36Embracingtheunknowndisentanglingthecomplex

HowcanIstandonthegroundeverydayandnotfeelitspower?HowcanIlivemylifesteppingonthisstuffandnotwonderatit? —W.B.Logan1Soilmicrobialbiomassrivalstheabovegroundbio-mass ofplantsoranimals,withsoiloftencontaining1,000kgofmicrobialbiomasscarbonperhectare2,3.Thesesoilmicroorganismshavecrucialrolesinnutrientcycling,themaintenanceofsoilfertilityandsoilcarbonsequestration,andthesoilmicrobiomehasbothdirectandindirecteffectsonthehealthofplantsandanimalsinterrestrialecosystems.Theimportanceofthesoilmicro-biomehasbeenrecognizedformorethanacentury4,andthereisalonghistoryofresearchthatdescribesthemicroorganismsthatinhabitsoil,theirmetaboliccapa-bilitiesandtheirinfluenceonsoilfertility.Infact,manyoftheimportantdiscoveriesmadebymicrobiologists—includingthediscoveryofantibioticsanduniquemicrobialmetabolicpathways(forexample,nitrogengasfixationandammoniaoxidation)—werelargelyderivedfromworkwithsoilmicroorganisms.Recentmethodologicaladvanceshaveenabledresearcherstochartthefullextentofsoilmicrobialdiver-sityandtobuildamorecomprehensiveunderstandingofspecificmicrobialcontrolsonsoilprocesses.Inpar-ticular,DNA-basedandRNA-basedanalysesofthesoilmicrobiomearenowrelativelycommonandhavegreatlyexpandedwhatisknownaboutthephylogeneticandtaxonomicstructureofsoilmicrobialcommunities.Itisnowrecognizedthattypicalculture-basedapproachessubstantiallyunderestimatesoilmicrobialdiversityandthatsoilscontainabroaddiversityofmicrobialtaxafromallthreedomainsoflife,themajorityofwhichremainuncharacterized5–8.InthisReview,Isummarizewhathasbeenlearnedfromrecentworkonthesoilmicrobiome,discussingwhatmicroorganismsliveinsoil,whatfactorsaffectthecompositionofthesoilmicrobiomeacrossspaceandtime,andwhyitremainsdifficulttolinkspecificsoilmicrobialtaxatomanysoilprocesses.Ithenfocusonrecentadvancesinourconceptualunderstandingofsoilmicrobialcommunitiesandtheirmetaboliccapa-bilities,andemphasizehowwecancontinuetoleveragegenomic,metagenomicandmarkergenedatatoinfertheecologicalattributesofundescribedsoilmicrobialtaxa.Next,Idiscussthechallengesandopportunitiesassociatedwitheffortsthataimtomanagesoilmicro-bialcommunitiestomaximizeagriculturalproductiv-ityandsustainability.Last,thisReviewhighlightskeyresearchdirectionsthatcouldshapethefutureofbasicandappliedresearchintothesoilmicrobiome.StructureofthesoilmicrobiomeSoilisnotasingleenvironment;rather,itencompassesawiderangeofenvironmentsthatcancontaindistinctmicrobialcommunities(FIG. 1).Distinctsoilenviron-mentsmaybeonlymicrometrestomillimetresapart,buttheycandifferconsiderablyintheirabioticcharacter-istics,microbialabundances,ratesofmicrobialactivityandmicrobialcommunitycomposition.1DepartmentofEcologyand EvolutionaryBiology,UniversityofColorado,334 UCB,Boulder,Colorado 80309,USA.2CooperativeInstituteforResearchinEnvironmentalSciences,216UCB,UniversityofColorado,Boulder,Colorado80309,[e-mail]:10.1038/nrmicro.2017.87Publishedonline21Aug2017SoilmicrobiomeAgeneraltermdescribingallmicroorganismsthatcanbefoundinsoil,includingarchaea,bacteria,viruses,fungi,protistsandothermicrobialeukaryotes.Embracingtheunknown:disentanglingthecomplexitiesofthesoilmicrobiomeNoahFierer1,2Abstract|Soilmicroorganismsareclearlyakeycomponentofbothnaturalandmanagedecosystems.Despitethechallengesofsurvivinginsoil,agramofsoilcancontainthousandsofindividualmicrobialtaxa,includingvirusesandmembersofallthreedomainsoflife.Recentadvancesinmarkergene,genomicandmetagenomicanalyseshavegreatlyexpandedourabilitytocharacterizethesoilmicrobiomeandidentifythefactorsthatshapesoilmicrobialcommunitiesacrossspaceandtime.However,althoughmostsoilmicroorganismsremainundescribed,wecanbegintocategorizesoilmicroorganismsonthebasisoftheirecologicalstrategies.Thisisanapproachthatshouldprovefruitfulforleveraginggenomicinformationtopredictthefunctionalattributesofindividualtaxa.Thefieldisnowpoisedtoidentifyhowwecanmanipulateandmanagethesoilmicrobiometoincreasesoilfertility,improvecropproductionandimproveourunderstandingofhowterrestrialecosystemswillrespondtoenvironmentalchange.MICROBIOMENATUREREVIEWS|MICROBIOLOGYADVANCEONLINEPUBLICATION|1REVIEWS©2017MacmillanPublishersLimited,partofSpringerNature.Allrightsreserved.RhizosphereThesoillocatedincloseproximitytoplantroots,which typicallyhasmoreplant-derivedcarbonandahighermicrobialbiomassthan thesurroundingnon-rhizosphereor‘bulk’soil.SoilhorizonsDistinctlayersinasoildepthprofilethataretypicallydefinedonthebasisofphysicalorchemicalcharacteristics.Characteristicsofthesoilenvironment.Attheglobalscale,soilenvironmentalconditionsarehighlyvari-able.Decadesofresearchhasshownthattheproper-tiesofsurfacesoils—includingpH,organiccarbonconcentration,salinity,textureandavailablenitro-gen concentration—exhibitanenormousrange.Thisvariationisaproductofthemainfactorsthataffectsoilformation:namely,climate,organisms(includingbothmacroorganismsandmicroorganisms),relief,parentmaterialandtime(asreviewedinREF. 9).Eveninagivensoilprofile,environmentalconditionscanvaryconsiderablyacrossthedistinctmicrobialhabi-tatsfoundinsoil,includingt