METHANO GENE SIS CHAPMAN & HALL MICROBIOLOGY SERIES Physiology I Ecology I Molecular Biology I Biotechnology Series Editors C. A. Reddy Department of Microbiology & Public Health Michigan State University East Lansing, MI 48824-110 1 A. M. Chakrabarty Department of Microbiology & Immunology University of Illinois Medical Center 835 S. Wolcott Avenue Chicago, IL 60612 Amold L. Demain Rm. 56-123 Massachusetts Institute of Technology Cambridge, MA 02139 James M. Tiedje Center for Microbiology Ecology Department of Crop & Soil Sciences Michigan State University East Lansing, MI 48824 METHANOGENESIS B & ECOLOGY, PHYSIOLOGY, IOCHEMISTRY GENETICS EDITEDBY James G. Ferry SPRINGER-SCIENCE+BUSINESS MEDIA, B.V. © 1993 Springer Science+Bnsiness Media Dordrecht Softcover re print of the hardcover Ist edition 1993 Originally pnblished by Chapman & Hali, Inc. in 1993 AII rights reserved. No part of this book may be reprinted or reproduced or utilized in any form or by any electronic, mechanical, orother means, now known or hereafter invented, includ ing photocopy ing and recording, or by an information storage or retrieval system, without permission in writing from the publishers. Library of Congress Cataloging in Publication Data Methanogenesis / editor, James G. Ferry. p. cm.-(Microbial metabolism) Includes bibliographical references. 1. Methanobacteriaceae. 2. Methane-Metabolism. 3. Microbial metabolism. 1. Ferry, J.G. II. Series. (DNLM: 1. Methanogens. 2. Methane. QW 4 M5915 1993] QR.M46M48 1993 589.9-<1c20 DNLMlDLC for Library of Congress 93-6676 CIP ISBN 978-1-4613-6013-1 ISBN 978-1-4615-2391-8 (eBook) DOI 10.1007/978-1-4615-2391-8 Contents Preface vii James G. Ferry Contributors ix An Historical Overview of Methanogenesis Ralph S. Wolfe Part I: MICROBIOLOGY 33 1. Diversity and Taxonomy of Methanogens 35 David R. Boone, William B. Whitman and Pierre Rouviere 2. Microscopy 81 G. Dennis Sprott and Terry J. Beveridge 3. Physiological Ecology of Methanogens 128 Stephen H. Zinder Part II: BIOCHEMISTRY 207 4. Reactions and Enzymes Involved in Methanogenesis from CO 2 ~~ ~ Rudolf K. Thauer, Reiner Hedderich and Reinhard Fischer 5. Conversion of Methanol and Methylamines to Methane and Carbon Dioxide 253 Jan T. Keltjens and Godfried D. Vogels 6. Fermentation of Acetate 304 James G. Ferry vi Contents 7. Redox Enzymes of Methanogens: Physicochemical Properties of Selected, Purified Oxidoreductases 335 David A. Grahame and Thressa C. Stadtman 8. Bioenergetics of Methanogenesis 360 Volker Milller, Michael Blaut and Gerhard Gottschalk Part III: BIOSYNTHESIS 407 9. Biosynthesis of the Coenzymes in Methanogens 409 Robert H. White and Dan Zhou 10. Anabolic Pathways in Methanogens 445 Peter G. Simpson and William B. Whitman 11. Nitrogen and Phosphorus Metabolism of Methanogens 473 Edward DeMoli Part IV: GENETICS 491 12. Structure and Organization of Genes 493 John N. Reeve Index 529 Preface The study of methane-producing microbes has witnessed unprecedented growth in its relatively short history. The stimulus for this interest originates from the broad impact methanogens have on the wider world of biological inquiry including the environment, early evolution, biochemistry, and molecular biology. Methanogens are found in nearly every conceivable anaerobic environment from the rumen and the intestines of humans to hot springs and the deep ocean floor, from sewage digestors and landfills to aquatic sediments. Methanogens grow at temperatures from 5 to 11 oDe and salinities ranging from freshwater to brine, a finding which has helped to redefine the environmental limits for life. Methanogens function in the global cycling of carbon; each year approximately 400 metric tons of methane are produced as an end product in the degradation of organic matter entering diverse anaerobic habitats. The methane is oxidized to CO in aerobic zones, but an undetermined amount escapes into the upper 2 atmosphere. Recent increases in the ruminant population and human activities have led to an increase in atmospheric methane, a major greenhouse gas. Early studies on methane-producing microbes gave the first clue that led to the recent proposal of a new higher taxon for all life, which includes the Archaea, Bacteria, and Eucarya domains. The methanogens are the largest, most diverse, and best-studied group in the Archaea. The wealth of information on cell wall components, ultrastructure, and phylogenetics of methanogens has made a key contribution toward understanding the early origins and evolution of the Archaea. The study of methanogens has also contributed to a broader understanding of the