Eugene Rosenberg

Editor-in-Chief
Edward F. DeLong
Stephen Lory
Erko Stackebrandt
Fabiano Thompson
Editors

The Prokaryotes
Other Major Lineages of Bacteria and
the Archaea
Fourth Edition

1 3Reference
The Prokaryotes
Eugene Rosenberg (Editor-in-Chief)
Edward F. DeLong, Stephen Lory, Erko Stackebrandt and Fabiano Thompson (Eds.)

The Prokaryotes
Other Major Lineages of Bacteria and the Archaea

Fourth Edition

With 253 Figures and 207 Tables

Editor-in-Chief
Eugene Rosenberg
Department of Molecular Microbiology 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
Massachusetts Institute of Technology and Cell Cultures
Cambridge, MA, USA Braunschweig, Germany
Center for Microbial Oceanography: 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 Fundao, Rio de Janeiro, Brazil
Department of Microbiology and Immunobiology
Harvard Medical School
Boston, MA, USA

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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 prokaryote life. 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 lives 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 thatafter a lifetime of studyit 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 eukaryote cell evolved as a chimera of certain prokaryote parts is a generally accepted concept today. Higher as well
as lower eukaryotes 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 microbiologists will again show its appreciation through use of these volumessuch 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 plants. 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 taxonomy, 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 611, 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 Quinones, 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 (19701974), full
professor (19752005), and professor emeritus (2006present). 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
animals 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 marine
biology 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. DeLongs scientific
interests focus primarily on central questions in marine microbial genomics, biogeochemistry, ecology, and evolution. A large part of
DeLongs 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 (19721977), 1978 with Carl Woese at the University of Illinois,
Urbana Champaign, and from 1979 to 1983 he was a member of Karl Schleifers 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 (19841990), at the
University of Queensland, Brisbane, Australia (19901993), and at the Technical University Braunschweig, where he also was the
director of the DSMZ-German Collection of Microorganisms and Cell Cultures GmbH (19932009). 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 (19821983) and his work has been awarded by the Academy of Science at
Gottingen, Bergeys Trust (Bergeys Award and Bergeys 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 Fundao
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 VibrionaceaeIUMS 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 Phylum Nanoarchaeota . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 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 Armatimonadetes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 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 Chlamydiae . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 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 Chrysiogenaceae . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 533

Max M. Haggblom . Elisabetta Bini

42 The Family Cryomorphaceae . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 539

John P. Bowman

43 The Family Cyclobacteriaceae . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 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 Caldithrix . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 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 Fibrobacteres . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 641

Eugene Rosenberg

51 The Family Flavobacteriaceae . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 643

Mark J. McBride
xviii Table of Contents

52 The Phylum Gemmatimonadetes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 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 Planctomycetes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 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 Cyanobacteria . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 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 Halkjr 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 Synergistetes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 931

Estelle Jumas-Bilak . Helene Marchandin

75 The Family Thermaceae . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 955

Luciana Albuquerque . Milton S. da Costa

76 The Phylum Thermotogae . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 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