The Prokaryotes: Prokaryotic Biology and Symbiotic Associations

629 Pages·2013·18.556 MB·English

by  Carl R. Woese (auth.), Eugene Rosenberg, Edward F. DeLong, Stephen Lory, Erko Stackebrandt, Fabiano Thompson (eds.)

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9 783642 301933 4th Ed. Reference
The Prokaryotes

Eugene Rosenberg (Editor-in-Chief)
Edward F. DeLong, Stephen Lory, Erko Stackebrandt and Fabiano Thompson (Eds.)
The Prokaryotes
Prokaryotic Biology and Symbiotic Associations
Fourth Edition
With183Figuresand62Tables
Editor-in-Chief
EugeneRosenberg
DepartmentofMolecularMicrobiologyandBiotechnology
TelAvivUniversity
TelAviv,Israel
Editors
EdwardF.DeLong FabianoThompson
DepartmentofBiologicalEngineering LaboratoryofMicrobiology,InstituteofBiology,Centerfor
MassachusettsInstituteofTechnology HealthSciences
Cambridge,MA,USA FederalUniversityofRiodeJaneiro(UFRJ)
IlhadoFunda˜o,RiodeJaneiro,Brazil
StephenLory
DepartmentofMicrobiologyandImmunology
HarvardMedicalSchool
Boston,MA,USA
ErkoStackebrandt
LeibnizInstituteDSMZ-GermanCollectionofMicroorganisms
andCellCultures
Braunschweig,Germany
ISBN978-3-642-30193-3 ISBN978-3-642-30194-0(eBook)
ISBN978-3-642-30195-7(printandelectronicbundle)
DOI10.1007/978-3-642-30194-0
SpringerHeidelbergNewYorkDordrechtLondon
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4thedition:©Springer-VerlagBerlinHeidelberg2013
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Foreword
Thepurposeofthisbriefforewordisunchangedfromthefirstedition;itissimplytomakeyou,thereader,hungryforthescientific
feastthatfollows.These11volumes(planned)ontheprokaryotesofferanexpandedscientificmenuthatdisplaysthebiochemical
depthandremarkablephysiologicalandmorphologicaldiversityofprokaryotelife.Thesizeofthevolumesmightinitiallydiscourage
theunpreparedmindfrombeingattractedtothestudyofprokaryotelife,forthislandmarkassemblagethoroughlydocumentsthe
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.
Volumes 6–11, organized by Erko Stackebrandt and Fabiano Thompson, contain chapters on each of the ca. 300 known
prokaryoticfamilies.Eachchapterpresentsboththehistoricalandcurrenttaxonomyofhighertaxa,mostlyabovethegenuslevel;
molecular analyses (e.g., DDH, MLSA, riboprinting, and MALDI-TOF); genomic and phenetic properties of the taxa covered;
genome analyses including nonchromosomal genetic elements; phenotypic analyses; methods for the enrichment, isolation, and
maintenanceofmembersofthefamily;ecologicalstudies;clinicalrelevance;andapplications.
Asinthethirdedition,thevolumesinthefourtheditionareavailablebothashardcopiesande-books,andaseReferences.The
advantagesoftheonlineversionincludenorestrictionofcolorillustrations,thepossibilityofupdatingchapterscontinuouslyand,
mostimportantly,librariescanplacetheirsubscribedcopiesontheirservers,makingitavailabletotheircommunityinofficesand
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.