The Fungal Community Its Organization and Role in the Ecosystem Third Edition docx

The Fungal
Community
Its Organization and Role
in the Ecosystem
Third Edition
MYCOLOGY SERIES
Editor
J. W. Bennett
Professor
Department of Cell and Molecular Biology
Tulane University
New Orleans, Louisiana
Founding Editor
Paul A. Lemke
1.
Viruses and Plasmids in Fungi,
edited by Paul A. Lemke
2.
The Fungal Community: Its Organization and Role in the Ecosystem,
edited by Donald
T. Wicklow and George C. Carroll
3.
Fungi Pathogenic for Humans and Animals (in three parts),
edited by Dexter H. Howard
4.
Fungal Differentiation: A Contemporary Synthesis,
edited by John E. Smith
5.
Secondary Metabolism and Differentiation in Fungi,
edited by Joan W. Bennett and

Alex Ciegler
6.
Fungal Protoplasts,
edited by John F. Peberdy and Lajos Ferenczy
7.
Viruses of Fungi and Simple Eukaryotes,
edited by Yigal Koltin and Michael J. Leibowitz
8.
Molecular Industrial Mycology: Systems and Applications for Filamentous Fungi,
edited by Sally A. Leong and Randy M. Berka
9.
The Fungal Community: Its Organization and Role in the Ecosystem, Second Edition,
edited by George C. Carroll and Donald T. Wicklow
10.
Stress Tolerance of Fungi,
edited by D. H. Jennings
11.
Metal Ions in Fungi,
edited by Gü'fcnther Winkelmann and Dennis R. Winge
12.
Anaerobic Fungi: Biology, Ecology, and Function,
edited by Douglas O. Mountfort and
Colin G. Orpin
13.
Fungal Genetics: Principles and Practice,
edited by Cees J. Bos
14.
Fungal Pathogenesis: Principles and Clinical Applications,
edited by Richard A.
Calderone and Ronald L. Cihlar

15.
Molecular Biology of Fungal Development,
edited by Heinz D. Osiewacz
16.
Pathogenic Fungi in Humans and Animals: Second Edition,
edited by Dexter H. Howard
17.
Fungi in Ecosystem Processes,
John Dighton
18.
Genomics of Plants and Fungi,
edited by Rolf A. Prade and Hans J. Bohnert
19.
Clavicipitalean Fungi: Evolutionary Biology, Chemistry, Biocontrol, and Cultural Impacts,
edited by James F. White Jr., Charles W. Bacon, Nigel L. Hywel-Jones, and Joseph W.
Spatafora
20.
Handbook of Fungal Biotechnology, Second Edition,
edited by Dilip K. Arora
21.
Fungal Biotechnology in Agricultural, Food, and Environmental Applications,
edited
by Dilip K. Arora
22.
Handbook of Industrial Mycology,
edited by Zhiqiang An
23.
The Fungal Community: Its Organization and Role in the Ecosystem, Third Edition,
edited by John Dighton, James F. White, and Peter Oudemans
The Fungal

Community
Its Organization and Role
in the Ecosystem
Third Edition
edited by
John Dighton
James F. White
Peter Oudemans

Published in 2005 by
CRC Press
Taylor & Francis Group
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Boca Raton, FL 33487-2742
© 2005 by Taylor & Francis Group, LLC
CRC Press is an imprint of Taylor & Francis Group
No claim to original U.S. Government works
Printed in the United States of America on acid-free paper
10987654321
International Standard Book Number-10: 0-8247-2355-4 (Hardcover)
International Standard Book Number-13: 978-0-8247-2355-2 (Hardcover)
This book contains information obtained from authentic and highly regarded sources. Reprinted material is quoted with
permission, and sources are indicated. A wide variety of references are listed. Reasonable efforts have been made to publish
reliable data and information, but the author and the publisher cannot assume responsibility for the validity of all materials
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No part of this book may be reprinted, reproduced, transmitted, or utilized in any form by any electronic, mechanical, or
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Library of Congress Cataloging-in-Publication Data

The Fungal community : its organization and role in the ecosystem / edited by John
Dighton, James F. White, Peter Oudemans. — 3rd ed.
p. cm. — (Mycology)
Includes bibliographical references and index.
ISBN 0-8247-2355-4 (alk. paper)
I. Dighton, J. (John) II. White, James F. (James Francis), 1953- III. Oudemans, Peter.
IV. Mycology series.
QK604.2.C64F86 2005

579.5'17—dc22 2004061821

Visit the Taylor & Francis Web site at

and the CRC Press Web site at

Taylor & Francis Group
is the Academic Division of T&F Informa plc.

