56Theoccurrenceofpotatocommonscabcorrelates

RESEARCHOpenAccessTheoccurrenceofpotatocommonscabcorrelateswiththecommunitycompositionandfunctionofthegeocaulospheresoilmicrobiomeWencongShi1,2,MingcongLi1,2,GuangshanWei3,4,RenmaoTian5,CuipingLi1,2,BingWang2,6,RongshanLin2,6,ChunyuShi1,7,XiuliChi8,BoZhou2,6*andZhengGao1,2,5*AbstractBackground:Soilmicroorganismscanmediatetheoccurrenceofplantdiseases.Potatocommonscab(CS)isarefractorydiseasecausedbypathogenicStreptomycesthatoccursworldwide,butlittleisknownabouttheinteractionsbetweenCSandthesoilmicrobiome.Inthisstudy,foursoil-rootsystemcompartments(geocaulospheresoil(GS),rhizospheresoil(RS),root-zonesoil(ZS),andfurrowsoil(FS))wereanalyzedforpotatoplantswithnaturallyhigh(H)andlow(L)scabseveritylevels.WeaimedtodeterminethecompositionandputativefunctionofthesoilmicrobiomeassociatedwithpotatoCS.Results:ThecopynumbersofthescabphytotoxinbiosyntheticgenetxtABandthebacterial16SrRNAgeneaswellasthediversityandcompositionofeachofthefoursoil-rootsystemcompartmentswereexamined;GSwastheonlycompartmentthatexhibitedsignificantdifferencesbetweentheHandLgroups.ComparedtotheHgroup,theLgroupexhibitedalowertxtABgenecopynumber,lowerbacterial16Scopynumber,higherdiversity,higherco-occurrencenetworkcomplexity,andhighercommunityfunctionsimilaritywithintheGSmicrobiome.ThecommunitycompositionandfunctionoftheGSsampleswerefurtherrevealedbyshotgunmetagenomicsequencing.Variovorax,Stenotrophomonas,andAgrobacteriumwerethemostabundantgenerathatweresignificantlyandpositivelycorrelatedwiththescabseveritylevel,estimatedabsoluteabundance(EAA)ofpathogenicStreptomyces,andtxtABgenecopynumber.Incontrast,Geobacillus,Curtobacterium,andunclassifiedGeodermatophilaceaeweresignificantlynegativelycorrelatedwiththesethreeparameters.ComparedtothefunctionprofilesintheLgroup,severalgenesinvolvedin“ABCtransporters,”the“bacterialsecretionsystem,”“quorumsensing(QS),”“nitrogenmetabolism,”andsomemetabolismbycytochromeP450wereenrichedintheHgroup.Incontrast,someantibioticbiosynthesispathwayswereenrichedintheLgroup.Basedonthedifferencesincommunitycompositionandfunction,asimplemodelwasproposedtoexplaintheputativerelationshipsbetweenthesoilmicrobiomeandCSoccurrence.(Continuedonnextpage)*Correspondence:[e-mail];[e-mail]1StateKeyLaboratoryofCropBiology,ShandongAgriculturalUniversity,Tai’an271018,China2CollegeofLifeSciences,ShandongAgriculturalUniversity,Tai’an271018,ChinaFulllistofauthorinformationisavailableattheendofthearticle©TheAuthor(s).2019OpenAccessThisarticleisdistributedunderthetermsoftheCreativeCommonsAttribution4.0InternationalLicense(),whichpermitsunrestricteduse,distribution,andreproductioninanymedium,providedyougiveappropriatecredittotheoriginalauthor(s)andthesource,providealinktotheCreativeCommonslicense,andindicateifchangesweremade.TheCreativeCommonsPublicDomainDedicationwaiver()appliestothedatamadeavailableinthisarticle,unlessotherwisestated.Shietal.Microbiome(2019)7:14(Continuedfrompreviouspage)Conclusions:TheGSmicrobiomewascloselyassociatedwithCSseverityinthesoil-rootsystem,andtheoccurrenceofCSwasaccompaniedbychangesincommunitycompositionandfunction.ThedifferentialfunctionsprovidenewcluestoelucidatethemechanismunderlyingtheinteractionbetweenCSoccurrenceandthesoilmicrobiome,andvaryingcommunitycompositionsprovidenovelinsightsintoCSoccurrence.Keywords:Soilmicrobiome,Commonscab,Geocaulospheresoil,Metagenome,MicrobialcommunitycompositionandfunctionBackgroundSoilmicroorganisms,whichcloselyinteractwithplants,areanimportantfactoraffectingplanthealth[1–3].Theemergenceandpropagationofplantpathogenscauseplantdiseases,andinturn,soilmicroorganismscanpre-ventplantdiseasesandinhibitpathogenstomaintainplanthealth[4,5].Usingmicroorganismstocontrolplantdiseaseshasbeensuccessfulinmanyways,andbiocontrolisconsideredadesirableapproachforcontrollingsoil-bornediseases[6–9].Manybiocontrolagentsforplantpathogenshavebeendevelopedandapplied,butduetothecomplexityofthesoilenvironmentandofsoilmi-crobialinteractions,theeffectivenessofbiocontrolagentsoftendiffersunderlaboratoryandnaturalenvironmentconditions.Toensurethatthebiocontrolofplantdiseaseismorestableandmoreeffectiveinthenaturalenviron-ment,aclearunderstandingofhowpathogens,biocontrolstrains,andsoilmicroorganismsinteractisnecessary.Therefore,itisofgreatsignificancetostudythesoilmi-crobialcommunitytocontrolplantdiseases.Inthelastdecade,anincreasingnumberofstudieshavefocusedontheroleofthesoilmicrobialcommu-nityinthefieldofplantdiseasepreventionandtreat-ment[3,10–12].Diseaseoccurrenceisoftenaccompaniedbychangesinthemicrobialcommunity,suchasalteredmicrobialabundance,composition,andfunction[13,14],soadditionaleffortstorehabilitatethemicrobialcommunitymaybemoreeffectiveatcuringplantdiseasesthansimplycontrollingpathogenpopula-tions.Researchindicatesthatthediversityofsoilmicro-bialcommunitiesiscloselyrelatedtoplantdiseaseresistance,andhighmicrobialdiversityprovidesplantswithgreaterprote