Fungi and Food Spoilage John I

Fungi and Food Spoilage John I. Pitt l Ailsa D. Hocking

Fungi and Food Spoilage

13 John I. Pitt Ailsa D. Hocking Honorary Research Fellow Honorary Research Fellow CSIRO Food and Nutritional Sciences CSIRO Food and Nutritional Sciences North Ryde, NSW 2113 North Ryde, NSW 2113 Australia Australia [email protected] [email protected]

ISBN 978-0-387-92206-5 e-ISBN 978-0-387-92207-2 DOI 10.1007/978-0-387-92207-2 Springer Dordrecht Heidelberg London New York

Library of Congress Control Number: 2009920217

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Springer is part of Springer ScienceþBusiness Media (www.springer.com) Preface to the Third Edition

In contrast to the second edition, the third edition of ‘‘Fungi and Food Spoilage’’ is evolutionary rather than revolutionary. The second edition was intended to cover almost all of the species likely to be encountered in mainstream food supplies, and only a few additional species have been included in this new edition. The third edition represents primarily an updating – of taxonomy, physiology, mycotoxin production and ecology. Changes in taxonomy reflect the impact that molecular methods have had on our understanding of classification but, it must be said, have not radically altered the overall picture. The improvements in the understanding of the physiology of food spoilage fungi have been relatively small, reflecting perhaps the lack of emphasis on physiology in modern micro- biological science. Much remains to be understood about the specificity of particular fungi for particular substrates, of the influence of water activity on the growth of many of the species treated, and even on such basic parameters as cardinal temperatures for growth and the influence of pH and preservatives. Since 1997, a great deal has been learnt about the specificity of mycotoxin production and in which commodities and products-specific mycotoxins are likely to occur. Changes in our understanding of the ecology of the included species are also in most cases evolutionary. A great number of papers have been published on the ecology of foodborne fungi in the past few years, but with few exceptions the basic ecology of the included species remains. Recent changes in our understanding of foodborne fungi include the realisa- tion that Aspergillus carbonarius is a major source of ochratoxin A in the world food supply, that A. westerdijkiae and not A. ochraceus is the other common Aspergillus species making this toxin and that these species are responsible for ochratoxin A in foods outside the cool temperate regions, where Penicillium verrucosum is the important species. In recent years a number of new species have been found to be capable of producing aflatoxin, but the fact remains that most aflatoxin in the global food supply is produced by A. flavus and A. para- siticus. The taxonomy of Fusarium species is still undergoing major revision. However, the renaming of Fusarium moniliforme as F. verticillioides is the only change of importance here. Recent publications have improved our understanding of species – mycotoxin relationships within Fusarium.

v vi Preface to the Third Edition

Among the colleagues who helped us to prepare this edition, we wish to particularly thank Dr Anne-Laure Markovina, now of the University of Sydney, who assisted in literature searches and some cultural and photographic work, and Mr N.J. Charley who has continued his excellent work of curating the FRR culture collection, on which so much of the descriptive work in this book is based. Preface to the First Edition

This book is designed as a laboratory guide for the food microbiologist to assist in the isolation and identification of common foodborne fungi. We emphasise the fungi which cause food spoilage, but also devote space to the fungi commonly encountered in foods at harvest, and in the food factory. As far as possible, we have kept the text simple, although the need for clarity in the descriptions has necessitated the use of some specialised mycological terms. The identification keys have been designed for use by microbiologist with little or no prior knowledge of mycology. For identification to genus level, they are based primarily on the cultural and physiological characteristics of fungi grown under a standard set of conditions. The microscopic features of the various fungi become more important when identifying isolates at the species level. Nearly all of the species treated have been illustrated with colony photographs, together with photomicrographs or line drawings. The photomicrographs were taken using a Zeiss WL microscope fitted with Nomarski interference contrast optics. We are indebted to Mr W. Rushton and Ms L. Burton, who printed the many hundreds of photographs used to make up the figures in this book. We also wish to express our appreciation to Dr D.L. Hawksworth, Dr A.H.S. Onions and Dr B.C. Sutton of the Commonwealth Mycological Institute, Kew, Surrey, UK, Professor P.E. Nelson and the staff of the Fusarium Research Center, University of Pennsylvania, USA and Dr L.W. Burgess of the University of Sydney, who generously provided facilities, cultures and advice on some of the genera studied.

