant diseases.
- Emphasises the functional biology of fungi, with examples from recent research.
- Includes a clear illustrative account of the features and significance of the main fungal groups.
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Contents
Preface
Chapter 1 Introduction: the fungi and fungal activities
The place of fungi in the “tree of life” – setting the scene
The characteristic features of fungi: defining the fungal kingdom
The major activities of fungi: pathogens, symbionts, and saprotrophs
Fungi in biotechnology
Online resources
General texts
Cited references
Chapter 2 The diversity of fungi and fungus-like organisms
Overview of the fungi and fungus-like organisms
The true fungi (Kingdom Mycota)
The fungus-like organisms
Online resources
Reference texts
Cited references
Chapter 3 Fungal structure and ultrastructure
Overview: the structure of a fungal hypha
Fungal ultrastructure
The hypha as part of a colony
The structure of yeasts
Fungal walls and wall components
Septa
The fungal nucleus
Cytoplasmic organelles
The cytoskeleton and molecular motors
Cited references
Chapter 4 Fungal growth
Apical growth of fungal hyphae
Spore germination and the orientation of hyphal tip growth
The yeast cell cycle
Kinetics of fungal growth
Commercial production of fungal biomass (Quorn™ mycoprotein)
Cited references
Chapter 5 Differentiation and development
Mould-yeast dimorphism
Infection structures of plant pathogens
Sclerotia
Nutrient-translocating organs
Asexual reproduction
Sexual development
Cited references
Chapter 6 Fungal nutrition
The nutrient requirements of fungi
The carbon and energy sources of fungi
Fungal adaptations for nutrient capture
The breakdown of cellulose: a case study of extracellular enzymes
Mineral nutrient requirements: nitrogen, phosphorus, and iron
Efficiency of substrate utilization
Fungi that cannot be cultured
General texts
Cited references
Chapter 7 Fungal metabolism and fungal products
How do fungi obtain energy in different conditions?
Coordination of metabolism: balancing the pathways
Mobilizable and energy storage compounds of fungi
Chitin synthesis
Lysine biosynthesis
Secondary metabolism
Cited references
Chapter 8 Environmental conditions for growth, and tolerance of extremes
Some introductory comments
Temperature and fungal growth
Hydrogen ion concentration and fungal growth
Oxygen and fungal growth
Water availability and fungal growth
Light
Cited references
Chapter 9 Fungal genetics, molecular genetics, and genomics
Overview: the place of fungi in genetical research
Neurospora and classical (mendelian) genetics
Structure and organization of the fungal genome
Genetic variation in fungi
Molecular approaches to population structure
Applied molecular genetics of fungi
And back to the genome
Expressed sequence tags and microarray technology
Online resources
General texts
Cited references
Chapter 10 Fungal spores, spore dormancy, and spore dispersal
General features of fungal spores
Spore dormancy and germination
Spore dispersal
Dispersal and infection behavior of zoospores
Zoospores as vectors of plant viruses
Dispersal of airborne spores
Air sampling devices and human health
Cited references
Chapter 11 Fungal ecology: saprotrophs
A theoretical model: the concept of life-history strategies
The biochemical and molecular toolbox for fungal ecology
A “generalized” decomposition sequence
The fungal community of composts
Fungal decomposers in the root zone
Fungal communities in decaying wood
Cited references
Chapter 12 Fungal interactions: mechanisms and practical exploitation
The terminology of species interactions
Antibiotics and their roles in species interactions
Antibiotics and disease control by Trichoderma species
Hyphal interference
Mycoparasites: fungi that parasitize other fungi
Competitive interactions on plants
Commensalism and mutualism
Online resources
General texts
Cited references
Chapter 13 Fungal symbiosis
The major types of symbiosis involving fungi
Mycorrhizas
Lichens
Geosiphon pyriforme
Fungus–insect mutualisms
Cited references
Chapter 14 Fungi as plant pathogens
The major types of plant-pathogenic fungi: setting the scene
Necrotrophic pathogens of immature or compromised hosts
Host-specialized necrotrophic pathogens
Vascular wilt diseases
Smut fungi
Fungal endophytes and their toxins
Phytophthora diseases
Biotrophic plant pathogens
Online resources
General texts
Cited references
Chapter 15 Fungal parasites of insects and nematodes
The insect-pathogenic fungi
The nematode-destroying fungi
Online resources
Cited references
Chapter 16 “The moulds of man”
Major fungal pathogens of humans and other mammals
Dermatophytic fungi
Opportunistic and incidental pathogens
Endemic dimorphic fungi
Pneumocystis species
Online resources
General texts
Cited references
Chapter 17 Principles and practice of controlling fungal growth
Control through the management of environmental and biological factors
Biological and integrated control
Chemical control of fungi
Principal cellular targets of antifungal agents
Fungicides used for plant disease control
Antifungal antibiotics used for plant disease control
Control of fungal infections of humans
Online resources
General texts
Cited references
Sources
Chapter 1
Chapter 2
Chapter 3
Chapter 4
Chapter 5
Chapter 6
Chapter 7
Chapter 8
Chapter 9
Chapter 10
Chapter 11
Chapter 12
Chapter 13
Chapter 14
Chapter 15
Chapter 16
Chapter 17
Systematic index
General index
© 2006 by J.W. Deacon© 1980, 1984, 1997 by Blackwell Publishing Ltd
BLACKWELL PUBLISHING350 Main Street, Malden, MA 02148-5020, USA9600 Garsington Road, Oxford OX4 2DQ, UK550 Swanston Street, Carlton, Victoria 3053, Australia
The right of J.W. Deacon to be identified as the Author of this Work has been asserted in accordance with the UK Copyright, Designs, and Patents Act 1988.
All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, electronic, mechanical, photocopying, recording or otherwise, except as permitted by the UK Copyright, Designs, and Patents Act 1988, without the prior permission of the publisher.
First edition published 1980Second edition published 1984Third edition published 1997Fourth edition published 2006 by Blackwell Publishing Ltd
1 2005
Library of Congress Cataloging-in-Publication Data
Deacon, J.W.
Fungal biology / J.W. Deacon.—4th ed
p. ; cm.
Rev. ed. of: Modern mycology. 3rd ed. 1997.
