For further volumes:http://www.springer.com/series/11224

Fungal Biology

Series Editors:Vijai Kumar Gupta, PhDMolecular Glycobiotechnology Group, Department of Biochemistry,School of Natural Sciences, National University of Ireland Galway,Galway, Ireland

Maria G. Tuohy, PhDMolecular Glycobiotechnology Group, Department of Biochemistry,School of Natural Sciences, National University of Ireland Galway,Galway, Ireland

Vijai Kumar Gupta • Maria G. Tuohy Editors

Manimaran Ayyachamy

Anthonia O’Donovan • Kevin M. Turner Associate Editors

Laboratory Protocols in Fungal Biology

Current Methods in Fungal Biology

Editors Vijai Kumar Gupta Molecular Glycobiotechnology Group Department of BiochemistrySchool of Natural Sciences National University of Ireland Galway Galway , Ireland

Assistant Professor of BiotechnologyDepartment of ScienceMITS University Lakshmangarh (Sikar), Rajasthan, India

Maria G. Tuohy Molecular Glycobiotechnology Group Department of BiochemistrySchool of Natural Sciences National University of Ireland Galway Galway , Ireland

ISBN 978-1-4614-2355-3 ISBN 978-1-4614-2356-0 (eBook) DOI 10.1007/978-1-4614-2356-0 Springer New York Heidelberg Dordrecht London

Library of Congress Control Number: 2012951631

© Springer Science+Business Media, LLC 2013 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, speci fi cally the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on micro fi lms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. Exempted from this legal reservation are brief excerpts in connection with reviews or scholarly analysis or material supplied speci fi cally for the purpose of being entered and executed on a computer system, for exclusive use by the purchaser of the work. Duplication of this publication or parts thereof is permitted only under the provisions of the Copyright Law of the Publisher’s location, in its current version, and permission for use must always be obtained from Springer. Permissions for use may be obtained through RightsLink at the Copyright Clearance Center. Violations are liable to prosecution under the respective Copyright Law. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a speci fi c statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. While the advice and information in this book are believed to be true and accurate at the date of publication, neither the authors nor the editors nor the publisher can accept any legal responsibility for any errors or omissions that may be made. The publisher makes no warranty, express or implied, with respect to the material contained herein.

Printed on acid-free paper

Springer is part of Springer Science+Business Media (www.springer.com)

Associate EditorsManimaran AyyachamyMolecular Glycobiotechnology Group Department of BiochemistrySchool of Natural SciencesNational University of Ireland Galway Galway, Ireland

Anthonia O’DonovanMolecular Glycobiotechnology Group Department of BiochemistrySchool of Natural SciencesNational University of Ireland GalwayGalway, Ireland

Kevin M. TurnerManufacturing Sciences and TechnologyThe Pfi zer Biotech Campus at Grange Castle Pfizer Ireland PharmaceuticalsDublin, Ireland

v

Foreword

Fungi represent the fi fth kingdom of organisms, which is characterized—sec-ond only to prokaryotes—by a huge number of diverse species. Even more, fungi have developed a tremendous variety in lifestyles, biochemical proper-ties, and morphological characters, the latter having been a permanent chal-lenge for de fi ning species and their identi fi cation. They have conquered practically all habitats, from deep sea water to desert soil, and from prokary-otes to mammals, leading to an array of positive but also negative impacts on mankind. On the negative side, fungi are known as pathogens of plants—a situation which seriously affects crop plantations all around the earth—but also of higher fungi, of lower eukaryotes, and of all animals up to mammals and men. Also, their versatile metabolism provided them with ef fi cient abili-ties to colonize almost all material, leading to biodeterioration of various organic materials including paintings and covers, which allowed them to settle in buildings and fl ats resulting in indoor contamination as a major problem of today. Yet there are also numerous bene fi ts: many fungi are known as bene fi cial symbionts of plants, such as plant tissue endosymbionts and mycorrhizas. In fact, the earth would be devoid of plants in the absence of the latter. Finally several fungi have been domesticated by humans, either for their use in agri-culture (such as for biocontrol of plant or invertebrate pathogens or in plant growth protection and stimulation), for the preparation of feed- and foodstuff, and as ef fi cient producers of biotechnological products such as primary metab-olites, numerous enzymes, and antibiotics. In the area of modern molecular biotechnology, fungi such as Pichia pastoris have become important high-throughput hosts for the production of recombinant proteins of bacterial to human origin. Last but not least, fungi like Saccharomyces cerevisiae, Neurospora crassa , and Aspergillus nidulans have become model systems for basic biochemical and genetic research, and an impressing amount of our text-book knowledge would not be available without them. In the current genomic age, elucidation of the genome inventory of about 50 multicellular asco- and basidiomycetes and the same number of yeasts has been completed and opened new avenues for their investigation.

