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Applied Microbiology VOLUME 60 This Page Intentionally Left Blank ADVANCES in Applied Microbiology ADVANCES IN Applied Microbiology VOLUME 60 This page intentionally left blank ADVANCES IN Applied Microbiology Edited by ALLEN I. LASKIN Somerset, New Jersey SIMA SARIASLANI Wilmington, Delaware GEOFFREY M. GADD Dundee, United Kingdom VOLUME 60 AMSTERDAM • BOSTON • HEIDELBERG • LONDON NEW YORK • OXFORD • PARIS • SAN DIEGO SAN FRANCISCO • SINGAPORE • SYDNEY • TOKYO Academic Press is an imprint of Elsevier Academic Press is an imprint of Elsevier 525 B Street, Suite 1900, San Diego, California 92101-4495, USA 84 Theobald’s Road, London WC1X 8RR, UK This book is printed on acid-free paper. Copyright ß 2006, Elsevier Inc. All Rights Reserved. No part of this publication may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopy, recording, or any information storage and retrieval system, without permission in writing from the Publisher. The appearance of the code at the bottom of the first page of a chapter in this book indicates the Publisher’s consent that copies of the chapter may be made for personal or internal use of specific clients. This consent is given on the condition, however, that the copier pay the stated per copy fee through the Copyright Clearance Center, Inc. (www.copyright.com), for copying beyond that permitted by Sections 107 or 108 of the U.S. Copyright Law. This consent does not extend to other kinds of copying, such as copying for general distribution, for advertising or promotional purposes, for creating new collective works, or for resale. Copy fees for pre-2006 chapters are as shown on the title pages. If no fee code appears on the title page, the copy fee is the same as for current chapters. 0065-2164/2006 $35.00 Permissions may be sought directly from Elsevier’s Science & Technology Rights Department in Oxford, UK: phone: (þ44) 1865 843830, fax: (þ44) 1865 853333, E-mail: [email protected]. You may also complete your request on-line via the Elsevier homepage (http://elsevier.com), by selecting ‘‘Support & Contact’’ then ‘‘Copyright and Permission’’ and then ‘‘Obtaining Permissions.’’ For information on all Academic Press publications visit our Web site at www.books.elsevier.com ISBN-13: 978-0-12-002662-3 ISBN-10: 0-12-002662-7 PRINTED IN THE UNITED STATES OF AMERICA 06070809987654321 CONTENTS Microbial Biocatalytic Processes and Their Development JOHN M. WOODLEY I. Introduction ............................................................................ 1 II. Rationale for the Use of Microbial Biocatalysts ................................... 2 III. Mode of Operation .................................................................... 4 IV. Conversions Particularly Suited to Microbial Biocatalysts ..................... 5 V. Processing Considerations for the Application of Microbial Biocatalysts .... 6 VI. Bioprocess Development ............................................................. 9 VII. Future Outlook ......................................................................... 12 VIII. Concluding Remarks .................................................................. 13 References ............................................................................... 13 Occurrence and Biocatalytic Potential of Carbohydrate Oxidases ERIK W. VAN HELLEMOND,NICOLE G. H. LEFERINK,DOMINIC P. H. M. HEUTS, MARCO W. FRAAIJE, AND WILLEM J. H. VAN BERKEL I. Introduction ............................................................................ 17 II. Physiological Role and Catalytic Properties ....................................... 20 III. Biocatalytical Applications .......................................................... 41 IV. Conclusions and Future Prospects .................................................. 45 References ............................................................................... 45 Microbial Interactions with Humic Substances J. IAN VAN TRUMP,YVONNE SUN, AND JOHN D. COATES I. Introduction ............................................................................ 56 II. Source and Chemistry of Humic Substances ...................................... 56 III. Interactions Between Humic Substances and Microorganisms ................. 61 IV. The Biochemistry of Microbial HS Reduction and Oxidation .................. 71 V. Microbes, Contaminants, and HS: Remediation Promise, Remediation Concerns ................................................................ 76 VI. Conclusions ............................................................................. 86 References ............................................................................... 86 v vi CONTENTS Significance of Microbial Interactions in the Mycorrhizosphere GARY D. BENDING,THOMAS J. ASPRAY, AND JOHN M. WHIPPS I. Introduction ............................................................................ 