Bergey's Manual® of Systematic Bacteriology: The Proteobacteria (Part C) PDF
Preview Bergey's Manual® of Systematic Bacteriology: The Proteobacteria (Part C)
(cid:1) BERGEY’S MANUAL OF Systematic Bacteriology Second Edition Volume Two The Proteobacteria Part C The Alpha-, Beta-, Delta-, and Epsilonproteobacteria (cid:1) 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 permissionofthepublisher(SpringerScience(cid:3)BusinessMedia,Inc.,233SpringStreet,NewYork,NY 10013,USA),exceptforbriefexcerptsinconnectionwithreviewsorscholarlyanalysis.Useinconnection with any form of information storage and retrieval, electronic adaptation, computer software, or by similarordissimilarmethodologynowknownorhereafterdevelopedisforbidden. Theuseinthispublicationoftradenames,trademarks,servicemarks,andsimilarterms,evenifthey arenotidentifiedassuch,isnottobetakenasanexpressionofopinionastowhetherornottheyare subjecttoproprietaryrights. PrintedintheUnitedStatesofAmerica. (APEX/MVY) 9 8 7 6 5 4 3 2 1 springeronline.com 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 (cid:1) 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 (cid:1) 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 (cid:1) Preface to the First Edition of Bergey’s Manual of Determinative Bacteriology Theelaboratesystemofclassificationofthebacteriaintofamilies, TheCommitteedesirestoexpressitsappreciationandthanks tribesandgenerabyaCommitteeonCharacterizationandClas- to those members of the society who gave valuable aid in the sificationoftheSocietyofAmericanBacteriologists(1911,1920) compilation of material and the classification of certain has made it very desirable to be able to place in the hands of species.. . . studentsamoredetailedkeyfortheidentificationofspeciesthan Theassistanceofallbacteriologistsisearnestlysolicitedinthe any that is available at present. The valuable book on “Deter- correction of possible errors in the text; in the collection of minative Bacteriology” by Professor F. D. Chester, publishedin descriptionsofallbacteriathatmayhavebeenomittedfromthe 1901, is now of very little assistance to the student,and allpre- text;in supplyingmoredetaileddescriptionsofsuchorganisms vious classifications are of still less value, especially as earlier as are described incompletely; and in furnishing complete de- systemsofclassificationwerebasedentirelyonmorphologicchar- scriptions of new organisms that may be discovered, or in di- acters. recting the attention of the Committee to publications of such It is hoped that this manual will serve tostimulateeffortsto newly describedbacteria. perfect the classification of bacteria, especially by emphasizing David H. Bergey, Chairman the valuable features as well as the weaker points in the new Francis C. Harrison system which the Committee of the Society of American Bacte- RobertS. Breed riologistshaspromulgated.TheCommitteedoesnotregardthe Bernard W. Hammer classification of species offered here as in any sense final, but Frank M. Huntoon merely a progress report leading to more satisfactoryclassifica- Committeeon Manual. tion in the future. August,1923. xiii
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