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The

Eugene Rosenberg (Editor-in-Chief) Edward F. DeLong, Stephen Lory, Erko Stackebrandt and Fabiano Thompson (Eds.)

The Prokaryotes

Other Major Lineages of and the

Fourth Edition

With 253 Figures and 207 Tables Editor-in-Chief Eugene Rosenberg Department of Molecular and Biotechnology Tel Aviv University Tel Aviv, Israel

Editors Edward F. DeLong Erko Stackebrandt Department of Biological Engineering Leibniz Institute DSMZ-German Collection of Microorganisms Institute of Technology and Cell Cultures Cambridge, MA, USA Braunschweig, Germany Center for Microbial : Research and Education Fabiano Thompson University of Hawaii Laboratory of Microbiology, Institute of Biology, Center for Manoa, Honolulu, HI, USA Health Sciences Federal University of Rio de Janeiro (UFRJ) Stephen Lory Ilha do Funda˜o, Rio de Janeiro, Brazil Department of Microbiology and Immunobiology Harvard Medical School Boston, MA, USA

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ISBN 978-3-642-38953-5 ISBN 978-3-642-38954-2 (eBook) ISBN 978-3-642-38955-9 (print and electronic bundle) DOI 10.1007/978-3-642-38954-2 Springer Heidelberg New York Dordrecht London

Library of Congress Control Number: 2014949495

3rd edition: © Springer Science+Business Media, LLC 2006 4th edition: © Springer-Verlag Berlin Heidelberg 2014 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. Exempted from this legal reservation are brief excerpts in connection with reviews or scholarly analysis or material supplied specifically for the purpose of being entered and executed on a computer system, for exclusive use by the purchaser of the work. Duplication of this publication or parts thereof is permitted only under the provisions of the Copyright Law of the Publisher’s location, in its current version, and permission for use must always be obtained from Springer. Permissions for use may be obtained through RightsLink at the Copyright Clearance Center. Violations are liable to prosecution under the respective Copyright Law. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. While the advice and information in this book are believed to be true and accurate at the date of publication, neither the authors nor the editors nor the publisher can accept any legal responsibility for any errors or omissions that may be made. The publisher makes no warranty, express or implied, with respect to the material contained herein.

Printed on acid-free paper

Springer is part of Springer ScienceþBusiness Media (www.springer.com) Foreword

The purpose of this brief foreword is unchanged from the first edition; it is simply to make you, the reader, hungry for the scientific feast that follows. These 11 volumes on the prokaryotes offer an expanded scientific menu that displays the biochemical depth and remarkable physiological and morphological diversity of . The size of the volumes might initially discourage the unprepared mind from being attracted to the study of prokaryote life, for this landmark assemblage thoroughly documents the wealth of present knowledge. But in confronting the reader with the state of the art, the Handbook also defines where more work needs to be done on well-studied bacteria as well as on unusual or poorly studied organisms. This edition of The Prokaryotes recognizes the almost unbelievable impact that the work of Carl Woese has had in defining a phylogenetic basis for the microbial world. The concept that the ribosome is a highly conserved structure in all cells and that its nucleic acid components may serve as a convenient reference point for relating all living things is now generally accepted. At last, the phylogeny of prokaryotes has a scientific basis, and this is the first serious attempt to present a comprehensive treatise on prokaryotes along recently defined phylogenetic lines. Although evidence is incomplete for many microbial groups, these volumes make a statement that clearly illuminates the path to follow. There are basically two ways of doing research with microbes. A classical approach is first to define the phenomenon to be studied and then to select the organism accordingly. Another way is to choose a specific organism and go where it leads. The pursuit of an unusual microbe brings out the latent hunter in all of us. The intellectual challenges of the chase frequently test our ingenuity to the limit. Sometimes the quarry repeatedly escapes, but the final capture is indeed a wonderful experience. For many of us, these simple rewards are sufficiently gratifying so that we have chosen to spend our scientific studying these unusual creatures. In these endeavors, many of the strategies and tools as well as much of the philosophy may be traced to the Delft School, passed on to us by our teachers, Martinus Beijerinck, A. J. Kluyver, and C. B. van Niel, and in turn passed on by us to our students. In this school, the principles of the selective, enrichment culture technique have been developed and diversified; they have been a major force in designing and applying new principles for the capture and isolation of microbes from nature. For me, the ‘‘organism approach’’ has provided rewarding adventures. The organism continually challenges and literally drags the investigator into new areas where unfamiliar tools may be needed. I believe that organism-oriented research is an important alternative to problem-oriented research, for new concepts of the future very likely lie in a study of the breadth of microbial life. The physiology, biochemistry, and ecology of the microbe remain the most powerful attractions. Studies based on classical methods as well as modern genetic techniques will result in new insights and concepts. To some readers, this edition of The Prokaryotes may indicate that the field is now mature, that from here on it is a matter of filling in details. I suspect that this is not the case. Perhaps we have assumed prematurely that we fully understand microbial life. Van Niel pointed out to his students that—after a lifetime of study—it was a very humbling experience to view in the microscope a sample of microbes from nature and recognize only a few. Recent evidence suggests that microbes have been evolving for nearly 4 billion years. Most certainly, those microbes now domesticated and kept in captivity in culture collections represent only a minor portion of the species that have evolved in this time span. Sometimes we must remind ourselves that evolution is actively taking place at the present moment. That the cell evolved as a chimera of certain prokaryote parts is a generally accepted concept today. Higher as well as lower evolved in contact with prokaryotes, and evidence surrounds us of the complex interactions between eukaryotes and prokaryotes as well as among prokaryotes. We have so far only scratched the surface of these biochemical interrelationships. Perhaps the legume nodule is a pertinent example of nature caught in the act of evolving the ‘‘nitrosome,’’ a unique nitrogen-fixing organelle. The study of prokaryotes is proceeding at such a fast pace that major advances are occurring yearly. The increase of this edition to four volumes documents the exciting pace of discoveries. To prepare a treatise such as The Prokaryotes requires dedicated editors and authors; the task has been enormous. I predict that the scientific community of will again show its appreciation through use of these volumes—such that the pages will become ‘‘dog-eared’’ and worn as students seek basic information for the hunt. These volumes belong in the laboratory, not in the library. I believe that a most effective way to introduce students to microbiology is for them to isolate microbes from nature, that is, from their habitats in soil, water, clinical specimens, or . The Prokaryotes enormously simplifies this process and should encourage the construction of courses that contain a wide spectrum of diverse topics. For the student as well as the advanced investigator, these volumes should generate excitement. Happy hunting!

