The MycotaEdited byK. Esser

The Mycota

I Growth, Differentiation and Sexuality1st edition ed. by J.G.H. Wessels and F. Meinhardt2nd edition ed. by U. Kues and R. Fischer

II Genetics and BiotechnologyEd. by U. Kuck

III Biochemistry and Molecular BiologyEd. by R. Brambl and G. Marzluf

IV Environmental and Microbial Relationships1st edition ed. by D. Wicklow and B. Soderstrom2nd edition ed. by C.P. Kubicek and I.S. Druzhinina

V Plant Relationships1st edition ed. by G. Carroll and P. Tudzynski2nd edition ed. by H.B. Deising

VI Human and Animal Relationships1st edition ed. by D.H. Howard and J.D. Miller2nd edition ed. by A.A. Brakhage and P.F. Zipfel

VII Systematics and Evolution1st edition ed. by D.J. McLaughlin, E.G. McLaughlin, and P.A. Lemke†

2nd edition ed. by D. McLaughlin and J.W. Spatafora

VIII Biology of the Fungal CellEd. by R.J. Howard and N.A.R. Gow

IX Fungal AssociationsEd. by B. Hock

X Industrial Applications1st edition ed. by H.D. Osiewacz2nd edition ed. by M. Hofrichter

XI Agricultural ApplicationsEd. by F. Kempken

XII Human Fungal PathogensEd. by J.E. Domer and G.S. Kobayashi

XIII Fungal GenomicsEd. by A.J.P. Brown

XIV Evolution of Fungi and Fungal-like OrganismsEd. by S. Poggeler and J. Wostemeyer

XV Physiology and Genetics: Selected Basic and Applied AspectsEd. by T. Anke and D. Weber

The MycotaA Comprehensive Treatiseon Fungi as Experimental Systemsfor Basic and Applied Research

Edited by K. Esser

Industrial Applications2nd Edition

Volume Editor:M. Hofrichter

X

Series Editor

Professor Dr. Dr. h.c. mult. Karl EsserAllgemeine BotanikRuhr-Universitat44780 Bochum, Germany

Tel.: +49 (234)32-22211Fax.: +49 (234)32-14211e-mail: Karl.Esser@rub.de

Volume Editor

Professor Dr. Martin HofrichterDepartment of Bio- and Environmental SciencesInternational Graduate School of ZittauMarkt 2302763 Zittau, Germany

Tel.: +49 3583276121Fax: +49 3583612734e-mail: hofrichter@ihi-zittau.de

Library of Congress Control Number: 2010936279

ISBN 978-3-642-11457-1 e-ISBN 978-3-642-11458-8

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Karl Esser(born 1924) is retired Professor of General Botany and Directorof the Botanical Garden at the Ruhr-Universitat Bochum(Germany). His scientific work focused on basic research inclassical and molecular genetics in relation to practicalapplication. His studies were carried out mostly on fungi.Together with his collaborators he was the first to detectplasmids in higher fungi. This has led to the integration offungal genetics in biotechnology. His scientific work wasdistinguished by many national and international honors,especially three honorary doctoral degrees.

Martin Hofrichter(born 1966) studied biology (with a focus on microbiology,bioorganic chemistry and ecology) at the Friedrich SchillerUniversity of Jena, Germany. His doctoral thesis dealt with thedegradation of aromatic compounds by the mold Penicilliumfrequentans. After completing his PhD in 1994 he worked on thecatalytic system of manganese peroxidase produced by basidio-mycetous fungi in Jena and Helsinki (Finland) and became alecturer at the University of Jena in 1999. In the years 2000 and2001 he worked at the University of Helsinki on the fungaldecomposition of lignin, humic materials and organopollutantsand became a Senior Research Fellow of the Academy of Finland.He became a Professor for Environmental Biotechnology at theInternational Graduate School of Zittau (Germany) in December2001 and head of the Department of Bio- and EnvironmentalSciences in 2010. His research stays include the University ofLa Plata (Argentina), the Vietnamese Academy of Science andTechnology and the Al-Farabi University of Almaty (Kazakhstan).His research examines various aspects of secreted fungalenzymes, with special emphasis on aromatic peroxygenasesrecently discovered in his lab.