In view of this steadily increased interest in fungi, also the methods needed for their isolation and identi fi cation, as well as their genetic manipulation and monitoring of gene expression and protein production, have become re fi ned and complemented. This book aims at presenting an inventory of techniques and methods that are currently in use for studying fungi: it contains 57 chap-ters dedicated to description of these techniques, starting from concepts of

vi Foreword

cultivation, enumeration, and visualization of fungi; molecular approaches for detection and quanti fi cation; measurement of relevant enzymes and meth-ods for their application; and the use of bioinformatic tools to investigate fungal genomes.

As a professional reference, this book is aimed at all people who work with fungi and should be useful both to academic institutions and research teams, as well as to teachers, graduate and postgraduate students. Vienna , Austria Prof. Christian P. Kubicek

vii

Foreword

It gives me immense pleasure to write a foreword for Laboratory Protocols in Fungal Biology of Springer, USA edited by Dr. Vijai Kumar Gupta and Dr. Maria G. Tuohy. After going through the content of this laboratory proto-col, I feel that it is a wonderful attempt done by Dr. Gupta to compile together all the information about the subject that will be highly useful to all mycolo-gists around the globe. I am sure that this volume will be highly useful to all those concerned with fungi and their biology, including environmental and public health of fi cers and professionals in the fi eld of interest. The volume is really exhaustive covering almost all the aspects of fungal biology. It will also be of interest to postgraduate students in this fi eld and also for one and all interested in Fungi. Additionally it will be of great market value. This effort of Dr. Gupta’s is admirable.

Varanasi, India Prof. R. S. Upadhyay

ix

Preface

The interaction between fungi and their environment is central to many natu-ral processes that occur in the biosphere. The hosts and habitats of these eukaryotic microorganisms are very diverse; fungi are present in every eco-system on Earth. The fungal kingdom is equally diverse, consisting of seven different known phyla. Yet detailed knowledge is limited to relatively few species. The relationship between fungi and humans has been characterized by the juxtaposed viewpoints of fungi as infectious agents of much dread and their exploitation as highly versatile systems for a range of economically important biotechnological applications. Understanding the biology of differ-ent fungi in diverse ecosystems as well as their interactions with living and nonliving is essential to underpin effective and innovative technological developments.

The tools and techniques of molecular biology, once reserved for mam-malian and bacterial systems, have been adapted and optimized for the analy-sis of fungal species at the molecular level. Rapid screening techniques based on screening speci fi c regions in the DNA of fungi have been used in species comparison and identi fi cation and are now being extended across fungal phyla with the ultimate goal being the assembly of the “Fungal Tree of Life” by the US National Science Foundation. Within a decade after the Human Genome Sequence was published, genome sequencing technology has been adapted to yield the complete genome sequences of not only fungi of com-merce and medical relevance, but other more isoteric species. Post-genomics approaches and systems biology are now also being applied to understanding the details of fungal biology and the interactions between fungi, their hosts, and their environment. The majority of fungi are multicellular eukaryotic sys-tems and therefore may be excellent model systems by which to answer fun-damental biological questions. A greater understanding of the cell biology of these versatile eukaryotes will underpin efforts to engineer (e.g., “humanize”) certain fungal species to provide novel cell factories for production of pro-teins for pharmaceutical applications. Finally, renewed interest in all aspects of the biology and biotechnology of fungi may also enable the development of “one pot” microbial cell factories to meet consumer energy needs into the twenty fi rst century. To realize this potential and to truly understand the diver-sity and biology of these eukaryotes, continued development of scienti fi c tools and techniques is essential.

This publication aims to provide a detailed compendium of analytical methods used to investigate different aspects of mycology, including fungal

x Preface

biology and biochemistry, genetics, phylogenetics, genomics, proteomics, molecular enzymology, and biotechnological applications, in a manner that re fl ects the many recent developments of relevance to scientists investigating the Kingdom of Fungi.

Galway, Ireland Vijai Kumar GuptaMaria G. Tuohy

Manimaran AyyachamyAnthonia O’Donovan

Kevin M. Turner

xi

Contents

1 Safety Norms and Regulations in Handling Fungal Specimens......................................................................... 1Finola E. Cliffe

2 Methods of Cryopreservation in Fungi ...................................... 9Ladislav Homolka

3 Long-Term Preservation of Fungal Cultures in All-Russian Collection of Microorganisms (VKM): Protocols and Results .................................................................................... 17Svetlana M. Ozerskaya, Natalya E. Ivanushkina, Galina A. Kochkina, Svetlana S. Eremina, Alexander N. Vasilenko, and Nadezhda I. Chigineva

4 Fungal Specimen Collection and Processing ............................. 67Anthonia O’Donovan, Vijai Kumar Gupta, and Maria G. Tuohy

