The Prokaryotes Third Edition The Prokaryotes A Handbook on the Biology of

Third Edition

Volume 1: Symbiotic Associations, Biotechnology, Applied

Martin Dworkin (Editor-in-Chief), Stanley Falkow, Eugene Rosenberg, Karl-Heinz Schleifer, Erko Stackebrandt (Editors) Editor-in-Chief Professor Dr. Martin Dworkin Department of Microbiology University of Minnesota Box 196 University of Minnesota Minneapolis, MN 55455-0312 USA

Editors Professor Dr. Stanley Falkow Professor Dr. Karl-Heinz Schleifer Department of Microbiology Department of Microbiology and Immunology Technical University Munich Stanford University Medical School 80290 Munich 299 Campus Drive, Fairchild D039 Germany Stanford, CA 94305-5124 USA Professor Dr. Erko Stackebrandt DSMZ- German Collection of Professor Dr. Eugene Rosenberg and Cell Cultures GmbH Department of Molecular Microbiology Mascheroder Weg 1b and Biotechnology 38124 Braunschweig Tel Aviv University Germany Ramat-Aviv 69978 Israel

Library of Congress Control Number: 2005928710

ISBN-10: 0-387-25476-5 e-ISBN 0-387-•••••-• Printed on acid-free paper. ISBN-13: 978-0387-25476-0

© 2006 Springer Science+Business Media, Inc. All rights reserved. This work may not be translated or copied in whole or in part without the written permission of the publisher (Springer Science+Business Media, Inc., 233 Spring Street, New York, NY 10013, USA), except for brief excerpts in connection with reviews or scholarly analysis. Use in connection with any form of information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed is forbidden. The use in this publication of trade names, trademarks, service marks, and similar terms, even if they are not identified as such, is not to be taken as an expression of opinion as to whether or not they are subject to proprietary rights.

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987654321 springer.com Preface

Each of the first two editions of The Prokaryotes has referred to the present took a bold step. The first edition, published in era of microbiology as its third golden age—the 1981, set out to be an encyclopedic, synoptic era of “integrative microbiology.” Essentially all account of the world of the prokaryotes—a col- microbiologists now speak a common language. lection of monographic descriptions of the So that the boundaries that previously separated genera of bacteria.The Archaea had not yet been subdisciplines from each other have faded: phys- formalized as a group. For the second edition in iology has become indistinguishable from patho- 1992, the editors made the decision to organize genesis; ecologists and molecular geneticists the chapters on the basis of the molecular phy- speak to each other; biochemistry is spoken by logeny championed by , which all; and—mirabile dictu!—molecular biologists increasingly provided a rational, evolutionary are collaborating with taxonomists. basis for the of the prokaryotes. In But before these molecular dissections of addition, the archaea had by then been recog- complex processes can be effective there must be nized as a phylogenetically separate and distin- a clear view of the organism being studied. And guishable group of the prokaryotes. The two it is our goal that these chapters in The Prokary- volumes of the first edition had by then otes provide that opportunity. expanded to four. The third edition was arguably There is also yet a larger issue. Microbiology the boldest step of all. We decided that the mate- is now confronted with the need to understand rial would only be presented electronically. The increasingly complex processes. And the modus advantages were obvious and persuasive. There operandi that has served us so successfully for would be essentially unlimited space. There 150 years—that of the pure culture studied under would be no restrictions on the use of color illus- standard laboratory conditions—is inadequate. trations. Film and animated descriptions could be We are now challenged to solve problems of made available. The text would be hyperlinked multimembered populations interacting with to external sources. Publication of chapters each other and with their environment under would be seriati—the edition would no longer constantly variable conditions. Carl Woese has have to delay publication until the last tardy pointed out a useful and important distinction author had submitted his or her chapter. Updates between empirical, methodological reductionism and modifications could be made continuously. and fundamentalist reductionism. The former And, most attractively, a library could place its has served us well; the latter stands in the way of subscribed copy on its server and make it avail- our further understanding of complex, interact- able easily and cheaply to all in its community. ing systems. But no matter what kind of synop- One hundred and seventy chapters have thus far tic systems analysis emerges as our way of been presented in 16 releases over a six-year understanding host–parasite relations, ecology, period. The virtues and advantages of the online or multicellular behavior, the understanding of edition have been borne out. But we failed to the organism as such is sine qua non. And in that predict the affection that many have for holding context, we are pleased to present to you the a bound, print version of a book in their hands. third edition of The Prokaryotes. Thus, this print version of the third edition shall accompany the online version. Martin Dworkin We are now four years into the 21st century. Editor-in-Chief Indulge us then while we comment on the chal- lenges, problems and opportunities for microbi- ology that confront us. Contents

Preface v Contributors xxvii

Volume 1 1. Essays in Prokaryotic Biology

1.1 How We Do, Don’t and Should Look at Bacteria and Bacteriology 3 carl r. woese

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

1.3 Defining Taxonomic Ranks 29 erko stackebrandt

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

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

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

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

1.8 Cell-Cell Interactions 221 dale kaiser

1.9 Prokaryotic Genomics 246 b. w. wren

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

1.11 Origin of Life: RNA World versus Autocatalytic Anabolism 275 günter wächtershäuser viii Contents

1.12 Biotechnology and Applied Microbiology 284 eugene rosenberg

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

2. Symbiotic Associations

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

2.2 Symbiotic Associations between Ciliates and Prokaryotes 364 hans-dieter görtz

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

2.4 Symbiotic Associations Between Termites and Prokaryotes 439 andreas brune

2.5 Marine Chemosynthetic Symbioses 473 colleen m. cavanaugh, zoe p. mckiness, irene l.g. newton and frank j. stewart

3. Biotechnology and Applied Microbiology

3.1 Organic Acid and Solvent Production 509 palmer rogers, jiann-shin chen and mary jo zidwick

3.2 Amino Acid Production 754 hidehiko kumagai

3.3 Microbial Exopolysaccharides 764 timothy harrah, bruce panilaitis and david kaplan

3.4 Bacterial Enzymes 775 wim j. quax

3.5 Bacteria in Food and Beverage Production 795 michael p. doyle and jianghong meng

3.6 Bacterial Pharmaceutical Products 810 arnold l. demain and giancarlo lancini

3.7 Biosurfactants 832 eugene rosenberg

3.8 Bioremediation 848 ronald l. crawford Contents ix

3.9 Biodeterioration 862 ji-dong gu and ralph mitchell

3.10 Microbial Biofilms 902 dirk de beer and paul stoodley

Index 937

Volume 2 1. Ecophysiological and Biochemical Aspects

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

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

1.3 The Phototrophic Way of Life 32 jörg overmann and ferrau garcia-pichel

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

1.5 Bacterial Behavior 102 judith armitage

1.6 Prokaryotic Life Cycles 140 martin dworkin

1.7 Life at High Temperatures 167 rainer jaenicke and reinhard sterner

1.8 Life at Low Temperatures 210 siegfried scherer and klaus neuhaus

1.9 Life at High Salt Concentrations 263 aharon oren

1.10 Alkaliphilic Prokaryotes 283 terry ann krulwich

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

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

1.13 Acetogenic Prokaryotes 354 harold l. drake, kirsten küsel and carola matthies x Contents

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

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

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

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

1.18 Hydrocarbon-Oxidizing Bacteria 564 eugene rosenberg

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

1.20 Aerobic Methylotrophic Prokaryotes 618 mary e. lidstrom

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

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

1.23 The Denitrifying Prokaryotes 769 james p. shapleigh

1.24 Dinitrogen-Fixing Prokaryotes 793 esperanza martinez-romero

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

1.26 Magnetotactic Bacteria 842 stefan spring and dennis a. bazylinski

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

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

1.29 The Metabolic Pathways of Biodegradation 956 lawrence p. wackett

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

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

1.32 Bacterial Stress Response 1012 eliora z. ron

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

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

Index 1081

Volume 3 A: Archaea

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

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

3. Sulfolobales 23 harald huber and david prangishvili

4. Desulfurococcales 52 harald huber and karl o. stetter

5. The Order Thermococcales 69 costanzo bertoldo and garabed antranikian

6. The Genus Archaeoglobus 82 patricia hartzell and david reed

7. Thermoplasmatales 101 harald huber and karl o. stetter

8. The Order Halobacteriales 113 aharon oren

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

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

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

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

13. Methanococcales 257 william b. whitman and christian jeanthon

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

15. Phylogenetic and Ecological Perspectives on Uncultured Crenarchaeota and Korarchaeota 281 scott 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 297 erko stackebrandt and peter schumann

1.1.2 The Family Bifidobacteriaceae 322 bruno biavati and paola mattarelli

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

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

1.1.5 The Family Succinivibrionaceae 419 erko stackebrandt and robert hespell

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

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

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

1.1.9 The Genus Actinoplanes and Related Genera 623 gernot vobis

1.1.10 The Family Actinosynnemataceae 654 david p. labeda

1.1.11 The Families Frankiaceae, Geodermatophilaceae, Acidothermaceae and Sporichthyaceae 669 philippe normand Contents xiii 1.1.12 The Family Thermomonosporaceae: Actinocorallia, Actinomadura, Spirillospora and Thermomonospora 682 reiner michael kroppenstedt and michael goodfellow

