Microbial Biotechnology Principles and Applications

Transcription

1 Microbial Biotechnology Principles and Applications Third Edition

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3 Microbial Biotechnology Principles and Applications Third Edition Editor Lee Yuan Kun World Scientific NEW JERSEY LONDON SINGAPORE BEIJING SHANGHAI HONG KONG TAIPEI CHENNAI

4 Published by World Scientific Publishing Co. Pte. Ltd. 5 Toh Tuck Link, Singapore USA office: 27 Warren Street, Suite , Hackensack, NJ UK office: 57 Shelton Street, Covent Garden, London WC2H 9HE Library of Congress Cataloging-in-Publication Data Microbial biotechnology : principles and applications / edited by Yuan Kun Lee,, Singapore. -- 3rd edition. pages cm Includes bibliographical references and index. ISBN (hardcover : alk. paper) -- ISBN (pbk. : alk. paper) 1. Microbial biotechnology. I. Lee, Y. K. (Yuan Kun) TP M53M '2--dc British Library Cataloguing-in-Publication Data A catalogue record for this book is available from the British Library. Copyright 2013 by World Scientific Publishing Co. Pte. Ltd. All rights reserved. This book, or parts thereof, may not be reproduced in any form or by any means, electronic or mechanical, including photocopying, recording or any information storage and retrieval system now known or to be invented, without written permission from the Publisher. For photocopying of material in this volume, please pay a copying fee through the Copyright Clearance Center, Inc., 222 Rosewood Drive, Danvers, MA 01923, USA. In this case permission to photocopy is not required from the publisher. Typeset by Stallion Press enquiries@stallionpress.com Printed in Singapore.

5 Preface Life science research and industry is developing rapidly all over the world. Microbial biotechnology is increasingly being regarded as a core subject in most university and polytechnic life science courses. There are already a number of excellent general textbooks on microbiology and biotechnology in the market that deal with the basic principles of the field. In order to complement these general textbooks, this book aims to focus on the applications of microbial biotechnological principles. A teachingbased format is adopted, whereby working problems, as well as answers to frequently asked questions are included to supplement the main text. This textbook also includes real life examples on how the application of microbial biotechnological principles has achieved breakthroughs in both research and industrial production. The rapidly expanding molecular biology, genetic, protein and metabolic techniques and approaches have significant impact on the Microbial biotechnology; this leads to the addition of three new chapters in the third edition of this textbook. They are the Chapter 3: Application of -Omics Technologies in Microbial Fermentation, Chapter 5: Microbial Genome Mining for Identifying Antimicrobial Targets, and the Chapter 21: Bacterial Biofilm: Molecular Characterization and Impacts on Water Management. The Chapter 1: Microbial Screening and Chapter 15: Transgenic Plants are re-written as fresh chapters. For completion, Part VI is expanded to include Biomining (Chapter 23: Microbial Biomining). Most of the others chapters are updated in this new edition. Although this textbook is written for university undergraduates and polytechnic students, it contains sufficient details to be used as a reference book v

6 vi Microbial Biotechnology: Principles and Applications for postgraduate students and lecturers. It may also service as a source book for corporate planners, managers and applied research personnel. Lee Yuan Kun Editor

7 Contents Preface List of Contributors Part I Principles of Microbial Biotechnology 1 Chapter 1 Microbial Screening 3 Allan Lim and Tan Hai-Meng Chapter 2 Bioprocess Technology 21 Lee Yuan Kun Chapter 3 Application of -Omics Technologies in Microbial Fermentation 71 Victor Wong Vai-Tak, Faraaz Noor Khan Yusufi and Lee Dong-Yup Chapter 4 Enzymology 95 Theresa Tan May Chin and Deng Lih Wen Chapter 5 Microbial Genome Mining for Identifying Antimicrobial Targets 117 Kishore R. Sakharkar, Jayaraman Premkumar, Meena K. Sakharkar and Vincent T. K. Chow Chapter 6 Manipulation of Genes 135 Azlinda Anwar, Too Heng-Phon and Chua Kim Lee v xi vii