5 Chemical and Molecular Methods for Detection of Toxigenic Fungi and Their Mycotoxins from Major Food Crops .............................................................. 73S. Chandra Nayaka, M. Venkata Ramana, A.C. Udayashankar, S.R. Niranjana, C.N. Mortensen, and H.S. Prakash

6 Identification Key for the Major Growth Forms of Lichenized Fungi...................................................................... 91Jeyabalan Sangeetha and Devarajan Thangadurai

7 Microscopic Methods for Analytical Studies of Fungi .............. 113De-Wei Li

8 Scanning Electron Microscopy for Fungal Sample Examination .................................................................... 133Eduardo Alves, Gilvaine Ciavareli Lucas, Edson Ampélio Pozza, and Marcelo de Carvalho Alves

9 High-Resolution Imaging and Force Spectroscopy of Fungal Hyphal Cells by Atomic Force Microscopy .............. 151Biplab C. Paul, Hui Ma, Laelie A. Snook, and Tanya E.S. Dahms

xii Contents

10 Use of Fourier-Transform Infrared (FTIR) Microscopy Method for Detection of Phyto-Fungal Pathogens ...................................................................................... 161Vitaly Erukhimovitch and Mahmoud Huleihel

11 Diagnosis of Parasitic Fungi in the Plankton: Technique for Identifying and Counting Infective Chytrids Using Epifluorescence Microscopy ........................................................ 169Télesphore Sime-Ngando, Serena Rasconi, and Mélanie Gerphagnon

12 Fungal Cell Wall Analysis ........................................................... 175Pilar Pérez and Juan C. Ribas

13 Histopathological Technique for Detection of Fungal Infections in Plants ....................................................................... 197Vijai Kumar Gupta and Brejesh Kumar Pandey

14 Development of Media for Growth and Enumeration of Fungi from Water .................................................................... 201Segula Masaphy

15 Sabouraud Agar for Fungal Growth .......................................... 211Janelle M. Hare

16 A Method for the Formation of Candida Biofilms in 96 Well Microtiter Plates and Its Application to Antifungal Susceptibility Testing ............................................ 217Christopher G. Pierce, Priya Uppuluri, and Jose L. Lopez-Ribot

17 Screening for Compounds Exerting Antifungal Activities ....... 225Jean-Paul Ouedraogo, Ellen L. Lagendijk, Cees A.M.J.J. van den Hondel, Arthur F.J. Ram, and Vera Meyer

18 Fluorescence In Situ Hybridization of Uncultured Zoosporic Fungi ................................................... 231Télesphore Sime-Ngando, Marlène Jobard, and Serena Rasconi

19 Staining Techniques and Biochemical Methods for the Identification of Fungi ..................................................... 237Jeyabalan Sangeetha and Devarajan Thangadurai

20 Protocol for the In Vivo Quantification of Superoxide Radical in Fungi ........................................................................... 259Konstantinos Grintzalis, Ioannis Papapostolou, and Christos Georgiou

21 Isolation of Intact RNA from Sorted S. cerevisiae Cells for Differential Gene Expression Analysis ................................. 265Jeannette Vogt, Frank Stahl, Thomas Scheper, and Susann Müller

22 Quantitative PCR Analysis of Double-Stranded RNA-Mediated Gene Silencing in Fungi.................................... 279José J. de Vega-Bartol, Vega Tello, Jonathan Niño, Virginia Casado, and José M. Díaz-Mínguez

xiiiContents

23 Semi-Nested PCR Approach to Amplify Large 18S rRNA Gene Fragments for PCR-DGGE Analysis of Soil Fungal Communities ........................................................ 289Miruna Oros-Sichler and Kornelia Smalla

24 Proteomic Protocols for the Study of Filamentous Fungi ........ 299Raquel González Fernández and Jesús V. Jorrín Novo

25 Detection and Quantification of Endoprotease Activity Using a Coomassie Dye-Binding Assay ...................................... 309Anthony J. O’Donoghue and Cathal S. Mahon

26 Protocol of a LightCycler™ PCR Assay for Detection and Quantification of Aspergillus fumigatus DNA in Clinical Samples of Neutropenic Patients.............................. 315Birgit Spiess and Dieter Buchheidt

27 Application of Polymerase Chain Reaction and PCR-Based Methods Targeting Internal Transcribed Spacer Region for Detection and Species-Level Identification of Fungi........... 321K. Lily Therese, R. Bagyalakshmi, and H.N. Madhavan

28 Real-Time PCR Assay in Fungi .................................................. 331Naomichi Yamamoto

29 Quantitative Sampling Methods for the Analysis of Fungi: Air Sampling ................................................................ 337Mary C. O’Loughlin, Katherine D. Turner, and Kevin M. Turner

30 Transformation of Filamentous Fungi in Microtiter Plate....... 343Bianca Gielesen and Marco van den Berg

31 Molecular Fingerprinting of Fungal Communities in Soil ....... 349Roberto A. Geremia and Lucie Zinger

32 Development of Microsatellite Markers from Fungal DNA Based on Shotgun Pyrosequencing ................................... 357Shaobin Zhong