Ralph S. Wolfe Department of Microbiology University of Illinois at Urbana-Champaign

Preface

During most of the twentieth century, microbiologists studied pure cultures under defined laboratory conditions in order to uncover the causative agents of disease and subsequently as ideal model systems to discover the fundamental principles of genetics and biochemistry. Microbiology as a discipline onto itself, e.g., microbial ecology, diversity, and evolution-based , has only recently been the subject of general interest, partly because of the realization that microorganisms play a key role in the environment. The development and application of powerful culture-independent molecular techniques and bioinformatics tools has made this development possible. The fourth edition of the Handbook of the Prokaryotes has been updated and expanded in order to reflect this new era of microbiology. The first five volumes of the fourth edition contain 34 updated and 43 entirely new chapters. Most of the new chapters are in the two new sections: Prokaryotic Communities and Bacteria in Human Health and Disease. A collection of microorganisms occupying the same physical habitat is called a ‘‘community,’’ and several examples of bacterial communities are presented in the Prokaryotic Communities section, organized by Edward F. DeLong. Over the last decade, important advances in molecular biology and bioinformatics have led to the development of innovative culture-independent approaches for describing microbial communities. These new strategies, based on the analysis of DNA directly extracted from environmental samples, circumvent the steps of isolation and culturing of microorganisms, which are known for their selectivity leading to a nonrepresentative view of prokaryotic diversity. Describing bacterial communities is the first step in understanding the complex, interacting microbial systems in the natural world. The section on Bacteria in Human Health and Disease, organized by Stephen Lory, contains chapters on most of the important bacterial diseases, each written by an expert in the field. In addition, there are separate general chapters on identification of pathogens by classical and non-culturing molecular techniques and virulence mechanisms, such as adhesion and bacterial toxins. In recognition of the recent important research on beneficial bacteria in human health, the section also includes chapters on gut microbiota, prebiotics, and probiotics. Together with the updated and expanded chapter on Bacterial Pharmaceutical Products, this section is a valuable resource to graduate students, teachers, and researchers interested in medical microbiology. Volumes 6–11, organized by Erko Stackebrandt and Fabiano Thompson, contain 265 chapters in total on each of the ca. 300 known prokaryotic families, in some cases even higher taxa. Each chapter presents both the historical and current taxonomy of these taxa, mostly above the genus level; molecular analyses (e.g., DDH, MLSA, riboprinting, and MALDI-TOF); genomic and phenetic properties of the taxa covered; genome analyses including nonchromosomal genetic elements; phenotypic analyses; methods for the enrichment, isolation, and maintenance of members of the family; ecological studies; clinical relevance; and applications. As in the third edition, the volumes in the fourth edition are available both as hard copies and as eReferences. The advantages of the online version include no restriction of color illustrations, the possibility of updating chapters continuously and, most importantly, libraries can place their subscribed copies on their servers, making it available to their community in offices and laboratories. The editors thank all the chapter authors and the editorial staff of Springer, especially Hanna Hensler-Fritton, Isabel Ullmann, Daniel Quin˜ones, Alejandra Kudo, and Audrey Wong, for making this contribution possible.