1.1.13 The Family Streptosorangiaceae 725 michael goodfellow and erika teresa quintana

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

1.1.15 Corynebacterium—Nonmedical 796 wolfgang liebl

1.1.16 The Genus Corynebacterium—Medical 819 alexander von graevenitz and kathryn bernard

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

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

1.1.19 The Genus Mycobacterium—Medical 919 beatrice saviola and william bishai

1.1.20 Mycobacterium leprae 934 thomas m. shinnick

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

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

1.1.23 Renibacterium 972 hans-jürgen busse

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

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

1.1.26 The Family Dermatophilaceae 1002 erko stackebrandt

1.1.27 The Genus Brevibacterium 1013 matthew d. collins

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

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

Index 1115

Volume 4 1. Firmicutes (Gram-Positive Bacteria) 1.2 Firmicutes with Low GC Content of DNA

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

1.2.2 The Genus Streptococcus—Oral 76 jeremy m. hardie and robert a. whiley

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

1.2.4 Streptococcus pneumoniae 149 elaine tuomanen

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

1.2.6 The Genus Enterococcus: Medical Importance 175 donald j. leblanc

1.2.7 The Genus Lactococcus 205 michael teuber and arnold geis

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

1.2.9 Genera Leuconostoc, Oenococcus and Weissella 267 johanna björkroth and wilhelm holzapfel

1.2.10 The Genera Lactobacillus and Carnobacterium 319 walter p. hammes and christian hertel

1.2.11 Listeria monocytogenes and the Genus Listeria 403 nadia khelef, marc lecuit, carmen buchrieser, didier cabanes, olivier dussurget and pascale cossart

1.2.12 The Genus Brochothrix 473 erko stackebrandt and dorothy jones

1.2.13 The Genus Erysipelothrix 488 erko stackebrandt, annette c. reboli and w. edmund farrar Contents xv

1.2.14 The Genus Gemella 507 matthew d. collins

1.2.15 The Genus Kurthia 515 erko stackebrandt, ronald m. keddie and dorothy jones

1.2.16 The Genus Bacillus—Nonmedical 526 ralph a. slepecky and h. ernest hemphill

1.2.17 The Genus Bacillus—Insect Pathogens 559 donald p. stahly, robert e. andrews and allan a. yousten

1.2.18 The Genus Bacillus—Medical 605 w. edmund farrar and annette c. reboli

1.2.19 Genera Related to the Genus Bacillus—Sporolactobacillus, Sporosarcina, Planococcus, Filibacter and Caryophanon 627 dieter claus, dagmar fritze and miloslav kocur

1.2.20 An Introduction to the Family Clostridiaceae 650 juergen wiegel, ralph tanner and fred a. rainey

1.2.21 Neurotoxigenic Clostridia 674 cesare montecucco, ornella rossetto and michel r. popoff

1.2.22 The Enterotoxic Clostridia 693 bruce a. mcclane, francisco a. uzai, mariano e. fernandez miyakawa, david lyerly and tracy wilkins

1.2.23 Clostridium perfringens and Histotoxic Disease 748 julian i. rood

1.2.24 The Genera Desulfitobacterium and Desulfosporosinus: Taxonomy 766 stefan spring and frank rosenzweig

1.2.25 The Genus Desulfotomaculum 782 friedrich widdel

1.2.26 The Anaerobic Gram-Positive Cocci 790 takayuki ezaki, na li and yoshiaki kawamura

1.2.27 The Order Haloanaerobiales 804 aharon oren

1.2.28 The Genus Eubacterium and Related Genera 818 william g. wade

1.2.29 The Genus Mycoplasma and Related Genera (Class Mollicutes) 831 shmuel razin

1.2.30 The Phytopathogenic Spiroplasmas 897 jacqueline fletcher, ulrich melcher and astri wayadande xvi Contents 1.3 Firmicutes with Atypical Cell Walls

1.3.1 The Family Heliobacteriaceae 943 michael t. madigan

1.3.2 Pectinatus, Megasphaera and Zymophilus 957 auli haikara and ilkka helander

1.3.3 The Genus Selenomonas 974 robert p. hespell, bruce j. paster and floyd e. dewhirst

1.3.4 The Genus Sporomusa 983 john a. breznak

1.3.5 The Family Lachnospiraceae, Including the Genera Butyrivibrio, Lachnospira and Roseburia 994 michael cotta and robert forster

1.3.6 The Genus Veillonella 1014 paul kolenbrander

1.3.7 Syntrophomonadaceae 1033 martin sobieraj and david r. boone

2. Cyanobacteria

2.1 The Cyanobacteria—Isolation, Purification and Identification 1045 john b. waterbury

2.2 The Cyanobacteria—Ecology, Physiology and Molecular Genetics 1066 yehuda cohen and michael gurevitz

2.3 The Genus Prochlorococcus 1091 anton f. post

Index 1103

Volume 5 3.

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

3.1. Alpha Subclass

3.1.1 The Phototrophic 41 johannes f. imhoff Contents xvii

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

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

3.1.4 The Genus Agrobacterium 91 ann g. matthysse

3.1.5 The Genus Azospirillum 115 anton hartmann and jose ivo baldani

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

3.1.7 The Genus Beijerinckia 151 jan hendrick becking

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

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

3.1.10 The Manganese-Oxidizing Bacteria 222 kenneth h. nealson

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

3.1.12 The Genus Phenylobacterium 250 jürgen eberspächer and franz lingens

3.1.13 Methylobacterium 257 peter n. green

3.1.14 The Methanotrophs—The Families Methylococcaceae and Methylocystaceae 266 john bowman

3.1.15 The Genus Xanthobacter 290 juergen wiegel

3.1.16 The Genus Brucella 315 edgardo moreno and ignacio moriyón

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

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

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

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

3.1.21 The Genus Wolbachia 547 markus riegler and scott l. o’neill

3.1.22 Aerobic Phototrophic Proteobacteria 562 vladimir v. yurkov

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

3.2. Beta Subclass

3.2.1 The Phototrophic Betaproteobacteria 593 johannes f. imhoff

3.2.2 The Neisseria 602 daniel c. stein

3.2.3 The Genus Bordetella 648 alison weiss

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

3.2.5 The Genus Spirillum 701 noel r. krieg

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

3.2.7 Comamonas 723 anne willems and paul de vos

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

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

3.2.10 The Genus Derxia 751 jan hendrick becking

3.2.11 The Genera Leptothrix and Sphaerotilus 758 stefan spring

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

3.2.13 The Genus Thiobacillus 814 lesley a. robertson and j. gijs kuenen

3.2.14 The Genera Simonsiella and Alysiella 830 brian p. hedlund and daisy a. kuhn

3.2.15 Eikenella corrodens and Closely Related Bacteria 842 edward j. bottone and paul a. granato

3.2.16 The Genus Burkholderia 850 donald e. woods and pamela a. sokol

3.2.17 The Nitrite-Oxidizing Bacteria 863 aharon abeliovich

3.2.18 The Genera Azoarcus, Azovibrio, Azospira and Azonexus 875 barbara reinhold-hurek and thomas hurek

Index 000

Volume 6 3. Proteobacteria 3.3. Gamma Subclass

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

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

3.3.3 The Genus Escherichia 60 rodney a. welch

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

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

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

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

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

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

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

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

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

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

3.3.14 Yersinia pestis and Bubonic Plague 399 bob brubaker

3.3.15 Erwinia and Related Genera 443 clarence i. kado

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

3.3.17 The Family Vibrionaceae 495 j. j. farmer iii

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

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

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

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

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

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

3.3.25 Xylophilus 741 ann willems and monique gillis Contents xxi

3.3.26 The Genus Acinetobacter 746 kevin towner

3.3.27 The Family Azobacteriaceae 759 jan hendrick becking

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

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

3.3.30 The Genus Deleya 836 karel kersters

3.3.31 The Genus Frateuria 844 jean swings

3.3.32 The Chromatiaceae 846 johannes f. imhoff

3.3.33 The Family Ectothiorhodospiraceae 874 johannes f. imhoff

3.3.34 Oceanospirillum and Related Genera 887 josé m. gonzález and william b. whitman

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

3.3.36 The Genus Psychrobacter 920 john p. bowman

3.3.37 The Genus Leucothrix 931 thomas d. brock

3.3.38 The Genus Lysobacter 939 hans reichenbach

3.3.39 The Genus Moraxella 958 john p. hays

3.3.40 Legionella Species and Legionnaire’s Disease 988 paul h. edelstein and nicholas p. cianciotto

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

3.3.42 The Genus Pasteurella 1062 henrik christensen and magne bisgaard

3.3.43 The Genus Cardiobacterium 1091 sydney m. harvey and james r. greenwood xxii Contents

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

3.3.45 The Genus Francisella 1119 francis nano and karen elkins

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

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

3.3.48 The Genus Thiomargarita 1156 schulz

Index 1164

Volume 7 3. Proteobacteria 3.4. Delta Subclass

3.4.1 The Genus Pelobacter 5 bernhard schink

3.4.2 The Genus Bdellovibrio 12 edouard jurkevitch

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

3.5. Epsilon Subclass

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

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

3.5.3 The Genus Wolinella 178 jörg simon, roland gross, oliver klimmek and achim kröger

4. Spirochetes

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

4.2 The Genus Treponema 211 steven j. norris, bruce j. paster, annette moter and ulf b. göbel

4.3 The Genus Borrelia 235 melissa caimano

4.4 The Genus Leptospira 294 ben adler and solly faine

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

4.6 The Genus Brachyspira 330 thaddeus b. stanton

5. Chlorobiaceae

5.1 The Family Chlorobiaceae 359 jörg overmann

6. Bacteroides and Cytophaga Group

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

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

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

6.4 The Genus Flavobacterium 481 jean-françois bernardet and john bowman

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

6.6 The Genera Flavobacterium, Sphingobacterium and Weeksella 539 barry holmes

6.7 The Order Cytophagales 549 hans reichenbach

6.8 The Genus Saprospira 591 hans reichenbach

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

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

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

6.12 The Genera Chryseobacterium and Elizabethkingia 638 jean-françois bernardet, celia 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 677 john p. bowman

