Environmental Molecular Diagnostics - Alaska Department of

363 Pages·2013·3.85 MB·English

by  Sidney Huffman

Technical and Regulatory Guidance
Environmental Molecular Diagnostics
New Site Characterization and Remediation Enhancement Tools
April2013
Prepared by
TheInterstateTechnology&RegulatoryCouncil
EnvironmentalMolecularDiagnosticsTeam
ABOUT ITRC
TheInterstateTechnology and Regulatory Council (ITRC) isapublic-privatecoalition working to reducebar-
riersto theuseof innovativeenvironmental technologiesand approachesso that compliancecostsarereduced
and cleanup efficacy ismaximized.ITRCproducesdocumentsand training that broaden and deepen technical
knowledgeand expeditequality regulatory decision making whileprotecting human health and theenvir-
onment.With privateand publicsector membersfrom all 50 statesand theDistrict of Columbia,ITRCtruly
providesanational perspective.Moreinformation on ITRCisavailableat www.itrcweb.org. ITRCisapro-
gram of theEnvironmental Research Instituteof theStates(ERIS),a501(c)(3) organization incorporated in
theDistrict of Columbiaand managed by theEnvironmental Council of theStates(ECOS).ECOS isthe
national,nonprofit,nonpartisan association representing thestateand territorial environmental commissioners.
Itsmission isto serveasachampion for states; to provideaclearinghouseof information for stateenvir-
onmental commissioners; to promotecoordination in environmental management; and to articulatestatepos-
itionson environmental issuesto Congress,federal agencies,and thepublic.
DISCLAIMER
Thismaterial wasprepared asan account of work sponsored by an agency of theUnited StatesGovernment.
Neither theUnited StatesGovernment nor any agency thereof,nor any of their employees,makesany war-
ranty,expressor implied,or assumesany legal liability or responsibility for theaccuracy,completeness,or use-
fulnessof any information,apparatus,product,or processdisclosed,or representsthat itsusewould not
infringeprivately owned rights.Referenceherein to any specificcommercial product,process,or serviceby
tradename,trademark,manufacturer,or otherwisedoesnot necessarily constituteor imply itsendorsement,
recommendation,or favoring by theUnited StatesGovernment or any agency thereof.Theviewsand opin-
ionsof authorsexpressed herein do not necessarily stateor reflect thoseof theUnited StatesGovernment or
any agency thereof and no official endorsement should beinferred.Theinformation provided in documents,
training curricula,and other print or electronicmaterialscreated by theInterstateTechnology and Regulatory
Council (ITRC) (“ITRCProducts”) isintended asageneral referenceto help regulatorsand othersdevelop a
consistent approach to their evaluation,regulatory approval,and deployment of environmental technologies.
Theinformation in ITRCProductswasformulated to bereliableand accurate.However,theinformation is
provided "asis" and useof thisinformation isat theusers’ own risk.
ITRCProductsdo not necessarily addressall applicablehealth and safety risksand precautionswith respect to
particular materials,conditions,or proceduresin specificapplicationsof any technology.Consequently,ITRC
recommendsconsulting applicablestandards,laws,regulations,suppliersof materials,and material safety data
sheetsfor information concerning safety and health risksand precautionsand compliancewith then-applicable
lawsand regulations.  ITRC,ERIS and ECOS shall not beliablein theevent of any conflict between inform-
ation in ITRCProductsand such laws,regulations,and/or other ordinances.  ITRCProduct content may be
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acting upon or using thisinformation.ITRC,ERIS,and ECOS do not endorseor recommend theuseof spe-
cifictechnology or technology provider through ITRCProducts.  Referenceto technologies,products,or ser-
vicesoffered by other partiesdoesnot constituteaguaranteeby ITRC,ERIS,and ECOS of thequality or
valueof thosetechnologies,products,or services.Information in ITRCProductsisfor general referenceonly;
it should not beconstrued asdefinitiveguidancefor any specificsiteand isnot asubstitutefor consultation
with qualified professional advisors.
EMD-2
Environmental Molecular Diagnostics
New Site Characterization and Remediation Enhancement Tools
April2013
Prepared by
TheInterstateTechnology&RegulatoryCouncil
EnvironmentalMolecularDiagnosticsTeam
Copyright2013InterstateTechnology&RegulatoryCouncil
50F StreetNW,Suite350,Washington,DC 20001
Permissionisgrantedtorefertoorquotefromthispublicationwiththecustomaryacknow-
ledgmentofthesource.Thesuggestedcitationforthisdocumentisasfollows:
ITRC (InterstateTechnology&RegulatoryCouncil).2013.EnvironmentalMolecularDiagnostics,
New SiteCharacterizationandRemediationEnhancementTools.EMD-2.Washington,
D.C.:InterstateTechnology&RegulatoryCouncil,EnvironmentalMolecularDiagnostics
Team.www.itrcweb.org.
AlltablesandfiguresfromITRC unlessotherwisenoted.
