Hydrocarbon and Lipid Microbiology Protocols: Ultrastructure and Imaging

178 Pages·2016·5.121 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
Ultrastructure and Imaging
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
Ultrastructure and Imaging
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
andMediterraneanInstitute
forAdvancedStudies
(IMEDEA,UIB-CSIC)
PalmadeMallorca,Spain
ISSN1949-2448 ISSN1949-2456 (electronic)
SpringerProtocolsHandbooks
ISBN978-3-662-49132-4 ISBN978-3-662-49134-8 (eBook)
DOI10.1007/978-3-662-49134-8
LibraryofCongressControlNumber:2016938230
#Springer-VerlagBerlinHeidelberg2016
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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.
Inanattempttocapturetheessenceofgreasymicrobiology,theHandbookofHydrocarbonandLipid
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
andofconsiderableservicetothecommunityanditsresearchendeavours,asevidencedbythelarge
number of chapter downloads. Volume 5 of the handbook, unlike volumes 1–4 which summarize
currentknowledgeonhydrocarbon microbiology, consistsofa collectionofexperimentalprotocols
andappendicespertinenttoresearchonthetopic.
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
UltrastructureandImaging. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
ManfredAuer
ElectronMicroscopyProtocolsfortheStudyofHydrocarbon-Producing
andHydrocarbon-DecomposingMicrobes:ClassicalandAdvancedMethods. . . . . . . . 5
KamnaJhambandManfredAuer
ProtocolforLaserScanningMicroscopyofMicroorganismsonHydrocarbons. . . . . . 29
ThomasR.NeuandJohnR.Lawrence
FluorescenceMicroscopyforMicrobiology. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
GabriellaMolinari
ImagingBacterialCellsandBiofilmsAdheringtoHydrophobicOrganic
Compound–WaterInterfaces. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
AlexisCanette,PriscillaBranchu,Re´gisGrimaud,andMurielleNa¨ıtali
Bacteria-MineralColloidInteractionsinBiofilms:AnUltrastructural
andMicroanalyticalApproach.. . . .. . . .. . .. . . .. . . .. . . .. . . .. . . .. . .. . . .. . . .. 85
HeinrichLu¨nsdorf
IdentificationofMicroorganismsinHydrocarbon-ContaminatedAquifer
SamplesbyFluorescenceInSituHybridization(CARD-FISH). . . . . . . . . . . . . . . . . . . 103
SchattenhoferMartha,ValerieHubalek,andAnnelieWendeberg
StudiesoftheEcophysiologyofSingleCellsinMicrobialCommunities
by(Quantitative)MicroautoradiographyandFluorescenceInSitu
Hybridization(MAR-FISH). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
MartaNierychlo,JeppeLundNielsen,andPerHalkjærNielsen
ProtocolforInSituDetectionofFunctionalGenesofMicroorganisms
byTwo-PassTSA-FISH. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131
KengoKubotaandShujiKawakami
vii
viii Contents
Three-DimensionalVisualisationandQuantificationofLipids
inMicroalgaeUsingConfocalLaserScanningMicroscopy. . . . . . . . . . . . . . . . . . . . . . 145
NarinChansawang,BoguslawObara,RichardJ.Geider,andPierrePhilippeLaissue
ACorrelativeLight-ElectronMicroscopy(CLEM)Protocol
fortheIdentificationofBacteriainAnimalTissue,Exemplified
byMethanotrophicSymbiontsofDeep-SeaMussels. . . . . . . . . . . . . . . . . . . . . . . . . . . 163
SvenR.LamingandSe´bastienDuperron
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
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