8 viii Microbial Biotechnology: Principles and Applications Chapter 7 Applications of Bioinformatics and Biocomputing to Microbiological Research 211 Paxton Loke and Sim Tiow Suan Chapter 8 Quantitative Real Time PCR (QPCR) 241 Too Heng-Phon and Azlinda Anwar Part II Food Production Involving Microorganisms and Their Products 267 Chapter 9 Fermented Foods 269 Desmond K. O Toole and Lee Yuan Kun Chapter 10 Food Involving Yeast and Ethanol Fermentation 335 Desmond K. O Toole and Lee Yuan Kun Chapter 11 Fungal Solid State Cultivation 379 Desmond K. O Toole Chapter 12 Food Ingredients 395 Desmond K. O Toole and Lee Yuan Kun Chapter 13 Enzyme Modified Food Products 423 Desmond K. O Toole and Lee Yuan Kun Annex Regulation of Foods Involving Genetically Engineered 436 Microorganisms Desmond K. O Toole and Lee Yuan Kun Part III Microbes in Agrobiotechnology 441 Chapter 14 Microbes and Livestock 443 Jimmy Kwang and He Fang Chapter 15 Transgenic Plants 521 Hong Yan and Bu Yun Ping Part IV Microbes in Medical Biotechnology 585 Chapter 16 Diagnostic Clinical Microbiology 587 Vincent T. K. Chow, Tim J. J. Inglis and Song Keang Peng

9 Contents ix Chapter 17 Microbes: Friends or Foes? 641 Vincent T. K. Chow, Tim J. J. Inglis and Song Keang Peng Part V Microbes in Environmental Biotechnology 671 Chapter 18 Municipal Wastewater Treatment 673 Chu Lee Man and Wong Po-Keung Chapter 19 Industrial Wastewater Treatment 719 Wong Po-Keung and Chu Lee Man Chapter 20 Municipal and Industrial Solid Waste Treatment 753 Wong Po-Keung and Chu Lee Man Chapter 21 Bacterial Biofilm: Molecular Characterization and Impacts on Water Management 777 Teng Wee Lin, Gao Pingping and Chang Siao Yun Annex Regulatory Issues on Application of Natural 796 and Genetically Engineered Microbes in Environmental Biotechnology Wong Po-Keung and Chu Lee Man Part VI Microbes in Alternative Energy and in Mining 799 Chapter 22 Microorganisms and Production of Alternative Energy 801 Lee Yuan Kun Chapter 23 Microbial Biomining 817 Yew Wen Shan Part VII Patenting Microbial Biotechnology 835 Chapter 24 Patenting Inventions in Microbiology 837 John Candlish Index 855

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11 List of Contributors Anwar, Azlinda, BSc (Hons), PhD Program in Infectious Diseases, Duke-NUS Graduate Medical School 8 College Rd, Singapore azlinda.anwar@duke-nus.edu.sg Bu, Yun Ping, BSc, PhD Temasek Life Sciences Laboratory 1 Research Link, Singapore Buyp@tll.org.sg Candlish, John, PhD, LLM Faculty of Medicine and Health Sciences, University of Malaysia Sarawak, Kuching, East Malaysia jkcandlish@yahoo.com.sg Chang, Siao Yun, BSc (Hons), PhD Technology & Water Quality Office, Public Utilities Board (PUB) 82 Toh Guan Road East, WaterHub, Singapore Siao_Yun_ Chang@pub.gov.sg Chow, Vincent T. K., MBBS, MSc, Dip Microbiology, FRC Path, MD, PhD Infectious Diseases Program Department of Microbiology, Yong Loo Lin School of Medicine National University Health System xi

12 xii Microbial Biotechnology: Principles and Applications Kent Ridge, Singapore Chu, Lee Man, BSc (Hons), PhD Department of Biology, The Chinese University of Hong Kong Shatin, NT, Hong Kong SAR, China Chua, Kim Lee, BSc (Hons), Dip Ed, PhD Department of Biochemistry, Yong Loo Lin School of Medicine MD 7, 8 Medical Drive, Singapore kim_lee_chua@nuhs.edu.sg Deng, Lih Wen, BSc (Hons), PhD Department of Biochemistry, Yong Loo Lin School of Medicine MD 7, 8 Medical Drive, Singapore bchdlw@nus.edu.sg Gao, Pingping, BSc, PhD Technology & Water Quality Office, Public Utilities Board (PUB) 82 Toh Guan Road East, WaterHub, Singapore pingping_ gao@pub.gov.sg He, Fang Institute of Molecular Agrobiology 1 Research Link, Singapore Hong, Yan, BSc, PhD Temasek Life Sciences Laboratory 1 Research Link, Singapore hongy@tll.org.sg

