Eugene Rosenberg Editor-in-Chief Edward F. DeLong Stephen Lory Erko Stackebrandt Fabiano Thompson Editors The Prokaryotes Other Major Lineages of Bacteria and the Archaea Fourth Edition 1 3 Reference The Prokaryotes Eugene Rosenberg (Editor-in-Chief) Edward F. DeLong, Stephen Lory, Erko Stackebrandt and Fabiano Thompson (Eds.) The Prokaryotes Other Major Lineages of Bacteria and the Archaea Fourth Edition With253Figuresand207Tables Editor-in-Chief EugeneRosenberg DepartmentofMolecularMicrobiologyandBiotechnology TelAvivUniversity TelAviv,Israel Editors EdwardF.DeLong ErkoStackebrandt DepartmentofBiologicalEngineering LeibnizInstituteDSMZ-GermanCollectionofMicroorganisms MassachusettsInstituteofTechnology andCellCultures Cambridge,MA,USA Braunschweig,Germany CenterforMicrobialOceanography:ResearchandEducation FabianoThompson UniversityofHawaii LaboratoryofMicrobiology,InstituteofBiology,Centerfor Manoa,Honolulu,HI,USA HealthSciences FederalUniversityofRiodeJaneiro(UFRJ) StephenLory IlhadoFunda˜o,RiodeJaneiro,Brazil DepartmentofMicrobiologyandImmunobiology HarvardMedicalSchool Boston,MA,USA Videostothisbookcanbeaccessedat http://www.springerimages.com/videos/978-3-642-38953-5 ISBN978-3-642-38953-5 ISBN978-3-642-38954-2(eBook) ISBN978-3-642-38955-9(printandelectronicbundle) DOI10.1007/978-3-642-38954-2 SpringerHeidelbergNewYorkDordrechtLondon LibraryofCongressControlNumber:2014949495 3rdedition:©SpringerScience+BusinessMedia,LLC2006 4thedition:©Springer-VerlagBerlinHeidelberg2014 Thisworkissubjecttocopyright.AllrightsarereservedbythePublisher,whetherthewholeorpartofthematerialisconcerned,specificallytherightsof translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or informationstorageandretrieval,electronicadaptation,computersoftware,orbysimilarordissimilarmethodologynowknownorhereafterdeveloped. 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Whiletheadviceandinformationinthisbookarebelievedtobetrueandaccurateatthedateofpublication,neithertheauthorsnortheeditorsnorthepublisher canacceptanylegalresponsibilityforanyerrorsoromissionsthatmaybemade.Thepublishermakesnowarranty,expressorimplied,withrespecttothe materialcontainedherein. Printedonacid-freepaper SpringerispartofSpringerScienceþBusinessMedia(www.springer.com) Foreword Thepurposeofthisbriefforewordisunchangedfromthefirstedition;itissimplytomakeyou,thereader,hungryforthescientific feastthatfollows.These11volumesontheprokaryotesofferanexpandedscientificmenuthatdisplaysthebiochemicaldepthand remarkable physiological and morphological diversity of prokaryote life. The size of the volumes might initially discourage the unprepared mind from being attracted to the study of prokaryote life, for this landmark assemblage thoroughly documents the wealthofpresentknowledge.Butinconfrontingthereaderwiththestateoftheart,theHandbookalsodefineswheremorework needstobedoneonwell-studiedbacteriaaswellasonunusualorpoorlystudiedorganisms. This edition of The Prokaryotes recognizes the almost unbelievable impact that the work of Carl Woese has had in defining aphylogeneticbasisforthemicrobialworld.Theconceptthattheribosomeisahighlyconservedstructureinallcellsandthatits nucleicacidcomponentsmayserveasaconvenientreferencepointforrelatingalllivingthingsisnowgenerallyaccepted.Atlast,the phylogenyofprokaryoteshasascientificbasis,andthisisthefirstseriousattempttopresentacomprehensivetreatiseonprokaryotes along recently defined phylogenetic lines. Although evidence is incomplete for many microbial groups, these volumes make astatementthatclearlyilluminatesthepathtofollow. Therearebasicallytwowaysofdoingresearchwithmicrobes.Aclassicalapproachisfirsttodefinethephenomenontobestudied andthentoselecttheorganismaccordingly.Anotherwayistochooseaspecificorganismandgowhereitleads.Thepursuitofan unusualmicrobebringsoutthelatenthunterinallofus.Theintellectualchallengesofthechasefrequentlytestouringenuitytothe limit.Sometimesthequarryrepeatedlyescapes,butthefinalcaptureisindeedawonderfulexperience.Formanyofus,thesesimple rewards are sufficiently gratifying so that