33 Multiplex and Quantifiable Detection of Infectious Fungi Using Padlock Probes, General qPCR, and Suspension Microarray Readout ......................................... 363Magnus Jobs, Ronnie Eriksson and Jonas Blomberg

34 Rapid Deletion Plasmid Construction Methods for Protoplast and Agrobacterium-based Fungal Transformation Systems .............................................................. 375María D. García-Pedrajas, Zahi Paz, David L. Andrews, Lourdes Baeza-Montañez, and Scott E. Gold

35 Improved Transformation Method for Alternaria Brassicicola and Its Applications ................................................ 395Yangrae Cho, Akhil Srivastava, and Christopher Nguyen

xiv Contents

36 Methods for High-Quality DNA Extraction from Fungi .......... 403Vijai Kumar Gupta, Maria G. Tuohy, and Rajeeva Gaur

37 Production of Recombinant Proteins from Pichia pastoris: Interfacing Fermentation and Immobilized Metal Ion Affinity Chromatography ............................................................ 407Berend Tolner, Gaurav Bhavsar, Bride Foster, Kim Vigor, and Kerry Chester

38 Development of a Real-Time Quantitative PCR Assay for the Assessment of Uncultured Zoosporic Fungi .................. 421Télesphore Sime-Ngando and Marlène Jobard

39 Nucleic and Protein Extraction Methods for Fungal Exopolysaccharide Producers ..................................................... 427Jochen Schmid, Dirk Mueller-Hagen, Volker Sieber, and Vera Meyer

40 Directed Evolution of a Fungal Xylanase for Improvement of Thermal and Alkaline Stability .............................................. 435Dawn Elizabeth Stephens, Suren Singh, and Kugen Permaul

41 Genome Shuffling Protocol for the Pentose-Fermenting Yeast Scheffersomyces stipitis ...................................................... 447Paramjit K. Bajwa, Nicole K. Harner, Terri L. Richardson, Sukhdeep Sidhu, Marc B. Habash, Jack T. Trevors, and Hung Lee

42 Detection and Identification of Fungal Microbial Volatile Organic Compounds by HS-SPME-GC–MS ............... 455Bernhard Kluger, Susanne Zeilinger, Gerlinde Wiesenberger, Denise Schöfbeck, and Rainer Schuhmacher

43 Transformation Methods for Slow-Growing Fungi .................. 467Suman Mukherjee and Rebecca Creamer

44 Enzymatic Saccharification of Lignocellulosic Biomass ........... 475Manimaran Ayyachamy, Vijai Kumar Gupta, Finola E. Cliffe, and Maria G. Tuohy

45 Protoplast Fusion Techniques in Fungi ...................................... 483Annie Juliet Gnanam

46 Large-Scale Production of Lignocellulolytic Enzymes in Thermophilic Fungi ................................................................. 489Manimaran Ayyachamy, Mary Shier, and Maria G. Tuohy

47 Panfungal PCR Method for Detection of Aflatoxigenic Molds ................................................................. 495Malik M. Ahmad, Pravej Alam, M.Z. Abdin, and Saleem Javed

48 Protocols for the Quantification of dsDNA and Its Fragmentation Status in Fungi ...................................... 501Ioannis Papapostolou, Konstantinos Grintzalis, and Christos Georgiou

xvContents

49 Rapid Identification and Detection of Pathogenic Fungi by Padlock Probes ............................................................. 505Clement K.M. Tsui, Bin Wang, Cor D. Schoen, and Richard C. Hamelin

50 Drug-Induced Permeabilization in Fungi .................................. 519Maria D. Mayan, Alexandra McAleenan, and Priscilla Braglia

51 Extraction and Characterization of Taxol: An Anticancer Drug from an Endophytic and Pathogenic Fungi ..................... 523M. Pandi, P. Rajapriya, and P.T. Manoharan

52 Identification of Mycotoxigenic Fungi Using an Oligonucleotide Microarray................................................... 529Eugenia Barros

53 DNA Microarray-Based Detection and Identification of Fungal Specimens .................................................................... 535Minna Mäki

54 Bioinformatic Protocols and the Knowledge-Base for Secretomes in Fungi ............................................................... 545Gengkon Lum and Xiang Jia Min

55 High-Throughput Functional Annotation and Data Mining of Fungal Genomes to Identify Therapeutic Targets ................ 559Gagan Garg and Shoba Ranganathan

56 Application of Support Vector Machines in Fungal Genome and Proteome Annotation ............................................................ 565Sonal Modak, Shimantika Sharma, Prashant Prabhakar, Akshay Yadav, and V.K. Jayaraman

57 Bioinformatics Tools for the Multilocus Phylogenetic Analysis of Fungi .......................................................................... 579Devarajan Thangadurai and Jeyabalan Sangeetha