Includes bibliographical references and index.
ISBN-13: 978-1-4051-3066-0 (pbk. : alk. paper)
ISBN-10: 1-4051-3066-0 (pbk. : alk. paper)
1. Mycology. 2. Fungi.
[DNLM: 1. Fungi. 2. Mycology. QK 603 D278i 2006] I. Deacon, J.W.
Modern mycology. II. Title.
QK603.D4 2006579.5—dc22
2005004137
A catalogue record for this title is available from the British Library.
For further information onBlackwell Publishing, visit our website:www.blackwellpublishing.com
Preface
Fungal Biology (4th edition) is the successor to three previous editions of “Modern Mycology.” The text has been fully updated and expanded to cover many new developments in fungal biology. Each of the 17 chapters is largely independent, with a clear theme and crossreferencing, so that the text can be used to focus on selected topics.
The early chapters deal with the unique structure and organization of fungi and fungus-like organisms, including modern experimental approaches in fungal biology, and the many ways in which fungi respond to environmental cues. These chapters also cover the diversity of fungi, and fungal products including immunosuppressants, antibiotics, and mycotoxins that contaminate food.
Recent developments in fungal genetics, molecular genetics, and genomics are discussed within the framework of a “biochemical and molecular toolbox,” using in-depth examples such as the roles of viruslike double-stranded RNA for the control of chestnut blight, and the population dynamics of Dutch elm disease. Major sections of the text deal with the development of fungi as commercial biological control agents of plant pathogens and insect pests. In addition, one of the three new chapters deals with the symbiotic associations of fungi with plants and animals, and the biology of lichens. Plant pathogens and plant defense also are covered in depth, using selected examples of all the major pathosystems.
Two final chapters are devoted to the “moulds of man,” covering the biology, pathogenicity, and virulence factors of the major fungal diseases of humans, and the antifungal drugs used to treat these conditions.
This text is designed to appeal to both undergraduates and postgraduates. The emphasis throughout is on the functional biology of fungi, with several examples from recent research, and many tables and illustrations. The text is supported by a comprehensive website (available via www.blackwellpublishing.com/deacon), with over 600 images, many in color, including “Special Focus Topics” and “Profiles of Significant or Interesting Fungi.” My own images are identified, and can be used freely, without restriction. The website also has a large interactive (randomized) test bank of multiplechoice questions, designed to aid self-assessment and reinforcement of key learning outcomes.
I wish to thank many colleagues who have contributed to this book by providing images and resources. They include many of my doctorate students, and Nick Read’s research group at the University of Edinburgh, who have been supportive throughout.
Jim DeaconEdinburgh
Chapter 1
Introduction: the fungi and fungal activities
The place of fungi in the “tree of life” – setting the scene
Carl Woese of the University of Illinois at Urbana-Champaign, USA, has championed the use of molecular phylogenetics. The basis of this is to identify genes that are present in all living organisms and that have an essential role, so they are likely to be highly conserved, accumulating only small changes (mutations and back mutations) over large spans of evolutionary time. Comparisons of these sequences can then indicate the relationships between different organisms. There are limitations and uncertainties in this approach, because of the potential for lateral gene transfer between species and because there are known to be variable rates of gene evolution between different groups of organisms. However several highly conserved genes and gene families can be used to provide comparative data.
Most phylogenetic analyses are based primarily on the genes that code for the production of ribosomal RNA. Ribosomes are essential components of all living organisms because they are the sites of protein synthesis. They occur in large numbers in all cells, and they are composed of a mixture of RNA molecules (which have a structural role in the ribosome) and proteins. In prokaryotes (non-nucleate cells) the ribosomes contain three different size bands of ribosomal RNA (rRNA), defined by their sedimentation rates (S values, also known as Svedberg units) during centrifugation in a sucrose solution. These three rRNAs are termed 23S, 16S, and 5S. In eukaryotes (nucleate cells) there are also three rRNAs (28S, 18S, and 5.8S). The genes encoding all of these rRNAs are found in multiple copies in the genome, and the different rRNA genes can be used to resolve differences between organisms at different levels.
For most phylogenetic analyses the genes that code for 16S rRNA (of prokaryotes) and the equivalent 18S rRNA (of eukaryotes) are used. These small subunit rDNAs contain enough information to distinguish between organisms across the phylogenetic spectrum. Using this approach, several different phylogenetic trees have been generated, but many of them are essentially similar, and one example is shown in Fig. 1.1.
Several points arise from Fig. 1.1, both in general terms and specifically relating to fungi.
Ribosomal DNA sequence analysis clearly demonstrates that there are three evolutionarily distinct groups of organisms, above the level of kingdom. These three groups – the
Bacteria, Archaea
, and
Eucarya
(eukaryotes) – are termed
domains
and the differences between them are matched by many differences in cellular structure and physiology.
Beneath the level of domains, there is still uncertainty about the taxonomic ranks that should be assigned to organisms. Plants, animals, and fungi are almost universally regarded as separate
kingdoms
(Whittaker 1969). But, arguably, this status could also apply to the many “kingdoms” of bacteria, especially the enormous
Proteobacteria
kingdom which includes most Gram-negative bacteria. And, it could be argued that the many separate groups of unicellular eukaryotes (amoebae, slime moulds, flagellates, etc.) should also be regarded as kingdoms, based on their apparently long-term separation as judged by rDNA sequence divergence. However, many of these lower eukaryotes are still poorly studied, so they are often referred to collectively as “protists,” pending further resolution of their relationships.
The major multicellular organisms – the
animals, plants
, and
fungi
– form a cluster at the very top of the Eucarya Domain, so they are often termed the “
crown eukaryotes
”. The interesting feature of these groups is that they seem to have diverged from one another at roughly the same time, and then underwent a major, rapid expansion and diversification. The time when this happened,
roughly half a billion years ago
, coincides with the period when the land surfaces were colonized by primitive plants such as bryophytes (mosses and liverworts) and when there were only three major continental land masses: (i) a land mass including present-day North America and Europe, located near the equator; (ii) part of modern Siberia, towards the north; (iii) a land mass consisting of present-day South America, Africa, Antarctica, India, and Australia in the southern hemisphere.