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v

Preface

The third edition of

The Fungal Community

has been compiled by a new set of editors. The
three of us were impressed with the quality and content of the previous two editions and
hope that we have matched the work of George Carroll and Don Wicklow in this new volume.
The aims and objectives of this volume are explained in our introductory chapter,
but in brief, we have tried to address some of the current discussions in ecology (diversity
and function, scaling issues, disturbance, invasive species) from a fungal perspective. In
order to be able to address these issues, we need appropriate techniques to identify fungi,
determine their abundance, determine their associations among themselves and other organ-
isms, measure their individual and community function, and be able to scale these measures
from the microscopic level of the individual hyphal or fungal cell through local to landscape
and ecosystem levels. The chapters of this edition have advanced toward addressing these
aspects of mycology and beyond, but they are by no means all-encompassing. We apologize
if some areas are missing, but the size of this volume speaks for the complexity and
dimension of aspects relating to the functional role of fungal communities in ecosystems,
and this book would be overwhelmingly large if we included more. There is a huge body
of literature in both mycological and ecological journals that pertains to the themes con-
tained herein, and we praise our authors for their extensive bibliographies, which will steer
interested readers to some of the most recent publications in their specific areas.

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vii

Editors

John Dighton

is a professor in the Institute of Marine and Coastal Sciences (Cook College)
and Biology Department (Camden) and director of the Pinelands Field Station of Rutgers
University. He is the author of

Fungi in Ecosystem Processes

(2003) and author or coauthor
of over 100 journal articles on soil ecology and mycology. He is a member of the British
Mycological Society, the Mycological Society of America, and the Ecological Society of
America. John Dighton is on the editorial board of

Mycological Research, Soil Biology
and Biochemistry,

and

Bartonia

. He received his B.Sc. degree as an external student of
London University in botany and zoology, an M.Sc. degree in ecology from Durham
University, and a Ph.D. in ecology from London University.

James F. White, Jr.

, is a professor of plant biology and pathology at Cook College,
Rutgers University, New Brunswick, New Jersey. He is the editor or coeditor of several
books, including

The Clavicipitalean Fungi

(2004),

Microbial Endophytes

(2000), and

Biotechnology of Acremonium Endophytes of Grasses

(1994). He is the author or coauthor
of over 130 journal articles and book chapters, and 50 abstracts, posters, and invited
lectures. He is a member of the American Phytopathological Society, the Mycological
Society of America, and the American Society for Microbiology. Dr. White is an associate
editor of the mycological journal

Mycologia

and was a founding member and past secretary
of the International Symbiosis Society. Dr. White received a B.S. degree in botany and an
M.S. degree in mycology and plant pathology from Auburn University, Alabama, and a
Ph.D. degree in mycology and botany from the University of Texas, Austin.

Peter Oudemans

is an associate professor in the Department of Plant Biology and
Pathology at Rutgers University and is stationed at the Philip E. Marucci Center for
Blueberry and Cranberry Research and Extension. His research goals are aimed at the
biology and control of fungal diseases of the blueberry and cranberry. To accomplish these
goals, he uses remote sensing and geographic information system methodologies to detect,
map, quantify, and track plant pathogens, as well as other interacting factors that influence
crop quality and yield. In addition to research, he teaches classes in plant pathology and
mycology, as well as a colloquium course entitled “Agriculture in the Pinelands.” He
received his training at the University of New Brunswick (B.S.), the University of Guelph
(M.S.), and the University of California (Ph.D.), as well as postgraduate training at Duke
University and the University of Kansas.

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ix

Acknowledgments

We thank



all our authors for their contributions and for helping to make the process of
editing this volume as painless as possible. We hope that we have not put too much pressure
on any of them. We also extend a debt of gratitude to Magnus Anusiem, Vanessa McCowan,
and other members of our laboratories who have helped us with collating and indexing
this book.

