Bergey's Manual of Systematic Bacteriology 2nd Ed Vol 2 Proteobacteria Part C The Alpha-, Beta-, Delta and Epsilonproteobacteria

1414 Pages·2005·79.44 MB·English

by  George Garrity (Editor)

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BERGEY’S MANUAL OF
Systematic
Bacteriology
Second Edition
Volume Two
The Proteobacteria
Part C
The Alpha-, Beta-, Delta-, and
Epsilonproteobacteria
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BERGEY’S MANUAL OF
Systematic
Bacteriology
Second Edition
Volume Two
The Proteobacteria
Part C
The Alpha-, Beta-, Delta-, and
Epsilonproteobacteria
Don J. Brenner
Noel R. Krieg
James T. Staley
EDITORS, VOLUME TWO
George M. Garrity
EDITOR-IN-CHIEF
EDITORIAL BOARD
James T. Staley, Chairman, David R. Boone, Vice Chairman,
Don J. Brenner, Paul De Vos, George M. Garrity, Michael Goodfellow,
Noel R. Krieg, Fred A. Rainey, Karl-Heinz Schleifer
WITH CONTRIBUTIONS FROM 222 COLLEAGUES
GeorgeM.Garrity,Sc.D.
Bergey’sManualTrust
DepartmentofMicrobiologyandMolecularGenetics
MichiganStateUniversity
EastLansing,MI48824-4320
USA
LibraryofCongressControlNumber:2005926296
ISBN-10:0-387-24145-0
ISBN-13:978-0387-24145-6
Printedonacid-freepaper.
(cid:2)2005,1984–1989Bergey’sManualTrust
Allrightsreserved.Thisworkmaynotbetranslatedorcopiedinwholeorinpartwithoutthewritten
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This volume is dedicated to our colleagues,
David R. Boone, Don J. Brenner,
Richard W. Castenholz, and Noel R. Krieg, who
retired from the Board of Trustees of Bergey’s Manual
Trust as this edition was in preparation. We deeply
appreciate their efforts as editors and authors; they
have devoted their time and many years in helping
the Trust meet its objectives.
EDITORIAL BOARD AND TRUSTEES
OF BERGEY’S MANUAL TRUST
JamesT.Staley,Chairman
DavidR.Boone,ViceChairman
GeorgeM.Garrity
PaulDeVos
MichaelGoodfellow
FredA.Rainey
Karl-HeinzSchleifer
DonJ.Brenner,Emeritus
RichardW.Castenholz,Emeritus
JohnG.Holt,Emeritus
NoelR.Krieg,Emeritus
JohnListon,Emeritus
JamesW.Moulder,Emeritus
R.G.E.Murray,Emeritus
CharlesF.Niven,Jr.,Emeritus
NorbertPfennig,Emeritus
PeterH.A.Sneath,Emeritus
JosephG.Tully,Emeritus
StanleyT.Williams,Emeritus
Preface to Volume Two of the Second Edition of
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Bergey’s Manual of Systematic Bacteriology
Thereisalong-standingtraditionfortheEditorsofBergey’sMan- theirmanuscripts.WewouldalsoliketothankDrs.HansTru¨per,
ual to open their respective editions with the observation that Brian Tindall, and Jean Euze´by for their assistance on matters
the new edition is a departure from the earlier ones. As this of nomenclatureand etymology.
volume goes to press, however, we recognize a need to deviate We would like to express our thanks to the Department of
fromthispractice,byofferingaseparateprefacetoeachvolume MicrobiologyandMolecularGeneticsatMichiganStateUniver-
within this edition. In part, this departure is necessary because sity for housing our headquarters and editorial office and for
the size and complexity ofthis editionfarexceededourexpec- providingacongenialandsupportiveenvironmentformicrobial
tations, as has the amount of time that has elapsed between systematics. We would also like to thank Connie Williams not
publicationof the first volumeof this edition and this volume. onlyforherexpertsecretarialassistance,butalsoforunflagging
Earlier, we noted that systematic procaryotic biology is a dy- dedication to the mission of Bergey’s Manual Trust and Drs.
namic field, driven by constant theoretical and methodological JuliaBellandDeniseSearlesfortheirexperteditorialassistance
advances that will ultimately lead to a more perfect and useful anddiligenceinverifyingcountlesspiecesofcriticalinformation
classificationscheme.Clearly,thepacehasbeenacceleratingas and to Dr. Timothy G. Lilburn for constructing many of the
evidenced in the super-linear rate at which new taxa are being phylogenetictreesusedinthisvolume.Wealsoextendourthanks
described. Much of the increase can be attributed to rapid ad- to Alissa Wesche, Matt Chval and Kristen Johnson for their as-
vances in sequencing technology, which has brought about a sistancein compilationof the bibliography.