Currently, the earliest
fossil evidence of fungi
dates to the Ordovician period, between 460 and 455 million years ago, but it is almost certain that aquatic fungi would have been present before that time, perhaps dating back to about 1 billion years ago. The Chytridiomycota are widely believed to be among the most ancient of the presently known fungi – not least because they have motile flagellate cells, indicating their dependence on free water. By contrast, in the Devonian period (417–354 million years ago) there is abundant evidence of fossil fungi associated with primitive land plants. For example, representatives of several major groups of fungi have been found in the Rhynie Chert deposits of Aberdeenshire, Scotland, representing the Devonian era. The early fossil fungi of the Rhynie deposits are very well preserved and, intriguingly, occur in close association with the underground organs of early land plants. These early terrestrial fungi, belonging to a newly defined group, the Glomeromycota (see
Fig. 2.4
), are remarkably similar to the arbuscular mycorrhizal fungi that colonize the roots of nearly 80% of present-day land plants (
Fig. 1.2
). So it seems that these fungi co-evolved with early land plants, and that their hyphae could have facilitated the uptake of mineral nutrients and water from soil, just as they do today (Lewis 1987; Chapter 13).
Having made the case for a long-term association between fungi and land plants, we need to correct a widely held misconception: there is now
strong evidence that fungi are more closely related to animals than to plants
(Baldauf & Palmer 1993). The fungi evolved as an early branch from the animal lineage, and both groups probably have a common origin in one of the simple unicellular eukaryotes. Currently it is believed that the most likely common ancestor of both the fungal and the animal kingdoms is a protozoan of the group termed choanoflagellates, also known as the collar-flagellates (
Fig. 1.3
). These resemble both the earliest branch of animals (the sponges) and the earliest branch of fungi (the chytrids). It is a humbling thought that humans should have evolved from something like this!
Fig. 1.1 A representation of the Universal Phylogenetic Tree, based on comparisons of the genes encoding smallsubunit (16S or 18S) ribosomal RNA. The lengths of the lines linking organisms to their nearest branch point represent inferred evolutionary distances (rRNA gene sequence divergence). (Based on a diagram in Woese (2000) but showing only a few of the major groups of organisms.)
Fig. 1.2 (a) A present-day “club-moss,” Lycopodium, which represents a primitive member of the ferns (pteridophytes), and (b,c) two fossil pteridophytes (Asteroxylon mackiei, and Rhynia major) from the Rhynie chert deposits. (d) Swollen vesicles of a presentday mycorrhizal fungus are remarkably similar to vesicles found in fossils from the Rhynie deposits (417–354 million years ago).
Fig. 1.3Codosiga gracilis, a member of the choanoflagellates (organisms with a single flagellum and a collar), considered to be the common ancestors of both fungi and animals. (Based on a drawing from: http://microscope.mbl.edu/scripts/microscope.php?func=imgDetai l&imageID=4575)
The characteristic features of fungi: defining the fungal kingdom
To begin this section we must make an important distinction between the true fungi and a range of fungus-like organisms that have traditionally been studied by mycologists, but are fundamentally different from fungi. Here we will focus on the true fungi, often termed the Mycota or Eumycota. We will discuss the fungus-like organisms in Chapter 2.
All true fungi have a range of features that clearly separate them from other organisms and that serve to define the fungal kingdom (Mycota). These features are outlined below:
All fungi are
eukaryotic
. In other words, they have membrane-bound nuclei containing several chromosomes, and they have a range of membranebound cytoplasmic organelles (mitochondria, vacuoles, etc.). Other characterisitics, shared by all eukaryotes, include: cytoplasmic streaming, DNA that contains noncoding regions termed introns, membranes that typically contain sterols, and ribosomes of the 80S type in contrast to the 70S ribosomes of bacteria (“S” refers to Svedberg units, as mentioned earlier).
Fungi typically grow as filaments, termed
hyphae
(singular: hypha), which extend only at their extreme tips. So, fungi exhibit
apical growth
in contrast to many other filamentous organisms (e.g. filamentous green algae) which grow by repeated cell divisions within a chain of cells (intercalary growth). Fungal hyphae branch repeatedly behind their tips, giving rise to a network termed a
mycelium
. However, some fungi grow as single-celled yeasts (e.g.
Saccharomyces cerevisiae
) which reproduce by budding, and some can switch between a yeast phase and a hyphal phase in response to environmental conditions. These
dimorphic fungi
(with two shapes) include several species that are serious pathogens of humans (Chapter 16). They often grow as yeast-like cells for proliferation in the body fluids but convert to hyphae for invasion of the tissues (
Fig. 1.4
).
Fungi are
heterotrophs
(chemo-organotrophs). In other words, they need preformed organic compounds as energy sources and also as carbon skeletons for cellular synthesis. The cell wall prevents fungi from engulfing food by phagocytosis, so fungi absorb simple, soluble nutrients through the wall and cell membrane. In many cases this is achieved by secreting enzymes at the hyphal tips to degrade complex polymers and then absorbing the simple, soluble nutrients released by the depolymerase (polymer-degrading) enzymes.
Fungi have a distinctive range of
wall components
, which typically including
chitin
and
glucans
(polymers of glucose with predominantly β-1,3 and β-1,6 linkages). Short lengths of cellulose (a β-1,4-linked polymer of glucose) have been detected in some fungal walls, especially in some of the primitive fungi. However fungi differ from plants because they do not have cellulose-rich cell walls.
Fungi have a characteristic range of soluble carbohydrates and storage compounds, including
mannitol
and other sugar alcohols,
trehalose
(a disaccharide of glucose), and glycogen. These compounds are similar to those of some animals – notably the arthropods – but are different from those of plants.
Fungi typically have
haploid nuclei
– an important difference from almost all other eukaryotes. However, fungal hyphae often have several nuclei within each hyphal compartment, and many budding yeasts are diploid. These differences in nuclear status and nuclear arrangements have important implications for fungal genetics (Chapter 9).
Fungi reproduce by both sexual and asexual means, and typically produce
spores
. Fungal spores vary enormously in shape, size and other properties, related to their various roles in dispersal or dormant survival (Chapter 10).