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xi

Contributors

Ann E. Arnold

Department of Biology
Duke University
Durham, North Carolina, USA

Charles W. Bacon

Toxicology and Mycotoxin Research
Unit
Russell Research Center
Athens, Georgia, USA

Felix Bärlocher

Mount Allison University
Sackville, New Brunswick, Canada

James W. Baxter

Department of Biological Sciences
Sacramento State University

Sacramento, California, USA

Jayne Belnap

U.S. Geological Survey
Moab, Utah, USA

James D. Bever

Department of Biology
Indiana University
Bloomington, Indiana, USA

Martin I. Bidartondo

Imperial College London
and
Royal Botanic Gardens
Kew, UK

Joseph F. Bischoff

National Center for Biotechnology
Information
National Institutes of Health
Bethesda, Maryland, USA

Euan P. Burford

Division of Environmental and Applied

Biology
Biological Sciences Institute
School of Life Sciences
University of Dundee
Dundee, Scotland, UK

Lei Cai

Centre for Research in Fungal Diversity
Department of Ecology and Biodiversity
The University of Hong Kong
Hong Kong

John W.G. Cairney

Centre for Horticulture and Plant Sciences
University of Western Sydney
New South Wales, Australia

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xii

Andrew W. Claridge

Department of Conservation and
Environment
Parks and Wildlife Division
Queanbeyan, New South Wales, Australia

Keith Clay

Department of Biology
Indiana University
Bloomington, Indiana, USA

Kirk J. Czymmek

Department of Biological Sciences
University of Delaware
Newark, Delaware, USA

John Dighton

Rutgers University Pinelands Field
Station
New Lisbon, New Jersey, USA

Daniel M. Durall

Biology Department
Okanagan University College
Kelowna, British Columbia, Canada

Louise M. Egerton-Warburton

Chicago Botanic Garden
Glencoe, Illinois, USA

Nataliya Ellanska

M.M. Grisko National Botanical Garden
NAN Ukraine
Kiev, Ukraine

Roger D. Finlay

Department of Forest Mycology and
Pathology
Swedish University of Agricultural
Sciences
Uppsala, Sweden

Marina Fomina

Division of Environmental and Applied
Biology
Biological Sciences Institute
School of Life Sciences
University of Dundee
Dundee, Scotland, UK

Geoffrey M. Gadd

Division of Environmental and Applied
Biology
Biological Sciences Institute
School of Life Sciences
University of Dundee
Dundee, Scotland, UK

Monique Gardes

Laboratoire Evolution et Diversité
Biologique
Université Paul Sabatier
Toulouse, France

Erast Golovko

M.M. Grisko National Botanical Garden
NAN Ukraine
Kiev, Ukraine

Everett M. Hansen

Department of Botany and Plant Pathology
Oregon State University
Corvallis, Oregon, USA

Kurt Haselwandter

Department of Microbiology
University of Innsbruck
Innsbruck, Austria

David L. Hawksworth

MycoNova
The Yellow House
Mataelpino
Madrid, Spain

Joan M. Henson

Department of Microbiology
Montana State University
Bozeman, Montana, USA

Edward A. Herre

Smithsonian Tropical Research Institute
Balboa, Republic of Panama

Bradley I. Hillman

Department of Plant Biology and
Pathology
Rutgers University
New Brunswick, New Jersey, USA

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xiii

Erik A. Hobbie

Complex Systems Research Center

University of New Hampshire
Durham, New Hampshire, USA

Kevin D. Hyde

Centre for Research in Fungal Diversity
Department of Ecology and Biodiversity
The University of Hong Kong
Hong Kong

Rajesh Jeewon

Centre for Research in Fungal Diversity
Department of Ecology and Biodiversity
The University of Hong Kong
Hong Kong

Melanie D. Jones

Biology Department
Okanagan University College
Kelowna, British Columbia, Canada

Ari Jumpponen

Division of Biology
Kansas State University
Manhattan, Kansas, USA

Tamar Kis-Papo

Institute of Evolution
The University of Haifa
Mount Carmel, Israel



Donald Y. Kobayashi

Department of Plant Biology and
Pathology
Rutgers University
New Brunswick, New Jersey, USA

Ingrid Kottke

Eberhard-Karls University Tuebingen
Botanical Institute
Systematic Botany
Mycology and Botanical Garden
Tuebingen, Germany

Damond A.



