Encyclopedia of microbiology, vol.1 4th edition edition thomas m. schmidt - Instantly access the com

Page 1


https://ebookmass.com/product/encyclopedia-of-microbiology-

Instant digital products (PDF, ePub, MOBI) ready for you

Download now and discover formats that fit your needs...

Encyclopedia of Interfacial Chemistry: Surface Science and Electrochemistry (Vol 1 - Vol 7) Klaus Wandelt (Editor)

https://ebookmass.com/product/encyclopedia-of-interfacial-chemistrysurface-science-and-electrochemistry-vol-1-vol-7-klaus-wandelt-editor/

ebookmass.com

Encyclopedia of Biomedical Engineering (vol. 1-3) Min Wang

https://ebookmass.com/product/encyclopedia-of-biomedical-engineeringvol-1-3-min-wang/

ebookmass.com

Aquaculture Microbiology John Thomas

https://ebookmass.com/product/aquaculture-microbiology-john-thomas/

ebookmass.com

Constitutional Change in the European Union: Towards a Federal Europe Andrew Duff

https://ebookmass.com/product/constitutional-change-in-the-europeanunion-towards-a-federal-europe-andrew-duff/

ebookmass.com

Garfield (Griffin Brothers Book 3) Kathi S. Barton

https://ebookmass.com/product/garfield-griffin-brothers-book-3-kathis-barton/

ebookmass.com

Intelligent Vehicular Networks and Communications. Fundamentals, Architectures and Solutions 1st Edition

Anand Paul

https://ebookmass.com/product/intelligent-vehicular-networks-andcommunications-fundamentals-architectures-and-solutions-1st-editionanand-paul/ ebookmass.com

18 Tiny Deaths Bruce Goldfarb

https://ebookmass.com/product/18-tiny-deaths-bruce-goldfarb/

ebookmass.com

In Search of Truth Sharon Wray

https://ebookmass.com/product/in-search-of-truth-sharon-wray-2/

ebookmass.com

Falling for French Kisses: A fish out of water sweet romcom in the city of love (Falling in Paris, a Sweet Romantic Comedy Book 1) Elsie Woods

https://ebookmass.com/product/falling-for-french-kisses-a-fish-out-ofwater-sweet-romcom-in-the-city-of-love-falling-in-paris-a-sweetromantic-comedy-book-1-elsie-woods/

ebookmass.com

Breaking Failure: How to Break the Cycle of Business

Failure and Underperformance Using Root Cause, Failure

Mode and Effects Analysis, and an Early Warning System

Alexander Edsel https://ebookmass.com/product/breaking-failure-how-to-break-the-cycleof-business-failure-and-underperformance-using-root-cause-failuremode-and-effects-analysis-and-an-early-warning-system-alexander-edsel/ ebookmass.com

ENCYCLOPEDIAOF MICROBIOLOGY

FOURTHEDITION

VOLUME1

A-C

ENCYCLOPEDIAOF MICROBIOLOGY

FourthEdition

EDITORINCHIEF

TOMSCHMIDT

DepartmentsofInternalMedicineandEcology&EvolutionaryBiology UniversityofMichigan

VOLUME1

Elsevier

Radarweg29,POBox211,1000AEAmsterdam,Netherlands TheBoulevard,LangfordLane,Kidlington,OxfordOX51GB,UnitedKingdom 50HampshireStreet,5thFloor,CambridgeMA02139,UnitedStates

Copyright © 2019ElsevierInc.Allrightsreserved

Nopartofthispublicationmaybereproducedortransmittedinanyformorbyanymeans,electronicormechanical,including photocopying,recording,oranyinformationstorageandretrievalsystem,withoutpermissioninwritingfromthepublisher.Detailsonhow toseekpermission,furtherinformationaboutthePublisher’spermissionspoliciesandourarrangementswithorganizationssuchasthe CopyrightClearanceCenterandtheCopyrightLicensingAgency,canbefoundatourwebsite: www.elsevier.com/permissions

ThisbookandtheindividualcontributionscontainedinitareprotectedundercopyrightbythePublisher(otherthanasmaybenoted herein).

Notices

Knowledgeandbestpracticeinthisfieldareconstantlychanging.Asnewresearchandexperiencebroadenourunderstanding,changesin researchmethods,professionalpractices,ormedicaltreatmentmaybecomenecessary.

Practitionersandresearchersmayalwaysrelyontheirownexperienceandknowledgeinevaluatingandusinganyinformation,methods, compounds,orexperimentsdescribedherein.Inusingsuchinformationormethodstheyshouldbemindfuloftheirownsafetyandthe safetyofothers,includingpartiesforwhomtheyhaveaprofessionalresponsibility.

Tothefullestextentofthelaw,neitherthePublishernortheauthors,contributors,oreditors,assumeanyliabilityforanyinjuryand/or damagetopersonsorpropertyasamatterofproductsliability,negligenceorotherwise,orfromanyuseoroperationofanymethods, products,instructions,orideascontainedinthematerialherein.

LibraryofCongressCataloging-in-PublicationData

AcatalogrecordforthisbookisavailablefromtheLibraryofCongress

BritishLibraryCataloguing-in-PublicationData

AcataloguerecordforthisbookisavailablefromtheBritishLibrary

ISBN978-0-12-811736-1

Forinformationonallpublications visitourwebsiteat http://store.elsevier.com

Publisher: OliverWalter

AcquisitionEditor: PriscillaBraglia

ContentProjectManagers: PaulaDaviesandJustinTaylor

AssociateContentProjectManagers: RamalakshmiBoobalanandFahmidaSultana

Designer: MilesHitchen

EDITOR-IN-CHIEF

Thomas(Tom)Schmidt isamicrobialphysiologistandecologistwhostudies diversemicrobesandmicrobialcommunities.TomreceivedaPhDfromThe OhioStateUniversityandconductedpostdoctoralresearchatScrippsInstituteof OceanographyandIndianaUniversity.Hespentmuchofhiscareerstudyingthe ecologyofmicrobesinsoilthatareresponsiblefortheexchangeofgreenhouse gaseswiththeatmosphere.Morerecently,hejoinedtheUniversityofMichigan andfocusedhisresearchonthehumanmicrobiome.Hisjointappointmentin theDepartmentsofInternalMedicineandEcology&EvolutionaryBiology reflectshisexpertiseinapplyingecologicalandevolutionaryprinciplestounderstandthefunctioningofcomplexmicrobialcommunities.

