Hydrocarbon and Lipid Microbiology Protocols: Genetic, Genomic and System Analyses of Communities

291 Pages·2017·5.7 MB·English

by  Terry J. McGenity

Terry J. McGenity
Kenneth N. Timmis
Balbina Nogales Editors
Hydrocarbon and
Lipid Microbiology
Protocols
Genetic, Genomic and System
Analyses of Communities
Springer Protocols Handbooks
More information about this series at http://www.springer.com/series/8623
Terry J. McGenity Kenneth N. Timmis Balbina Nogales
(cid:129) (cid:129)
Editors
Hydrocarbon and Lipid
Microbiology Protocols
Genetic, Genomic and System Analyses
of Communities
Scientific Advisory Board
JackGilbert,IanHead,MandyJoye,VictordeLorenzo,
JanRoelofvanderMeer,ColinMurrell,JoshNeufeld,
RogerPrince,JuanLuisRamos,WilfredRo¨ling,
HeinzWilkes,MichailYakimov
Editors
TerryJ.McGenity KennethN.Timmis
SchoolofBiologicalSciences InstituteofMicrobiology
UniversityofEssex TechnicalUniversityBraunschweig
Colchester,Essex,UK Braunschweig,Germany
BalbinaNogales
DepartmentofBiology
UniversityoftheBalearicIslands
andMediterraneanInstituteforAdvanced
Studies(IMEDEA,UIB-CSIC)
PalmadeMallorca,Spain
ISSN1949-2448 ISSN1949-2456 (electronic)
SpringerProtocolsHandbooks
ISBN978-3-662-50449-9 ISBN978-3-662-50450-5 (eBook)
DOI10.1007/978-3-662-50450-5
LibraryofCongressControlNumber:2016938230
#Springer-VerlagBerlinHeidelberg2017
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Preface to Hydrocarbon and Lipid Microbiology
Protocols1
Allactivecellularsystemsrequirewaterastheprincipalmediumandsolventfortheirmetabolicand
ecophysiological activities. Hydrophobic compounds and structures, which tend to exclude water,
althoughprovidinginteraliaexcellentsourcesofenergyandameansofbiologicalcompartmental-
ization, present problems of cellular handling, poor bioavailability and, in some cases, toxicity.
Microbesbothsynthesizeandexploitavastrangeofhydrophobicorganics,whichincludesbiogenic
lipids, oils and volatile compounds, geochemically transformed organics of biological origin
(i.e.petroleumandotherfossilhydrocarbons)andmanufacturedindustrialorganics.Theunderlying
interactionsbetweenmicrobesandhydrophobiccompoundshavemajorconsequencesnotonlyfor
thelifestylesofthemicrobesinvolvedbutalsoforbiogeochemistry,climatechange,environmental
pollution, human health and a range of biotechnological applications. The significance of this
“greasymicrobiology”isreflectedinboththescaleandbreadthofresearchonthevariousaspects
ofthetopic.Despitethis,therewas,asfarasweknow,notreatiseavailablethatcoversthesubject.
In an attempt to capture the essence of greasy microbiology, the Handbook of Hydrocarbon and
Lipid Microbiology (http://www.springer.com/life+sciences/microbiology/book/978-3-540-77584-
3) was published by Springer in 2010 (Timmis 2010). This five-volume handbook is, we believe,
uniqueandofconsiderableservicetothecommunityanditsresearchendeavours,asevidencedby
the large number of chapter downloads. Volume 5 of the handbook, unlike volumes 1–4 which
summarizecurrentknowledgeonhydrocarbonmicrobiology,consistsofacollectionofexperimen-
talprotocolsandappendicespertinenttoresearchonthetopic.
Asecondeditionofthehandbookisnowinpreparationandadecisionwastakentosplitoff
themethodssectionandpublishitseparatelyaspartoftheSpringerProtocolsprogram(http://
www.springerprotocols.com/). The multi-volume work Hydrocarbon and Lipid Microbiology
Protocols, while rooted in Volume 5 of the Handbook, has evolved significantly, in terms of
range of topics, conceptual structure and protocol format. Research methods, as well as
instrumentationandstrategicapproachestoproblemsandanalyses,areevolvingatanunprec-
edented pace, which can be bewildering for newcomers to the field and to experienced
researchers desiring to take new approaches to problems. In attempting to be comprehensive
– a one-stop source of protocols for research in greasy microbiology – the protocol volumes
inevitablycontainbothsubject-specificandmoregenericprotocols,includingsamplinginthe
field, chemical analyses, detection of specific functional groups of microorganisms and com-
munity composition, isolation and cultivation of such organisms, biochemical analyses and
activity measurements, ultrastructure and imaging methods, genetic and genomic analyses,
1AdaptedinpartfromthePrefacetoHandbookofHydrocarbonandLipidMicrobiology.