Index ...................................................................................................... 593

xvii

Contributors

M. Z. Abdin Department of Biotechnology , Jamia Hamdard University , New Delhi , Delhi , India

Malik M. Ahmad Department of Biotechnology , Jamia Hamdard University , New Delhi , Delhi , India

Pravej Alam Department of Biotechnology , Jamia Hamdard University , New Delhi , Delhi , India

Eduardo Alves Department of Phytopathology , Federal University of Lavras , Lavras , Minas Gerais , Brazil

David L. Andrews Department of Plant Pathology , University of Georgia , Athens , GA , USA

Manimaran Ayyachamy Department of Biochemistry, School of Natural Sciences , National University of Ireland , Galway , Ireland

Lourdes Baeza-Montañez Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Consejo Superior de Investigaciones Cientí fi cas (IHSM-UMA-CSIC), Estación Experimental “La Mayora” , Algarrobo-Costa , Málaga , Spain

R. Bagyalakshmi Sankara Nethralaya, Larsen and Toubro Microbiology Research Centre , Chennai , Tamil Nadu , India

Paramjit K. Bajwa School of Environmental Sciences , University of Guelph , Guelph , ON , Canada

Eugenia Barros Department of Biosciences , Council for Scienti fi c and Industrial Research (CSIR) , Brummeria , Pretoria , South Africa

Gaurav Bhavsar Department of Oncology , University College London Cancer Institute , London , UK

Jonas Blomberg Department of Medical Sciences , Uppsala Academic Hospital, Uppsala University , Uppsala , Sweden

Priscilla Braglia Sir William Dunn School of Pathology , University of Oxford , Oxford , UK

Dieter Buchheidt Third Department of Internal Medicine , Mannheim University Hospital , Mannheim , Germany

xviii Contributors

Virginia Casado Department of Microbiologia y Genetica—CIALE , Universidad de Salamanca , Salamanca , Spain

Kerry Chester Department of Oncology , University College London Cancer Institute , London , UK

Nadezhda I. Chigineva All-Russian Collection of Microorganisms (VKM IBPM RAS, Pushchino, Russia), G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Science , Pushchino , Moscow Region , Russia

Yangrae Cho Department of Plant and Environmental Protection Sciences , University of Hawaii at Manoa , Honolulu , HI , USA

Finola E. Cliffe Department of Biochemistry , School of Natural Sciences, National University of Ireland Galway , Galway , Ireland

Rebecca Creamer Department of Entomology, Plant Pathology, and Weed Science , New Mexico State University , Las Cruces , NM , USA

Tanya E.S. Dahms Department of Chemistry and Biochemistry , University of Regina , Regina , SK , Canada

Marcelo de Carvalho Alves Department of Soil and Rural Engineering , Campus of the Federal University of Mato Grosso, Federal University of Mato Grosso , Cuiaba , Mato Grosso , Brazil

José J. de Vega-Bartol Department of Microbiologia y Genetica—CIALE , Universidad de Salamanca , Salamanca , Spain

José M. Díaz-Mínguez Department of Microbiologia y Genetica—CIALE , Centro Hispano Luso de Investigaciones Agrarias, Universidad de Salamanca , Salamanca , Spain

Svetlana S. Eremina All-Russian Collection of Microorganisms (VKM IBPM RAS, Pushchino, Russia), G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Science , Pushchino , Moscow Region , Russia

Ronnie Eriksson Livsmedelsverket , Uppsala , Sweden

Vitaly Erukhimovitch Analytical Equipment Unit , Ben-Gurion University of the Negev , Beer-Sheva , Israel

Raquel González Fernández Department of Biochemistry and Molecular Biology , University of Córdoba , Córdoba , Spain

Bride Foster Department of Oncology , University College London Cancer Institute , London , UK

María D. García-Pedrajas Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Consejo Superior de Investigaciones Cientí fi cas (IHSM-UMA-CSIC), Estación Experimental “La Mayora” , Málaga , Spain

Gagan Garg Department of Chemistry and Biomolecular Sciences , Macquarie University , Sydney , NSW , Australia

xixContributors

Rajeeva Gaur Department of Microbiology , Dr. R.M.L. Avadh University , Faizabad , Uttar Pradesh , India

Christos Georgiou Department of Biology , University of Patras , Patras , Achaia , Greece

Roberto A. Geremia Laboratoire d’Ecologie Alpine, CNRS/UJF, Université Joseph Fourier , Grenoble , France

Mélanie Gerphagnon Université Blaise Pascal , Aubière , France

Bianca Gielesen DSM Biotechnology Center , Delft , Zuid Holland , The Netherlands

Annie Juliet Gnanam College of Natural Science , Institute for Cellular and Molecular Biology, University of Texas at Austin , Austin , TX , USA

