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首页 伯杰细菌鉴定手册第九版(英文版)-bergeysoutline

伯杰细菌鉴定手册第九版(英文版)-bergeysoutline.pdf

伯杰细菌鉴定手册第九版(英文版)-bergeysoutline

桃小仙
2011-12-18 0人阅读 举报 0 0 暂无简介

简介:本文档为《伯杰细菌鉴定手册第九版(英文版)-bergeysoutlinepdf》,可适用于人文社科领域

DOI:bergeysoutlineTAXONOMICOUTLINEOFTHEPROKARYOTESBERGEY’SMANUAL®OFSYSTEMATICBACTERIOLOGY,SECONDEDITIONReleaseMayGeorgeMGarrityJuliaABellandTimothyGLilburnGeorgeMGarrityBergey’sManualTrustandDepartmentofMicrobiologyandMolecularGeneticsMichiganStateUniversityEastLansing,MI–JuliaABellFoodSafetyandToxicologyCenterMichiganStateUniversityEastLansing,MI–TimothyGLilburnBioinformaticsGroupAmericanTypeCultureCollectionManassas,VA©Bergey’sManualTrustAllrightsreservedThisworkmaynotbetransferredorcopiedinwholeorinpartwithoutwrittenpermissionofthepublisher,(SpringerNewYork,IncSpringStreet,NewYork,NY,USA),exceptforbriefexcerptsinconnectionwithreviewsorscholarlyanalysisUseinconnectionwithanyformofinformationstorageandretrieval,electronicadaptation,computersoftwareorbysimilarmethodologynowknownorhereafterdevelopedisforbiddenWhiletheadviceandinformationcontainedwithinthisdocumentarebelievedtobetrueandaccurateatthetimeofpublication,neithertheauthors,thepublisher,norBergey’sManualTrustcanacceptanylegalresponsibilityforanyerrorsoromissionsthatmaybemadeThepublishermakesnowarranty,expressorimplied,withrespecttothematerialcontainedhereinThisdocumentwasproducedbytheeditorialofficeofBergey’sManualTrustusingEpicDocumentArchitectandEpicEditor(Version,ArborText,AnnArbor,MI)andaprototypedocumenttypedefinitiondevelopedexpresslyfortaxonomichierarchiesDOIbergeysoutlineSpringerNewYorkBerlinHeidelbergTaxonomicOutlineoftheProkaryotesReleaseBergey’sManual®ofSystematicBacteriology,ndEditionGEORGEMGARRITY,JULIAABELLANDTIMOTHYGLILBURNBackgroundTheclassificationpresentedbelowwasinitiatedintheearlysintheeditorialofficeofBergey’sManualTrustasapreliminarystepinorganizingthecontentofthesecondeditionofBergey’sManualofSystematicBacteriology(theSystematics)Theprimaryobjectivewastodeviseaclassificationthatwouldreflectthephylogenyofprokaryotes,asdefinedbySrDNAsequenceanalysis,whilesimultaneouslyplacingallofthevalidlynamedmembersofagiventaxonintotheclassificationatasinglepoint,basedonthesequenceofthetypestrain,typespecies,ortypegenusUnderidealconditions,suchataskwouldberelativelystraightforwardAllspeciesassignedtoagenuswouldbeinagreementwiththephylogeneticmodelandthiswouldbereflectedinthenomenclatureFurthermore,eachspecieswouldbearasinglenamethatwouldreflectbothitstaxonomicandphylogeneticpositionHowever,wefindthisnottobethecaseasthereareanumberofexistinggenera(eg,Clostridium,Aquaspirillum)thatareparaphyleticbasedontheSrDNAmodelItisourviewthatsuchinstancesindicateaneedfortaxonomicrevisionInaddition,priortaxonomicrevisionshaveledtonumerousinstancesinwhichthesamespeciesmaybearmorethanonevalidlypublishedname,indicatingdifferencesintaxonomicopinionToensurecompleteness,wehaveoptedtoincludethemajorityofthesesynonymswithintheOutlinePlacementofspecieswithintheOutlineisdictatedbythegenusnameratherthanthepositionwithinanygivenphylogeneticmodelWebelievethatperiodicpublicationofupdatedversionsofthisOutlinewillprovidethecommunitywithanindicationoftheprogressthathasbeenmadeinresolvingsuchproblems,aswellaspointingoutanyremainingornewdiscrepanciesthathaveoccurredbetweenrevisionsTherefore,anyreferencetotheoutlineshouldincludethereleasenumber,thepublicationdate,andthedigitalobjectidentifier(theDOI)ofthereleasebeingreferencedTechnicalnotesReleasecoincideswiththepublicationofVolumeofthesecondeditionoftheSystematicsAsstatedearlier,wecontinuetosearchthetaxonomicliteratureandthepublicdatabasesfornew,highqualitySrDNAsequences(definedas>nts,<ambiguity,andfewerthanmissingpositions)andhaveaddedthesesequencestoourphylogeneticmodelsInthisrelease,welistuniquesequencesthatareassociatedwithtypestrainsandsynonymsWehavealsoaddednewspeciesnewcombinations,newgenera,newfamilies,neworder,andnewclasstoourtaxonomicmodelNewadditionsaresummarizedinTableThetaxonomicmodelWithinthisclassification,werecognizetwoprokaryoticdomains:theArchaeaandBacteriaThedomainsaredividedintophylawhichareinturndividedintoclasses,orders(exceptfortheCyanobacteriaforwhichweusetherankofsubdivision),families,andgeneraIntheActinobacteria,subclassesandsubordersarerecognized,andsubordersoccurwithintheMyxococcalesTherankofkingdomisnotusedtoavoidpossibleconflictswiththeBotanicalCode,wheresomeoverlapexistsReadersareadvisedthattheCodeofProkaryoticNomenclaturedoesnotcovertaxaabovetheClass,eventhoughthedomainandphylumnamesappearingintheOutlineandintheManualhaveappearedinValidationListAsofMay,validlynamedprokaryoticspeciesappearedeitherintheApprovedListofBacterialNames(Skermanetal,),inoriginalpaperspublishedintheInternationalJournalofSystematicBacteriologyortheInternationalJournalofSystematicandEvolutionaryMicrobiology,orinValidationLists–InthisversionoftheOutline,weextendourlistofsynonymstobyincludingforthcomingassertionsofsynonymythatwillappearinVolumeoftheSystematicsReadersshouldbeawarethat,insomecases,wehaveoptedtoexcludesomenamesthathavenotfoundwidespreadusage,eventhoughthosenamesarevalidlypublishedAmoredetaileddiscussionofthehistoricalaspectsofthiseffortarepresentedinthefirstreleaseoftheOutlineandbyGarrityandHoltinVolumeoftheSystematicsListswerepublishedintheInternationalJournalofSystematicBacteriologyandlistsintheInternationalJournalofSystematicandEvolutionaryMicrobiology,()(),(),(),(),(),,(),,,(),,(),,()(),,,(),,,(),,,(),,,(),,,(),,,(),,,(),,,(),,,(),,,(),,,(),,,(),,,,,(),,,,,(),,,,,(),,,,,:(),©Bergey’sManualTrustAllrightsreservedTaxonomicOutlineoftheProcaryotesAdoptionofahierarchicalclassificationpresentsseveraldifficultiesthatmustalsoberecognizedBydefinition,eachspeciesmustbeamemberofsuccessivelyhigherranks(sixofwhicharerecognizedforthemajorityoftaxainthesecondeditionoftheSystematics)Yetthereisconsiderablereluctanceamongmanycontemporarysystematicprocaryoticbiologiststoplacenewspeciesandgeneraintohighertaxa,especiallyattheintermediatelevels(family,order,andclass)becauseofuncertaintyofphylogeneticmodelsIncompilingandmaintainingtheoutlinewehaveoftenhadtodealwithinstanceswherenewspecieswerevariouslyassignedtoaclassordomainwithoutbeingascribedmembershipinanyoftheinterveningtaxaThismaybeattributedtoalackofclearrulesfordelineatinghighertaxaItmayalsoreflecttheinherentlimitationsoftheSrRNAgenefordefiningahighertaxonomicstructure,especiallywhencontemporaryphylogenetictechniques,whichrelyontreegraphsastheprincipalinterpretivedevice,areusedtoanalyzesmallandinherentlybiaseddatasetsWehavealsoobservedagenerallackofconsistencyindefiningtheboundariesofgenerabasedonSrDNAsequenceanalysisThisisparticularlyproblematicinbushyareasoftheARBandRDPtreeswhereuncertaintyofbranchingorderishighandcleardemarcationoftaxonomicgroupsisimpossibleintheabsenceofothersupportingdataIndealingwithsuchproblems,wehavefilledinthemissingtaxatocompletethehierarchyNamesofhighertaxaarebasedlargelyonpriority,exceptininstanceswheresuchastrategymightleadtounnecessaryconfusion(eg,Helicobacteraceaeratherthan“Wolinellaceae”)ConsiderableefforthasbeenspentinconfirmingtheplacementofgenerawithinhighertaxaEachofthesehighertaxahasalsobeenscrutinizedforphylogeneticcoherencesoastoavoidparaphyleticorpolyphyleticgroupingswhereverpossibleHowever,sinceSrDNAsequencesarenotyetavailableforallvalidlynamedspecies,somesuchinstanceswillremainfortheforeseeablefutureWehaveannotatedthespeciesleveloutlineinmanyareastoprovideuserssomeinsightintoourrationaleforplacementsthatmightbedeemedcontroversialortoalertthereadertoproblemsconcerningthevalidityorlegitimacyofnamesReadersareinvitedtopassalonganycommentsorobservations–alongwithsupportingdata–regardingotherpotentialmisplacementsorerrorsDespitesomelimitations,itisourviewthattheuseofthewellestablishedphylogenybasedontheSrRNAgeneprovidesamarkedimprovementovertheearlierartificialclassificationsofprokaryotesThetechnique(SrDNAsequencing)isuniversallyapplicableandprovidesasingletypeofdatathatwillsoonbeavailableforallvalidlynamedspeciesGiventherapidadvancementsinsequencingtechnology,weexpectthatsequencesofothergeneswillfollowinthenearfutureandhelpinresolvingtheplacementofproblemtaxaInterpretationofthetaxonomicoutlineAtpresent,thetwoprocaryoticdomainshavebeensubdividedintophyla,twoofwhichoccurwithintheArchaeaTheremainingphylaareascribedtotheBacteriaThefactthattheArchaeaanddeeplybranchingBacteriaarepresentedfirstisbasedlargelyontheearlyversionsoftheRDPtreeSincethebranchingorderofspecieswithingeneraisfrequentlyambiguousandthedatasetisknowntobeincomplete,theuseofphylogenetictreesasaguidefororderingtaxa,bothintheoutlineandtheSystematicsManualprovedtobeuntenableThus,wehaveadoptedamoreworkableandallinclusivestrategyThetypetaxonalwaysappearsfirstWithinlowertaxa,membersoftherankwillusuallyappearinalphabeticalorderThehierarchicalnumberingschemeusedintheoutlineisarbitrary,especiallyatthelowerlevelsItisalsosubjecttochangeasnewtaxaaredescribedandexistingtaxareclassifiedTherefore,weadviseagainstusingthenumberingschemeasanorganizationalormnemonicdeviceDecodingtheentriesWithinthisdocument,aswellaswithintheSystematics,wefollowtheAmericanstyleforrenderingLatinizednamesRegardlessofrank,allnamesappearinitalicsThesuperscriptALindicatesthatthenamewasincludedontheApprovedListsofBacterialNamespublishedinThesuperscriptVPindicatesthatthenamewasvalidlypublishedintheInternationalJournalofSystematicBacteriology(nowtheInternationalJournalofSystematicandEvolutionaryMicrobiology)orappearedononeofthevalidationlistspublishedinthatjournalNamesappearinginquoteshavenostandinginnomenclature,althoughtheymayhavebeeneffectivelypublishedelsewhereNamesfollowedwithsuperscriptedNPareindicativeofproposalsfornewtaxathatwillappearintheforthcomingsecondvolumeoftheSystematicsInthecaseofspeciesnames,eachisfollowedwiththeauthorityforthenameandyearoftheoriginaldescription,inabbreviatedformThetypestrain(species),typespecies(genus),typegenus(familyandorder),andtypeorder(classandabove)areindicatedbyanuppercaseT,enclosedinparenthesesandinsuperscriptNewtaxa(recentlyadded)arehighlightedinredtypeandthosewhichhavebeenrelocatedwithintheoutlineasaresultofcommentsfromexpertsappearinmagentaReadersshouldunderstandthatthetaxaarenot,inrealitymoved,butarethesubjectofalternativetaxonomicviewsItislikelythatthisnumberunderstatesthetruenumberofphylumlevellineageswithintheBacteriaHugenholtzrecognizesatleastfourotherphylawithintheFirmicutesBergey’sManualofSystematicBacteriology,ndEditionIntheunabridgedversionoftheoutlinethatincludesspeciesnamesandassociatedinformation,proposalsfornewcombinationstypicallyresultinmultiplechangeswithinthetaxonomyThenewnameisfollowedbythebasonym,whichisidentifiedbythesymbol<precedingtheoldnameBasonymsarealsohomotypicsynonyms(formerlyreferredtoasobjectivesynonyms)bydefaultTominimizeredundancy,wewillnotidentifythemassuchTheoldnameisalsoretainedwithintheoutline,intheoriginallocationHowever,oldernamesareprecededbyadaggersymbol(†)andshouldbeconsidereddeprecatedundermostcircumstancesFollowingtheoldnameandinformationaboutthetaxonomicauthoritythenewnameappearsingreentypeprecededbyanarrow(>)Ininstancesofsynonymy,thesynonyms(eitherhomotypicorheterotypic)areidentifiedassuchandprecededbyanequalssign(=)Synonymsarefurthercategorizedaseitherseniororjunior,indicatingpriorityMoredetailedinformationregardingthetopicsofsynonymyandpriorityareavailableintheInternationalCodeofNomenclatureofBacteria(Revision)andinMinutesoftheJudicialCommissiononProkaryoticNomenclaturepublishedintheInternationalJournalofSystematicandEvolutionaryMicrobiologyImmediatelyfollowingthenomenclaturesectionofeachentryfollowskeyinformationregardingthetypestrain,includingtheoriginalstraindesignation,whenreported,andallknowndepositsinmajorculturecollectionsEachsuchdepositissetoffbyasmallverticalbar(|)IfoneormorehighqualitySrDNAsequenceshavebeenreportedforthatstrain,informationregardingthosesequenceswillfollowThefirstvaluewillbetheGenBank,EMBLorDDBJaccessionnumber(s)ThiswillbefollowedbytheRDPshortidentifier,whichistypicallyanalphanumericabbreviationderivedfromthespeciesnameEachsuchtripletissetofffromothersbythesmallverticalbar(|)CitationGarrity,GM,JABellandTGLilburn()TaxonomicOutlineoftheProkaryotesBergey’sManualofSystematicBacteriology,SecondEdition,Release,SpringerVerlag,NewYorkpagesDOI:bergeysoutlineAcknowledgmentsWealsowouldliketoacknowledgeDrsWolfgangLudwigandKarlHeinzSchleifer(TechnicalUniversityofMunich),SeanTurner(NCBI),PhilipHugenholtz(UCBerkeley),andJamesColeandQiongWang(RDPCenterforMicrobialEcology,MichiganState)fortheirnumerousandhelpfuldiscussionsonresolvingdiscrepanciesbetweentheBergey’sOutlineandthephylogeneticreferencetreesanduncoveringannotationerrorsDrsJeanEuzéby(ÉcoleNationaleVétérinairedeToulouse),BrianTindall(DeutscheSammlungvonMikroorganismenundZellkulturen,GmbH)andAharonOrenfornumeroushelpfulandspiritedcommentsonnomenclatureandeditorialremarksWewouldalsoliketoextendourthankstoDrsDavidBoone,PaulDeVos,MichaelGoodfellow,NoelKreig,FredRainey,ErkoStackebrandt,JamesStaley,JosephTully,andWilliamWhitmanfortheirhelpfuldiscussionsandconstructivecommentsThisdocumentwasdevelopedandismaintainedasanXMLinstanceofacustomdocumenttypedefinitionfortaxonomichierarchiesusingEpicArchitectandEpicEditor,Version,(ArborText,AnnArbor,MI)TheDTDwasauthoredbyGeorgeMGarrity(MichiganStateUniversity,EastLansing,MI)andCatherineLyons