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

6.15 The Genus Capnocytophaga 709 e. r. leadbetter

6.16 The Genera Rhodothermus, Thermonema, Hymenobacter and Salinibacter 712 aharon oren

7. Chlamydia

7.1 The Genus Chlamydia—Medical 741 murat 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 757 naomi ward, james t. staley, john a. fuerst, stephen giovannoni, heinz schlesner and erko stackebrandt

9. Thermus

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

10. Chloroflexaceae and Related Bacteria

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

10.2 The Genus Thermoleophilum 843 jerome j. perry

10.3 The Genus Thermomicrobium 849 jerome j. perry Contents xxv

10.4 The Genus Herpetosiphon 854 natuschka lee and hans reichenbach

11. Verrucomicrobium

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

12. Thermotogales

12.1 Thermotogales 899 robert huber and michael hannig

13. Aquificales

13.1 Aquificales 925 robert huber and wolfgang eder

14. Phylogenetically Unaffiliated Bacteria

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

14.2 The Genus Propionigenium 955 bernhard schink

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

14.4 Large Symbiotic Spirochetes: Clevelandia, Cristispira, Diplocalyx, Hollandina and Pillotina 971 and gregory hinkle

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

14.6 The Genus Toxothrix 986 peter hirsch

14.7 The Genus Gallionella 990 hans h. hanert

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

14.9 The Genus Brachyarcus 998 peter hirsch xxvi Contents

14.10 The Genus Pelosigma 1001 peter hirsch

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

14.12 The Genus Fusobacterium 1016 tor hofstad

Index 1029 Contributors

Sharon Abbott Burt E. Anderson Microbial Diseases Laboratory Department of Medical Microbiology and Berkeley, CA 94704 Immunology USA College of Medicine University of South Florida Aharon Abeliovich Tampa, FL 33612 Department of Biotechnology Engineering USA Institute for Applied Biological Research Environmental Biotechnology Institute Robert E. Andrews Ben Gurion University Department of Microbiology 84105 Beer-Sheva University of Iowa Israel Iowa City, IA 52242 USA

David G. Adams David R. Arahal School of Biochemistry and Microbiology Colección Española de Cultivos Tipo (CECT) University of Leeds Universidad de Valencia Leeds LS2 9JT Edificio de Investigación UK 46100 Burjassot (Valencia) Spain Ben Adler Monash University John Archer Faculty of Medicine, Nursing and Health Department of Genetics Sciences Downing Street Department of Microbiology Cambridge University Clayton Campus Cambridge CB2 3EH Victoria, 3800 UK Australia M.J. Arduino Garabed Antranikian Center for Infectious Diseases Technical University Hamburg-Harburg Centers for Disease Control Institute of Technical Microbiology Atlanta, GA 30333 D-21073 Hamburg USA Germany Judith Armitage Department of Biochemistry Raymond Akhurst Microbiology Unit CSIRO Entomology University of Oxford Black Mountain OX1 3QU Oxford ACT 2601 Canberra UK Australia Ingo Autenrieth Rudolf Amann Institut für Medizinische Mikrobiologie Max Planck Institute for Marine Microbiology Universitatsklinikum Tuebingen D-28359 Bremen D-72076 Tuebingen Germany Germany xxviii Contributors

Hans-Dietrich Babenzien Edward A. Bayer Leibniz-Institut für Gewässerökologie und Department of Biological Chemistry Binnenfischereiim Forschungsverbund Weizmann Institute of Science Berlin Rehovot 76100 12587 Berlin Israel Germany

Werner Back Dennis A. Bazylinski Lehrstuhl für Technologie der Brauerei I Department of Microbiology, Immunology and Technische Universität München Preventive Medicine D-85354 Freising-Weihenstephan Iowa State University Germany Ames, IA 55001 USA Margo Baele Department of Pathology Jan Hendrick Becking Bacteriology and Poultry Diseases Stichting ITAL Faculty of Veterinary Medicine Research Institute of the Ministry of Ghent University Agriculture and Fisheries B-9820 Merelbeke 6700 AA Wageningen Belgium The Netherlands

Jose Ivo Baldani EMBRAPA-Agrobiology Robert Belas Centro Nacional de Pesquisa de Agrobiologia The University of Maryland Biotechnology Seropedica, 23851-970 Institute CP 74505 Rio de Janeiro Center of Marine Biotechnology Brazil Baltimore, MD 21202 USA David L. Balkwill Department of Biomedical Sciences Birgitta Bergman College of Medicine Department of Botany Florida State University Stockholm University Tallahassee, FL 32306-4300 SE-106 91 Stockholm USA Sweden Horia Banciu Department of Biotechnology Kathryn Bernard Delft University of Technology Special Bacteriology Section 2628 BC Delft National Microbiology Laboratory Health Canada Tammy Bannerman Winnipeg R3E 3R2 School of Allied Medical Professions Canada Division of Medical Technology The Ohio State University Columbus, OH 43210 Jean-François Bernardet USA Unité de Virologie et Immunologie Moléculaires Institut National de la Recherche Bonnie L. Bassler Agronomique (INRA) Department of Molecular Biology Domaine de Vilvert Princeton University 78352 Jouy-en-Josas cedex Princeton, NJ 08544-1014 France USA

Paul Baumann Costanzo Bertoldo Department of Microbiology Technical University Hamburg-Harburg University of California, Davis Institute of Technical Microbiology Davis, CA 95616-5224 D-21073 Hamburg USA Germany Contributors xxix

Karl A. Bettelheim Adam S. Bonin National Escherichia coli Reference Portland State University Laboratory Portland OR 97207 Microbiological Diagnostic Unit USA Public Health Laboratory Department of Microbiology and Immunology David R. Boone University of Melbourne Department of Biology Melbourne Environmental Science and Engineering Victoria 3010 Oregon Graduate Institute of Science and Australia Technology Portland State University Bruno Biavati Portland, OR 97207-0751 Istituto di Microbiologia Agraria USA 40126 Bologna Italy Diana Borenshtein Magne Bisgaard Massachusetts Institute of Technology Department of Veterinary Microbiology Cambridge, MA 02139-4307 Royal Veterinary and Agricultural University USA 1870 Frederiksberg C Denmark Edward J. Bottone Division of Infectious Diseases William Bishai The Mount Sinai Hospital Departments of Molecular Microbiology and One Gustave L. Levy Place Immunology, International Health, and New York, NY 10029 Medicine USA Center for Tuberculosis Research Johns Hopkins School of Hygiene and Public Timothy L. Bowen Health Department of Microbiology Baltimore, MD 21205-2105 University of Georgia USA Athens, GA 30602 USA Johanna Björkroth Department of Food and Environmental Hygiene John Bowman Faculty of Veterinary Medicine Australian Food Safety Centre for Excellence University of Helsinki School of Agricultural Science FIN-00014 Helsinki Hobart, Tasmania, 7001 Finland Australia

Eberhard Bock John A. Breznak Institute of General Botany Department of Microbiology and Molecular Department of Microbiology Genetics University of Hamburg Michigan State University D-22609 Hamburg East Lansing, MI 48824-1101 Germany USA Noël Boemare Ecologie Microbienne des Insectes et Stephanie Bringer-Meyer Interactions Hôte-Pathogène Institut Biotechnologie UMR EMIP INRA-UMII Forschungszentrum Jülich IFR56 Biologie cellulaire et Porcessus D-52425 Jülich infectieux Germany Université Montpellier II 34095 Montpellier Sylvain Brisse France Unité Biodiversité des Bactéries Pathogènes Emergentes Antje Boetius U 389 INSERM Max-Planck-Institut für Marine Mikrobiologie Institut Pasteur D-28359 Bremen 75724 Paris Germany France xxx Contributors

Thomas D. Brock Didier Cabanes Department of Bacteriology Department of Immunology and Biology of University of Wisconsin-Madison Infection Madison, WI 53706 Molecular Microbiology Group USA Institute for Molecular and Cellular Biology 4150-180 Porto Robert Brubaker Portugal Department of Microbiology Michigan State University Melissa J. Caimano East Lansing, MI 48824 Center for Microbial Pathogenesis USA and Department of Pathology Franz Brümmer and Biologisches Institut/Zoologie Department of Genetics and Development Universität Stuttgart University of Connecticut Health Center D-70569 Stuttgart Farmington, CT 06030-3205 Germany USA

Yves V. Brun Ercole Canale-Parnola Department of Biology Department of Microbiology Indiana University University of Massachusetts Bloomington, IN 47405-6801 Amherst, MA 01003 USA USA

