The ProkaryotesThird Edition

The ProkaryotesA Handbook on the Biology of Bacteria

Third Edition

Volume 3: Archaea. Bacteria: Firmicutes, Actinomycetes

Martin Dworkin (Editor-in-Chief), Stanley Falkow, Eugene Rosenberg,Karl-Heinz Schleifer, Erko Stackebrandt (Editors)

Editor-in-ChiefProfessor Dr. Martin DworkinDepartment of MicrobiologyUniversity of MinnesotaBox 196University of MinnesotaMinneapolis, MN 55455-0312USA

EditorsProfessor Dr. Stanley FalkowDepartment of Microbiologyand ImmunologyStanford University Medical School299 Campus Drive, Fairchild D039Stanford, CA 94305-5124USA

Professor Dr. Eugene RosenbergDepartment of Molecular Microbiologyand BiotechnologyTel Aviv UniversityRamat-Aviv 69978Israel

Professor Dr. Karl-Heinz SchleiferDepartment of MicrobiologyTechnical University Munich80290 MunichGermany

Professor Dr. Erko StackebrandtDSMZ- German Collection of Microorganismsand Cell Cultures GmbH Mascheroder Weg 1b38124 BraunschweigGermany

Library of Congress Control Number: 91017256

Volume 3ISBN-10: 0-387-25493-5ISBN-13: 978-0387-25493-7e-ISBN: 0-387-30743-5Print + e-ISBN: 0-387-33489-0DOI: 10.1007/0-387-30743-5

Volumes 17 (Set)ISBN-10: 0-387-25499-4ISBN-13: 978-0387-25499-9e-ISBN: 0-387-30740-0Print + e-ISBN: 0-387-33488-2

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URLs in The Prokaryotes: Uncommon Web sites have been listed in the text. However, the following Web siteshave been referred to numerous times and have been suppressed for aesthetic purposes: www.bergeys.org;www.tigr.org; dx.doi.org; www.fp.mcs.anl.gov; www.ncbi.nlm.nih.gov; www.genome.ad.jp; www.cme.msu.edu;umbbd.ahc.umn.edu; www.dmsz.de; and www.arb-home.de. The entirety of all these Web links have been main-tained in the electronic version.

Preface

Each of the first two editions of The Prokaryotestook a bold step. The first edition, published in1981, set out to be an encyclopedic, synopticaccount of the world of the prokaryotesa col-lection of monographic descriptions of thegenera of bacteria.The Archaea had not yet beenformalized as a group. For the second edition in1992, the editors made the decision to organizethe chapters on the basis of the molecular phy-logeny championed by Carl Woese, whichincreasingly provided a rational, evolutionarybasis for the taxonomy of the prokaryotes. Inaddition, the archaea had by then been recog-nized as a phylogenetically separate and distin-guishable group of the prokaryotes. The twovolumes of the first edition had by thenexpanded to four. The third edition was arguablythe boldest step of all. We decided that the mate-rial would only be presented electronically. Theadvantages were obvious and persuasive. Therewould be essentially unlimited space. Therewould be no restrictions on the use of color illus-trations. Film and animated descriptions could bemade available. The text would be hyperlinkedto external sources. Publication of chapterswould be seriatithe edition would no longerhave to delay publication until the last tardyauthor had submitted his or her chapter. Updatesand modifications could be made continuously.And, most attractively, a library could place itssubscribed copy on its server and make it avail-able easily and cheaply to all in its community.One hundred and seventy chapters have thus farbeen presented in 16 releases over a six-yearperiod. The virtues and advantages of the onlineedition have been borne out. But we failed topredict the affection that many have for holdinga bound, print version of a book in their hands.Thus, this print version of the third edition shallaccompany the online version.

We are now four years into the 21st century.Indulge us then while we comment on the chal-lenges, problems and opportunities for microbi-ology that confront us.

Moselio Schaechter has referred to the presentera of microbiology as its third golden agetheera of integrative microbiology. Essentially allmicrobiologists now speak a common language.So that the boundaries that previously separatedsubdisciplines from each other have faded: phys-iology has become indistinguishable from patho-genesis; ecologists and molecular geneticistsspeak to each other; biochemistry is spoken byall; andmirabile dictu!molecular biologistsare collaborating with taxonomists.

But before these molecular dissections ofcomplex processes can be effective there must bea clear view of the organism being studied. Andit is our goal that these chapters in The Prokary-otes provide that opportunity.

There is also yet a larger issue. Microbiologyis now confronted with the need to understandincreasingly complex processes. And the modusoperandi that has served us so successfully for150 yearsthat of the pure culture studied understandard laboratory conditionsis inadequate.We are now challenged to solve problems of multimembered populations interacting witheach other and with their environment underconstantly variable conditions. Carl Woese haspointed out a useful and important distinctionbetween empirical, methodological reductionismand fundamentalist reductionism. The formerhas served us well; the latter stands in the way ofour further understanding of complex, interact-ing systems. But no matter what kind of synop-tic systems analysis emerges as our way ofunderstanding hostparasite relations, ecology,or multicellular behavior, the understanding ofthe organism as such is sine qua non. And in thatcontext, we are pleased to present to you thethird edition of The Prokaryotes.

Martin DworkinEditor-in-Chief

Foreword

The purpose of this brief foreword is unchangedfrom the first edition; it is simply to make you,the reader, hungry for the scientific feast thatfollows. These four volumes on the prokaryotesoffer an expanded scientific menu that displaysthe biochemical depth and remarkable physio-logical and morphological diversity of prokary-ote life. The size of the volumes might initiallydiscourage the unprepared mind from beingattracted to the study of prokaryote life, for thislandmark assemblage thoroughly documents thewealth of present knowledge. But in confrontingthe reader with the state of the art, the Hand-book also defines where more work needs to bedone on well-studied bacteria as well as onunusual or poorly studied organisms.

This edition of The Prokaryotes recognizesthe almost unbelievable impact that the work ofCarl Woese has had in defining a phylogeneticbasis for the microbial world. The concept thatthe ribosome is a highly conserved structure inall cells and that its nucleic acid components may serve as a convenient reference point forrelating all living things is now generallyaccepted. At last, the phylogeny of prokaryoteshas a scientific basis, and this is the first seriousattempt to present a comprehensive treatise onprokaryotes along recently defined phylogeneticlines. Although evidence is incomplete for manymicrobial groups, these volumes make a state-ment that clearly illuminates the path to follow.

There are basically two ways of doing researchwith microbes. A classical approach is first todefine the phenomenon to be studied and thento select the organism accordingly. Another wayis to choose a specific organism and go where itleads. The pursuit of an unusual microbe bringsout the latent hunter in all of us. The intellectualchallenges of the chase frequently test our inge-nuity to the limit. Sometimes the quarry repeat-edly escapes, but the final capture is indeed awonderful experience. For many of us, thesesimple rewards are sufficiently gratifying so thatwe have chosen to spend our scientific livesstudying these unusual creatures. In theseendeavors many of the strategies and tools as

well as much of the philosophy may be traced tothe Delft School, passed on to us by our teach-ers, Martinus Beijerinck, A. J. Kluyver, and C. B.van Niel, and in turn passed on by us to ourstudents.

In this school, the principles of the selective,enrichment culture technique have been devel-oped and diversified; they have been a majorforce in designing and applying new principlesfor the capture and isolation of microbes fromnature. For me, the organism approach hasprovided rewarding adventures. The organismcontinually challenges and literally drags theinvestigator into new areas where unfamiliartools may be needed. I believe that organism-oriented research is an important alternative toproblem-oriented research, for new concepts ofthe future very likely lie in a study of the breadthof microbial life. The physiology, biochemistry,and ecology of the microbe remain the mostpowerful attractions. Studies based on classicalmethods as well as modern genetic techniqueswill result in new insights and concepts.

To some readers, this edition of the TheProkaryotes may indicate that the field is nowmature, that from here on it is a matter of fillingin details. I suspect that this is not the case.Perhaps we have assumed prematurely that wefully understand microbial life. Van Niel pointedout to his students thatafter a lifetime ofstudyit was a very humbling experience toview in the microscope a sample of microbesfrom nature and recognize only a few. Recentevidence suggests that microbes have beenevolving for nearly 4 billion years. Most certainlythose microbes now domesticated and kept incaptivity in culture collections represent only aminor portion of the species that have evolved inthis time span. Sometimes we must remind our-selves that evolution is actively taking place atthe present moment. That the eukaryote cellevolved as a chimera of certain prokaryote partsis a generally accepted concept today. Higher aswell as lower eukaryotes evolved in contact withprokaryotes, and evidence surrounds us of thecomplex interactions between eukaryotes and

prokaryotes as well as among prokaryotes. Wehave so far only scratched the surface of thesebiochemical interrelationships. Perhaps thelegume nodule is a pertinent example of naturecaught in the act of evolving the nitrosome,a unique nitrogen-fixing organelle. Study ofprokaryotes is proceeding at such a fast pace thatmajor advances are occurring yearly. Theincrease of this edition to four volumes docu-ments the exciting pace of discoveries.

To prepare a treatise such as The Prokaryotesrequires dedicated editors and authors; the taskhas been enormous. I predict that the scientificcommunity of microbiologists will again show itsappreciation through use of these volumessuch that the pages will become dog-eared andworn as students seek basic information for the

viii Foreword

hunt.These volumes belong in the laboratory, notin the library. I believe that a most effective wayto introduce students to microbiology is for themto isolate microbes from nature, i.e., from theirhabitats in soil, water, clinical specimens, orplants. The Prokaryotes enormously simplifiesthis process and should encourage the construc-tion of courses that contain a wide spectrum ofdiverse topics. For the student as well as theadvanced investigator these volumes shouldgenerate excitement.

Happy hunting!

Ralph S. WolfeDepartment of Microbiology

University of Illinois at Urbana-Champaign

Contents

Preface vForeword by Ralph S. Wolfe viiContributors xxix

Volume 11. Essays in Prokaryotic Biology

1.1 How We Do, Dont and Should Look at Bacteria and Bacteriology 3carl r. woese

1.2 Databases 24wolfgang ludwig, karl-heinz schleifer and erko stackebrandt

1.3 Defining Taxonomic Ranks 29erko stackebrandt

1.4 Prokaryote Characterization and Identification 58hans g. trper and karl-heinz schleifer

1.5 Principles of Enrichment, Isolation, Cultivation, and Preservation of Prokaryotes 80jrg overmann

1.6 Prokaryotes and Their Habitats 137hans g. schlegel and holger w. jannasch

1.7 Morphological and Physiological Diversity 185stephen h. zinder and martin dworkin

1.8 Cell-Cell Interactions 221dale kaiser

1.9 Prokaryotic Genomics 246b. w. wren

1.10 Genomics and Metabolism in Escherichia coli 261margrethe haugge serres and monica riley

1.11 Origin of Life: RNA World versus Autocatalytic Anabolism 275gnter wchtershuser

1.12 Biotechnology and Applied Microbiology 284eugene rosenberg

1.13 The Structure and Function of Microbial Communities 299david a. stahl, meredith hullar and seana davidson

2. Symbiotic Associations

2.1 Cyanobacterial-Plant Symbioses 331david g. adams, birgitta bergman, s. a. nierzwicki-bauer,a. n. rai and arthur schler

