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个人简介

石良,博士,教授,博士生导师,2016年引进到中国地质大学(武汉)环境学院的全职特聘教授。

研究领域

地质微生物学,主要包括以下两个方面: A.微生物-矿物之间的胞外电子传导机理(Extracellularelectrontransfermechanismsbetweenmicroorganismsandminerals)。作为一个非常重要的生物地球化学反应,微生物-矿物之间的电子传导直接影响到矿物的形成和风化,以及环境中污染物的转化,迁移和降解。另外,与常见的、位于细胞内的电子传递链不同,微生物-矿物之间的电子传导涉及到电子由细胞内传导到位于细胞外矿物表面的独特过程。这一特殊的电子传导过程可用来修复环境中污染物;低品位贵金属(铜、金等)的提取;生产电、氢气和生物燃料;室温合成新型的纳米材料和防治钢锈蚀。正是由于其在生物地球化学过程中的重要性,在生物电子传导过程中的特殊性和在生物技术中的多种应用性,微生物-矿物之间的电子传导近年来已成为地质微生物学、生物地球化学和多个基础学科以及应用科学研究的焦点和热点。因此,开展微生物-矿物之间胞外电子传导机理的研究,对提升从分子水平上认识微生物胞外电子传导过程、传导后对矿物的影响和开发利用与微生物胞外电子传导相关的生物技术,均具有重要意义。 B.地质微生物群系:地表下微生物种群的组分和功能(Geomicrobiome:themicrobialcompositionandfunctioninsubsurfaceenvironment)。目前,微生物学领域正经历由单分子、单菌株研究到群系研究的演变。这场革命性的转变将为有效利用微生物扭转全球暖化、防治人类疾病、增加粮食产量、保障饮水安全、治理环境污染和发展生物经济提供科学依据和技术保证。正是这些原因,世界各发达国家都在积极主导和推动与微生物群系相关的研究。在地表下,生活着数量庞大(>5×1029和20%地球生物总量)、种类众多和尚未发现的微生物。它们是全球微生物群系的一个重要组成部分,并且直接参与多种重要的地质化学反应。因此,地表下微生物种群的组分和功能正成为地质微生物学界关注的热点和前沿领域,其研究成果对准确预测微生物种群与地质环境之间的相互作用、建立精确的污染物反应迁移模型和科学应用地质微生物群系,都有着极其重要的意义。

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6.AHTanzil,STSultana,SRSaunders,LShi,EMarsiliandHBeyenal1.2016.Biologicalsynthesisofnanoparticlesinbiofilms。EnzymeandMicrobialTechnology(accepted). 7.HWei,JDai,MXia,MFRomine,LShi,ABeliaev,JMTiedje,KHNealson,JKFredrickson,JZhouandDQiu.2016.FunctionalrolesofCymAandNapCinreductionofnitrateandnitritebyShewanellaputrefaciensW3-18-1.Microbiology16:930-941. 8.SYang,YLiu,LiuC,LShi,JShang,HShan,JMZachara,JKFredrickson,DKennedy,CTResch,CThompsonandSFansler.2016.Nitratebioreductioninredox-variablelowpermeabilitysediments.ScienceoftheTotalEnvironment539:186-195. 9.YLiu,JKFredrickson,JMZacharaandLShi*.2015.DirectinvolvementofombB,omaBandomcBgenesinextracellularreductionofFe(III)byGeobactersulfurreducensPCA.FrontierinMicrobiology6:1075. 10.ZWang,ZShi,LShi,GFWhite,DJRichardson,TAClarke,JKFredricksonandJMZachara.2015.Effectsofsolubleflavinonheterogeneouselectrontransferbetweensurface-exposedbacterialcytochromesandironoxides.2015.GeochimicaetCosmochimicaActa163:299-310. 11.MEdwards,GWhite,MNorman,ATome-Fernandez,EAinsworth,LShi,JKFredrickson,JMZachara,JButt,DJRichardsonandTAClarke.2015.Redoxlinkedflavinsitesinextracellulardecahemeproteinsinvolvedinmicrobe-mineralelectrontransfer.ScientificReports5:11677. 12.CBeckwith,MJEdwards,MLawes,LShi,JNButt,DJRichardsonandTAClarke.2015.CharacterisationofMtoDfromSideroxydanslithotrophicus:acytochromecelectronshuttleusedinlithoautotrophicgrowth.FrontierinMicrobiology6:332. 13.JLee,JKFredrickson,AEPlymale,ACDohnalkova,CTResch,JPMcKinleyandLShi.2015.AnautotrophicH2-oxidizing,nitrate-respiring,Tc(VII)-reducingAcidovoraxsp.isolatedfromasubsurfaceoxic-anoxictransitionzone.EnvironmentalMicrobiologyReports7:395-403. 14.LShi*,JKFredricksonandJMZachara.2014.Genomicanalysesofbacterialporin-cytochromegeneclusters.FrontierinMicrobiology5:657. 15.YLiu,ZWang,JLiu,CLevar,MJEdwards,JTBabauta,DWKennedy,ZShi,HBeynal,DRBond,TAClarke,JNButt,DJRichardson,KMRosso,JMZachara,JKFredricksonandLShi*.2014.Atrans-outermembraneporin-cytochromeproteincomplexforextracellularelectrontransferbyGeobactersulfurreducensPCA.EnvironmentalMicrobiologyReports6:776-785. 