The Yeast Handbook Carlos Rosa, Gábor Péter (Eds.)
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The Yeast Handbook Carlos Rosa, Gábor Péter (Eds.) Biodiversity and Ecophysiology of Yeasts With 40 Figures and 43 Tables Dr. Gábor Péter Professor Carlos Rosa Budapest University of Economic Departmento de Microbiologia Sciences and Public Administration ICB, CP 486 Faculty of Food Sciences Universidade Federal de Minas Gerais National Collection of Agricultural and Belo Horizonte, MG Industrial Microorganisms 31270-901 Somloi út 14-16 Brazil H-1118 Budapest Hungary Cover pictures by courtesy of: Vincent Robert, Centraalbureau voor Schimmelcultures (CBS), The Netherlands Carlos Rosa, Universidade Federal de Minas Gerais, Brazil ISBN-10 3-540-26100-1 Springer Berlin Heidelberg New York ISBN-13 978-3-540-26100-1 Springer Berlin Heidelberg New York Library of Congress Control Number: 2005930628 This work is subject to copyright. All rights are reserved, whether the whole or part of the mate- rial is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recita- tion, broadcasting, reproduction on microfilm or in any other way, and storage in data banks. Duplication of this publication or parts thereof is permitted only under the provisions of the German Copyright Law of September 9, 1965, in its current version, and permission for use must always be obtained from Springer. Violations are liable to prosecution under the German Copyright Law. Springer-Verlag is a part of Springer Science+Business Media springeronline.com © Springer-Verlag Berlin Heidelberg 2006 Printed in Germany The use of general descriptive names, registered names, trademarks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. Editor: Dr. Sabine Schreck, Heidelberg Desk Editor: Anette Lindqvist, Heidelberg Production: SPI Publisher Services Typesetting: SPI Publisher Services Cover Design: Design & Production, Heidelberg Printed on acid-free paper 39/3152-HM 543210 Preface Biological diversity or biodiversity, according to the United Nations Convention on Biological Diversity, “means the variability among living organisms from all sources including, inter alia, terrestrial, marine and other aquatic ecosystems and the eco- logical complexes of which they are part” and includes genetic diversity, species diversity, and ecological diversity. Authors trying to estimate the number of extant yeast species usually come to the conclusion that, similarly to other groups of microorganisms, a very small proportion of the yeasts, possibly only 1% of the species, have been described. Studies on “yeast biodiversity” are more focused on taxonomic inventories, with emphasis on the description of novel species. Approximately 30% of known yeast species were described from a single strain, and information about the ecology and the genetic and physiological variability of these yeasts is missing or incomplete. In the last few decades an increasing number of new yeast habitats have been explored. As a result, a large body of ecological information has been accumulated and the number of known yeast species has increased rapidly. The volume “Biodiversity and ecophysiology of yeasts” provides a comprehensive and up-to- date overview of several areas in the field of yeast biodiversity and ecology. The chapters are written by respected experts in various fields. The first chapters approach yeast biodiversity from different points of view, including phylogenetics and genomics. Some aspects of sugar and nitrogen metabolism are also discussed. Separate chapters are devoted to stress responses of yeasts, to environmental factors influencing them, to antagonistic interactions among them, to methods used for investigating yeast biodiversity, and to the role of culture collections in handling the ever-increasing number of yeast strains and relevant data. The chapters dealing with yeast communities from different habitats include reviews on yeasts from invertebrates, the phylloplane, soil, freshwater and marine ecosystems, cactophilic communities, as well as Antarctic and tropical forest ecosys- tems. In some chapters the effect of human activity on yeast communities is also considered. The black yeasts are treated in a separate chapter, and finally the role of yeast biodiversity in biotechnology is reviewed. We gratefully acknowledge the contributors to this book. We hope that it will provide a useful overview of the biodiversity and ecophysiology of yeasts, and that it will stimulate increasing efforts in yeast biodiversity research. Carlos Rosa Gábor Péter May 2005 Acknowledgements C.A. Rosa acknowledges the CNPq (Conselho Nacional de Desenvolvimento Científico e Tecnológico) for support of research on yeast biodiversity. Special thanks are extended to J.R. Nicoli, R.P. Martins, F.A. Silveira, M.A. Lachance, B.M. Borelli, A.O. Medeiros, L.C.R.S. Teixeira, I.C.A. Lacerda, B.S. Missagia, I.G. Gabler and F.C.O. Gomes for assistance during the review process of this book. Contents 1 Yeast Biodiversity: How Many and How Much? Marc-André Lachance . 