97 II. The Mycorrhizosphere as a Soil Compartment ................................... 98 III. The Physical and Chemical Environment of the Mycorrhizosphere .......... 99 IV. Interactions Between Microbes and Symbionts Prior to and During Mycorrhiza Formation ................................................................ 102 V. Interactions Between Mycorrhizas and Free-Living Nonpathogenic Organisms ........................................................... 109 VI. Pathogen Interactions with Mycorrhizas .......................................... 115 VII. Conclusions ............................................................................ 120 References .............................................................................. 121 Escherich and Escherichia HERBERT C. FRIEDMANN I. Introduction ............................................................................ 134 II. The Naming of Bacteria and the ‘‘Mystery’’ of ‘‘E.’’ ............................. 134 III. A Paradox: The Golden Age of Bacteriology, and Persistence of Noncontagious Notions of Transmissible Diseases .............................. 135 IV. The Invention of the Word ‘‘Bacteriology’’ and the Rapid Rise of Bacteriology as a Distinct Discipline ............................................... 137 V. Theodor Escherich’s Life ............................................................. 138 VI. First Studies with Bacterium coli commune: Search for the Bacterial Cause of Infantile Diarrhea ............................................... 154 VII. Escherichia: Vagaries of a Name .................................................... 168 VIII. Escherich’s Neglect of His Discovery of Campylobacter jejuni and of Some Other Bacteria .......................................................... 172 IX. Extensive Studies with E. coli, Long Before the Advent of Molecular Biology ..................................................................... 174 X. Summary ................................................................................ 182 References .............................................................................. 184 INDEX .......................................................................................... 197 CONTENTS OF PREVIOUS VOLUMES ............................................................. 205 Microbial Biocatalytic Processes and Their Development JOHN M. WOODLEY Department of Biochemical Engineering, University College London Torrington Place, London WC1E 7JE, United Kingdom I. Introduction 1 II. Rationale for the Use of Microbial Biocatalysts 2 III. Mode of Operation 4 IV. Conversions Particularly Suited to Microbial Biocatalysts 5 A. Conversions as Part of a ‘‘Cell Factory’’ 5 B. Reactions Involving Cofactor‐Requiring Enzymes 5 V. Processing Considerations for the Application of Microbial Biocatalysts 6 A. Industrial Process Requirements 6 B. Reactions Using Organic Solvent‐Based Media 7 C. Oxygen‐Requiring Reactions 7 D. Substrate Access 8 E. Product Recovery 8 VI. Bioprocess Development 9 VII. Future Outlook 12 A. Cell Engineering 12 B. Toward Bulk Chemical Bioprocessing 12 VIII. Concluding Remarks 13 References 13 I. Introduction With recent advances in genomic and genetic engineering, interest in the use of biocatalysis for industrial synthetic chemistry is growing rapidly. Likewise, the range of characterized enzymes and the applica- tions of biocatalysts continue to expand (Rich et al., 2002). In particular, biocatalysis is starting to fulfill its promise as a key tool for the produc- tion of optically pure small organic molecules (for the pharmaceutical and agrochemical sector), in part due to the high chemo‐, regio‐, and stereospecificity and selectivity inherent in enzymatic reactions. In addition, the use of microbial (whole‐cell) catalysts containing these enzymes for biocatalytic synthesis is gaining considerable industrial interest. Microbial processes offer possibilities for biocatalysis, which cannot always be met by use of isolated enzymes. The cellular environ- ment protects the protein, which may lead to improved catalyst stability. Furthermore, reactions involving expensive cofactors [e.g., NADH 1 ADVANCES IN APPLIED MICROBIOLOGY, VOLUME 60 0065-2164/06 $35.00 Copyright 2006, Elsevier Inc. All rights reserved. DOI: 10.1016/S0065-2164(06)60001-4 2 JOHN M. WOODLEY or NAD(P)H] and multistep conversions can be simplified in a whole‐ cell format. However, despite the increased interest from chemists in the appli- cation of enzymes and whole‐cell catalysts, it remains the case that the majority of biocatalytic processes implemented in recent years use isolated enzymes. In this chapter, the focus is on microbial conversions with particular emphasis on the
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