Kyllo

Smithsonian Tropical Research Institute
Ancon, Republic of Panama

Otto L. Lange

Julius-von-Sachs Institute für
Biowissenschaften
University of Würzburg
Würzburg, Germany

Adrian Leuchtmann

Geobotanisches Institut ETH
Zurich, Switzerland

Kathy J. Lewis

Department of Forestry
University of Northern British Columbia
Prince George, British Columbia, Canada

Erik Lilleskov

USDA Forest Service
Forestry Sciences Laboratory
Houghton, Michigan, USA

Björn D. Lindahl

Department of Forest Mycology and
Pathology
Swedish University of Agricultural

Sciences
Uppsala, Sweden

D. Jean Lodge

Center for Forest Mycology Research
USDA Forest Service
Forest Products Laboratory
Luquillo, Puerto Rico

John Lussenhop

Biological Sciences Department
University of Illinois at Chicago
Chicago, Illinois, USA

Philip Lyons

Department of Natural Sciences
University of Houston–Downtown
Houston, Texas, USA

Zuleyka Maynard

Smithsonian Tropical Research Institute
Balboa, Republic of Panama

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xiv

Bruce A. McDonald

Institute of Plant Sciences
Phytopathology Group
ETH Zentrum/LFW
Zürich, Switzerland

Luis C. Mejia

Smithsonian Tropical Research Institute
Balboa, Republic of Panama

Julian I. Mitchell

School of Biological Sciences
University of Portsmouth
Portsmouth, UK



Sherri J. Morris

Biology Department
Bradley University
Peoria, Illinois, USA

Gregory M. Mueller

Department of Botany
Field Museum of Natural History
Chicago, Illinois, USA

Peter Oudemans

Philip Maricci Center for Blueberry and
Cranberry Research
Rutgers University
Chatsworth, New Jersey, USA

Jean-François Ponge

Museum National d’Histoire Naturelle
Brunoy, France

Regina S. Redman

Department of Biology
University of Washington
Seattle, Washington, USA

David M. Rizzo

Department of Plant Pathology
University of California
Davis, California, USA

Nancy Robbins

Department of Plant Biology
Rutgers University
New Brunswick, New Jersey, USA

G. Philip Robertson

Department of Crop and Soil Sciences
Michigan State University, Lansing
and
W.K. Kellogg Biological Station
Michigan State University
Hickory Corners, Michigan, USA

Russell J. Rodriguez

U.S. Geological Survey
WFRC
Seattle, Washington, USA

Enith Rojas

Smithsonian Tropical Research Institute
Balboa, Republic of Panama

Jennifer A. Rudgers

Department of Biology
Indiana University
Bloomington, Indiana, USA

Liliane Ruess

Institute of Zoology
Technical University of Darmstadt
Darmstadt, Germany

Christopher L. Schardl

Department of Plant Pathology
University of Kentucky
Lexington, Kentucky, USA

John Paul Schmit

Department of Plant Biology
University of Illinois at
Urbana–Champaign
Urbana, Illinois, USA

Peggy A. Schultz

Department of Biology
Indiana University
Bloomington, Indiana, USA

Robert L. Sinsabaugh

Biology Department
University of New Mexico

Albuquerque, New Mexico, USA

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xv

Jeffrey K. Stone

Department of Botany and Plant Pathology
Oregon State University
Corvallis, Oregon, USA

Mary E. Stromberger

Department of Soil and Crop Sciences
Colorado State University
Fort Collins, Colorado, USA

Michael J. Swift

Tropical Soil Biology and Fertility Institute
of CIAT
Nairobi, Kenya
and
Institut de Recherche pour le
Developpement
Montpellier, France

James M. Trappe

Department of Forest Science
Oregon State University
Corvallis, Oregon, USA

Kathleen K. Treseder

Department of Ecology and Evolutionary
Biology and Department of Earth System
Science
University of California
Irvine, California, USA

Amy R. Tuininga

Department of Biological Sciences
Louis Calder Center
Fordham University
Armonk, New York, USA

Katarzyna Turnau

Institute of Botany of the Jagiellonian
University
Krakow, Poland

Sunshine A. Van Bael

Smithsonian Tropical Research Institute
Balboa, Republic of Panama

Milton Wainwright

Department of Molecular Biology and
Biotechnology
University of Sheffield
Sheffield, UK

Roy Watling

Caledonian Mycological Enterprises
and
Royal Botanic Garden
Edinburgh, Scotland, UK

James F. White, Jr.

