ADVANCES IN Applied Microbiology VOLUME 53 ThisPageIntentionallyLeftBlank ADVANCES IN Applied Microbiology Edited by ALLEN I. LASKIN Somerset, New Jersey JOAN W. BENNETT New Orleans, Lousiana GEOFFREY M. GADD Dundee, United Kingdom VOLUME 53 This book is printed on acid-free paper. Copyright ß 2003, 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. (222 Rosewood Drive, Danvers, Massachusetts 01923), 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-2003 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. 0065-2164/2003 $35.00 Permissions may be sought directly from Elsevier’s Science & Technology Rights Department in Oxford, UK: phone: (+44) 1865 843830, fax: (+44) 1865 853333, e-mail: [email protected]. You may also complete your request on-line via the Elsevier homepage (http://elsevier.com), by selecting ‘‘Customer Support’’ and then ‘‘Obtaining Permissions.’’ Elsevier Academic Press 525 B Street, Suite 1900, San Diego, California 92101-4495, USA 84 Theobald’s Road, London WC1X 8RR, UK http://www.academicpress.com International Standard Book Number: 0-12-002655-4 PRINTED IN THE UNITED STATES OF AMERICA 03 04 05 06 07 08 9 8 7 6 5 4 3 2 1 CONTENTS Biodegradation of Organic Pollutants in the Rhizosphere LIZ J. SHAW AND RICHARD G. BURNS I. Introduction ............................................................................ 1 II. The Rhizosphere Environment and Microbial Ecology .......................... 2 III. Fate of Organic Pollutants in the Rhizosphere .................................... 7 IV. Mechanisms of Enhanced Biodegradation ......................................... 22 V. Specific and Nonspecific Interactions between Plant and Microbe ............ 34 VI. Stimulating and Initiating Rhizosphere Activity ................................. 37 VII. Conclusions ............................................................................. 43 VIII. Glossary of Latin Plant Names ....................................................... 46 References ............................................................................... 47 Anaerobic Dehalogenation of Organohalide Contaminants in the Marine Environment MAX M. HA¨ GGBLOM,YOUNG-BOEM AHN,DONNA E. FENNELL,LEE J. KERKHOF, AND SUNG-KEUN RHEE I. Introduction—The Halogen Cycle .................................................. 61 II. Microbial Transformation of Organohalides and the Influence of Electron Donors and Alternate Electron Acceptors .............................. 63 III. Molecular and Biochemical Characterization of Dehalogenating Consortia in Marine Environments ................................................. 69 IV. Detection of Putative Reductive Dehalogenase-Encoding Genes in Dehalogenating Consortia and Marine Sediments ................................ 71 V. Dehalogenation by Anaerobic Bacteria in Marine Sponges—Natural Sources of Dehalogenating Bacteria .......................... 73 VI. In Situ Enhancement of Anaerobic Microbial Dechlorination of Polychlorinated Dibenzo-p-dioxins and Dibenzofurans in Marine and Estuarine Sediments .................................................... 75 VII. Summary ................................................................................ 78 References ............................................................................... 78 v vi CONTENTS Biotechnological Application of Metal-Reducing Microorganisms JONATHAN R. LLOYD,DEREK R. LOVLEY, AND LYNNE E. MACASKIE I. Introduction ............................................................................ 85 II. Fe(III) and Mn(IV) Reduction ........................................................ 86 III. Reduction of Other Transition Metals ............................................. 92 IV. Reduction of Metalloids .............................................................. 108 V. Reduction and Bioremediation of Actinides and Fission Products ........... 112 VI. Future Directions ...................................................................... 118 References .............................................................................. 119 Determinants of Freeze Tolerance in Microorganisms, Physiological Importance, and Biotechnological Applications AN TANGHE,PATRICK VAN DIJCK, AND JOHAN M. THEVELEIN I. Introduction ............................................................................ 129 II. Freeze–Thaw Events .................................................................. 131 III. Freeze–Thaw Injury ................................................................... 134 IV. Microbial Freeze-Tolerance Mechanisms .......................................... 136 V. Physiological Importance of Microbial Freeze-Tolerance Mechanisms ....... 147 VI. Biotechnological Applications of Microbial Freeze-Tolerance Mechanisms and Freeze-Tolerant Microorganisms .............................. 149 VII. Concluding Remarks .................................................................. 160 References .............................................................................. 161 Fungal Osmotolerance P. HOOLEY,D.A.FINCHAM,M.P.WHITEHEAD, AND N. J. W. CLIPSON I. Introduction ............................................................................ 177 II. Physiological Mechanisms of Osmotolerance .................................... 179 III. Control of Osmotic Responses at the Molecular Level .......................... 183 IV. Conclusions ............................................................................ 199 References .............................................................................. 204 Mycotoxin Research in South Africa M. F. DUTTON I. South Africa—A Short Guide ....................................................... 213 II. Introduction to South African Mycotoxin Research ............................. 215 III. Mycotoxins and Agriculture in South Africa ..................................... 220 IV. Chronic Disease ........................................................................ 223 V. Conclusion on Currently Investigated Chronic Disease ......................... 232 References .............................................................................. 232 CONTENTS vii Electrophoretic Karyotype Analysis in Fungi J. BEADLE,M.WRIGHT,L.MCNEELY, AND J. W. BENNETT I. Introduction ............................................................................ 243 II. Background ............................................................................. 244 III. Techniques ............................................................................. 245 IV. Chromosome Numbers and Size .................................................... 256 V. Applications of PFGE ................................................................. 258 VI. Limitations of PFGE for Fungal Karyotype Analysis ............................. 260 VII. Summary ................................................................................ 263 References ............................................................................... 264 Tissue Infection and Site-Specific Gene Expression in Candida albicans CHANTAL FRADIN AND BERNARD HUBE I. Introduction ............................................................................ 271 II. Secretory Lipases of C. albicans ...................................................... 273 III. Agglutinin-Like Proteins of C.albicans.............................................. 275 IV. Secretory Proteinases of C. albicans .................................................. 276 V. Why Gene Families (Part I)? ......................................................... 277 VI. Why Gene Families (Part II)? ........................................................ 282 VII. Genome-Wide Transcriptional Profiling ........................................... 284 VIII. Summary ................................................................................ 288 References ............................................................................... 288 LuxS and Autoinducer-2: Their Contribution to Quorum Sensing and Metabolism in Bacteria KLAUS WINZER,KIM R. HARDIE, AND PAUL WILLIAMS I. Introduction ............................................................................ 292 II. Overview of Bacterial Cell-to-Cell Communication .............................. 292 III. Biochemistry of AI-2 Formation ..................................................... 295 IV. The Structure of AI-2 ................................................................. 298 V. LuxS: Crystal Structure and Enzymatic Properties ............................... 304 VI. The Metabolic Role of LuxS ......................................................... 311 VII. The Location