Fig. 1.4Candida albicans, a common dimorphic fungus that grows on the mucosal membranes of humans. Normally it is found as a budding yeast (a), but the yeast cells can produce hyphae (b) for invasion of the tissues.
In summary, we can define fungi by the following characteristic features (Table 1.1):
eukaryotic
typically grow as hyphae, with apical growth, but sometimes as yeasts
heterotrophic – they depend on pre-formed organic nutrients
typically have a haploid genome
have walls composed primarily of chitin and glucans
absorb soluble nutrients through the cell wall and plasma membrane
produce spores.
Table 1.1 Comparison of some features of fungi with those of animals and plants.
The major activities of fungi: pathogens, symbionts, and saprotrophs
As we have already seen, all fungi require organic nutrients for their energy source and as carbon nutrients for cellular synthesis. But a broad distinction can be made according to how these nutrients are obtained: (i) by growing as a parasite (or a pathogen – a disease-causing agent) of another living organism; (ii) by growing as a symbiont in association with another organism; or (iii) by growing as a saprotroph (saprophyte) on nonliving materials. These topics are covered in detail in Chapters 11–14.
Fungal parasites of plants
The fungal (or fungus-like) parasites of plants are enormously significant, accounting for more than 70% of all the major crop diseases, and for many devastating epidemics. To cite just a few examples:
Potato blight caused by the fungus-like organism
Phytophthora infestans
destroyed the potato crops of Ireland in the 1840s, leading to the starvation of up to one million people, and large-scale emigration to the rest of Europe and the USA. Even today the control of
P. infestans
and its close relatives, the downy mildew fungi, accounts for about 15% of world fungicide sales.
The Advance of the Fungi
by E. C. Large (1940) provides a fascinating and highly readable account of potato blight and its legacy.
Dutch elm disease, caused by
Ophiostoma novo-ulmi
and
O. ulmi
(Chapter 10), has destroyed most of the common elm (
Ulmus procera
) trees in Britain and Western Europe in the last 30 years, as it did in North America earlier in the 1900s. Similarly, chestnut blight caused by the fungus
Cryphonectria parasitica
(Chapter 9) has devastated the native American chestnut (
Castanea dentata
) population in the USA – an epidemic that can be traced to the first recorded diseased chestnut tree in the New York Zoological Garden in 1904 (Chapter 9). And, at the time of writing, a new species of
Phytophthora
(
P. ramorum
) is causing sudden oak death in southwestern USA and has already spread to several parts of Europe (Chapter 14).
Fungal symbionts of plants
Many fungi form symbiotic associations with plants, in which both of the partners are likely to benefit. The two most important examples are lichens and mycorrhizas. Lichens are intimate associations between two organisms – a photosynthetic partner (a green alga or a cyanobacterium) and a fungus – which together produce a thallus that can withstand some of the most inhospitable environments on Earth (Fig. 1.5). Typically, the fungus encases and protects the photosynthetic cells, and also absorbs mineral nutrients from trace levels in the environment, while the photosynthetic partner provides the fungus with carbon nutrients. There are about 13,500 lichen species across the globe, and they play essential roles as pioneer colonizers of habitats where no other organisms can grow, including rock surfaces and unstable, arid mineral soils (Chapter 13).
Mycorrhizas are intimate associations between fungi and the roots or other underground organs of plants. There are many types of mycorrhizal fungi, which have evolved independently of one another and which serve different roles. In almost all cases these fungi depend on the plant for a supply of carbon nutrients, while the plants depend on the fungi for a supply of mineral nutrients (phosphorus, nitrogen) from the soil. As we will see in Chapter 13, phosphorus is often the critical limiting factor for plant growth, because soil phosphates rapidly form insoluble complexes with organic matter or with divalent cations (Ca2+, Mg2+) and cannot easily diffuse to the plant roots. Mycorrhizal fungi help to alleviate this problem by providing an extensive hyphal network for capturing mineral nutrients and transporting them back to the roots. However, some other mycorrhizal fungi serve a quite different role. Orchids and some nonphotosynthetic plants are absolutely dependent on fungi for all or part of the plant’s life, because the plant feeds on sugars supplied by a soil fungus.
Lichens and mycorrhizas are not the only examples of symbiosis. In recent years many plants have been found to harbor symptomless endophytic fungi within the plant walls or intercellular spaces. These fungi apparently do no harm to the plants. Instead they can be beneficial because they help to activate plant defense genes and produce insect anti-feedant compounds such as the ergot alkaloids. But this is a double-edged sword, because the toxins can cause serious damage to grazing animals such as horses, cattle, and sheep (Chapter 11).
Fungal pathogens of humans
In contrast to the many fungal parasites of plants, there are only some 200 fungi that infect humans or other warm-blooded animals. In fact, humans have a high degree of innate immunity to fungi, with the exception of the dermatophytic fungi which commonly cause infections of the skin, nails, and hair. However, the situation changes drastically when the immune system is compromised, and this is becoming common in patients with AIDS, transplant patients whose immune system is purposefully suppressed, patients suffering from cancer or advanced diabetes, and patients undergoing prolonged corticosteroid therapy. In any of these circumstances there is a significant chance of infection from fungi that pose no serious threat to healthy people. For example, the widespread and extremely common airborne fungus Aspergillus fumigatus normally grows on composts and in soil, but it has become one of the most significant invasive fungi in deep surgical procedures, and the survival rate can be as low as 30%. Many other fungi that can grow at 37°C have spores that are small enough to enter the lungs and reach the alveoli. These fungi were virtually unknown until recently but are now extremely common causes of infection in immunodeficient patients. For example, the fungus-like organism Pneumocystis jiroveci (previously named P. carinii) commonly causes pneumonia in patients infected with the human immunodeficiency virus (HIV). The onset of this disease in patients with HIV is regarded as one of the “AIDS-defining” symptoms.
Fig. 1.5 A sign in Arches National Park, Utah, USA. Get your boots off our microbes!
Only a handful of antifungal drugs are available to treat the major human mycoses, and most need to be administered at low doses over a prolonged time to avoid excessive toxicity. Many of these drugs are expensive so they offer little hope to the poorest people in the developing world. Chapter 16 is devoted to the mycoses of humans, and Chapter 17 deals with the drugs available to treat these conditions.
