Consequences of Microbial Interactions with Hydrocarbons, Oils, and Lipids: Biodegradation and Bioremediation PDF
Preview Consequences of Microbial Interactions with Hydrocarbons, Oils, and Lipids: Biodegradation and Bioremediation
Handbook of Hydrocarbon and Lipid Microbiology Series Editors: Kenneth N. Timmis (Editor-in-Chief) Matthias Boll · Otto Geiger · Howard Goldfine · Tino Krell Sang Yup Lee · Terry J. McGenity · Fernando Rojo Diana Z. Sousa · Alfons J. M. Stams · Robert J. Steffan · Heinz Wilkes Robert J. Steffan Editor Consequences of Microbial Interactions with Hydrocarbons, Oils, and Lipids: Biodegradation and Bioremediation Handbook of Hydrocarbon and Lipid Microbiology SeriesEditors KennethN.Timmis(Editor-in-Chief) FernandoRojo EmeritusProfessor CSIC InstituteofMicrobiology CentroNacionaldeBiotecnología TechnicalUniversityBraunschweig Madrid,Spain Braunschweig,Germany DianaZ.Sousa MatthiasBoll LaboratoryofMicrobiology InstituteofBiology/Microbiology WageningenUniversityandResearch UniversityofFreiburg Wageningen,TheNetherlands Freiburg,Germany AlfonsJ.M.Stams OttoGeiger LaboratoryofMicrobiology CentrodeCienciasGenómicas WageningenUniversityandResearch UniversidadNacionalAutónomade Wageningen,TheNetherlands México CentreofBiologicalEngineering Cuernavaca,Morelos,Mexico UniversityofMinho HowardGoldfine Braga,Portugal DepartmentofMicrobiology RobertJ.Steffan UniversityofPennsylvania BlueCrabLureCompany Philadelphia,PA,USA CapeCoral,FL,USA TinoKrell HeinzWilkes DepartmentofEnvironmental ICBM Protection CarlvonOssietzkyUniversity EstaciónExperimentaldelZaidín Oldenburg,Niedersachsen,Germany ConsejoSuperiordeInvestigaciones Científicas Granada,Granada,Spain SangYupLee Dept.Chem.Engineer.andBioProcess KoreaAdv.Inst.ScienceandTechn. Taejon,Korea(Republicof) TerryJ.McGenity SchoolofBiologicalSciences UniversityofEssex Colchester,UK This handbook is the unique and definitive resource of current knowledge on the diverse and multifaceted aspects of microbial interactions with hydrocarbons and lipids, the microbial players, the physiological mechanisms and adaptive strategies underlying microbial life and activities at hydrophobic material:aqueous liquid interfaces, and the multitude of health, environmental and biotechnological conse- quencesoftheseactivities. ScientificAdvisoryBoard Victor de Lorenzo, Eduardo Diaz, Otto Geiger, Ian Head, Sang Yup Lee, Terry McGenity,ColinMurrell,BalbinaNogales,RogerPrince,JuanLuisRamos,Wilfred Röling,ElioraRon,BurkhardTümmler,JanRoelofvanderMeer,WillyVerstraete, FriedrichWiddel,HeinzWilkesandMichailYakimov. Moreinformationaboutthisseriesathttp://www.springer.com/series/13884 Robert J. Steffan Editor Consequences of Microbial Interactions with Hydrocarbons, Oils, and Lipids: Biodegradation and Bioremediation With50Figuresand25Tables Editor RobertJ.Steffan BlueCrabLureCompany CapeCoral,FL,USA ISBN978-3-319-50432-2 ISBN978-3-319-50433-9(eBook) ISBN978-3-319-50434-6(printandelectronicbundle) https://doi.org/10.1007/978-3-319-50433-9 ©SpringerNatureSwitzerlandAG2019 Thisworkissubjecttocopyright.AllrightsarereservedbythePublisher,whetherthewholeorpartofthe materialisconcerned,specificallytherightsoftranslation,reprinting,reuseofillustrations,recitation, broadcasting,reproductiononmicrofilmsorinanyotherphysicalway,andtransmissionorinformation storageandretrieval,electronicadaptation,computersoftware,orbysimilarordissimilarmethodology nowknownorhereafterdeveloped. Theuseofgeneraldescriptivenames,registerednames,trademarks,servicemarks,etc.inthispublication doesnotimply,evenintheabsenceofaspecificstatement,thatsuchnamesareexemptfromtherelevant protectivelawsandregulationsandthereforefreeforgeneraluse. Thepublisher,theauthors,andtheeditorsaresafetoassumethattheadviceandinformationinthisbook arebelievedtobetrueandaccurateatthedateofpublication.Neitherthepublishernortheauthorsorthe