The Prokaryotes: Other Major Lineages of Bacteria and The Archaea

1018 Pages·2014·35.66 MB·English

by  Eugene Rosenberg

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
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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.