Eugene Rosenberg Editor-in-Chief

About the Editors

Eugene Rosenberg (Editor-in-Chief) Department of Molecular Microbiology and Biotechnology Tel Aviv University Tel Aviv Israel

Eugene Rosenberg holds a Ph.D. in biochemistry from Columbia University (1961) where he described the chemical structures of the capsules of Hemophilus influenzae, types B, E, and F. His postdoctoral research was performed in organic chemistry under the guidance of Lord Todd in Cambridge University. He was an assistant and associate professor of microbiology at the University of California at Los Angeles from 1962 to 1970, where he worked on the biochemistry of Myxococcus xanthus. Since 1970, he has been in the Department of Molecular Microbiology and Biotechnology, Tel Aviv University, as an associate professor (1970–1974), full professor (1975–2005), and professor emeritus (2006–present). He has held the Gol Chair in Applied and Environmental Micro- biology since 1989. He is a member of the American Academy of Microbiology and European Academy of Microbiology. He has been awarded a Guggenheim Fellowship, a Fogarty International Scholar of the NIH, the Pan Lab Prize of the Society of Industrial Microbiology, the Proctor & Gamble Prize of the ASM, the Sakov Prize, the Landau Prize, and the Israel Prize for a ‘‘Beautiful Israel.’’ His research has focused on myxobacteriology; hydrocarbon microbiology; surface-active polymers from Acinetobacter; biore- mediation; coral microbiology; and the role of symbiotic microorganisms in the adaptation, development, behavior, and evolution of and plants. He is the author of about 250 research papers and reviews, 9 books, and 16 patents. x About the Editors

Edward F. DeLong Department of Biological Engineering Massachusetts Institute of Technology Cambridge, MA USA and Center for Microbial Oceanography: Research and Education University of Hawaii, Manoa Honolulu, HI USA

Edward DeLong received his bachelor of science in bacteriology at the University of California, Davis, and his Ph.D. in at Scripps Institute of Oceanography at the University of California, San Diego. He was a professor at the University of California, Santa Barbara, in the Department of Ecology for 7 years, before moving to the Monterey Bay Aquarium Research Institute where he was a senior scientist and chair of the science department, also for 7 years. He has worked for the past 10 years as a professor at the Massachusetts Institute of Technology in the Department of Biological Engineering, and the Department of Civil and Environmental Engineering, and in August 2014 joined the University of Hawaii as a professor of oceanography. DeLong’s scientific interests focus primarily on central questions in marine microbial genomics, biogeochemistry, ecology, and evolution. A large part of DeLong’s efforts have been devoted to the study of microbes and microbial processes in the ocean, combining laboratory and field- based approaches. Development and application of genomic, biochemical, and metabolic approaches to study and exploit microbial communities and processes is his other area of interest. DeLong is a fellow in the American Academy of Arts and Science, the U.S. National Academy of Science, and the American Association for the Advancement of Science. About the Editors xi

Stephen Lory Department of Microbiology and Immunobiology Harvard Medical School Boston, MA USA

Stephen Lory received his Ph.D. degree in microbiology from the University of California in Los Angeles in 1980. The topic of his doctoral thesis was the structure-activity relationships of bacterial exotoxins. He carried out his postdoctoral research on the basic mechanism of protein secretion by Gram-negative bacteria in the Bacterial Physiology Unit at Harvard Medical School. In 1984, he was appointed assistant professor in the Department of Microbiology at the University of Washington in Seattle, becoming full professor in 1995. While at the University of Washington, he developed an active research program in host-pathogen interactions including the role of bacterial adhesion to mammalian cells in virulence and regulation of gene expression by bacterial pathogens. In 2000, he returned to Harvard Medical School where he is currently a professor of microbiology and immunobiology. He is a regular reviewer of research projects on various scientific panels of governmental and private funding agencies and served for four years on the Scientific Council of Institute Pasteur in Paris. His current research interests include evolution of bacterial virulence, studies on post-translational regulation of gene expression in Pseudomonas, and the development of novel antibiotics targeting multi-drug- resistant opportunistic pathogens. xii About the Editors

Erko Stackebrandt Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures Braunschweig Germany