Department of



Plant Biology and
Pathology
Cook College–Rutgers University
New Brunswick, New Jersey, USA

John Zak

Department of Biological Sciences
Texas Tech University
Lubbock, Texas, USA

Valentina A. Zakharchenko

Institute of Microbiology and Virology
National Academy of Sciences of the
Ukraine
Kiev, Ukraine

Jiasui Zhan

Scottish Crop Research Institute
Invergowrie
Dundee, Scotland, UK

Nelli N. Zhdanova

Institute of Microbiology and Virology
National Academy of Sciences of the
Ukraine
Kiev, Ukraine

Alga Zuccaro

Institute of Microbiology
Technical University of Braunschweig
Braunschweig, Germany

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xvii

Contents

Introduction 1

John Dighton, James F. White, Jr., and Peter Oudemans

SECTION 1 Structure of Fungal Communities
1

Linking Function between Scales of Resolution 13

Sherri J. Morris and G. Philip Robertson

2

Fungal Communities: Their Diversity and Distribution 27

David L. Hawksworth and Gregory M. Mueller

3

Freshwater Fungal Communities 39

Felix Bärlocher

4

Marine Fungal Communities 61

Tamar Kis-Papo

5

Tropical Fungi 93

Kevin D. Hyde, Lei Cai, and Rajesh Jeewon

6

Lichens and Microfungi in Biological Soil Crusts: Community Structure,
Physiology, and Ecological Functions 117

Jayne Belnap and Otto L. Lange

7

Mycorrhizal Fungi in Successional Environments: A Community Assembly
Model Incorporating Host Plant, Environmental, and Biotic Filters 139

Ari Jumpponen and Louise M. Egerton-Warburton

8

Fungal Communities: Relation to Resource Succession 169

Jean-François Ponge

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xviii

9

Emerging Perspectives on the Ecological Roles of Endophytic Fungi
in Tropical Plants 181

Sunshine A. Van Bael, Zuleyka Maynard, Enith Rojas, Luis C. Mejia,
Damond A. Kyllo, Edward A. Herre, Nancy Robbins, Joseph F. Bischoff,
and Ann E. Arnold

10

Classical Methods and Modern Analysis for Studying Fungal Diversity 193

John Paul Schmit and D. Jean Lodge

11

Fungal Diversity in Molecular Terms: Profiling, Identification, and
Quantification in the Environment 215

Martin I. Bidartondo and Monique Gardes

12

Analytical and Experimental Methods for Estimating Population Genetic
Structure of Fungi 241

Jiasui Zhan and Bruce A. McDonald

13

Interspecific Interaction Terminology: From Mycology to General Ecology 265

Amy R. Tuininga

SECTION 2 Function of Fungal Communities
14

Fungal Activity as Determined by Microscale Methods with Special
Emphasis on Interactions with Heavy Metals 287

Katarzyna Turnau and Ingrid Kottke

15

Exploring Fungal Activity with Confocal and Multiphoton Microscopy 307

Kirk J. Czymmek

16

Enzymatic Activities of Mycelia in Mycorrhizal Fungal Communities 331

Björn D. Lindahl, Roger D. Finlay, and John W.G. Cairney

17

Fungal Enzymes at the Community Scale 349

Robert L. Sinsabaugh

18

Using Isotopic Tracers to Follow Carbon and Nitrogen Cycling of Fungi 361

Erik A. Hobbie

19

Diversity-Functioning Relationships in Ectomycorrhizal Fungal
Communities 383

James W. Baxter and John Dighton

20

Fungi, Bacteria, and Viruses as Pathogens of the Fungal Community 399

Donald Y. Kobayashi and Bradley I. Hillman

21

Fungal Endophytes in Terrestrial Communities and Ecosystems 423

Jennifer A. Rudgers and Keith Clay

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xix

22

Mechanisms of Arbuscular Mycorrhizal Mediation of Plant–Plant
Interactions 443

James D. Bever and Peggy A. Schultz

23

Impacts of Plant Pathogenic Fungi on Plant Communities 461

Everett M. Hansen and Jeffrey K. Stone

24

The

Epichloë

Endophytes of Grasses and the Symbiotic Continuum 475

Christopher L. Schardl and Adrian Leuchtmann

25

Evolutionary Development of the Clavicipitaceae 505

Joseph F. Bischoff and James F. White, Jr.

26

Ecological Fitness Factors for Fungi within the Balansieae and Clavicipiteae 519

Charles W. Bacon and Philip Lyons

27

Fungal Communities of Seaweeds 533

Alga Zuccaro and Julian I. Mitchell

28

Trophic Interactions of Fungi and Animals 581

Liliane Ruess and John Lussenhop

29

Sporocarp Mycophagy: Nutritional, Behavioral, Evolutionary,
and Physiological Aspects 599

Andrew W. Claridge and James M. Trappe

30

Hypogeous Fungi: Evolution of Reproductive and Dispersal Strategies
through Interactions with Animals and Mycorrhizal Plants 613