TomisafellowoftheAmericanAcademyforMicrobiologyandwasdirector oftheMarineBiologicalLaboratory’sMicrobialDiversityCourseinWoodsHole. Throughthatcourseandinhislaboratory,hehashelpednumerousscientists incorporatemolecularapproachesintotraditionalstrategiesforstudyingthe microbialworld.Hecurrentlyteachesauniversitycoursethatmergeshisresearchandteachinggoalsby engagingstudentsinacoordinatedstudyoftheeffectsofdietonthegutmicrobiome,andhedirectsagraduate programthatcombineslaboratorysciencesandmodeling.Tomwasasectioneditorforpreviouseditionsofthe EncyclopediaofMicrobiology andwasdelightedtoassumetheroleaseditor-in-chieftohelpbringthemicrobial worldtoanexpandingaudience.

EDITORIALBOARD

BiancaBrahamsha isaresearchmicrobiologistatScrippsInstitutionof OceanographyattheUniversityofCalifornia,SanDiego.Shewasabiology andhistorymajoratGoucherCollege,earnedherPhDinmicrobiologyat CornellUniversity,andcarriedoutpostdoctoralworkinmoleculargeneticsas anAmericanCancerSocietyfellowattheUniversityofChicago.Herresearch interestshavecenteredonbacterialmotility,thegeneticsandphysiologyof marinecyanobacteria,andontheinteractionsbetweencyanobacteriaandtheir eukaryoticpredators.

James(Jim)Brown wasborninAtlanta,Georgia,andlivedinDadeCity (Florida),Bloomington(Indiana),Lima(Peru),andMuncie(Indiana)while growingup.Fromthebeginning,hehadanintenseinterestinnature,including anythingfoundinthewoods,rivers,beachoroceanthatwerealwaysnearby. JimattendedBallStateUniversitybeginningin1976.Asinglelectureon microbialdiversityinageneralmicrobiologyclass,followedbytheannouncementofthediscoveryoftheArchaea(GeorgeFoxandCarlWoese,1977), sparkedhislastinginterestinmicrobiology.Thisledtoundergraduateresearch examining Beggiatoa inasulfurspringinFrenchLick,Indiana.Afterreceiving hisBSinbiologyin1980,hejoinedthegraduateprograminmicrobiology atMiamiUniversity,whereheworkedonplanttissueculturemRNAswith Prof.RonaldTreick.AfterobtaininganMSdegreein1982,hemovedtothe MCDBiologyProgramatTheOhioStateUniversitytoworkonthemolecular biologyofmethanogenicArchaeaintheDepartmentofMicrobiologywithProf.JohnReeve.Whilethere,Jim workedonpolyadenylationofmRNAs,RNApolymerase,andpromotersinArchaea,andreceivedhisPhDin 1988.JimthenwenttoIndianaUniversityfor5yearsofpostdoctoralworkinProf.NormanPace’slabonthe comparativeanalysisofthestructureofabacterialribozyme,RNaseP.

InJanuaryof1994,JimstartedasanassistantprofessorintheDepartmentofMicrobiologyandmovedto NorthCarolinaStateUniversity.ResearchinJim’slabfocusedonthecomparativesequenceandbiochemical analysisofRNA,andinparticularRNasePinArchaea.StudentsintheBrownlabdevelopedahigh-resolution modelforthestructureofthisRNA,howitchangedoverthediversificationoftheArchaea,theproteinsubunits associatedwiththeRNA,andhowtheycontributetothefunctionoftheholoenzyme.Jimdeveloped,teaches, andwrotethetextbookforasenior-levelundergraduatelabcourseinmicrobialdiversity.JimisnowProfessor EmeritusintheDepartmentofBiologicalSciencesatNCStateUniversity.

Jimhasasonandtwodaughters,andismarriedtoMelanieLee-Brown,professorofbiologyanddirectorof ResearchandCreativeEndeavorsatGuilfordCollege.Forfun,Jimenjoysskinandscubadiving,driving(i.e., workingon)his1968LotusSuperSeven,andrestoringvintageracingbicycles.JimandMelaniehavebeen renovatinganabandonedfishinglodgeonNorthCaicosIsland(TurksandCaicosIslands,BWI),whichwillbe reopenedsoonasabedandbreakfast.

LarryForney isauniversitydistinguishedprofessorandamemberofthe AmericanAcademyofMicrobiologywithacademicappointmentsintheDepartmentofBiologicalSciencesandBioinformaticsandComputationalBiologyatthe UniversityofIdaho.Dr.Forneyisanevolutionaryecologistwhoconductsresearch onthecomplexarrayoffactorsthatinfluencethefunction,composition,structure,andtemporaldynamicsofbacterialcommunitiesinawidearrayofhabitats. Inrecentyearshehaslargelyfocusedonthecommunityecologyofthehuman vaginaacrossawoman’slifetimewithaneyeonunderstandinghowchangesin communitystructureandfunctionaffectawoman’srisktobacterialvaginosis, sexuallytransmittedinfections,andpre-termbirth,andhowhostfactorsshape thesecommunities.Hisresearchextendstounderstandingthemutation-selection processesthatgoverntheoccurrenceandpersistenceofgeneticdiversityofbacterialpopulationsinspatiallystructuredenvironmentssuchasmicrobialbiofilms andporousmedia.Thesestudieshaveshownthatspatialstructurecreatesconditionsinwhichmutationfrequenciesarehighandselectivesweepsareprotracted,whichleadstoextraordinary withinspeciesdiversitythatincreasestheresilienceofpopulationstoenvironmentalchanges.

RobertHaselkorn wastheF.L.Pritzkerdistinguishedserviceprofessorof moleculargeneticsandcellbiologyattheUniversityofChicago,retiringseveral yearsago.HewasanundergraduateatPrinceton,agraduatestudentatHarvard, andapostdoctorateinCambridge,England.Hestartedhisteachingcareerat Chicagoin1961inbiophysics,extendinglatertomicrobiology,biochemistry, andchemistry.Hisresearchinterestshavecenteredonheterocystdifferentiation innitrogen-fixingcyanobacteria,inbacterialgenomics,andintheenzyme acetyl-CoAcarboxylaseinplants,parasites,andpeople.Heisamemberofthe NationalAcademyofSciences,afellowoftheAmericanAcademyofArtsand Sciences,andamemberoftheAmericanPhilosophicalSociety.Amongother externalactivitieshewasafounderandadviserfor20yearstotheInternational CenterforGeneticEngineeringandBiotechnology,locatedinItalyandIndia.For thepast15yearsHaselkornandhiswifeMargothavebeenworkingonselection andsupportingaspeakerfortheHaselkornLectureattheUniversityofChicago, anawardtheyhaveendowed.ManyoftheHaselkornLecturershavebeenNobelPrizewinnersorwillbesoon.

