Table Of ContentHandbook 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
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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
