genomics, metabolomics and secretomics. In sum, the book contains fascinating and essential information on various fungal metabolites and their industrial.
Fungal Biomolecules
Fungal Biomolecules Sources, Applications and Recent Developments Edited by
Dr. Vijai Kumar Gupta Molecular Glycobiotechnology Group, Discipline of Biochemistry, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
Prof. Robert L. Mach Institute of Chemical Engineering and Technical Biosciences, Vienna University of Technology, Vienna, Austria
Prof. S. Sreenivasaprasad Department of Life Sciences and Institute of Biomedical and Environmental Science and Technology, University of Bedfordshire, Bedfordshire, Uk
This edition first published 2015 © 2015 by John Wiley & Sons, Ltd. Registered Office John Wiley & Sons, Ltd, The Atrium, Southern Gate, Chichester, West Sussex, PO19 8SQ, UK Editorial Offices 9600 Garsington Road, Oxford, OX4 2DQ, UK The Atrium, Southern Gate, Chichester, West Sussex, PO19 8SQ, UK 111 River Street, Hoboken, NJ 07030-5774, USA For details of our global editorial offices, for customer services and for information about how to apply for permission to reuse the copyright material in this book please see our website at www.wiley.com/wiley-blackwell. The right of the author to be identified as the author of this work has been asserted in accordance with the UK Copyright, Designs and Patents Act 1988. All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, electronic, mechanical, photocopying, recording or otherwise, except as permitted by the UK Copyright, Designs and Patents Act 1988, without the prior permission of the publisher. Designations used by companies to distinguish their products are often claimed as trademarks. All brand names and product names used in this book are trade names, service marks, trademarks or registered trademarks of their respective owners. The publisher is not associated with any product or vendor mentioned in this book. Limit of Liability/Disclaimer of Warranty: While the publisher and author(s) have used their best efforts in preparing this book, they make no representations or warranties with respect to the accuracy or completeness of the contents of this book and specifically disclaim any implied warranties of merchantability or fitness for a particular purpose. It is sold on the understanding that the publisher is not engaged in rendering professional services and neither the publisher nor the author shall be liable for damages arising herefrom. If professional advice or other expert assistance is required, the services of a competent professional should be sought. Library of Congress Cataloging-in-Publication Data Fungal biomolecules : sources, applications, and recent developments / editors, Dr. Vijai Kumar Gupta, Prof. Robert L. Mach, Prof. S. Sreenivasaprasad. pages cm Includes bibliographical references and index. ISBN 978-1-118-95829-2 (cloth) 1. Biofilms. 2. Fungal enzymes–Research. 3. Aspergillus–Research. I. Gupta, Vijai Kumar, editor. II. Mach, Robert Ludwig, editor. III. Sreenivasaprasad, S., editor. QR100.8.B55F86 2015 579′.17–dc23 2014042236 A catalogue record for this book is available from the British Library. Wiley also publishes its books in a variety of electronic formats. Some content that appears in print may not be available in electronic books. Cover images top right, going clockwise: 1) ‘Turkeytail’ image by Bill Welch, used with permission. 2) Image by Drs V.K. Gupta, A. O’Donovan and M.G. Tuohy, MGBG, Discipline of Biochemistry, National University of Ireland Galway, Galway, Ireland, used with permission. 3) Aspergillus fumigatus from Centers for Disease Control and Prevention: http://phil.cdc.gov/phil/details.asp 4) Aspergillus niger by R.H. Chichewicz, P. Larson, and G. Strout, used with permission. Set in 10/12pt Minion by SPi Publisher Services, Pondicherry, India 1 2015
Contents Contributorsix Foreword
xiii
Preface
xvii
Section 1 Fungi as cell factories
1
Chapter 1 Fungal biofilms: An overview Virginia Medeiros de Siqueira
3
Chapter 2 Fungal biomolecules for the food industry Quang D. Nguyen, Erika Bujna, Gabriella Styevkó, Judit M. Rezessy-Szabó and Ágoston Hoschke Chapter 3 Fungal biocatalysts in the textile industry: Whole‐cell systems in real textile wastewater treatment Federica Spina, Valeria Tigini, Valeria Prigione and Giovanna Cristina Varese
11
39
Chapter 4 Discovery of fungal enzymes and pathways Aleksandra Mitrovic and Anton Glieder
