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Letter*,FalkHildebrand4,21,SofiaK.Forslund4,16,17,JenniferL.Anderson2,NadejdaA.Soudzilovskaia5,PeterM.Bodegom5,JohanBengtsson-Palme6,7,18,StenAnslan1,8,LuisPedroCoelho4,HeleryHarend1,JaimeHuerta-Cepas4,19,MarnixH.Medema9,Miar.Maltz10,SunilMundra11,PålAxelOlsson12,MariPent1,SergeiPõlme1,ShinichiSunagawa4,20,Martinryberg2,Lehotedersoo13*&PeerBork4,14,15*SoilsharboursomeofthemostdiversemicrobiomesonEarthandareessentialforbothnutrientcyclingandcarbonstorage.Tounderstandsoilfunctioning,itisnecessarytomodeltheglobaldistributionpatternsandfunctionalgenerepertoiresofsoilmicroorganisms,aswellasthebioticandenvironmentalassociationsbetweenthediversityandstructureofbothbacterialandfungalsoilcommunities1–4.Hereweshow,byleveragingmetagenomicsandmetabarcodingofglobaltopsoilsamples(189sites,7,560subsamples),thatbacterial,butnotfungal,geneticdiversityishighestintemperatehabitatsandthatmicrobialgenecompositionvariesmorestronglywithenvironmentalvariablesthanwith geographicdistance.WedemonstratethatfungiandbacteriashowglobalnichedifferentiationthatisassociatedwithcontrastingdiversityresponsestoprecipitationandsoilpH.Furthermore,weprovideevidenceforstrongbacterial–fungalantagonism,inferredfromantibiotic-resistancegenes,intopsoilandoceanhabitats,indicatingthesubstantialroleofbioticinteractionsinshapingmicrobialcommunities.Ourresultssuggestthatbothcompetitionandenvironmentalfilteringaffecttheabundance,compositionandencodedgenefunctionsofbacterialandfungalcommunities,indicatingthattherelativecontributionsofthesemicroorganismstoglobalnutrientcyclingvariesspatially.Bacteriaandfungidominateterrestrialsoilhabitatsintermsofbio-diversity,biomassandtheirinfluenceoveressentialsoilprocesses5.Specificrolesofmicrobialcommunitiesinbiogeochemicalprocessesarereflectedbytheirtaxonomiccomposition,bioticinteractionsandgenefunctionalpotential1–4.Althoughmicrobial-biogeographystudieshavefocusedlargelyonsingletaxonomicgroups,andonhowtheirdiversityandcompositionrespondtolocalabioticsoilfactors(forexample,pH6,7),globalpatternsandtheimpactofbioticinteractionsonmicrobialbiogeographyremainrelativelyunexplored.Inadditiontoconstraintsimposedbyenvironmentalfactors,bioticinteractionsmaystronglyinfluencebacterialcommunities.Forexample,tooutcompetebacteria,manyfungaltaxasecretesubstantialamountsofantimicro-bialcompounds8,whichmay selectforantibiotic-resistantbacteriaandeffectivelyincreasethe relativeabundanceof antibiotic-resistancegenes(ARGs).HereweusedmetagenomicsandDNAmetabarcoding(16S,18Sandinternaltranscribedspacer(ITS)rRNAgenemarkers),soilchemistryandbiomassassessments(phospholipidfattyacidsanalyses(PLFAs))todeterminetherelationshipsamonggenetic(functionalpotential),phylogeneticandtaxonomicdiversityandabundanceinresponsetobioticandabioticfactorsin189topsoilsamples,coveringallterrestrialregionsandbiomesoftheworld9(ExtendedDataFig. 1a,SupplementaryTable 1).Altogether,58,000topsoilsubsampleswerecollectedfrom0.25-haplotsfrom1,450sites(40subsamplespersite),harbouringhomogeneousvegetationthatwereminimallyaffectedbyhumans.Weminimizedbiasesandshortcomingsinsampling10aswellastechnicalvariation,includingbatcheffects11,byusinghighlystand-ardized collectionandprocessingprotocols.Fromthetotalcollection,189representativesiteswereselectedforthisanalysis.Wevalidatedourmainfindingsinexternaldatasets,includinganindependentsoildataset(145topsoilsamples;SupplementaryTable 1)thatfollowedthesamesamplingandsequencingprotocol.Usingmetagenomics,weconstructedagenecatalogueforsoils,bycombiningournewlygenerateddatawithpublishedsoilmetage-nomes(n=859,SupplementaryTable1)andidentified159,907,547uniquegenes(orfragmentsthereof).Only0.51%ofthese160mil-liongenesoverlappedwiththosefrompublishedgenomesandlargegut12andocean13genecataloguesthataremuchclosertosaturation(SupplementaryTable2),indicatingthatthefunctionalpotentialofsoilmicrobiomesisenormouslyvastandundersampled.Forfunctionalanalysis,weannotatedgenesandfunctionalmodulesviaorthologousgroupsusingtheeggNOGdatabase14.Foreachsample,wealsocon-structedtaxonomicprofilesattheclassandphylumlevelsforbothbacteriaandfungifromrelativeabundanceofrRNAgenesinmetagen-omicdatasets(miTags15),complementedbyoperationaltaxonomicunits(OTUs)thatwerebasedonclustering18SrRNAandITS16genesforsoilfungiand16SrRNAgenesforsoilbacteriaat97%similaritythreshold(see Methods‘Metagenomicsandmetabarcodinganalyses’).Intotal,34,52216S-basedbacterial,2,08618S-basedand33,476ITS-basedfungalOTUswereanalysedinthecontextofgeographicspaceand16edaphicandclimaticparameters weredeterminedforeachsamplingsite(see Methods‘Statisticalanalyses’).Archaeawerepoorlyrepresentedinourmetabarcodingdata (lessthan1%ofOTUs)andmetagenomicsdata(lessthan1%of miTags)andhenceareexcludedfrommostanalyses.Weexaminedwhetherthelatitudinaldiversitygradient(LDG),atrendofincreasingdiversityfromthepolestothetropicsseeninmanymacroscopicorganisms,especiallyplants17,appliestomicrobialglobaldistributionpat
本文标题:51Structureandfunctionoftheglobaltopsoilm
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