Sulfate-Reducing Bacteria

347 Pages·1995·14.392 MB·English

by  Larry L. Barton, Francisco A. Tomei (auth.), Larry L. Barton (eds.)

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