51
Chapter 5 Fungal laccase in the textile industry Susana Rodríguez‐Couto
63
Section 2 Production of recombinant peptides
73
Chapter 6 Lignocellulose‐degrading enzymes: An overview of the global market Paula M. D. Jaramillo, Helder A. R. Gomes, Antonielle V. Monclaro, Caio O. G. Silva and Edivaldo X. F. Filho
75
Chapter 7 Recent advancements in the role of volatile organic compounds from fungi Lourdes Macías‐Rodríguez, Hexon Ángel Contreras‐Cornejo, Jesús Salvador López‐Bucio and José López‐Bucio
87
Chapter 8 Peptaibiotics and peptaibols from fungi Susanne Zeilinger
101
v
vi
Contents
Section 3 Fungal secondary metabolites and synthesis
115
Biosynthesis of silver nanoparticles by fungi Ana Olívia de Souza and Alexandre Gomes Rodrigues
117
Chapter 10 Fungal biomolecules as modulators of growth and pathogenesis Rajesh N. Patkar and Naweed I. Naqvi
137
Chapter 11 Fungi as a source of antitumour agents Shin Yee Fung and Nget Hong Tan
145
Chapter 12 Fungal mycotoxins: an overview Svetlana V. Malysheva, José Diana Di Mavungu and Sarah De Saeger
153
Chapter 13 Fungal pigments: An overview Marcela C. Pagano and Partha P. Dhar
173
Chapter 14 An overview regarding bioherbicide and their production methods by fermentation Rodrigo Klaic, Raquel C. Kuhn, Edson L. Foletto, Valéria Dal Prá, Rodrigo J. S. Jacques, Jerson V. C. Guedes, Helen Treichel, Altemir J. Mossi, Débora Oliveira, J. Vladimir Oliveira, Sérgio L. Jahn and Marcio A. Mazutti
183
Chapter 9
Section 4 Regulation of fungal secondary metabolism
201
Chapter 15 The role of nutrients in fungal development and pathogenesis YiZhen Deng, Fan Yang and Naweed I. Naqvi
203
Chapter 16 Role of nitrogen sources in regulation of fungal secondary metabolism Bidisha Sharma and Dhruva Kumar Jha
213
Chapter 17 Regulatory genes in fungal secondary metabolism Jaswinder Kaur and Catherine Collins
225
Chapter 18 Fungal metabolic diversity Andrei Stecca Steindorff, Gabriela F. Persinoti, Valdirene Neves Monteiro and Roberto Nascimento Silva
239
Chapter 19 Secreted biomolecules in fungal plant pathogenesis Neil Andrew Brown and Kim E. Hammond‐Kosack
263
Contents
vii
Section 5 Developments and advancements
311
Chapter 20 Fungal molecular taxonomy: an overview Marcela C. Pagano and Luiz H. Rosa
313
Chapter 21 Fungal biomolecules in wines and beer industries Carlos Roberto Felix and Eliane Ferreira Noronha
323
Chapter 22 Biosorption and bioaccumulation of chromium VI by different fungal species Dhara Shukla and Padma S. Vankar
333
Chapter 23 Fungal biomolecules in plant growth promotion Hexon Angel Contreras‐Cornejo, Lourdes Macías‐Rodríguez and José López‐Bucio
345
Chapter 24 Fungal biomolecules and their implications Andleeb Zehra, Manish Kumar Dubey, Arti Tiwari, Mukesh Meena, Punam Kumari, Vivek Kumar Singh, Vijai Kumar Gupta and R. S. Upadhyay
363
Index
377
Contributors Neil Andrew Brown Faculdade de Ciências Farmacêuticas de Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
Ana Olívia de Souza Laboratório de Bioquimica e Biofísica, Instituto Butantan, Avenida Vital Brazil, São Paulo, Brazil
Erika Bujna Department of Brewing and Distilling, Faculty of Food Science, Corvinus University of Budapest, Budapest, Hungary
Partha P. Dhar Plant Production Department, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
Catherine Collins Shannon Applied Biotechnology Centre, Limerick Institute of Technology, Moylish Park, Limerick, Ireland
José Diana Di Mavungu Laboratory of Food Analysis, Department of Bio‐analysis, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
Hexon Ángel Contreras‐Cornejo Instituto de Investigaciones Químico‐Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, México Valéria Dal Prá Department of Chemical Engineering, Federal University of Santa Maria, Santa Maria, Brazil YiZhen Deng Temasek Life Sciences Laboratory and Department of Biological Sciences, National University of Singapore, Singapore Sarah De Saeger Laboratory of Food Analysis, Department of Bio‐analysis, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium Virginia Medeiros de Siqueira Microbial Resources Division (DRM), Research Center for Chemistry, Biology and Agriculture (CPQBA), Campinas University (UNICAMP), Campinas, SP, Brazil