16.SPirbandian,SEBarchinger,KMLeung,HSByun,YJangir,RABouhenni,SBReed,MFRomine,DASaffarini,LShi,YAGorby,JHGolbeck,andMYEl-Naggar.2014.ShewanellaoneidensisMR-1nanowiresareoutermembraneandperiplasmicextensionsoftheextracellularelectrontransportcomponents.ProceedingsoftheNationalAcademyofSciencesoftheUnitedStatesofAmerica111:12883-12888.(http://www.pnnl.gov/science/highlights/highlight.asp?id=3779). 17.MJEdwards,NBaiden,AJohs,STTomanicek,LLiang,LShi,JKFredrickson,JMZachara,AJGates,JNButt,DJRichardsonandTAClarke.2014.TheX-raystructureofShewanellaoneidensisOmcArevealsnewinsightatmicrobe-mineralinterface.FEBSLetter588:1886-1890. 18.HSByun,S.Pirbadian,ANakano,LShiandMYEl-Naggar.2014.KineticMonteCarlosimulationsandmolecularconductancemeasurementsofthebacterialdecahemecytochromeMtrF.ChemElectroChem1:1932-1939. 19.GFWhite,ZShi,LShi,ZWang,ACDohnalkova,MJMarshall,JKFredrickson,JMZachara,JNButt,DJRichardsonandTAClarke.2013.Rapidelectronexchangebetweensurface-exposedbacterialcytochromesandFe(III)minerals.ProceedingsoftheNationalAcademyofSciencesoftheUnitedStatesofAmerica110(16):6346-6351.(http://news.sciencemag.org/sciencenow/2013/03/scienceshot-the-original-iron-lu.html). 20.JLiu,CIPearce,CLiu,ZWang,LShi,EArenholzandKMRosso.2013.Fe3-xTixO4nanoparticlesastunableprobesofmicrobialmetaloxidation.JournaloftheAmericanChemicalSociety135(24):8896-8907. 21.DGGMcMillan,SJMarritt,MAFirer-Sherwood,LShi,DJRichardson,SDEvans,SJElliott,JNButtandLJCJeuken.2013.Protein-proteininteractionregulatesthedirectionofcatalysisandelectrontransferinaredoxenzymecomplex.JournaloftheAmericanChemicalSociety135(28):10650-10656. 22.VKodali,MHLittke,SCTilton,JGTeeguarden,LShi,CWFrevert,WWang,JGPoundsandBDThrall.2013.Dysregulationofmacrophageactivationprofilesbyengineerednanoparticles.ACSNano7(8):6997–7010. 23.ZShi,JM.Zachara,ZWang,LShiandJKFredrickson.2013.Reductivedissolutionofgoethiteandhematitesuspendedparticlesbyreducedflavins.GeochimicaetCosmochimicaActa121:139-154. 24.YWang,PCSevinc,SMBelchik,JKFredrickson,LShiandHPLu.2013.Single-cellimagingandspectroscopicanalysesofCr(VI)reductiononthesurfaceofbacterialcells.Langmuir29(3):950-956. 25.AJGates,SJMarritt,JMBradley,LShi,DGMcMillan,LJJeuken,DJRichardsonandJNButt.2013.Electrodeassembliescomposedofredoxcascadesfrommicrobialrespiratoryelectrontransferchains.BiochemicalSocietyTransactions41(5):1249-1253. 26.LShi*,KMRosso,JMZacharaandJKFredrickson.2012.MtrextracellularelectrontransferpathwaysinFe(III)-reducingorFe(II)-oxidizingbacteria:agenomicperspective.BiochemicalSocietyTransactions40(6):1261-1267. 27.LShi*,KMRosso,TAClarke,DJRichardson,JMZacharaandJKFredrickson.2012.MolecularunderpinningsofFe(III)oxidereductionbyShewanellaoneidensisMR-1.FrontiersinMicrobiology3:50.doi:10.3389/fmicb.2012.00050. 28.JLiu,ZWang,SMBelchik,MJEdwards,CLiu,DWKennedy,EDMerkley,MSLipton,JNButt,DJRichardson,JMZachara,JKFredrickson,KMRossoandLShi*.2012.IdentificationandcharacterizationofMtoA:adecahemec-typecytochromeoftheneutrophilicFe(II)-oxidizingbacteriumSideroxydanslithotrophicusES-1.FrontiersinMicrobiology3:37.doi:10.3389/fmicb.2012.00037. 