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Series Preface

Mycology, the study of fungi, originated as a sub discipline of botany and was adescriptive discipline, largely neglected as an experimental science until the earlyyears of this century. A seminal paper by Blakeslee in 1904 provided evidence for selfincompatibility, termed “heterothallism”, and stimulated interest in studies related tothe control of sexual reproduction in fungi by mating-type specificities. Soon to followwas the demonstration that sexually reproducing fungi exhibit Mendelian inheritanceand that it was possible to conduct formal genetic analysis with fungi. The namesBurgeff, Kniep and Lindegren are all associated with this early period of fungalgenetics research.These studies and the discovery of penicillin by Fleming, who shared a Nobel Prize

in 1945, provided further impetus for experimental research with fungi. Thus began aperiod of interest in mutation induction and analysis of mutants for biochemicaltraits. Such fundamental research, conducted largely with Neurospora crassa, led tothe one gene: one enzyme hypothesis and to a second Nobel Prize for fungal researchawarded to Beadle and Tatum in 1958. Fundamental research in biochemical geneticswas extended to other fungi, especially to Saccharomyces cerevisiae, and by the mid-1960s fungal systems were much favored for studies in eukaryotic molecular biologyand were soon able to compete with bacterial systems in the molecular arena.The experimental achievements in research on the genetics and molecular biology of

fungi have benefited more generally studies in the related fields of fungal biochemistry,plant pathology, medical mycology, and systematics. Today, there is much interest inthe genetic manipulation of fungi for applied research. This current interest inbiotechnical genetics has been augmented by the development of DNA-mediatedtransformation systems in fungi and by an understanding of gene expression andregulation at the molecular level. Applied research initiatives involving fungi extendbroadly to areas of interest not only to industry but to agricultural and environmentalsciences as well.It is this burgeoning interest in fungi as experimental systems for applied as well as

basic research that has prompted publication of this series of books under the titleThe Mycota. This title knowingly relegates fungi into a separate realm, distinct fromthat of either plants, animals, or protozoa. For consistency throughout this Series ofVolumes the names adopted for major groups of fungi (representative genera inparentheses) areas follows:

Pseudomycota

Division: Oomycota (Achlya, Phytophthora, Pythium)Division: Hyphochytriomycota

Eumycota

Division: Chytridiomycota (Allomyces)Division: Zygomycota (Mucor, Phycomyces, Blakeslea)

Division: DikaryomycotaSubdivision: Ascomycotina

Class: Saccharomycetes (Saccharomyces, Schizosaccharomyces)Class: Ascomycetes (Neurospora, Podospora, Aspergillus)

Subdivision: BasidiomycotinaClass: Heterobasidiomycetes (Ustilago, Tremella)Class: Homobasidiomycetes (Schizophyllum, Coprinus)

We have made the decision to exclude from The Mycota the slime molds which,although they have traditional and strong ties to mycology, truly represent nonfungalforms insofar as they ingest nutrients by phagocytosis, lack a cell wall during theassimilative phase, and clearly show affinities with certain protozoan taxa.The Series throughout will address three basic questions: what are the fungi, what

dothey do, and what is their relevance to human affairs? Such a focused andcomprehensive treatment of the fungi is long overdue in the opinion of the editors.A volume devoted to systematics would ordinarily have been the first to appear in

this Series. However, the scope of such a volume, coupled with the need to giveserious and sustained consideration to any reclassification of major fungal groups,has delayed early publication. We wish, however, to provide a preamble on the natureoff ungi, to acquaint readers who are unfamiliar with fungi with certain characteristicsthat are representative of these organisms and which make them attractive subjectsfor experimentation.The fungi represent a heterogeneous assemblage of eukaryotic microorganisms.

Fungal metabolism is characteristically heterotrophic or assimilative for organiccarbon and some nonelemental source of nitrogen. Fungal cells characteristicallyimbibe or absorb, rather thaningest, nutrients and they have rigid cellwalls. The vastmajority of fungi are haploid organisms reproducing either sexually or asexuallythrough spores. The spore forms and details on their method of production have beenused to delineate most fungal taxa. Although there is amultitude of spore forms,fungal spores are basically only of two types: (i) asexual spores are formed followingmitosis (mitospores) and culminate vegetative growth, and (ii) sexual spores areformed following meiosis (meiospores) and are borne in or upon specializedgenerative structures, the latter frequently clustered in a fruit body. The vegetativeforms of fungi are either unicellular, yeasts are an example, or hyphal; the latter maybe branched to form an extensive mycelium.Regardless of these details, it is the accessibility of spores, especially the direct

recovery of meiospores coupled with extended vegetative haploidy, that have madefungi especially attractive as objects for experimental research.The ability of fungi, especially the saprobic fungi, to absorb and grow on rather

simple and defined substrates and to convert these substances, not only into essentialmetabolites but into important secondary metabolites, is also noteworthy. Themetabolic capacities of fungi have attracted much interest in natural productschemistry and in the production of antibiotics and other bioactive compounds. Fungi,especially yeasts, are important in fermentation processes. Other fungi are importantin the production of enzymes, citric acid and other organic compounds as well as inthe fermentation of foods.Fungi have invaded every conceivable ecological niche. Saprobic forms abound,