Andreas Brune Elisabeth Carniel Max Planck Institute for Terrestrial Laboratoire des Yersinia Microbiology Institut Pasteur Marburg 75724 Paris Germany France Brita Bruun Colleen Cavanaugh Department of Clinical Microbiology Bio Labs Hillerød Hospital Harvard University DK 3400 Hillerød Cambridge, MA 02138 Denmark USA Carmen Buchrieser Laboratoire de Génomique des Wendy Champness Microorganismes Pathogènes Department of Microbiology Institut Pasteur Michigan State University 75724 Paris East Lansing, MI 48824-1101 France USA

Hans-Jürgen Busse Jiann-Shin Chen Institut für Bakteriology, Mykologie, und Department of Biochemistry Hygiene Virginia Polytechnic Institute and Veterinärmedizinische Universität Wien State University—Virginia Tech A-1210 Vienna Blacksburg, VA 24061-0308 Austria USA

Patrick Butaye Zhongying Chen CODA-CERVA-VAR Department of Biology 1180 Brussels University of North Carolina Belgium Chapel Hill, NC 27514 USA Gerald I. Byrne Department of Medical Microbiology and Qi Cheng Immunology University of Western Sydney University of Wisconsin—Madison Penrith South Madison, WI 53706 NSW 1797 USA Australia Contributors xxxi

Henrik Christensen Mike Cotta Department of Veterinary Microbiology USDA-ARS North Regional Research Royal Veterinary and Agricultural University Center Denmark Peoria, IL 61604-3902 USA Nicholas P. Cianciotto Department of Microbiology and Immunology Ron Crawford Northwestern University School of Medicine Food Research Center Chicago, IL University of Idaho USA Moscow, ID 83844-1052 USA Josephine E. Clark-Curtiss Department of Biology Washington University Cecil S. Cummins St. Louis, MO 63130-7246 Department of Anaerobic Microbiology USA Virginia Polytechnic Institute and State University Dieter Claus Blacksburg, VA 24061 Deutsche Sammlung von Mikroorganismen USA D-3300 Braunschweig-Stockheim Germany Heribert Cypionka Institut für Chemie und Biologie des Meeres P. Patrick Cleary Fakultät 5, Mathematik und Department of Microbiology Naturwissenschaften University of Minnesota Medical School Universität Oldenburg Minneapolis, MN 55455 D-26111 Oldenburg USA Germany Yehuda Cohen Milton S. da Costa Department of Molecular and Microbial M. Fernanda Nobre Ecology Centro de Neurociências e Biologia Celular Institute of Life Science Departamento de Zoologia Hebrew University of Jerusalem Universidade de Coimbra 91904 Jerusalem 3004-517 Coimbra Israel Portugal Matthew D. Collins Institute of Food Research Seana Davidson Reading Lab, Early Gate University of Washington UK Civil and Environmental Engineering Seattle, WA 98195-2700 Guy Cornelis USA Microbial Pathogenesis Unit Université Catholique de Louvain and Scott C. Dawson Christian de Duve Institute of Cellular Department of Molecular and Cellular Pathology Biology B1200 Brussels University of California-Berkeley Belgium Berkeley, CA 94720 USA Pascale Cossart Unité des Interactions Bactéries-Cellules INSERM U604 Dirk de Beer Institut Pasteur Max-Planck-Institute for Marine Microbiology 75724 Paris D-28359 Bremen France Germany

Milton S. da Costa Jan A.M. de Bont Department of Zoologia Department of Food Science Universidade de Coimbra Agricultural University 3049 Coimbra 6700 EV Wageningen Portugal The Netherlands xxxii Contributors

Maria H. Deinema Harold L. Drake Laboratory of Microbiology Department of Ecological Microbiology Agricultural University BITOEK, University of Bayreuth 6703 CT Wageningen D-95440 Bayreuth The Netherlands Germany

Jozef de Ley Patrick R. Dugan Laboratorium voor Microbiologie en Idaho National Engineering Laboratory Microbiële Genetica EG & G Idaho Rijksuniversiteit Ghent Idaho Falls, ID 83415 B-9000 Ghent USA Belgium Paul V. Dunlap Edward F. DeLong Department of Molecular Science Chair Cellular and Developmental Biology Monterey Bay Aquarium Research Institute University of Michigan Moss Landing, CA 95039 Ann Arbor, MI 48109-1048 USA USA

Arnold Demain Olivier Dussurget Department of Biology Unité des Interactions Bactéries-Cellules Massachusetts Institute of Technology INSERM U604 Cambridge, MA 02139 Institut Pasteur USA 75724 Paris France Paul de Vos Department of Biochemistry, Physiology and Martin Dworkin Microbiology University of Minnesota Medical School Universiteit Gent Department of Microbiology B-9000 Gent Minneapolis, MN 55455 Belgium USA

Luc Devriese Faculty of Veterinary Medicine Jürgen Eberspächer B982 Merelbeke Institut fur Mikrobiologie Belgium Universitat Hohenheim D-7000 Stuttgart 70 Germany Floyd E. Dewhirst Forsyth Dental Center 140 Fenway Paul H. Edelstein Boston, MA 02115 Department of Pathology and Laboratory USA Medicine University of Pennsylvania Medical Center Leon M.T. Dicks Philadelphia, PA 19104-4283 Department of Microbiology USA University of Stellenbosch ZA-7600 Stellenbosch South Africa Wolfgang Eder Lehrstuhl für Mikrobiologie Universität Regensburg Michael Doyle 93053 Regensburg College of Agricultural and Environmental Germany Sciences Center for Food Safety and Quality Enhancement Karen Elkins University of Georgia CBER/FDA Griffin, GA 30223-1797 Rockville, MD 20852 USA USA Contributors xxxiii

Craig D. Ellermeier Doran L. Fink Department of Microbiology Edward Mallinckrodt Department of Pediatrics University of Illinois and Department of Molecular Microbiology Urbana, IL 61801 Washington University School of Medicine and St. Louis, Missouri 63110 Department of Molecular and Cellular USA Biology Harvard University Jacqueline Fletcher Cambridge, MA 02138 Department of Entomology and Plant USA Pathology Oklahoma State University Lyudmila Evtushenko Stillwater, OK All-Russian Collection of Microorganisms USA Institute of Biochemistry and Physiology of the Russian, Academy of Sciences Puschino Robert Forster Moscow Region, 142290 Bio-Products and Bio-Processes Program Russia Agriculture and Agri-Food Canada Lethbridge Research Centre Lethbridge T1J 4B1 Takayuki Ezaki Canada Bacterial Department Gifu University Medical School 40 Tsukasa M. Pilar Francino Machi Gifu City Evolutionary Genomics Department Japan DOE Joint Genome Institute Walnut Creek, CA 94598 Solly Faine USA Monash University Faculty of Medicine, Nursing and Health Charles M.A.P. Franz Sciences Institute of Hygiene and Toxicology Department of Microbiology BFEL Clayton Campus D-76131 Karlsruhe Victoria, 3800 Germany Australia David N. Fredricks J.J. Farmer VA Palo Alto Healthcare System Center for Infectious Diseases Palo Alto, CA 94304 Centers for Disease Control USA Atlanta, GA 30333 USA J.K. Fredrickson W. Edmund Farrar Pacific Northwest National Laboratory Department of Medicine Richland, Washington 99352 Medical University of South Carolina USA Charleston, SC 29425 USA Bärbel Friedrich Institut für Biologie/Mikrobiologie Mariano E. Fernandez Miyakawa Homboldt-Universität zu Berlin California Animal Health and Food Safety Chaussesstr. 117 Laboratory D-10115 Berlin University of California, Davis Germany San Bernardino, CA 92408 USA Thomas R. Fritsche Associate Director Eugenio Ferrari The Jones Group/JMI Laboratories Genencor International, Inc. 345 Beaver Kreek Centre, Suite A Palo Alto, CA 94304 North Liberty, IA 52317 USA USA xxxiv Contributors

Dagmar Fritze Frank C. Gibson Deutsche Sammlung von Mikroorganismen Department of Medicine D-3300 Braunschweig-Stockheim Section of Infectious Diseases Germany and ‘ Department of Microbiology John A Fuerst Boston University School of Medicine Department of Microbiology and Parasitology Boston, MA 02118 University of Queensland USA Brisbane Queensland 4072 Monique Gillis Australia Laboratorium voor Mikrobiologie Universiteit Gent Hiroshi Fukushima B-9000 Gent Public Health Institute of Shimane Prefecture Belgium 582-1 Nishihamasada, Matsue Shimane 690-0122 Stephen Giovannoni Japan Department of Microbiology Oregon State University Jorge E. Galan Corvallis, OR 97331 Boyer Center Molecular Medicine USA Yale University School of Medicine New Haven, CT 06536-0812 Frank Oliver Glöckner USA Max-Planck-Institut für Marine Mikrobiologie D-28359 Bremen Germany Jean-Louis Garcia Laboratoire ORSTOM de Microbiologie des Ulf B. Göbel Anaérobies Institut für Mikrobiologie und Hygiene Université de Provence Universitaetsklinikum Chariteacute CESB-ESIL Humboldt-Universitaet zu Berlin 13288 Marseille D-10117 Berlin France Germany