ACKNOWLEDGEMENTS
ThemembersoftheInterstateTechnologyandRegulatoryCouncil(ITRC)EnvironmentalMolecu-
larDiagnostics(EMD)Teamwishtoacknowledgetheindividuals,organizations,andagenciesthat
contributedtothisTechnicalandRegulatoryGuidanceDocument.Theteamrecognizesthegreat
valueofteamworkandthankseveryonewhoparticipated—namedandunnamed, ITRC staff,
ITRC PointofContact,orteammember—fortheiroutstandingeffortonthisproject.
TheEMD teamappreciatestheongoingsupportfromseveralagenciesandorganizations.Aspart
ofthebroaderITRC effort,theEMD TeameffortisfundedprimarilybytheU.S. Departmentof
Energy.AdditionalfundingandsupporthavebeenprovidedbytheU.S.DepartmentofDefense
andtheU.S.EnvironmentalProtectionAgency.ITRC operatesasacommitteeoftheEnvir-
onmentalResearchInstituteoftheStates(ERIS),aSection501(c)(3)publiccharitythatsupports
theEnvironmentalCounciloftheStates(ECOS)throughitseducationalandresearchactivities.
ThegoaloftheseactivitiesistoimprovetheenvironmentintheUnitedStatesand toprovidea
forumforstateenvironmentalpolicymakers.
TheEMD TeamthankstheITRC externalreviewersandthepeerreviewerswhocontributedcom-
mentsandsuggestionsthatwereofgreathelptotheteaminfinalizingthisguidance.TheEMD
Teamalsowishestothankthereviewersandcontributorsofthecasestudies.
TheEMD Teamrecognizestheeffortsandimportantcontributionsofthefollowingstateenvir-
onmentalpersonnel:
RobertMueller,New JerseyDepartmentofEnvironmentalProtection,EMD TeamLeader
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JamesFish,AlaskaDepartmentofEnvironmentalConservation
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ChristineBrown,SaraMichael,andClaudioSorrentino;CaliforniaDepartmentofToxic
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SubstanceControl
CleetCarlton,CaliforniaRegionalWaterQualityControlBoard
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UndineJohnson,GeorgiaEnvironmentalProtectionDivision
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RichardAho,MichiganMCSWMA
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RameshBelani,PennsylvaniaDepartmentofEnvironmentalProtection
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KimberlyWilson,SouthCarolinaDepartmentofHealthandEnvironmentalControl
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TheEMD Teamrecognizestheeffortsandvaluablecontributionsofthefollowingstakeholderand
academicrepresentatives:
PeterStrauss,PMStrauss&Associates
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MichaelHyman,NorthCarolinaStateUniversity
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PaulPhilp,UniversityofOklahoma
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FrankLöfflerandElizabethPadilla-Crespo,UniversityofTennessee
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KerrySublette,UniversityofTulsa
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JenniferWeidhaas,WestVirginiaUniversity
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TheEMD Teamrecognizestheeffortsandvaluablecontributionsofthefollowingfederalper-
sonnel:
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AdriaBodour,AFCEE
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AnnMiracleandM.HopeLee,DOE,PacificNorthwestNationalLaboratory
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HansStrooandPaulHatzinger,SERDP/ESTCP
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CherylA.Hawkins,USEPA
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DavidLattier,USEPA
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CarmenLebrón,U.S.Navy
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Finally,theEMD Teamrecognizestheeffortsandvaluablecontributionsofthefollowingcon-
sultantsandindustryrepresentatives:
JunLu,RebeccaMora,ChadRoper,andHarvinderSingh;AECOMEnvironment
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JessicaGoin,AnchorQEA
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CaitlinBell,ARCADIS
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RamonaDarlington,BattelleMemorialInstitute
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StephanieFiorenzaandDavidTsao,BP
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StephenKoenigsberg,BrownandCaldwell
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TamzenMacbethandRyanWymore,CDMSmith
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DavidDuncklee,DunckleeandDunham
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WilliamBerti,DuPont
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IoanaPetrisor,CardnoEntrix
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EricRaes,EngineeringandLandPlanningAssociates,Inc.
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DevonRowe,ENVIRON
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ErikPetrovskisandTashaKamegai-Karadi,GeosyntecConsultants
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AaronPeacock,Haley&Aldrich,Inc.
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SophiaDrugan,Kleinfelder,Inc.
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BrettBaldwinandDoraOgles,MicrobialInsights,Inc.
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PatMcLoughlin,Microseeps,Inc.
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LesleyHayWilson,SageRiskSolutions,LLC
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ChristopherGlenn,TreadwellRollo
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YiWang,Zymax
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GregDavis
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EXECUTIVE SUMMARY
Environmentalmoleculardiagnostics(EMDs)isacollectivetermthatdescribesagroupof
advancedandemergingtechniquesusedtoanalyzethebiologicalandchemicalcharacteristicsof
environmentalsamples.Overthelastdecade,greatadvanceshavebeenmadeinadaptingand
applyingEMDsforenvironmentalsitemanagement.EMDsarebecomingincreasinglypowerful,
andstandardizedmethodsarebeingdeveloped.Asaresult,theiruseisincreasingrapidly,anda
growingneedexistsfortechnicalinformationandtrainingonEMDs.EMDsprovideadditionaland
oftenuniqueinformationthatsupplementsconventionaldata.Thepurposeofthistechnicalandreg-
ulatoryguidancedocumentisto:
ProvideobjectiveguidanceonthebestpracticesforusingEMDs
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DemonstrateappropriateusesofEMDs,includingtheirstrengthsandlimitations
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Explainhow toevaluate,apply,andinterprettheresultsofEMDs.
