Diversity of Microbial Toluene Degradation Pathways
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Advances in APPLIED MICROBIOLOGY VOLUME 64 This page intentionally left blank Advances in APPLIED MICROBIOLOGY VOLUME 64 Edited by ALLEN I. LASKIN Somerset, New Jersey, USA SIMA SARIASLANI Wilmington, Delaware, USA GEOFFREY M. GADD Dundee, Scotland, UK 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 84 Theobald’s Road, London WC1X 8RR, UK 30 Corporate Drive, Suite 400, Burlington, MA 01803, USA First edition 2008 Copyright # 2008 Elsevier Inc. 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, mechani- cal, photocopying, recording or otherwise without the prior written permission of the publisher Permissions may be sought directly from Elsevier’s Science & Technol- ogy Rights Department in Oxford, UK: phone (+44) (0) 1865 843830; fax(+44)(0)1865853333;email:[email protected] you can submit your request online by visiting the Elsevier web site at http://elsevier.com/locate/permissions, and selecting, Obtaining permission to use Elsevier material Notice No responsibility is assumed by the publisher for any injury and/or damage to persons or property as a matter of products liability, negli- gence or otherwise, or from any use or operation of any methods, products, instructions or ideas contained in the material herein. Because of rapid advances in the medical sciences, in particular, independent verification of diagnoses and drug dosages should be made ISBN: 978-0-12-374338-1 ISSN: 0065-2164 For information on all Academic Press publications visit our website at books.elsevier.com Printed and bound in USA 08 09 10 11 12 10 9 8 7 6 5 4 3 2 1 CONTENTS Contributors ix 1. Diversity of Microbial Toluene Degradation Pathways R. E. Parales, J. V. Parales, D. A. Pelletier, and J. L. Ditty I. Introduction 2 II. Dioxygenase Mediated Pathway: Pseudomonas putida F1 4 A. Pathway details and enzymology 4 B. Genetics and regulation 8 III. Toluene 2-Monooxygenase Pathway: Burkholderia vietnamiensis G4 12 A. Pathway details and enzymology 12 B. Genetics and pathway regulation 14 IV. Toluene-3-monooxygenase Pathway: Ralstonia pickettii PKO1 15 V. Toluene-4-monooxygenase Pathway: Pseudomonas mendocina KR1 20 VI. A Strain with Multiple Toluene Degradation Pathways: Burkholderia sp. Strain JS150 25 VII. A Nonspecific Toluene Monooxygenase Pathway: Pseudomonas stutzeri OX1 28 A. Pathway details and enzymology 28 B. Pathway regulation 32 VIII. TOL Pathway: Pseudomonas putida mt-2 33 A. Pathway and enzymology 34 B. Genetics and regulation 40 IX. A Fungal Toluene Degradation Pathway 43 X. Anaerobic Toluene Pathway: Thauera aromatica K172 47 A. Pathway details and enzymology 47 B. Genetics and regulation 52 XI. Conclusions 52 Acknowledgments 55 References 55 2. Microbial Endocrinology: Experimental Design Issues in the Study of Interkingdom Signalling in Infectious Disease Primrose P. E. Freestone and Mark Lyte I. Microbial Endocrinology as a New Scientific Discipline 76 A. Overview and goal of review 76 v vi Contents B. The stress response and its influence on the immune system and the infectious agent 77 C. Mechanisms by which stress-related neuroendocrine hormones can enhance bacterial growth and virulence 79 D. The spectrum of catecholamine responsive bacteria 84 E. Catecholamine specificity in enteric bacteria 85 F. Molecular analyses of bacterial catecholamine responsiveness 88 II. Experimental Design Issues in the Study of Microbial Endocrinology 89 A. Medium comparability 90 B. Bacterial inoculum size and its influence on stress neurohormone responsiveness 92 C. The importance of neuroendocrine hormone concentration 94 D. Neuroendocrine stress neurohormone assay methodologies 97 III. Conclusions and Future Directions 101 References 102 3. Molecular Genetics of Selenate Reduction by Enterobacter cloacae SLD1a-1 Nathan Yee and Donald Y. Kobayashi I. Introduction 108 II. Physiology and Biochemistry of E. cloacae SLD1a-1 108 III. Basic Systems of Molecular Genetics in Facultative Se-reducing Bacteria 110 A. Growth of E. cloacae SLD1a-1 on selenate-containing agar plates 110 B. Direct cloning experiments 110 C. Gene specific mutagenesis 112 D. Random mutagenesis using transposons 113 IV. Genetic Analysis of Selenate Reduction in E. cloacae SLD1a-1 115 V. A Molecular Model for Selenate Reduction in E. cloacae SLD1a-1 118 VI. Conclusions and Future Prospects 120 Acknowledgments 120 References 120 4. Metagenomics of Dental Biofilms Peter Mullany, Stephanie Hunter, and Elaine Allan I. Introduction 126 II. Isolation of Metagenomic DNA 126 III. Sample Collection and Processing 126 IV. DNA Extraction 128 V. Preparation