2.2 Symbiotic Associations Between Ciliates and Prokaryotes 364hans-dieter grtz

2.3 Bacteriocyte-Associated Endosymbionts of Insects 403paul baumann, nancy a. moran and linda baumann

2.4 Symbiotic Associations Between Termites and Prokaryotes 439andreas brune

2.5 Marine Chemosynthetic Symbioses 475colleen m. cavanaugh, zoe p. mckiness, irene l.g. newton andfrank j. stewart

3. Biotechnology and Applied Microbiology

3.1 Organic Acid and Solvent Production 511palmer rogers, jiann-shin chen and mary jo zidwick

3.2 Amino Acid Production 756hidehiko kumagai

3.3 Microbial Exopolysaccharides 766timothy harrah, bruce panilaitis and david kaplan

3.4 Bacterial Enzymes 777wim j. quax

3.5 Bacteria in Food and Beverage Production 797michael p. doyle and jianghong meng

3.6 Bacterial Pharmaceutical Products 812arnold l. demain and giancarlo lancini

3.7 Biosurfactants 834eugene rosenberg

3.8 Bioremediation 850ronald l. crawford

x Contents

3.9 Biodeterioration 864ji-dong gu and ralph mitchell

3.10 Microbial Biofilms 904dirk de beer and paul stoodley

Index 939

Volume 21. Ecophysiological and Biochemical Aspects

1.1 Planktonic Versus Sessile Life of Prokaryotes 3kevin c. marshall

1.2 Bacterial Adhesion 16itzhak ofek, nathan sharon and soman n. abraham

1.3 The Phototrophic Way of Life 32jrg overmann and ferran garcia-pichel

1.4 The Anaerobic Way of Life 86ruth a. schmitz, rolf daniel, uwe deppenmeier andgerhard gottschalk

1.5 Bacterial Behavior 102judith armitage

1.6 Prokaryotic Life Cycles 140martin dworkin

1.7 Life at High Temperatures 167rainer jaenicke and reinhard sterner

1.8 Life at Low Temperatures 210siegfried scherer and klaus neuhaus

1.9 Life at High Salt Concentrations 263aharon oren

1.10 Alkaliphilic Prokaryotes 283terry ann krulwich

1.11 Syntrophism among Prokaryotes 309bernhard schink and alfons j.m. stams

1.12 Quorum Sensing 336bonnie l. bassler and melissa b. miller

1.13 Acetogenic Prokaryotes 354harold l. drake, kirsten ksel and carola matthies

Contents xi

1.14 Virulence Strategies of Plant Pathogenic Bacteria 421barbara n. kunkel and zhongying chen

1.15 The Chemolithotrophic Prokaryotes 441donovan p. kelly and anne p. wood

1.16 Oxidation of Inorganic Nitrogen Compounds as an Energy Source 457eberhard bock and michael wagner

1.17 The H2-Metabolizing Prokaryotes 496edward schwartz and brbel friedrich

1.18 Hydrocarbon-Oxidizing Bacteria 564eugene rosenberg

1.19 Cellulose-Decomposing Bacteria and Their Enzyme Systems 578edward a. bayer, yuval shoham and raphael lamed

1.20 Aerobic Methylotrophic Prokaryotes 618mary e. lidstrom

1.21 Dissimilatory Fe(III)- and Mn(IV)-Reducing Prokaryotes 635derek lovley

1.22 Dissimilatory Sulfate- and Sulfur-Reducing Prokaryotes 659ralf rabus, theo a. hansen and friedrich widdel

1.23 The Denitrifying Prokaryotes 769james p. shapleigh

1.24 Dinitrogen-Fixing Prokaryotes 793esperanza martinez-romero

1.25 Root and Stem Nodule Bacteria of Legumes 818michael j. sadowsky and p. h. graham

1.26 Magnetotactic Bacteria 842stefan spring and dennis a. bazylinski

1.27 Luminous Bacteria 863paul v. dunlap and kumiko kita-tsukamoto

1.28 Bacterial Toxins 893vega masignani, mariagrazia pizza and rino rappuoli

1.29 The Metabolic Pathways of Biodegradation 956lawrence p. wackett

1.30 Haloalkaliphilic Sulfur-Oxidizing Bacteria 969dimitry yu. sorokin, horia banciu, lesley a. robertson andj. gijs kuenen

1.31 The Colorless Sulfur Bacteria 985lesley a. robertson and j. gijs kuenen

xii Contents

1.32 Bacterial Stress Response 1012eliora z. ron

1.33 Anaerobic Biodegradation of Hydrocarbons Including Methane 1028friedrich widdel, antje boetius and ralf rabus

1.34 Physiology and Biochemistry of the Methane-Producing Archaea 1050reiner hedderich and william b. whitman

Index 1081

Volume 3A: Archaea

1. The Archaea: A Personal Overview of the Formative Years 3ralph s. wolfe

2. Thermoproteales 10harald huber, robert huber and karl o. stetter

3. Sulfolobales 23harald huber and david prangishvili

4. Desulfurococcales 52harald huber and karl o. stetter

5. The Order Thermococcales 69costanzo bertoldo and garabed antranikian

6. The Genus Archaeoglobus 82patricia hartzell and david w. reed

7. Thermoplasmatales 101harald huber and karl o. stetter

8. The Order Halobacteriales 113aharon oren

9. The Methanogenic Bacteria 165william b. whitman, timothy l. bowen and david r. boone

10. The Order Methanomicrobiales 208jean-louis garcia, bernard ollivier and william b. whitman

11. The Order Methanobacteriales 231adam s. bonin and david r. boone

12. The Order Methanosarcinales 244melissa m. kendall and david r. boone

Contents xiii

13. Methanococcales 257william b. whitman and christian jeanthon

14. Nanoarchaeota 274harald huber, michael j. hohn, reinhard rachel andkarl o. stetter

15. Phylogenetic and Ecological Perspectives on Uncultured Crenarchaeota and Korarchaeota 281scott c. dawson, edward f. delong and norman r. pace

B: Bacteria

1. Firmicutes (Gram-Positive Bacteria)

1.1. Firmicutes with High GC Content of DNA

1.1.1 Introduction to the Taxonomy of Actinobacteria 297erko stackebrandt and peter schumann

1.1.2 The Family Bifidobacteriaceae 322bruno biavati and paola mattarelli

1.1.3 The Family Propionibacteriaceae: The Genera Friedmanniella,Luteococcus, Microlunatus, Micropruina, Propioniferax,Propionimicrobium and Tessarococcus 383erko stackebrandt and klaus p. schaal

1.1.4 Family Propionibacteriaceae: The Genus Propionibacterium 400erko stackebrandt, cecil s. cummins and john l. johnson

1.1.5 The Family Succinivibrionaceae 419erko stackebrandt and robert b. hespell

1.1.6 The Family Actinomycetaceae: The Genera Actinomyces, Actinobaculum,Arcanobacterium, Varibaculum and Mobiluncus 430klaus p. schaal, atteyet f. yassin and erko stackebrandt

1.1.7 The Family Streptomycetaceae, Part I: Taxonomy 538peter kmpfer

1.1.8 The Family Streptomycetaceae, Part II: Molecular Biology 605hildgund schrempf

1.1.9 The Genus Actinoplanes and Related Genera 623gernot vobis

1.1.10 The Family Actinosynnemataceae 654david p. labeda

1.1.11 The Families Frankiaceae, Geodermatophilaceae, Acidothermaceae and Sporichthyaceae 669philippe normand

xiv Contents

1.1.12 The Family Thermomonosporaceae: Actinocorallia, Actinomadura,Spirillospora and Thermomonospora 682reiner michael kroppenstedt and michael goodfellow

1.1.13 The Family Streptosporangiaceae 725michael goodfellow and erika teresa quintana

1.1.14 The Family Nocardiopsaceae 754reiner michael kroppenstedt and lyudmila i. evtushenko

1.1.15 CorynebacteriumNonmedical 796wolfgang liebl

1.1.16 The Genus CorynebacteriumMedical 819alexander von graevenitz and kathryn bernard

1.1.17 The Families Dietziaceae, Gordoniaceae, Nocardiaceae and Tsukamurellaceae 843michael goodfellow and luis angel maldonado

1.1.18 The Genus MycobacteriumNonmedical 889sybe hartmans, jan a.m. de bont and erko stackebrandt

1.1.19 The Genus MycobacteriumMedical 919beatrice saviola and william bishai

1.1.20 Mycobacterium leprae 934thomas m. shinnick

1.1.21 The Genus Arthrobacter 945dorothy jones and ronald m. keddie

1.1.22 The Genus Micrococcus 961miloslav kocur, wesley e. kloos and karl-heinz schleifer

1.1.23 Renibacterium 972hans-jrgen busse

1.1.24 The Genus Stomatococcus: Rothia mucilaginosa, basonymStomatococcus mucilaginosus 975erko stackebrandt

1.1.25 The Family Cellulomonadaceae 983erko stackebrandt, peter schumann and helmut prauser

1.1.26 The Family Dermatophilaceae 1002erko stackebrandt

1.1.27 The Genus Brevibacterium 1013matthew d. collins

1.1.28 The Family Microbacteriaceae 1020lyudmila i. evtushenko and mariko takeuchi

Contents xv

1.1.29 The Genus Nocardioides 1099jung-hoon yoon and yong-ha park

Index 1115

Volume 41. Firmicutes (Gram-Positive Bacteria)

1.2 Firmicutes with Low GC Content of DNA

1.2.1 The Genera Staphylococcus and Macrococcus 5friedrich gtz, tammy bannerman and karl-heinz schleifer

1.2.2 The Genus StreptococcusOral 76jeremy m. hardie and robert a. whiley

1.2.3 Medically Important Beta-Hemolytic Streptococci 108p. patrick cleary and qi cheng

1.2.4 Streptococcus pneumoniae 149elaine tuomanen

1.2.5 The Genus Enterococcus: Taxonomy 163luc devriese, margo baele and patrick butaye

1.2.6 Enterococcus 175donald j. leblanc

1.2.7 The Genus Lactococcus 205michael teuber and arnold geis

1.2.8 The Genera Pediococcus and Tetragenococcus 229wilhelm h. holzapfel, charles m. a. p. franz, wolfgang ludwig,werner back and leon m. t. dicks

1.2.9 Genera Leuconostoc, Oenococcus and Weissella 267johanna bjrkroth and wilhelm h. holzapfel

1.2.10 The Genera Lactobacillus and Carnobacterium 320walter p. hammes and christian hertel

1.2.11 Listeria monocytogenes and the Genus Listeria 404nadia khelef, marc lecuit, carmen buchrieser, didier cabanes,olivier dussurget and pascale cossart

1.2.12 The Genus Brochothrix 477erko stackebrandt and dorothy jones

1.2.13 The Genus Erysipelothrix 492erko stackebrandt, annette c. reboli and w. edmund farrar

xvi Contents

1.2.14 The Genus Gemella 511matthew d. collins

1.2.15 The Genus Kurthia 519erko stackebrandt, ronald m. keddie and dorothy jones

1.2.16 The Genus BacillusNonmedical 530ralph a. slepecky and h. ernest hemphill

1.2.17 The Genus BacillusInsect Pathogens 563donald p. stahly, robert e. andrews and allan a. yousten

1.2.18 The Genus BacillusMedical 609w. edmund farrar and annette c. reboli

1.2.19 Genera Related to the Genus BacillusSporolactobacillus,Sporosarcina, Planococcus, Filibacter and Caryophanon 631dieter claus, dagmar fritze and miloslav kocur

1.2.20 An Introduction to the Family Clostridiaceae 654jrgen wiegel, ralph tanner and fred a. rainey

1.2.21 Neurotoxigenic Clostridia 679cesare montecucco, ornella rossetto and michel r. popoff

1.2.22 The Enterotoxic Clostridia 698bruce a. mcclane, francisco a. uzai,mariano e. fernandez miyakawa, david lyerly andtracy wilkins

1.2.23 Clostridium perfringens and Histotoxic Disease 753julian i. rood

1.2.24 The Genera Desulfitobacterium and Desulfosporosinus: Taxonomy 771stefan spring and frank rosenzweig

1.2.25 The Genus Desulfotomaculum 787friedrich widdel

1.2.26 The Anaerobic Gram-Positive Cocci 795takayuki ezaki, na (michael) li and yoshiaki kawamura

1.2.27 The Order Haloanaerobiales 809aharon oren

1.2.28 The Genus Eubacterium and Related Genera 823william g. wade

1.2.29 The Genus Mycoplasma and Related Genera (Class Mollicutes) 836shmuel razin

1.2.30 The Phytopathogenic Spiroplasmas 905jacqueline fletcher, ulrich melcher and astri wayadande

Contents xvii

1.3 Firmicutes with Atypical Cell Walls

1.3.1 The Family Heliobacteriaceae 951michael t. madigan

1.3.2 Pectinatus, Megasphaera and Zymophilus 965auli haikara and ilkka helander

1.3.3 The Genus Selenomonas 982robert b. hespell, bruce j. paster and floyd e. dewhirst

1.3.4 The Genus Sporomusa 991john a. breznak

1.3.5 The Family Lachnospiraceae, Including the Genera Butyrivibrio,Lachnospira and Roseburia 1002michael cotta and robert forster