majorshiftinhowweviewtherelationshipsamongBacteriaand A project such as the Systematics Manual also requires the
Archaea. While the possibility of a universally applicablenatural strong and continuedsupportofadedicatedpublisher,andwe
classificationwasevidentastheFirstEditionwasinpreparation, have been most fortunate in this regard. We would also like to
it is only recently that the sequence databases became large express our gratitude to Springer-Verlag for supporting our ef-
enough, and the taxonomic coverage broad enough to make forts and for the development of the Bergey’s DocumentType
suchanarrangementfeasible.Wehavereliedheavilyuponthese Definition (DTD). We would especially like to thank our Exec-
datainorganizingthecontentsofthiseditionofBergey’sManual utive Editor, Dr. William Curtis for his courage, patience, un-
of Systematic Bacteriology, which will follow a phylogenetic frame- derstanding, and support; Catherine Lyonsforherexpertisein
work based on analysis of the nucleotide sequenceofthesmall designinganddevelopingourDTD,andJeriLambertandLeslie
ribosomalsubunitRNA,ratherthanaphenotypicstructure.This Grossberg of Impressions Book and Journal Services for their
departs from the First Edition, as well as the Eighth and Ninth efforts during the pre-production and production phases. We
EditionsoftheDeterminativeManual.Whiletherationaleforpre- would also like to acknowledge the support of ArborText,Inc.,
senting the content ofthisedition insuchamannershouldbe forprovidinguswithstate-of-the-artSGMLdevelopmentanded-
evidenttomostreaders,theyshouldbearinmindthatthisedi- iting tools at reduced cost. Lastly, I would like to express my
tion,asinallprecedingonesrepresentsaprogressreport,rather personalthankstomyfellowtrusteesforprovidingmewiththe
than a final classificationof procaryotes. opportunity to participate in this effort, to Drs. Don Brenner,
TheEditorsremindthereadersthattheSystematicsManualis NoelKrieg,andJamesStaleyfortheirenormouseffortsasvolume
a peer-reviewed collection of chapters, contributed by authors editorsandtomywife,Nancy,anddaughter,Jane,fortheircon-
who were invited by the Trust to share their knowledge and tinued patience,toleranceand support.
expertiseofspecifictaxa.Citationshouldrefertotheauthor,the Comments on this edition are welcomed and should be di-
chaptertitle,andinclusivepagesratherthantotheEditors.The rected to Bergey’s Manual Trust, Department of Microbiology
Trustisindebtedtoallofthecontributorsandreviewers,without andMolecularGenetics,6162BiomedicalandPhysicalSciences
whomthisworkwouldnotbepossible.TheEditorsaregrateful Building, Michigan State University, East Lansing, MI, USA
for the time and effort that each expended on behalf of the 48824-4320.Email:[email protected]
entirescientificcommunity.Wealsothanktheauthorsfortheir
good grace in accepting comments, criticisms, and editing of George M. Garrity
ix

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Preface to the First Edition of Bergey’s Manual of
Systematic Bacteriology
ManymicrobiologistsadvisedtheTrustthataneweditionofthe Advisory Committees, composed of prominent taxonomic au-
Manual was urgently needed. Of great concern to us was the thoritiestowhomwearemostgrateful.Authorswerechosenon
steadily increasing time interval between editions; this interval the basis of constant surveillance of the literature of bacterial
reachedamaximumof17yearsbetweentheseventhandeighth systematics and by recommendations from our Advisory Com-
editions. To be useful the Manual must reflect relatively recent mittees.
information; a new edition is soon dated or obsolete in parts Theactivationofthe1976Codehadintroducedsomenovel
becauseofthenearlyexponentialrateatwhichnewinformation problems.Wedecidedtoincludenotonlythosegenerathathad
accumulates. A new approach to publication was needed, and beenpublishedintheApprovedListsofBacterialNamesinJan-
from this conviction came our plan to publish the Manual as a uary 1980 or that had been subsequently validly published,but
sequence of four subvolumes concerned with systematic bacte- also certain genera whose names had no current standing in
riology as it applies to taxonomy. The four subvolumes are di- nomenclature.Wealsodecidedtoincludedescriptionsofcertain
videdroughlyasfollows:(a)theGram-negativesofgeneral,med- organismswhichhadnoformaltaxonomicnomenclature,such
icalorindustrialimportance;(b)theGram-positivesotherthan as the endosymbionts of insects. Our goal was to omit no im-
actinomycetes; (c) the archaeobacteria, cyanobacteria and re- portant group of cultivated bacteria and also to stimulate taxo-
maining Gram-negatives; and (d) the actinomycetes. The Trust nomic research on “neglected” groups and on some groups of
believed that more attention and care could be given to prep- undoubted bacteria that have not yet been cultivated and sub-
aration of the various descriptions within each subvolume,and jected to conventionalstudies.