Erko Stackebrandt holds a Ph.D. in microbiology from the Ludwig-Maximilians University Munich (1974). During his postdoctoral research, he worked at the German Culture Collection in Munich (1972–1977), 1978 with Carl Woese at the University of Illinois, Urbana Champaign, and from 1979 to 1983 he was a member of Karl Schleifer’s research group at the Technical University, Munich. He habilitated in 1983 and was appointed head of the Departments of Microbiology at the University of Kiel (1984–1990), at the University of Queensland, Brisbane, Australia (1990–1993), and at the Technical University Braunschweig, where he also was the director of the DSMZ-German Collection of Microorganisms and Cell Cultures GmbH (1993–2009). He is involved in systematics, and molecular phylogeny and ecology of Archaea and Bacteria for more than 40 years. He has been involved in many research projects funded by the German Science Foundation, German Ministry for Science and Technology, and the European Union, working on pure cultures and microbial communities. His projects include work in soil and peat, Mediterranean coastal waters, North Sea and Baltic Sea, Antarctic Lakes, Australian soil and artesian wells, formation of stromatolites, as well as on giant ants, holothurians, rumen of cows, and the digestive tract of koalas. He has been involved in the description and taxonomic revision of more than 650 bacteria taxa of various ranks. He received a Heisenberg stipend (1982–1983) and his work has been awarded by the Academy of Science at Go¨ttingen, Bergey’s Trust (Bergey’s Award and Bergey’s Medal), the Technical University Munich, the Australian Society for Microbiology, and the American Society for Microbiology. He held teaching positions in Kunming, China; Budapest, Hungary; and Florence, Italy. He has published more than 600 papers in refereed journals and has written more than 80 book chapters. He is the editor of two Springer journals and served as an associate editor of several international journals and books as well as on national and international scientific and review panels of the German Research Council, European Science Foundation, European Space Agency, and the Organisation for Economic Co-Operation and Development. About the Editors xiii

Fabiano Thompson Laboratory of Microbiology Institute of Biology Center for Health Sciences Federal University of Rio de Janeiro (UFRJ) Ilha do Funda˜o Rio de Janeiro Brazil

Fabiano Thompson became a professor of the Production Engineer Program (COPPE-UFRJ) in 2014 and the director of research at the Institute of Biology, Federal University of Rio de Janeiro (UFRJ), in 2012. He was an oceanographer at the Federal University of Rio Grande (Brazil) in 1997. He received his Ph.D. in biochemistry from Ghent University (Belgium) in 2003, with emphasis on marine microbial taxonomy and biodiversity. Thompson was an associate researcher in the BCCM/LMG Bacteria Collection (Ghent University) in 2004; professor of genetics in 2006 at the Institute of Biology, UFRJ; and professor of marine biology in 2011 at the same university. He has been a representative of UFRJ in the National Institute of Metrology (INMETRO) since 2009. Thompson is the president of the subcommittee on the Systematics of –IUMS and an associate editor of BMC Genomics and Microbial Ecology. The Thompson Lab in Rio currently performs research on marine microbiology in the Blue Amazon, the realm in the southwestern Atlantic that encompasses a variety of systems, including deep sea, Cabo Frio upwelling area, Amazonia river-plume continuum, mesophotic reefs, Abrolhos coral reef bank, and Oceanic Islands (Fernando de Noronha, Saint Peter and Saint Paul, and Trindade).

Table of Contents

Section I Archaea ...... 1

1 The Archaea: A Personal Overview of the Formative Years ...... 3 Ralph S. Wolfe

2 The Family Acidilobaceae ...... 9 Maria Prokofeva . Alexander Merkel . Alexander Lebedinsky . Elizaveta Bonch-Osmolovskaya