1.3.6 The Genus Veillonella 1022paul kolenbrander

1.3.7 Syntrophomonadaceae 1041martin sobierj and david r. boone

2. Cyanobacteria

2.1 The CyanobacteriaIsolation, Purification and Identification 1053john b. waterbury

2.2 The CyanobacteriaEcology, Physiology and Molecular Genetics 1074yehuda cohen and michael gurevitz

2.3 The Genus Prochlorococcus 1099anton f. post

Index 1111

Volume 53. Proteobacteria

Introduction to the Proteobacteria 3karel kersters, paul de vos, monique gillis, jean swings,peter van damme and erko stackebrandt

3.1. Alpha Subclass

3.1.1 The Phototrophic Alpha-Proteobacteria 41johannes f. imhoff

xviii Contents

3.1.2 The Genera Prosthecomicrobium and Ancalomicrobium 65gary e. oertli, cheryl jenkins, naomi ward, frederick a. rainey,erko stackebrandt and james t. staley

3.1.3 Dimorphic Prosthecate Bacteria: The Genera Caulobacter,Asticcacaulis, Hyphomicrobium, Pedomicrobium, Hyphomonasand Thiodendron 72jeanne s. poindexter

3.1.4 The Genus Agrobacterium 91ann g. matthysse

3.1.5 The Genus Azospirillum 115anton hartmann and jose ivo baldani

3.1.6 The Genus Herbaspirillum 141michael schmid, jose ivo baldani and anton hartmann

3.1.7 The Genus Beijerinckia 151jan hendrick becking

3.1.8 The Family Acetobacteraceae: The Genera Acetobacter, Acidomonas,Asaia, Gluconacetobacter, Gluconobacter, and Kozakia 163karel kersters, puspita lisdiyanti, kazuo komagata andjean swings

3.1.9 The Genus Zymomonas 201hermann sahm, stephanie bringer-meyer and georg a. sprenger

3.1.10 The Manganese-Oxidizing Bacteria 222kenneth h. nealson

3.1.11 The Genus Paracoccus 232donovan p. kelly, frederick a. rainey and ann p. wood

3.1.12 The Genus Phenylobacterium 250jrgen eberspcher and franz lingens

3.1.13 Methylobacterium 257peter n. green

3.1.14 The MethanotrophsThe Families Methylococcaceae and Methylocystaceae 266john p. bowman

3.1.15 The Genus Xanthobacter 290jrgen wiegel

3.1.16 The Genus Brucella 315edgardo moreno and ignacio moriyn

3.1.17 Introduction to the Rickettsiales and Other Intracellular Prokaryotes 457david n. fredricks

3.1.18 The Genus Bartonella 467michael f. minnick and burt e. anderson

Contents xix

3.1.19 The Order Rickettsiales 493xue-jie yu and david h. walker

3.1.20 The Genus Coxiella 529robert a. heinzen and james e. samuel

3.1.21 The Genus Wolbachia 547markus riegler and scott l. oneill

3.1.22 Aerobic Phototrophic Proteobacteria 562vladimir v. yurkov

3.1.23 The Genus Seliberia 585jean m. schmidt and james r. swafford

3.2. Beta Subclass

3.2.1 The Phototrophic Betaproteobacteria 593johannes f. imhoff

3.2.2 The Neisseria 602daniel c. stein

3.2.3 The Genus Bordetella 648alison weiss

3.2.4 Achromobacter, Alcaligenes and Related Genera 675hans-jrgen busse and andreas stolz

3.2.5 The Genus Spirillum 701noel r. krieg

3.2.6 The Genus Aquaspirillum 710bruno pot, monique gillis and jozef de ley

3.2.7 Comamonas 723anne willems and paul de vos

3.2.8 The Genera Chromobacterium and Janthinobacterium 737monique gillis and jozef de ley

3.2.9 The Genera Phyllobacterium and Ochrobactrum 747jean swings, bart lambert, karel kersters and barry holmes

3.2.10 The Genus Derxia 751jan hendrick becking

3.2.11 The Genera Leptothrix and Sphaerotilus 758stefan spring

3.2.12 The Lithoautotrophic Ammonia-Oxidizing Bacteria 778hans-peter koops, ulrike purkhold, andreas pommerening-rser,gabriele timmermann and michael wagner

xx Contents

3.2.13 The Genus Thiobacillus 812lesley a. robertson and j. gijs kuenen

3.2.14 The Genera Simonsiella and Alysiella 828brian p. hedlund and daisy a. kuhn

3.2.15 Eikenella corrodens and Closely Related Bacteria 840edward j. bottone and paul a. granato

3.2.16 The Genus Burkholderia 848donald e. woods and pamela a. sokol

3.2.17 The Nitrite-Oxidizing Bacteria 861aharon abeliovich

3.2.18 The Genera Azoarcus, Azovibrio, Azospira and Azonexus 873barbara reinhold-hurek and thomas hurek

Index 893

Volume 63. Proteobacteria

3.3. Gamma Subclass

3.3.1 New Members of the Family Enterobacteriaceae 5j. michael janda

3.3.2 Phylogenetic Relationships of Bacteria with Special Reference toEndosymbionts and Enteric Species 41m. pilar francino, scott r. santos and howard ochman

3.3.3 The Genus Escherichia 60rodney a. welch

3.3.4 The Genus Edwardsiella 72sharon l. abbott and j. michael janda

3.3.5 The Genus Citrobacter 90diana borenshtein and david b. schauer

3.3.6 The Genus Shigella 99yves germani and philippe j. sansonetti

3.3.7 The Genus Salmonella 123craig d. ellermeier and james m. slauch

3.3.8 The Genus Klebsiella 159sylvain brisse, francine grimont and patrick a. d. grimont

Contents xxi

3.3.9 The Genus Enterobacter 197francine grimont and patrick a. d. grimont

3.3.10 The Genus Hafnia 215megan e. mcbee and david b. schauer

3.3.11 The Genus Serratia 219francine grimont and patrick a. d. grimont

3.3.12 The Genera Proteus, Providencia, and Morganella 245jim manos and robert belas

3.3.13 Y. enterocolitica and Y. pseudotuberculosis 270elisabeth carniel, ingo autenrieth, guy cornelis,hiroshi fukushima, franoise guinet, ralph isberg,jeannette pham, michael prentice, michel simonet,mikael skurnik and georges wauters

3.3.14 Yersinia pestis and Bubonic Plague 399robert brubaker

3.3.15 Erwinia and Related Genera 443clarence i. kado

3.3.16 The Genera Photorhabdus and Xenorhabdus 451noel boemare and raymond akhurst

3.3.17 The Family Vibrionaceae 495j. j. farmer, iii

3.3.18 The Genera Vibrio and Photobacterium 508j. j. farmer, iii and f. w. hickman-brenner

3.3.19 The Genera Aeromonas and Plesiomonas 564j. j. farmer, iii, m. j. arduino and f. w. hickman-brenner

3.3.20 The Genus Alteromonas and Related Proteobacteria 597valery v. mikhailov, lyudmila a. romanenko andelena p. ivanova

3.3.21 Nonmedical: Pseudomonas 646edward r. b. moore, brian j. tindall, vitor a. p. martins dos santos,dietmar h. pieper, juan-luis ramos and norberto j. palleroni

3.3.22 Pseudomonas aeruginosa 704timothy l. yahr and matthew r. parsek

3.3.23 Phytopathogenic Pseudomonads and Related Plant-Associated Pseudomonads 714milton n. schroth, donald c. hildebrand andnickolas panopoulos

3.3.24 Xylophilus 741anne willems and monique gillis

xxii Contents

3.3.25 The Genus Acinetobacter 746kevin towner

3.3.26 The Family Azotobacteraceae 759jan hendrick becking

3.3.27 The Genera Beggiatoa and Thioploca 784andreas teske and douglas c. nelson

3.3.28 The Family Halomonadaceae 811david r. arahal and antonio ventosa

3.3.29 The Genus Deleya 836karel kersters

3.3.30 The Genus Frateuria 844jean swings

3.3.31 The Chromatiaceae 846johannes f. imhoff

3.3.32 The Family Ectothiorhodospiraceae 874johannes f. imhoff

3.3.33 Oceanospirillum and Related Genera 887jos m. gonzlez and william b. whitman

3.3.34 Serpens flexibilis: An Unusually Flexible Bacterium 916robert b. hespell

3.3.35 The Genus Psychrobacter 920john p. bowman

3.3.36 The Genus Leucothrix 931thomas d. brock

3.3.37 The Genus Lysobacter 939hans reichenbach

3.3.38 The Genus Moraxella 958john p. hays

3.3.39 Legionella Species and Legionnaires Disease 988paul h. edelstein and nicholas p. cianciotto

3.3.40 The Genus Haemophilus 1034doran l. fink and joseph w. st. geme, iii

3.3.41 The Genus Pasteurella 1062henrik christensen and magne bisgaard

3.3.42 The Genus Cardiobacterium 1091sydney m. harvey and james r. greenwood

Contents xxiii

3.3.43 The Genus Actinobacillus 1094janet i. macinnes and edward t. lally

3.3.44 The Genus Francisella 1119francis nano and karen elkins

3.3.45 Ecophysiology of the Genus Shewanella 1133kenneth h. nealson and james scott

3.3.46 The Genus Nevskia 1152heribert cypionka, hans-dietrich babenzien,frank oliver glckner and rudolf amann

3.3.47 The Genus Thiomargarita 1156heide n. schulz

Index 1165

Volume 73. Proteobacteria

3.4 Delta Subclass

3.4.1 The Genus Pelobacter 5bernhard schink

3.4.2 The Genus Bdellovibrio 12edouard jurkevitch

3.4.3 The Myxobacteria 31lawrence j. shimkets, martin dworkin and hans reichenbach

3.5. Epsilon Subclass

3.5.1 The Genus Campylobacter 119trudy m. wassenaar and diane g. newell

3.5.2 The Genus Helicobacter 139jay v. solnick, jani l. orourke, peter van damme and adrian lee

3.5.3 The Genus Wolinella 178jrg simon, roland gross, oliver klimmek and achim krger

4. Spirochetes

4.1 Free-Living Saccharolytic Spirochetes: The Genus Spirochaeta 195susan leschine, bruce j. paster and ercole canale-parola

xxiv Contents

4.2 The Genus Treponema 211steven j. norris, bruce j. paster, annette moter andulf b. gbel

4.3 The Genus Borrelia 235melissa j. caimano

4.4 The Genus Leptospira 294ben adler and solly faine

4.5 Termite Gut Spirochetes 318john a. breznak and jared r. leadbetter

4.6 The Genus Brachyspira 330thaddeus b. stanton

5. Chlorobiaceae

5.1 The Family Chlorobiaceae 359jrg overmann

6. Bacteroides and Cytophaga Group

6.1 The Medically Important Bacteroides spp. in Health and Disease 381c. jeffrey smith, edson r. rocha and bruce j. paster

6.2 The Genus Porphyromonas 428frank c. gibson and caroline attardo genco

6.3 An Introduction to the Family Flavobacteriaceae 455jean-franois bernardet and yasuyoshi nakagawa

6.4 The Genus Flavobacterium 481jean-franois bernardet and john p. bowman

6.5 The Genera Bergeyella and Weeksella 532celia j. hugo, brita bruun and piet j. jooste

6.6 The Genera Flavobacterium, Sphingobacterium and Weeksella 539barry holmes

6.7 The Order Cytophagales 549hans reichenbach

6.8 The Genus Saprospira 591hans reichenbach

6.9 The Genus Haliscomenobacter 602eppe gerke mulder and maria h. deinema

6.10 Sphingomonas and Related Genera 605david l. balkwill, j. k. fredrickson and m. f. romine

Contents xxv

xxvi Contents

6.11 The Genera Empedobacter and Myroides 630celia j. hugo, brita bruun and piet j. jooste

6.12 The Genera Chryseobacterium and Elizabethkingia 638jean-franois bernardet, celia j. hugo and brita bruun

6.13 The Marine Clade of the Family Flavobacteriaceae: The Genera Aequorivita, Arenibacter, Cellulophaga, Croceibacter, Formosa,Gelidibacter, Gillisia, Maribacter, Mesonia, Muricauda, Polaribacter,Psychroflexus, Psychroserpens, Robiginitalea, Salegentibacter,Tenacibaculum, Ulvibacter, Vitellibacter and Zobellia 677john p. bowman