Fungal parasites as biological control agents
Fungi parasitize many types of host, including other fungi (mycoparasites, Chapter 12), insects (entomopathogens, Chapter 15), and nematodes (nematophagous fungi, Chapter 15). In the past, such fungi might have been regarded as curiosities, but now they are recognized as being significant population regulators of their hosts and as potential biological control (biocontrol) agents of major pests or plant pathogens. We discuss biocontrol at many points in this book, notably in Chapters 12 and 17.
Fungal saprotrophs
Fungi are particularly important in the decomposition of cellulose, which represents about 40% of plant cell wall material and is the most abundant natural polymer on Earth. Grazing animals (ruminants) also consume significant amounts of cellulose, but this is broken down in the rumen (in effect, a large anaerobic fermentation vessel) and the rumen fungi are thought to play a significant role in the decomposition process. The breakdown of polymers by fungi is intimately linked to hyphal growth which provides both penetrating power and the coordinated release of extracellular enzymes and subsequent reabsorption of the enzymic breakdown products (Chapter 6). But different fungi are adept at degrading different types of polymer, so fungal saprotrophs often grow in complex, mixed communities reflecting their different enzymic capabilities (Chapter 11).
Although the decomposer fungi play vital roles in the recycling of major nutrients, they can also be significant spoilage agents. A well-known example is the dry-rot fungus, Serpula lacrymans, which is a major cause of timber decay in buildings (Chapter 5). Similarly the “sooty moulds” that commonly grow on kitchen and bathroom walls are extremely difficult to eradicate (Fig. 1.6). They utilize the soluble cellulose gels that are used as stabilizers in emulsion paints or as wallpaper pastes. These common fungi include species of Alternaria, Cladosporium and Sydowia polyspora (previously called Aureobasidium pullulans) which discolor the walls because of their darkly pigmented hyphae and spores. However, their natural habitat is the surface of leaves or the decaying stalk tissues of plants, and they occur in buildings only because they find similar conditions (and substrates) to those in their natural environment (Chapter 8). Public health authorities are now paying increasing attention to safety in the workplace, and particularly to the potential roles of fungi in “sick building syndrome,” which has been linked (tenuously) to infant cot death. The conditions in underventilated buildings can certainly promote the growth of moulds, including Stachybotrys chartarum, another common sooty mould. But there is no definitive evidence to link these fungi to sick building syndrome.
Fig. 1.6 Part of a bathroom ceiling where the paint has flaked away, revealing extensive growth and sporulation of sooty moulds.
Some saprotrophic fungi pose a serious threat to human and animal welfare by growing on stored food products and producing mycotoxins. These are a diverse range of fungal secondary metabolites, often found in improperly stored materials. For example, aflatoxins are commonly produced in groundnuts and cottonseed meal. They are among the most potent known carcinogens and are strongly implicated in hepatomas. Similarly, the toxins produced by several Fusarium species on grain crops are implicated in esophageal cancer in Africa, and in kidney carcinomas. The pathways leading to the production of these compounds are discussed in Chapter 7; the maintenance of safe storage conditions is covered in Chapter 8.
Fungi in biotechnology
Fungi have many traditional roles in biotechnology, but also some novel roles, and there is major scope for their future commercial development (Wainwright 1992). Some of these roles are outlined below.
Foods and food flavorings
In 1994 the total world production of edible mushrooms was estimated to be over 5 million tonnes, with a value of US $14 billion. Much of the mushroom-growing industry is based on strains of the common cultivated mushroom Agaricus bisporus (or A. brunnescens) discussed in Chapters 5 and 11. But Lentinula edodes (the Shiitake mushroom, which is grown on logs; Fig. 1.7), Volvariella volvacea (the padi straw mushroom, which is grown on rice straw), and Pleurotus ostreatus (the oyster mushroom, Fig. 1.8) are traditionally grown in Japan and southeast Asia, and are now widely available in western supermarkets.
Fig. 1.7 (a,b) Commercial culture of the shiitake mushroom, Lentinula edodes, on inoculated logs. (Courtesy of Robert L. Anderson (photographer) and USDA Forest Service; www.forestryimages.org)
Fungi are used to produce several traditional foods and beverages, including alcoholic drinks (ethanol from the yeast Saccharomyces cerevisiae) and bread, where the yeast produces CO2 for raising the dough. Penicillium roqueforti is used in the later stages of production of the blue-veined cheeses such as Stilton and Roquefort, to which it imparts a characteristic flavor. P. camemberti is used to produce the soft cheeses such as Camembert and bries; it grows on the cheese surface, forming a “crust,” and produces proteases which progressively degrade the cheese to give the soft consistency. Less well known but equally significant is the role of fungi in the fermentation of traditional foods around the world. For example, Rhizopus oligosporus is used to convert cooked soybean “grits” to a nutritious staple food, called tempeh (Fig. 1.8). This involves only a short (24–36 hour) incubation time, during which the fungus degrades some of the fat and also degrades a trypsin inhibitor in soybeans, so that the naturally high protein content of this crop is more readily available in the diet, and a “flatulence factor” is broken down during this process. The food termed gari is part of the staple diet in southern Nigeria; it is produced from the high-yielding root crop, cassava, perhaps better known in its processed form, tapioca. Raw cassava contains a toxic cyanogenic glycoside termed linamarin, which is removed during a prolonged and largely uncontrolled fermentation in village communities. Much of this process involves bacteria, but the fungus Galactomyces geotrichum (asexual stage: Geotrichum candidum) gives the product its desired flavor. Details of the production of several traditional Asian fermented foods can be found in Nout & Aidoo (2002).
A major development in recent years has been the introduction of an entirely new type of food, termed Quorn™ mycoprotein (Fig. 1.9). This is produced commercially by growing a fungus (Fusarium venanatum) in large fermentation vessels, then harvesting the fungal hyphae and processing them into meat-like chunks and various oven-ready meals. Quorn (as it is now called) is widely available in British and European supermarkets. It has an almost ideal nutritional profile, with a high protein content, low fat content, and absence of cholesterol (Table 1.2). The production of Quorn is discussed in detail in Chapter 4.