vii Preface to the Second Edition

In planning for the second edition of ‘‘Fungi and Food Spoilage’’, we decided that the book would benefit from a larger format, which would permit improved illustrations, and from some expansion of the text, in both numbers of species treated and overall scope. These aims have been realised. The Crown Quarto size has allowed us to include substantially larger, clearer illustrations. Many new photographs and photomicrographs have been added, the latter taken using a Zeiss Axioscop microscope fitted with Nomarski differential interference contrast optics. We have taken the opportunity to include more than 40 additional species descriptions, to add a new section on mycotoxin production for each species and to update and upgrade all of the text. Since the first edition, changes in the climate for stabilising fungal nomenclature have resulted in development of a list of ‘‘Names in Current Use’’ for some important genera, including Aspergillus and Penicillium. Names of species used in the second edition are taken from that list, which was given special status by the International Botanical Congress, Tokyo, 1994. Names used in this edition have priority over any other names for a particular species. Publication of a list of ‘‘Authors of Fungal Names’’ (P.M. Kirk and A.E. Ansell, Index of Fungi, Supplement: 1–95, 1992) has also stabilised names of authorities for all fungal species. Abbreviations of authors’ names used in this edition conform to those recommended by Kirk and Ansell. Some progress in standardisation of methods and media has also been made, primarily through the efforts of the International Commission on Food Mycology. The first edition included some 400 references. When we began revisionary work, we felt that the number of references in the area of food mycology had probably doubled or increased by perhaps 150% during the intervening years. In fact, this second edition includes over 1900 references, almost a five-fold increase over the 1985 edition! This provides a clear indication that interest in, and study of, food mycology has greatly increased in recent years. Modern referencing systems have enabled us to expand information from tropical sources, especially in Asia and Africa, but we are conscious of the fact that treatment of fungi found in foods on a worldwide basis remains rather incomplete. We gratefully acknowledge support and assistance from colleagues who have contributed to this new edition. Ms J.C. Eyles formatted and printed the camera

ix x Preface to the Second Edition ready copy, Ms C. Heenan collated, arranged and formatted the illustrations and Mr N.J. Charley looked after the culture collection, culture growth and colony photography. Without this level of support, the book would not have been completed. Contents

1 Introduction ...... 1 2 The Ecology of Fungal Food Spoilage ...... 3 2.1 Water Activity ...... 3 2.2 Hydrogen Ion Concentration...... 4 2.3 Temperature ...... 5 2.4 Gas Tension ...... 7 2.5 Consistency...... 8 2.6 Nutrient Status ...... 8 2.7 Specific Solute Effects ...... 8 2.8 Preservatives ...... 9 2.9 Conclusions: Food Preservation ...... 9 3 Naming and Classifying Fungi ...... 11 3.1 Taxonomy and Nomenclature: Biosystematics ...... 11 3.2 Hierarchical Naming ...... 12 3.3 Zygomycotina...... 12 3.4 Ascomycotina...... 13 3.5 Basidiomycotina...... 15 3.6 The Ascomycete – Conidial Fungus Connection ...... 15 3.7 Dual Nomenclature ...... 15 3.8 Practical Classification of Fungi ...... 16 4 Methods for Isolation, Enumeration and Identification ...... 19 4.1 Sampling...... 19 4.2 Enumeration Techniques ...... 19 4.2.1 Direct Plating...... 20 4.2.2 Dilution Plating ...... 21 4.2.3 Incubation Conditions...... 22 4.3 Sampling Surfaces ...... 22 4.4 Air Sampling ...... 23 4.5 Isolation Techniques ...... 23 4.5.1 Yeasts ...... 23 4.5.2 Moulds...... 24 4.5.3 Short Term Storage ...... 24 4.6 Choosing a Suitable Medium ...... 25 4.6.1 General Purpose Enumeration Media...... 26 4.6.2 Selective Isolation Media...... 27 4.6.3 Techniques for Yeasts ...... 30 4.6.4 Techniques for Heat-Resistant Fungi ...... 32 4.6.5 Other Plating Techniques ...... 33 4.7 Estimation of Fungal Biomass ...... 34 4.7.1 Chitin...... 34 4.7.2 Ergosterol ...... 35 4.7.3 Impedimetry and Conductimetry ...... 37

