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Sulfate-Reducing Bacteria PDF

347 Pages·1995·14.392 MB·English
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Sulfate-Reducing Bacteria BIOTECHNOLOGY HANDBOOKS Series Editors: Tony Atkinson and Roger F. Sherwood Centre for Applied Microbiology and Research Division of Biotechnology Salisbury, Wiltshire, England Volume 1 PENICILLIUM AND ACREMONIUM Edited by John F. Peberdy Volume 2 BACILLUS Edited by Colin R. Harwood Volume 3 CLOSTRIDIA Edited by Nigel P. Minton and David J. Clarke Volume 4 SACCHAROMYCES Edited by Michael F. Tuite and Stephen G. Oliver Volume 5 METHANE AND METHANOL UTILIZERS Edited by J. Colin Murrell and Howard Dalton Volume 6 PHOTOSYNTHETIC PROKARYOTES Edited by Nicholas H. Mann and Noel G. Carr Volume 7 ASPERGILLUS Edited by j. E. Smith Volume 8 SULFATE-REDUCING BACTERIA Edited by Larry L. Barton Volume 9 THERMUS SPECIES Edited by Richard Sharp and Ralph Williams A Continuation Order Plan is available ror this series. A continuation order will bring delivery or each new volume immediately upon publication. Volumes are billed only upon actual shipment. For rurther inrormation please contact the publisher. Sulfate-Reducing Bacteria Edited by Larry L. Barton University of New Mexico Albuquerque. New Mexico Springer Science+Business Media, LLC Library of Congress Cataloging-in-Publication Data Sulfate-raducing bacteria / edited by Larry L. Barton, p. cm. — (Biotechnology handbooks ; v. 8) Includes bibliographical references and Index. ISBN 978-1-4899-1584-9 1. Sulphur bacteria. I. Barton, Larry. II. Series. QR92.S8S84 1995 589.9'6—dc20 95-15113 CIP ISBN 978-1-4899-1584-9 ISBN 978-1-4899-1582-5 (eBook) DOI 10.1007/978-1-4899-1582-5 © 1995 Springer Science+Business Media New York Originally published by Plenum Press, New York in 1995 Softcover reprint of the hardcover 1st edition 1995 10 98765432 All rights reserved No part of this book may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, microfilming, recording, or otherwise, without written permission from the Publisher Contributors J. M. Akagi • Department of Microbiology, The University of Kansas, Lawrence, Kansas 66045 Larry L. Barton • Department of Biology, University of New Mexico, Albuquerque, New Mexico 87131 Liang Chen • Department of Biochemistry, The University of Geor gia, Athens, Georgia 30605 Heribert Cypionka • Carl von Ossietzky Universitat Oldenburg, In stitut fur Chemie und Biologies des Meeres, D-26111 Oldenburg, Ger many Richard Devereux • United States Environmental Protection Agen cy, Environmental Research Laboratory, Gulf Breeze, Florida 32561 Burt D. Ensley • Phytotech, Newton, Pennsylvania 18940 Guy D. Fauque • Centre d'Oceanologie de Marseille, Universite d'Aix-Marseille II, F-13288 Marseille Cedex 9, France W. Allan Hamilton • Molecular and Cell Biology, Marischal College University, Aberdeen AB9 lAS, Scotland T. R.Jack • Novacor Research and Technology Corporation, Calgary, Alberta, Canada, T2E 7K7 Jasper Kunow • Laboratorium fur Mikrobiologie des Fachbereichs Biologie der Philipps-Universitat Marburg, and Max-Planck-Institut fur Terrestrische Mikrobiologie, Marburg, D-35043 Marburg, Germany Whonchee Lee • Center for Biofilm Engineering, Montana State University, Bozeman, Montana 59717-0398 Jean Le Gall • Department of Biochemistry, The University of Geor gia, Athens, Georgia 30605 Ming-Y. Liu • Department of Biochemistry, The University of Geor gia, Athens, Georgia 30605 Erko Stackebrandt • Deutsche Sammlung von Mikroorganismen und Zellkulturen, Mascheroder, Weg IB, 38124 Braunschweig, Germany David A. Stahl • College of Veterinary Medicine, Department of Vet erinary Pathobiology, University of Illinois, Urbana, Illinois 61801 v vi CONTRIBUTORS Joseph M. Suflita • Department of Botany and Microbiology, The University of Oklahoma, Norman, Oklahoma 73019 Rudolf K. Thauer • Laboratorium fUr Mikrobiologie des Fach bereichs Biologie der Philipps-Universitat and Max-Planck-Institut fUr Terrestrische Mikrobiologie, Marburg, D-35043 Marburg, Germany Francisco A. Tomei • Army Environmental Policy Institute, Cham paign, Illinois 61821 Walter M. A. M. van Dongen • Department of Biochemistry, Agri cultural University, Dreyenlaan 3, 6703 HA Wageningen, The Nether lands D. W. S. Westlake • Westec Microbes Ltd., Victoria, British Colum bia, Canada V9C lX4 Preface Over the years, sulfate-reducing bacteria (SRB) have been examined from many different perspectives. In several areas research has been highly active and molecular mechanisms have been developed, while research in other areas has progressed at a markedly slower rate. This book was initiated with the objective of summarizing the information available on the SRB with the intent that biology of the bacteria would be linked with biochemistry processes. This approach should enable us to identify and define appropriate questions for future research. The first chapter provides an overview of the sulfate-reducing eu bacteria, while the second chapter summarizes the activities of the sulfate-reducing archaebacteria. Included in these two chapters are an enumeration of key enzymes that are unique to these bacteria and use