The Fungal Community Its Organization and Role in the Ecosystem Fourth Edition MYCOLOGY SERIES Editor J. W. Bennett Professor Department of Plant Biology and Pathology Rutgers University New Brunswick, New Jersey 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 Güfcnther 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 24. Fungi: Experimental Methods in Biology, Ramesh Maheshwari 25. Food Mycology: A Multifaceted Approach to Fungi and Food, edited by Jan Dijksterhuis and Robert A. Samson 26. The Aspergilli: Genomics, Medical Aspects, Biotechnology, and Research Methods, edited by Gustavo H. Goldman and Stephen A. Osmani 27. Defensive Mutualism in Microbial Symbiosis, edited by James F. White, Jr. and Mónica S. Torres 28. Fungi: Experimental Methods In Biology, Second Edition, Ramesh Maheshwari 29. Fungal Cell Wall: Structure, Synthesis, and Assembly, Second Edition, José Ruiz-Herrera 30. Polyamines in Fungi: Their Distribution, Metabolism, and Role in Cell Differentiation and Morphogenesis, Laura Valdes-Santiago and José Ruiz-Herrera 31. Fungi in Ecosystem Processes, Second Edition, John Dighton 32. The Fungal Community: Its Organization and Role in the Ecosystem, Fourth Edition, John Dighton and James F. White The Fungal Community Its Organization and Role in the Ecosystem Fourth Edition edited by John Dighton James F. White Front cover: Image courtesy of Björn Lindahl. Used with permission. All rights reserved. CRC Press Taylor & Francis Group 6000 Broken Sound Parkway NW, Suite 300 Boca Raton, FL 33487-2742 © 2017 by Taylor & Francis Group, LLC CRC Press is an imprint of Taylor & Francis Group, an Informa business No claim to original U.S. Government works Printed on acid-free paper Version Date: 20160927 International Standard Book Number-13: 978-1-4987-0665-0 (Hardback) This book contains information obtained from authentic and highly regarded sources. Reasonable efforts have been made to publish reliable data and information, but the author and publisher cannot assume responsibility for the validity of all materials or the consequences of their use. The authors and publishers have attempted to trace the copyright holders of all material reproduced in this publication and apologize to copyright holders if permission to publish in this form has not been obtained. If any copyright material has not been acknowledged please write and let us know so we may rectify in any future reprint. 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Trademark Notice: Product or corporate names may be trademarks or registered trademarks, and are used only for identification and explanation without intent to infringe. Library of Congress Cataloging-in-Publication Data Names: Dighton, John, editor. | White, James F. (James Francis), 1953- , editor. Title: The fungal community : its organization and role in the ecosystem / [edited by] John Dighton and James F. White. Description: Fourth edition. | Boca Raton : Taylor & Francis, 2016. | Series: Mycology series Identifiers: LCCN 2016027059| ISBN 9781498706650 (hardback : alk. paper) | ISBN a 9781498706674 (e-book) Subjects: LCSH: Fungal communities. | Fungi-- Ecology. Classification: LCC QK604.2.C64 F86 2016 | DDC 579.5-- dc23 LC record available at https://lccn.loc.gov/2016027059 Visit the Taylor & Francis Web site at http://www.taylorandfrancis.com and the CRC Press Web site at http://www.crcpress.com Contents Introduction ...........................................................................................................................................................................xiii Editors ....................................................................................................................................................................................xv Contributors .........................................................................................................................................................................xvii Part I Integrating Genomics and Metagenomics into Community Analysis Chapter 1 Molecular Community Ecology of Arbuscular Mycorrhizal Fungi ........................................................................................3 Joe D. Taylor, Thorunn Helgason, and Maarja Öpik Chapter 2 Comparative and Functional Genomics of Ectomycorrhizal Symbiosis ...............................................................................27 Joske Ruytinx and Francis Martin Chapter 3 Early Fungi: Evidence from the Fossil Record ......................................................................................................................37 Michael Krings, Thomas N. Taylor, and Carla J. Harper Chapter 4 Evolution of Lichens ...............................................................................................................................................................53 H. Thorsten Lumbsch and Jouko Rikkinen Part II Recent Advances in Fungal Endophyte Research Chapter 5 A Novel Framework for Decoding Fungal Endophyte Diversity ..........................................................................................65 Natalie Christian, Briana K. Whitaker, and Keith Clay Chapter 6 Foliar Endophyte Communities and Leaf Traits in Tropical Trees .......................................................................................79 Sunshine Van Bael, Catalina Estrada, and A. Elizabeth Arnold Chapter 7 Community Assembly of Phyllosphere Endophytes: A Closer Look at Fungal Life Cycle Dynamics, Competition, and Phytochemistry in the Shaping of the Fungal Community ............................................................................................95 Christopher B. Zambell and James F. White Chapter 8 Interactions between Fungal Endophytes and Bacterial Colonizers of Fescue Grass .........................................................109 Elizabeth Lewis Roberts and Christopher Mark Adamchek vii viii CONTENTS Part III Fungal Communities in Terrestrial Ecosystems Chapter 9 Geomycology: Geoactive Fungal Roles in the Biosphere .....................................................................................................121 Geoffrey Michael Gadd Chapter 10 Lichens and Microfungi in Biological Soil Crusts: Structure and Function Now and in the Future ...................................137 Jayne Belnap and Otto L. Lange Chapter 11 Ecology of Fungal Phylloplane Epiphytes ............................................................................................................................159 Katalin Malcolm and John Dighton Chapter 12 Wood Decay Communities in Angiosperm Wood ...............................................................................................................169 Lynne Boddy, Jennifer Hiscox, Emma C. Gilmartin, Sarah R. Johnston, and Jacob Heilmann-Clausen Chapter 13 Lichens in Natural Ecosystems .............................................................................................................................................191 Darwyn Coxson and Natalie Howe Part IV Fungal Communities in Marine and Aquatic Ecosystems Chapter 14 Diversity and Role of Fungi in the Marine Ecosystem ........................................................................................................207 Chandralata Raghukumar Chapter 15 Aquatic Hyphomycete Communities in Freshwater ............................................................................................................225 Kandikere R. Sridhar Chapter 16 The Ecology of Chytrid and Aphelid Parasites of Phytoplankton .......................................................................................239 Thomas G. Jephcott, Floris F. van Ogtrop, Frank H. Gleason, Deborah J. Macarthur, and Bettina Scholz Chapter 17 Crown Oomycetes Have Evolved as Effective Plant and Animal Parasites ........................................................................257 Agostina V. Marano, Frank H. Gleason, Sarah C. O. Rocha, Carmen L. A. Pires-Zottarelli, and José I. de Souza CONTENTS ix Part V Fungal Adaptations to Stress and Conservation Chapter 18 Adaptations of Fungi and Fungal-Like Organisms for Growth under Reduced Dissolved Oxygen Concentrations ...........275 Sandra Kittelmann, Cathrine S. Manohar, Ray Kearney, Donald O. Natvig, and Frank H. Gleason Chapter 19 Fungi in Extreme and Stressful Environments ....................................................................................................................293 Sharon A. Cantrell Chapter 20 Reaching the Wind: Boundary Layer Escape as a Constraint on Ascomycete Spore Dispersal .........................................309 Anne Pringle, Michael Brenner, Joerg Fritz, Marcus Roper, and Agnese Seminara Chapter 21 Who Cares? The Human Perspective on Fungal Conservation ............................................................................................321 Elizabeth S. Barron Part VI Fungal–Faunal Interactions Chapter 22 Belowground Trophic Interactions ........................................................................................................................................333 Amy Treonis Chapter 23 Mycophagy and Spore Dispersal by Vertebrates .................................................................................................................347 Alessandra Zambonelli, Francesca Ori, and Ian Hall Chapter 24 The Fungal Spore: Myrmecophilous Ophiocordyceps as a Case Study ...............................................................................359 João P. M. Araújo and David P. Hughes Chapter 25 Coevolution of Fungi and Invertebrates ...............................................................................................................................369 Xingzhong Liu, Lin Wang, and Meichun Xiang Chapter 26 Fungal Diversity of Macrotermes–Termitomyces Nests in Tsavo, Kenya ...........................................................................377 Jouko Rikkinen and Risto Vesala x CONTENTS Chapter 27 Emerging Mycoses and Fungus-Like Diseases of Vertebrate Wildlife ...............................................................................385 Hannah T. Reynolds, Daniel Raudabaugh, Osu Lilje, Matthew Allender, Andrew N. Miller, and Frank H. Gleason Chapter 28 Geomyces and Pseudogymnoascus: Emergence of a Primary Pathogen, the Causative Agent of Bat White-Nose Syndrome .............................................................................................................................................................................405 Michelle L. Verant, Andrew M. Minnis, Daniel L. Lindner, and David S. Blehert Part VII Fungal Communities, Climate Change, and Pollution Chapter 29 Mycorrhizal Fungi and Accompanying Microorganisms in Improving Phytoremediation Techniques ..............................419 Piotr Rozpądek, Agnieszka Domka, and Katarzyna Turnau Chapter 30 Effects of Toxic Metals on Chytrids, Fungal-Like Organisms, and Higher Fungi ..............................................................433 Linda Henderson, Erna Lilje, Katie Robinson, Frank H. Gleason, and Osu Lilje Chapter 31 The Fungal Community in Organically Polluted Systems ...................................................................................................459 Hauke Harms, Lukas Y. Wick, and Dietmar Schlosser Chapter 32 Fungal Communities and Climate Change ...........................................................................................................................471 Jennifer M. Talbot Part VIII Fungi in the Built Environment Chapter 33 Decomposition of Wooden Structures by Fungi ...................................................................................................................491 Benjamin W. Held Chapter 34 Fungal Degradation of Our Cultural Heritage ......................................................................................................................501 John Dighton Chapter 35 Microorganisms for Safeguarding Cultural Heritage ..........................................................................................................509 Edith Joseph, Saskia Bindschedler, Monica Albini, Lucrezia Comensoli, Wafa Kooli, and Lidia Mathys