29.MJEdwards,AHall,LShi,JKFredrickson,JMZachara,JNButt,DJRichardsonandTAClarke.2012.Thecrystalstructureoftheextracellular11-hemecytochromeUndArevealsaconserved10-hememotifanddefinedbindingsiteforsolubleironchelates.Structure20:1275-1284. 30.ZShi,JMZachara,LShi,ZWang,DAMoore,DWKennedyandJKFredrickson.2012.Redoxreactionsofreducedflavinmononucleotide(FMN),riboflavin(RBF),andanthraquinone-2,6-disulfonate(AQDS)withferrihydriteandlepidocrocite.EnvironmentalScience&Technology46:11644-11652. 31.SMarritt,TGLowe,JBye,DGGMcMillan,LShi,JFredrickson,JZachara,DJRichardson,MRCheesman,LJCJeukenandJNButt.2012.AfunctionaldescriptionofCymA,thekey-stoneforanaerobicrespiratoryflexibilityinShewanella.BiochemicalJournal444:465–474. 32.BCao,PD.Majors,BAhmed,RSRenslow,ADohnalkova,CPSylvia,LShi,SKjelleberg,JKFredricksonandHalukBeyenal.2012.Biofilmshowsspatiallystratifiedmetabolicresponsestocontaminantexposure.EnvironmentalMicrobiology14:2901-2910. 33.DJRichardson,JNButt,JKFredrickson,JMZachara,LShi,MJEdwards,GWhite,NBaiden,AJGates,SJMarrittandTAClarke.2012.‘Porin-cytochrome’modelformicrobe-to-mineralelectrontransfer.MolecularMicrobiology85:201-212. 34.BMFonseca,MTien,M.Rivera,LShiandROLouro.2012.Efficientandselectiveisotopiclabelingofhemestofacilitatethestudyofmultihemeproteins.BioTechniques:doi:10.2144/000113859. 35.EMerkley,BAnderson,JPark,SBelchik,LShi,MMonroe,RSmithandMLipton.2012.Detectionandidentificationofhemec-modifiedpeptidesbyhistidineaffinitychromatography,high-performanceliquidchromatography-massspectrometry,anddatabasesearching.JournalofProteomeResearch11(12):6147-6158. 36.GFWhite,ZShi,LShi,ACDohnakova,JKFredrickson,JMZachara,JNButt,DJRichardsonandTAClarke.2012.Developmentofaproteoliposomemodeltoprobetransmembraneelectron-transferreactions.BiochemicalSocietyTransactions40(6):1257-1260. 37.SMarritt,DGGMcMillan,LShi,JKFredrickson,JMZachara,DJRichardson,LJCJeukenandJNButt.2012.TherolesofCymAinsupportoftherespiratoryflexibilityofShewanellaoeidensisMR-1.BiochemicalSocietyTransactions40(6):1217-1221. 38.MBreuer,PZaezycki,LShi,TAClarke,MJMarcus,JNButt,DJRichardson,JKFredrickson,JMZachara,JBlumbergerandKMRosso.2012.MolecularstructureandfreeenergylandscapefromelectrontransportinthedecahaemcytochromeMtrF.BiochemicalSocietyTransactions40(6):1198-12603. 39.DJRichardson,MEdwards,GWhite,NBaiden,RSHartshorne,JFredrickson,LShi,JZachara,AGates,JNButtandTAClarke.2012.ExploringthebiochemistryattheextracellularredoxfrontierofbacterialmineralFe(III)respiration.BiochemicalSocietyTransactions40(3):493-500. 40.HYang,HGandhi,LShi,HWKreuzer,NEOstromandELHegg.2012.Usinggaschromatography-isotoperatiomassspectrometrytodeterminethefractionationfactorforH2productionbyhydrogenases.RapidCommunicationsinMassSpectrometry26:61-68. 41.AEPlymale,VBailey,JKFredrickson,SHeald,EBuck,LShi,ZWang,CResch,DMooreandHBolton.2012.BioticandabioticreductionandsolubilizationofPu(IV)O2•xH2O(am)asaffectedbyAQDSandEDTA.EnvironmentalScience&Technology46(4):2132-2140. 