Manish Kumar Dubey Laboratory of Mycopathology and Microbial Technology, Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi, India Carlos Roberto Felix Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, Distrito Federal, Brazil Edivaldo X. F. Filho Laboratory of Enzymology, Department of Cellular Biology, University of Brasília, Brasília, Brazil Edson L. Foletto Department of Chemical Engineering, Federal University of Santa Maria, Santa Maria, Brazil Shin Yee Fung Department of Molecular Medicine and CENAR, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
ix
x
Contributors
Anton Glieder Austrian Centre for Industrial Biocatalysis (ACIB GmbH), Graz, Austria
Raquel C. Kuhn Department of Chemical Engineering, Federal University of Santa Maria, Santa Maria, Brazil
Helder A. R. Gomes Laboratory of Enzymology, Department of Cellular Biology, University of Brasília, Brasília, Brazil
Punam Kumari Laboratory of Mycopathology and Microbial Technology, Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi, India
Jerson V. C. Guedes Department of Plant Protection, Federal University of Santa Maria, Santa Maria, Brazil Vijai Kumar Gupta Molecular Glycobiotechnology Group, Discipline of Biochemistry, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland Kim E. Hammond‐Kosack Department of Plant Biology and Crop Science, Rothamsted Research, Harpenden, United Kingdom Ágoston Hoschke Department of Brewing and Distilling, Faculty of Food Science, Corvinus University of Budapest, Budapest, Hungary Rodrigo J. S. Jacques Department of Soil Science, Federal University of Santa Maria, Santa Maria, Brazil Sérgio L. Jahn Department of Chemical Engineering, Federal University of Santa Maria, Santa Maria, Brazil Paula M. D. Jaramillo Laboratory of Enzymology, Department of Cellular Biology, University of Brasília, Brasília, Brazil Dhruva Kumar Jha Microbial Ecology Laboratory, Department of Botany, Gauhati University, Guwahati, India Jaswinder Kaur Shannon Applied Biotechnology Centre, Limerick Institute of Technology, Moylish Park, Limerick, Ireland Rodrigo Klaic Department of Chemical Engineering, Federal University of Santa Maria, Santa Maria, Brazil
Jesús Salvador López‐Bucio Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México José López‐Bucio Instituto de Investigaciones Químico‐Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, México Lourdes Macías‐Rodríguez Instituto de Investigaciones Químico‐Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, México Svetlana V. Malysheva Laboratory of Food Analysis, Department of Bio‐analysis, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium Marcio A. Mazutti Department of Chemical Engineering, Federal University of Santa Maria, Santa Maria, Brazil Mukesh Meena Laboratory of Mycopathology and Microbial Technology, Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi, India Aleksandra Mitrovic Austrian Centre for Industrial Biocatalysis (ACIB GmbH), Graz, Austria Antonielle V. Monclaro Laboratory of Enzymology, Department of Cellular Biology, University of Brasília, Brasília, Brazil Valdirene Neves Monteiro Universidade Estadual de Goiás, Unidade Universitária de Ciências Exatas e Tecnológicas da Universidade Estadual de Goiás‐UnUCET, Anápolis, Brazil
Altemir J. Mossi Federal University of Fronteira Sul, Erechim, Av. Dom João Hoffmann, Erechim, Brazil Naweed I. Naqvi Temasek Life Sciences Laboratory and Department of Biological Sciences, National University of Singapore, Singapore and School of Biological Sciences, Nanyang Technological University, Singapore Quang D. Nguyen Department of Brewing and Distilling, Faculty of Food Science, Corvinus University of Budapest, Budapest, Hungary Eliane Ferreira Noronha Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, Distrito Federal, Brazil Débora Oliveira Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, Brazil J. Vladimir Oliveira Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, Brazil Marcela C. Pagano Nano‐Espectroscopy Laboratory, Physics Department, ICEx, Institute of Exact Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil Rajesh N. Patkar Temasek Life Sciences Laboratory and Department of Biological Sciences, National University of Singapore, Singapore Gabriela F. Persinoti Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
Contributors
xi
