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

260 Pages·2017·7.35 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 Pure Cultures
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 Pure Cultures
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
ISBN978-3-662-50433-8 ISBN978-3-662-50435-2 (eBook)
DOI10.1007/978-3-662-50435-2
LibraryofCongressControlNumber:2016938230
#Springer-VerlagBerlinHeidelberg2017
Thisworkis subjectto copyright.Allrightsarereservedbythe Publisher,whetherthe wholeorpartofthe materialis
concerned,specificallytherightsoftranslation,reprinting,reuseofillustrations,recitation,broadcasting,reproductionon
microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation,
computersoftware,orbysimilarordissimilarmethodologynowknownorhereafterdeveloped.
Theuseofgeneraldescriptivenames,registerednames,trademarks,servicemarks,etc.inthispublicationdoesnotimply,
evenintheabsenceofaspecificstatement,thatsuchnamesareexemptfromtherelevantprotectivelawsandregulationsand
thereforefreeforgeneraluse.
Thepublisher,theauthorsandtheeditorsaresafetoassumethattheadviceandinformationinthisbookarebelievedtobe
trueandaccurateatthedateofpublication.Neitherthepublishernortheauthorsortheeditorsgiveawarranty,expressor
implied,withrespecttothematerialcontainedhereinorforanyerrorsoromissionsthatmayhavebeenmade.
Printedonacid-freepaper
ThisSpringerimprintispublishedbySpringerNature
TheregisteredcompanyisSpringer-VerlagGmbHBerlinHeidelberg
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.
petroleum and other fossil hydrocarbons) and manufactured industrial organics. The underlying
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, unique and of considerable service to the community and its research endeavours, as
evidencedbythelargenumberofchapterdownloads.Volume5ofthe handbook,unlikevolumes
1–4whichsummarizecurrentknowledgeonhydrocarbonmicrobiology,consistsofacollectionof
experimentalprotocolsandappendicespertinenttoresearchonthetopic.
Asecondeditionofthehandbookisnowinpreparationandadecisionwastakentosplitoffthe
methods section and publish it separately as part of the Springer Protocols program (http://www.
springerprotocols.com/).Themulti-volumeworkHydrocarbonandLipidMicrobiologyProtocols,
whilerootedinVolume5oftheHandbook,hasevolvedsignificantly, intermsofrange oftopics,
conceptual structure and protocol format. Research methods, as well as instrumentation and
strategic approaches to problems and analyses, are evolving at an unprecedented 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
researchingreasymicrobiology–theprotocolvolumesinevitablycontainbothsubject-specificand
more generic protocols, including sampling in the field, chemical analyses, detection of specific
functionalgroupsofmicroorganismsandcommunitycomposition,isolationandcultivationofsuch
organisms, biochemical analyses and activity measurements, ultrastructure and imaging methods,
geneticandgenomicanalyses,systemsandsyntheticbiologytoolusage,diverseapplications,and
1AdaptedinpartfromthePrefacetoHandbookofHydrocarbonandLipidMicrobiology.
v
vi PrefacetoHydrocarbonandLipidMicrobiologyProtocols
theexploitationofbioinformatic,statisticalandmodellingtools.Thus,whiletheworkisaimedat
researchers working on the microbiologyof hydrocarbons, lipids and other hydrophobic organics,
much of it will be equally applicable to research in environmental microbiology and, indeed,
microbiologyingeneral.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 themselves, and to
generous ad hoc advisors like Wei Huang, Manfred Auer and Lars Blank. We also express our
appreciationofJuttaLindenbornofSpringerwhosteeredthisworkwithprofessionalism,patience
andgoodhumour.
Colchester,Essex,UK TerryJ.McGenity
Braunschweig,Germany KennethN.Timmis
PalmadeMallorca,Spain BalbinaNogales
Reference
TimmisKN(ed)(2010)Handbookofhydrocarbonandlipidmicrobiology.Springer,Berlin,Heidelberg
Contents
IntroductiontoGenetic,GenomicandSystemAnalysesofPureCultures. . . . . . . . . . . 1
V´ıctordeLorenzo
BroadeningtheSEVAPlasmidRepertoiretoFacilitateGenomic
EditingofGram-NegativeBacteria. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
Toma´sAparicio,V´ıctordeLorenzo,andEstebanMart´ınez-Garc´ıa
ProtocolsonRegulationofGeneExpression. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
Sof´ıaHerna´ndez-Arranz,RuggeroLaRosa,RenataMoreno,
EmmaSevilla,LuisYuste,andFernandoRojo
Genetic,Genomic,andSystemAnalysesforPureCulturesand
Communities:Protocol–Ultra-High-ThroughputTransposon
ScanningofBacterialGenomes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
Cle´menceRoggoandJanRoelofvanderMeer
Knock-In-Leave-Behind(KILB):GeneticGraftingofProtease-
CleavingSequencesintoPermissiveSitesofProteinswitha
Tn5-BasedTranspositionSystem. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
Bele´nCallesandV´ıctordeLorenzo
DeepSequencingtoStudyMicrobialTranscriptomicResponses
toHydrocarbonDegradation/Production/Stress. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
JuhyunKimandV´ıctordeLorenzo
ShotgunProteomicsforHydrocarbonMicrobiology. . . . . . . . . . . . . . . . . . . . . . . . . . . 97
EricaM.Hartmann,Jean-CharlesGaillard,andJeanArmengaud
InteratomicCharacterizationofProtein–ProteinInteractionsin
Membrane-AssociatedMega-complexes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103
Jose´ ManuelBorrero-deAcun˜a,LotharJ€ansch,ManfredRohde,
KennethN.Timmis,DieterJahn,andMartinaJahn
LipidomicAnalysisofBacteriabyThin-LayerChromatographyand
LiquidChromatography/MassSpectrometry. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125
HowardGoldfineandZiqiangGuan
AccurateMicrobialGenomeAnnotationUsinganIntegrated
andUser-FriendlyEnvironmentforCommunityExpertise
ofGeneFunctions:TheMicroScopePlatform. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141
EugeniBelda,DavidVallenet,andClaudineMe´digue
vii
viii Contents
ApproachesforDisplayingCompleteTranscriptomesof
EnvironmentalBacteria. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 171
JuanCarlosOliveros
APracticalProtocolforGenome-ScaleMetabolicReconstructions. . . . . . . . . . . . . . . . 197
JuanNogales
GC-MS-BasedDeterminationofMassIsotopomerDistributionsfor
13C-BasedMetabolicFluxAnalysis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 223
AndreasSchmitz,BirgittaE.Ebert,andLarsM.Blank
AnalysisoftheHierarchicalandMetabolicRegulationofFlux
ThroughMetabolicPathways. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 245
WilfredF.M.Ro¨ling,LucasFillinger,andUlissesNunesdaRocha
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) and the Postgraduate Research Institute for Sedimentology
(UniversityofReading).Hisoverarchingresearch interestistounder-
stand how microbial communities function and interact to influence
major biogeochemical processes. He worked as a postdoc with Ken
TimmisattheUniversityofEssex,wherehewasinspiredtoinvestigate
microbialinteractionswithhydrocarbonsatmultiplescales,fromcommunitiestocells,andasboth
asourceoffoodandstress.Hehasbroadinterestsinmicrobialecologyanddiversity,particularly
withrespecttocarboncycling(especiallythesecondmostabundantlyproducedhydrocarboninthe
atmosphere, 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