v
vi PrefacetoHydrocarbonandLipidMicrobiologyProtocols
systems and synthetic biology tool usage, diverse applications, and the exploitation of bioin-
formatic,statisticalandmodellingtools.Thus,whiletheworkisaimedatresearchersworking
onthemicrobiologyofhydrocarbons,lipidsandotherhydrophobicorganics,muchofitwillbe
equally applicable to research in environmental microbiology and, indeed, microbiology in
general.This,webelieve,isasignificantstrengthofthesevolumes.
We are extremely grateful to the members of our Scientific Advisory Board, who have
made invaluable suggestions of topics and authors, as well as contributing protocols them-
selves,andtogenerousadhocadvisorslikeWeiHuang,ManfredAuerandLarsBlank.Wealso
express our appreciation of Jutta Lindenborn of Springer who steered this work with profes-
sionalism,patienceandgoodhumour.
Colchester,Essex,UK TerryJ.McGenity
Braunschweig,Germany KennethN.Timmis
PalmadeMallorca,Spain BalbinaNogales
Reference
TimmisKN(ed)(2010)Handbookofhydrocarbonandlipidmicrobiology.Springer,Berlin,Heidelberg
Contents
IntroductiontoGenetic,Genomic,andSystemAnalysesforCommunities. . . . . . . . . . 1
JackA.GilbertandNicoleM.Scott
GenomicAnalysisofPureCulturesandCommunities. . . . . . . . . . . . . . . . . . . . . . . . . . 5
StepanV.Toshchakov,IlyaV.Kublanov,EnzoMessina,
MichailM.Yakimov,andPeterN.Golyshin
ProtocolsforMetagenomicLibraryGenerationandAnalysis
inPetroleumHydrocarbonMicrobeSystems. . . . .. . . . . . . . .. . . . . . . . .. . . . . . . .. . 29
StephanieM.Moormann,JarradT.Hampton-Marcell,
SarahM.Owens,andJackA.Gilbert
PreparationandAnalysisofMetatranscriptomicLibraries
inPetroleumHydrocarbonMicrobeSystems. . . . .. . . . . . . . .. . . . . . . . .. . . . . . . .. . 51
JarradT.Hampton-Marcell,AngelFrazier,StephanieM.Moormann,
SarahM.Owens,andJackA.Gilbert
ProkaryoticMetatranscriptomics. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
DaniloPe´rez-PantojaandJavierTamames
DefiningaPipelineforMetaproteomicAnalyses. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99
JosephA.Christie-Oleza,DespoinaSousoni,JeanArmengaud,
ElizabethM.Wellington,andAlexandraM.E.Jones
MetabolicProfilingandMetabolomicProceduresforInvestigating
theBiodegradationofHydrocarbons. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111
VincentBonifay,EgemenAydin,DenizF.Aktas, JanSunner,
andJosephM.Suflita
GeneratingEnrichedMetagenomesfromActiveMicroorganisms
withDNAStableIsotopeProbing. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163
CarolinaGrob,MartinTaubert,AlexandraM.Howat,OliverJ.Burns,
YinChen,JoshD.Neufeld,andJ.ColinMurrell
DNA-andRNA-BasedStableIsotopeProbingofHydrocarbonDegraders. . . . . . . . . . 181
TillmannLueders
ProtocolforPerformingProteinStableIsotopeProbing(Protein-SIP)
Experiments. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 199
NicoJehmlichandMartinvonBergen
vii
viii Contents
ProteinExtractionfromContaminatedSoilsandSediments. . . . . . . . . . . . . . . . . . . . . 215
MercedesV.DelPozo,Mo´nicaMart´ınez-Mart´ınez,andManuelFerrer
AnalysisoftheRegulationoftheRateofHydrocarbonandNutrient
FlowThroughMicrobialCommunities. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 233
WilfredF.M.Ro¨ling,LucasFillinger,andUlissesNunesdaRocha
ConstructingandAnalyzingMetabolicFluxModelsofMicrobial
Communities. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 247
Jose´ P.Faria,TahminehKhazaei,JanakaN.Edirisinghe,PamelaWeisenhorn,
SamuelM.D.Seaver,NealConrad,NomiHarris,MatthewDeJongh,
andChristopherS.Henry
ProtocolforEvaluatingthePermissivenessofBacterialCommunities
TowardConjugalPlasmidsbyQuantificationandIsolation
ofTransconjugants. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 275
UliKlu¨mper,ArnaudDechesne,andBarthF.Smets
About the Editors
Terry J. McGenity is a Reader at the University of Essex, UK. His
Ph.D., investigating the microbial ecology of ancient salt deposits
(University of Leicester), was followed by postdoctoral positions at
the Japan Marine Science and Technology Centre (JAMSTEC, Yoko-
suka)andthePostgraduateResearchInstituteforSedimentology(Uni-
versityofReading). Hisoverarching researchinterest istounderstand
how microbial communities function and interact to influence major
biogeochemicalprocesses.HeworkedasapostdocwithKenTimmisat
theUniversityofEssex,wherehewasinspiredtoinvestigatemicrobial
interactionswithhydrocarbonsatmultiplescales,fromcommunitiestocells,andasbothasourceof
foodandstress.Hehasbroadinterestsinmicrobialecologyanddiversity,particularlywithrespect
tocarboncycling(especiallythesecondmostabundantlyproducedhydrocarbonintheatmosphere,
isoprene), and is driven to better understand how microbes cope with, or flourish in hypersaline,
desiccatedandpoly-extremeenvironments.