42.SJTomanicek,AJohs,MSSawhney,AGardberg,LShiandLLiang.2012.CrystallizationandpreliminaryX-raycrystallographicstudiesoftheoutermembranecytochromeOmcAofShewanellaoneidensisMR-1.ActaCrystallographicaSectionFStructuralBiologyandCrystallizationCommunications68(Pt1):53-55. 43.LShi*,SMBelchik,AEPlymale,SHeald,ACDohnalkova,KSybirna,HBottin,TCSquier,JMZacharaandJKFredrickson.2011.Purificationandcharacterizationof[NiFe]-hydrogenaseofShewanellaoneidensisMR-1.AppliedandEnvironmentalMicrobiology77:5584-5590. 44.LShi*,SMBelchik,ZWang,DWKennedy,ACDohnalkova,MJMarshall,JMZacharaandJKFredrickson.2011.IdentificationandcharacterizationofUndAHRCR-6,anoutermembraneendecahemec-typecytochromeofShewanellasp.strainHRCR-6.AppliedandEnvironmentalMicrobiology77:5521-5523. 45.SMBelchik,DWKennedy,ACDohnalkova,YWang,PCSevinc,HWu,YLin,HPLu,JKFredricksonandLShi*.2011.ExtracellularreductionofhexavalentchromiumbycytochromesMtrCandOmcAofShewanellaoneidensisMR-1.AppliedandEnvironmentalMicrobiology77:4035-4011. 46.YQian,LShiandMTien.2011.SO2907,aputativeTonB-dependentreceptor,isinvolvedindissimilatoryironreductionbyShewanellaoneidensisMR-1.JournalofBiologicalChemistry286:33973-33980. 47.TAClarke,MEdwards,AJGates,AHall,GWhite,JBradley,CReardon,LShi,ABeliaev,MMarshall,ZWang,N.Watmough,JFredrickson,JZachara,JuleaNButtandDJRichardson.2011.Thestructureofabacterialcellsurfacedeca-hemeelectronconduit.ProceedingsofNationalAcademyofScienceoftheUnitedStatesofAmerica108:9384-9389.(http://www.nature.com/nchembio/journal/v7/n7/full/nchembio.606.html). 48.BCao,BAhmed,DWKennedy,ZWang,LShi,MJMarshall,JKFredrickson,NGIsern,PDMajorsandHBeyenal.2011.ContributionofextracellularpolymericsubstancesfromShewanellasp.HRCR-1biofilmstoU(VI)immobilization.EnvironmentalScience&Technology45:5483-5490. 49.BCao,LShi,RBrown,YXiong,JKFredrickson,MFRomine,MJMarshall,MSLiptonandHBeyenal..2011.ExtracellularpolymericsubstancesfromShewanellasp.HRCR-1biofilms:characterizationbyinfraredspectroscopyandproteomics.EnvironmentalMicrobiology13:1018-1031. 50.YXiong,BChen,LShi,JFredrickson,DBigelowandTSquier.2011.TargetedproteindegradationofoutermembranedecahemecytochromeMtrCmetalreductaseinShewanellaoneidensisMR-1measuredusingbiarsenicalprobeCrAsH-EDT2.Biochemistry50:9738-9751. 51.HZhang,FYang,WQian,RNBrown,YWang,MEMonroe,SOPurvine,RJMoore,LShi,JKFredrickson,LPasa-Tolic,RDSmith,andMSLipton.2011.Identificationofc-typeheme-containingpeptidesusingnon-activatedIMACresinenrichmentandhigher-energycollisionaldissociation.AnalyticalChemistry83:7260-7268. 52.AJohs,LShi,TDroubay,JFAnknerandLLiang.2010.Characterizationofthedecahemec-typecytochromeOmcAinsolutionandonhematitesurfacesbysmallangleX-rayscatteringandneutronreflectometry.BiophysicalJournal98:3035-4043. 53.HZhang,RNBrown,WQian,MEMonroe,SOPurvine,RJMoore,MAGritsenko,LShi,MFRomine,JKFredrickson,LPasa-Tolic,RDSmith,andMSLipton.2010.Quantitativeanalysisofcellsurfacemembraneproteinsusingmembrane-impermeablechemicalprobecoupledwith18Olabeling.JournalofProteomeResearch9:2160-2169. 54.CLReardon,ACDohalkova,PNachimuthu,DWKennedy,DASaffarini,BWArey,LShi,ZWang,DMoore,JSMcLean,DMoyles,MJMarshall,JMZachara,JKFredrickson,ASBeliaev.2010.Roleofouter-membranecytochromesMtrCandOmcAinthebiomineralizationofferrihydritebyShewanellaoneidensisMR-1.Geobiology8:56-68. 