especially in the decay of organic debris. Pathogenic forms exist with both plant andanimal hosts. Fungi even grow on other fungi. They are found in aquatic as well assoil environments, and their spores may pollute the air. Some are edible; others are

viii Series Preface

poisonous. Many are variously associated with plants as copartners in the formationof lichens and mycorrhizae, as symbiotic endophytes or as overt pathogens.Association with animal systems varies; examples include the predaceous fungi thattrap nematodes, the micro fungi that grow in the anaerobic environment of therumen, the many insect associated fungi and the medically important pathogensafflicting humans. Yes, fungi are ubiquitous and important.There are many fungi, conservative estimates are in the order of 100,000 species,

and there are many ways to study them, from descriptive accounts of organismsfound in nature to laboratory experimentation at the cellular and molecular level. Allsuch studies expand our knowledge of fungi and of fungal processes and improve ourability to utilize and to control fungi for the benefit of humankind.We have invited leading research specialists in the field of mycology to contributeto

this Series. We are especially indebted and grateful for the initiative and leadershipshown by the Volume Editors in selecting topics and assembling the experts. We haveall been a bit ambitious in producing these Volumes on a timely basis and there in liesthe possibility of mistakes and oversights in this first edition. We encourage thereadership to draw our attention to any error, omission or inconsistency in this Seriesin order that improvements can be made in any subsequent edition.Finally, we wish to acknowledge the willingness of Springer-Verlag to host this

project, which is envisioned to require more than 5 years of effort and the publicationof at least nine Volumes.

Bochum, Germany KARL ESSERAuburn, AL, USA PAUL A. LEMKE

April 1994 Series Editors

Series Preface ix

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Addendum to the Series Preface

During the Fourth International Mycological Congress in Regensburg (1989) whilerelaxing in a beer garden with Paul Lemke (USA), Dr. Czeschlik (Springer-Verlag)discussed with us the possibility to publish a series about Fungi. We both were at firstsomewhat reserved, but after a comprehensive discussion this idea looked promising.We decided to name this new series The Mycota.Then Paul Lemke and I created a program involving seven volumes covering a wide

area of Mycology. The first volume was presented in 1994 at the Fifth InternationalMycological Congress in Vancover (Canada). The other volumes followed step bystep. After the early death of Paul Lemke (1995) I proceeded alone as Series Editor.However for Vols. X-XII I received support by Joan Bennett.Since evidently the series was well accepted by the scientific community and since

the broad area of Fungi was not completely covered, it was decided to proceed witheight more volumes. In addition, second editions of eight volumes were published.I would like to thank Springer-Verlag, represented by Drs. Czeschlik and

Schlitzberger for their support and cooperation.

Bochum, Germany KARL ESSERMay 2010

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Volume Preface to the Second Edition

For more than 5000 years mankind has been using fungi in the production of beveragesand food, and the basics of these techniques are nowadays still the same as in ancienttimes. Thus already the Sumerians and Egyptians made use of yeasts to make beer, wineand bread. Fruiting bodies of basidiomycetes and ascomycetes, colloquially calledmushrooms, have contributed to man’s alimentation and medicine for centuries. Whilethese mushrooms were initially still collected in forests, they were later cultivated ona larger scale in different regions of the world. Today, these traditional processes areperformed on an industrial scale along with the manufacturing of the products ofmodern fungal biotechnology, such as organic acids, antibiotics, secondary metabolitesand biotransformation products, as well as enzymes. Furthermore fungi and theirenzymes can be applied for the processing of lignocelluloses and textiles or for bio-remediation purposes. This issue of The Mycota deals with all these applications offungi and tries to give an overview on recent achievements in this sector, not leastagainst the background of rapidly developing white biotechnology and the growing fieldof modern molecular biology. In this context, the second edition of this book both triesto continue the excellent concept of the first edition by updating respective chapters andto introduce fresh ideas by supplementing new chapters.The first section of the book (Chapters 1–4), describes the state of the art in the

production and conservation of food and beverages using traditional processes ofindustrial mycology. In this context, both classic Oriental and European productssuch as beer, wine, cheese and bread as well as Asian fermented food like tofu, tempeor soy sauce are dealt with. These products are produced on a scale of millions oftonnes and represent the largest market for fungal biotechnology. Chapter 4 addressesthe cultivation of edible mushrooms with focus on the production of fruiting bodiesfrom lignocellulose-degrading basidiomycetes. So far, mushroom cultivation is themost economically successful method for bioprocessing lignocelluloses and manycommercial systems operate throughout the world.The second section (Chapters 5–13) is devoted to the production of fungal

