The Prokaryotes: Prokaryotic Communities and Ecophysiology

548 Pages·2013·18.263 MB·English

by  Dr. David A. Stahl, Jason J. Flowers, Meredith Hullar, Seana Davidson (auth.), Eugene Rosenberg, Edward F. DeLong, Stephen Lory, Erko Stackebrandt, Fabiano Thompson (eds.)

The Prokaryotes

Eugene Rosenberg (Editor-in-Chief)
Edward F. DeLong, Stephen Lory, Erko Stackebrandt and Fabiano Thompson (Eds.)
The Prokaryotes
Prokaryotic Communities and Ecophysiology
Fourth Edition
With179Figuresand43Tables
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
ISBN978-3-642-30122-3 ISBN978-3-642-30123-0(eBook)
ISBN978-3-642-30124-7(printandelectronicbundle)
DOI10.1007/978-3-642-30123-0
SpringerHeidelbergNewYorkDordrechtLondon
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3rdedition:©SpringerScience+BusinessMedia,LLC2006
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.
x AbouttheEditors
EdwardF.DeLong
DepartmentofBiologicalEngineering
MassachusettsInstituteofTechnology
Cambridge,MA
USA
Edward DeLong received his bachelor of science in bacteriology at the University of California, Davis, and his Ph.D. in marine
biology at Scripps Institute of Oceanography at the University of California, San Diego. He was a professor at the University of
California,SantaBarbara,intheDepartmentofEcologyfor7years,beforemovingtotheMontereyBayAquariumResearchInstitute
wherehewasaseniorscientistandchairofthesciencedepartment,alsofor7years.HenowservesasaprofessorattheMassachusetts
Institute of Technology in the Department of Biological Engineering, where he holds the Morton and Claire Goulder Family
Professorship in Environmental Systems. DeLong’s scientific interests focus primarily on central questions in marine microbial
genomics,biogeochemistry,ecology,andevolution.AlargepartofDeLong’seffortshavebeendevotedtothestudyofmicrobesand
microbial processes in the ocean, combining laboratory and field-based approaches. Development and application of genomic,
biochemical,andmetabolicapproachestostudyandexploitmicrobialcommunitiesandprocessesishisanotherareaofinterest.
DeLong is a fellow in the American Academy of Arts and Science, the U.S. National Academy of Science, and the American
AssociationfortheAdvancementofScience.