Valeria Prigione Department of Life Sciences and Systems Biology, Mycotheca Universitatis Taurinensis, University of Turin, Turin, Italy Judit M. Rezessy‐Szabó Department of Brewing and Distilling, Faculty of Food Science, Corvinus University of Budapest, Budapest, Hungary Alexandre Gomes Rodrigues Laboratório de Bioquimica e Biofísica, Instituto Butantan, Avenida Vital Brazil, São Paulo, Brazil Susana Rodríguez‐Couto CEIT, Unit of Environmental Engineering, San Sebastian, and IKERBASQUE, Basque Foundation for Science, Bilbao, Spain Luiz H. Rosa Department of Microbiology, ICB, Federal University of Minas Gerais, Belo Horizonte, Brazil Bidisha Sharma Microbial Ecology Laboratory, Department of Botany, Gauhati University, Guwahati, India Dhara Shukla Facility for Ecological and Analytical Testing (FEAT), Indian Institute of Technology, Kanpur, India Caio O. G. Silva Laboratory of Enzymology, Department of Cellular Biology, University of Brasília, Brasília, Brazil Roberto Nascimento Silva Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil Vivek Kumar Singh Laboratory of Mycopathology and Microbial Technology, Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi, India
xii
Contributors
Federica Spina Department of Life Sciences and Systems Biology, Mycotheca Universitatis Taurinensis, University of Turin, Turin, Italy
Padma S. Vankar Facility for Ecological and Analytical Testing (FEAT), Indian Institute of Technology, Kanpur, India
Andrei Stecca Steindorff Departamento de Biologia Celular, Universidade de Brasília, Brasília, Distrito Federal, Brazil
Giovanna Cristina Varese Department of Life Sciences and Systems Biology, Mycotheca Universitatis Taurinensis, University of Turin, Turin, Italy
Gabriella Styevkó Department of Brewing and Distilling, Faculty of Food Science, Corvinus University of Budapest, Budapest, Hungary
R. S. Upadhyay Laboratory of Mycopathology and Microbial Technology, Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi, India
Nget Hong Tan Department of Molecular Medicine and CENAR, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
Fan Yang Temasek Life Sciences Laboratory and Department of Biological Sciences, National University of Singapore, Singapore
Valeria Tigini Department of Life Sciences and Systems Biology, Mycotheca Universitatis Taurinensis, University of Turin, Turin, Italy
Andleeb Zehra Laboratory of Mycopathology and Microbial Technology, Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi, India
Arti Tiwari Laboratory of Mycopathology and Microbial Technology, Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi, India
Susanne Zeilinger Institute of Chemical Engineering, Research Area of Biotechnology and Microbiology, Vienna University of Technology, Wien, Austria
Helen Treichel Federal University of Fronteira Sul, Erechim, Av. Dom João Hoffmann, Erechim, Brazil
Foreword Fungi prevail in microscopic as well as macroscopic life forms and perform a wide range of biochemical activities probably highest among the microscopic organisms. Their omnipresence and evolutionary ancestry to plants highlight their significance on Earth. Current understanding of fungi has provided an opportunity to acknowledge their wide range of activities in industrial, therapeutic, agricultural and environmental applications. Every year, newer facts emerge on numerous domains of mycological studies. Fungi perform their tasks through secretion of many chemically diverse secondary metabolites (SMs), hydrolytic enzymes and proteins. It is highly essential that the recent concepts be compiled at regular intervals for a consolidated update on all the new revelations. Fungal Biomolecules is therefore an indispensable tool planned to accelerate the pace of the current research regarding the diverse roles of fungal biomolecules. This is also crucial as fungal taxonomy is noticeably altered with biotechnological interventions in the fungal genome. The book encompasses a wide range of topics related to biomolecules synthesized and secreted by various fungi useful in industrial, pharmaceutical and agricultural sectors. At the same time, some chapters reflect the toxic effects of some biomolecules secreted particularly by pathogenic fungi on human and environmental health. Detailed discussion on topics like fungal biofilm is significant as it describes the molecular basis of how fungi unite to perform specific tasks by withstanding the challenges posed by external environment. Topics such as the role of fungi in plant growth promotion and disease management (e.g. biocontrol agents and biofertilizers) are mutually related to biofilm formation. Similarly, topics related to fungal enzymes have highlighted the significance of such enzymes in textile industries and environmental clean‐ up programmes through absorption of toxic heavy metals from soil, sludge and industrial wastes. Novel