JennieC.Hunter-Cevera receivedherPhDfromRutgersUniversityin1978 (microbialphysiologyandbiochemistry),anMSinmicrobialecologyin1972, andaBSinbiologyfromWestVirginiaUniversityin1970.Sheisthefounderof HunterandAssociates,aconsultingfirmfocusingonfindingintegrativesolutionstocomplexproblemsinvolvingsustainabilityinthelifesciencesarena. FromJulyof2009toAugust2012,shewastheexecutivevicepresidentof DiscoveryandAnalyticalSciences(DAS),CorporateDevelopmentandGovernmentRelations.Shehas22yearsofexperienceinthepharmaceuticaland biotechnologyindustries(E.R.SquibbandSons,CetusCorporation,GeoBiotics, andUniversalFoods).Shewastheco-founderofTheBioticNetworkandBlueSkyLaboratorythatcontractedwithbiotechnologyandpharmaceuticalcompaniesonbasicandappliednaturalproductresearch.Dr.Hunter-Ceverawasan

employeefor5yearswiththeDepartmentofEnergyastheheadoftheLawrenceBerkeleyNationalLaboratory’ s CenterforEnvironmentalBiotechnology.Sheworkedinacademiafor10yearsasthepresidentoftheUniversity ofMarylandBiotechnologyInstituteand2yearsastheInterimProvostofMountSt.Mary’sUniversity.Shealso servedasprojectmanagerforUCDavis’sCIFAR(CenterforIndustrialFoodandAgriculturalResearch).Shehas publishedmanypapersandchapters,andservedassenioreditorofthe JournalofIndustrialMicrobiologyand Biotechnology for10years.Sheisaco-sectionheadofmicrobiologyforFacultyof1000.Sheholds15patentsand specializesinareasofscreendesignforthediscoveryofnaturalcompoundsintheareaofhumantherapeutics, biodefense,sustainableagriculture,bioremediation,andbiocatalysisforindustrialprocessesinthefoodand clothingindustries.

WhileinMaryland,sheservedasamemberoftheExecutiveCommitteeforGovernorErhlich ’stransition team,hisCommitteeonscience,technology,engineering,andmaths,andwastheTechnologyRepresentative forGovernorGlendenningontheSouthernGovernor’sAssociation,andsheservedontheTechnology EconomicDevelopmentCorporation,TEDCO(BoardofDirectorsfor4yearsandwasChairfor2years).Dr. Hunter-CeveraalsoservedontheAdvisoryBoardfortheMarylandIndustrialPartnerships,theMDBio’sBoard ofDirectors,andtheMDBioFoundationfor10yearsandontheBioITCoalitionfor5years.Sheservedasan EntremedBoardMemberfor10yearsandservedontheExecutiveCommitteefor2years.Shewasaboard memberforPatientswithPower,asoftwarecompanythatdesignsprogramsforcancerpatientstomakethebest decisionsfortheirtreatments.JenniealsoservedasactingsecretaryforMaryland ’sHigherEducationCommissionin2015.

SheisamemberofseveralprofessionalsocietiesandhasservedaspresidentoftheSocietyforIndustrial Microbiology,theInternationalMarineBiotechnologyAssociation,andtheUnitedStatesFederationofCulture Collections.Dr.HunterhasservedonmanynationalcommitteesandcommissionsandwasChairofthe NationalResearchCouncil’sCommitteeonLargeScaleProductionofBiofuelsfromAlgae.Shealsochairedtwo otherNRCCommittees:StandingCommitteeonDOD’sTranslationalMedicineandtheDOE’sGenometoLife forBiofuels.

SheistherecipientofseveralawardsandhonorsincludingMaryland’sTop50InfluentialPeople(2007, 2009)andMaryland’sTop100Women(2003,2006,2009),AmericanSocietyforMicrobiology ’sPorterAward fordistinguishedresearchinmicrobialsystematicsandtaxonomy,electedasaSIMfellow,amemberoftheASM AcademyofMicrobiology,andanAAASfellow.SheisalsoaWVUDistinguishedAlumniAwardeeandNath lecturerandservedasanentrepreneurialcoachfortheUNCExecutiveMBAprogram.Shewasawardedan HonoraryDoctoratefromWestVirginiaUniversity,May2013,andtheRutgersCookCollegeDennisM.Fenton DistinguishedGraduateAlumniAwardin2014.

ShecurrentlyservesontheInternationalAdvisoryCouncilforBrazil’sFundaçãoDomCabralwhichisa world-classBrazilianbusinessschoolthatdevelopsstrategicthinkingskillsofexecutives,entrepreneurs,and public-sectormanagers.Inaddition,Jennieserved6yearsontheEdisonAwardsSteeringCommitteeand currentlyservesontheEdisonAwardsAdvisoryBoard.

StanleyMaloy isaprofessorofmicrobiologyandassociatevicepresidentfor researchandinnovationatSanDiegoStateUniversity.Stanley’sresearchhas focusedonbacterialandphagegeneticsandphysiology,evolutionofinfectious diseases,anddevelopmentofantimicrobialsandvaccines.Inaddition,hehas consultedwithlargeandsmallcompaniesinmultiplesectors,playedarole instartingseveralBiotechcompanies,andservedleadershiprolesinmultiple start-upcompanies.

Dr.McCormick earnedherPhDinmicrobiologyinthetopicareaofintestinal ecology,andcompletedpostdoctoraltrainingatHarvardMedicalSchool.She remainedonthefacultyofHarvardMedicalSchoolwhereshewasanassociate professorofpediatricgastroenterology,anddirectorofresearchfortheMucosal ImmunologyandBiologyResearchCenteratMassachusettsGeneralHospital. In2008,shejoinedtheUniversityofMassachusettsMedicalSchoolwheresheis professorandvicechairoftheDepartmentofMicrobiologyandPhysiological Systems.Dr.McCormickisalsothefoundingexecutivedirectoroftheUniversity ofMassachusettsCenterforMicrobiomeResearch,whichsheestablishedin 2014.Dr.McCormickisoneoftheoriginalpioneersinthefieldnowknown ascellularmicrobiology.Herworkprovidedthefirstevidencethatepithelialcells inresponsetopathogencontactorchestrateapro-inflammatoryprogram,which recruitsinflammatorycells.Dr.McCormickhassinceidentifiednew,previously unidentifiedandunexpectedvirulencemechanismsthatarekeytotheinflammatoryresponse,leadingtoboth novelbiologicalprinciplesofhost–microbeinteractionsandtherapeuticinterventionstrategiesforthetreatmentinflammatoryboweldisease,andcancer.Herworkcontinuestoidentifynovelwaysinwhichmicrobes interactwiththeintestinalepithelium,publishingover100originalresearchpapersandopinionpiecesinthis area.Dr.McCormickisanelectedfellowoftheAmericanAcademyofMicrobiology,isontheBoardofEditors for Gastroenterology,and GutMicrobes,andservesasamemberoffourEditorialReviewBoards.

