Applied Microbiology and Molecular Biology in Oilfield Systems: Proceedings from the International Symposium on Applied Microbiology and Molecular Biology in Oil Systems (ISMOS-2), 2009 PDF
Preview Applied Microbiology and Molecular Biology in Oilfield Systems: Proceedings from the International Symposium on Applied Microbiology and Molecular Biology in Oil Systems (ISMOS-2), 2009
Applied Microbiology and Molecular Biology in Oilfield Systems Applied Microbiology and Molecular Biology in Oilfield Systems Proceedings from the International Symposium on Applied Microbiology and Molecular Biology in Oil Systems (ISMOS-2), 2009 Edited by Corinne Whitby DepartmentofBiologicalSciences,UniversityofEssex, Colchester,UK Torben Lund Skovhus DanishTechnologicalInstitute, DTIOil&Gas,Aarhus, Denmark 1 3 Editors CorinneWhitby TorbenLundSkovhus UniversityofEssex DanishTechnologicalInstitute DepartmentofBiologicalSciences DTIOil&Gas KongsvangAllé29 WivenhoePark DK-8000Aarhus Colchester Denmark CO43SQEssex [email protected] UnitedKingdom [email protected] ISBN978-90-481-9251-9 e-ISBN978-90-481-9252-6 DOI10.1007/978-90-481-9252-6 SpringerDordrechtHeidelbergLondonNewYork LibraryofCongressControlNumber:2010932402 ©SpringerScience+BusinessMediaB.V.2011 Nopartofthisworkmaybereproduced,storedinaretrievalsystem,ortransmittedinanyformorby anymeans,electronic,mechanical,photocopying,microfilming,recordingorotherwise,withoutwritten permissionfromthePublisher,withtheexceptionofanymaterialsuppliedspecificallyforthepurpose ofbeingenteredandexecutedonacomputersystem,forexclusiveusebythepurchaserofthework. Coverillustration:GraphicsproducedbyJennieOjczyk,JODesign,Ildved,Denmark, [email protected] Printedonacid-freepaper SpringerispartofSpringerScience+BusinessMedia(www.springer.com) Preface This book provides a combined theoretical and practical approach to molecular microbiology studies in oil reservoirs and related downstream processing plants and is written by some of the world’s leading authorities in this area from both academia and the oil and petroleum industry. The book is based on specific case studies and encapsulates the ethos of the ‘International Symposium on Applied MicrobiologyandMolecularBiologyinOilSystems(ISMOS)’.Thetextexplains how each method works and the type of information that can be obtained. This is ofdirectrelevancetoreservoirengineers,productionchemists,corrosionmanagers, field technicians and microbiologists, who are working in the oil and petroleum industry.ThetextbeginswithChapter2,whichaddressespracticalissuesrelatingto samplingfromoilfieldsystemsandthetypesofsamplestobecollected.Specifically, thefocusisontheimportanceofcorrectsamplingtechniques,howtomaintainsam- ple integrity, for example, from offshore facilities, until the samples are processed in the laboratory. Details are also given on methodologies relating to DNA/RNA extractionandPCRamplificationofnucleicacidsfromfieldsamples. Chapters 3–11 introduce each molecular approach in turn and explain the type of information that can be obtained, depending on the specific microbiological or technical questions that are being addressed. For example, if the question is ‘which microbial community is present in a sample?’ then possible molecular approaches which could be applied include PCR, DNA fingerprinting, fluorescent in situ hybridisation (FISH) and cloning and sequencing. If the question is ‘how manymicroorganismsarepresentinasample?’thenquantitativePCR(qPCR)that targets a specific gene may be applied. In order to address the question of ‘which microorganisms are active in a sample?’ then approaches such as the use of RNA analysestargetingfunctionalgenesmaybeapplied.Thiscategorisationofeachtech- niqueisratheranoversimplificationandindeedinformationfromonemethodmay addressmorethanoneofthesemicrobiologicalquestions.Forexample,whileFISH enables the identification and localisation of microbes within their environment, quantitativedataontheirrelativeabundancecanalsobeobtained,ifspecificprobes are applied. Details are also given on the recent developments of next-generation sequencingmethodsandmicroarrayswhichenablevastamountsofdatatobegen- erated very quickly and will allow us to significantly advance our knowledge of oilfieldmicrobiologyinthefuture.However,theproductionofsuchlargedatasets v vi Preface requires more sophisticated bioinformatics software and user expertise in order to processit,understanditandapplyit,inordertobenefittheindustry. Chapters12–19givedetailsoftheproblemscausedbymicrobesinoilfieldsys- tems such as biocorrosion (MIC) and reservoir souring. The text focuses on how molecularmicrobiologicalmethods(MMM)offeranovelapproachformonitoring theinsitumicrobialcommunitiesinordertomitigatepotentialproblemscausedby microbes in the future, as well as to determine the efficacy of possible treatment strategies (e.g. nitrate, biocides, scavenging of H S, pigging/cleaning and corro- 2 sion/scale inhibitors). In addition to the problems caused by microbes, Chapters 20–25considerthebeneficialimplicationsofspecificmicrobialprocessesandhow MMMmaybeusedtofurtherexploitthese.Thisincludestheuseofmicroorganisms inbioremediationandbiorefiningandbioprocessingforpetroleumoilupgrade,the exploitationofmicroorganismsinoilrecovery,i.e.microbial-enhancedoilrecovery (MEOR)andusinganaerobicmicrobialprocessesforobtainingmethanefromoil. Chapters 26–28 describe novel fuels for the future, including the development of biofuels and the removal of naphthenic acids for both heavy oil upgrade and the bioremediation of contaminated tailing pond waters. Finally, in the Appendix, detailsareprovidedforthemethodologiesusedbythecontributingauthorsasguide- linesfornon-specialistusersworkingintheoilandpetroleumindustry.Currently, there are other methods, such as stable isotopes, proteomics and metabolomics, whichmayalsohavethepotentialtofurtheradvanceourunderstandingofmicrobial ecologyandtheirprocessesinthesub-surface.Thus,incomplexoilsystems,where manyphysicochemicalparametersaredrivingthemicrobialcommunitiesandtheir activities, it is important to adopt a polyphasic approach which combines molec- ular microbiological studies, with physiological and biochemical analyses of the microorganisms,alongsideadetailedcharacterisationoftheirenvironment.Sucha combined approach of analytical technologies will enhance oil production, extend life time of aging equipment/facilities, increase personnel safety and more effi- ciently protect the environment. Therefore, the energy sector will greatly benefit fromthewidespreadimplementationofMMMinthenearfuture. Acknowledgements Wewouldliketothankallofthecontributorstothisbookandalsotothereviewers fortheirusefulcommentsandsuggestions. Colchester,UK CorinneWhitby Aarhus,Denmark TorbenLundSkovhus vii Contents PartI Introduction,SamplingandProcedures 1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 CorinneWhitbyandTorbenLundSkovhus 2 SamplingandNucleic ExtractionProcedures fromOil ReservoirSamples . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 GeertM.vanderKraan,MaartendeRidder,BartP.Lomans, andGerardMuyzer PartII ApplicationofMolecularMicrobiologicalMethods totheOilIndustry 3 Application of Molecular Microbiological Methods totheOilIndustrytoAnalyseDNA,RNAandProteins . . . . . . . 19 SeanM.Caffrey 4 WhichMicrobialCommunitiesArePresent?Importance ofSelectingAppropriatePrimersandProbesforUsein MolecularMicrobiologicalMethods(MMM)inOilfields . . . . . . 27 KetilBerntSørensen 5 WhichMicrobialCommunitiesarePresent?Application ofPCR-DGGE:CaseStudyonanOilfieldCoreSample . . . . . . 33 GeertM.vanderKraan,FlorisBuijzen, CorA.T.Kuijvenhoven,andGerardMuyzer 6 WhichMicrobialCommunitiesArePresent?Application ofCloneLibraries:SyntrophicAcetateDegradationto MethaneinaHigh-TemperaturePetroleumReservoir– Culture-Basedand16SrRNAGenesCharacterisation . . . . . . . 45 NatalyaM.Shestakova,ValeriyS.Ivoilov,TatianaP.Tourova, SergeyS.Belyaev,AndreiB.Poltaraus,andTamaraN.Nazina ix
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