3 The Class Archaeoglobi ...... 15 Kristen Brileya . Anna-Louise Reysenbach

4 The Family Caldisphaeraceae ...... 25 Takashi Itoh

5 The Family Ferroplasmaceae ...... 29 Olga V. Golyshina

6 The Family Fervidicoccaceae ...... 35 Anna Perevalova . Alexander Lebedinsky . Elizaveta Bonch-Osmolovskaya

7 The Family Halobacteriaceae ...... 41 Aharon Oren

8 The Methanogenic Bacteria ...... 123 William B. Whitman . Timothy L. Bowen . David R. Boone

9 The Family Methanobacteriaceae ...... 165 Aharon Oren

10 The Family Methanocalculaceae ...... 195 Aharon Oren

11 The Family Methanocaldococcaceae ...... 201 Aharon Oren

12 The Family Methanocellaceae ...... 209 Sanae Sakai . Ralf Conrad . Hiroyuki Imachi

13 The Family Methanococcaceae ...... 215 Aharon Oren

14 The Family Methanocorpusculaceae ...... 225 Aharon Oren

15 The Family Methanomicrobiaceae ...... 231 Aharon Oren

16 The Family Methanopyraceae ...... 247 Aharon Oren xvi Table of Contents

17 The Family Methanoregulaceae ...... 253 Aharon Oren

18 The Family Methanosarcinaceae ...... 259 Aharon Oren

19 The Family Methanospirillaceae ...... 283 Aharon Oren

20 The Family Methanothermaceae ...... 291 Aharon Oren

21 The Family Methanotrichaceae ...... 297 Aharon Oren

22 The Family Methermicoccaceae ...... 307 Aharon Oren

23 The ...... 311 Harald Huber . Lydia Kreuter

24 The Family Picrophilaceae ...... 319 Anna-Louise Reysenbach . Kristen Brileya

25 The Family Sulfolobaceae ...... 323 Sonja-Verena Albers . Bettina Siebers

26 The Phylum Thaumarchaeota ...... 347 Michaela Stieglmeier . Ricardo J. E. Alves . Christa Schleper

27 The Order Thermococcales and the Family Thermococcaceae ...... 363 Gerrit J. Schut . Gina L. Lipscomb . Yejun Han . Jaspreet S. Notey . Robert M. Kelly . Michael M. W. Adams

28 The Family Thermoplasmataceae ...... 385 Anna-Louise Reysenbach . Kristen Brileya

29 The Family Thermoproteaceae ...... 389 Takashi Itoh

Section II Bacteria ...... 403

30 The Family Acidobacteriaceae ...... 405 Barbara J. Campbell

31 The Phylum Aquificae ...... 417 Radhey S. Gupta

32 The Phylum ...... 447 Kevin C. Y. Lee . Peter F. Dunfield . Matthew B. Stott

33 The Genus Bacteroides ...... 459 Hannah M. Wexler Table of Contents xvii

34 The Family Brachyspiraceae ...... 485 Eugene Rosenberg

35 The Family Brevinemataceae ...... 487 Eugene Rosenberg

36 The Family Caldisericaceae ...... 489 Koji Mori . Nobuyuki Fujita

37 The Family Chitinophagaceae ...... 493 Eugene Rosenberg

38 The Phylum ...... 497 Stephen Lory

39 The Family Chlorobiaceae ...... 501 Johannes F. Imhoff

40 The Phylum Chloroflexi, the Family Chloroflexaceae, and the Related Phototrophic Families Oscillochloridaceae and Roseiflexaceae ...... 515 Satoshi Hanada