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ThedocumentprovidesdetaileddescriptionsofeachofthemajorEMDs,alongwithcasestudies
oftheirusesandrecommendationsregardingtheappropriateusesofthesetechniques.Inaddition,
appendicesareincludedtoaddressthefrequentlyaskedquestionsregardingtheunderlyingscience,
includingstableisotopechemistryandfundamentalmolecularbiology,sothatinterestedproject
managers, stakeholdersandregulatorscaneasilyfindtheinformationneededtounderstandthe
basisforeachoftheindividualEMDs.
TYPES OF EMDS
EMDscanbeclassifiedintotwomajorcategoriesofanalyticaltechniques:chemicaltechniques,
specificallycompoundspecificisotopeanalysis(CSIA),andavarietyofmolecularbiologicaltech-
niques(MBTs).CSIA measurestheamountsofstableisotopes(typicallycarbon, hydrogen,or
chlorine)incontaminantstodeterminetheextentofspecificchemicalandbiochemicalreactions
impactingthecontaminant.Asacontaminantdegradesthroughnaturalorengineeredprocesses,the
relativeamountofeachstableisotopeinthecontaminantcanchange.Incontrast,theisotopiccom-
positionofcontaminantsislargelyunaffectedbyprocessessuchasdilutionthatdonotresultin
degradationofthecontaminant.CSIA thereforecanbeusefulforansweringseveralimportantques-
tionsregardingachemical’ssource,degradationmechanisms,andrateofdegradation.
MBTsevaluatethetypes,abundance,andbiochemicalcapabilitiesofmicroorganismspresentin
theenvironment.Often,themicroorganismsresponsibleforthedegradationofspecificcon-
taminantscannotbedetectedandquantifiedbyconventionalmethodsandMBTscanovercome
theselimitations.SeveraltypesofMBTsareavailable-somecanbeusedtodetectknownmicroor-
ganisms,othersarealsousefulforquantification,somecanbeusedtodeterminewhethermicroor-
ganismsareactivelydegradingspecificcontaminants,andsomecanidentifycurrentlyunknown
microorganismsinvolvedindegradation.
Todate,themostcommonlyusedMBTsarepolymerasechainreaction(PCR),quantitativePCR
(qPCR)andreversetranscriptase-qPCR (RT-qPCR),andDNA microarrays.Howeverother
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MBTshaveusesaswell,includingfluorescenceinsituhybridization(FISH),enzymeactivity
probes(EAPs)andstableisotopeprobing(SIP).Therearealsoseveralpotentiallyusefulmicrobial
fingerprintingtechniques,includingphospholipidfattyacid(PLFA)analysis,denaturinggradient
gelelectrophoresis(DGGE),andterminalrestrictionfragmentlengthpolymorphism(T-RFLP).
EMDshaveapplicationineachphaseofenvironmentalsitemanagement,includingsitechar-
acterization,remediation,monitoring,andclosureactivities(SeeFigureES-1).EMDscanprovide
uniqueinformationvaluableinconjunctionwithmoreconventionaldata.
FigureES-1.Overview ofEMDs.
USINGEMDS
EMDshavebeenusedathundredsofenvironmentalcleanupsitesintheUS (and alsoatsites
aroundtheworld).FigureES-2includescumulativedatafornumbersofprojectsbystatefrom
2009to2012.Thedataarefromtwocommerciallaboratories,sothedatamaynotfullyrepresent
theactualnumberofEMD projectscompletedduringthattime.Thestateswereassignedtothepro-
jectsbasedontheinformationavailabletothelaboratories.Thereisuncertaintyinsomeofthepro-
jectlocationsbecauseofclientconfidentiality.Themapisintendedtoprovidearelative
understandingoftheusageofEMDsatthistime,andnottoprovidedefinitivenumbersofprojects.
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FigureES-2.EMD projectsbystate.
EMDscanprovidethefollowingbenefits:
Improvethemanagementofcontaminatedsites
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Determinewhetherbioticorabioticdegradationisoccurringatasite
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Identifyspecificcontaminantsourcesorrevealwhethermultiplesourcesofcontaminationare
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present(forinstance, isotopicfractionation)
Improveevaluationanddecisionmakingforremediationstrategies
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Identifydegradationpathwaysandtheirdegreeofcompletion
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Identifytheneedforenhancementssuchaschemicalamendmentsorbioaugmentation
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Estimatedegradationrates,forinstance,CSIA usingtheRayleighequation(see Appendix
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C.12)
Aidinmonitoringprogramdecisions
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Providecomplementarydatatosupportsiteclosureandothersitemanagementdecisions
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FigureES-3describespotentialusesofEMDsineachphaseofsitemanagement.
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