6.14 Capnophilic Bird Pathogens in the Family Flavobacteriaceae:Riemerella, Ornithobacterium and Coenonia 695peter van damme, h. m. hafez and k. h. hinz

6.15 The Genus Capnocytophaga 709e. r. leadbetter

6.16 The Genera Rhodothermus, Thermonema, Hymenobacterand Salinibacter 712aharon oren

7. Chlamydia

7.1 The Genus ChlamydiaMedical 741murat v. kalayoglu and gerald i. byrne

8. Planctomyces and Related Bacteria

8.1 The Order Planctomycetales, Including the Genera Planctomyces,Pirellula, Gemmata and Isosphaera and the Candidatus Genera Brocadia, Kuenenia and Scalindua 757naomi ward, james t. staley, john a. fuerst, stephen giovannoni,heinz schlesner and erko stackebrandt

9. Thermus

9.1 The Genus Thermus and Relatives 797milton s. da costa, frederick a. rainey and m. fernanda nobre

10. Chloroflexaceae and Related Bacteria

10.1 The Family Chloroflexaceae 815satoshi hanada and beverly k. pierson

10.2 The Genus Thermoleophilum 843jerome j. perry

10.3 The Genus Thermomicrobium 849jerome j. perry

10.4 The Genus Herpetosiphon 854natuschka lee and hans reichenbach

11. Verrucomicrobium

11.1 The Phylum Verrucomicrobia: A Phylogenetically Heterogeneous Bacterial Group 881heinz schlesner, cheryl jenkins and james t. staley

12. Thermotogales

12.1 Thermotogales 899robert huber and michael hannig

13. Aquificales

13.1 Aquificales 925robert huber and wolfgang eder

14. Phylogenetically Unaffiliated Bacteria

14.1 Morphologically Conspicuous Sulfur-Oxidizing Eubacteria 941jan w. m. la rivire and karin schmidt

14.2 The Genus Propionigenium 955bernhard schink

14.3 The Genus Zoogloea 960patrick r. dugan, daphne l. stoner and harvey m. pickrum

14.4 Large Symbiotic Spirochetes: Clevelandina, Cristispira, Diplocalyx,Hollandina and Pillotina 971lynn margulis and gregory hinkle

14.5 Streptobacillus moniliformis 983james r. greenwood and sydney m. harvey

14.6 The Genus Toxothrix 986peter hirsch

14.7 The Genus Gallionella 990hans h. hanert

14.8 The Genera Caulococcus and Kusnezovia 996jean m. schmidt and georgi a. zavarzin

14.9 The Genus Brachyarcus 998peter hirsch

Contents xxvii

14.10 The Genus Pelosigma 1001peter hirsch

14.11 The Genus Siderocapsa (and Other Iron- and Maganese-Oxidizing Eubacteria) 1005hans h. hanert

14.12 The Genus Fusobacterium 1016tor hofstad

14.13 Prokaryotic Symbionts of Amoebae and Flagellates 1028kwang w. jeon

Index 1039

xxviii Contents

Contributors

Burt E. AndersonDepartment of Medical Microbiology and

ImmunologyCollege of MedicineUniversity of South FloridaTampa, FL 33612USA

Robert E. AndrewsDepartment of MicrobiologyUniversity of IowaIowa City, IA 52242USA

Garabed AntranikianTechnical University Hamburg-HarburgInstitute of Technical MicrobiologyD-21073 HamburgGermany

David R. ArahalColeccin Espaola de Cultivos Tipo (CECT)Universidad de ValenciaEdificio de Investigacin46100 Burjassot (Valencia)Spain

M. J. ArduinoCenter for Infectious DiseasesCenters for Disease ControlAtlanta, GA 30333USA

Judith ArmitageDepartment of BiochemistryMicrobiology UnitUniversity of OxfordOX1 3QU OxfordUK

Ingo AutenriethInstitut fr Medizinische MikrobiologieUniversitatsklinikum TuebingenD-72076 TuebingenGermany

Sharon L. AbbottMicrobial Diseases LaboratoryBerkeley, CA 94704USA

Aharon AbeliovichDepartment of Biotechnology EngineeringInstitute for Applied Biological ResearchEnvironmental Biotechnology InstituteBen Gurion University84105 Beer-ShevaIsrael

Soman N. AbrahamDirector of Graduate Studies in PathologyDepartments of Pathology, Molecular Genetics

and Microbiology, and ImmunologyDuke University Medical CenterDurham, NC 27710USA

David G. AdamsSchool of Biochemistry and MicrobiologyUniversity of LeedsLeeds LS2 9JTUK

Ben AdlerMonash UniversityFaculty of Medicine, Nursing and Health

SciencesDepartment of MicrobiologyClayton CampusVictoria, 3800Australia

Raymond AkhurstCSIRO EntomologyBlack MountainACT 2601 CanberraAustralia

Rudolf AmannMax Planck Institute for Marine MicrobiologyD-28359 BremenGermany

xxx Contributors

Hans-Dietrich BabenzienLeibniz-Institut fr Gewsserkologie und

Binnenfischereiim Forschungsverbund Berlin

12587 BerlinGermany

Werner BackLehrstuhl fr Technologie der Brauerei ITechnische Universitt MnchenD-85354 Freising-WeihenstephanGermany

Margo BaeleDepartment of PathologyBacteriology and Poultry DiseasesFaculty of Veterinary MedicineGhent UniversityB-9820 MerelbekeBelgium

Jose Ivo BaldaniEMBRAPA-AgrobiologyCentro Nacional de Pesquisa de AgrobiologiaSeropedica, 23851-970CP 74505 Rio de JaneiroBrazil

David L. BalkwillDepartment of Biomedical SciencesCollege of MedicineFlorida State UniversityTallahassee, FL 32306-4300USA

Horia BanciuDepartment of BiotechnologyDelft University of Technology2628 BC Delft

Tammy BannermanSchool of Allied Medical ProfessionsDivision of Medical TechnologyThe Ohio State UniversityColumbus, OH 43210USA

Bonnie L. BasslerDepartment of Molecular BiologyPrinceton UniversityPrinceton, NJ 08544-1014USA

Linda BaumannSchool of NursingClinical Science CenterUniversity of WisconsinMadison, WI 53792-2455USA

Paul BaumannDepartment of MicrobiologyUniversity of California, DavisDavis, CA 95616-5224USA

Edward A. BayerDepartment of Biological ChemistryWeizmann Institute of ScienceRehovot 76100Israel

Dennis A. BazylinskiDepartment of Microbiology, Immunology and

Preventive MedicineIowa State UniversityAmes, IA 55001USA

Jan Hendrick BeckingStichting ITALResearch Institute of the Ministry of

Agriculture and Fisheries6700 AA WageningenThe Netherlands

Robert BelasThe University of Maryland Biotechnology

InstituteCenter of Marine BiotechnologyBaltimore, MD 21202USA

Birgitta BergmanDepartment of BotanyStockholm UniversitySE-106 91 StockholmSweden

Kathryn BernardSpecial Bacteriology SectionNational Microbiology LaboratoryHealth CanadaWinnipeg R3E 3R2Canada

Jean-Franois BernardetUnit de Virologie et Immunologie

MolculairesInstitut National de la Recherche

Agronomique (INRA)Domaine de Vilvert78352 Jouy-en-Josas cedexFrance

Contributors xxxi

Costanzo BertoldoTechnical University Hamburg-HarburgInstitute of Technical MicrobiologyD-21073 HamburgGermany

Bruno BiavatiIstituto di Microbiologia Agraria40126 BolognaItaly

Magne BisgaardDepartment of Veterinary MicrobiologyRoyal Veterinary and Agricultural University1870 Frederiksberg CDenmark

William BishaiDepartments of Molecular Microbiology and

Immunology, International Health, andMedicine

Center for Tuberculosis ResearchJohns Hopkins School of Hygiene and Public

HealthBaltimore, MD 21205-2105USA

Johanna BjrkrothDepartment of Food and Environmental

HygieneFaculty of Veterinary MedicineUniversity of HelsinkiFIN-00014 HelsinkiFinland

Eberhard BockInstitute of General BotanyDepartment of MicrobiologyUniversity of HamburgD-22609 HamburgGermany

Noel BoemareEcologie Microbienne des Insectes etInteractions Hte-PathogneUMR EMIP INRA-UMIIIFR56 Biologie cellulaire et Porcessus

infectieuxUniversit Montpellier II34095 MontpellierFrance

Antje BoetiusMax-Planck-Institut fr Marine MikrobiologieD-28359 BremenGermany

Adam S. BoninPortland State UniversityPortland OR 97207USA

David R. BooneDepartment of BiologyEnvironmental Science and EngineeringOregon Graduate Institute of Science and

TechnologyPortland State UniversityPortland, OR 97207-0751USA

Diana BorenshteinMassachusetts Institute of TechnologyCambridge, MA 02139-4307USA

Edward J. BottoneDivision of Infectious DiseasesThe Mount Sinai HospitalOne Gustave L. Levy PlaceNew York, NY 10029USA

Timothy L. BowenDepartment of MicrobiologyUniversity of GeorgiaAthens, GA 30602USA

John P. BowmanAustralian Food Safety Centre for ExcellenceSchool of Agricultural ScienceHobart, Tasmania, 7001Australia

John A. BreznakDepartment of Microbiology and Molecular

GeneticsMichigan State UniversityEast Lansing, MI 48824-1101USA

Stephanie Bringer-MeyerInstitut BiotechnologieForschungszentrum JlichD-52425 JlichGermany

Sylvain BrisseUnit Biodiversit des Bactries Pathognes

EmergentesU 389 INSERMInstitut Pasteur75724 ParisFrance

Thomas D. BrockDepartment of BacteriologyUniversity of Wisconsin-MadisonMadison, WI 53706USA

xxxii Contributors

Robert BrubakerDepartment of MicrobiologyMichigan State UniversityEast Lansing, MI 48824USA

Andreas BruneMax Planck Institute for Terrestrial

MicrobiologyMarburgGermany

Brita BruunDepartment of Clinical MicrobiologyHillerd HospitalDK 3400 HillerdDenmark

Carmen BuchrieserLaboratoire de Gnomique des

Microorganismes PathognesInstitut Pasteur75724 ParisFrance

Hans-Jrgen BusseInstitut fr Bakteriology, Mykologie, und

HygieneVeterinrmedizinische Universitt WienA-1210 ViennaAustria

Patrick ButayeCODA-CERVA-VAR1180 BrusselsBelgium

Gerald I. ByrneDepartment of Medical Microbiology and

ImmunologyUniversity of WisconsinMadisonMadison, WI 53706USA

Didier CabanesDepartment of Immunology and Biology of

InfectionMolecular Microbiology GroupInstitute for Molecular and Cellular Biology4150-180 PortoPortugal

Melissa CaimanoCenter for Microbial PathogenesisandDepartment of PathologyandDepartment of Genetics and DevelopmentUniversity of Connecticut Health CenterFarmington, CT 06030-3205USA

Ercole Canale-ParolaDepartment of MicrobiologyUniversity of MassachusettsAmherst, MA 01003USA

Elisabeth CarnielLaboratoire des YersiniaInstitut Pasteur75724 ParisFrance

Colleen M. CavanaughBio LabsHarvard UniversityCambridge, MA 02138USA

Jiann-Shin ChenDepartment of BiochemistryVirginia Polytechnic Institute and

State UniversityVirginia TechBlacksburg, VA 24061-0308USA

Zhongying ChenDepartment of BiologyUniversity of North CarolinaChapel Hill, NC 27514USA

Qi ChengUniversity of Western SydneyPenrith SouthNSW 1797Australia

Henrik ChristensenDepartment of Veterinary MicrobiologyRoyal Veterinary and Agricultural UniversityDenmark