James M. Trappe and Andrew W. Claridge

SECTION 3 Human Impacts on Fungal Communities and Their Function
31

Human Impacts on Biodiversity and Ecosystem Services: An Overview 627

Michael J. Swift

32

Oligotrophic Growth of Fungi 643

Milton Wainwright

33

Fungal Communities of Desert Ecosystems: Links to Climate Change 659

John Zak

34

Symbiotic Lifestyle Expression by Fungal Endophytes and the Adaptation
of Plants to Stress: Unraveling the Complexities of Intimacy 683

Russell J. Rodriguez, Regina S. Redman, and Joan M. Henson

35

Biological Soil Crusts and Global Changes: What Does the Future Hold? 697

Jayne Belnap and Otto L. Lange

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xx

36

Nutrient Acquisition Strategies of Fungi and Their Relation to Elevated
Atmospheric CO

2

713

Kathleen K. Treseder

37

Toxic Metals and Fungal Communities 733

Marina Fomina, Euan P. Burford, and Geoffrey M. Gadd

38

Radionuclides and Fungal Communities 759

Nelli N. Zhdanova, Valentina A. Zakharchenko, and Kurt Haselwandter

39

How Do Composition, Structure, and Function of Mycorrhizal Fungal
Communities Respond to Nitrogen Deposition and Ozone Exposure? 769

Erik A. Lilleskov

40

Micromycete Associations in the Rhizosphere of Steppe and
Agrophytocenose Plants 803

Erast Golovko and Nataliya Ellanska

41

Fungal Communities of Agroecosystems 813

Mary E. Stromberger

42

Effects of Forest Management on Fungal Communities 833

Daniel M. Durall, Melanie D. Jones, and Kathy J. Lewis

43

Exotic Species and Fungi: Interactions with Fungal, Plant, and Animal
Communities 857

David M. Rizzo

SECTION 4 Preserving Fungal Communities
44

Fungal Conservation: Some Impressions — A Personal View 881

Roy Watling

Species Index 897
Subject Index 911

DK3133_bookTOC.fm Page xx Monday, April 18, 2005 11:33 AM

1

Introduction

John Dighton

Rutgers University Pinelands Field Station, New Lisbon, New Jersey, USA

James F. White, Jr.

Department of Plant Biology and Pathology, Cook College–Rutgers University,

New Brunswick, New Jersey, USA

Peter Oudemans

Phillip Maruccie Center for Blueberry and Cranberry Research, Rutgers University,
Chatsworth, New Jersey, USA

THE THOUGHTS BEHIND THIS VOLUME

Why is it that it took three people to edit this third edition of

The Fungal Community

when it has so eloquently been done by two people in the past? Are we so much less
competent? Perhaps so, but we would like to think that in the interval between the last
edition and this a number of new technological advances have been made, allowing us to
have more tools, or toys, to play with to study fungi and fungal communities, and we are
not all familiar with all methods available. Thus, among us, we hope that we have
assembled a mixture of authors who can address some of the questions regarding the
observations, characterizations, and functional attributes of fungal assemblages and their
interactions with both the environment and other organisms. In addition, the ecological
literature has expanded to ask questions of global and local biodiversity, highlight the
problems of exotic species, reopen the debate about diversity and function, and become
more aware of the functional rather than taxonomic methods of classification.
All of these factors impact our way of looking at communities, interactions between
species, and community function. New tools, particular molecular methods of identifica-
tion of individuals and the phylogenetic relations of these individuals, and the molecular
identification of functional regulators allow us to investigate the functional aspects of
individuals and groups of individuals (communities) in different ways than in the past.

DK3133_Intro.fm Page 1 Wednesday, April 13, 2005 11:57 AM

2 Dighton, White, and Oudemans

The speed at which these new technologies are evolving makes it difficult for one
individual to be able to be conversant with the details of all methods, their utility,
limitations, and applications.
Thus, we hope that among the three of us we may be able to show a degree of
competence in some of the subject areas we encompass in this volume. We have attempted
to address a number of current ecological concepts and approach the concept of fungal
communities from an ecological perspective, rather than a fungicentric view. We hope that
the melding of ideas, methods, and results promoted by our contributors will point to
directions in which mycology should proceed in the future.