55.LShi*,DJRichardson,ZWang,SNKerisit,KMRosso,JMZacharaandJKFredrickson*.2009.TherolesofoutermembranecytochromesofShewanellaandGeobacterinextracellularelectrontransfer.EnvironmentalMicrobiologyReports.1:220-227. 56.LShi*,SMChowdhury,HSSmallwood,HYoon,HMMottaz-Brewer,ADNorbeck,JEMcDermott,TRWClauss,FHeffron,RDSmithandJAdkins*.2009.ProteomicinvestigationofthetimecourseresponsesofRAW264.7macrophagestoinfectionwithSalmonellaentrica.InfectionandImmunity77:3227–3233. 57.LShi*,CAnsong,HSSmallwood,LRommereim,JEMcDermott,HMBrewer,ADNorbeck,RTaylor,JKGustin,FHeffron,RDSmith,andJNAdkins*.2009.ProteomeofSalmonellaentericaserotypeTyphimuriumgrowninalowMg2+/pHmedium.JournalofProteomeandBioinformatics2(9):388-397. 58.RSHartshorne,CLReardon,DRoss,JNuester,TAClarke,AJGates,PCMills,JKFredrickson,JMZachara,LShi,ASBeliaev,MJMarshall,MTien,SBrantley,JNButtandDJRichardson.2009.Characterizationofanelectronconduitbetweenbacteriaandtheextracellularenvironment.ProceedingsofNationalAcademyofScienceoftheUnitedStatesofAmerica106(52):22169-22174.(http://sciencenow.sciencemag.org/cgi/content/full/2009/1217/3). 59.SMChowdhury,LShi,HYoon,LMRommereim,ADNorbeck,KJAuberry,JNAdkins,FHeffron,andRDSmith.2009.Amethodforinvestigatingprotein-proteininteractionsrelatedtoSalmonellatyphimuriumpathogenesis.JournalofProteomeResearch.8:1504-1514. 60.LMeitl,CMEggleston,NKhare,PJSColberg,CLReardonandLShi.2009.ElectrochemicalinteractionofShewanellaoneidensisMR-1anditsoutermembranecytochromesOmcAandMtrCwithhematiteelectrodes.GeochimicaetCosmochimicaActa.73:5292-5307. 61.BHLower,RYongsunthon,LShi,LWildling,HJGruber,CLReardon,GEPinchuk,TCDroubay,JFBoily,andSKLower.2009.Antibody-recognitionforcemicroscopyshowsthatOmcAandMtrCcytochromesareexpressedontheoutersurfaceofShewanellaoneidensisMR-1.AppliedandEnvironmentalMicrobiology.75:2931-2935(CoverofMay1stissueofAEM). 62.RCTaylor,MSinghal,JWeller,SKhoshnevis,LShi,JMcDermott.2009.Anetworkinferenceworkflowappliedtovirulence-relatedprocessesinSalmonellatyphimurium.AnnalsoftheNYAcademyofSciences.1158:143-158. 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67.LShi*,SDeng,MJMarshall,ZWang,DWKennedy,ACDohnalkova,HMMottaz,EAHill,YAGorby,ASBeliaev,DJRichardson,JMZacharaandJKFredrickson*.2008.DirectinvolvementoftypeIIsecretionsysteminextracellulartranslocationofShewanellaoneidensisoutermembranecytochromesMtrCandOmcA.JournalofBacteriology190:5512-5516. 68.BHLower,RDLins,ZOestreicher,TPStraatsma,MFHochellaJr.,LShiandSKLower.2008.Invitroevolutionofapeptidewithahematitebindingmotifthatmayconstituteanaturalmetal-oxidebindingarchetype.EnvironmentalScience&Technology.42:3821-3827. 69.HZhang,XTang,GMunske,NZakharova,.Yang,CZheng,MWolff,NTolic,GAnderson,LShi,MMarshall,JKFredricksonandJBruce.2008.InvivoidentificationofoutermembraneproteinOmcA-MtrCinteractionnetworkinShewanellaoneidensisMR-1cellsusingnovelhydrophobicchemicalcross-linkers.JournalofProteomeResearch.7:1712-1720. 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