Dr.Mobley receivedhisBSdegreeinbiologyfromEmoryUniversityin1975 andhisPhDdegreeinmicrobiologyandimmunologyfromUniversityof Louisvillein1981.Heconductedpostdoctoraltraininginbiologicalchemistry andthenbacterialgeneticsintheCenterforVaccineDevelopmentatthe UniversityofMarylandSchoolofMedicine.Heservedonthefacultyatthe UniversityofMarylandSchoolofMedicinefrom1984until2004intheDivision ofInfectiousDiseases(1984 –97)andthentheDepartmentofMicrobiologyand Immunology(1997–2004)whereheledthegraduateprogram.Duringthat time,heheldajointappointmentintheDepartmentofBiochemistryand MolecularBiologyandtrainedgraduatestudentsinthatprogram.In2004, MobleymovedtotheUniversityofMichigantochairtheDepartmentofMicrobiologyandImmunologyandwasinstalledastheinauguralFrederickG.Novy CollegiateProfessorofMicrobiologyandImmunology.

Dr.Mobley’sresearchinterestsfocusonthemolecularmechanismsofbacterial pathogenesisandonthefundamentalbasicresearchthatwilllaythegroundworkforfuturetherapeuticsand vaccines.Hislabstudiesvirulencemechanismsofuropathogenic Escherichiacoli and Proteusmirabilis thatcause uncomplicatedandcomplicatedurinarytractinfections,respectively,and,intherecentpast, Helicobacterpylori thatcausesgastritisandpepticulcerdisease.For E.coli and Proteusmirabilis,hislabisfocusedonidentifying surface-exposedproteinsthatarebothsynthesizedbythebacteriaduringaurinarytractinfectionandconserved amonguropathogenic E.coliandProteus strains.Usingtheseconservedantigens,hislabisdeterminingtheefficacy ofcandidateproteinsascomponentsofamultivalentsubunitvaccinetoprotectagainsturinarytractinfection.

Dr.MobleyisafellowoftheAmericanAcademyofMicrobiologyandafellowoftheAmericanAssociation fortheAdvancementofScienceandamemberandpastpresidentoftheAssociationofMedicalSchool Microbiology&ImmunologyChairs.HewastherecipientoftheinauguralUniversityofMichiganPostdoctoral AssociationExcellenceinMentorshipAwardin2012.Heisamemberoftheeditorialreviewboardsof Infection andImmunityandMicrobiologySpectrum andhasservedasastudysectionmemberfortheNationalInstitutes ofHealth.Dr.Mobleywasawardedandnamedadistinguisheduniversityprofessorin2015.Thisisthe University’smostprestigiousprofessorshipestablishedtorecognizeseniorfacultywithexceptionalscholarly achievements,nationalandinternationalreputationsforacademicexcellence,andsuperiorrecordsofteaching, mentoring,andservice.

Dr.Mobleyhaspublished255peer-reviewedarticleswhichhavebeencitedintheliteratureover18,000 timesasofJune2019,aswellas49bookchaptersand5books.Hehastrained29PhDstudentsand 38postdoctoralfellows,andhasdelivered232invitedlecturesin21countries.

CarlosPedrós-Alió graduatedinbiologyattheAutonomousUniversityof BarcelonaandgothisPhDinbacteriologyattheUniversityofWisconsin–Madison.AfterapostdoctoralstayattheAutonomousUniversityhebecame anassistantprofessorofmicrobiology.HemovedtotheMarineSciencesInstitute(CSIC,Barcelona)in1989wherehewasaresearchprofessorsince2000. In2016hemovedtotheNationalCenterforBiotechnology(CSIC,Madrid). Dr.Pedrós-Alió ’sinterestistounderstandtheecologyofaquaticmicroorganisms.Around2005hestartedtousegenomicsasatooltogeneratehypotheses thatcouldlaterbetestedexperimentally.Healsolikestostudyextremeenvironmentssuchashypersalinesystems,thermalsprings,orpolarwaters.Another interestisinfindingthemechanismsmaintainingalargenumberofrarebacteria inaquaticecosystems.Heisalsointerestedinoutreach,relationshipsbetweenart andscience,biologyofspirituality,fictionwriting,andbirding.

LISTOFCONTRIBUTORSFORVOLUME1

StephenTAbedon

DepartmentofMicrobiology,TheOhioStateUniversity, Mansfield,OH,UnitedStates

Shin-IchiAizawa

PrefecturalUniversityofHiroshima,Hiroshima,Japan

JBAlbaneseJr. TerrapinBeerCompany,Athens,GA,UnitedStates

BirgitEAlber

OhioStateUniversity,Columbus,OH,USA

Sonja-VerenaAlbers UniversityofFreiburg,Freiburg,Germany

GregoryGAnderson

IndianaUniversity PurdueUniversityIndianapolis, Indianapolis,IN,UnitedStates

JudithPArmitage UniversityofOxford,Oxford,UnitedKingdom

PhilippAssmy NorwegianPolarInstitute,FramCenter,Tromsø, Norway

DBermudes

CaliforniaStateUniversity,Northridge,CA,UnitedStates

EmanueleGBiondi AixMarseilleUniversity,Marseille,France

MarcusBlohs MedicalUniversityofGraz,Graz,Austria

AMBrandt

HarvardMedicalSchool,HarvardUniversity,Boston, MA,USA

AlejandraBravo InstituteofBiotechnology,Cuernavaca,Morelos,Mexico

AndreasBreitwieser UniversityofNaturalResourcesandLifeSciencesVienna, Vienna,Austria

SusanneBrenzinger LeidenUniversity,Leiden,ZuidHolland,TheNetherlands

ArianeBriegel

LeidenUniversity,Leiden,ZuidHolland,TheNetherlands

AlitaRBurmeister YaleUniversity,NewHaven,CT;BEACONCenterfor theStudyofEvolutioninAction,EastLansing,MI, UnitedStates

KatrinaCampbell Queen'sUniversityBelfast,Belfast,UnitedKingdom

Ivan Cepicka CharlesUniversity,Prague,CzechRepublic Y-CCheng YaleUniversitySchoolofMedicine,NewHaven, CT,USA

SusanECohen

CaliforniaStateUniversity,LosAngeles,LosAngeles,CA, UnitedStates

PCourvalin InstitutPasteur,Paris,France

AlanCunningham TeagascFoodResearchCentre,Moorepark,Cork,Ireland; Queen'sUniversityBelfast,Belfast,UnitedKingdom

PatrickDCurtis UniversityofMississippi,University,MS,UnitedStates

FelipeDargent UniversityofOttawa,Ottawa,ON,Canada

OhanaYdeAssisCosta NetherlandsInstituteofEcology(NIOO-KNAW), DepartmentofMicrobialEcology,Wageningen,the Netherlands

JamieSDepelteau LeidenUniversity,Leiden,ZuidHolland,The Netherlands

NinaDombrowski

RoyalNetherlandsInstituteforSeaResearch,andUtrecht University,DenBurg,theNetherlands