xi xii Contents

4.7.4 Adenosine Triphosphate (ATP) ...... 37 4.7.5 Fungal Volatiles...... 37 4.7.6 Immunological Techniques ...... 38 4.7.7 Molecular Methods ...... 40 4.8 Identification Media and Methods...... 41 4.8.1 Standard Methodology ...... 41 4.8.2 Plating Regimen ...... 41 4.8.3 Inoculation ...... 41 4.8.4 Additional Media and Methods ...... 42 4.8.5 Identification of Fusarium Species...... 43 4.8.6 Yeasts...... 44 4.9 Examination of Cultures ...... 45 4.9.1 Colony Diameters ...... 45 4.9.2 Colony Characters...... 45 4.9.3 Preparation of Wet Mounts for Microscopy...... 46 4.9.4 Staining ...... 46 4.9.5 Microscopes and Microscopy ...... 47 4.10 Preservation of Fungi ...... 48 4.10.1 Lyophilisation ...... 48 4.10.2 Other Storage Techniques ...... 49 4.11 Housekeeping in the Mycological Laboratory...... 50 4.11.1 Culture Mites...... 50 4.11.2 Problem Fungi...... 51 4.11.3 Pathogens and Laboratory Safety ...... 51 5 Primary Keys and Miscellaneous Fungi ...... 53 5.1 The General Key ...... 54 5.1.1 Notes on the General Key ...... 55 5.2 Miscellaneous Fungi...... 56 5.3 Genus Acremonium Link...... 58 5.4 Genus Alternaria Nees: Fr...... 60 5.5 Genus Arthrinium Kunze ...... 64 5.6 Genus Aureobasidium Viala and G. Boyer ...... 65 5.7 Genus Bipolaris Shoemaker ...... 67 5.8 Genus Botrytis P. Micheli: Fr...... 68 5.9 Genus Chaetomium Kunze ...... 70 5.10 Genus Chrysonilia Arx...... 73 5.11 Genus Cladosporium Link...... 75 5.12 Genus Colletotrichum Corda ...... 81 5.13 Genus Curvularia Boedijn...... 82 5.14 Genus Drechslera S.Ito...... 85 5.15 Genus Endomyces Reess...... 86 5.16 Genus Epicoccum Link ...... 88 5.17 Genus Fusarium Link...... 89 5.18 Genus Geotrichum Link:Fr...... 122 5.19 Genus Hyphopichia Arx and van der Walt...... 124 5.20 Genus Lasiodiplodia Ellis and Everh...... 125 5.21 Genus Monascus Tiegh...... 127 5.22 Genus Moniliella Stolk and Dakin ...... 129 5.23 Genus Nigrospora Zimm...... 131 Contents xiii

5.24 Genus Pestalotiopsis Steyaert ...... 133 5.25 Genus Phoma Sacc...... 134 5.26 Genus Stemphylium Wallr...... 136 5.27 Genus Trichoconiella B.L. Jain...... 137 5.28 Genus Trichoderma Pers...... 139 5.29 Genus Trichothecium Link ...... 140 5.30 Genus Ulocladium Preuss ...... 142 6 Zygomycetes ...... 145 6.1 Genus Absidia Tiegh...... 148 6.2 Genus Cunninghamella Matr...... 149 6.3 Genus Mucor P. Micheli: Fr...... 151 6.4 Genus Rhizomucor (Lucet and Costantin) Vuill...... 157 6.5 Genus Rhizopus Ehrenb...... 158 6.6 Genus Syncephalastrum J. Schrot...... ¨ 165 6.7 Genus Thamnidium Link ...... 167 7 Penicillium and Related Genera ...... 169 7.1 Genus Byssochlamys Westling ...... 170 7.2 Genus Eupenicillium F. Ludw...... 175 7.3 Genus Geosmithia Pitt ...... 182 7.4 Genus Paecilomyces Bainier ...... 183 7.5 Genus Scopulariopsis Bainier ...... 187 7.6 Genus Talaromyces C.R. Benj...... 188 7.7 Genus Penicillium Link...... 194 7.7.1 Penicillium subgenus Aspergilloides Dierckx ...... 196 7.7.2 Penicillium subgenus Furcatum Pitt...... 207 7.7.3 Penicillium subgenus Penicillium ...... 223 7.7.4 Penicillium subgenus Biverticillium Dierckx ...... 263 8 Aspergillus and Related Teleomorphs...... 275 8.1 Genus Emericella Berk...... 279 8.2 Genus Eurotium Link: Fr...... 281 8.3 Genus Neosartorya Malloch and Cain ...... 292 8.4 Genus Aspergillus Fr.: Fr...... 295 9 Xerophiles ...... 339 9.1 Genus Basipetospora G.T. Cole and W.B. Kendr...... 340 9.2 Genus Chrysosporium Corda ...... 342 9.3 Genus Eremascus Eidam...... 347 9.4 Genus Polypaecilum G.Sm...... 348 9.5 Genus Wallemia Johan-Olsen...... 350 9.6 Genus Xeromyces L.R. Fraser ...... 353 10 Yeasts...... 357 11 Fresh and Perishable Foods ...... 383 11.1 Spoilage of Living, Fresh Foods ...... 383 11.2 Fruits ...... 383 11.2.1 Citrus Fruits ...... 384 11.2.2 Pome Fruits ...... 385 11.2.3 Stone Fruits ...... 386 xiv Contents

