64Croppingpracticesmanipulateabundancepattern

RESEARCHOpenAccessCroppingpracticesmanipulateabundancepatternsofrootandsoilmicrobiomememberspavingthewaytosmartfarmingKyleHartman1,2,MarcelG.A.vanderHeijden1,2,4,RaphaëlA.Wittwer1,SamiranBanerjee1,Jean-ClaudeWalser3andKlausSchlaeppi1*AbstractBackground:Harnessingbeneficialmicrobespresentsapromisingstrategytooptimizeplantgrowthandagriculturalsustainability.Littleisknowntowhichextentandhowspecificallysoilandplantmicrobiomescanbemanipulatedthroughdifferentcroppingpractices.Here,weinvestigatedsoilandwheatrootmicrobialcommunitiesinacroppingsystemexperimentconsistingofconventionalandorganicmanagements,bothwithdifferenttillageintensities.Results:Whilemicrobialrichnesswasmarginallyaffected,wefoundpronouncedcroppingeffectsoncommunitycomposition,whichwerespecificfortherespectivemicrobiomes.Soilbacterialcommunitieswereprimarilystructuredbytillage,whereassoilfungalcommunitiesrespondedmainlytomanagementtypewithadditionaleffectsbytillage.Inroots,managementtypewasalsothedrivingfactorforbacteriabutnotforfungi,whichweregenerallydeterminedbychangesintillageintensity.Toquantifyan“effectsize”formicrobiotamanipulation,wefoundthatabout10%ofvariationinmicrobialcommunitieswasexplainedbythetestedcroppingpractices.Croppingsensitivemicrobesweretaxonomicallydiverse,andtheyrespondedinguildsoftaxatothespecificpractices.Thesemicrobesalsoincludedfrequentcommunitymembersormembersco-occurringwithmanyothermicrobesinthecommunity,suggestingthatcroppingpracticesmayallowmanipulationofinfluentialcommunitymembers.Conclusions:Understandingtheabundancepatternsofcroppingsensitivemicrobespresentsthebasistowardsdevelopingmicrobiotamanagementstrategiesforsmartfarming.Forfuturetargetedmicrobiotamanagement—e.g.,tofostercertainmicrobeswithspecificagriculturalpractices—anextstepwillbetoidentifythefunctionaltraitsofthecroppingsensitivemicrobes.Keywords:Soilandrootmicrobiomes,Microbialco-occurrence,Networkanalysis,Croppingpractices,Microbiotamanagement,SmartfarmingBackgroundAgriculturalintensificationhasresultedinanincreasedproductionofstaplecropssuchaswheat,rice,andmaizeandleadtogreaterfoodsecurityforacontinu-ouslygrowingworldpopulation[1,2].Despitethesebenefits,thereisincreasingawarenessabouttheadverseenvironmentalimpactsarisingfromtheintensiveprac-ticesofmodernagriculture.Theseincludeincreasedgreenhousegasemissionsandnutrientleachingasaresultofintensivefertilizerapplication[3],increasedsoilerosion[4],anddetrimentaleffectsonbiodiversity[5,6].Toalleviatesuchdeleteriouseffects,anecologicalintensificationhasbeenproposedthatfocusesonmeet-ingstandardsofenvironmentalqualitywhilepromotingandmaintainingorganismsthatprovidebeneficialeco-systemservices[7,8].Anumberofpracticesimprovethesustainabilityofagriculture,includingorganicfarm-ing[9]andreducedorno-tillage[10].Thesepracticesaimtoenhancesoilfertilitywhilemaintainingcropyieldsthroughsupportingadiverseandactivesoilbiota[11].Soilbiotaincludesmicrobessuchasbacteriaandfungithatcollectivelyfunctionasamicrobiome.Bacteria*Correspondence:[e-mail]1Plant-SoilInteractions,DepartmentofAgroecologyandEnvironment,Agroscope,Zurich,SwitzerlandFulllistofauthorinformationisavailableattheendofthearticle©TheAuthor(s).2018OpenAccessThisarticleisdistributedunderthetermsoftheCreativeCommonsAttribution4.0InternationalLicense(),whichpermitsunrestricteduse,distribution,andreproductioninanymedium,providedyougiveappropriatecredittotheoriginalauthor(s)andthesource,providealinktotheCreativeCommonslicense,andindicateifchangesweremade.TheCreativeCommonsPublicDomainDedicationwaiver()appliestothedatamadeavailableinthisarticle,unlessotherwisestated.Hartmanetal.Microbiome(2018)6:14DOI10.1186/s40168-017-0389-9andfungiregulatemanyecosystemprocessesandplaykeyrolesinnutrientcyclingthroughdecompositionoforganicmatter,andtransformationandfixationofim-portantsoilnutrientslikenitrogenandphosphorus[12].Asidefromtheenvironmentalbenefitsoforganicagri-culture[13]andlessintensivetillageregimes[10],thereisstilldebateabouttheeffectsofthesecroppingpracticesonbelowgroundmicrobialcommunities.Ingeneral,arablemanagementaffectscommunitycompositionanddiver-sity;althoughsucheffectsmaydependonthemicrobialkingdombeingstudiedandthedifferentfarmingsystemsbeingcompared[14,15].However,therearefewagricul-turalexperimentscomparingconventionalandorganicfarmingpractices[16]andfewerthatcomparedifferentmanagementtypesandtillageintensities[17].Therefore,anagriculturalexperimentcombiningthesetwoaspectsatasinglesiteallowstoseparatetheeffectsofmanagementtypeandtillageonmicrobialcommunitiesandminimizevariationcausedbysoilspatialheterogeneity.TheFarmingSystemandTillageexperiment(FAST)wasestablishedin2009nearZürichtoaddressthisforthemainarablecrop-pingsystemsinSwitzerland(Additionalfile1:Fig.S1).Thesecroppingsystemsare,namely,conventional(C)andorganic(O)managementtypes,withdifferenttillagein-tensities(no-tillage(NT),reduced-tillage(RT),andinten-sivetillage(IT)).TheFASTexperim