LEggeling

InstituteofBio-andGeosciences,IBG-1,Biotechnology, Juelich,Germany

LarryEErickson

KansasStateUniversity,Manhattan,KS,UnitedStates

AEspinel-Ingroff

VirginiaCommonwealthUniversityMedicalCenter, Richmond,VA,UnitedStates

HFan

RutgersUniversityRobertWoodJohnsonMedicalSchool, Piscataway,NJ,USA

MariaIFerrante

AntonDohrnZoologicalStation,Napoli,Italy

LSFrost UniversityofAlberta,Edmonton,AB,Canada

Shun-IchiFukushima

TokyoMetropolitanUniversity,Hachioji,Tokyo,Japan

FerranGarcia-Pichel

SchoolofLifeSciencesandCenterforFundamentaland AppliedMicrobiomics,BiodesignInstitute,ArizonaState University,Tempe,AZ,UnitedStates

SarjeetSGill

UniversityofCalifornia,Riverside,CA,UnitedStates

SusanSGolden

UniversityofCalifornia,SanDiego,CA,UnitedStates

CristinaGonzalez-Martin

UniversityInstituteofTropicalDiseasesandPublicHealth oftheCanaryIslands;UniversityofLaLaguna – ULL, CanaryIslands,Spain

GDGriffin

OakRidgeNationalLaboratory,OakRidge,TN,USA

JuliaEGrimwade

FloridaInstituteofTechnology,Melbourne,FL,United States

Ji-DongGu

TheUniversityofHongKong,HongKong,PRChina

NealDHammer

MichiganStateUniversity,EastLansing,MI,UnitedStates

SatoshiHanada

TokyoMetropolitanUniversity,Hachioji,Tokyo, Japan

MAHarrison

UniversityofGeorgia,Athens,GA,UnitedStates

RolandKHartmann

Philipps-UniversityMarburg,Marburg,Germany

PaulHyman DepartmentofBiologyandToxicology,AshlandUniversity, Ashland,OH,UnitedStates

NassimaIllikoud SECALIM,INRA,Oniris,UniversityBrittanyLoire, Nantes,France

IlseDJacobsen LeibnizInstituteforNaturalProductResearchand InfectionBiology,HansKnöllInstitute,Jena, Germany

EmmanuelJaffrès SECALIM,INRA,Oniris,UniversityBrittanyLoire, Nantes,France

KenFJarrell Queen'sUniversity,Kingston,ON,Canada

ElizabethEJefferys UniversityofOxford,Oxford,UnitedKingdom

AnnEJerse

UniformedServicesUniversity,Bethesda,MD, UnitedStates

EAJohnson UniversityofWisconsin,Madison,WI,USA

DSJones

MassachusettsInstituteofTechnology,Cambridge,MA, USA

NanakoKanno

TokyoMetropolitanUniversity,Hachioji,Tokyo, Japan

MarioKapitan LeibnizInstituteforNaturalProductResearchand InfectionBiology,HansKnöllInstitute,Jena,Germany

ReesKassen UniversityofOttawa,Ottawa,ON,Canada

EKhan

MedicalCollegeofWisconsin,ClinicalCancerCenter, Milwaukee,WI,USA

AndreasKlingl BiocenterLMUMunich,Planegg-Martinsried,Germany

Anne-MarieKrachler UniversityofTexasMcGovernMedicalSchoolatHouston, Houston,TX,UnitedStates

MartKrupovic PasteurInstitute,Paris,France

JGijsKuenen

DelftUniversityofTechnology,Delft,TheNetherlands

EikoEKuramae

NetherlandsInstituteofEcology(NIOO-KNAW), DepartmentofMicrobialEcology,Wageningen,the Netherlands

MichaelILatz

UniversityofCaliforniaSanDiego,LaJolla,CA,United States

AlanCLeonard

FloridaInstituteofTechnology,Melbourne,FL,United States

JennyLindström

UniversityofGothenburg,Gothenburg,Sweden

PMaharom

TheJohnsHopkinsHealthSystem,Baltimore,MD,USA

AlexanderMahnert

MedicalUniversityofGraz,Graz,Austria

HMarkel

UniversityofMichiganMedicalSchool,AnnArbor,MI,USA

SandraMartínez-García

UniversityofVigo,Vigo,Spain

OliviaMcAuliffe

TeagascFoodResearchCentre,Moorepark,Cork,Ireland

TEMcKnight

OakRidgeNationalLaboratory,OakRidge,TN,USA

CDMeehan

UniversityofMichiganMedicalSchool,AnnArbor,MI,USA

CameronNeilMelton

IndianaUniversity PurdueUniversityIndianapolis, Indianapolis,IN,UnitedStates

NishaMohanan

UniversityofManitoba,Winnipeg,Manitoba,Canada

ChristineMoissl-Eichinger MedicalUniversityofGraz,Graz,Austria

MarinaMontresor

AntonDohrnZoologicalStation,Napoli,Italy

NNanninga UniversiteitvanAmsterdam,Amsterdam,TheNetherlands

MariaJNiemiec

LeibnizInstituteforNaturalProductResearchand InfectionBiology,HansKnöllInstitute,Jena,Germany

KimOrth

UniversityofTexasSouthwesternMedicalCenter,Dallas, TX,UnitedStates

EPaintsil

YaleUniversitySchoolofMedicine,NewHaven,CT,USA

StephanePelletier

St.JudeChildren'sResearchHospital,Memphis,TN, UnitedStates

BPérichon

InstitutPasteur,Paris,France

TMPerl

TheJohnsHopkinsMedicine,Baltimore,MD,USA

JaronePinhassi

LinnaeusUniversity,Kalmar,Sweden

JeanneSPoindexter

ColumbiaUniversity,NewYork,NY,UnitedStates

MelaniePolke

LeibnizInstituteforNaturalProductResearchand InfectionBiology,HansKnöllInstitute,Jena,Germany

DietmarPum

UniversityofNaturalResourcesandLifeSciencesVienna, Vienna,Austria

SanjayRam UniversityofMassachusettsMedicalSchool,Worcester, MA,UnitedStates

GiancarloRanalli

DepartmentofBioscienceandTerritory(DIBT),University ofMolise,Pesche(IS),Italy

EricaLRaterman

UniformedServicesUniversity,Bethesda,MD,UnitedStates

MartaRibeiro

UniversityofPorto,Porto,Portugal

KPSaalbach UniversityofOsnabrueck,Osnabrueck,Germany

HSahm

InstituteofBio-andGeosciences,IBG-1,Biotechnology, Juelich,Germany

MiltonHSaierJr. UniversityofCaliforniaatSanDiego,LaJolla,CA, UnitedStates

CaitlinSande UniversityofGuelph,Guelph,ON,Canada

TulasiSatyanarayana

NetajiSubhasInstituteofTechnology,NewDelhi,India

PSavard

CHUMSt-LucHospital,Montreal,QC,Canada

ClaudioScazzocchio

UniversityofParis-Sud,Orsay,France;Departmentof Microbiology,ImperialCollegeLondon,London,United Kingdom;InstituteforIntegrativeBiologyoftheCell (I2BC),Gif-sur-Yvette,France