(Explicatrixllc,Sterling,NJ)andisinteroperablewiththeBergey’sManualDTDThisresearchwassupportedinpartbytheBiologicalandEnvironmentalResearchProgram(BER),USDepartmentofEnergy,GrantNoDEFGERLapageetal,()ASMPress,Washington,DCWiththisreleaseoftheOutline,wehaveimplementedachangeintheprefixoftheformerInstituteofFermentation,Osakaculturecollection(IFO)tothenewdesignationastheNITE(NationalInstituteofTechnologyandEvaluation)BiologicalResourceCenter(NBRC)TaxonomicOutlineoftheProcaryotesRankTaxonPhylumClassClassAnaerolineaeChloroflexiOrderAnaerolinaelesChloroflexiAnaerolineaeFamilyAnaerolinaeceeaChloroflexiAnaerolineaeHydrogenimonaceaeProteobacteriaEpsilonproteobacteriaThermodesulfobiaceaeFirmicutesClostridiaGenusAeriscardoviaActinobacteriaActinobacteriaAestuariibacterProteobacteriaGammaproteobacteriaAlistipesBacteroidetesBacteroidetesAnaerolineaChloroflexiAnaerolineaeAnaerotruncusFirmicutesClostridiaAquicellaProteobacteriaGammaproteobacteriaArsenicicoccusActinobacteriaActinobacteriaBalneariumAquificaeAquificaeBelliellaBacteroidetesSphingobacteriaBryantellaFirmicutesClostridiaCaldanaerobacterFirmicutesClostridiaCaldilineaChloroflexiAnaerolineaeCaldithrixDeferribacteresDeferribacteresDesulfatibacillumProteobacteriaDeltaproteobacteriaFulvimarinaProteobacteriaAlphaproteobacteriaGillisiaBacteroidetesFlavobacteriaHespelliaFirmicutesClostridiaHongiellaBacteroidetesSphingobacteriaHydrogenimonasProteobacteriaEpsilonproteobacteriaHylemonellaProteobacteriaBetaproteobacteriaKerstersiaProteobacteriaBetaproteobacteriaMesoniaBacteroidetesFlavobacteriaMethanomethylovoransEuryarchaeotaMethanomicrobiaNitratireductorProteobacteriaAlphaproteobacteriaOceanicaulisProteobacteriaAlphaproteobacteriaOceanisphaeraProteobacteriaGammaproteobacteriaOttowiaProteobacteriaBetaproteobacteriaParasporobacteriumFirmicutesClostridiaPhytoplasmaFirmicutesMollicutesPropionicimonasActinobacteriaActinobacteriaRhabdochlamydiaChlamydiaeChlamydiaeSalinibacteriumActinobacteriaActinobacteriaBergey’sManualofSystematicBacteriology,ndEditionRankTaxonPhylumClassSilicibacterProteobacteriaAlphaproteobacteriaSoehngeniaFirmicutesClostridiaSulfurimonasProteobacteriaEpsilonproteobacteriaThalassolituusProteobacteriaGammaproteobacteriaThermodesulfatatorThermodesulfobacteriaThermodesulfobacteriaThermodesulfobiumFirmicutesClostridiaWautersiaProteobacteriaBetaproteobacteriaXylanibacteriumActinobacteriaActinobacteriaYaniaActinobacteriaActinobacteriaSpeciesAchromobacterdenitrificansProteobacteriaBetaproteobacteriaAchromobacterinsolitusProteobacteriaBetaproteobacteriaAchromobacterspaniusProteobacteriaBetaproteobacteriaActinomaduramexicanaActinobacteriaActinobacteriaActinomadurameyeriiActinobacteriaActinobacteriaActinomyceshongkongensisActinobacteriaActinobacteriaAeriscardoviaaeriphilaActinobacteriaActinobacteriaAeromicrobiummarinumActinobacteriaActinobacteriaAeromonassimiaeProteobacteriaGammaproteobacteriaAeropyrumcaminiCrenarchaeotaThermoproteiAestuariibacterhalophilusProteobacteriaGammaproteobacteriaAestuariibactersalexigensProteobacteriaGammaproteobacteria

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  • 113.14.56.211 大家不要搞错了,这是分类手册,不是鉴定手册!!!!伯杰鉴定手册现在还没出第九版!

    2012-05-25 23:19:48

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伯杰细菌鉴定手册第九版(英文版)-bergeysoutline

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