sulfate as the final electron acceptors. Taxonomic relationships, path ways for sulfate reduction, electron transport, cell energetics, and genet ics of these specialized bacteria are addressed in five separate chapters. This information provides an insight into life processes of the SRB. In fact, it is apparent from these chapters that the depth of knowledge of biochemical and physiological processes of the sulfate reducers is so great that these organisms may be used as model systems for under standing anaerobic activities. The broad topics of ecology, biocorrosion, bioremediation, and problems in industry related to SRB are skillfully reviewed in the last four chapters. Many of these highly dynamic pro cesses assume a new dimension in light of the information provided here detailing chemical activities of SRB. The reader will notice the breadth and complexity of the various topics. Without the cooperation from the authors of these chapters, it would be difficult or perhaps impossible to provide an accurate assess ment of the activities of SRB. This book was written for advanced under graduates, graduate students, engineers, scientists, and other profes sionals. For readers seeking additional information, a substantial num ber of references are given to original literature and recent reviews. Larry L. Barton Albuquerque, New Mexico vii Contents Chapter 1 Characteristics and Activities of Sulfate-Reducing Bacteria... . ..... ........ .... ...... .. .... .... .... .... .. 1 Larry L. Barton and Francisco A. Tomei 1. Introduction ............................................ 1 2. Diversity of Bacteria ..................................... 2 2.1. Biology ............................................ 2 2.2. Cell Characteristics .................................. 2 3. Growth................................................ 3 3.1. Cultivation ......................................... 3 3.2. Stress Response ..................................... 6 3.3. Identification ....................................... 7 3.4. Isolation ........................................... 7 3.5. Detection............................................ 8 4. Biochemical Activities. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8 4.1. Enzymes ........................................... 8 4.2. Immobilization of Enzymes .......................... 9 4.3. Metabolic Products .................................. 9 4.4 Transformation Reaction ............................ 15 4.5. Energy Technology ................................. 18 5. Interactions with Plants and Animals ...................... 20 6. Perspectives . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22 Chapter 2 Sulfate-Reducing Archaea 33 Rudolf K. Thauer and Jasper Kunow 1. Introduction: Discovery of Archaeoglobus ................... 33 2. Phylogenetic Position among the Archaea . . . . . . . . . . . . . . . . . . 34 ix x CONTENTS 3. Morphology and Components of Cellular Structures. . . . .. . . 37 4. Habitats and Growth Requirements ....................... 38 5. Coenzymes, Enzymes, and Metabolic Pathways ............. 39 5.1. Coenzymes......................................... 39 5.2. Enzymes ........................................... 40 5.3. Metabolic Pathways. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43 6. Assimilatory Sulfate Reduction in Archaea .. . . . . . . . . . . . . . . . 43 References .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45 Chapter 3 Taxonomic Relationships 49 Erko Stackebrandt, David A. Stahl, and Richard Devereux 1. Introduction ........................................... 49 2. Traditional Classification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51 2.1. The Mesophilic Gram-Negative Sulfate Reducers ... 53 2.2. The Thermophilic Gram-Negative Sulfate Reducers 57 2.3. The Gram-Positive Sulfate Reducers ............... 59 2.4. The Archaeal Sulfate Reducers.. . . . . . . . . . . . . . . . . . . 60 3. The Phylogeny of the Mesophilic Gram-Negative Bacterial Sulfate-Reducers ....................................... 61 3.1. The Family "Desulfovibrionaceae" ................... 63 3.2. The Family "Desulfobateriaceae" .................... 64 4. The Phylogeny of the Thermophilic Gram-Negative Bacteria ............................................... 65 5. The Phylogeny of the Gram-Positive Sulfate Reducers ..... 66 6. The Phylogeny of the Archaeal Sulfur Reducers .......... 69 7. The Analysis of Genetic Markers other than the 16S rONA 70 7.1. Ferredoxin...................................... 71 7.2. Cytochrome c .............. ......... .. ... . ..... . . 72 7.3. Hydrogenases ................................... 72 8. Determinative Tools and New Developments. . . . . . .. . . . . . . 73 8.1. Lipid Biomarkers ................................ 73 8.2. The Use of Nucleic Acid Hybridization for Determinative Studies ............................ 74 8.3. Gene Probes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75 9. Origin and Evolution of Sulfate-Reducing Bacteria in Relationship to the Biosphere ........................... 77 10. Uncultured Novel Sulfate-Reducing Bacteria. . . .. . . . . . . . . . 78

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