metabolites and enzymes representing value-added products used in medicine,agriculture or food and textile industry. In addition to metabolites such as �-lactams(Chapter 5) and other antibiotics (Chapter 6), ergot alkaloids (Chapter 9), citric andother organic acids (Chapter 10) as well as vitamins (Chapter 11), all of which havesuccessfully been in use for decades, this section is also dedicated to promising fungalmetabolites, such as new insecticidal and nematicidal metabolites (Chapter 7) andimmunosurppressants (Chapter 8), which may be exploited in the near future.Chapter 12 deals with mushroom flavors and is probably the most comprehensivecompilation on this topic published over the past ten years. I am particularly pleasedabout the contribution of the world’s leading enzyme manufacturer, NovozymesA/S, to this book (Chapter 13), which deals with industrial enzymes from fungi, theirlarge-scale production and application.

Section three (Chapters 14–18) presents the state of the art and recent developments infungal biotransformation of small molecules, the bioconversion and treatment of ligno-celluloses and the use of fungi in metal recovery. The use of fungi for whole-cellbiotransformations is a well-developed field of fungal biotechnology and enables orfacilitates access to complex bioactive compounds – both commercial drugs and candi-dates – due to their capacity to catalyze regio- and stereoselective reactions on smallmolecules. Numerous examples are presented in Chapter 14 and show that traditionalbiotransformation remains a viable and feasible option to derivatize natural products in aspecific way. Lignocelluloses represent the major resource of renewable organic matterand their gentle, i.e. preferably biological disintegration will be a prerequisite for thedevelopment of suitable technologies converting them to chemical feedstock, for example,second-generation biofuels. To reach this ambitious goal, a profound knowledge of theunderlying biochemical reactions is required. Therefore Chapter 15 focuses, in first place,on the basics of lignocellulose degradation by white-rot and brown-rot fungi. Though notall details of these radical mediated processes have been elucidated so far, importantprogress has been made towards the understanding of their enzymatic basis over the lastyears. Powerful hydrolytic enzymes (cellulases, xylanases) are produced by the modelfungus Aspergillus niger and their production, optimization and application is describedin Chapter 16. Not least, the removal of pitch deposits from pulp, disturbing the paper-making process, by lipases is a good example for the introduction of an innovative fungalproduct to the market (Chapter 17). The final chapter of this section shows that fungalbiomass can be used to accumulate and remove different cations, which makes it pro-mising for recovering valuable metals from dilute solutions and purify waste water.The final section (Chapters 19–22) introduces some innovative recent develop-

ments in the field of applied mycology, among others, the preparation of fungalbioherbicides (Chapter 19), recent genomic approaches for the identification ofbiopolymer degrading enzymes (Chapter 20), new trends in using oxidative enzymesfrom fungi in chemical synthesis (Chapter 21) and new attempts to transfer fungalremediation technologies into practice (Chapter 22).The new impetus given to fungal biotechnology in recent years has come from the

rapid developments in genetic engineering which introduce the possibility of tailoringorganisms: (i) to optimize the production of established or novel metabolites andenzymes of commercial importance and (ii) to transfer genetic material from oneorganism to another. In particular, Chapters 10, 16 and 20 take these developments indifferent fields into account.From the onset of the conception of this book, it was obvious that the range of topics

we wished to include virtually necessitated drawing on the expertise of a considerablenumber of scientists from different countries. I was aware that the adoption of such amulti-author format entailed risks that might be impact negatively on the uniformityand timetable for completion of the book. However, when this book is viewed in itstotality, I believe that the overall quality and usefulness of its contents vindicates thedecision to ask colleagues from all over the world to contribute to this book.I am very grateful to the many authors and experts in the field of applied mycology

and fungal biotechnology who wrote chapters for this book. Their expertise, enthusiasmand the costly time which they devoted to their writing is highly appreciated.Last but not least, I would like to express my gratitude to the series editor Karl Esser

and Andrea Schlitzberger from the publisher Springer for their excellent support andthe customary professionalism.

Zittau, Germany MARTIN HOFRICHTER

June 2010 Volume Editor

xiv Volume Preface to the Second Edition

Volume Preface to the First Edition

The fungi, including yeast and mycelial species, are a very heterogeneous group ofeukaryotic microorganisms with a broad potential of applications in various fields ofindustrial mycology. The use of yeast in food and beverage production dates backto ancient times. Thousands of years before Christ, the Sumerians, Babyloniansand Egyptians used yeast to produce bread and alcoholic beverages. Today, yeastand other fungi are also the basic organisms used for the production, processing andconservation of food, both at the household and the industrial scale. The productionof antibiotics and chemicals is another more recent field in which fungi play aparamount role. Today, from the economic point of view, fungi dominatebiotechnology. It can be expected that this will not change in the near future sincethere is a growing interest to use these organisms for various novel applications.In this issue of The Mycota, an overview is provided on both the state of the art intraditional fields of industrial mycology as well as on the evaluation of novel appli-cations of fungi in agriculture, environmental biology and medicine. Chapters 1–3 aredevoted to the traditional use of fungi in the production and processing of food andbeverages. Different aspects dealing with the specific needs to control the quality ofproducts, to improve production processes and to introduce novel products on themarket are dealt with.In the second section of the book, an overview of different fungal metabolites and