editorsgiveawarranty,expressorimplied,withrespecttothematerialcontainedhereinorforanyerrors oromissionsthatmayhavebeenmade.Thepublisherremainsneutralwithregardtojurisdictionalclaims inpublishedmapsandinstitutionalaffiliations. ThisSpringerimprintispublishedbytheregisteredcompanySpringerNatureSwitzerlandAG Theregisteredcompanyaddressis:Gewerbestrasse11,6330Cham,Switzerland Preface Formanydecadesscientistshavestudiedthebiotransformationofhydrocarbonsby microorganisms.Thisresearchoftenbeginswithmicrocosmstudiesthatevaluatethe transformationofchemicalsinsimulatedenvironments,andsometimesleadstothe isolationofindividualmicrobesthatcantransformthetargetchemicalinsomeway. Thesestudiesthencanleadtobiochemicalanalysestoidentifyspecifictransforma- tion reactions and the responsible enzymes, and to genetic studies to identify and analyze the underlying genetic basis of the observed biotransformations. As illus- trated in some of the chapters presented in this volume, these genetic studies can evenleadtodeepunderstandingsoftheintricatenetworksofregulatorycontrolthat allow microorganisms to balance carbon and energy flow even while surviving in chemically rich hostile environments. The use of modern “omic” techniques (e.g., genomics,proteomics,metabolomics,etc.)nowallowsscientiststoevaluatesomeof these regulatory and biochemical processes at the community level and even in actualenvironmentalsamples.Althoughsomeofthisresearchhasledtofundamen- tal understandings of universal principles or mechanisms, much of the work is targetedtoward understandingthefate ofchemicalsinnatureandthedevelopment of techniques for remediating polluted environments. Together, these studies form thefoundationofthefieldsofbioremediationandbiologicalwastetreatmentwhich involvethepurposefulapplicationofmicrobialcatalyststoremediatecontaminated environmentsortreatchemicalwastestreams,respectively. Inthisvolume,webringtogetherinternationalexpertstodiscussthestateofthe art in the bioremediation of hydrocarbons. The volume begins with a forward- lookingintroductiontothefieldofbioremediationthatprovidesapathforwardfor the use of modern molecular and biochemical tools to improve the treatment of environmentalpollutants.Ithenprovideafirst-handperspectiveonthemanyfactors that drive the selection and application of advanced technologies at actual remedi- ationsites.Afteracomprehensivechapterabouthowactualcontaminatedindustrial sites can be used to enhance bioremediation research, several chapters provide insightintohydrocarbonbiodegradationinspecificenvironments,includingmarine systems, groundwater, shale oil formations, and soils. Other chapters focus on specific hydrocarbon remediation techniques, including natural attenuation, biostimulation, bioaugmentation, co-metabolism, and surfactant enhancement. Twochaptersfocusonspecificclassesofpollutants,ether-containinghydrocarbons v vi Preface (e.g.,MTBE,1,4-dioxane,etc.)andplastics,thathavebeenintherecentforefrontof research because of their recalcitrance and public interest. Another comprehensive chapter summarizes decades of research on the genetic regulation of toluene bio- degradation in Pseudomonas, and it brings us full circle back to our introductory chapterthatinformsusofhowmodern“omic”data,builtonthefoundationofsuch landmarkbasicresearch,canimproveremediationinthefuture.Finally,thevolume ends with a very detailed chapter on the use of chemostats to generate essential kinetics data for evaluating biodegradation. This chapter should become a go-to instruction manual for this somewhat lost art that still has great potential for evaluating,understanding,andimprovingpollutionbiodegradation. Iamextremelygratefultotheauthorswhosharedtheirvaluabletimetocontribute tothisexcellentcollectionofchaptersonhydrocarbonbiodegradationandbioreme- diation.ForthoseofyouthatIhaveknownthroughouryearsofinteractions,Ilook forwardtoseeingyouagaininthenot-too-distantfuture,andtothoseofyouIhave