Nicholas P. CianciottoDepartment of Microbiology and ImmunologyNorthwestern University School of MedicineChicago, ILUSA

Dieter ClausDeutsche Sammlung von MikroorganismenD-3300 Braunschweig-StockheimGermany

P. Patrick ClearyDepartment of MicrobiologyUniversity of Minnesota Medical SchoolMinneapolis, MN 55455USA

Contributors xxxiii

Yehuda CohenDepartment of Molecular and Microbial

EcologyInstitute of Life ScienceHebrew University of Jerusalem91904 JerusalemIsrael

Matthew D. CollinsInstitute of Food ResearchReading Lab, Early GateUK

Guy CornelisMicrobial Pathogenesis UnitUniversit Catholique de Louvain andChristian de Duve Institute of Cellular

PathologyB1200 BrusselsBelgium

Pascale CossartUnit des Interactions Bactries-CellulesINSERM U604Institut Pasteur75724 ParisFrance

Michael CottaUSDA-ARS North Regional Research

CenterPeoria, IL 61604-3902USA

Ronald L. CrawfordFood Research CenterUniversity of IdahoMoscow, ID 83844-1052USA

Cecil S. CumminsDepartment of Anaerobic MicrobiologyVirginia Polytechnic Institute and State

UniversityBlacksburg, VA 24061USA

Heribert CypionkaInstitut fr Chemie und Biologie des MeeresFakultt 5, Mathematik und

NaturwissenschaftenUniversitt OldenburgD-26111 OldenburgGermany

Milton S. da CostaM. Fernanda NobreCentro de Neurocincias e Biologia CelularDepartamento de ZoologiaUniversidade de Coimbra3004-517 CoimbraPortugal

Rolf DanielDepartment of General MicrobiologyInstitute of Microbiology and Genetics37077 GttingenGermany

Seana DavidsonUniversity of WashingtonCivil and Environmental EngineeringSeattle, WA 98195-2700USA

Scott C. DawsonDepartment of Molecular and Cellular

BiologyUniversity of California-BerkeleyBerkeley, CA 94720USA

Dirk de BeerMax-Planck-Institute for Marine MicrobiologyD-28359 BremenGermany

Jan A.M. de BontDepartment of Food ScienceAgricultural University6700 EV WageningenThe Netherlands

Maria H. DeinemaLaboratory of MicrobiologyAgricultural University6703 CT WageningenThe Netherlands

Jozef de LeyLaboratorium voor Microbiologie en

Microbile GeneticaRijksuniversiteit GhentB-9000 GhentBelgium

Edward F. DeLongScience ChairMonterey Bay Aquarium Research InstituteMoss Landing, CA 95039USA

xxxiv Contributors

Arnold L. DemainDepartment of BiologyMassachusetts Institute of TechnologyCambridge, MA 02139USA

Uwe DeppenmeierDepartment of Biological Sciences University of WisconsinMilwaukee, WI 53202USA

Paul de VosDepartment of Biochemistry, Physiology and

MicrobiologyUniversiteit GentB-9000 GentBelgium

Luc DevrieseFaculty of Veterinary MedicineB982 MerelbekeBelgium

Floyd E. DewhirstForsyth Dental Center140 FenwayBoston, MA 02115USA

Leon M. T. DicksDepartment of MicrobiologyUniversity of StellenboschZA-7600 StellenboschSouth Africa

Michael P. DoyleCollege of Agricultural and Environmental

SciencesCenter for Food Safety and Quality

EnhancementUniversity of GeorgiaGriffin, GA 30223-1797USA

Harold L. DrakeDepartment of Ecological MicrobiologyBITOEK, University of BayreuthD-95440 BayreuthGermany

Patrick R. DuganIdaho National Engineering LaboratoryEG & G IdahoIdaho Falls, ID 83415USA

Paul V. DunlapDepartment of MolecularCellular and Developmental BiologyUniversity of MichiganAnn Arbor, MI 48109-1048USA

Olivier DussurgetUnit des Interactions Bactries-CellulesINSERM U604Institut Pasteur75724 ParisFrance

Martin DworkinUniversity of Minnesota Medical SchoolDepartment of MicrobiologyMinneapolis, MN 55455USA

Jrgen EberspcherInstitut fur MikrobiologieUniversitat HohenheimD-7000 Stuttgart 70Germany

Paul H. EdelsteinDepartment of Pathology and Laboratory

MedicineUniversity of Pennsylvania Medical

CenterPhiladelphia, PA 19104-4283USA

Wolfgang EderLehrstuhl fr MikrobiologieUniversitt Regensburg93053 RegensburgGermany

Karen ElkinsCBER/FDARockville, MD 20852USA

Craig D. EllermeierDepartment of MicrobiologyUniversity of IllinoisUrbana, IL 61801andDepartment of Molecular and Cellular

BiologyHarvard UniversityCambridge, MA 02138USA

Contributors xxxv

Lyudmila I. EvtushenkoAll-Russian Collection of MicroorganismsInstitute of Biochemistry and Physiology of the

Russian, Academy of SciencesPuschinoMoscow Region, 142290Russia

Takayuki EzakiBacterial DepartmentGifu University Medical School40 TsukasaMachi Gifu CityJapan

Solly FaineMonash UniversityFaculty of Medicine, Nursing and Health

SciencesDepartment of MicrobiologyClayton CampusVictoria, 3800Australia

J. J. Farmer, IIICenter for Infectious DiseasesCenters for Disease ControlAtlanta, GA 30333USA

W. Edmund FarrarDepartment of MedicineMedical University of South CarolinaCharleston, SC 29425USA

Mariano E. Fernandez MiyakawaCalifornia Animal Health and Food Safety

LaboratoryUniversity of California, DavisSan Bernardino, CA 92408USA

Doran L. FinkEdward Mallinckrodt Department of Pediatrics

and Department of Molecular MicrobiologyWashington University School of MedicineSt. Louis, Missouri 63110USA

Jacqueline FletcherDepartment of Entomology and Plant

PathologyOklahoma State UniversityStillwater, OKUSA

Robert ForsterBio-Products and Bio-Processes ProgramAgriculture and Agri-Food CanadaLethbridge Research CentreLethbridge T1J 4B1Canada

M. Pilar FrancinoEvolutionary Genomics DepartmentDOE Joint Genome InstituteWalnut Creek, CA 94598USA

Charles M. A. P. FranzInstitute of Hygiene and ToxicologyBFELD-76131 KarlsruheGermany

David N. FredricksVA Palo Alto Healthcare SystemPalo Alto, CA 94304USA

J. K. FredricksonPacific Northwest National LaboratoryRichland, Washington 99352USA

Brbel FriedrichInstitut fr Biologie/MikrobiologieHomboldt-Universitt zu BerlinChaussesstr. 117D-10115 BerlinGermany

Dagmar FritzeDeutsche Sammlung von MikroorganismenD-3300 Braunschweig-StockheimGermany

John A. FuerstDepartment of Microbiology and

ParasitologyUniversity of QueenslandBrisbaneQueensland 4072Australia

Hiroshi FukushimaPublic Health Institute of Shimane

Prefecture582-1 Nishihamasada, MatsueShimane 690-0122Japan

xxxvi Contributors

Jean-Louis GarciaLaboratoire ORSTOM de Microbiologie des

AnarobiesUniversit de ProvenceCESB-ESIL13288 MarseilleFrance

Ferran Garcia-PichelAssociate ProfessorArizona State UniversityTempe, AZ 85281USA

Arnold GeisInstitut fr MikrobiologieBundesanstalt fr MilchforschungD-24121 KielGermany

Caroline Attardo GencoDepartment of MedicineSection of Infectious Diseases

and Department of MicrobiologyBoston University School of MedicineBoston, MA 02118USA

Yves GermaniInstitut PasteurUnit Pathognie Microbienne MolculaireandRseau International des Instituts PasteurParis 15France

Frank C. GibsonDepartment of MedicineSection of Infectious Diseasesand Department of MicrobiologyBoston University School of MedicineBoston, MA 02118USA

Monique GillisLaboratorium voor MikrobiologieUniversiteit GentB-9000 GentBelgium

Stephen GiovannoniDepartment of MicrobiologyOregon State UniversityCorvallis, OR 97331USA

Frank Oliver GlcknerMax-Planck-Institut fr Marine MikrobiologieD-28359 BremenGermany

Ulf B. GbelInstitut fr Mikrobiologie und HygieneUniversitaetsklinikum ChariteacuteHumboldt-Universitaet zu BerlinD-10117 BerlinGermany

Jos M. GonzlezDepartment de Microbiologia y Biologia

CelularFacultad de FarmaciaUniversidad de La Laguna38071 La Laguna, TenerifeSPAIN

Michael GoodfellowSchool of BiologyUniverstiy of NewcastleNewcastle upon Tyre NE1 7RUUK

Friedrich GtzFacultt fr BiologieInstitut fr Microbielle GenetikUniversitt TbingenD-72076 TbingenGermany

Hans-Dieter GrtzDepartment of ZoologyBiologisches InstitutUniversitt StuttgartD-70569 StuttgartGermany

Gerhard GottschalkInstitut fr Mikrobiologie und GenetikGeorg-August-Universitt GttingenD-37077 GttingenGermany

P. H. GrahamDepartment of Soil, Water, and ClimateSt. Paul, MN 55108USA

Paul A. GranatoDepartment of Microbiology and ImmunologyState University of New York Upstate Medical

UniversitySyracus, NY 13210USA

Peter N. GreenNCIMB LtdAB24 3RY AberdeenUK

Contributors xxxvii

James R. GreenwoodBio-Diagnostics LaboratoriesTorrance, CA 90503USA

Francine GrimontUnite 199 INSERMInstitut Pasteur75724 ParisFrance

Patrick A. D. GrimontInstitut Pasteur75724 ParisFrance

Roland GrossInstitut fr MikrobiologieJohann Wolfgang Goethe-UniversittFrankfurt am MainGermany

Ji-Dong GuLaboratory of Environmental ToxicologyDepartment of Ecology & BiodiversityandThe Swire Institute of Marine ScienceUniversity of Hong KongHong Kong SARP.R. ChinaandEnvironmental and Molecular MicrobiologySouth China Sea Institute of OceanographyChinese Academy of SciencesGuangzhou 510301P.R. China

Franoise GuinetLaboratoire des YersiniaInstitut Pasteur75724 ParisFrance

Michael GurevitzDepartment of BotanyLife Sciences InstituteTel Aviv UniversityRamat Aviv 69978Israel

H. M. HafezInstitute of Poultry DiseasesFree University BerlinBerlinGerman

Auli HaikaraVTT BiotechnologyTietotie 2, EspooFinland

Walter P. HammesInstitute of Food TechnologyUniversitt HohenheimD-70599 StuttgartGermany

Satoshi HanadaResearch Institute of Biological ResourcesNational Institute of Advanced Industrial

Science and Technology (AIST)Tsukuba 305-8566Japan

Hans H. HanertInstitut fr MikrobiologieTechnische Univeristt BraunschweigD-3300 BraunschweigGermany

Michael HannigLehrstuhl fr MikrobiologieUniversitt RegensburgD-93053 RegensburgGermany

Theo A. HansenMicrobial Physiology (MICFYS)Groningen UniversityRijksuniversiteit GroningenNL-9700 AB GroningenThe Netherlands

Jeremy M. HardieDepartment of Oral MicrobiologySchool of Medicine & DentistryLondon E1 2ADUK

Timothy HarrahBioengineering CenterTufts UniversityMedford, MA 02155USA

Anton HartmannGSF-National Research Center for

Environment and HealthInstitute of Soil EcologyRhizosphere Biology DivisionD-85764 Neuherberg/MuenchenGermany

Sybe HartmansDepartment of Food ScienceAgricultural University Wageningen6700 EV WageningenThe Netherlands

xxxviii Contributors

Patricia HartzellDepartment of Microbiology, Molecular

Biology, and BiochemistryUniversity of IdahoMoscow, ID 83844-3052USA

Sydney M. HarveyNichols Institute Reference Laboratories32961 Calle PerfectoSan Juan Capistrano, CA 92675USA