Fungal metabolites
Metabolites can be grouped into two broad categories (Chapter 7):
Primary metabolites
: the intermediates or end products of the common metabolic pathways of all organisms (sugars, amino acids, organic acids, glycerol, etc.) and which are essential for the normal cellular functions of fungi.
Secondary metabolites
: a diverse range of compounds formed by specific pathways of particular organisms; they are not essential for growth, although they can confer an advantage to the organisms that produce them (e.g. antibiotics, fungal toxins, etc.).
Fig. 1.8 (a) A tray of exotic mushrooms from a supermarket in the UK, including shiitake (centre) and the oyster mushroom, Pleuotus ostreatus, reputed to be an aphrodisiac. (b) An attempt to produce a homemade cake of tempeh, which tasted only marginally better than it looks.
Table 1.2 Nutritional composition of Quorn™ mycoprotein, compared with traditional protein sources. (Data from Trinci 1992.)
Fig. 1.9 Quorn: (a) the package and (b) one of several products: “Fillets in a Mediterranean marinade with tomato, red wine, and herbs.”
Several metabolites of both groups are produced commercially from fungal cultures (Turner 1971; Turner & Aldridge 1983). One of the best examples of a fungal primary metabolite is citric acid, with an estimated global production of 900,000 tons in the year 2000 (Ruijter et al. 2002). Citric acid produced on this vast scale is the mainstay of the soft drinks industry (lemonade, etc.) because it has a tart taste and also enhances flavor, reduces sweetness, and has antioxidant and preservative qualities. Specially selected, overproducing strains of Aspergillus niger are used for the commercial production of citric acid, but several other conditions are necessary – the cultures must contain high levels of readily metabolizable sugars (up to 20% or more) and the concentration of either phosphate or nitrogen must be kept low, to limit the amount of fungal growth. In these conditions 80% or more of the sugar supplied to the cultures is converted into citric acid, which is then exported from the cells and accumulates in the culture medium. The effect of this is to lower the pH of the culture medium to 3.0 or less, which the fungus tolerates well. This secretion of the acid is a crucial feature, because fungal cells tightly regulate their internal pH. Recent evidence indicates that cells of A. niger maintain their intracellular pH at 7.7 when the cells are exposed to external pH levels ranging from 1.5 to 6.
Other organic acids are produced commercially by fungal fermentations. Gluconic acid (estimated annual global production of 50,000–100,000 tons) is used mainly as a food additive, and is produced by specific strains of A. niger, grown at normal pH. This acid is produced by the direct oxidation of glucose, catalyzed by the enzyme glucose oxidase. Itaconic acid (global production 70,000–80,000 tons) is produced by Aspergillus terreus and is used as a co-polymer in the manufacture of paints, adhesives, etc.
Table 1.3 Some valuable secondary metabolites produced commercially from fungi.
Metabolite
Fungal source
Application
Penicillins
Penicillium chrysogenum
Antibacterial
Cephalosporins
Acremonium chrysogenum
Antibacterial
Griseofulvin
Penicillium griseofulvum
Antifungal
Fusidin
Fusidium coccineum
Antibacterial
Ciclosporins
Tolypocladium spp
.
Immunosuppressants
Zearalenone
Gibberella zeae
Cattle growth promoter
Gibberellins
Gibberella fujikuroi
Plant hormone
Ergot alkaloids and related compounds
Claviceps purpurea related fungi
and
Many effects including: antimigraine, vasoconstriction, vasodilation, antihypertension, anti-Parkinson, psychiatric disorders
In some respects the production of citric acid and itaconic acid is similar to the production of ethanol by Saccharomyces spp. – the basis of the alcoholic drinks industry. Both types of product accumulate in the culture medium when growth is restricted by some factor but when the biochemical machinery continues to operate, like the engine of a car taken out of gear. For example, ethanol accumulates as a metabolic endproduct when yeast is grown in a sugar-rich medium favoring metabolism, but in anaerobic conditions that limit cell growth.
In contrast to the bulk metabolites mentioned above, a vast range of secondary metabolites are produced by fungi, and they include several high-value products with pharmaceutical applications. A small selection of these is shown in Table 1.3. The best-known examples are the penicillins – a group of structurally related β-lactam antibiotics that are synthesized naturally from small peptides. As explained in Chapter 7, the naturally occurring penicillins such as penicillin G (produced by Penicillium chrysogenum) have a relatively narrow spectrum of activity. But a wide range of other penicillins can be produced by chemical modification of the natural penicillins. All modern penicillins are semisynthetic compounds; they are obtained initially from fermentation cultures but are then structurally modified for specific desirable properties. Schmidt (2002) reviewed the manufacture and therapeutic aspects of β-lactam antibiotics, including the cephalosporins which are structurally related to the penicillins. Remarkably, despite their age (the penicillins were first produced commercially in the late 1940s), the β-lactam antibiotics still share 50% of the world market for systemic antibiotics, with sales in 1998 worth about US $4 billion for penicillins and about US $7 billion for the more recently developed cephalosporins.
Several non-β-lactam antibiotics are also produced by fungi. They include griseofulvin (from the fungus P. griseofulvum) which has been used for several years to treat dermatophyte infections of the skin, nails and hair of humans, although recently it has been replaced by less toxic drugs (Chapter 17). Fusidic acid (from various fungi) has been used to control staphylococci that have become resistant to penicillin, and there is renewed interest in a range of other natural fungal products for treating the systemic fungal infections of humans (Chapter 17). Ciclosporins from various fungi (but principally from species of Tolypocladium) are used as immunosuppressants to prevent organ rejection in transplant surgery. In fact, 17 different fungal taxa are reported to produce ciclosporins. Another powerful immunosuppressant is the antibiotic gliotoxin (from Trichoderma virens), which is better known for its role in biological control of plant pathogenic fungi (Chapter 12). The production and use of these immunosuppressants was reviewed by Kürnsteiner et al. (2002). As a final example, the ergot alkaloids and related toxins of the ergot fungus, Claviceps purpurea (Chapter 14), have many important pharmacological applications (Keller & Tudzynski 2002). The fourmembered ring structure of the D-lysergic acid derivatives of ergot alkaloids mimic the ring structures of neurotransmitters (dopamine, epinephrine (adrenaline), and serotonin: Fig. 1.10). However, at present many of the ergot derivatives are too nonspecific in their modes of action to meet their true potential in treating human disorders.