enzymes is given. This is a huge field of applied mycology.Therefore, only someexamples from different groups of compounds are provided, emphasizing the widerange of valuable substances produced by fungi. First, metabolites directed againstbacteria as well as against insects and nematodes are introduced in Chapters 4–6.Whereas the first group of metabolites contains the classical antibiotics which havebeen so efficiently used in medicine over more than half a century, the lattersubstances have not developed into commercial products, but have importantpotential as plant protectants. Chapters 7 and 8 are devoted to the pharmaceuticallyimportant agents, immunosuppressants and the ergot alkaloids. In particular, the useof the former to prevent the rejection of transplanted organs is of prime relevance inthe corresponding field of modern medicine. The search for improved substances andthe development of improved strains following classical and modern strategies iscurrently the subject of intensive investigations.The same is true for the production ofergot alkaloids, which are produced as the result of the complex interaction betweena fungus and a higher plant. Chapter 9 summarizes current knowledge about planthormones produced by fungi. The potential applications of plant hormones inagriculture and plant protection are discussed. The production of organic acids isanother ‘‘classical’’ field of applied mycology. It is introduced in Chapter 10, whichfocuses on citric acid, the major organic acid produced on an industrial scale.Chapters 11 and 12 deal with vitamins as essential micronutrients and withcarotinoids, important food supplements. As in the production of other compounds,

these compounds will only be produced via fungal fermentation if the costs arecompetitive with the chemical production. A detailed knowledge of the biochemistryand molecular biology underlying the synthesis of these compounds is thusimportant. The last chapter of this section (Chapter 13) deals with enzymes, anothergroup of compounds traditionally produced by fungi. In this chapter, emphasis is onplant cell degrading enzymes which have wide applications in the food and feed aswell as in the paper and pulp industry.In the next seetion of this book, Chapters 14–18 focus on the use of fungi for con-

verting different substrates or for recovering substances from solutions, Chapter 14deals with the use of fungi Ior catalyzing specific reactions, leading to the conversionof a certain substrate to a specific product.This field of applied mycology is welldeveloped. However, there still remains a huge potential for improvement since manybiocatalytic activities of fungi are unknown or are not used economically. Manypossibilities to improve strains and processes can be envisaged, Chapters 15–17summarize developments to utilize the ability of many fungi to disassemble complexpolymers like lignin, cellulose and coal. These processes are very important forrecycling organic material and are of particular industrial significance, e.g. in paperproduction, Biosolubilization of low-rank coal to a fluid form for transportation isanother example. However, although in principle possible, the economic use of thisapproach rernains to be demonstrated. Chapter 18 deals with the ability of fungi toremove different metals from dilute solutions. In principle, biosorption is a suitableapproach to purify wastewater and recycle it efficiently.The last three chapters of this Volume (Chapters 19–21) present examples of more

recent concepts which, in the near future, may have an important impact on industrialmycology. Chapter 19 summarizes the strategies and developments in the field ofweed control. The goal is the controlled damage of weed populations by fungal plantpathogens. From this chapter it becomes clear that currently there are a varietyof problems and constraints that need to be overcome before bioherbicides will beable to compete with chemical herbicides. The genetic engineering of ‘‘unsuitable’’pathogens into effective biocontrol agents seems to be one promising strategy. Inaddition to the construction of suitable bioherbicides, their conservation is anotherimportant practical issue. Chapter 20 deals with the problern of developiug myco-herbicides. Finally, Chapter 21 provides an overview of the concept to use mycelialfungi as biological systems to produce heterologous proteins. The use of specificspecies, for which a huge body of experience exists aud which are classified as beingsafe, appears to be very promising. Within the next decade this concept may open newavenues iu iudustrial mycology.I hope that, although additional topics could have been iucluded in this issue, the

selection of issues presented here provides a good overview of both traditional as wellmodern and future aspects of applied mycology. I also hope that this Volume will beof interest not only to researchers working iu the immediate field of industrialmycology,but also to biologists and graduate students wishing to acquire an overviewof the potential applications of fungi in the various fields of life sciences.Finally, I would like to express my gratitude to all authors for their important

contributions to this book.