Arnold Geis Jose M. Gonzalez Institut für Mikrobiologie Department de Microbiologia y Biologia Bundesanstalt für Milchforschung Celular D-24121 Kiel Facultad de Farmacia Germany Universidad de La Laguna 38071 La Laguna, Tenerife Caroline Attardo Genco SPAIN Department of Medicine Section of Infectious Diseases Michael Goodfellow and Department of Microbiology School of Biology Boston University School of Medicine Universtiy of Newcastle Boston, MA 02118 Newcastle upon Tyre NE1 7RU USA UK

Yves Germani Friedrich Götz Institut Pasteur Facultät für Biologie Unité Pathogénie Microbienne Moléculaire Institut für Microbielle Genetik and Universität Tübingen Réseau International des Instituts Pasteur D-72076 Tübingen Paris 15 Germany France Hans-Dieter Görtz Bill Ghiorse Department of Zoology Department of Microbiology Biologisches Institut Cornell University Universität Stuttgart Ithaca, NY 14853-8101 D-70569 Stuttgart USA Germany Contributors xxxv

Jan Gottschal Françoise Guinet Lab. Mikrobiologie Laboratoire des Yersinia Rijksunivnsiteit Groningen Institut Pasteur NL-9751 NN Haven 75724 Paris The Netherlands France

Gerhard Gottschalk Michael Gurevitz Institut für Mikrobiologie und Genetik Department of Botany Georg-August-Universität Göttingen Life Sciences Institute D-37077 Göttingen Tel Aviv University Germany Ramat Aviv 69978 Israel Paul A. Granato Department of Microbiology and Immunology H. M. Hafez State University of New York Upstate Medical Institute of Poultry Diseases University Free University Berlin Syracus, NY 13210 Berlin USA German

Peter Green Auli Haikara NCIMB Ltd VTT Biotechnology AB24 3RY Aberdeen Tietotie 2, Espoo UK Finland

James R. Greenwood Walter P. Hammes Bio-Diagnostics Laboratories Institute of Food Technology Torrance, CA 90503 Universität Hohenheim USA D-70599 Stuttgart Germany

Francine Grimont Satoshi Hanada Unite 199 INSERM Research Institute of Biological Resources Institut Pasteur National Institute of Advanced Industrial 75724 Paris Science and Technology (AIST) France Tsukuba 305-8566 Japan Patrick Grimont Institut Pasteur Hans Helmut Hanert 75724 Paris Institut für Mikrobiologie France Technische Univeristät Braunschweig D-3300 Braunschweig Roland Gross Germany Institut für Mikrobiologie Johann Wolfgang Goethe-Universität Michael Hannig Frankfurt am Main Lehrstuhl für Mikrobiologie Germany Universität Regensburg D-93053 Regensburg Ji-Dong Gu Germany Laboratory of Environmental Toxicology Department of Ecology & Biodiversity T.A. Hansen and Microbial Physiology (MICFYS) The Swire Institute of Marine Science Groningen University University of Hong Kong Rijksuniversiteit Groningen Hong Kong SAR NL-9700 AB Groningen P.R. China The Netherlands and Environmental and Molecular Microbiology Jeremy Hardie South China Sea Institute of Oceanography Department of Oral Microbiology Chinese Academy of Sciences School of Medicine & Dentistry Guangzhou 510301 London E1 2AD P.R. China UK xxxvi Contributors

Timothy Harrah Christian Hertel Bioengineering Center Institute of Food Technology Tufts University Universität Hohenheim Medford, MA 02155 D-70599 Stuttgart USA Germany

Anton Hartmann Robert B. Hespell GSF-National Research Center for Northern Regional Research Center, ARS Environment and Health US Department of Agriculture Institute of Soil Ecology Peoria, IL 61604 Rhizosphere Biology Division USA D-85764 Neuherberg/Muenchen Germany F.W. Hickmann-Brenner Center for Infectious Diseases Sybe Hartmans Centers for Disease Control Department of Food Science Atlanta, GA 30333 Agricultural University Wageningen USA 6700 EV Wageningen The Netherlands Donald C. Hildebrand Patricia Hartzell Department of Plant Pathology Department of Microbiology, Molecular University of California-Berkeley Biology, and Biochemistry Berkeley, CA 94720 University of Idaho USA Moscow, ID 83844-3052 USA Gregory Hinkle Department of Botany Sydney M. Harvey University of Massachusetts Nichols Institute Reference Laboratories Amherst, MA 01003 32961 Calle Perfecto USA San Juan Capistrano, CA 92675 USA K.H. Hinz Clinic for Poultry John P. Hays School of Veterinary Medicine Department of Medical Microbiology and D-30559 Hannover Infectious Diseases Germany Erasmus MC 3015 GD Rotterdam Peter Hirsch The Netherlands Institut für Allgemeine Mikrobiologie Universität Kiel Brian P. Hedlund D-2300 Kiel Department of Biological Sciences Germany University of Nevada, Las Vegas Las Vegas, NV 89154-4004 Tor Hofstad USA Department of Microbiology and Robert A. Heinzen Immunology Department of Molecular Biology University of Bergen University of Wyoming N-5021 Bergen Laramie, WY 82071-3944 Norway USA Michael J. Hohn Ilkka Helander Lehrstuhl für Mikrobiologie VTT Biotechnology Universität Regensburg Tietotie 2, Espoo D-93053 Regensburg Finland Germany

H. Ernest Hemphill Barry Holmes Department of Biology Central Public Health Laboratory Syracuse University National Collection of Type Cultures Syracuse, NY 13244 London NW9 5HT USA UK Contributors xxxvii

Wilhelm H. Holzapfel Elena Ivanova Federal Research Centre of Nutrition Senior Researcher in Biology Institute of Hygiene and Toxicology Laboratory of Microbiology D-76131 Karlsruhe Pacific Institute of Bioorganic Chemistry of the Germany Far-Eastern Branch of the Russian Academy of Sciences 690022 Vladivostok Harald Huber Russia Lehrstuhl für Mikrobiologie Universität Regensburg D-93053 Regensburg Rainer Jaenicke Germany 6885824 Schwalbach a. Ts. Germany Robert Huber and Lehrstuhl für Mikrobiologie Institut für Biophysik und Physikalische Universität Regensburg Biochemie D-93053 Regensburg Universität Regensburg Germany Regensburg Germany and Celia J. Hugo School of Crystallography Department of Microbial, Biochemical and Birbeck College Food Biotechnology University of London University of the Free State London, UK Bloemfontein South Africa J. Michael Janda Microbial Diseases Laboratory Meredith Hullar Division of Communicable Disease Control University of Washington California Department of Health Services Seattle, WA Berkeley, CA 94704-1011 USA USA

Thomas Hurek Christian Jeanthon Laboratory of General Microbiology UMR CNRS 6539–LEMAR University Bremen Institut Universitaire Europeen de la Mer 28334 Bremen Technopole Brest Iroise Germany 29280 Plouzane France Barbara Iglewski Department of Microbiology and Immunology Cheryl Jenkins University of Rochester Medical Center Department of Microbiology Rochester, NY 14642-0001 University of Washington USA Seattle, WA 98195 USA

Johannes F. Imhoff Marine Mikrobiologie John L. Johnson Institut für Meereskunde an der Universität Department of Anaerobic Microbiology Kiel Virginia Polytechnic Institute and State D-24105 Kiel University Germany Blacksburg, VA 24061 USA

Ralph Isberg Department of Molecular Biology and Dorothy Jones Microbiology Department of Microbiology Tufts University School of Medicine University of Leicester, School of Medicine Boston, MA 02111 Lancaster LE1 9HN USA UK xxxviii Contributors

P.J. Jooste Yoshiaki Kawamura Department of Biotechnology and Food Department of Microbiology Technology Regeneration and Advanced Medical Tshwane University of Technology Science Pretoria 0001 Gifu University Graduate School of South Africa Medicine Gifu 501-1194 Edouard Jurkevitch Japan Department of Plant Pathology and Microbiology Ronald M. Keddie Faculty of Agriculture Craigdhu Food & Environmental Quality Services Fortrose The Hebrew University Ross-shire IV 10 8SS 76100 Rehovot UK Israel Donovan Kelly Clarence Kado University of Warwick Department of Plant Pathology Department of Biological Sciences University of California, Davis CV4 7AL Coventry Davis, CA 95616-5224 UK USA Melissa M. Kendall Dale Kaiser Department of Biology Department of Biochemistry Portland State University Stanford University School of Medicine Portland, OR 97207-0751 Stanford, CA 94305-5329 USA USA Karel Kersters Laboratorium voor Mikrobiologie Murat V. Kalayoglu Department of Biochemistry Department of Medical Microbiology and Physiology and Microbiology Immunology Universiteit Gent University of Wisconsin—Madison B-9000 Gent Madison, WI 53706 Belgium USA Nadia Khelef P. Kämpfer Unité des Interactions Bactéries-Cellules Institut für Angewandte Mikrobiologie INSERM U604 Justus Liebig-Universität Institut Pasteur D-35392 Gießen 75724 Paris Germany France

Otto Kandler Kumiko Kita-Tsukamoto Institut Botanik Ocean Research Institute Universität München University of Tokyo D-80638 München Tokyo 164 Germany Japan

Jim Kaper Staffan Kjelleberg Center for Vaccine Development School of Microbiology & Immunology University of Maryland School of Medicine University of New South Wales Baltimore, MD 21201 2052 Sydney USA Australia