Kenneth N. Timmis read microbiology and obtained his Ph.D. at
Bristol University, where he became fascinated with the topics of
environmental microbiology and microbial pathogenesis, and their
interfacepathogenecology.Heundertookpostdoctoraltrainingatthe
Ruhr-University Bochum with Uli Winkler, Yale with Don Marvin,
andStanfordwithStanCohen,atthelattertwoinstitutionsasaFellow
oftheHelenHayWhitneyFoundation,whereheacquiredthetoolsand
strategiesofgeneticapproachestoinvestigatemechanismsandcausal
relationships underlying microbial activities. He was subsequently
appointedHeadofanIndependentResearchGroupattheMaxPlanck
InstituteforMolecularGeneticsinBerlin,thenProfessorofBiochem-
istry in the University of Geneva Faculty of Medicine. Thereafter, he became Director of the
Division of Microbiology at the National Research Centre for Biotechnology (GBF)/now the
Helmholtz Centre for Infection Research (HZI) and Professor of Microbiology at the Technical
UniversityBraunschweig.Hisgrouphasworkedformanyyears,interalia,onthebiodegradationof
oil hydrocarbons, especially the genetics and regulation of toluene degradation, pioneered the
genetic designand experimental evolutionof novel catabolic activities,discovered the new group
of marine hydrocarbonoclastic bacteria, and conducted early genome sequencing of bacteria that
ix
x AbouttheEditors
becameparadigmsofmicrobesthatdegradeorganiccompounds(PseudomonasputidaandAlcani-
voraxborkumensis).Hehashadtheprivilegeandpleasureofworkingwithandlearningfromsome
of the most talented young scientists in environmental microbiology, a considerable number of
whicharecontributingauthorstothisseries,andinparticularBalbinaandTerry.HeisFellowofthe
RoyalSociety,MemberoftheEMBO,RecipientoftheErwinSchro¨dingerPrize,andFellowofthe
AmericanAcademyofMicrobiologyandtheEuropeanAcademyofMicrobiology.Hefoundedthe
journals Environmental Microbiology, Environmental Microbiology Reports and Microbial Bio-
technology.KennethTimmisiscurrentlyEmeritusProfessorintheInstituteofMicrobiologyatthe
TechnicalUniversityofBraunschweig.
BalbinaNogalesisaLecturerattheUniversityoftheBalearicIslands,
Spain. Her Ph.D. at the Autonomous University of Barcelona (Spain)
investigated antagonistic relationshipsinanoxygenicsulphur photosyn-
thetic bacteria. This was followed by postdoctoral positions in the
researchgroupsofKen Timmisatthe GermanNationalBiotechnology
Institute (GBF, Braunschweig, Germany) and the University of Essex,
where she joinedTerryMcGenity aspostdoctoralscientist.Duringthat
time, she worked in different researchprojects on community diversity
analysisofpollutedenvironments.Aftermovingtohercurrentposition,
herresearchisfocusedonunderstandingmicrobialcommunitiesinchronicallyhydrocarbon-polluted
marineenvironments,andelucidatingtheroleinthedegradationofhydrocarbonsofcertaingroupsof
marinebacterianotrecognizedastypicaldegraders.