LITTLE AND LARGE: SCALE IN PERSPECTIVE

Fungi are regarded as microorganisms. Their individual components, hyphal filaments,
are microscopic. However, by their nature of excreting enzymes, low-molecular-weight
organic acids, etc., they have an influence on a larger sphere than the space occupied by
their biomass. Together with the extensive growth of hyphae through the substrate colo-
nized by the fungal mycelium (Rayner, 1998), information (carbon and nutrients) can be
effectively translocated by them (Jennings, 1990; Wells and Boddy, 1995; Wells et al.,
2001). Thus, the influence of fungi extends to a macrolevel of space (Rayner, 1992). In
conjunction with vascular and other plants, the influence of fungi can extend to the
landscape level. How can we translate among scales of resolution influenced by fungi?
How can we translate the activities occurring at the surface of individual hyphae into
macroscale effects. How can we account for macroscale perturbations and heterogeneity
on physiological and biochemical changes in the fungal hyphae at the cellular level?

The
influence of scale and heterogeneity in the ecosystem is a confounding factor in our
attempts to understand ecology and community functioning. However, these factors are
inherent in ecosystems, and we need to be able to identify them and develop tools to use
the unique properties that these variables provide to ecosystems. How are ecologists
overcoming these problems? Can we apply the same ecological principles to investigate
fungal communities at each of these scales, and how does observation at each scale allow
us to interpret what is going on at the scale above or below that which we are observing?
This is one of the more intangible questions of ecology, but it allows us to think about
experiments and observations required to transcend these scales (O’Neill, 1988; O’Neill
et al., 1991; Friese et al., 1997). This subject runs throughout this volume and is introduced
in Chapter 1 by Morris and Robertson, where they relate the function of fungi and fungal
communities at different scales of observation or measurement.

WHAT IS A FUNGAL COMMUNITY?

What do we really mean by a community? We may take the definition of Whittaker (1975):
“an assemblage of populations of plants, animals, bacteria and fungi that live in an
environment and interact with one another, forming together a distinctive living system,
with its own composition, structure, environmental relations, development and function.”
Using this definition, it seems impossible to consider the structure and development of
fungal communities without investigating their interactions with other organisms and the
environment. A good discussion of the properties and dynamics of communities can be
found in Peter Morin’s book

Community Ecology

(1999). A view of fungal communities,
their identification in relation to plant phytosociological taxonomy, and a call for mycol-

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Introduction 3

ogists to become more precise in their definitions of fungal communities come from
Chapter 2 by Hawksworth and Mueller, and later from Chapter 13 by Tuininga. Fungal
communities are inextricably related to communities and populations of plants and animals
in the ecosystem. The effect of fungi on other organisms and the effects of other organisms
on fungi are important aspects of community analysis in any ecosystem. In this respect,
we have chapters that describe interactions between fungi and plants (Chapter 9 by Van
Bael et al. and Chapter 21 by Rudgers and Clay, for endophytes; Chapter 22 by Bever
and Schultz, with plant communities; Chapter 27 by Zuccaro and Mitchell, for seaweeds),
fungal interactions with animals (Chapter 28 by Ruess and Lussenhop, for invertebrates;
Chapter 29 by Trappe and Claridge

,

for vertebrates), and interactions with microbial
communities in biological soil crusts (Chapter 6 by Belnap and Lange). These interactions
encompass the broad spectrum of competition, predation, mutualism, commensalism, and
amensalism found in all communities.

IDENTIFICATION AND CHARACTERIZATION OF A FUNGAL
COMMUNITY

How do we characterize communities of fungi? Methods required to identify individuals
within the community include classical methods of direct observation (largely restricted
to the identification of fruiting structures), culturing methods (linked to direct observa-
tions), and molecular/biochemical methods. Are these methods mutually exclusive? Is each

of the methods robust? For example, the identification of species and communities based
on fruiting structures (mushrooms) provides information only on mushroom distribution
and abundance, saying little about the abundance, distribution, and interactions of other
parts of the mycelium, which is usually the functional component of the organism. Isolation
techniques are media dependent. How many replicate media are required to adequately
extract and identify all species that are present in the environment under study? Many
times a single medium or sometimes two media are used. Is this adequate?
Some of the classical methods for the study of fungal communities are discussed
by Schmit and Lodge in Chapter 10. More recently, molecular methods of DNA extraction
and comparison with known DNA libraries have become in vogue. However, how adequate
and robust are these methods when used in isolation? Because the methods have become
more available and easier to use, is sample preparation before extraction influenced by
quality control protocols? Can extraneous DNA amplified from inadequately prepared
source material confuse the interpretation of molecular profiles obtained? Are all molecular
profiles checked against DNA extracted from isolated fungi that have been identified by
classical techniques? Is this degree of rigor really required, or can we get by with a quick
and dirty global DNA extraction? These questions are addressed in Chapter 11 by Bidar-
tondo and Gardes. In order to determine who is where, there is also a need to identify
where an individual organism and population reside. Molecular tools are being used to
allow us to identify where similar and dissimilar genetic information in the same species
exists, identifying population demography. These methods are described by Zhan and
McDonald in Chapter 12.
Terminology used to describe interactions between organisms and populations is
complex in all fields. In fungal ecology, the terminology is probably as complex as in
other disciplines, or even more so. Terminology has changed over time, and common
terminology has been used to mean different things by different people (Cooke and Rayner,
1984). In Chapter 13, Tuininga attempts to unravel some of these complexities and suggests
a revision of the terminology that may lead to less ambiguity in the future.