Frankfurt, Germany H.D. OSIEWACZT

July 2001 Volume Editor

xvi Volume Preface to the First Edition

Contents

Traditional Food and Beverage Fermentation

1 Production of Bread, Cheese and Meat . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3KLAUS GORI, METTE DINES CANTOR, MOGENS JAKOBSEN, LENE JESPERSEN

2 Asian Fungal Fermented Food . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29M.J. ROBERT NOUT, KOFI E. AIDOO

3 Production of Beer and Wine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59WINFRIED HARTMEIER, MONIKA REISS

4 Production of Edible Mushrooms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79RAMESH CHANDRA UPADHYAY, MANJIT SINGH

Metabolites and Enzymes

5 The �-Lactam Antibiotics: Current Situation and Future Prospectsin Manufacture and Therapy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101FRANK-RAINER SCHMIDT

6 Non-�-Lactam Antibiotics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 123GERHARD ERKEL

7 Insecticidal and Nematicidal Metabolites from Fungi . . . . . . . . . . . . . . . . . . . . . . . . . . 151HEIDRUN ANKE

8 Immunomodulators . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 165HESHAM EL ENSHASY

9 Ergot Alkaloids . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 195DANIEL G. PANACCIONE

10 Production of Organic Acids by Filamentous Fungi . . . . . . . . . . . . . . . . . . . . . . . . . . . . 215CHRISTIAN P. KUBICEK, PETER PUNT, JAAP VISSER

11 Production of Vitamin B2 and a Polyunsaturated Fatty Acid by Fungi . . . . . . 235K.-PETER STAHMANN

12 Fungal Flavours . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 249MARCO A. FRAATZ, HOLGER ZORN

13 Industrial Applications of Fungal Enzymes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 269LARS H. ØSTERGAARD, HANS SEJR OLSEN

Biotransformations, Lignocellulose Conversion and Recoveryof Metals from Solution

14 Fungal Biotransformations in Pharmaceutical Sciences . . . . . . . . . . . . . . . . . . . . . . . . 293WOLFGANG HÜTTEL, DIRK HOFFMEISTER

15 Fungal Biodegradation of Lignocelluloses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 319ANNELE HATAKKA, KENNETH HAMMEL

16 (Hemi-)Cellulose Degrading Enzymes and Their Encoding Genesfrom Aspergillus and Trichoderma . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 341RONALD P. DE VRIES, EVY BATTAGLIA, PEDRO M. COUTINHO, BERNARD HENRISSAT,JAAP VISSER

17 Fungi and Their Enzymes for Pitch Control in the Pulpand Paper Industry . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 357ANA GUTIÉRREZ, JOSÉ C. DEL RÍO, ÁNGEL T. MARTÍNEZ

18 Biosorption of Metals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 379MARTIN ZIMMERMANN, KLAUS WOLF

Recent Developments and New Strategies

19 Bioherbicides . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 395ALICE L. PILGERAM, DAVID C. SANDS

20 Genomic Approaches for Identification of the BiopolymerDegrading Enzyme Network of Aspergillus niger . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 407R.M. VAN DER KAAIJ, A.F.J. RAM, P. SCHAAP, P.J. PUNT

21 New Trends in Fungal Biooxidation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 425MARTIN HOFRICHTER, RENÉ ULLRICH

22 Fungal Soil Bioremediation: Developments Towards Large-ScaleApplications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 451KARI STEFFEN, MARJA TUOMELA

Biosystematic Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 469

Subject Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 477

xviii Contents

List of Contributors

KOFI E. AIDOO

(e-mail: k.aidoo@gcal.ac.uk)Food Research Laboratories, School of Biological and Biomedical Sciences, GlasgowCaledonian University, Cowcaddens Road, Glasgow, G4 0BA, United Kingdom

HEIDRUN ANKE

(e-mail: anke@ibwf.de, Tel.: +49 631-3167210, Fax: +49 631-3167215)Institute for Biotechnology and Drug Research, IBWF e.V., Erwin-Schroedinger-Strasse 56, 67663 Kaiserslautern, Germany

EVY BATTAGLIA

Microbiology, Utrecht University, Utrecht, The Netherlands

METTE DINES CANTOR

Department of Food Science, Faculty of Life Sciences, University of Copenhagen,Rolighedsvej 30, 1958 Frederiksberg C, Denmark

PEDRO M. COUTINHO

AFMB – UMR 6098 CNRS/Universites Aix-Marseille I and II, Marseille, France

RONALD P. DE VRIES

(e-mail: r.devries@cbs.knaw.nl, Tel.: +31 302122689, Fax: +31 302612097)CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands

JOSE C. DEL RIO

Instituto de Recursos Naturales y Agrobiologıa, CSIC, Po Box 1052, 41080 Seville,Spain