notyetmet,Ilookforwardtothechancetosomedaythankyouinpersonforyour helpinthiseffort. CapeCoral,FL,USA RobertJ.Steffan Acknowledgment More than 30 years ago as a budding scientist having just received my Ph.D., I arrived at the National Institute for Biotechnology (GBF) in Braunschweig, Ger- many, for my postdoctoral studies under the direction of Professor Kenneth N. Timmis. We were a new group then that grew rapidly, and with that growth was the need for everyone to accept significant levels of responsibility so that the group could become established and prosper. Professor Timmis provided me with manyopportunitiesatthattime,includingthechancetomentorstudents,managemy own small group, review manuscripts, and to help organize conferences. These opportunities and others offered by him throughout my career made me a better scientistandamoreactivememberofthescientificcommunity.Thiseditorialeffort may be my last chance to work with Professor Timmis in a scientific capacity as I fadeintoretirement.IthankKenfortheopportunitytoeditthisvolume,andforhis manyyearsoffriendship,mentoring,andcollaboration. vii Contents 1 BiodegradationandBioremediation:AnIntroduction .......... 1 VíctordeLorenzo 2 DevelopingBioremediationTechnologiesforCommercial Application:AnInsider’sView ............................ 21 RobertJ.Steffan 3 UtilityofIndustrialExperimentalSitesforDeveloping Analytical,Monitoring,andRemediationTechnologies ......... 33 D.L.FreedmanandR.Yu 4 BioremediationofMarineOilSpills ........................ 45 RogerC.PrinceandRonaldM.Atlas 5 OilBiodegradationinDeepMarineBasins .................. 71 TerryC.HazenandStephenM.Techtmann 6 BiostimulationStrategiesforEnhancedBioremediationof MarineOilSpillsIncludingChronicPollution ................ 89 MariaNikolopoulouandNicolasKalogerakis 7 WeatheredHydrocarbonBiotransformation:Implications forBioremediation,Analysis,andRiskAssessment ............ 99 S.Cipullo,K.J.Brassington,S.J.T.Pollard,andF.Coulon 8 RoleofBiosurfactants ................................... 117 ElioraZ.RonandE.Rosenberg 9 Plant-EndophytePartnershipstoAssistPetroleum HydrocarbonRemediation ............................... 123 S.Thijs,N.Weyens,P.Gkorezis,andJ.Vangronsveld ix x Contents 10 RemovalofHydrocarbonsandOtherRelatedChemicals viatheRhizosphereofPlants ............................. 157 LázaroMolina,PietervanDillewijn,EstrellaDuque,CraigDaniels, TinoKrell,ManuelEspinosa-Urgel,MaríaIsabelRamos-González, SaraRodríguez-Conde,MiguelA.Matilla,ReginaWittich, JuanLuisRamos,andAnaSegura 11 NaturalAttenuationofHydrocarbonCompoundsin Groundwater .......................................... 171 StevenF.Thornton 12 InSituGroundwaterBioremediation ....................... 197 TerryC.Hazen 13 MicrobiologyofOil-andNaturalGas-ProducingShale Formations:AnOverview ................................ 215 ChristopherG.Struchtemeyer 14 CometabolicBioremediation .............................. 233 TerryC.Hazen 15 AnaerobicBiodegradationofHydrocarbons:Metagenomics andMetabolomics ...................................... 249 LisaM.GiegandCourtneyR.A.Toth 16 GenomicResponsesofPseudomonasputidatoAromatic Hydrocarbons ......................................... 287 VíctordeLorenzoandHirenJoshi 17 BiodegradationofEtherPollutants ........................ 303 AmieMcElroyandMichaelHyman 18 PlasticBiodegradation:ChallengesandOpportunities ......... 333 NickWierckx,TanjaNarancic,ChristianEberlein,RenWei, OliverDrzyzga,AudreyMagnin,HendrikBallerstedt, ShaneT.Kenny,EricPollet,LucAvérous,KevinE.O’Connor, WolfgangZimmermann,HermannJ.Heipieper,AuxiliadoraPrieto, JoséJiménez,andLarsM.Blank 19 DeterminationofKineticParametersandMetabolicModes UsingtheChemostat .................................... 363 RichBodenandLeeP.Hutt Index .................................................... 405
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