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4 Dighton, White, and Oudemans

Descriptions of fungal communities are represented here at a variety of spatial scales:
from biome;

γ

-diversity (Chapter 4 by Kis-Papo, Chapter 5 by Hyde et al.) through
landscape;

β

-diversity (Chapter 3 by Bärlocher and Chapter 6 by Belnap and Lange

)

to
local; and

α

-diversity (Chapter 27 by Zuccaro and Mitchell). For discrete, mobile organ-
isms, changes in resources usually lead to a redistribution of individuals and populations
to areas or niches that are most suitable for their existence and controlled by birth, death,
and rates of emigration and immigration. In addition to spore or propagule dispersal,
nonmobile organisms, such as fungi, frequently occupy niche space by the growth of single
individuals and compete with other individuals by chemical warfare. Do the dynamics of
these communities follow the same rules of density-dependent regulation and Lotka–Vol-
terra models of species interactions (see Morin, 1999)?

The development of communities depends also on time. During fungal community
development the nature of the resources available to the fungi also changes. This is explored
in an evolutionary context by Van Bael et al. in Chapter 9 and over the time course of
decomposition (Chapter 8 by Ponge). The relative influences of different factors affecting
the outcome of intraspecific interactions, leading to changes in community structure, are
known as assembly rules (Drake, 1990) and are discussed here, in reference to mycorrhizal
fungi, by Jumpponen and Egerton-Warburton in Chapter 7. These temporal changes in
community structure of nondiscrete, nonmotile organisms may differ from those classically
thought of by ecologists. In the decomposer community, for example, niche breadth is
changed over time by the fungal community occupying that niche (Swift, 1976), leading
to a sequential change in fungal communities occupying the same resource (Ponge, 1990,
1991; Frankland, 1992, 1998), as discussed here by Ponge (Chapter 8). Are assembly rules
for fungal communities the same as for other plant and animal communities?

FUNCTIONALITY IN FUNGAL COMMUNITIES

Characterization of the fungal community can tell us the nature of the components of the
community; for example, information can be gained by molecular profiling. But what degree
of functional information is gained from physiological and biochemical profiling, such as
BIOLOG (Winding, 1994) of FUNGILOG (Zak et al., 1994; Dobranic and Zak, 1999)? Do
these methods actually provide us with the true function of the community as it is

in vivo

, or
are community constituents influenced by the media upon which they are isolated and grown
prior to the biochemical profiling? An alternative to thinking in classical Linnean taxonomic
terms is to think in terms of guilds (Root, 1967) or functional groups, where organisms are
grouped on the basis of their functional attributes, irrespective of their taxonomic status. How
much of the function of fungal communities can be explained in terms of, for example, enzyme

expression (see Chapter 16 by Lindahl et al. and Chapter 17 by Sinsabaugh)? These biochem-
ical changes in the environment created by the presence of fungal hyphae are at the local or
microscale, despite the fact that they can be integrated over larger scales and have landscape
effects (Dighton, 2003). As fungi are microorganisms, detection of changes in the local
environment under the influence of an individual hyphum is limited because analytical tech-
niques are usually designed for measures of changes in the chemistry of the environment
(Dighton et al., 2001). Turnau and Kottke (Chapter 14) and Czymmek (Chapter 15) provide
methods where the influence of single fungal hyphae may be measured, and Lindahl et al.
(Chapter 16) describe influences at the local scale of mycorrhizal root surfaces.
At the larger scale of resolution, Sinsabaugh (Chapter 17) shows how the interactions
between fungi and bacteria can lead to larger changes in soil enzyme activity and expres-
sion, acting in a true community sense. Eric Hobbie (Chapter 18) introduces us to the use

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