John P. HaysDepartment of Medical Microbiology and

Infectious DiseasesErasmus MC3015 GD RotterdamThe Netherlands

Reiner HedderichMax Planck Institute fr Terrestriche

MikrobiologieD-35043 MarburgGermany

Brian P. HedlundDepartment of Biological SciencesUniversity of Nevada, Las VegasLas Vegas, NV 89154-4004USA

Robert A. HeinzenDepartment of Molecular BiologyUniversity of WyomingLaramie, WY 82071-3944USA

Ilkka HelanderVTT BiotechnologyTietotie 2, EspooFinland

H. Ernest HemphillDepartment of BiologySyracuse UniversitySyracuse, NY 13244USA

Christian HertelInstitute of Food TechnologyUniversitt HohenheimD-70599 StuttgartGermany

Robert B. HespellNorthern Regional Research Center, ARSUS Department of AgriculturePeoria, IL 61604USA

F. W. Hickman-BrennerCenter for Infectious DiseasesCenters for Disease ControlAtlanta, GA 30333USA

Donald C. HildebrandDepartment of Plant PathologyUniversity of California-BerkeleyBerkeley, CA 94720USA

Gregory HinkleDepartment of BotanyUniversity of MassachusettsAmherst, MA 01003USA

K. H. HinzClinic for PoultrySchool of Veterinary MedicineD-30559 HannoverGermany

Peter HirschInstitut fr Allgemeine MikrobiologieUniversitt KielD-2300 KielGermany

Tor HofstadDepartment of Microbiology and

ImmunologyUniversity of BergenN-5021 BergenNorway

Michael J. HohnLehrstuhl fr MikrobiologieUniversitt RegensburgD-93053 RegensburgGermany

Barry HolmesCentral Public Health LaboratoryNational Collection of Type CulturesLondon NW9 5HTUK

Wilhelm H. HolzapfelFederal Research Centre of NutritionInstitute of Hygiene and ToxicologyD-76131 KarlsruheGermany

Contributors xxxix

Harald HuberLehrstuhl fr MikrobiologieUniversitt RegensburgD-93053 RegensburgGermany

Robert HuberLehrstuhl fr MikrobiologieUniversitt RegensburgD-93053 RegensburgGermany

Celia J. HugoDepartment of Microbial, Biochemical and

Food BiotechnologyUniversity of the Free StateBloemfonteinSouth Africa

Meredith HullarUniversity of WashingtonSeattle, WAUSA

Thomas HurekLaboratory of General MicrobiologyUniversity Bremen28334 BremenGermany

Johannes F. ImhoffMarine MikrobiologieInstitut fr Meereskunde an der Universitt

KielD-24105 KielGermany

Ralph IsbergDepartment of Molecular Biology and

MicrobiologyTufts University School of MedicineBoston, MA 02111USA

Elena P. IvanovaSenior Researcher in BiologyLaboratory of MicrobiologyPacific Institute of Bioorganic Chemistry of the

Far-Eastern Branch of the Russian Academyof Sciences

690022 VladivostokRussia

Rainer Jaenicke6885824 Schwalbach a. Ts.GermanyandInstitut fr Biophysik und Physikalische

BiochemieUniversitt RegensburgRegensburgGermanyandSchool of CrystallographyBirbeck CollegeUniversity of LondonLondon, UK

J. Michael JandaMicrobial Diseases LaboratoryDivision of Communicable Disease ControlCalifornia Department of Health ServicesBerkeley, CA 94704-1011USA

Holger W. JannaschWoods Hole Oceanographic InstitutionWoods Hole, MA 02543USA

Christian JeanthonUMR CNRS 6539LEMARInstitut Universitaire Europeen de la MerTechnopole Brest Iroise29280 PlouzaneFrance

Cheryl JenkinsDepartment of MicrobiologyUniversity of WashingtonSeattle, WA 98195USA

John L. JohnsonDepartment of Anaerobic MicrobiologyVirginia Polytechnic Institute and State

UniversityBlacksburg, VA 24061USA

Dorothy JonesDepartment of MicrobiologyUniversity of Leicester, School of MedicineLancaster LE1 9HNUK

xl Contributors

Piet J. JoosteDepartment of Biotechnology and Food

TechnologyTshwane University of TechnologyPretoria 0001South Africa

Edouard JurkevitchDepartment of Plant Pathology and

MicrobiologyFaculty of AgricultureFood & Environmental Quality ServicesThe Hebrew University76100 RehovotIsrael

Clarence I. KadoDepartment of Plant PathologyUniversity of California, DavisDavis, CA 95616-5224USA

Dale KaiserDepartment of BiochemistryStanford University School of MedicineStanford, CA 94305-5329USA

Murat V. KalayogluDepartment of Medical Microbiology and

ImmunologyUniversity of WisconsinMadisonMadison, WI 53706USA

Peter KmpferInstitut fr Angewandte MikrobiologieJustus Liebig-UniversittD-35392 GieenGermany

David KaplanDepartment of Chemcial and Biological

EngineeringTufts UniversityMedford, MA 02115USA

Yoshiaki KawamuraDepartment of MicrobiologyRegeneration and Advanced Medical

ScienceGifu University Graduate School of

MedicineGifu 501-1194Japan

Ronald M. KeddieCraigdhuFortroseRoss-shire IV 10 8SSUK

Donovan P. KellyUniversity of WarwickDepartment of Biological SciencesCV4 7AL CoventryUK

Melissa M. KendallDepartment of BiologyPortland State UniversityPortland, OR 97207-0751USA

Karel KerstersLaboratorium voor MikrobiologieDepartment of BiochemistryPhysiology and MicrobiologyUniversiteit GentB-9000 GentBelgium

Nadia KhelefUnit des Interactions Bactries-CellulesINSERM U604Institut Pasteur75724 ParisFrance

Kumiko Kita-TsukamotoOcean Research InstituteUniversity of TokyoTokyo 164Japan

Oliver KlimmekJohann Wolfgang Goethe-Universitt

FrankfurtInstitut fr MikrobiologieD-60439 FrankfurtGermany

Wesley E. KloosDepartment of GeneticsNorth Carolina State UniversityRaleigh, NC 27695-7614USA

Miloslav KocurCzechoslovak Collection of MicroorganismsJ.E. Purkyne University662 43 BrnoCzechoslovakia

Contributors xli

Paul KolenbranderNational Institute of Dental ResearchNational Institute of HealthBethesda, MD 20892-4350USA

Kazuo KomagataLaboratory of General and Applied

MicrobiologyDepartment of Applied Biology and

ChemistryFaculty of Applied BioscienceTokyo University of AgricultureTokyo, Japan

Hans-Peter KoopsInstitut fr Allgemeine BotanikAbteilung MikrobiologieUniversitt HamburgD-22069 HamburgGermany

Noel R. KriegDepartment of BiologyVirginia Polytechnic InstituteBlacksburg, VA 24061-0406USA

Achim KrgerInstitut fr MikrobiologieBiozentrum NiederurselD-60439 Frankfurt/MainGermany

Reiner Michael KroppenstedtDeutsche Sammlung von Mikroorganismen

und ZellkulturenD-3300 BraunschweigGermany

Terry Ann KrulwichDepartment of BiochemistryMount Sinai School of MedicineNew York, NY 10029USA

J. Gijs KuenenDepartment of BiotechnologyDelft University of Technology2628BC DelftThe Netherlands

Daisy A. KuhnDepartment of BiologyCalifornia State UniversityNorthridge, CA 91330USA

Hidehiko KumagaiDivision of Applied SciencesGraduate School of AgricultureKyoto UniversityKitashirakawa606 8502 KyotoJapan

Barbara N. KunkelDepartment of BiologyWashington UniversitySt. Louis, MO 63130USA

Kirsten KselDepartment of Ecological MicrobiologyBITOEK, University of BayreuthD-95440 BayreuthGermany

David P. LabedaMicrobial Genomics and Bioprocessing

Research UnitNational Center for Agricultural Utilization

ResearchAgricultural Research ServiceU.S. Department of AgriculturePeoria, IL 61604USA

Edward T. LallyLeon Levy Research Center for Oral BiologyUniversity of PennsylvaniaPhiladelphia, Pennsylvania, 19104-6002USA

Bart LambertPlant Genetic Systems N.V.J. Plateaustraat 22B-9000 GhentBelgium

Raphael LamedDepartment of Molecular Microbiology and

BiotechnologyGeorge S. Wise Faculty of Life SciencesTel Aviv UniversityRamat Aviv 69978Israel

Giancarlo LanciniConsultant, Vicuron Pharmaceutical21040 Gerenzano (Varese)Italy

Jan W. M. la RivireInstitut fr MikrobiologieUniversitt GttingenD-3400 GttingenGermany

xlii Contributors

Jared R. LeadbetterEnvironmental Science and EngineeringCalifornia Institute of TechnologyPasadena, CA 91125-7800USA

Donald J. LeBlancID GenomicsPharmacia CorporationKalamazoo, MI 49001USA

Marc LecuitUnit des Interactions Bactries-CellulesINSERM U604Institut Pasteur75724 ParisFrance

Adrian LeeSchool of Microbiology & ImmunologyUniversity of New South WalesSydney, New South Wales2052 Australia

Natuschka LeeLehrstuhl fr MikrobiologieTechnische Universitt MnchenD-85350 FreisingGermany

Susan LeschineDepartment of MicrobiologyUniversity of MassachusettsAmherst, MA 01003-5720USA

Na (Michael) LiDivision of BiostatisticsSchool of Public HealthUniversity of MinnesotaMinneapolis, MN 55455USA

Mary E. LidstromDepartment of Chemical EngineeringUniversity of WashingtonSeattle, WA 98195USA

Wolfgang LieblInstitut fr Mikrobiologie und GenetikGeorg-August-UniversittD-37077 GttingenGermany

Franz LingensInstitut fur MikrobiologieUniversitat HohenheimD-7000 Stuttgart 70Germany

Puspita LisdiyantiLaboratory of General and Applied

MicrobiologyDepartment of Applied Biology and

ChemistryFaculty of Applied BioscienceTokyo University of AgricultureTokyo, Japan

Derek LovleyDepartment of MicrobiologyUniversity of MassachusettsAmherst, MA 01003USA

Wolfgang LudwigLehrstuhl fr MikrobiologieTechnische Universitt MnchenD-85350 FreisingGermany

David LyerlyTechLab, Inc.Corporate Research CenterBlacksburg VA 24060-6364USA

Janet I. MacinnesUniversity of GuelphGuelph N1G 2W1Canada

Michael T. MadiganDepartment of MicrobiologyMailcode 6508Southern Illinois UniversityCarbondale, IL 62901-4399USA

Luis Angel MaldonadoSchool of BiologyUniversidad Nacional Autonoma de Mexico

(UNAM)Instituto de Ciencias del Mar y LimnologiaCiudad Universitaria CP04510 Mexico DFMexico

Jim ManosThe University of Maryland Biotechnology

InstituteCenter of Marine BiotechnologyBaltimore, MD 21202

Lynn MargulisDepartment of BotanyUniversity of MassachusettsAmherst, MA 01003USA

Contributors xliii

Kevin C. MarshallSchool of MicrobiologyUniversity of New South WalesKensingtonNew South Wales 2033Australia

Esperanza Martinez-RomeroCentro de Investigacion sobre Fijacion de

NitrogenoCuernavaca MorMexico

Vitor A. P. Martins dos SantosGesellschaft fr Biotechnologische ForschungDivision of MicrobiologyBraunschweig D-38124Germany

Vega MasignaniIRIS, Chiron SpA53100 SienaItaly

Paola MattarelliIstituto di Microbiologia Agraria40126 BolognaItaly

Carola MatthiesDepartment of Ecological MicrobiologyBITOEK, University of BayreuthD-95440 BayreuthGermany

Ann G. MatthysseDepartment of BiologyUniversity of North CarolinaChapel Hill, NC 27599USA

Megan E. McBeeBiological Engineering DivisionMassachusetts Institute of TechnologyCambridge, MAUSA