we have chosen to spend our scientific lives studying these unusual creatures. In these endeavors,manyofthestrategiesandtoolsaswellasmuchofthephilosophymaybetracedtotheDelftSchool,passedontousbyour teachers,MartinusBeijerinck,A.J.Kluyver,andC.B.vanNiel,andinturnpassedonbyustoourstudents. Inthisschool,theprinciplesoftheselective,enrichmentculturetechniquehavebeendevelopedanddiversified;theyhavebeen amajorforceindesigningandapplyingnewprinciplesforthecaptureandisolationofmicrobesfromnature.Forme,the‘‘organism approach’’hasprovidedrewardingadventures.Theorganismcontinuallychallengesandliterallydragstheinvestigatorintonewareas whereunfamiliar toolsmaybeneeded.Ibelievethatorganism-orientedresearchisanimportantalternativetoproblem-oriented research,fornewconceptsofthefutureverylikelylieinastudyofthebreadthofmicrobiallife.Thephysiology,biochemistry,and ecology of the microbe remain the most powerful attractions. Studies based on classical methods as well as modern genetic techniqueswillresultinnewinsightsandconcepts. Tosomereaders,thiseditionofTheProkaryotesmayindicatethatthefieldisnowmature,thatfromhereonitisamatteroffilling indetails.Isuspectthatthisisnotthecase.Perhapswehaveassumedprematurelythatwefullyunderstandmicrobiallife.VanNiel pointedouttohisstudentsthat—afteralifetimeofstudy—itwasaveryhumblingexperiencetoviewinthemicroscopeasampleof microbesfromnatureandrecognizeonlyafew.Recentevidencesuggeststhatmicrobeshavebeenevolvingfornearly4billionyears. Mostcertainly,thosemicrobesnowdomesticatedandkeptincaptivityinculturecollectionsrepresentonlyaminorportionofthe speciesthathaveevolvedinthistimespan.Sometimeswemustremindourselvesthatevolutionisactivelytakingplaceatthepresent moment.Thattheeukaryotecellevolvedasachimeraofcertainprokaryotepartsisagenerallyacceptedconcepttoday.Higheraswell aslowereukaryotesevolvedincontactwithprokaryotes,andevidencesurroundsusofthecomplexinteractionsbetweeneukaryotes andprokaryotesaswellasamong prokaryotes.Wehavesofaronlyscratchedthesurfaceofthesebiochemicalinterrelationships. Perhapsthelegumenoduleisapertinentexampleofnaturecaughtintheactofevolvingthe‘‘nitrosome,’’auniquenitrogen-fixing organelle.Thestudyofprokaryotesisproceedingatsuchafastpacethatmajoradvancesareoccurringyearly.Theincreaseofthis editiontofourvolumesdocumentstheexcitingpaceofdiscoveries. ToprepareatreatisesuchasTheProkaryotesrequiresdedicatededitorsandauthors;thetaskhasbeenenormous.Ipredictthatthe scientificcommunityof microbiologists will again showits appreciation through use of these volumes—such that thepages will become‘‘dog-eared’’andwornasstudentsseekbasicinformationforthehunt.Thesevolumesbelonginthelaboratory,notinthe library.Ibelievethatamosteffectivewaytointroducestudentstomicrobiologyisforthemtoisolatemicrobesfromnature,thatis, from their habitats in soil, water, clinical specimens, or plants. The Prokaryotes enormously simplifies this process and should encourage the construction of courses that contain a wide spectrum of diverse topics. For the student as well as the advanced investigator,thesevolumesshouldgenerateexcitement. Happyhunting! RalphS.Wolfe DepartmentofMicrobiology UniversityofIllinoisatUrbana-Champaign Preface Duringmostofthetwentiethcentury,microbiologistsstudiedpureculturesunderdefinedlaboratoryconditionsinordertouncover the causative agents of disease and subsequently as ideal model systems to discover the fundamental principles of genetics and biochemistry. Microbiology as a discipline onto itself, e.g., microbial ecology, diversity, and evolution-based taxonomy, has only recentlybeenthesubjectofgeneralinterest,partlybecauseoftherealizationthatmicroorganismsplayakeyroleintheenvironment. Thedevelopmentandapplicationofpowerfulculture-independentmolecular techniquesandbioinformaticstoolshasmadethis developmentpossible.ThefourtheditionoftheHandbookoftheProkaryoteshasbeenupdatedandexpandedinordertoreflectthis neweraofmicrobiology. Thefirstfivevolumesofthefourtheditioncontain34updatedand43entirelynewchapters.Mostofthenewchaptersareinthe