Scott E. Gold United States Department of Agriculture—Agricultural Research Unit (USDA–ARS), Toxicology and Mycotoxin Research Unit , Athens Georgia , USA

Konstantinos Grintzalis Department of Biology , University of Patras , Patras , Achaia , Greece

Vijai Kumar Gupta Molecular Glycobiotechnology Group, Department of Biochemistry, School of Natural Sciences , National University of Ireland Galway , Galway , Ireland

Assistant Professor of Biotechnology, Department of Science, Faculty of Arts, Science & Commerce, MITS University, Rajasthan, India

Marc B. Habash School of Environmental Sciences, University of Guelph , Guelph , ON , Canada

Richard C. Hamelin Department of Forest Sciences , The University of British Columbia , Vancouver , BC , Canada

Laurentian Forestry Centre, Natural Resources Canada , Quebec , QC , Canada

Janelle M. Hare Department of Biology and Chemistry , Morehead State University , KY , USA

Nicole K. Harner School of Environmental Sciences, University of Guelph , Guelph , ON , Canada

Ladislav Homolka Department of Ecology of Microorganisms , Institute of Microbiology, Academy of Sciences of the Czech Republic , Prague , Czech Republic

Mahmoud Huleihel Department of Virology and Developmental Genetics , Ben-Gurion University of the Negev , Beer-Sheva , Israel

Natalya E. Ivanushkina All-Russian Collection of Microorganisms (VKM IBPM RAS, Pushchino, Russia), G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Science , Pushchino , Moscow Region , Russia

xx Contributors

Saleem Javed Department of Biochemistry , Jamia Hamdard University , New Delhi , India

V. K. Jayaraman Scienti fi c and Engineering Computing Group (SECG), Centre for Development of Advanced Computing (C-DAC), University of Pune , Pune , Maharashtra , India

Marlène Jobard LMGE UMR CNRS , U.F.R. Sciences et Technologies , Aubière Cedex , France

Magnus Jobs School of Health and Social Studies , Högskolan Dalarna, Uppsala University , Falun , Sweden

Bernhard Kluger Department for Agrobiotechnology (IFA-Tulln) , University of Natural Resources and Life Sciences Vienna , Tulln , Austria

Galina A. Kochkina All-Russian Collection of Microorganisms (VKM IBPM RAS, Pushchino, Russia), G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Science , Pushchino , Moscow Region , Russia

Christian P. Kubicek Department of Chemical Engineering , Vienna University of Technology , Vienna , Austria

Ellen L. Lagendijk Department of Molecular Microbiology and Biotechnology , Leiden University , Leiden , The Netherlands

Hung Lee University of Guelph, School of Environmental Sciences , Guelph , ON , Canada

De-Wei Li Valley Laboratory , The Connecticut Agricultural Experiment Station , Windsor , CT , USA

Jose L. Lopez-Ribot Department of Biology , South Texas Center for Emerging Infectious Diseases, The University of Texas at San Antonio , San Antonio , TX , USA

Gilvaine Ciavareli Lucas Department of Phytopathology , Federal University of Lavras , Lavras , Minas Gerais , Brazil

Departamento de Fitopatologia, Universidade Federal de Lavras, Caixa postal, Lavras, Minas Gerais, Brazil

Gengkon Lum Department of Computer Science and Information Systems , Youngstown State University , Youngstown , OH , USA

Hui Ma Department of Chemistry, National University of Singapore, Singapore

Alexandra McAleenan Clinical Sciences Centre , Imperial College London , London , UK

H. N. Madhavan Sankara Nethralaya, Larsen and Toubro Microbiology Research Centre , Chennai , Tamil Nadu , India

Cathal S. Mahon Department of Pharmaceutical Chemistry , University of California—San Francisco , San Francisco , CA , USA

xxiContributors

Minna Mäki Program Leader, NAT, Orion Diagnostica Oy, Espoo, Finland

P. T. Manoharan Department of Botany , Vivekananda College , Madurai , Tamil Nadu , India

Segula Masaphy Department of Applied Microbiology and Mycology , MIGAL , Kiryat Shmona , Israel

Maria D. Mayan Fundación CHUAC, Biomedical Research Center—INIBIC , A Coruña , Galicia , Spain

Vera Meyer Department of Applied and Molecular Microbiology , Berlin University of Technology , Berlin , Germany

Xiang Jia Min Department of Biological Sciences , Center for Applied Chemical Biology, Youngstown State University , Youngstown , OH , USA

Sonal Modak Bioinformatics Centre , University of Pune , Pune , Maharashtra , India

C. N. Mortensen Department of Agriculture and Ecology , University of Copenhagen , Copenhagan , Taastrup , Denmark

Dirk Mueller-Hagen Department of Applied and Molecular Microbiology , Technische Universität Berlin , Berlin , Germany

Suman Mukherjee Laboratory of Biochemistry and Genetics, NIDDK , National Institutes of Health , Bethesda , MD , USA