Bruce A. McClaneDepartment of Molecular Genetics and

BiochemistryUniversity of Pittsburgh School of MedicinePittsburgh, PA 15261USA

Zoe P. McKinessDepartment of Organic and Evolutionary

BiologyHarvard UniversityCambridge, MA 02138USA

Ulrich MelcherDepartment of Biochemistry and Molecular

BiologyOklahoma State UniversityStillwater, OKUSA

Jianghong MengNutrition and Food ScienceUniversity of MarylandCollege Park, MD 20742-7521USA

Valery V. MikhailovPacific Institute of Bioorganic ChemistryFar-Eastern Branch of the Russian Academy of

Sciences690022 VladivostokRussia

Melissa B. Miller, Ph.D.Department of Pathology and Laboratory

MedicineUniversity of North Carolina at Chapel HillChapel Hill, NC 27599USA

Michael F. MinnickDivision of Biological SciencesUniversity of MontanaMissoula, MT 59812-4824USA

Ralph MitchellLaboratory of Microbial EcologyDivision of Engineering and Applied

SciencesHarvard UniversityCambridge, MA 02138USA

Cesare MontecuccoProfessor of General PathologyVenetian Institute for Molecular Medicine35129 PadovaItaly

Edward R. B. MooreThe Macaulay InstituteEnvironmental Sciences GroupAberdeen AB158QHUKandCulture Collection University of Gteborg

(CCUG)Department of Clinical BacteriologyUniversity of GteborgGteborg SE-416 43Sweden

xliv Contributors

Nancy A. MoranUniversity of ArizonaDepartment of Ecology and Evolutionary

BiologyTucson, AZ 85721USA

Edgardo MorenoTropical Disease Research Program

(PIET)Veterinary School, Universidad NacionalCosta Rica

Ignacio MoriynDepartment of MicrobiologyUniversity of Navarra32080 PamplonaSpain

Annette MoterInstitut fr Mikrobiologie und HygieneUniversitaetsklinikum ChariteacuteHumboldt-Universitt zu BerlinD-10117 BerlinGermany

Eppe Gerke MulderLaboratory of MicrobiologyAgricultural University6703 CT WageningenThe Netherlands

Yasuyoshi NakagawaBiological Resource Center (NBRC)Department of BiotechnologyNational Institute of Technology and

EvaluationChiba 292-0818Japan

Francis NanoDepartment of Biochemistry & MicrobiologyUniversity of VictoriaVictoria V8W 3PGCanada

Kenneth H. NealsonDepartment of Earth SciencesUniversity of Southern CaliforniaLos Angeles, CA 90033USA

Douglas C. NelsonDepartment of MicrobiologyUniversity of California, DavisDavis, CA 95616USA

Klaus NeuhausDepartment of Pediatrics, Infection, Immunity,

and Infectious Diseases UnitWashington University School of MedicineSt. Louis, MO 63110USA

Diane G. NewellVeterinary Laboratory Agency (Weybridge)AddlestoneNew HawSurrey KT1 53NBUK

Irene L. G. Newton Department of Organismic and Evolutionary

BiologyHarvard UniversityCambridge, MA 02138USA

S.A. Nierzwicki-BauerDepartment of BiologyRensselaer Polytechnic InstituteTroy, NYUSA

M. Fernanda NobreDepartamento de ZoologiaUniversidade de Coimbra3004-517 CoimbraPortugal

Philippe NormandLaboratoire dEcologie MicrobienneUMR CNRS 5557Universit Claude-Bernard Lyon 169622 VilleurbanneFrance

Steven J. NorrisDepartment of Pathology and Laboratory

Medicine and Microbiology and MolecularGenetics

University of Texas Medical Scvhool atHouston

Houston, TX 77225USA

Howard OchmanDepartment of Biochemistry and Molecular

BiophysicsUniversity of ArizonaTucson, AZ 85721USA

Gary E. OertliMolecular and Cellular BiologyUnviersity of WashingtonSeattle, WA 98195-7275USA

Contributors xlv

Itzhak OfekDepartment of Human MicrobiologyTel Aviv University69978 Ramat AvivIsrael

Bernard OllivierLaboratoire ORSTOM de Microbiologie des

AnarobiesUniversit de ProvenceCESB-ESIL13288 MarseilleFrance

Scott L. ONeillDepartment of Epidemiology and Public

HealthYale University School of MedicineNew Haven, CT 06520-8034USA

Aharon OrenDivision of Microbial and Molecular

EcologyThe Institute of Life SciencesandMoshe Shilo Minerva Center for Marine

BiogeochemistryThe Hebrew University of Jerusalem91904 JerusalemIsrael

Jani L. ORourkeSchool of Microbiology and ImmunologyUniversity of New South WalesSydney, NSW 2052Australia

Jrg OvermannBereich MikrobiologieDepartment Biologie ILudwig-Maximilians-Universitt MnchenD-80638 MnchenGermany

Norman R. PaceDepartment of Molecular, Cellular and

Developmental BiologyUnversity of ColoradoBoulder, CO 80309-0347USA

Norberto J. PalleroniRutgers UniversityDepartment of Biochemistry and

MicrobiologyNew Brunswick 08901-8525New JerseyUSA

Bruce PanilaitisDepartment of Chemcial and Biomedical

EngineeringTufts UniversityMedford, MA 02155USA

Nickolas PanopoulosDepartment of Plant PathologyUniversity of California-BerkeleyBerkeley, CA 94720USA

Yong-Ha ParkKorean Collection for Type CulturesKorea Research Institute of Bioscience &

BiotechnologyTaejon 305-600Korea

Matthew R. ParsekUniversity of IowaIowa City, IA 52242USA

Bruce J. PasterDepartment of Molecular GeneticsThe Forsyth InstituteBoston, MA 02115USA

Jerome J. Perry3125 Eton RoadRaleigh, NC 27608-1113USA

Jeannette PhamThe CDS Users GroupDepartment of MicrobiologySouth Eastern Area Laboratory ServicesThe Prince of Wales Hospital CampusRandwick NSW 2031Australia

Harvey M. PickrumProctor and Gamble CompanyMiami Valley LaboratoriesCincinnatti, OH 45239USA

Dietmar H. PieperGesellschaft fr Biotechnologische ForschungDivision of MicrobiologyBraunschweig D-38124Germany

Beverly K. PiersonBiology DepartmentUniversity of Puget SoundTacoma, WA 98416USA

xlvi Contributors

Mariagrazia PizzaIRIS, Chiron SpA53100 SienaItaly

Jeanne S. PoindexterDepartment of Biological SciencesBarnard College/Columbia UniversityNew York, NY 10027-6598USA

Andreas Pommerening-RserInstitut fr Allgemeine BotanikAbteilung MikrobiologieUniversitt HamburgD-22069 HamburgGermany

Michel R. PopoffUnit des Toxines MicrobiennesInstitut Pasteur75724 ParisFrance

Anton F. PostDepartment of Plant and Environmental

SciencesLife Sciences InstituteHebrew UniversityGivat Ram91906 JerusalemIsrael

Bruno PotLaboratorium voor Microbiologie en

Microbile GeneticaRijksuniversiteit GhentB-9000 GhentBelgium

David PrangishviliDepartment of MikrobiologyUniversitity of RegensburgD-93053 RegensburgGermany

Helmut PrauserDSMZ-German Collection of

Microorganisms and Cell Cultures GmbHD-38124 BraunschweigGermany

Michael PrenticeBarts and the London School of Medicine and

DentistryDepartment of Medical MicrobiologySt. Bartholomews HospitalLondon EC1A 7BEUK

Ulrike PurkholdLehrstuhl fr MikrobiologieTechnische Universitt MnchenD-80290 MunichGermany

Wim J. QuaxDepartment of Pharmaceutical BiologyUniversity of GroningenGroningen 9713AVThe Netherlands

Erika Teresa QuintanaSchool of BiologyUniverstiy of NewcastleNewcastle upon Tyne NE1 7RUUK

Ralf RabusMax-Planck-Institut fr Marine MikrobiologieD-28359 BremenGermany

Reinhard RachelLehrstuhl fr MikrobiologieUniversitt RegensburgD-93053 RegensburgGermany

A. N. RaiBiochemistry DepartmentNorth-Eastern Hill UniversityShillong 793022India

Frederick A. RaineyDepartment of Biological SciencesLouisiana State UniversityBaton Rouge, LA 70803USA

Juan-Luis RamosEstacin Experimental del ZaidinDepartment of Biochemistry and Molecular

and Cell Biology of PlantsGranada E-18008Spain

Rino RappuoliIRIS Chiron Biocine ImmunobiologieResearch Institute Siena53100 SienaItaly

Shmuel RazinDepartment of Membrane and Ultrastructure

ResearchThe Hebrew University-Hadassah Medical

SchoolJerusalem 91120

Contributors xlvii

Annette C. ReboliDepartment of MedicineHahneman University HospitalPhiladelphia, PA 19102USA

David W. ReedBiotechnology DepartmentIdaho National Engineering and

Environmental Laboratory (INEEL)Idaho Falls, ID 83415-2203USA

Hans ReichenbachGBFD-3300 BraunschweigGermany

Barbara Reinhold-HurekLaboratory of General MicrobiologyUniversitt BremenLaboratorium fr Allgemeine MikrobiologieD-28334 BremenGermany

Markus RieglerIntegrative Biology SchoolUniversity of QueenslandAustralia

Monica RileyMarine Biological LabWoods Hole, MA 02543USA

Lesley A. RobertsonDepartment of BiotechnologyDelft University of Technology2628 BC DelftThe Netherlands

Edson R. RochaDepartment of Microbiology and ImmunologyEast Carolina UniversityGreenville, NC 27858-4354USA

Palmer RogersDepartment of MicrobiologyUniversity of Minnesota Medical SchoolMinneapolis, MN 55455USA

Lyudmila A. RomanenkoSenior Researcher in BiologyLaboratory of MicrobiologyPacific Institute of Bioorganic Chemistry of the

Far-Eastern Branch of the Russian Academyof Sciences

Vladivostoku, 159Russia

M. F. RominePacific Northwest National LaboratoryRichland, WA 99352USA

Eliora Z. RonDepartment of Molecular Microbiology and

BiotechnologyThe George S. Wise Faculty of Life SciencesTel Aviv UniversityRamat Aviv69978 Tel AvivIsrael

Julian I. RoodAustralian Bacterial Pathogenesis ProgramDepartment of MicrobiologyMonash UniversityVictoria 3800Australia

Eugene RosenbergDepartment of Molecular Microbiology &

BiotechnologyTel Aviv UniversityRamat Aviv69978 Tel AvivIsrael

Frank RosenzweigDivision of Biological SciencesUniversity of MontanaMissoula, MT 59812-4824USA

Ornella RossettoCentro CNR Biomembrane and Dipartimento

di Scienze Biomediche35100 PadovaItaly

Michael J. SadowskyDepartment of Soil, Water, and ClimateUniversity of MinnesotaMinneapolis, MN 55455USA

Hermann SahmInstitut BiotechnologieForschungszentrum JlichD-52425 JlichGermany

Joseph W. St. Gemer, IIIDepartment of Molecular MicrobiologyWashington University School of MedicineSt. Louis, MO 63110USA

xlviii Contributors

James E. SamuelDepartment of Medical Microbiology and

ImmunologyCollege of MedicineTexas A&M University System Health Science

CenterCollege Station, TX, 77843-1114USA

Philippe J. SansonettiUnit de PathognieMicrobienne MolculaireInstitut Pasteur75724 ParisFrance

Scott R. SantosDepartment of Biochemistry & Molecular

BiophysicsUniversity of ArizonaTucson, AZ 85721USA

Beatrice SaviolaDepartments of Molecular Microbiology and

ImmunologyJohns Hopkins School of Hygiene and Public

HealthBaltimore, MD 21205-2105USA

Klaus P. SchaalInstitut fr MedizinischeMikrobiologie und ImmunologieUniversitt BonnD-53105 BonnGermany

David B. SchauerBiological Engineering Division and Division

of Comparative MedicineMassachusetts Institute of TechnologyCambridge, MA 02139USA

Siegfried SchererDepartment fr Biowienschaftliche

GrundlagenWienschaftszentrum WeihenstephanTechnische Universitt MnchenD-85354 Freising, Germany