41 The Family ...... 533 Max M. Ha¨ggblom . Elisabetta Bini

42 The Family Cryomorphaceae ...... 539 John P. Bowman

43 The Family ...... 551 Anil Kumar Pinnaka . Naga Radha Srinivas Tanuku

44 The Family Cytophagaceae ...... 577 Mark J. McBride . Weifeng Liu . Xuemei Lu . Yongtao Zhu . Weixin Zhang

45 The Phylum Deferribacteres and the Genus ...... 595 Corentine Alauzet . Estelle Jumas-Bilak

46 The Family Deinococcaceae ...... 613 Eugene Rosenberg

47 The Family Desulfurobacteriaceae ...... 617 Takuro Nunoura

48 The Phylum Dictyoglomi ...... 627 P. L. Bergquist . H. W. Morgan

49 The Family Elusimicrobiaceae ...... 637 Andreas Brune

50 The Phylum ...... 641 Eugene Rosenberg

51 The Family Flavobacteriaceae ...... 643 Mark J. McBride xviii Table of Contents

52 The Phylum ...... 677 Satoshi Hanada . Yuji Sekiguchi

53 The Class Holophagaceae ...... 683 Yukiyo Fukunaga . Natsuko Ichikawa

54 The Family Hydrogenothermaceae ...... 689 Ken Takai . Satoshi Nakagawa

55 The Family Ignavibacteriaceae ...... 701 Takao Iino

56 The Family Lentisphaeraceae ...... 705 Jang-Cheon Cho

57 The Family Leptospiraceae ...... 711 Mathieu Picardeau

58 The Family Marinilabiaceae ...... 731 Eugene Rosenberg

59 The Family Nitrospiraceae ...... 733 Holger Daims

60 The Family Opitutaceae ...... 751 Jorge L. M. Rodrigues . Jantiya Isanapong

61 The Family Parachlamydiaceae ...... 757 Eugene Rosenberg

62 The Phylum ...... 759 Noha H. Youssef . Mostafa S. Elshahed

63 The Family Porphyromonadaceae ...... 811 Mitsuo Sakamoto

64 The Family Prevotellaceae ...... 825 Eugene Rosenberg

65 The Genus Prochlorococcus, Phylum ...... 829 Debbie Lindell

66 The Family Puniceicoccaceae ...... 847 Jaewoo Yoon

67 The Family Rhodothermaceae ...... 849 Sanghwa Park . Yokota Akira . Kazuhiro Kogure

68 The Family Rikenellaceae ...... 857 Joerg Graf

69 The Family Rubritaleaceae ...... 861 Eugene Rosenberg

70 The Family Saprospiraceae ...... 863 Simon Jon McIlroy . Per Halkjær Nielsen Table of Contents xix

71 The Family Simkaniaceae ...... 891 Karin D. E. Everett

72 The Family Sphingobacteriaceae ...... 907 Antonietta Lambiase

73 The Phylum Spirochaetaceae ...... 915 Ali Karami . Meysam Sarshar . Reza Ranjbar . Rahim Sorouri Zanjani

74 The Phylum ...... 931 Estelle Jumas-Bilak . He´le`ne Marchandin

75 The Family Thermaceae ...... 955 Luciana Albuquerque . Milton S. da Costa

76 The Phylum ...... 989 Vaibhav Bhandari . Radhey S. Gupta

77 The Family Verrucomicrobiaceae ...... 1017 Jaewoo Yoon

78 The Family Victivallaceae ...... 1019 Caroline M. Plugge . Erwin G. Zoetendal

79 The Family Waddliaceae ...... 1023 Ludovic Pilloux . Gilbert Greub

List of Contributors

Michael M. W. Adams P. L. Bergquist Department of Biochemistry & Molecular Biology Department of Chemistry and Biomolecular Sciences University of Georgia Macquarie University Athens, GA North Ryde, NSW USA Australia and Department of Molecular Medicine & Pathology Yokota Akira University of Auckland Medical School Department of Biology, Faculty of Mathematics and Natural Auckland Sciences New Zealand University of Indonesia Depok Indonesia Vaibhav Bhandari Department of Biochemistry and Biomedical Sciences McMaster University Corentine Alauzet Hamilton, ON EA 7300, Equipe d’Accueil Stress Immunite´ Pathoge`nes Canada Faculte´ de Me´decine Universite´ de Lorraine Vandoeuvre–les–Nancy Elisabetta Bini France Department of Biochemistry and Microbiology and School of Environmental and Biological Sciences Laboratoire de Bacte´riologie Rutgers University Centre Hospitalier et Universitaire de Nancy New Brunswick, NJ Nancy USA France Elizaveta Bonch-Osmolovskaya Winogradsky Institute of Microbiology Sonja-Verena Albers Russian Academy of Sciences Max Planck Institute for Terrestrial Microbiology Moscow Marburg Russia Germany

David R. Boone Luciana Albuquerque Department of Biology, Environmental Science and Center for Neuroscience and Cell Biology Engineering University of Coimbra Oregon Graduate Institute of Science and Technology Coimbra Portland State University Portugal Portland, OR USA

Ricardo J. E. Alves Department of Ecogenomics and Systems Biology/Archaea Timothy L. Bowen Biology and Ecogenomics Group Department of Microbiology University of Vienna University of Georgia Vienna Athens, GA Austria USA xxii List of Contributors

John P. Bowman Mostafa S. Elshahed Food Safety Centre, Tasmanian Institute of Agriculture Department of Microbiology and Molecular Genetics University of Tasmania Oklahoma State University Sandy Bay, Hobart, TAS Stillwater, OK Australia USA

Kristen Brileya Department of Biology Karin D. E. Everett Portland State University Editorial Advisory Board Portland, OR Veterinary Microbiology, Elsevier USA Lynnwood, WA USA

Andreas Brune Max Planck Institute for Terrestrial Microbiology Nobuyuki Fujita Marburg Biological Resource Center Germany National Institute of Technology and Evaluation (NBRC) Kisarazu, Chiba Barbara J. Campbell Japan Department of Biological Sciences Clemson University Clemson, SC Yukiyo Fukunaga USA Biological Resource Center National Institute of Technology and Evaluation (NBRC) Kisarazu, Chiba Jang-Cheon Cho Japan Department of Biological Sciences Inha University Incheon Olga V. Golyshina Republic of Korea School of Biological Sciences Bangor University Ralf Conrad Bangor Max Planck Institute for Terrestrial Microbiology UK Marburg Germany Joerg Graf Milton S. da Costa Department of Molecular and Cell Biology Department of Life Sciences University of Connecticut University of Coimbra Storrs, CT Coimbra USA Portugal