and effective methods of environmental clean‐up with biosynthesized nanoparticles are also discussed for detoxification of industrial wastes. The chapters regarding discoveries of enzymatic pathways, fungal metabolic diversity and regulation of metabolic pathways provide ample information on the topic of biosynthesis of fungal metabolites. While the chapter related to mycotoxins has highlighted the detrimental aspects of fungal metabolites, the chapters on medicinal properties of fungal metabolites have added therapeutic value to the book by incorporating a human factor and highlighting the possibilities of treating dreadful human diseases using such fungal metabolites. Most of these topics are addressed with a deep molecular insight. The book also incorporates the molecular basis of fungal taxonomy which is a higher dimension of structural classification of fungi and also includes chapters demonstrating the exciting possibilities of improving the fungal strains through genetic manipulations. The chapter on the employment of bioinformatic approaches for understanding modern mycology has emphasized the role of bioinformatics in the fungal genomics, metabolomics and secretomics. In sum, the book contains fascinating and essential information on various fungal metabolites and their industrial applications. The book is a very fine compilation of the recent concepts of fungal biomolecules which, I believe, will have a wide readership of students, researchers, academicians, industrialists and environmentalists interested in harnessing the potential of fungal biomolecules. H.B. Singh Professor Department of Mycology and Plant Pathology Institute of Agricultural Sciences Banaras Hindu University Varanasi, India
xiii
xiv
Foreword
According to molecular phylogeneticists, the establishment of terrestrial eukaryotes was possible only through symbiotic associations between fungi and simple photosynthesizing organisms (phototrophs), and the two most common symbioses active today are lichens and arbuscular mycorrhizae. Recent estimates even suggest a much earlier colonization of land than thought before, around 1000 million years ago, by green algae and major lineages of fungi thereby affecting Earth’s atmosphere, climate and evolution of animals (D.S. Heckman et al., Science 293, 2001). According to these estimates, it is evident that fungi must have evolved a plethora of strategies to efficiently use all possible substrates including their plant hosts – may they be nutrient rich or nutrient poor, difficult to penetrate or easy to access. From the fungal point of view, humans are just more than another substrate that can be used to allow their colony to proliferate and reproduce. Humans when compared to hard substrates such as lignin‐containing wood or dry soils with little organic matter are ‘easy to crack’ for fungal cells. Since the first settlements, humans have used these metabolic capacities of fungi to preserve food and beverages by fermentation, to produce hallucinogenic alcohols for use in religious ceremonies and to process fibres used in clothing and building materials. Medieval folk medicine has already documented about the wound‐healing properties of moulded bread soaked in vinegar which was used for superficial inflammations – the first application of fungal metabolites as antibiotics. All these cultural techniques were developed by trial‐and‐error‐ based approaches, and they eventually led to the development of biotechnology‐based methods that we currently use for food processing and preparation and for medical, environmental or agricultural applications. For humankind, fungi are both beneficial and harmful. This book provides an overview on the basic concepts and recent research related to the roles of fungal metabolites as a key for understanding both sides of the medal: the beneficial environmental functions and biotechnological or medical applications, and the detrimental pathogenic mechanisms and their role as important virulence factors or harmful toxins. I give here a non‐chronological synopsis of research results and opinions expressed by the authors of the individual chapters with the aim of showing how fascinating and diverse fungal lifestyles are and how interesting it is to do research with these organisms.