David Kaplan Oliver Klimmek Department of Chemcial and Biological Johann Wolfgang Goethe-Universität Engineering Frankfurt Tufts University Institut für Mikrobiologie Medford, MA 02115 D-60439 Frankfurt USA Germany Contributors xxxix

Wesley Kloos J. Gijs Kuenen Department of Genetics Department of Biotechnology North Carolina State University Delft University of Technology Raleigh, NC 27695-7614 2628BC Delft USA The Netherlands

Daisy A. Kuhn Miroslav Kocur Department of Biology Czechoslovak Collection of Microorganisms California State University J.E. Purkyneˇ University Northridge, CA 91330 662 43 Brno USA Czechoslovakia Hidehiko Kumagai Paul Kolenbrander Division of Applied Sciences National Institute of Dental Research Graduate School of Agriculture National Institute of Health Kyoto University Bethesda, MD 20892-4350 Kitashirakawa USA 606 8502 Kyoto Japan Kazuo Komagata Barbara N. Kunkel Laboratory of General and Applied Department of Biology Microbiology Washington University Department of Applied Biology and St. Louis, MO 63130 Chemistry USA Faculty of Applied Bioscience Tokyo University of Agriculture Kirsten Küsel Tokyo, Japan Department of Ecological Microbiology BITOEK, University of Bayreuth Hans-Peter Koops D-95440 Bayreuth Institut für Allgemeine Botanik Germany Abteilung Mikrobiologie Universität Hamburg David P. Labeda D-22069 Hamburg Microbial Genomics and Bioprocessing Germany Research Unit National Center for Agricultural Utilization Research Noel Krieg Agricultural Research Service Department of Biology U.S. Department of Agriculture Virginia Polytechnic Institute Peoria, IL 61604 Blacksburg, VA 24061-0406 USA USA Edward T. Lally Achim Kröger Leon Levy Research Center for Oral Biology Institut für Mikrobiologie University of Pennsylvania Biozentrum Niederursel Philadelphia, Pennsylvania, 19104-6002 D-60439 Frankfurt/Main USA Germany Bart Lambert Plant Genetic Systems N.V. Reiner M. Kroppenstedt J. Plateaustraat 22 Deutsche Sammlung von Mikroorganismen B-9000 Ghent und Zellkulturen Belgium D-3300 Braunschweig Germany Raphael Lamed Department of Molecular Microbiology and Terry Krulwich Biotechnology Department of Biochemistry George S. Wise Faculty of Life Sciences Mount Sinai School of Medicine Tel Aviv University New York, NY 10029 Ramat Aviv 69978 USA Israel xl Contributors

Jan W.M. la Rivière Franz Lingens Institut für Mikrobiologie Institut fur Mikrobiologie Universität Göttingen Universitat Hohenheim D-3400 Göttingen D-7000 Stuttgart 70 Germany Germany

Jared R. Leadbetter Environmental Science and Engineering Puspita Lisdiyanti California Institute of Technology Laboratory of General and Applied Pasadena, CA 91125-7800 Microbiology USA Department of Applied Biology and Chemistry Donald J. LeBlanc Faculty of Applied Bioscience ID Genomics Tokyo University of Agriculture Pharmacia Corporation Tokyo, Japan Kalamazoo, MI 49001 USA Derek Lovley Department of Microbiology Marc Lecuit University of Massachusetts Unité des Interactions Bactéries-Cellules Amherst, MA 01003 INSERM U604 USA Institut Pasteur 75724 Paris France Wolfgang Ludwig Lehrstuhl für Mikrobiologie Adrian Lee Technische Universität München School of Microbiology & Immunology D-85350 Freising University of New South Wales Germany Sydney, New South Wales 2052 Australia David Lyerly TechLab, Inc. Natuschka Lee Corporate Research Center Lehrstuhl für Mikrobiologie Blacksburg VA 24060-6364 Technische Universität München USA D-85350 Freising Germany Janet I. Macinnes Susan Leschine University of Guelph Department of Microbiology Guelph N1G 2W1 University of Massachusetts Canada Amherst, MA 01003-5720 USA Mike Madigan Na (Michael) Li Department of Microbiology Division of Biostatistics Mailcode 6508 School of Public Health Southern Illinois University University of Minnesota Carbondale, IL 62901-4399 Minneapolis, MN 55455 USA USA Luis Angel Maldonado Mary Lidstrom Laboratorio 4 Department of Chemical Engineering Unidad de Investigación en Plantas University of Washington Medicinales Seattle, WA 98195 Mexico USA

Wolfgang Liebl Jim Manos Institut für Mikrobiologie und Genetik The University of Maryland Biotechnology Georg-August-Universität Institute D-37077 Göttingen Center of Marine Biotechnology Germany Baltimore, MD 21202 Contributors xli

Esperanza Martinez-Romero Ulrich Melcher Centro de Investigacion sobre Fijacion de Department of Biochemistry and Molecular Nitrogeno Biology Cuernavaca Mor Oklahoma State University Mexico Stillwater, OK USA Vega Masignani IRIS, Chiron SpA Valery V. Mikhailov 53100 Siena Pacific Institute of Bioorganic Chemistry Italy Far-Eastern Branch of the Russian Academy of Sciences Luis Angel Maldonado 690022 Vladivostok School of Biology Russia Universidad Nacional Autonoma de Mexico (UNAM) Instituto de Ciencias del Mar y Limnologia James N. Miller Ciudad Universitaria CP Department of Microbiology and Immunity 04510 Mexico DF Center of Health Mexico University of California School of Medicine Los Angeles, CA 90024 Lynn Margulis USA Department of Botany University of Massachusetts Michael F. Minnick Amherst, MA 01003 Division of Biological Sciences USA University of Montana Missoula, MT 59812-4824 Vitor A.P. Martins dos Santos USA Gesellschaft für Biotechnologische Forschung Division of Microbiology Ralph Mitchell Braunschweig D-38124 Laboratory of Microbial Ecology Germany Division of Engineering and Applied Sciences Paola Mattarelli Harvard University Istituto di Microbiologia Agraria Cambridge, MA 02138 40126 Bologna USA Italy Cesare Montecucco Carola Matthies Professor of General Pathology Department of Ecological Microbiology Venetian Institute for Molecular Medicine BITOEK, University of Bayreuth 35129 Padova D-95440 Bayreuth Italy Germany

Ann Matthysse Edward Moore Department of Biology GBF University of North Carolina Arbeitsgruppe Mikrobielle Sekundästroffe Chapel Hill, NC 27599 D-38124 Braunschweig USA Germany

Megan E. McBee Edward R.B. Moore Biological Engineering Division The Macaulay Institute Massachusetts Institute of Technology Environmental Sciences Group Cambridge, MA Aberdeen AB158QH USA UK and Bruce A. McClane Culture Collection University of Göteborg Department of Molecular Genetics and (CCUG) Biochemistry Department of Clinical Bacteriology University of Pittsburgh School of Medicine University of Göteborg Pittsburgh, PA 15261 Göteborg SE-416 43 USA Sweden xlii Contributors

Edgardo Moreno Diane G. Newell Tropical Disease Research Program Veterinary Laboratory Agency (Weybridge) (PIET) Addlestone Veterinary School, Universidad Nacional New Haw Costa Rica Surrey KT1 53NB UK Ignacio Moriyón S.A. Nierzwicki-Bauer Department of Microbiology Department of Biology University of Navarra Rensselaer Polytechnic Institute 32080 Pamplona Troy, NY Spain USA

Annette Moter M. Fernanda Nobre Institut für Mikrobiologie und Hygiene Departamento de Zoologia Universitaetsklinikum Chariteacute Universidade de Coimbra Humboldt-Universität zu Berlin 3004-517 Coimbra D-10117 Berlin Portugal Germany Philippe Normand Laboratoire d’Ecologie Microbienne Eppe Gerke Mulder UMR CNRS 5557 Laboratory of Microbiology Université Claude-Bernard Lyon 1 Agricultural University 69622 Villeurbanne 6703 CT Wageningen France The Netherlands Steven J. Norris Yasuyoshi Nakagawa Department of Pathology and Laboratory Biological Resource Center (NBRC) Medicine and Microbiology and Molecular Department of Biotechnology Genetics National Institute of Technology and University of Texas Medical Scvhool at Evaluation Houston Chiba 292-0818 Houston, TX 77225 Japan USA

Howard Ochman Francis Nano Department of Biochemistry and Molecular Department of Biochemistry & Microbiology Biophysics University of Victoria University of Arizona Victoria V8W 3PG Tucson, AZ 85721 Canada USA

Kenneth H. Nealson Gary E. Oertli Department of Earth Sciences Molecular and Cellular Biology University of Southern California Unviersity of Washington Los Angeles, CA 90033 Seattle, WA 98195-7275 USA USA

Itzhak Ofek Douglas C. Nelson Department of Human Microbiology Department of Microbiology Tel Aviv University University of California, Davis 69978 Ramat Aviv Davis, CA 95616 Israel USA Bernard Ollivier Klaus Neuhaus Laboratoire ORSTOM de Microbiologie des Department of Pediatrics, Infection, Immunity, Anaérobies and Infectious Diseases Unit Université de Provence Washington University School of Medicine CESB-ESIL St. Louis, MO 63110 13288 Marseille USA France Contributors xliii