Susann Müller Department of Environmental Microbiology , Helmholtz Centre for Environmental Research—UFZ , Leipzig , Saxonia , Germany

S. Chandra Nayaka Department of Studies in Biotechnology , Asian Seed Health Centre, University of Mysore , Mysore , Karnataka , India

Christopher Nguyen Department of Plant and Environmental Protection Sciences , University of Hawaii at Manoa , Honolulu , HI , USA

Jonathan Niño Department of Microbiologia y Genetica—CIALE , Universidad de Salamanca , Villamayor , Salamanca , Spain

S. R. Niranjana Department of Studies in Biotechnology , University of Mysore , Mysore , Karnataka , India

Jesús V. Jorrín Novo Department of Biochemistry and Molecular Biology , University of Córdoba , Córdoba , Spain

Anthony J. O’Donoghue Department of Pharmaceutical Chemistry , University of California—San Francisco , San Francisco , CA , USA

Anthonia O’Donovan Discipline of Biochemistry , School of Natural Sciences, National University of Ireland , Galway , Ireland

Mary C. O’ Loughlin Department of Life Sciences , University of Limerick , Castletroy , Limerick , Ireland

Miruna Oros-Sichler Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institut , Braunschweig , Lower Saxony , Germany

xxii Contributors

Jean-Paul Ouedraogo Department Applied and Molecular Microbiology , Institute of Biotechnology, Berlin University of Technology , Berlin , Germany

Svetlana M. Ozerskaya All-Russian Collection of Microorganisms (VKM IBPM RAS, Pushchino, Russia) , G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Science , Pushchino , Moscow Region , Russia

Brejesh Kumar Pandey Molecular Plant Pathology Laboratory , Central Institute for Subtropical Horticulture, Indian Council of Agricultural Research , Lucknow , Uttar Pradesh , India

M. Pandi Department of Molecular Microbiology , School of Biotechnology, Madurai Kamaraj University , Madurai , Tamil Nadu , India

Ioannis Papapostolou Department of Biology , University of Patras , Patras , Achaia , Greece

Biplab C. Paul Department of Chemistry and Biochemistry, University of Regina, Regina, SK, Canada

Zahi Paz Department of Plant Pathology , University of Georgia , Athens , GA , USA

Pilar Pérez Departamento de Microbiología CSIC/Universidad de Salamanca , Instituto de Biología Funcional y Genómica (IBFG) , Salamanca , Spain

Kugen Permaul Department of Biotechnology and Food Technology , Durban University of Technology , Durban , Kwa-Zulu-Natal , South Africa

Christopher G. Pierce Department of Biology , South Texas Center for Emerging Infectious Diseases, The University of Texas at San Antonio , San Antonio , TX , USA

Edson Ampélio Pozza Departamento de Fitopatologia, Universidade Federal de Lavras, Caixa postal, Lavras, Minas Gerais, Brazil

Prashant Prabhakar Department of Biotechnology , Dr. D.Y. Patil University , Pune , Maharashtra , India

H. S. Prakash Department of Studies in Biotechnology , Asian Seed Health Centre, University of Mysore , Mysore , Karnataka , India

P. Rajapriya Department of Microbiology , Srinivasan College of Arts and Science , Perambalur , Tamil Nadu , India

Arthur F. J. Ram Department of Molecular Microbiology and Biotechnology , Leiden University , Leiden , BE , The Netherlands

M. Venkata Ramana Department of Studies in Microbiology , University of Mysore , Mysore , Karnataka , India

Shoba Ranganathan Department of Chemistry and Biomolecular Sciences , Macquarie University , Sydney , NSW , Australia

xxiiiContributors

Department of Biochemistry , Yong Loo Lin School of Medicine, National University of Singapore , Singapore , Singapore

Serena Rasconi Department of Biology , University of Oslo , Oslo , Norway

Juan C. Ribas Departamento de Microbiología CSIC/Universidad de Salamanca , Senior Scientist from the Spanish Research Council (Consejo Superior de Investigaciones Cientí fi cas, CSIC), Instituto de Biología Funcional y Genómica (IBFG) , Salamanca , Spain

Terri L. Richardson School of Environmental Sciences, University of Guelph , Guelph , ON , Canada

Jeyabalan Sangeetha Department of Zoology , Karnataka University, 580003, Dharwad, Karnataka, India

Thomas Scheper Chip Technology Institute for Technical Chemistry, University of Hannover , Hannover , Lower Saxony , Germany

Jochen Schmid Department of Chemistry of Biogenic Resources , Technische Universität München , Straubing , Bavaria , Germany

Cor D. Schoen Department of Bio-Interactions and Plant Health , Plant Research International B. V , Wageningen , The Netherlands

Denise Schöfbeck Department for Agrobiotechnology (IFA-Tulln) , University of Natural Resources and Life Sciences Vienna , Tulln , Austria