On the positive side, whole fungal cells play a significant role in human life. Siqueira describes some basic work on how fungi are engaged in biofilm formation (Chapter 1) and are used in the production of nutraceuticals (Chapter 24) . Apart from the degradation of recalcitrant organic matter, fungi play an important role in nutrient cycling in agricultural soils, which has been so far vastly underestimated or missed. This role – if properly exploited – may considerably contribute to higher fertilizer efficiency rates and thus savings in chemicals, environmental and energy costs (Gorfer et al., ISME J. 5, 2011). Along the same line, various authors have described the recent developments on how fungi can be used in different processes: Nguyen describes the role of fungi in food processing (Chapter 2), Shukla and Vankar describes the bioremediation of toxic chromium VI by various fungal species (Chapter 22) and Spina et al. elaborates on textile wastewater treatment (Chapter 3). Contreras‐ Cornejo et al. documents the beneficial interaction of fungi with plants which promotes plant growth (Chapter 23), a process that will also help agricultural production systems to become ‘greener’. To correlate fungal metabolic functions with fungal diversity in any environment (natural or artificial), a sound and reliable fungal detection system is necessary. As only a fraction of fungi grow under standard laboratory conditions, we traditionally chose molecular analysis systems, and a taxonomy based on molecular markers is necessary. Hence, an excellent chapter by Pagano and Rosa (Chapter 20) which deals with marker development and molecular taxonomy is included. Adding to the holistic view of the whole fungal cell as functional unit, the book also contains several chapters with updates on recent results and concepts on the use of fungi as a ‘cell factory’. As already outlined, the metabolic capacities of fungi have been employed by mankind ever since the prehistoric settlements, and refinement of techniques for a controlled use of fungi has dominated this ‘early‐days biotechnology’. Section 1, an important section that spans a wide area of fungal enzyme technology research, contains a chapter by Glieder (Chapter 4) that describes how new enzymatic functions can be discovered by studying dedicated metabolic pathways. Jaramillo et al. (Chapter 6) provide us with an overview on the importance and the global market of lignocellulose‐degrading enzymes. Without doubt, this class of secreted fungal proteins represents a major target of research for the use of lignocellulose as
energy source and as a basis for biomaterials. One should not forget that lignocellulosic biomass is the most abundantly available raw material on the Earth and thus the production of biofuels or biomaterials from cellulose and hemicellulose holds great promises. For this to come true, however, the efficiency of lignocellulose breakdown to fermentable hexoses and pentoses must increase, and research described by Rodriguez‐ Couto (Chapter 5), for example, targets laccases as key enzymes in this process because they oxidize lignin components, thereby making separation of lignin from cellulosic compounds easier and thus more economic. An interesting concept is described by de Souza and Rodrigues (Chapter 9) in which fungal surfaces are used to produce biogenic nanoparticles. As an example, they have chosen silver nanoparticles as they are known to have antimicrobial effects. The authors describe the actual understanding of the mechanisms that mediate the microbial synthesis of nanoparticles and the steps to be followed to better understand the processes and potential applications. More information on the general level of molecular events that regulate the metabolic processes and the expression of metabolic diversity is provided by Steindorff et al. in Chapter 18. Section 5 certainly provides important information for fungal biologists as it describes bioinformatic approaches for correct gene‐calling methods, a basis for biomining new metabolites from fungi. This section conceptually leads the reader to the second core area of this book, namely, the generation, function and toxicity of fungal SMs in saprophytic and pathogenic lifestyles. The concept of ‘secondary metabolites’ (e.g. pigments or volatile compounds) has not been explored much, as they may be produced already during primary metabolism (i.e. active growth phase). It is widely accepted that SMs (e.g. antibiotics and mycotoxins) are not essential for the growth, development and reproduction of fungi but help them to compete for space and nutrients, thus making them more competitive as saprophytes or pathogens in their natural environments. However, there are probably many more functions of SMs, and they may act as regulators of internal signalling or external communication, for example, quorum sensing. While there is still much space for the enthusiastic mycologist to discover additional roles of SMs, a large body of knowledge is available on the biosynthesis pathways and function of well‐known SMs such as mycotoxins, antibiotics or other bioactive molecules. This book leads the reader
Foreword
xv