Gilbert Greub Holger Daims Center for Research on Intracellular Bacteria (CRIB) Division of Microbial Ecology, Department of Institute of Microbiology Microbiology and Ecosystem Science University Hospital Center and University of Lausanne University of Vienna Lausanne Vienna Switzerland Austria

Peter F. Dunfield Radhey S. Gupta Department of Biological Sciences Department of Biochemistry and Biomedical Sciences University of Calgary McMaster University Calgary, AB Hamilton, ON Canada Canada List of Contributors xxiii

Max M. Ha¨ggblom Jantiya Isanapong Department of Biochemistry and Microbiology Department of Biology School of Environmental and Biological Sciences University of Texas Rutgers University Arlington, TX New Brunswick, NJ USA USA

Takashi Itoh Yejun Han Japan Collection of Microorganisms Department of Chemical and Biomolecular Engineering RIKEN BioResource Center North Carolina State University Tsukuba, Ibaraki Raleigh, NC Japan USA

Satoshi Hanada Estelle Jumas-Bilak Bioproduction Research Institute, National Institute UMR5119 ECOSYM, Equipe Pathoge`nes et Environnements of Advanced Industrial Science and Technology (AIST) UFR des Sciences pharmaceutiques et Biologiques Tsukuba, Ibaraki Universite´ Montpellier 1 Japan Montpellier France Harald Huber and Faculty of Biology and Preclinical Medicine Laboratoire d’Hygie`ne hospitalie`re Institute for Microbiology and Archaea Center Centre Hospitalier Re´gional Universitaire de Montpellier University Regensburg Montpellier Regensburg France Germany

Ali Karami Natsuko Ichikawa Molecular Biology Research Center Biological Resource Center Baqiyatallah University of Medical Sciences National Institute of Technology and Evaluation (NBRC) Tehran Tokyo Iran Japan

Takao Iino Robert M. Kelly Japan Collection of Microorganisms (RIKEN-BRC JCM) Department of Chemical and Biomolecular Engineering RIKEN Bioresource Center North Carolina State University Tsukuba, Ibaraki Raleigh, NC Japan USA

Hiroyuki Imachi Kazuhiro Kogure Subsurface Geobiology & Advanced Research (SUGAR) Department of Aquatic Bioscience Project, Extremobiosphere Research Program Atmosphere and Ocean Research Institute Institute of Biogeosciences The University of Tokyo Japan Agency for Marine-Earth Science & Kashiwa, Chiba Technology (JAMSTEC) Japan Yokosuka, Kanagawa Japan Lydia Kreuter Johannes F. Imhoff Faculty of Biology and Preclinical Medicine Marine Mikrobiologie Institute for Microbiology and Archaea Center Helmholtz Centre for Ocean Research University Regensburg Kiel Regensburg Germany Germany xxiv List of Contributors

Antonietta Lambiase He´le`ne Marchandin Department of Molecular Medicine and Health Biotechnology UMR5119 ECOSYM, Equipe Pathoge`nes et Environnements Medicine School, University of Naples ‘‘Federico II’’ UFR des Sciences pharmaceutiques et Biologiques Naples Universite´ Montpellier 1 Italy Montpellier France Alexander Lebedinsky and Winogradsky Institute of Microbiology Laboratoire de Bacte´riologie Russian Academy of Sciences Centre Hospitalier Re´gional Universitaire de Montpellier Moscow Montpellier Russia France

Kevin C. Y. Lee Extremophile Research Group Mark J. McBride GNS Science Department of Biological Sciences Taupo University of Wisconsin-Milwaukee New Zealand Milwaukee, WI and USA School of Biological Sciences University of Waikato Hamilton Simon Jon McIlroy New Zealand Department of Biotechnology, Chemistry, and Environmental Engineering Debbie Lindell Aalborg University Faculty of Biology Aalborg Technion – Israel Institute of Technology Denmark Haifa Israel Alexander Merkel Gina L. Lipscomb Winogradsky Institute of Microbiology Department of Biochemistry & Molecular Biology Russian Academy of Sciences University of Georgia Moscow Athens, GA Russia USA

Weifeng Liu H. W. Morgan The State Key Laboratory of Microbial Technology Thermophile Research Unit School of Life Science University of Waikato Shandong University Hamilton Jinan, Shandong New Zealand China

Stephen Lory Koji Mori Department of Microbiology and Immunobiology Biological Resource Center Harvard Medical School National Institute of Technology and Evaluation (NBRC) Boston, MA Kisarazu, Chiba USA Japan

Xuemei Lu The State Key Laboratory of Microbial Technology Satoshi Nakagawa School of Life Science Laboratory of Microbiology, Faculty of Fisheries Sciences Shandong University Hokkaido University Jinan, Shandong Hakodate, Hokkaido China Japan List of Contributors xxv