ChristinaSchilde UniversityofDundee,Dundee,UnitedKingdom

MAScidmore

CornellCollegeofVeterinaryMedicine,Ithaca, NY,USA

LúciaCSimões

UniversityofPorto,Porto;UniversityofMinho,Braga, Portugal

ManuelSimões UniversityofMinho,Braga,Portugal

AlastairGBSimpson DalhousieUniversity,Halifax,NS,Canada

UweBSleytr UniversityofNaturalResourcesandLifeSciencesVienna, Vienna,Austria

VictorSmetacek AlfredWegenerInstituteforPolarandMarineResearch, Bremerhaven,Germany

MarioSoberón

InstituteofBiotechnology,Cuernavaca,Morelos, Mexico

PGSohnle

MedicalCollegeofWisconsin,ClinicalCancerCenter, Milwaukee,WI,USA

ClaudiaSorlini DepartmentofFood,EnvironmentalandNutritional Sciences,UniversityofMilan,Milan,Italy

TanyaSoule DepartmentofBiology,PurdueUniversityFortWayne,Fort Wayne,IN,UnitedStates

AnjaSpang

UppsalaUniversity,Uppsala,Sweden;RoyalNetherlands InstituteforSeaResearch,andUtrechtUniversity,Den Burg,theNetherlands

EricVStabb UniversityofGeorgia,Athens,GA,UnitedStates

DNStratis-Cullum

USArmyResearchLaboratory,Adelphi,MD,USA

CWStratton VanderbiltUniversitySchoolofMedicine;Vanderbilt UniversityMedicalCenter,Nashville,TN, UnitedStates

FCTenover Cepheid,Sunnyvale,CA,USA

VeraThiel

TokyoMetropolitanUniversity,Hachioji,Tokyo,Japan

PaulETurner YaleUniversity,NewHaven,CT;BEACONCenterforthe StudyofEvolutioninAction,EastLansing,MI;YaleSchool ofMedicine,NewHaven,CT,UnitedStates

NadineBWäber Philipps-UniversityMarburg,Marburg,Germany

DavidWarrilow

QueenslandHealthForensicandScientificServices, Archerfield,QLD,Australia

DanelleWeakland UniversityofMichiganMedicalSchool,AnnArbor,MI, UnitedStates

SamanthaWear UniversityofGuelph,Guelph,ON,Canada

ChrisWhitfield UniversityofGuelph,Guelph,ON,Canada

MoniqueZagorec SECALIM,INRA,Oniris,UniversityBrittanyLoire, Nantes,France

ElisabettaZanardini DepartmentofScienceandHighTechnology,Universityof Insubria,Como,Italy

SUBJECTCLASSIFICATION

HISTORICAL

AIDS,Historical

Cholera,Historical

HistoricalPlague

HistoricalSmallpox

HistoryofMicrobiology

HistoryofVirology

Methods,Philosophyof

SpontaneousGeneration

Syphilis,Historical

Typhoid,Historical TyphusFeversandOtherRickettsialDiseases,Historical

MICROBIALDIVERSITY

Acidobacteria

AmitochondriateProtists(Diplomonads,ParabasalidsandOxymonads)

Amoebozoa

Aquificae

Archaea – AnIntroduction

Aspergillus:AMultifacetedGenus

BacillusThuringiensis:MechanismsandUse

Bacteriophage:Overview

Brochothrixthermosphacta

Caulobacter

Chlamydia

Chloroflexi

Clostridia

Cyanobacteria

Dictyostelium

Dinoflagellates

Escherichiacoli

GreenAlgae:ChlorophytaandStreptophyta

HaemophilusInfluenzae

HalophilicArchaea

Helicobacterpylori

Legionella and Bartonella

Leishmania

Listeriamonocytogenes

Mollicutes

Nanoarchaeota

Phylum Verrucomicrobia

Picoeukaryotes

Planctomycetes

PlantPathogens,Minor(Phytoplasmas)

Protozoa

Rhizobia

Spirochetes

Staphylococcus

StreptococcusPneumoniae Evolving – ImpactofAntibioticsandVaccines

Streptomyces

Trypanosomes

Viroids/Virusoids

PHYSIOLOGYANDGENOMICS

Archaellum

AutotrophicCO2Metabolism

BacterialandArchaealCellMembranes

BacterialandArchaealCellStructure

BacterialBioluminescence

BacterialCellCyclesandDivision

BacterialChemotaxis:ConservationandVariationonaTheme

BacterialDevelopment

BacterialFlagella

BioluminescenceinEukaryoticMicrobes

ChromosomeReplicationandSegregation

CircadianRhythmicityinProkaryotes

Conjugation,Bacterial

CRISPR –Cas9

CrystallineCellSurfaceLayers(S-Layers)

EnergyTransductionProcesses

FundamentalsofMetabolicSystemsBiology

GeneTransferAgents

GeneticallyModifiedOrganisms:GuidelinesandRegulationsforResearch

GlycogenBiosynthesis

HorizontalGeneTransfer:UptakeofExtracellularDNAbyBacteria

IntracellularStructuresofProkaryotes:Inclusions,Compartments,andAssemblages

IronMetabolism

LipidBiosynthesis

Magnetotaxis

Methanogenesis

MethylationandotherModificationsofNucleicAcidsandProteins

MicrobialSoluteTransporters

NitrogenAssimilationinBacteria

NoBonesAboutIt:TheBacterialCytoskeleton

NonflagellarBacterialMotility

OuterMembrane,Gram-NegativeBacteria

Peptidoglycan(Murein)

PhototaxisinArchaeaandBacteria

PhototrophyandPhototrophs

Pili,Fimbriae

PosttranscriptionalRegulation

RegulationofCarbonAssimilationinBacteria

RegulationofReplicationOriginFiring

RegulatoryRNAs

Restriction-ModificationSystems

RNAProcessing

SensoryTransductioninBacteria

Single-ParticleCryo-ElectronMicroscopy

Stress,Bacterial:GeneralandSpecific

StressResponses:Heat

SwimmingandSwarmingMotility

TheBacterialGlycome:FromMonomerstoComplexCarbohydratePolymers

TheSocialEvolutionofBacterialQuorumSensing

TranscriptionRegulationinBacteria

Transduction:TheTransferofHostDNAbyBacteriophages

TranslationalControlandFidelity

ECOLOGYANDEVOLUTION

AdaptationsofMicroorganismstoLowNutrientEnvironments:ManagingLifeintheOligotrophicOcean