Rainer Schuhmacher Department for Agrobiotechnology (IFA-Tulln) , University of Natural Resources and Life Sciences Vienna , Tulln , Austria

Shimantika Sharma Department of Biotechnology , Dr. D.Y. Patil University , Pune , Maharashtra , India

Mary Shier Department of Biochemistry , National University of Ireland , Galway , Ireland

Sukhdeep Sidhu School of Environmental Sciences, University of Guelph , Guelph , ON , Canada

Volker Sieber Chemistry of Biogenic Resources , Technische Universität München , Straubing , Bavaria , Germany

Télesphore Sime-Ngando UMR CNRS 6023, Université Blaise Pascal, Clermont II , Aubière , Cedex , France

Suren Singh Department of Biotechnology and Food Technology , Durban University of Technology , Durban , Kwa-Zulu-Natal , South Africa

Kornelia Smalla Julius Kühn Institut, Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics , Braunschweig , Lower Saxony , Germany

Laelie A. Snook Department of Human Health and Nutritional Sciences, Guelph, Ontario, Canada

xxiv Contributors

Birgit Spiess Third Department of Internal Medicine , Mannheim University Hospital , Mannheim , Germany

Akhil Srivastava Department of Plant and Environmental Protection Sciences , University of Hawaii at Manoa , Honolulu , HI , USA

Frank Stahl Chip Technology Institute for Technical Chemistry, University of Hannover , Hannover , Germany

Dawn Elizabeth Stephens Department of Biotechnology and Food Technology , Durban University of Technology , Durban , Kwa-Zulu-Natal , South Africa

Vega Tello Department of Microbiologia y Genetica—CIALE , Universidad de Salamanca , Salamanca , Spain

Devarajan Thangadurai Department of Botany , Karnataka University , Dharwad , Karnataka , India

K. Lily Therese Sankara Nethralaya, Larsen and Toubro Microbiology Research Centre, Vision Research Foundation , Chennai , Tamil Nadu , India

Berend Tolner Department of Oncology , University College London Cancer Institute , London , UK

Jack T. Trevors School of Environmental Sciences, University of Guelph , Guelph , ON , Canada

Clement K. M. Tsui Department of Forest Sciences , The University of British Columbia , Vancouver , BC , Canada

Maria G. Tuohy Department of Biochemistry, School of Natural Sciences , National University of Ireland , Galway , Ireland

Katherine D. Turner School of Natural Sciences , Centre for Chromosome Biology, National University of Ireland Galway , Galway , Ireland

Kevin M. Turner Manufacturing Sciences and Technology, P fi zer Ireland Pharmaceuticals, The P fi zer Biotech Campus at Grange Castle , Dublin , Ireland

A. C. Udayashankar Department of Studies in Biotechnology , Asian Seed Health Centre, University of Mysore , Mysore , Karnataka , India

R. S. Upadhyay Department of Botany , Centre of Advanced Study, Banaras Hindu University , Varanasi , Uttar Pradesh , India

Priya Uppuluri Department of Biology , South Texas Center for Emerging Infectious Diseases, The University of Texas at San Antonio , San Antonio , TX , USA

Marco van den Berg Applied Biochemistry and Screening , DSM Biotechnology Center , Delft , Zuid-Holland , The Netherlands

Cees A. M. J. J . van den Hondel Department of Molecular Microbiology and Biotechnology , Leiden University , Leiden , BE , The Netherlands

xxvContributors

Alexander N. Vasilenko All-Russian Collection of Microorganisms (VKM IBPM RAS, Pushchino, Russia), G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Science , Pushchino , Moscow Region , Russia

Kim Vigor Department of Oncology , University College London Cancer Institute , London , UK

Jeannette Vogt Department of Environmental Microbiology , Helmholtz Centre for Environmental Research—UFZ , Leipzig , Saxonia , Germany

Bin Wang Westmead Hospital, Centre of Virus Research, Westmead Millennium Institute, University of Sydney , Westmead , NSW , Australia

Gerlinde Wiesenberger Institute of Applied Genetics and Cell Biology , University of Natural Resources and Life Sciences Vienna , Tulln , Austria

Akshay Yadav Scienti fi c and Engineering Computing Group (SECG), Centre for Development of Advanced Computing (C-DAC) , University of Pune , Pune , Maharashtra , India

Naomichi Yamamoto Department of Environmental Health, Graduate School of Public Health, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, Korea

Susanne Zeilinger Research Area Gene Technology and Applied Biochemistry , Institute for Chemical Engineering, Vienna University of Technology , Vienna , Austria

Shaobin Zhong Department of Plant Pathology , North Dakota State University , Fargo , ND , USA

Lucie Zinger Laboratoire d’Ecologie Alpine, CNRS/UJF , Université Joseph Fourier , Grenoble , France