Scott L. O’Neill Yong-Ha Park Department of Epidemiology and Public Korean Collection for Type Cultures Health Korea Research Institute of Bioscience & Yale University School of Medicine Biotechnology New Haven, CT 06520-8034 Taejon 305-600 USA Korea

Jani L. O’Rourke Matthew R. Parsek School of Microbiology and Immunology University of Iowa University of New South Wales Iowa City, IA 52242 Sydney, NSW 2052 USA Australia Bruce J. Paster Aharon Oren Department of Molecular Genetics Division of Microbial and Molecular The Forsyth Institute Ecology Boston, MA 02115 The Institute of Life Sciences USA and Moshe Shilo Minerva Center for Marine Jerome J. Perry Biogeochemistry 3125 Eton Road The Hebrew University of Jerusalem Raleigh, NC 27608-1113 91904 Jerusalem USA Israel Jeanette Pham Jörg Overmann The CDS Users Group Bereich Mikrobiologie Department of Microbiology Department Biologie I South Eastern Area Laboratory Services Ludwig-Maximilians-Universität München The Prince of Wales Hospital Campus D-80638 München Randwick NSW 2031 Germany Australia Harvey M. Pickrum Norman Pace Proctor and Gamble Company Department of Molecular, Cellular and Miami Valley Laboratories Developmental Biology Cincinnatti, OH 45239 Unversity of Colorado USA Boulder, CO 80309-0347 USA Dietmar H. Pieper Gesellschaft für Biotechnologische Forschung Norberto J. Palleroni Division of Microbiology Rutgers University Braunschweig D-38124 Department of Biochemistry and Germany Microbiology New Brunswick 08901-8525 Beverly K. Pierson New Jersey Biology Department USA University of Puget Sound Tacoma, WA 98416 Bruce Panilaitis USA Department of Chemcial and Biomedical Engineering Mariagrazia Pizza Tufts University IRIS, Chiron SpA Medford, MA 02155 53100 Siena USA Italy

Nickolas Panopoulos Jeannette Pham Department of Plant Pathology Department of Microbiology University of California-Berkeley Prince of Wales Hospital Berkeley, CA 94720 Randwick N.S.W. 2031 USA Australia xliv Contributors

Jeanne Poindexter Wim J. Quax Department of Biological Sciences Department of Pharmaceutical Biology Barnard College/Columbia University University of Groningen New York, NY 10027-6598 Groningen 9713AV USA The Netherlands

Andreas Pommerening-Röser Erika Teresa Quintana Institut für Allgemeine Botanik School of Biology Abteilung Mikrobiologie Universtiy of Newcastle Universität Hamburg Newcastle upon Tyne NE1 7RU D-22069 Hamburg UK Germany Ralf Rabus Michel R. Popoff Max-Planck-Institut für Marine Mikrobiologie Unité des Toxines Microbiennes D-28359 Bremen Institut Pasteur Germany 75724 Paris France Reinhard Rachel Lehrstuhl für Mikrobiologie Anton F. Post Universität Regensburg Department of Plant and Environmental D-93053 Regensburg Sciences Germany Life Sciences Institute Hebrew University Justin Radolf Givat Ram Molecular Biology and Biochemistry 91906 Jerusalem University of Connecticut Health Center Israel Farmington, CT 06030-3205 USA Bruno Pot Laboratorium voor Microbiologie en A.N. Rai Microbiële Genetica Biochemistry Department Rijksuniversiteit Ghent North-Eastern Hill University B-9000 Ghent Shillong 793022 Belgium India

David Prangishvili Fred A. Rainey Department of Mikrobiology Department of Biological Sciences Universitity of Regensburg Louisiana State University D-93053 Regensburg Baton Rouge, LA 70803 Germany USA

Helmut Prauser Juan-Luis Ramos DSMZ-German Collection of Estación Experimental del Zaidin Microorganisms and Cell Cultures GmbH Department of Biochemistry and Molecular D-38124 Braunschweig and Cell Biology of Plants Germany Granada E-18008 Spain Michael Prentice Bart’s and the London School of Medicine and Rino Rappuoli Dentistry IRIS Chiron Biocine Immunobiologie Department of Medical Microbiology Research Institute Siena St. Bartholomew’s Hospital 53100 Siena London EC1A 7BE Italy UK Shmuel Razin Ulrike Purkhold Department of Membrane and Ultrastructure Lehrstuhl für Mikrobiologie Research Technische Universität München The Hebrew University-Hadassah Medical D-80290 Munich School Germany Jerusalem 91120 Contributors xlv

Annette C. Reboli M.F. Romine Department of Medicine Pacific Northwest National Laboratory Hahneman University Hospital Richland, WA 99352 Philadelphia, PA 19102 USA USA Eliora Z. Ron David W. Reed Department of Molecular Microbiology and Biotechnology Department Biotechnology Idaho National Engineering and The George S. Wise Faculty of Life Sciences Environmental Laboratory (INEEL) Tel Aviv University Idaho Falls, ID 83415-2203 Ramat Aviv USA 69978 Tel Aviv Israel Hans Reichenbach GBF D-3300 Braunschweig Julian I. Rood Germany Australian Bacterial Pathogenesis Program Department of Microbiology Barbara Reinhold-Hurek Monash University Laboratory of General Microbiology Victoria 3800 Universität Bremen Australia Laboratorium für Allgemeine Mikrobiologie D-28334 Bremen Eugene Rosenberg Germany Department of Molecular Microbiology & Biotechnology Markus Riegler Tel Aviv University Integrative Biology School Ramat Aviv University of Queensland 69978 Tel Aviv Australia Israel Monica Riley Frank Rosenzweig Marine Biological Lab Division of Biological Sciences Woods Hole, MA 02543 University of Montana USA Missoula, MT 59812-4824 Lesley A. Robertson USA Department of Biotechnology Delft University of Technology Ornella Rossetto 2628 BC Delft Centro CNR Biomembrane and Dipartimento The Netherlands di Scienze Biomediche 35100 Padova Edson R. Rocha Italy Department of Microbiology and Immunology East Carolina University Mike Sadowsky Greenville, NC 27858-4354 Department of Soil, Water, and Climate USA University of Minnesota Minneapolis, MN 55455 Palmer Rogers USA Department of Microbiology University of Minnesota Medical School Minneapolis, MN 55455 Hermann Sahm USA Institut Biotechnologie Forschungszentrum Jülich Lyudmila A. Romanenko D-52425 Jülich Senior Researcher in Biology Germany Laboratory of Microbiology Pacific Institute of Bioorganic Chemistry of the Joseph St. Geme Far-Eastern Branch of the Russian Academy Department of Molecular Microbiology of Sciences Washington University School of Medicine Vladivostoku, 159 St. Louis, MO 63110 Russia USA xlvi Contributors

Mirja Salkinoja-Salonen Bernhard Schink Department of Applied Chemistry & Fakultät für Biologie der Universität Konstanz Microbiology D-78434 Konstanz University of Helsinki Germany 00014 SF Finland Karl-Heinz Schleifer Lehrstruhl für Mikrobiologie James E. Samuel Technische Universität München Department of Medical Microbiology and D-85354 Freising Immunology Germany College of Medicine Texas A&M University System Health Science Heinz Schlesner Center Institut für Allgemeine Mikrobiologie College Station, TX, 77843-1114 Christian Albrechts Universität USA D-24118 Kiel Germany Philippe J. Sansonetti Unité de Pathogénie Michael Schmid Microbienne Moléculaire GSF-Forschungszentrum für Umwelt und Institut Pasteur Gesundheit GmbH 75724 Paris Institut für Bodenökologie France D-85764 Neuherberg Germany Scott R. Santos Department of Biochemistry & Molecular Jean M. Schmidt Biophysics Department of Botany and Microbiology University of Arizona Arizona State University Tucson, AZ 85721 Tempe, AZ 85287 USA USA Karin Schmidt Beatrice Saviola Institut für Mikrobiologie Departments of Molecular Microbiology and Georg-August-Universität Immunology D-3400 Göttingen Johns Hopkins School of Hygiene and Public Germany Health Baltimore, MD 21205-2105 Hildgund Schrempf USA FB Biologie/Chemie Universität Osnabrück Klaus P. Schaal 49069 Osnabrück Institut für Medizinische Germany Mikrobiologie und Immunologie Universität Bonn Milton N. Schroth D-53105 Bonn Department of Plant Pathology Germany University of California-Berkeley Berkeley, CA 94720 David Schauer USA Biological Engineering Division and Division of Comparative Medicine Heide N. Schulz Massachusetts Institute of Technology Institute for Microbiology Cambridge, MA 02139 University of Hannover USA D-30167 Hannover Germany Siegfried Scherer Department für Biowißenschaftliche Peter Schumann Grundlagen DSMZ-German Collection of Microorganisms Wißenschaftszentrum Weihenstephan and Cell Cultures GmbH Technische Universität München D-38124 Braunschweig D-85354 Freising, Germany Germany Contributors xlvii