Bernhard SchinkFakultt fr Biologie der Universitt KonstanzD-78434 KonstanzGermany

Hans G. SchlegelInstitut fr Mikrobiologie der Gessellschaft

fr Strahlen- und Umweltforschung mbHGttingenGermany

Karl-Heinz SchleiferLehrstruhl fr MikrobiologieTechnische Universitt MnchenD-85354 FreisingGermany

Heinz SchlesnerInstitut fr Allgemeine MikrobiologieChristian Albrechts UniversittD-24118 KielGermany

Michael SchmidGSF-Forschungszentrum fr Umwelt und

Gesundheit GmbHInstitut fr BodenkologieD-85764 NeuherbergGermany

Jean M. SchmidtDepartment of Botany and MicrobiologyArizona State UniversityTempe, AZ 85287USA

Karin SchmidtInstitut fr MikrobiologieGeorg-August-UniversittD-3400 GttingenGermany

Ruth A. SchmitzUniversity of GttingenD-3400 GttingenGermany

Hildgund SchrempfFB Biologie/ChemieUniversitt Osnabrck49069 OsnabrckGermany

Milton N. SchrothDepartment of Plant PathologyUniversity of California-BerkeleyBerkeley, CA 94720USA

Heide N. SchulzInstitute for MicrobiologyUniversity of HannoverD-30167 HannoverGermany

Contributors xlix

Peter SchumannDSMZ-German Collection of Microorganisms

and Cell Cultures GmbHD-38124 BraunschweigGermany

Arthur SchlerInstitut Botany64287 DarmstadtGermany

Edward SchwartzInstitut fr Biologie/MikrobiologieHomboldt-Universitt zu BerlinD-10115 BerlinGermany

James ScottGeophysical LaboratoryCarnegie Institution of WashingtonWashington, DC 20015USA

Margrethe Haugge SerresMarine Biological LabWoods Hole, MA 02543USA

James P. ShapleighDepartment of MicrobiologyCornell UniversityWing HallIthaca, NY 14853-8101USA

Nathan SharonThe Weizmann Institute of ScienceDepartment of Biological ChemistryIL-76100 RehovothIsrael

Lawrence J. ShimketsDepartment of MicrobiologyThe University of GeorgiaAthens, GA 30602-2605USA

Thomas M. ShinnickCenter for Infectious DiseasesCenters for Disease ControlAtlanta, GA 30333USA

Yuval ShohamDepartment of Food Engineering and

BiotechnologyTechnionIsrael Institute of TechnologyHaifa 32000Israel

Jrg SimonJohann Wolfgang Goethe-Universitt FrankfurtCampus RiedbergInstitute of Molecular BiosciencesMolecular Microbiology and BioenergeticsD-60439 FrankfurtGermany

Michel SimonetDpartment de Pathogense des Maladies

Infectieuses et ParasitairesInstitut de Biologie de Lille59021 LilleFrance

Mikael SkurnikDepartment of Medical BiochemistryUniversity of Turku20520 TurkuFinland

James M. SlauchDepartment of MicrobiologyCollege of MedicineUniversity of IllinoisandChemical and Life Sciences LaboratoryUrbana, IL 61801USA

Ralph A. SlepeckyDepartment of BiologySyracuse UniversitySyracuse, NY 13244USA

C. Jeffrey SmithDepartment of Microbiology and

ImmunologyEast Carolina UniversityGreenville, NC 27858-4354USA

Martin SobierjDepartment of BiologyEnvironmental Science and EngineeringOregon Graduate Institute of Science and

TechnologyPortland State UniversityPortland, OR 97291-1000USA

Pamela A. SokolDepartment of Microbiology and Infectious

DiseasesUniversity of Calgary Health Science CenterCalgary T2N 4N1Canada

l Contributors

Jay V. SolnickDepartment of Interanl Medicine (Infectious

Diseases) and MedicalMicrobiology and ImmunologyUniversity of California, DavisSchool of MedicineDavis, CA 95616USA

Dimitry Yu. SorokinDepartment of BiotechnologyDelft University of Technology2628 BC DelftThe NetherlandsandS.N. Winogradsky Institute of Microbiology117811 MoscowRussia

Georg A. SprengerInstitut BiotechnologieForschungszentrum JlichD-52425 JlichGermany

Stefan SpringDeutsche Sammlung von Mikroorganismen und

ZellkulturenD-38124 BraunschweigGermany

Erko StackebrandtDeutsche Sammlung von Mikroorganismen und

ZellkulturenD-38124 BraunschweigGermany

David A. StahlUniversity of WashingtonSeattle, WAUSA

Donald P. StahlyDepartment of MicrobiologyUniversity of IowaIowa City, IA 52242USA

James T. StaleyDepartment of MicrobiologyUniversity of WashingtonSeattle, WA 98105USA

Alfons J.M. StamsLaboratorium voor MicrobiologieWageningen UniversityNL-6703 CT WageningenThe Netherlands

Thaddeus B. StantonPHFSED Research UnitNational Animal Disease CenterUSDA-ARSAmes, IA 50010USA

Daniel C. SteinDepartment of Cell Biology and Molecular

GeneticsUniversity of MarylandCollege Park, MD 20742USA

Reinhard SternerUniversitaet RegensburgInstitut fuer Biophysik und Physikalische

BiochemieD-93053 RegensburgGermany

Karl O. StetterLehrstuhl fr MikrobiologieUniversitt RegensburgD-93053 RegensburgGermany

Frank J. StewartDepartment of Organic and Evolutionary

BiologyHarvard UniversityCambridge, MA 02138USA

Andreas StolzInstitut fr MikrobiologieUniversitt Stuttgart70569 StuttgartGermany

Daphne L. StonerIdaho National Engineering LaboratoryEG & G IdahoIdaho Falls, ID 83415USA

Paul StoodleyCenter for Biofilm EngineeringMontana State UniversityBozeman, MT 59717-3980USA

James R. SwaffordDepartment of Botany and MicrobiologyArizona State UniversityTempe, AZ 85287USA

Contributors li

Jean SwingsLaboratorium voor MicrobiologieDepartment of BiochemistryPhysiology and MicrobiologyBCCM/LMG Bacteria CollectionUniversiteit GentGentBelgium

Mariko TakeuchiInstitute for FermentationOsaka 532-8686Japan

Ralph TannerUniversity of OklahomaNorman, OK, 73019-0390USA

Andreas TeskeDepartment of Marine SciencesUniversity of North Carolina at Chapel HillChapel Hill, NC 27599USA

Michael TeuberETH-ZentrumLab Food MicrobiologyCH-8092 ZrichSwitzerland

Gabriele TimmermannInstitut fr Allgemeine BotanikAbteilung MikrobiologieUniversitt HamburgD-22069 HamburgGermany

Brian J. TindallDeutsche Sammlung von Mikroorganismen und

ZellkulturenBraunschweig D-38124Germany

Kevin TownerConsultant Clinical ScientistPublic Health LaboratoryUniversity HospitalNottingham NG7 2UHUK

Hans G. TrperInstitut fr Mikrobiologie und BiotechnologieD-53115 BonnGermany

Elaine TuomanenDepartment of Infectious DiseasesSt. Jude Childrens Research HospitalMemphis, TN 38105-2394USA

Francisco A. UzalCalifornia Animal Health and Food Safety

LaboratoryUniversity of California, DavisSan Bernardino, CA 92408USA

Peter Van dammeLaboraroorium voor MicrobiologieFaculteit WetenschappenUniversiteit GentB-9000 GentBelgium

Antonio VentosaDepartment of Microbiology and

ParasitologyFaculty of PharmacyUniversity of Sevilla41012 SevillaSpain

Gernot VobisCentro Regional Universitario BarilocheUniversidad Nacional de ComahueBarioloche 8400, Rio NegroArgentina

Alexander von GraevenitzDepartment of Medical MicrobiologyUniversity of ZrichGH-8028 ZrichSwitzerland

Gnther Wchtershuser80331 MunichGermany

Lawrence P. WackettDepartment of Biochemistry, Molecular

BiologyandBiophysics and Biological Process Technology

InstituteUniversity of MinnesotaSt. Paul, MN, 55108-1030USA

William G. WadeDepartment of MicrobiologyGuys CampusLondon, SE1 9RTUK

Michael WagnerLehrstuhl fr Mikrobielle kologieInstitut fr kologie und NaturschutzUniversitt WienA-1090 ViennaAustria

lii Contributors

David H. WalkerDepartment of PathologyUniversity of Texas Medical BranchGalveston, TX 77555-0609USA

Naomi WardThe Institute for Genomic ResearchRockville, MD 20850USA

Trudy M. WassenaarMolecular Microbiology and Genomics

Consultants55576 ZotzenheimGermany

John B. WaterburyWoods Hole Oceanographic InstitutionWoods Hole, MA 02543USA

Georges WautersUniversit Catholique de LouvainFacult de MdecineUnit de MicrobiologieB-1200 BruxellesBelgium

Astri WayadandeDepartment of Entomology and Plant

PathologyOklahoma State UniversityStillwater, OKUSA

Alison WeissMolecular Genetics, Biology and MicrobiologyUniversity of CincinnatiCincinnati, OH 45267USA

Rodney A. WelchMedical Microbiology and ImmunologyUniversity of WisconsinMadison, WI 53706-1532USA

William B. WhitmanDepartment of MicrobiologyUniversity of GeorgiaAthens, GA 30605-2605USA

Friedrich WiddelMax-Planck-Institut fr Marine MikrobiologieD-28359 BremenGermany

Jrgen WiegelUniversity of GeorgiaDepartment of MicrobiologyAthens, GA 30602USA

Robert A. WhileyQueen Mary, University of LondonLondon E1 4NSUK

Tracy WhilkinsTechLab, Inc.Corporate Research CenterBlacksburg VA 24060-6364USA

Anne WillemsLaboratorium voor MikrobiologieUniversiteit GentB-9000 GentBelgium

Carl R. WoeseDepartment of MicrobiologyUniversity of IllinoisUrbana, IL 61801USA

Ralph S. WolfeDepartment of MicrobiologyUniversity of IllinoisUrbana, IL 61801

Ann P. WoodDivision of Life SciencesKings College LondonLondon WC2R 2LSUK

Donald E. WoodsDepartment of Microbiology and Infectious

DiseasesUniversity of Calgary Health Science CenterCalgary T2N 4N1Canada

B. W. WrenDepartment of Infectious and Tropical

DiseasesLondon School of Hygiene and Tropical

MedicineLondon WC1E 7HTUK

Timothy L. YahrUniversity of IowaIowa City, IA 52242USA

Contributors liii

Atteyet F. YassinInstitut fr MedizinischeMikrobiologie und ImmunologieUniversitt BonnD-53105 BonnGermany

Jung-Hoon YoonKorean Collection for Type CulturesKorea Research Institute of Bioscience and

BiotechnologyYuson, Taejon 305-600Korea

Allan A. YoustenBiology DepartmentVirginia Polytechnic Institute and State

UniversityBlacksburg, VA 24061USA

Xue-Jie YuUniversity of Texas Medical BranchGalveston, TXUSA

Vladimir V. YurkovDepartment of MicrobiologyUniversity of ManitobaWinnipeg R3T 2N2Canada

Georgi A. ZavarzinInstitute of MicrobiologyAcademy of Sciences of the USSR117312 MoscowRussia

Mary Jo ZidwickCargill Biotechnology Development CenterFreshwater BuildingMinneapolis, MN 55440USA

Stephen H. ZinderDepartment of MicrobiologyCornell University272 Wing HallIthaca, NY 14853USA

CHAPTER 1The Archaea: A Personal Overview of the Formative Years

The Archaea: A Personal Overview of the Formative Years

RALPH S. WOLFE

a new scientific truth does not triumph by convinc-ing its opponents and making them see the light, butrather because its opponents eventually die, and a newgeneration grows up that is familiar with it. MaxPlanck

The year 2002 marks the 25th anniversary ofthe discovery of the Archaea. Data to supportthis discovery were presented in the Proceedingsof the National Academy of Science of October1977 (Fox et al., 1977). However, most peoplelearned abo