through the overwhelming literature by summarizing the role of nutrient sources in general (Chapter 15) and nitrogen in particular (Chapter 16) in SM formation. An overview of regulatory genes that participate in this process is provided by Catherine Collins in Chapter 17. Several groups of metabolites are discussed then in the book: volatile organic compounds described by Lopez‐ Bucino et al. (Chapter 7) may act as elicitors during the infection of plants by pathogens and may be necessary for biocontrol. Peptaibols are linear or cyclic peptides containing non‐proteinogenic amino acids, and the antibiotic or antitumor functions of such molecules produced, for example, by Trichoderma species are discussed in Chapter 8 by Susanne Zeilinger. More beneficial functions of fungal SMs as potential antitumor agents are also discussed by Shin‐Yee Fung in Chapter 11. Fungal pigments not only protect fungal cells themselves from DNA damage caused by UV light, but they are also produced in industrial processes because of their potential for use in industry, agriculture and medicine. Thus, biotechnological processes for efficient fungal pigment production represent an important research task (Chapter 13). Another long‐ standing research question is whether and how toxic fungal SMs, that is, mycotoxins, participate in the infection and establishment process of fungal pathogens. Svetlana Malysheva (Chapter 12) first provides a good overview on fungal mycotoxins and their biosynthetic pathways, and then Naweed Naqvi (Chapter 10) summarizes the role of fungal SMs as modulators for growth and pathogenesis. The implications of such biomolecules for fungal virulence are also discussed well by Upadhyay (Chapter 24), but similar types of metabolites may also function as plant growth promoters, as described by Lopez‐Bucio in Chapter 23. Are certain secretory proteins also secondary m etabolites? Probably not in classical terms, because we usually understand them as ‘small molecules’ (less than 1 kDa), but Hammond‐Kosack in Chapter 19 disagrees with the stringent definition of SMs by detailing how important secretory proteins are for pathogenesis. Data of a recent research on Ustilago maydis (Djamei et al., Nature 478, 2011; Djamei et al., PLoS Pathogens 8, 2012) underpin this view that even large proteins are secreted as ‘secondary metabolites’ into plant tissue to counteract plant defence systems. If space would permit, one could go on and on with many more chapters and examples of how diverse and fascinating fungal lifestyles are, how their primary
xvi
Foreword
and secondary metabolic capacities contribute to their ecological success and how mankind has over thousands of years professionally refined the knowledge on how to use these metabolic abilities for their own purposes. The lively chapters of this book deal comprehensively with both the beneficial and the harmful sides of the fungal world. I recommend it to all molecular mycologists and to anyone fascinated by the
superb metabolic diversity evolution can build up for the sake of an organism’s success in a competitive environment. Prof. Joseph Strauss BOKU University of Natural Resources and Life S ciences Vienna, Austria
Preface Fungi display an extraordinary level of structural and functional diversity with an estimated 1.5–5.1 million extant species. About 100,000 fungal species have so far been described. The number of species identified continues to increase particularly with the development and application of postgenomic methodologies to disentangle species aggregates and identify cryptic species. Fungi are one of the most important groups of eukaryotic organisms that are exploited for m etabolites of potential therapeutic value as well as applications in diverse industries such as food and textile. Fungi offer a rich and diverse source of biomolecules that continue to be explored for food, health and environmental applications through research and development of both public and private sectors. And the key to harnessing this fantastic natural resource is to maximize more collaborative efforts across these sectors. With this backdrop, this volume presents an exciting collection of chapters by active researchers across the globe covering a range of applications of fungi and their biomolecules, presented under various thematic sections. Sections 1 and 2 present recent research on fungi as cell factories in the production of enzymes and various metabolites and their use as biocatalysts and biofilms. The topics include discovery of fungal enzymes and pathways, applications in food and textile industries, peptides and peptaibols and recent advances in the role and analysis of volatile compounds. Sections 3 and 4 explore fungal secondary metabolism and regulation of synthesis with an array of research developments covered including metabolic
diversity, antimicrobial and antitumour agents, biosynthesis of nanoparticles, mycotoxins, the influence of nutrients, fungal secretome, the role of secretory proteins in pathogenesis and regulatory genes. Section 5 focuses on molecular approaches to the identification of fungal species that were hitherto difficult to distinguish reliably based on their phenotype. Furthermore, parallel developments in genetic methodologies that are continuing to emerge to improve the performance of fungal strains for industrial application are also presented. Section 6 covers various recent methodological and conceptual advances in understanding and exploiting fungal diversity and their interactions including bioinformatic approaches for the detection of fungal species and their biomolecules. Further chapters provide insights into key molecules and their implications, plant growth promotion and sustainable environmental management including recent advances and emerging areas. This volume provides a comprehensive coverage of exemplars of the diverse roles and applications of fungal biomolecules in food, health and the environment. Furthermore, with the collection of chapters providing a wider perspective from fungal metabolic diversity to the impact on ecosystem management, this volume would serve as an excellent reference for early career and experienced academics and researchers from both public and private sectors. Vijai Kumar Gupta Robert L. Mach S. Sreenivasaprasad
xvii