twonewsections:ProkaryoticCommunitiesandBacteriainHumanHealthandDisease.Acollectionofmicroorganismsoccupying thesamephysicalhabitatiscalleda‘‘community,’’andseveralexamplesofbacterialcommunitiesarepresentedintheProkaryotic Communities section, organized by Edward F. DeLong. Over the last decade, important advances in molecular biology and bioinformaticshaveledtothedevelopmentofinnovativeculture-independentapproachesfordescribingmicrobialcommunities. Thesenewstrategies,basedontheanalysisofDNAdirectlyextractedfromenvironmentalsamples,circumventthestepsofisolation andculturingofmicroorganisms,whichareknownfortheirselectivityleadingtoanonrepresentativeviewofprokaryoticdiversity. Describingbacterialcommunitiesisthefirststepinunderstandingthecomplex,interactingmicrobialsystemsinthenaturalworld. ThesectiononBacteriainHumanHealthandDisease,organizedbyStephenLory,containschaptersonmostoftheimportant bacterialdiseases,eachwrittenbyanexpertinthefield.Inaddition,thereareseparategeneralchaptersonidentificationofpathogens byclassicalandnon-culturingmoleculartechniquesandvirulencemechanisms,suchasadhesionandbacterialtoxins.Inrecognition of the recent important research on beneficial bacteria in human health, the section also includes chapters on gut microbiota, prebiotics,andprobiotics.TogetherwiththeupdatedandexpandedchapteronBacterialPharmaceuticalProducts,thissectionis avaluableresourcetograduatestudents,teachers,andresearchersinterestedinmedicalmicrobiology. Volumes6–11,organizedbyErkoStackebrandtandFabianoThompson,contain265chaptersintotaloneachoftheca.300 knownprokaryoticfamilies,insomecasesevenhighertaxa.Eachchapterpresentsboththehistoricalandcurrenttaxonomyofthese taxa,mostlyabovethegenuslevel;molecularanalyses(e.g.,DDH,MLSA,riboprinting,andMALDI-TOF);genomicandphenetic propertiesofthetaxacovered;genomeanalysesincludingnonchromosomalgeneticelements;phenotypicanalyses;methodsforthe enrichment,isolation,andmaintenanceofmembersofthefamily;ecologicalstudies;clinicalrelevance;andapplications. Asinthethirdedition,thevolumesinthefourtheditionareavailablebothashardcopiesandaseReferences.Theadvantagesof the online version include no restriction of color illustrations, the possibility of updating chapters continuously and, most importantly, libraries can place their subscribed copies on their servers, making it available to their community in offices and laboratories.TheeditorsthankallthechapterauthorsandtheeditorialstaffofSpringer,especiallyHannaHensler-Fritton,Isabel Ullmann,DanielQuin˜ones,AlejandraKudo,andAudreyWong,formakingthiscontributionpossible. EugeneRosenberg Editor-in-Chief About the Editors EugeneRosenberg(Editor-in-Chief) DepartmentofMolecularMicrobiologyandBiotechnology TelAvivUniversity TelAviv Israel EugeneRosenbergholdsaPh.D.inbiochemistryfromColumbiaUniversity(1961)wherehedescribedthechemicalstructuresofthe capsules of Hemophilus influenzae, types B, E, and F. His postdoctoral research was performed in organic chemistry under the guidanceofLordToddinCambridgeUniversity.HewasanassistantandassociateprofessorofmicrobiologyattheUniversityof CaliforniaatLosAngelesfrom1962to1970,whereheworkedonthebiochemistryofMyxococcusxanthus.Since1970,hehasbeenin the Department of Molecular Microbiology and Biotechnology, Tel Aviv University, as an associate professor (1970–1974), full professor(1975–2005),andprofessoremeritus(2006–present).HehasheldtheGolChairinAppliedandEnvironmentalMicro- biologysince1989.HeisamemberoftheAmericanAcademyofMicrobiologyandEuropeanAcademyofMicrobiology.Hehasbeen awarded a Guggenheim Fellowship, a Fogarty International Scholar of the NIH, the Pan Lab Prize of the Society of Industrial Microbiology,theProctor&GamblePrizeoftheASM,theSakovPrize,theLandauPrize,andtheIsraelPrizefora‘‘BeautifulIsrael.’’ Hisresearchhasfocusedonmyxobacteriology;hydrocarbonmicrobiology;surface-activepolymersfromAcinetobacter;biore- mediation;coralmicrobiology;andtheroleofsymbioticmicroorganismsintheadaptation,development,behavior,andevolutionof animalsandplants.Heistheauthorofabout250researchpapersandreviews,9books,and16patents.