13 List of Contributors xiii Inglis, Tim J. J., BM, DM, PhD, FRCPath, DTM&H, FRCPA School of Pathology and Laboratory Medicine University of Western Australia Crawley WA 6009, Perth, Australia Kwang, Jimmy, DVM, PhD Institute of Molecular Agrobiology 1 Research Link, Singapore kwang@tll.org.sg Lee, Dong-Yup, BSc (Hons), PhD Bioprocessing Technology Institute, A*STAR 20 Biopolis Way, #06 01 Centros, Singapore , and Department of Chemical and Biomolecular Engineering 4 Engineering Drive 4, Blk E5 #02 09, Singapore cheld@nus.edu.sg Lee, Yuan Kun, BSc (Hons), PhD Department of Microbiology, Yong Loo Lin School of Medicine 5 Science Drive 2, Singapore micleeyk@nus.edu.sg Lim, Allan, BSc (Hons), PhD Nestlé R&D Center Pte Ltd 15A, Changi Business Park Central 1 #05 02/03 Eightrium@Changi Business Park Singapore Allan.Lim@rdsg.nestle.com

14 xiv Microbial Biotechnology: Principles and Applications Loke, Paxton, BSc (Hons), PhD Ian Potter Hepatitis Research Laboratory The Macfarlane Burnet Institute for Medical Research and Public Health Commercial Road, Melbourne, Vic 3004, Australia O Toole, Desmond K., BSc, PhD Department of Biology and Chemistry, City University of Hong Kong 83 Tat Chee Avenue, Kowloon, Hong Kong, China d.k.otoole@gmail.com Premkumar, Jayaraman Biomedical Engineering Research Centre Nanyang Technological University, Singapore Sakharkar, Kishore R. Biomedical Engineering Research Centre Nanyang Technological University, Singapore Sakharkar, Meena K. Graduate School of Life and Environmental Sciences University of Tsukuba, Ibaraki, Japan Sim, Tiow Suan, BSc (Hons), PhD Department of Microbiology, Yong Loo Lin School of Medicine 5 Science Drive 2, Singapore tiow_suan_sim@nuhs.edu.sg Song, Keang Peng, BDS, PhD School of Science, Monash University Sunway Campus, Selangor, Malaysia song.keang.peng@sci.monash.edu.my

15 List of Contributors xv Tan, Hai Meng, BSc (Hons), PhD Kemin Industries (Asia) Pte Ltd 12 Senoko Drive, Singapore Tan, Theresa May Chin, BSc, PhD Department of Biochemistry, Yong Loo Lin School of Medicine MD 7, 8 Medical Drive, Singapore bchtant@nus.edu.sg Teng, Wee Lin BSc (Hons), PhD Technology & Water Quality Office, Public Utilities Board (PUB) 82 Toh Guan Road East, WaterHub, Singapore sarah_teng@pub.gov.sg Too, Heng-Phon, BSc, PhD Department of Biochemistry, Yong Loo Lin School of Medicine MD 7, 8 Medical Drive, Singapore , and Chemical and Pharmaceutical Engineering Singapore-Massachusetts Institute of Technology E , 4 Engineering Drive 3, Singapore bchtoohp@nus.edu.sg Wong, Po-Keung, BSc (Hons), PhD Department of Biology, The Chinese University of Hong Kong Shatin, NT, Hong Kong SAR, China pkwong@cuhk.edu.hk Wong, Victor Vai-Tak, BSc (Hons), PhD Bioprocessing Technology Institute, A*STAR 20 Biopolis Way, #06 01 Centros, Singapore , and Department of Chemical and Biomolecular Engineering 4 Engineering Drive 4, Blk E5 #02 09, Singapore victor.wong@lonza.com

16 xvi Microbial Biotechnology: Principles and Applications Yew, Wen Shan Department of Biochemistry, Yong Loo Lin School of Medicine MD 7, 8 Medical Drive, Singapore Yusufi, Faraaz Noor Khan, BSc (Hons), PhD Bioprocessing Technology Institute, A* STAR 20 Biopolis Way, #06-01 Centros, Singapore faraaz_yusufi@bti.a-star.edu.sg