biochemical world. A plethora of novel cofactors has emerged from investigations on the pathway of methanogenesis, and new metalloenzymes have been discovered. An understanding of the bioenergetics is just beginning to unfold viii Preface but already has revealed uncommon mechanisms for the generation of chemical gradients. Biochemical studies clearly indicate that the transcriptional and transla tional apparatus of the methanogens resembles that of the Eucarya more than the Bacteria. Although the field of methanogenesis has progressed from methods for the growth of these fastidious anaerobes to elegant studies of the novel biochemistry and into molecular biology, major interesting questions remain unanswered; for example, the mechanism of energy conservation and principles of gene expres sion. Today the field is at a threshold. The accomplishments of the past are pushing on the door to genetics. The development of a reliable genetic exchange system will soon catalyze another rapid expansion of research that will surely impact all aspects of methanogens. Events of the past predict that this new era will reveal still more processes that are unique to these microbes and afford new perspectives to the broader fields of biochemistry and molecular biology. This is the first book exclusively on the subject of methanogenesis. It is intended to provide the reader with a comprehensive view of the field, past and present, and indicate future directions. For the experienced, it is anticipated that the contents will provide fresh insights and, for those new to the field, will stimulate interest and research in new directions. The chapters that follow reveal the unusual and diverse ecology, microbiology, physiology, biochemistry, and molecular biology which characterizes these microbes. Finally, many factors have contributed to the success of this field not the least of which is a collegial scientifc community. I wish to thank the authors for their cooperation and advice. JAMES G. FERRY Blacksburg, Virginia Contributors Dr. Terrance J. Beveridge Dr. James Ferry Department of Microbiology Department of Anaerobic Microbi College of Biological Science ology University of Guelph Virginia Polytechnic Institute and Guelph, Ontario NIG 2Wl State University Canada Blacksburg, VA 24061-0305 Michael Blaut Reinhard Fischer Institut fUr Mikrobio1ogie der Uni- Philipps-Universitat Marburg versitat G6ttingen Fachbereich Biologie Grisebachstr. 8 Laboratorium fur Mikrobiologie W -3400 G6ttingen 0-3550 Marburg/Lanberge Germany Karl-von-FrischstraBe Germany Dr. David Boone Oregon Graduate Institute of Science Dr. David Grahame and Technology National Heart Institute 19600 N.W. Von Neumann Drive Building 3, Room 114 Beaverton, OR 97006-1999 Bethesda, MD 20892 Dr. L. Edward DeMoll Dr. Gerhard Gottschalk Department of Microbiology & Immu- Institut fUr Mikrobiologie nology Georg-August-Universitat University of Kentucky Grisebachstrasse 8 Chandler Medical Center 3400 G6ttingen Lexington, KT 40536-0084 Germany x Contributors R. Hedderich Dr. Rudolf K. Thauer Philipps-Universitat Marburg Philipps-Universitat Marburg Fachbereich Biologie Fachberiech Biologie Laboratorium fur Mikrobiologie Laboratorium fUr Microbiologie D-3550 Marburg/Lanberge D-3550 Marburg/Lanberge Karl-von-Frischestrasse Karl-von-Frisch Strasse Germany Germany Dr. Jan Keltjens Dr. Godfried Vogels Department of Microbiology Department of Microbiology University of Nijmegen University of Nijmegen Toernooiveld Toernooiveld NL-6525 Nijmegen NL-6525 Nijmegen The Netherlands The Netherlands Dr. Robert H. White Volker Muller Department of Biochemistry Institut fUr Mikrobiologie der Uni- Virginia Polytechnic Institute and versitat Gottingen State University Grisebachstr. 8 Blacksburg , VA 24061-0308 W-3400 Gottingen Germany Dr. William B. Whitman Department of Microbiology Dr. John N. Reeve University of Georgia Department of Microbiology Athens, GA 30602 The Ohio State University 484 West 12th Street Dr. Ralph S. Wolfe Columbus, OH 43210 Department of Microbiology University of Illinois Prof. Peter Simpson Burrill Hall Department of Microbiology 407 South Goodwin A venue University of Georgia Urbana, IL 61801 Athens, GA 30602 Dan Zhou Dr. G. Dennis Sprott Department of Biochemistry Division of Biological Sciences Virginia Polytechnic Institute and National Research Council of Canada State University Ottawa, Ontario KIA OR6 Blacksburg, VA 24061-0308 Canada Dr. Steve Zinder Dr. Thressa Stadtman Department of Microbiology National Heart Institute Stocking Hall Building 3, Room 103 Cornell University Bethesda, MD 20892 Ithaca, NY 14853