HESHAM EL ENSHASY(e-mail: hesham@utm.my)Chemical Engineering Pilot Plant (CEPP), Faculty of Chemical and Natural ResourcesEngineering, University Technology Malaysia (UTM), 81310 Skudai, Johor, Malaysia;and Bioprocess Development Department, Mubarak City for Scientific Research andTechnology Applications (MuCSAT), New Burg Al Arab, Alexandria, Egypt

GERHARD ERKEL(e-mail: erkel@ibwf.de, Tel.: +49 631-205-2881)Department of Biotechnology, University of Kaiserslautern, Paul-Ehrlich-Strasse 23,67663 Kaiserslautern, Germany

MARCO A. FRAATZ(e-mail: marco.fraatz@lcb.chemie.uni-giessen.de)Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen,Heinrich-Buff-Ring 58, 35392 Giessen, Germany

KLAUS GORI

(e-mail: klg@life.ku.dk, Tel.: +45 3533-3284, Fax: +45 3533-3214)Department of Food Science, Faculty of Life Sciences, University of Copenhagen,Rolighedsvej 30, 1958 Frederiksberg C, Denmark

ANA GUTIERREZ

(e-mail: anagu@irnase.csic.es, Tel.: +34 954624711, Fax: +34 954624002)Instituto de Recursos Naturales y Agrobiologıa, CSIC, Reina Mercedes 10, PO Box1052, 41080 Seville, Spain

KENNETH E. HAMMEL

(e-mail: kehammel@facstaff.wisc.edu, Tel.: +1 608-231-9528, Fax: +1 608-231-9262)USDA Forest Products Laboratory, University of Wisconsin, One Gifford PinchotDrive, Madison, WI 53726, USA

WINFRIED HARTMEIER

(e-mail: w.hartmeier@biotec.rwth-aachen.de)RWTH Aachen University, Lehrstuhl fur Biotechnologie, Worringer Weg 1, 52074Aachen, Germany

ANNELE HATAKKA

(e-mail: annele.hatakka@helsinki.fi, Tel.: +348 9-19159314, Fax: +358 9-19159322)Department of Food and Environmental Sciences, University of Helsinki, PO Box 56,Viikki Biocenter, Viikinkaari 9, 00014, Finland

BERNARD HENRISSAT

AFMB – UMR 6098 CNRS / Universites Aix-Marseille I and II, Marseille, France

DIRK HOFFMEISTER

(e-mail: dirk.hoffmeister@hki-jena.de, Tel.: +49 3641-532-1310, Fax: +49 3641-532-0812)Department of Pharmaceutical Biology at the Hans-Knoll-Institut, Friedrich-Schiller-Universitat Jena, Beutenbergstrasse 11a, 07745 Jena, Germany

MARTIN HOFRICHTER

(e-mail: hofrichter@ihi-zittau.de)International Graduate School of Zittau, Department of Bio- and EnvironmentalSciences, Markt 23, 02763 Zittau, Germany

WOLFGANG HUTTEL

Albert-Ludwigs-Universitat, Pharmaceutical and Medicinal Chemistry, Albertstrasse25, 79104 Freiburg, Germany

MOGENS JAKOBSEN(e-mail: moj@life.ku.dk, Tel.: +45 3533-3216, Fax: +45 3533-3214)Department of Food Science, Faculty of Life Sciences, University of Copenhagen,Rolighedsvej 30, 1958 Frederiksberg C, Denmark

xx List of Contributors

LENE JESPERSENDepartment of Food Science, Faculty of Life Sciences, University of Copenhagen,Rolighedsvej 30, 1958 Frederiksberg C, Denmark

CHRISTIAN P. KUBICEK

(e-mail: ckubicek@mail.zserv.tuwien.ac.at, Tel.: +43 1-58801-17250, Fax: +43 1-58801-17299)Research Area Gene Technology and Applied Biochemistry, Institute of ChemicalEngineering, Technische Universitat Wien, Getreidemarkt 9/166, 1060 Vienna, Austria

ANGEL T. MARTINEZ

Centro de Investigaciones Biologicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid Spain

M.J. ROBERT NOUT

(e-mail: rob.nout@wur.nl)Laboratory of Food Microbiology, Wageningen University, Bomenweg 2, 6703 HD,Wageningen, The Netherlands

HANS SEJR OLSEN

(e-mail: hso@novozymes.com)Novozymes A/S, Krogshøjvej 36, 2880 Bagsværd, Denmark

LARS H. ØSTERGAARD

(e-mail: laq@novozymes.com, Tel.: +45 444-60271)Novozymes A/S, Krogshøjvej 36, 2880 Bagsværd, Denmark