Even these few examples raise fascinating questions about the roles of fungal secondary metabolites. What functions do they serve in fungi and what competitive advantage do they confer? In recent years many of the genes encoding the secondary biosynthetic pathways have been identified and sequenced. This should lead both to an understanding of their roles and to the potential construction of transgenic strains that overproduce valuable metabolites.
Some of the polysaccharides of fungi have potential commercial value. Pullulan is an α-1,4-glucan (polymer of glucose) produced as an extracellular sheath by Sydowia polyspora (formerly Aureobasidium pullulans), one of the sooty moulds. This polymer is used in Japan to make a film-wrap for foods. A potential new market could develop from the discovery that fungal wall polymers or their partial breakdown products can be powerful elicitors of plant defense responses (Chapter 14) so they might be used to “immunize” plants. For example, the β-glucan fractions from walls of the yeast S. cerevisiae have this effect. So too does chitosan, the de-acetylated form of chitin in fungal cell walls (chapters 3 & 7). At present, chitosan is used on a large scale in Japan for clarifying sewage, but the source of this chitosan is crustacean shells. Fungi are an alternative, easily renewable source of this and other polymers.
Enzymes and enzymic conversions
Saprotrophic fungi and some plant-pathogenic fungi produce a range of extracellular enzymes with important commercial roles (Table 1.4). The pectic enzymes of fungi are used to clarify fruit juices, a fungal amylase is used to convert starch to maltose during breadmaking, and a fungal rennet is used to coagulate milk for cheese-making. A single fungus, Aspergillus niger, accounts for almost 95% of the commercial production of these and other bulk enzymes from fungi, although specific strains of the fungus have been selected for particular purposes. The methanol-utilizing yeasts (Candida lipolytica, Hansenula polymorpha, and Pichia pastoris) have potential commercial value because they produce large amounts of alcohol oxidase, which could be used as a bleaching agent in detergents. The wood-rotting fungus Phanerochaete chrysosporium is extremely active in degrading lignin; it has the potential to be developed for delignification of agricultural wastes and byproducts of the wood-pulping industry, so that the cellulose in these materials could be used as a cheap substrate for production of fuel alcohol by yeasts (Chapter 11).
Fig. 1.10 Structural similarities between three neurotransmitters (dopamine, noradrenaline, and serotonin) and the D-lysergic acid derivatives of ergot alkaloids.
Table 1.4 Some fungal enzymes produced commercially. (Based on Wainwright 1992.)
Enzyme
Fungal source
Application
α-Amylase
Aspergillus niger, A. oryzae
Starch conversions
Amyloglucosidase
A. niger
Starch syrups, dextrose foods
Pullulanase
Aureobasidium pullulans
Debranching of starch
Glucose aerohydrogenase
A. niger
Production of gluconic acid
Proteases (acid, neutral, alkaline)
Aspergillus spp. etc.
.
Breakdown of proteins (baking, brewing, etc.)
Invertase
Yeasts
Sucrose conversions
Pectinases
Aspergillus, Rhizopus
Clarifying fruit juices
Rennet
Mucor spp.
Milk coagulation
Glucose isomerase
Mucor, Aspergillus
High fructose syrups
Lipases
Mucor, Aspergillus, Penicillium
Dairy industry, detergents
Hemicellulase
A. niger
Baking, gums
Glucose oxidase
A. niger
Food processing
In addition to these examples of “bulk” enzymes, fungi have many internal enzymes and enzymic pathways that can be exploited for the bioconversion of compounds such as pharmaceuticals. For example, fungi are used for the bioconversion of steroids, because fungal enzymes perform highly specific dehydrogenations, hydroxylations and other modifications of the complex aromatic ring systems of steroids. Precursor steroids are fed to a fungus, held at low nutrient level either in culture or attached to an inert bed, so that the steroid is absorbed, transformed and then released into the culture medium from which it can be retrieved.
Heterologous gene products
Genetic engineering of fungi, particularly Saccharomyces cerevisiae, has developed to the stage where the cells can be used as factories to produce pharmaceutical products, by the introduction of foreign (heterologous) genes, as we already noted for the hepatitis B vaccine. There are several advantages in using yeast to synthesize such products. S. cerevisiae is already grown on a large industrial scale, so companies are familiar with its culture. It is a GRAS organism, i.e. “generally regarded as safe.” Its genome was the first to be sequenced, and its genetics and molecular genetics are well-researched (Chapter 9). Furthermore, yeast has a well-characterized secretory system for exporting gene products into a culture medium. Examples of heterologous gene products that have been produced experimentally from yeast include epidermal growth factor (involved in wound healing), atrial natriuretic factor (for management of hypertension), interferons (with antiviral and antitumor activity), and α-1-antitrypsin (for potential relief from emphysema). There are, however, disadvantages in using S. cerevisiae. In particular, this fungus is genetically quite different from other fungi and other eukaryotes, including its use of different codons for some amino acids, so it does not always correctly read the introduced genes. For this reason attention has switched to some other fungi, such as the fission yeast Schizosaccharomyces pombe and the filamentous fungus Emericella (Aspergillus) nidulans, for both of which the genomes have now been sequenced.
Online resources
Forestry Images. http://www.forestryimages.org. [Many high-quality images of fungi, diseases, forestry practices, etc.]
Fungal Biology. http://www.helios.bto.ed.ac.uk/bto/FungalBiology/ [The website for this book.]
Tree of Life Web Project. http://tolweb.org/tree?group=life. [A major source of information on fungal systematics and phylogeny.]
General texts
Alexopoulos, C.J., Mims, C.W. & Blackwell, M. (1996) Introductory Mycology, 4th edn. John Wiley, New York.
Carlile, M.J., Watkinson, S.C. & Gooday, G.W. (2001) The Fungi, 2nd edn. Academic Press, London.
Jennings, D.H. & Lysek, G. (1999) Fungal Biology: understanding the fungal lifestyle, 2nd edn. Bios, Oxford.
Kendrick, B. (2001) The Fifth Kingdom, 3rd edn. Mycologue Publications, Sidney, Canada.
