60Geographicpatternsofcooccurrencenetworkto

Seediscussions,stats,andauthorprofilesforthispublicationat:  in  TheISMEJournal·December2015DOI:10.1038/ismej.2015.261CITATIONS58READS5879authors,including:Someoftheauthorsofthispublicationarealsoworkingontheserelatedprojects:SoilmicobiologyViewprojectbiochareffectsonsoilmicrobialcommunityViewprojectBinMaZhejiangUniversity40PUBLICATIONS   492CITATIONS   SEEPROFILEMelissaDsouzaUniversityofChicago24PUBLICATIONS   160CITATIONS   SEEPROFILEJunLouZhejiangUniversity22PUBLICATIONS   119CITATIONS   SEEPROFILEYanHeZhejiangUniversity69PUBLICATIONS   938CITATIONS   SEEPROFILEAllcontentfollowingthispagewasuploadedbyJunLouon03March2016.Theuserhasrequestedenhancementofthedownloadedfile.OPENORIGINALARTICLEGeographicpatternsofco-occurrencenetworktopologicalfeaturesforsoilmicrobiotaatcontinentalscaleineasternChinaBinMa1,2,5,HaizhenWang1,2,5,MelissaDsouza3,JunLou1,YanHe1,2,ZhongminDai1,PhilipCBrookes1,JianmingXu1,2andJackAGilbert3,41CollegeofEnvironmentalandResourceSciences,ZhejiangUniversity,Hangzhou,China;2ZhejiangProvincialKeyLaboratoryofSubtropicalSoilandPlantNutrition,Hangzhou,China;3DepartmentofEcologyandEvolution,DepartmentofSurgery,UniversityofChicago,Chicago,IL,USAand4BioscienceDivision,ArgonneNationalLaboratory,Lemont,IL,USASoilmicrobiotaplayacriticalroleinsoilbiogeochemicalprocessesandhaveaprofoundeffectonsoilfunctions.Recentstudieshaverevealedmicrobialco-occurrencepatternsinsoilmicrobialcommunities,yetthegeographicpatternoftopologicalfeaturesinsoilmicrobialco-occurrencenetworksatthecontinentalscalearelargelyunknown.Here,weinvestigatedtheshiftsoftopologicalfeaturesinco-occurrencenetworksinferredfromsoilmicrobiotaalongacontinentalscaleineasternChina.Integratingarchaeal,bacterialandfungalcommunitydatasets,weinferredameta-communityco-occurrencenetworkandanalyzednode-levelandnetwork-leveltopologicalshiftsassociatedwithfiveclimaticregions.Bothnode-levelandnetwork-leveltopologicalfeaturesrevealedgeographicpatternswhereinmicroorganismsinthenorthernregionshadcloserrelationshipsbuthadalowerinteractioninfluencethanthoseinthesouthernregions.Wefurtheridentifiedtopologicaldifferencesassociatedwithtaxonomicgroupsanddemonstratedthatco-occurrencepatternswererandomforarchaeaandnon-randomforbacteriaandfungi.Giventhatmicrobialinteractionsmaycontributetosoilfunctionsmorethanspeciesdiversity,thisgeographicshiftoftopologicalfeaturesprovidesnewinsightintostudyingmicrobialbiogeographicpatterns,theirorganizationandimpactsonsoil-associatedfunction.TheISMEJournaladvanceonlinepublication,15January2016;doi:10.1038/ismej.2015.261IntroductionSoilmicrobiotaplaycriticalrolesinawiderangeofbiogeochemicalcyclesandcomprisethemajorpooloflivingbiomassinsoilecosystems(Miltneretal.,2012;Xuetal.,2013).Increasingevidenceindicatesthatavarietyofsoilfactorscanshapeandbeshapedbythemicrobiome,suggestingapromis-ingavenueforincreasingsoilhealthviadirectedmanipulationofthemicrobiome(Chaparroetal.,2012;Ellouzeetal.,2013).Characterizingthecapacityofthesoilmicrobiota,itsinteractionwithsoilfactorsanditscontributiontovarioussoilbiogeochemicalprocessesthereforehasthepotentialtoprovideimportantinsightsintosoilfunctions.Thiswouldcompriseasystems-levelunderstandingofcommunityfunctionandstructure(Fuhrman,2009).Toaddressthischallenge,researchershavestartedmappingthesoilmicrobiota(Hultmanetal.,2015;Panke-Buisseetal.,2015),andtheuseofhigh-throughputsequencinganalysishasallowedustocharacterizethecompositionandfunctionalattributesofsoilmicrobialcommunitiesacrossbroadspatialscales(FiererandJackson,2006;Batesetal.,2011;Fiereretal.,2013).Additionally,recentstudieshaverevealedco-occurrencepatternsinsoilmicro-bialcommunitiesacrossawiderangeofterrestrialecosystems(Barberánetal.,2012;Fiereretal.,2012).Networkanalyses-basedapproacheshaverecentlybeenusedtoinvestigateco-occurrencepatternsbetweenmicroorganismsincomplexenvironmentsrangingfromthehumanguttooceansandsoils(Ruanetal.,2006;FuhrmanandSteele,2008;Faustetal.,2012;Chowetal.,2013).Co-occurrencepatternsareubiquitousandparticularlyimportantinunderstandingmicrobialcommunitystructure,offeringnewinsightsintopotentialinteractionnetworks,andrevealingnichespacessharedbycommunitymembers(Steeleetal.,2011;FaustandRaes,2012;Karaetal.,2013).RecentstudieshaveCorrespondence:JMXu,CollegeofEnvironmentalandResourceSciences,ZhejiangUniversity,866YuhangtangRoad,Hangzhou310058,China.E-mail:[e-mail],DepartmentofEcologyandEvolution,DepartmentofSurgery,UniversityofChicago,900East57thStreet,Chicago60637,IL,USA.E-mail:[e-mail]21August2015;revised1December2015;accepted8December2015TheISMEJournal(2016),1–11©2016InternationalSocietyforMicrobialEcologyAllrightsreserved1751-7362/16