Per Halkjær Nielsen Anil Kumar Pinnaka Department of Biotechnology, Chemistry, and Microbial Type Culture Collection and Gene Bank Environmental Engineering CSIR – Institute of Microbial Technology Aalborg University Chandigarh Aalborg India Denmark Caroline M. Plugge Jaspreet S. Notey Laboratory of Microbiology Department of Chemical and Biomolecular Engineering Wageningen University North Carolina State University Wageningen Raleigh, NC The Netherlands USA

Maria Prokofeva Takuro Nunoura Winogradsky Institute of Microbiology Subsurface Geobiology and Advanced Research (SUGAR) Russian Academy of Sciences Project, Extremobiosphere Research Program Moscow Institute of Biogeosciences, Japan Agency for Marine-Earth Russia Science and Technology (JAMSTEC) Yokosuka, Kanagawa Japan Reza Ranjbar Molecular Biology Research Center Aharon Oren Baqiyatallah University of Medical Sciences Department of and Environmental Sciences Tehran The Institute of Life Sciences, The Hebrew University of Iran Jerusalem Jerusalem Anna-Louise Reysenbach Israel Department of Biology Portland State University Sanghwa Park Portland, OR Department of Aquatic Bioscience USA Atmosphere and Ocean Research Institute The University of Tokyo Kashiwa, Chiba Jorge L. M. Rodrigues Japan Department of Biology University of Texas Arlington, TX Anna Perevalova USA Winogradsky Institute of Microbiology Russian Academy of Sciences Moscow Eugene Rosenberg Russia Department of Molecular Microbiology and Biotechnology Mathieu Picardeau Tel Aviv University Institut Pasteur Tel Aviv Unite´ de Biologie des Spiroche`tes Israel Paris France Sanae Sakai Subsurface Geobiology & Advanced Research (SUGAR) Ludovic Pilloux Project, Extremobiosphere Research Program Center for Research on Intracellular Bacteria (CRIB) Institute of Biogeosciences Institute of Microbiology Japan Agency for Marine-Earth Science & University Hospital Center and University of Lausanne Technology (JAMSTEC) Lausanne Yokosuka, Kanagawa Switzerland Japan xxvi List of Contributors

Mitsuo Sakamoto Ken Takai Microbe Division/Japan Collection of Microorganisms Subsurface Geobiology Advanced Research (SUGAR) Project RIKEN BioResource Center Japan Agency for Marine-Earth Science & Tsukuba, Ibaraki Technology (JAMSTEC) Japan Yokosuka, Kanagawa Japan

Meysam Sarshar Molecular Biology Research Center Naga Radha Srinivas Tanuku Baqiyatallah University of Medical Sciences Regional Centre Tehran CSIR – National Institute of Oceanography Iran Visakhapatnam India

Christa Schleper Department of Ecogenomics and Systems Biology/Archaea Hannah M. Wexler Biology and Ecogenomics Group GLAVAHCS University of Vienna Los Angeles, CA Vienna USA Austria and David Geffen UCLA School of Medicine Los Angeles, CA Gerrit J. Schut USA Department of Biochemistry & Molecular Biology University of Georgia William B. Whitman Athens, GA Department of Microbiology USA University of Georgia Athens, GA Yuji Sekiguchi USA Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST) Ralph S. Wolfe Tsukuba, Ibaraki Department of Microbiology Japan University of Illinois at Urbana-Champaign Urbana, IL USA Bettina Siebers FB Chemie - Biofilm Centre Molekulare Enzymtechnologie und Biochemie Jaewoo Yoon Universita¨t Duisburg-Essen College of Pharmacy Essen Keimyung University Germany Daegu Republic of Korea Michaela Stieglmeier Department of Ecogenomics and Systems Biology/Archaea Noha H. Youssef Biology and Ecogenomics Group Department of Microbiology and Molecular Genetics University of Vienna Oklahoma State University Vienna Stillwater, OK Austria USA

Matthew B. Stott Rahim Sorouri Zanjani Extremophile Research Group Department of Microbiology, Faculty of Medicine GNS Science Baqiyatallah University of Medical Sciences Taupo Tehran New Zealand Iran List of Contributors xxvii

Weixin Zhang Erwin G. Zoetendal The State Key Laboratory of Microbial Technology Laboratory of Microbiology School of Life Science Wageningen University Shandong University Wageningen Jinan, Shandong The Netherlands China

Yongtao Zhu Department of Biological Sciences University of Wisconsin-Milwaukee Milwaukee, WI USA