11.2.4 Tomatoes and other Solanaceous Fruit...... 387 11.2.5 Melons and other Cucurbits ...... 387 11.2.6 Grapes ...... 388 11.2.7 Berries ...... 389 11.2.8 Figs ...... 389 11.2.9 Tropical Fruit ...... 390 11.3 Vegetables...... 391 11.3.1 Peas ...... 391 11.3.2 Beans ...... 391 11.3.3 Onions and Garlic ...... 391 11.3.4 Potatoes ...... 392 11.3.5 Roots and Tubers ...... 392 11.3.6 Yams ...... 392 11.3.7 Cassava ...... 392 11.3.8 Leafy and other Green Vegetables ...... 393 11.4 Dairy Foods ...... 393 11.5 Meats ...... 394 11.6 Cereals, Nuts and Oilseeds ...... 395 11.6.1 Wheat, Barley and Oats...... 395 11.6.2 Rice ...... 396 11.6.3 Maize ...... 396 11.6.4 Soybeans and Mung Beans ...... 397 11.6.5 Other Beans and Pulses ...... 398 11.6.6 Sunflower Seed ...... 398 11.6.7 Sorghum...... 398 11.6.8 Peanuts...... 398 11.6.9 Cashews and Brazil Nuts...... 399 11.6.10 Almonds, Hazelnuts, Walnuts and Pecans ...... 399 11.6.11 Pistachios ...... 399 11.6.12 Copra ...... 400 401 12 Spoilage of Stored, Processed and Preserved Foods ...... 12.1 Low Water Activity Foods: Dried Foods ...... 401 12.1.1 Cereals ...... 402 12.1.2 Flour ...... 403 12.1.3 Pasta...... 403 12.1.4 Bakery Products...... 403 12.1.5 Maize ...... 404 12.1.6 Soybeans, Mung Beans, other Beans and Chickpeas ...... 405 12.1.7 Nuts ...... 406 12.1.8 Peanuts...... 406 12.1.9 Hazelnuts, Walnuts, Pecans and Almonds ...... 407 12.1.10 Pistachio Nuts ...... 408 12.1.11 Other Nuts ...... 409 12.1.12 Coconut ...... 409 12.1.13 Spices ...... 410 12.1.14 Coffee Beans ...... 410 12.1.15 Cocoa...... 411 12.1.16 Dried Meat ...... 412 Contents xv

12.2 Low Water Activity Foods: Concentrated Foods ...... 412 12.2.1 Jams ...... 412 12.2.2 Dried Fruit...... 413 12.2.3 Fruit Cakes ...... 414 12.2.4 Confectionery ...... 415 12.2.5 Fruit Concentrates...... 415 12.2.6 Honey and Syrups ...... 416 12.3 Low Water Activity Foods: Salt Foods ...... 416 12.4 Intermediate Moisture Foods: Processed Meats ...... 417 12.5 Heat Processed Acid Foods ...... 418 12.6 Preserved Foods ...... 418 12.7 Cheese...... 419 Media Appendix ...... 423 Glossary...... 427 References ...... 431 Index ...... 503