1 2 Yeast Systematics and Phylogeny – Implications of Molecular Identification Methods for Studies in Ecology Cletus P. Kurtzman and Jack W. Fell . 11 3 Yeast Biodiversity and Culture Collections Vincent Robert, Joost Stalpers, Teun Boekhout and Shu-hui Tan . 31 4 Genomics and Biodiversity in Yeasts M. Bolotin-Fukuhara . 45 5 Methods for Investigating Yeast Biodiversity K. Boundy-Mills . 67 6 Sugar Metabolism in Yeasts: an Overview of Aerobic and Anaerobic Glucose Catabolism Fernando Rodrigues, Paula Ludovico and Cecília Leão . 101 7 Diversity of Nitrogen Metabolism Among Yeast Species: Regulatory and Evolutionary Aspects Francine Messenguy, Bruno André and Evelyne Dubois . 123 8 Environmental Factors Influencing Yeasts Tibor Deak . 155 9 Yeast Responses to Stresses An Tanghe, Bernard Prior and Johan M. Thevelein . 175 x Contents 10 Antagonistic Interactions Among Yeasts W.I. Golubev . 197 11 Yeasts in Soil Alfred Botha . 221 12 Yeast Biodiversity in Freshwater, Marine and Deep-Sea Environments Takahiko Nagahama . 241 13 Phylloplane Yeasts Á. Fonseca and J. Inácio . 263 14 Yeast and Invertebrate Associations Philip F. Ganter . 303 15 Yeasts in Extreme Environments Peter Raspor and Jure Zupan . 371 16 Yeast Biodiversity in the Antarctic Helen S. Vishniac . 419 17 Yeast Biodiversity in Tropical Forests of Asia Takashi Nakase, Sasitorn Jindamorakot, Somjit Am-in, Wanchern Potacharoen and Morakot Tanticharoen . 441 18 Yeast Communities in Tropical Rain Forests in Brazil and other South American Ecosystems Paula B. Morais, Fernando C. Pagnocca and Carlos A. Rosa . 461 19 The Biogeographic Diversity of Cactophilic Yeasts William T. Starmer, Virginia Aberdeen and Marc-André Lachance . 485 20 Black Yeasts and Meristematic Fungi: Ecology, Diversity and Identification Katja Sterflinger . 501 21 Yeasts as Indicators of Environmental Quality Allen N. Hagler . 515 22 Yeast Biodiversity and Biotechnology Pietro Buzzini and Ann Vaughan-Martini . 533 Index . 561 Chapter 1 Yeast Biodiversity: How Many and How Much? MARC-ANDRÉ LACHANCE Department of Biology, University of Western Ontario, London, ON, Canada N6A 5B7 (e-mail: [email protected]) 1.1 Introduction Biodiversity is now a common word. Harper and Hawksworth (1995) tabulated the frequency of use of the term in Biosis and reported its first occurrence in 1988 fol- lowed by an increase to approximately 900 by 1994. A similar search of the PubMed database yielded a cumulative total of 1,361 hits by the end of 2003. By comparison, the number of articles using the word “yeast” is approaching 100,000. If the present trend continues, by the year 2016 searches for either word will produce in excess of 36,000 hits for that year only. The task at hand is to make similar predictions about yeast biodiversity. Biodiversity means different things to different individuals. Gaston (1996) reviewed several definitions and concluded that the concept is an abstract expression of all aspects of the variety of life. Recent publications dealing with yeast diversity, had they appeared only 15 years earlier, might have used instead such terms as tax- onomy, ecology, or survey (Nout et al. 1997; Buzzini and Martini 2000; Fell et al. 2000; Poliakova et al. 2001; Gadanho et al. 2003; Granchi et al. 2003; Lachance et al. 2003a; Ganga and Martinez 2004; Renker et al. 2004) or even enzymology (Lamb et al. 1999). The Convention on Biological Diversity (Anonymous 1992) defines bio- logical diversity as “the variability among living organisms from all sources includ- ing, inter alia, terrestrial, marine and other aquatic ecosystems and the ecological complexes of which they are part; this includes diversity within species, between species and of ecosystems.” As with most things in our society, biodiversity became a tangible reality when it could be assigned a significant economic value. And as with most things in science, the recognition of biodiversity as a worthy research topic is predicated on measurability and the generation of testable hypotheses. The current urgency of the scientific study of biodiversity stems from the realization that only a small fraction (approximately 8%) of the total diversity of life is known (Stork 1999) and that species extinction is occurring at a measurable and increasing rate (Purvis and Hector 2000). 2 Marc-André Lachance 1.2 Measurement and Significance of Biodiversity 1.2.1 Levels of Diversity The inclusion of any level of biological