also that each subvolume could be prepared, published, and The invited authors were provided with instructions andex-
revised as the area demanded, more rapidly than could be the emplarychaptersinJune1980and,althoughtheintendeddead-
case if the Manual were to remain as a single, comprehensive lineforreceiptofmanuscriptswasMarch1981,allcontributions
volumeasinthepast.Moreover,microbiologistswouldhavethe were assembled inJanuary1982forthefinalpreparations.The
optionofpurchasingonlythatparticularsubvolumecontaining Manualwas forwardedto the publisherin June 1982.
the organismsin which they were interested. Some readers will note the consistent use of the stem -var
TheTrustalsobelievedthatthescopeoftheManualneeded instead of -type in words such as biovar, serovar and pathovar.
tobeexpandedtoincludemoreinformationofimportancefor This is in keeping with the recommendations of the Bacterio-
systematic bacteriology and bring together informationdealing logical Code and was done against the wishes of some of the
with ecology, enrichment and isolation, descriptions of species authors.
and their determinative characters, maintenance and preserva- We have deleted much of the synonymy of scientific names
tion, all focused on the illumination of bacterial taxonomy. To which was contained in past editions. The adoption ofthenew
reflectthischangeinscope,thetitleoftheManualwaschanged startingdateofJanuary1,1980andpublicationoftheApproved
andtheprimarypublicationbecomesBergey’sManualofSystematic Lists of Bacterial Names has made mention of past synonymy
Bacteriology. This contains not only determinative material such obsolete. We have included synonyms of a name only if they
as diagnostic keys and tables useful for identification, but also havebeenpublishedsincethenewstartingdate,oriftheywere
all of the detailed descriptive information and taxonomiccom- also on the Approved Listsand,in rare caseswithcertainpath-
ments. Upon completion of each subvolume, the purely deter- ogens, if the mention of an old name would help readers asso-
minative information will be assembled for eventualincorpora- ciate the organism with a clinical problem. If the reader is in-
tion into a much smaller publication which will continue the terested in tracing the history of a name we suggest he or she
original name of the Manual, Bergey’s Manual of Determinative consult past editions of the Manual or the Index Bergeyana and
Bacteriology, which will be a similar but improved version of the its Supplement. In citations of names we have used the abbrevia-
presentShorter Bergey’s Manual.So,intheendtherewillbetwo tion AL to denote the inclusion of the name on the Approved
publications,onesystematicandonedeterminativeincharacter. Lists of Bacterial Names and VP to show the name has been
An important task of the Trust was to decide which genera validlypublished.
should be covered in the first and subsequent subvolumes. We In the matter of citation of the Manual in the scientific lit-
were assisted in this decision by the recommendations of our erature we again stress the fact that the Manual is a collection
xi
xii PREFACETOTHEFIRSTEDITION
ofauthoredchaptersandthecitationshouldrefertotheauthor, (LM-03707) from the National Library of Medicine, National
the chapter title and its inclusivepages,not the Editor. Institutes of Health to assist in the preparation of this and the
Toallcontributors,thesincerethanksoftheTrustisdue;the next volumeof the Manualis gratefullyacknowledged.
Editor is especially grateful for the good grace with which the Anumberofindividualsdeservespecialmentionandthanks
authorsacceptedcomments,criticismsandeditingoftheirman- fortheirhelp.ProfessorThomasO.McAdoooftheDepartment
uscripts.Itisonlybecauseofthevoluntaryanddedicatedefforts ofForeignLanguagesandLiteraturesattheVirginiaPolytechnic
of these authors that the Manual can continue to serve the sci- InstituteandStateUniversityhasgiveninvaluableadviceonthe
ence of bacteriologyon an internationalbasis. etymology and correctness of scientific names. Those assisting
A number of institutions and individuals deserve special ac- theEditorintheBlacksburgofficewereR.MartinRoopII,Don
knowledgment from the Trust for their help in bringing about D.Lee,EileenC.FalkandMichaelW.Friedmanandtheirhelp
thepublicationofthisvolume.WearegratefultotheDepartment issincerelyappreciated.IntheAmesofficewewereablyassisted
of Biology of the Virginia Polytechnic Institute and State Uni- by Gretchen Colletti and Diane Triggs during the early period
versityforprovidingspace,facilitiesand,aboveall,tolerancefor of preparation and by Cynthia Pease during the major portion
thedivertedtimetakenbytheEditorduringthepreparationof of the editing process. Mrs. Pease has been responsible for the
the book. The Department of Microbiology at Iowa State Uni- construction of the List of References and her willingness to
versity of Science and Technology continues to provide a wel- handlethecumbersomedetailsoftexteditingonabigcomputer
come home for the main editorial offices and archives of the is gratefullyacknowledged.
Trust and we acknowledge their continued support. A grant John G. Holt