Hydrocarbon and Lipid Microbiology Protocols: Single-Cell and Single-Molecule Methods

209 Pages·2016·5.442 MB·English

by  Terry J. McGenity, Kenneth N. Timmis, Balbina Nogales (eds.)

Terry J. McGenity
Kenneth N. Timmis
Balbina Nogales Editors
Hydrocarbon and
Lipid Microbiology
Protocols
Single-Cell and
Single-Molecule Methods
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
Single-Cell and Single-Molecule Methods
Scientific Advisory Board
Jack Gilbert, Ian Head, Mandy Joye, Victor de Lorenzo,
Jan Roelof van der Meer, Colin Murrell, Josh Neufeld,
Roger Prince, Juan Luis Ramos, Wilfred Ro¨ling,
Heinz Wilkes, Michail Yakimov
Editors
TerryJ.McGenity KennethN.Timmis
SchoolofBiologicalSciences InstituteofMicrobiology
UniversityofEssex TechnicalUniversityBraunschweig
Colchester,Essex,UK Braunschweig,Germany
BalbinaNogales
DepartmentofBiology
UniversityoftheBalearicIslands
andMediterraneanInstitute
forAdvancedStudies
(IMEDEA,UIB-CSIC)
PalmadeMallorca,Spain
ISSN1949-2448 ISSN1949-2456 (electronic)
SpringerProtocolsHandbooks
ISBN978-3-662-49129-4 ISBN978-3-662-49131-7 (eBook)
DOI10.1007/978-3-662-49131-7
LibraryofCongressControlNumber:2016938230
#Springer-VerlagBerlinHeidelberg2016
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,
uniqueandofconsiderableservicetothecommunityanditsresearchendeavours,asevidencedby
the large number of chapter downloads. Volume 5 of the handbook, unlike volumes 1–4 which
summarizecurrentknowledgeonhydrocarbonmicrobiology,consistsofacollectionofexperimen-
talprotocolsandappendicespertinenttoresearchonthetopic.
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
IntroductiontoSingle-CellandSingle-MoleculeMethods. . . . . . . . . . . . . . . . . . . . . . . 1
WeiE.Huang
Single-CellCultivationinMicrofluidicDevices. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
SattarTaheri-AraghiandSuckjoonJun
Single-CellBacterialBioreporterAssaystoMeasureHydrocarbons. . . . . . . . . . . . . . . 17
RobinTecon
WholeGenomeAmplificationofSingleBacterialCells. . . . . . . . . . . . . . . . . . . . . . . . . 29
PaulScottandAlanW.Walker
DetectionofSpecificmRNAMoleculesinHydrocarbon-DegradingBacteria. . . . . . . . 43
JuhyunKimandV´ıctordeLorenzo
LocalizationofProteinsWithinIntactBacterialCellsUsingFluorescent
ProteinFusions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
VeronicaWellsRowlettandWilliamMargolin
SingleCellMicrobialEcophysiologywithRaman-FISH. . . . . . . . . . . . . . . . . . . . . . . . 65
DanielRead,WeiE.Huang,andAndrewS.Whiteley
Single-CellMetabolomics. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
YunWang,YizhiSong,IanP.Thompson,JianXu,andWeiE.Huang
MarryingSingleMoleculestoSingleCells:ProtocolsfortheStudy
oftheBacterialProto-ringComponentsEssentialforDivision. . . . . . . . . . . . . . . . . . . 91
A.Sa´nchez-Gorostiaga,A.I.Rico,P.Natale,M.Krupka,andM.Vicente
Single-CellBiotechnologyforUnculturedMicroorganisms. . . . . . . . . . . . . . . . . . . . . . 119
PeiranZhang,YizhiSong,IanP.Thompson,BoMa, JianXu,andWeiE.Huang
Single-CellandSystemsBiologyToolsforBiofuelProduction. . . . . . . . . . . . . . . . . . . . 133
TingtingWang*,YuetongJi*,YunWang,YuehuiHe,JingJia,QiangHu,
WeiE.Huang,andJianXu
DetectionofProtein-SynthesizingMicroorganismsintheEnvironment
viaBioorthogonalNoncanonicalAminoAcidTagging(BONCAT). . . . . . . . . . . . . . . . 145
RolandHatzenpichlerandVictoriaJ.Orphan
vii
viii Contents
FlowCytometricDeterminationofMicrobialAbundances
andItsUsetoObtainIndicesofCommunityStructure
andRelativeActivity. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 159
JosepM.GasolandXose´ AnxeluG.Mora´n
ProtocolsforVisualizingHorizontalGeneTransferinGram-Negative
BacteriaThroughNaturalCompetence. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 189
MelanieBlokesch
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