Arthur Schüßler Michel Simonet Institut Botany Départment de Pathogenèse des Maladies 64287 Darmstadt Infectieuses et Parasitaires Germany Institut de Biologie de Lille 59021 Lille Tom G. Schwan France Rocky Mountain Labs Hamilton MT 59840 Mikael Skurnik USA Department of Medical Biochemistry University of Turku Edward Schwartz 20520 Turku Institut für Biologie/Mikrobiologie Finland Homboldt-Universität zu Berlin D-10115 Berlin Germany James M. Slauch Department of Microbiology James Scott College of Medicine Geophysical Laboratory University of Illinois Carnegie Institution of Washington and Washington, DC 20015 Chemical and Life Sciences Laboratory USA Urbana, IL 61801 USA Margrethe Hauge Serres Marine Biological Lab Ralph Slepecky Woods Hole, MA 02543 Department of Biology USA Syracuse University Syracuse, NY 13244 Jim Shapiro USA Department of Biochemistry & Molecular Biology Cummings Life Sciences Center Lindsay Sly Department of Microbiology Chicago, IL 60637-4931 University of Queensland USA Brisbane 4072 Queensland James Shapleigh Australia Department of Microbiology Cornell University C. Jeffrey Smith Wing Hall Department of Microbiology and Ithaca, NY 14853-8101 Immunology USA East Carolina University Greenville, NC 27858-4354 Lawrence J. Shimkets USA Department of Microbiology The University of Georgia Martin Sobierj Athens, GA 30602-2605 Department of Biology USA Environmental Science and Engineering Oregon Graduate Institute of Science and Thomas M. Shinnick Technology Center for Infectious Diseases Portland State University Centers for Disease Control Portland, OR 97291-1000 Atlanta, GA 30333 USA USA

Yuval Shoham Pamela A. Sokol Department of Food Engineering and Department of Microbiology and Infectious Biotechnology Diseases Technion—Israel Institute of Technology University of Calgary Health Science Center Haifa 32000 Calgary T2N 4N1 Israel Canada xlviii Contributors

Jay V. Solnick Thaddeus B. Stanton Department of Interanl Medicine (Infectious PHFSED Research Unit Diseases) and Medical National Animal Disease Center Microbiology and Immunology USDA-ARS University of California, Davis Ames, IA 50010 School of Medicine USA Davis, CA 95616 USA Daniel C. Stein Department of Cell Biology and Molecular Dimitry Yu. Sorokin Genetics Department of Biotechnology University of Maryland Delft University of Technology College Park, MD 20742 2628 BC Delft USA The Netherlands and Reinhard Sterner S.N. Winogradsky Institute of Microbiology Universitaet Regensburg 117811 Moscow Institut fuer Biophysik und Physikalische Russia Biochemie D-93053 Regensburg Georg A. Sprenger Germany Institut Biotechnologie Forschungszentrum Jülich Karl O. Stetter D-52425 Jülich Lehrstuhl für Mikrobiologie Germany Universität Regensburg D-93053 Regensburg Stefan Spring Germany Deutsche Sammlung von Mikroorganismen und Zellkulturen Andreas Stolz D-38124 Braunschweig Institut für Mikrobiologie Germany Universität Stuttgart 70569 Stuttgart Erko Stackebrandt Germany Deutsche Sammlung von Mikroorganismen und Zellkulturen Daphne L. Stoner D-38124 Braunschweig Idaho National Engineering Laboratory Germany EG & G Idaho Idaho Falls, ID 83415 David A. Stahl USA University of Washington Seattle, WA Paul Stoodley USA Center for Biofilm Engineering Montana State University Donald P. Stahly Bozeman, MT 59717-3980 Department of Microbiology USA University of Iowa Iowa City, IA 52242 James R. Swafford USA Department of Botany and Microbiology Arizona State University James Staley Tempe, AZ 85287 Department of Microbiology USA University of Washington Seattle, WA 98105 Jean Swings USA Laboratorium voor Microbiologie Department of Biochemistry Alfons J.M. Stams Physiology and Microbiology Laboratorium voor Microbiologie BCCM/LMG Bacteria Collection Wageningen University Universiteit Gent NL-6703 CT Wageningen Gent The Netherlands Belgium Contributors xlix

Mariko Takeuchi Olli Tuovinen Institute for Fermentation Department of Microbiology Osaka 532-8686 The Ohio State University Japan Columbus, OH 43210-1292 USA Ralph Tanner University of Oklahoma Francisco A. Uzal Norman, OK, 73019-0390 California Animal Health and Food Safety USA Laboratory University of California, Davis Andreas Teske San Bernardino, CA 92408 Department of Marine Sciences USA University of North Carolina at Chapel Hill Chapel Hill, NC 27599 Peter Vandamme USA Laboraroorium voor Microbiologie Faculteit Wetenschappen Michael Teuber Universiteit Gent ETH-Zentrum B-9000 Gent Lab Food Microbiology Belgium CH-8092 Zürich Switzerland Antonio Ventosa Department of Microbiology and Gabriele Timmermann Parasitology Institut für Allgemeine Botanik Faculty of Pharmacy Abteilung Mikrobiologie University of Sevilla Universität Hamburg 41012 Sevilla D-22069 Hamburg Spain Germany Gernot Vobis Brian J. Tindall Centro Regional Universitario Bariloche Deutsche Sammlung von Mikroorganismen und Universidad Nacional de Comahue Zellkulturen Barioloche 8400, Rio Negro Braunschweig D-38124 Argentina Germany Alexander von Graevenitz Kevin Towner Department of Medical Microbiology Consultant Clinical Scientist University of Zürich Public Health Laboratory GH-8028 Zürich University Hospital Switzerland Nottingham NG7 2UH UK Günther Wächterhäuser 80331 Munich Hans G. Trüper Germany Institut für Mikrobiologie und Biotechnologie D-53115 Bonn Lawrence P. Wackett Germany Department of Biochemistry, Molecular Biology Joseph G. Tully and National Institute for Allergy and Infectious Biophysics and Biological Process Technology Diseases Institute Frederick Cancer Research Center University of Minnesota Frederick, MD 21701 St. Paul, MN, 55108-1030 USA USA

Elaine Tuomanen William G. Wade Department of Infectious Diseases Department of Microbiology St. Jude Children’s Research Hospital Guy’s Campus Memphis, TN 38105-2394 London, SE1 9RT USA UK l Contributors

Michael Wagner Friedrich Widdel Lehrstuhl für Mikrobielle Ökologie Max-Planck-Institut für Marine Mikrobiologie Institut für Ökologie und Naturschutz D-28359 Bremen Universität Wien Germany A-1090 Vienna Austria Jürgen Wiegel University of Georgia David H. Walker Department of Microbiology Department of Pathology Athens, GA 30602 University of Texas Medical Branch USA Galveston, TX 77555-0609 USA Robert A. Wiley Queen Mary, University of London Naomi Ward London E1 4NS The Institute for Genomic Research UK Rockville, MD 20850 USA Tracy Wilkins TechLab, Inc. Trudy M. Wassenaar Corporate Research Center Molecular Microbiology and Genomics Blacksburg VA 24060-6364 Consultants USA 55576 Zotzenheim Germany Anne Willems Laboratorium voor Mikrobiologie John B. Waterbury Universiteit Gent Woods Hole Oceanographic Institution B-9000 Gent Woods Hole, MA 02543 Belgium USA Carl R. Woese Georges Wauters Department of Microbiology Université Catholique de Louvain University of Illinois Faculté de Médecine Urbana, IL 61801 Unité de Microbiologie USA B-1200 Bruxelles Belgium Ralph S. Wolfe Astri Wayadande Department of Microbiology Department of Entomology and Plant University of Illinois Pathology Urbana, IL 61801 Oklahoma State University Stillwater, OK Anne P. Wood USA Division of Life Sciences King’s College London Alison Weiss London WC2R 2LS Molecular Genetics, Biology and Microbiology UK University of Cincinnati Cincinnati, OH 45267 Donald Woods USA Department of Microbiology and Infectious Diseases Rodney A. Welch University of Calgary Health Science Center Medical Microbiology and Immunology Calgary T2N 4N1 University of Wisconsin Canada Madison, WI 53706-1532 USA Brendan W. Wren Department of Infectious and Tropical William B. Whitman Diseases Department of Microbiology London School of Hygiene and Tropical University of Georgia Medicine Athens, GA 30605-2605 London WC1E 7HT USA UK Contributors li

Timothy L. Yahr Vladimir V. Yurkov University of Iowa Department of Microbiology Iowa City, IA 52242 University of Manitoba USA Winnipeg R3T 2N2 Canada Atteyet F. Yassin Institut für Medizinische Georgi A. Zavarzin Mikrobiologie und Immunologie Institute of Microbiology Universität Bonn Academy of Sciences of the USSR D-53105 Bonn 117312 Moscow Germany Russia Gerhard Zellner Jung-Hoon Yoon Institute of Hydrology Korean Collection for Type Cultures National Research Center for Environment Korea Research Institute of Bioscience and and Health Biotechnology D-85764 Neuherberg Yuson, Taejon 305-600 Germany Korea Mary Jo Zidwick Allan A. Yousten Cargill Biotechnology Development Center Biology Department Freshwater Building Virginia Polytechnic Institute and State Minneapolis, MN 55440 University USA Blacksburg, VA 24061 USA Stephen Zinder Department of Microbiology Xue-Jie Yu Cornell University University of Texas Medical Branch 272 Wing Hall Galveston, TX Ithaca, NY 14853 USA USA