of the Insert DNA for Cloning 128 A. Partial restriction digestion 129 B. Mechanical shearing of the DNA 129 VI. Removal of Human DNA 129 Contents vii VII. Metagenomic Library Construction 130 A. Construction of large insert metagenomic libraries 130 B. Construction of small insert libraries 132 C. Phage display 132 VIII. Limitations of Metagenomics 133 IX. Conclusions and Future Perspectives 134 References 134 5. Biosensors for Ligand Detection Alison K. East, Tim H. Mauchline, and Philip S. Poole I. Introduction 137 II. Induction Biosensors 139 A. General considerations for use of induction biosensors 139 B. Reporter genes 140 III. Molecular Biosensors 150 A. Optical biosensors 150 B. Electrical biosensors 159 IV. Conclusions and Future Prospects 160 Acknowledgments 160 References 160 6. Islands Shaping Thought in Microbial Ecology Christopher J. van der Gast I. Introduction 167 II. The Importance of Islands 169 A. Biogeographic islands for studies of bacterial diversity 169 B. Island biogeography 170 III. Species–Area Relationships 170 A. Microbial biogeography 171 B. Island size and bacterial diversity 172 IV. Beta Diversity 174 A. Smaller islands are less stable than larger ones 175 B. Species–time relationships 175 C. Distance–decay relationships 177 V. Opposing Perspectives on Community Assembly 177 VI. Conclusions 179 Acknowledgments 180 References 180 7. Human Pathogens and the Phyllosphere John M. Whipps, Paul Hand, David A. C. Pink, and Gary D. Bending I. Introduction 183 viii Contents II. Food Poisoning Outbreaks Associated with Consumption of Fresh and Minimally Processed Fresh Vegetables, Salads, and Fruit 185 III. Sources of Human Pathogens on Plants 186 IV. Ecology of Human Pathogens in Relation to Phyllosphere Contamination 189 A. Ecology and survival in sewage, manure, soil, and water 189 B. Ecology and survival in association with plants 190 C. Ecology and survival during processing 203 V. Conclusions and Future 208 Acknowledgments 209 References 209 8. Microbial Retention on Open Food Contact Surfaces and Implications for Food Contamination Joanna Verran, Paul Airey, Adele Packer, and Kathryn A. Whitehead I. Introduction 224 II. Microbial Attachment, Biofilm Formation, and Cell Retention 225 III. Surfaces (substrata) Encountered 226 IV. Factors Affecting Retention 227 A. Surface topography 227 B. Surface chemistry 230 C. Presence of organic material 231 V. Characterization of Surfaces 232 A. Topography 232 B. Chemistry 234 VI. Measuring Retention and Assessing Cleaning and Disinfection 234 A. Substratum preparation 234 B. Amount of retention 235 C. Strength of retention 238 D. Quantifying organic material 240 VII. Conclusions 241 References 241 Index 247 Contents of Previous Volumes 255 Color Plate Section CONTRIBUTORS Paul Airey School of Biology, Chemistry and Health Science, Manchester Metropolitan University, Manchester M1 5GD, United Kingdom. Elaine Allan Division of Microbial Diseases, Eastman Dental Institute, University College London, London WC1X 8LD, United Kingdom. Gary D. Bending Warwick HRI, University of Warwick, Wellesbourne, Warwick, CV35 9EF, United Kingdom. J. L. Ditty Department of Biology, University of St. Thomas, St. Paul, Minnesota 55105. Alison K. East Molecular Microbiology, John Innes Centre, Colney Lane, Norwich NR4 7UH, United Kingdom. Primrose P. E. Freestone Department of Infection, Immunity and Inflammation, University of Leicester School of Medicine, Leicester, United Kingdom. Paul Hand Warwick HRI, University of Warwick, Wellesbourne, Warwick, CV35 9EF, United Kingdom. Stephanie Hunter Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, United Kingdom. Donald Y. Kobayashi Department of Plant Biology and Pathology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901. Mark Lyte Department of Pharmacy Practice, School of Pharmacy, Texas Tech University Health Sciences Center, Lubbock, Texas 79430-8162. ix x Contributors Tim H. Mauchline School of Biological Sciences, University of Reading, Berkshire RG6 6AJ, United Kingdom. Peter Mullany Division of Microbial Diseases, Eastman Dental Institute, University College London, London WC1X 8LD, United Kingdom. Adele Packer School of Biology, Chemistry and Health Science, Manchester Metropolitan University, Manchester M1 5GD, United Kingdom. J. V. Parales Department of Microbiology, University of California, Davis, California 95616. R. E. Parales Department of Microbiology, University of California, Davis, California 95616. D. A. Pelletier Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831. David A. C. Pink Warwick HRI, University of Warwick, Wellesbourne, Warwick, CV35 9EF, United Kingdom.