DANIEL G. PANACCIONE(e-mail: danpan@wvu.edu, Tel.: +1 304-293-8819)Division of Plant and Soil Sciences, West Virginia University, PO Box 6108,Morgantown, WV 26506, USA

ALICE L. PILGERAM

(e-mail: pilgeram@montana.edu)Plant Sciences and Plant Pathology, Montana State University, 131 Plant BioScienceBuilding, Bozeman, MT 59717-31, USA

PETER J. PUNT

(e-mail: peter.punt@tno.nl)Department Food and Biotechnology Innovations, TNO Quality of Life, Utrechtseweg48, 3704HE, Zeist, The Netherlands; and Sylvius Laboratory, Institute of Biology,Leiden University, Sylviusweg 72, 2333BE Leiden, The Netherlands

A.F.J. RAM

(e-mail: a.f.j.ram@biology.leidenuniv.nl)Institute of Biology Leiden, Leiden University, Molecular Microbiology andBiotechnology, Sylviusweg 72, 2333BE Leiden, The Netherlands; and Kluyver Centrefor Genomics of Industrial Fermentation, PO Box 5057, 2600 GA, Delft, TheNetherlands

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MONIKA REISS

(e-mail: m.reiss@biotec.rwth-aachen.de)RWTH Aachen University, Lehrstuhl fur Biotechnologie, Worringer Weg 1, 52074Aachen, Germany

DAVID C. SANDS(e-mail: dsands@montana.edu, Tel.: +1 406-994-5151, Fax: +1 406-994-7600)Plant Sciences and Plant Pathology, Montana State University, 204 Plant BioScienceBuilding, Bozeman, MT 59717-0001, USA

PETER SCHAAP(e-mail: peter.schaap@wur.nl)Kluyver Centre for Genomics of Industrial Fermentation, PO Box 5057, 2600 GA, Delft,The Netherlands; and Laboratory of Microbiology, Section Fungal Genomics,Wageningen University, Dreijenplein 10, 6703 HB, Wageningen, The Netherlands

FRANK-RAINER SCHMIDT

(e-mail: frank-rainer.schmidt@sanofi-aventis.com, Tel.: 49 69-305-6757)Sanofi-Aventis Deutschland GmbH, Prozeßentwicklung Chemie, Bldg K607,Industriepark Hoechst, 65926 Frankfurt am Main, Germany

MANJIT SINGHDirectorate of Mushroom Research, Solan, 173213 Himachal Pradesh, India

K.-PETER STAHMANN

(e-mail: klaus-peter.stahmann@hs-lausitz.de, Tel.: 49 69-305-6757)Fachbereich Bio-, Chemie- und Verfahrenstechnik, Hochschule Lausitz (FH),Großenhainer Str. 57, 01958 Senftenberg, Germany

KARI STEFFEN(e-mail: kari.steffen@helsinki.fi)Department of Food and Environmental Sciences, University of Helsinki, PO Box 56,00014 Helsinki, Finland

MARJA TUOMELA

(e-mail: marja.tuomela@helsinki.fi)Department of Food and Environmental Sciences, University of Helsinki, PO Box 56,00014 Helsinki, Finland

RENE ULLRICH

(e-mail: ullrich@ihi-zittau.de)International Graduate School of Zittau, Department of Bio- and EnvironmentalSciences, Markt 23, 02763 Zittau, Germany

RAMESH CHANDRA UPADHYAY

(e-mail: rc_upadhyay@hotmail.com)Directorate of Mushroom Research, Solan, 173213 Himachal Pradesh, India

RACHEL M. VAN DER KAAIJ

(e-mail: rachel.vanderkaaij@tno.nl)Department Food and Biotechnology Innovations, TNO Quality of Life, Utrechtseweg48, 3704 HE, Zeist, The Netherlands

xxii List of Contributors

JAAP VISSER

(e-mail: dr.jaapvisser@planet.nl)Sylvius Laboratory, Institute of Biology, Leiden University, Sylviusweg 72, 2333BELeiden, The Netherlands; and Fungal Genetics and Technology Consultancy, PO Box396, 6700 AJ, Wageningen, The Netherlands

KLAUS WOLF

Institut fur Biologie IV (Mikrobiologie), Rheinisch-Westfalische TechnischeHochschule Aachen, Worringerweg, 52056 Aachen, Germany

MARTIN ZIMMERMANN

(e-mail: martin.zimmermann@rwth-aachen.de, Tel.: +49 241-8026607)Institut fur Biologie IV (Mikrobiologie), Rheinisch-Westfalische TechnischeHochschule Aachen, Worringerweg, 52056 Aachen, Germany

HOLGER ZORN

(e-mail: holger.zorn@lcb.chemie.uni-giessen.de)Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen,Heinrich-Buff-Ring 58, 35392 Giessen, Germany

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