AdaptiveRadiationinMicrobes

AlgalBlooms

BacteriophageEcology

EcologyofRareMicroorganisms

Ecology,Microbial

EndophyticMicrobes

EvolutionaryTheoryandExperimentsWithMicroorganisms

ExtremophilesandAcidicEnvironments

Extremophiles:ColdEnvironments

Extremophiles:DryEnvironments(IncludingCryptoendoliths)

Extremophiles:HotEnvironments

Extremophiles:HypersalineEnvironments

FreshwaterHabitats

GenomesFromUncultivatedMicroorganisms

IntracellularSymbiontsandParasites

MarineDeepBiosphere

MicrobialBiofilms

MicrobialCyclingofMethane

MicrobialEcologyoftheRumen

MicrobialMats:ImpactonGeology

MixotrophyAmongFreshwaterandMarineProtists

ModelsinMicrobialEcology

NitrogenCycle

OriginofLife,Theoriesof OverviewofPlantDiseases

Palaeontology,Microbial

Paramecium MolecularEvolution

PhosphorusDynamicsintheEnvironment

Plastics:ColonizationandDegradation

Quorum-SensinginBacteria

Rhizosphere

SecondaryandTertiaryEndosymbiosis

SedimentHabitats,IncludingWatery

TheEvolutionaryEcologyofMicrobes

VirusEvolution

PATHOGENESISANDIMMUNOLOGY

AdhesinsDuringInfection

AirborneInfectiousMicroorganisms

AntibioticResistance

AntifungalAgents

AntigenicVariationinBacterialPathogens

AntiviralAgents

Arboviruses

BacterialIronAcquisitionStrategies

BiofilmsandDisease:APersistentThreat

CapsulesandSecretedExtracellularPolysaccharides

Chlamydophilapneumoniae,APathogenCausingMoreThanPneumonia

CommensaltoPathogenTransitionof Candidaalbicans

Complement

CutaneousFungalInfections

DiagnosticMicrobiology

EmergingandReemergingInfectiousDiseases

EntamoebaHistolytica:BiologyandHostImmunity

EntericViruses

EpidemiologicalConceptsandHistoricalExamples

Exotoxins

FirstPrinciplesofClinicalMicrobiology:Collection,Handling,andDiagnostics

FungalBiofilms

FungalInfections,Systemic

GastrointestinalMicrobiologyintheNormalHost

GutMicrobiotainHumanHealthandDiseases

HemorrhagicFeverViruses

HepatitisViruses

Herpesviruses

HIVandRetroviruses

HowMicrobialPathogensSubvertHostInnateImmuneDefenses

HumanFungalInfections

Lipopolysaccharides(Endotoxins)

MedicallyRelevant MycoplasmasandUreaplasma

MicrobialAgentstoTreatCancer

MicrobiologyoftheCysticFibrosisAirway Mycotoxins

OralMicrobiology

PathogenSensing:Toll-LikeReceptorsandNODs(InnateImmunity)

PhageTherapy

Phagocytes(InnateImmunity)

PolyomavirusesandPapillomaviruses

Quinolones

Rabies

RespiratoryViruses

Retroviruses

RNAViruses:PlantPathogenic

RoleofBCellsandAntibodiesinControllingBacterialPathogens

SexuallyTransmittedDiseases

Toxoplasmosis

UnusualInfectiousAgents

TECHNOLOGICALADVANCESANDAPPLIEDMICROBIOLOGY

AminoAcidProduction

Amylases

AntimicrobialSusceptibilityTesting

BacterialTargetingofTumors

BacteriophagesandRapidDetectionofBacterialPathogens:ANovelApproach Beer/Brewing

Biocides

Biodeterioration – IncludingCulturalHeritage

BiologicalWarfare

Bioreactors

Biosensors

Bioterrorism

ContinuousCultures(Chemostats)

Corrosion,Microbial

DirectedEvolution

DNACloningStrategies

DrinkingWater

DrinkingWaterMicrobiology

FoodbornePathogenDetection,UsingRapidTechnologies

FungalExtracellularVesicles

GenomeSequenceDatabases:Annotation

GenomeSequenceDatabases:SequencingandAssembly

GenomeSequenceDatabases:TypesofDataandBioinformaticTools

GenomeSequencingofMicrobes

HeavyMetalPollutants:EnvironmentalandBiotechnologicalAspects

IndustrialBiotechnology(Overview)

IndustrialProductionofGlycosaminoglycans

InfectiousWasteManagement

InsecticidalToxinsfrom PhotorhabdusandXenorhabdus

MetalExtractionandBiomining

MicrobialAdhesion

MicrobialForensics

MicrobiologyofFermentedDairyProducts

MunicipalWaterTreatment

OrganicandFattyAcidProduction,Microbial PatentingofMicroorganisms

Pesticides,Microbial PhylogeneticMethods

Pigments,Microbial

Polysaccharides,Microbial

Solvent(Acetone–Butanol:AB)Production

TeachingResources,Microbiology

TechnologyAdvancesinMedicalMicrobiology

Trehalose:ACrucialMoleculeinthePhysiologyofFungi

TypeCultureCollectionstheirDatabases

VitaminsandVitamin-LikeCompounds:MicrobialProduction

WaterTreatment,Industrial Wine

Xylanases

PREFACE

Aswithpreviouseditionsofthe EncyclopediaofMicrobiology,the4theditiontakesonthechallengeofprovidinga contemporaryoverviewofmicrobes themostabundantanddiverseformsoflifeonEarth.Thesesingle-celled organismswerethefirstlifeformstoinhabitEarthandtheytransformedtheplanetanditsatmosphere.They continuetomaintainEarth’satmosphere,driveessentialprocessesinterrestrialandaquaticecosystems,and formintimaterelationshipswithallplantsandanimals.Microbescanreproducebydoublingevery20minutes orcanremaindormantformanythousandsofyears.TheycolonizeeveryknownhabitatonEarth,accounting forapproximatelyhalfofthelivingbiomassonourplanet.Microbesalsocausethemostdevastatingdiseases knowntohumansandarewinningtheantibioticwarwewageagainstthem.Yet,wecannotlivewithout microbesassymbiontsofhumansanddriversofEarth’sbiosphere.

Despitethecentralrolesofmicrobes,weareonlyjustbecomingawareofourlimitedknowledgeof interactionsamongmicrobes,otherorganisms,andtheenvironment.Moleculartechniquescontinuetolead arevolutioninourunderstandingofmicrobialdiversityandfunction,withthenew “bigdata” sciencesof genomics,transcriptomics,proteomics,andmetabolomicsnowbeingappliedtocommunitiesofmicrobes. Thesetechniquesprovidetheabilitytoidentifyandstudycomplexcommunitiesofmicrobesindiverse environmentsincludingthehumangut,forestsoil,water-treatmentbiofilters,andtheopenocean.