Turner, W.B. (1971) Fungal Metabolites. Academic Press, London.
Turner, W.B. & Aldridge, D.C. (1983) Fungal Metabolites. II. Academic Press, London.
Wainwright, M. (1992) An Introduction to Fungal Biotechnology. Wiley, Chichester.
Webster, J. (1980) Introduction to Fungi, 2nd edn. Cambridge University Press, Cambridge.
Cited references
Baldauf, S.L. & Palmer, J.D. (1993) Animals and fungi are each other’s closest relatives: congruent evidence from multiple proteins. Proceedings of the National Academy of Sciences, USA90, 11558–11562.
Hawksworth, D.L. (2001) The magnitude of fungal diversity: the 1.5 million species estimate revisited. Mycological Research105, 1422–1432.
Hawksworth, D.L. (2002) Mycological Research News. Mycological Research106, 514.
Keller, U. & Tudzynski, P. (2002) Ergot alkaloids. In: The Mycota X. Industrial Applications (H.D. Osiewicz, ed.), pp. 157–181. Springer-Verlag, Berlin.
Kürnsteiner, H., Zinner, M. & Kück, U. (2002) Immunosuppressants. In: The Mycota X. Industrial Applications (H.D. Osiewicz, ed.), pp. 129–155. Springer-Verlag, Berlin.
Kürnsteiner, H., Zinner, M. & Kück, U. (2002) Immunosuppressants. In: The Mycota X. Industrial Applications (H.D. Osiewicz, ed.), pp. 129–155. Springer-Verlag, Berlin.
Large, E.C. (1940) The Advance of the Fungi. Henry Holt, New York.
Lewis, D.H. (1987) Evolutionary aspects of mutualistic associations between fungi and photosynthetic organisms. In: Evolutionary Biology of the Fungi (eds Rayner, A.D.M., Brasier, C.M. & Moore, D.), pp. 161–178. Cambridge University Press, Cambridge.
Nout, M.J.R. & Aidoo, K.E. (2002) Asian fungal fermented food. In: The Mycota X. Industrial Applications (H.D. Osiewicz, ed.), pp. 23–47. Springer-Verlag, Berlin.
Ruijter, G.J.G., Kubicek, C.P. & Visser, J. (2002) Production of organic acids by fungi. In: The Mycota X. Industrial Applications (H.D. Osiewicz, ed.), pp. 213–230. Springer- Verlag, Berlin.
Schmidt, F.R. (2002) Beta-lactam antibiotics: aspects of manufacture and therapy. In: The Mycota X. Industrial Applications (H.D. Osiewicz, ed.), pp. 69–91. Springer- Verlag, Berlin.
Trinci, A.P.J. (1992) Myco-protein: a twenty-year overnight success story. Mycological Research96, 1–13.
Woese, C.R. (2000) Interpreting the universal phylogenetic tree. Proceedings of the National Academy of Sciences, USA97, 8392–8396.
Chapter 2
The diversity of fungi and fungus-like organisms
Overview of the fungi and fungus-like organisms
Within the Kingdom Fungi, the Ascomycota and the Basidiomycota have many features in common, pointing clearly to a common ancestry. The phylum Chytridiomycota has traditionally been characterized on the basis of motile cells with a single posterior flagellum. This phylum was redefined recently, based on sequence analysis of the nuclear genes encoding small subunit (SSU) ribosomal RNA (18S rDNA). This has revealed that some nonmotile fungi, previously assigned to the Zygomycota, are closely related to the Chytridiomycota and must be reassigned. An example is the fungus Basidiobolus ranarum (Chapter 4), now transferred to the Chytridiomycota. The status of Zygomycota (as currently defined after excluding the Glomeromycota) is still unclear. Some of its members may need to be separated into new groups.
Nevertheless, the current view is that all organisms within the Kingdom Fungi constitute a monophyletic group (all derived from a common ancestor), sharing several features with animals (see Table 1.1). Gene sequence analyses provide the basis for a natural phylogeny, especially when data for the SSU rDNA are supported by sequence analysis of other gene families, such as the tubulin and actin genes.
The Kingdom Straminipila (straminipiles, or stramenopiles) is now universally recognized as being distinct from the true fungi. It consists of one large and extremely important phylum, the Oomycota, and two small phyla, the Hyphochytridiomycota (with about 25 species) and Labyrinthulomycota (with about 40 species). The Phylum Oomycota is remarkable in many ways. It includes some of the most devastating plant pathogens, including Phytophthora infestans (potato blight), Phytophthora ramorum (sudden oak death in California), Phytophthora cinnamomi (the scourge of large tracts of Eucalyptus forest in Australia), and many other important plant pathogens, including Pythium and Aphanomyces spp. But perhaps most remarkable of all is the fact that Oomycota have evolved a lifestyle that resembles that of the true fungi in almost every respect. We discuss this group in detail later in this chapter and at several points in this book.
The fungus-like organisms of uncertain affinity include four types of organism: the acrasid cellular slime moulds, the dictyostelid cellular slime moulds, the plasmodial slime moulds (Myxomycota), and the plasmodiophorids. For most of their life these organisms lack cell walls, and they grow as either a naked protoplasmic mass or as amoeboid cells, converting to a walled form at the onset of sporulation. There is no evidence that they are related to fungi, but they have traditionally been studied by mycologists, and they have several interesting features, which are discussed towards the end of this chapter.
Against this background, we now consider the individual phyla in more detail.
The true fungi (Kingdom Mycota)
Chitridiomycota
The Chytridiomycota, commonly termed chytrids, number about 1000 species (Barr 1990) and are considered to be the earliest branch of the true fungi, dating back to about 1 billion years ago. They have cell walls composed mainly of chitin and glucans (polymers of glucose) and many other features typical of fungi (see Table 1.1). But they are unique in one respect, because they are the only true fungi that produce motile, flagellate zoospores. Typically, the zoospore has a single, posterior whiplash flagellum, but some of the chytrids that grow in the rumen of animals have several flagella (Chapter 8), and some other chytrids (e.g. Basidiobolus ranarum, recently transferred to the Chytridiomycota based on SSU rDNA analysis), have no flagella. This provides a good example of the value of DNA sequencing in determining the true phylogenetic relationships of organisms.