Giventheremarkablephysiologicalandphylogeneticdiversityofmicrobes,theircapacityforrapidevolution,andthepivotalroleofhost-associatedandenvironmentalmicrobiomes,itisdifficult,ifnotimpossible,to identifycontemporaryquestionsinbiologythatarenotinfluencedbymicrobes.Itisalsoincreasinglydifficult toassembleanencyclopediathatprovidescomprehensivecoverageofthevastuniverseofmicrobes.Despite thesechallenges,wehaveengagedtheexpertiseofscientistsaroundtheglobetoprovideanexceptional overviewofandperspectiveonthemicrobialworld.Thiseditionofthe EncyclopediaofMicrobiology willhelp readersdevelopaframeworkforunderstandingmicrobesandwillprovidereferencesdirectingreaderstothe primaryliteraturethatisneededforamorethoroughappreciationofspecifictopics.

Wehaveincludedanumberofarticleswhichprovideahistoricalperspectiveofmicrobiologythatisfocused ondisease oneofhumanity’searliestacknowledgmentofmicrobes.Thesehelpframemorecontemporary issuesinmicrobiologythathavemovedfarbeyondtherelativelysmallcollectionofmicrobesthatcausedisease. Ratherthansimplyalphabetizetopicsasintraditionalencyclopedias,articlesinthe4theditionarealsolisted underthefollowingthemesinaSubjectClassification:Historical,MicrobialDiversity,PhysiologyandGenomics,EcologyandEvolution,PathogenesisandImmunology,andTechnologicalAdvancesandAppliedMicrobiology.Wehopethishelpsreadersnavigatetheworkmoreeffectively.

Onbehalfofaninsightfulandcollegialeditorialteam,Ihopethatyouemergefromyourforaysintothe EncyclopediaofMicrobiology withsomeoftheawethatwesharefortheeleganceandpowerofthe microbialworld.

INTRODUCTION:MICROBIALDIVERSITY

Itiswhatwethinkweknowalreadythatoftenpreventsusfromlearning.

Oneofthedifficultlessonsforanyprofessionalscientististhat,asmuchasweknow,asgoodasourtoolsand questionsare,ourknowledgeiscrudeandfarsmallerthanweimaginedwhenwewerestudents.Particularly troublesomeisthatmostfundamentalaspectsofvariousscientificfieldsaresimplynotverywellunderstood. Thephysicistwonderswhat,exactly, “time” is,howspaceisstructured,andwhythePlanckConstantis 6.62607004x10 14 m 2 kg/sinsteadofanyothernumberyoumightcaretochoose.Chemistsargueabout thenatureofacovalentbond,orwhetherornottransitionstatesexistinreality.Biologistsareatalossto describehowlifeoriginated,orevenwhatexactlylife(inageneralsense)actuallyis.Inthemostimportantbook ofmoderntimes, “OntheOriginofSpecies,” CharlesDarwinclearly(butnotconcisely)deconstructstheideaof thebiological “species,” anddespitewhatmanyofuslearnedinschool,ourviewofthe “species” evenfor multicellularsexuallyreproducingcreaturesremainsmurky.Themodernreaderof “OntheOriginofSpecies ” mightbeforgivenforconcludingthatthereasonforthisisthatitistheactual biology ofspecies,andbyextension “life,” ourorigin,etc.,ratherthanourconceptsofthem,thatarefundamentallydisordered.

ThesubjectofthissectionoftheEncyclopediaisMicrobialDiversity.Whatdoesthismean?What is “microbialdiversity?”

Letusstartwith “microbial.” Literallyspeaking,theterm “microbial” meanssmalllivingthings,usually understoodtomeanlifetoosmalltoseewiththeunaidedeye.Thescientificfieldofmicrobiology,however, mostlyemergedfromourneedtosolvecrucialhealthdangerscreatedbyatinyfractionofmicrobes.Asaresult, “microbiology,” andso “microbes,” refertoBacteria(andinmoderntimestheArchaea),fungi,ascatteringof problematicsingle-celledorsmallmulticellulareukaryotes,andthephysiologicalsystemsofthehumanbody thatmanagesourinteractionswiththesecreatures.Thissellsthemicrobialworldveryshort.For85%ofthe historyofourplanet,lifewas entirely microbial,anditremains predominantly microbial.InthewordsofStephen J.Gould, “Welivenowinthe ‘AgeofBacteria.’ Ourplanethasalwaysbeeninthe ‘AgeofBacteria,’ eversincethefirst fossils bacteria,ofcourse wereentombedinrocksmorethan3billionyearsago.Onanypossible,reasonableorfair criterion,bacteriaare andalwayshavebeen thedominantformsoflifeonEarth.” Anotherviewofthiscomesfrom thephylogeneticperspective.Ifyouscrutinizeanyobjective/quantitative “TreeofLife,” basedonmolecular sequenceanalysisoranyothercriterionofchoice,youwillquicklydiscoverthatnonmicrobiallifeislimitedto thetipsofasmallnumberofotherwiseun-noteworthybranches.Onlyfromourself-centeredanthropocentric viewpointismicrobiologydistinguishablefrombiologyasawhole.

Andwhatof “diversity?” Livingthingsandtheirmorphology,structure,physiology,ecology,internal mechanisms,behavior,interactions,etc.,arefarmorediversethanmostofushavebeenledtobelieve.For example,ifyouthinkyouknowhowmitosisworks,lookitupin Giardia andbeamazed.Thenotionofwhat constitutesa “ gene ” inthekinetoplastof Trypanosoma requiresyoutothrowalmosteverythingyouthinkyou knowaboutmoleculargeneticsaway.Thenhavealookthroughthegenomeofthearchaeon Nanoarchaeum. These are justthetipsoficebergs;theseandmanymorecanbefoundwithinthechaptersthatfollow.Andyet allofthisdiversityrestsoveranalmostentirelyuniformbiochemistrythatspeakstothesharedancestryofall livingthingsonEarth.How,then,doweassessthe “diversity” oflivingthings?Historically,thismeant comparingthemorphologyofdifferentlivingthings;thiswastheoriginofLinnaeantaxonomyand,tobe fair,isveryusefulfororganismsonthehumansizescale.Morerecentlymolecularphylogeneticshasallowedus tomoreclearlyunderstandhowcreaturesarerelated,anddrawanobjectiveandquantitativegraphofthese

Turn static files into dynamic content formats.

Create a flipbook
Issuu converts static files into: digital portfolios, online yearbooks, online catalogs, digital photo albums and more. Sign up and create your flipbook.