72QuesttomapAfricassoilmicrobiomebegins

SVENTORFINN/PANOSBYSARAHWILDOnethousandziplockedbagsofsoilfromtencountrieswillformthebasisofthefirstlarge-scalesurveyofthemicrobiallifehiddenundergroundinsub-SaharanAfrica.TheleadersoftheAfricansoilmicrobiologyprojecthopethatthedatawillonedayhelptodrivebetteragriculturalprac-ticesandtoprotectecosystemsandcropsinthefaceofclimatechange.“Soilsarecriticalandsoilhealthisvitalforhumanandanimallivelihoods,”saysDonCowan,directoroftheCentreforMicrobialEcologyandGenomicsattheUniversityofPretoriainSouthAfrica.Helaunchedtheprojecton8Octoberattheconsortium’sfirstmeetinginPretoria.Researchersincreasinglyrecognizetheimportanceofsoilmicrobestoecologyandagriculture.Somebacteriaandfungicolonizeplantroots,promotingtheplant’sgrowth.Adiversepopulationofsoilmicrobeshelpstoregulateanecosystem’sclimate,andmain-tainsthefertilityofthesoilanditsabilitytosupportcrops.AndbiotechnologycompaniesincludingMonsantoaretestingadditivesthatcontainsoilmicrobesfortheirabilitytoimproveagriculturalproductivity.Yetthediversityandsheernumberofsoilmicrobes —aswellastheextenttowhichpopulationsvaryacrosstheplanet —isnotwellunderstood,saysmicrobialecologistNoahFierer,whoresearchesmicrobesindiverseenviron-mentsattheUni-versityofColoradoatBoulder.A2014studyofCentralParkinNewYorkrevealedthatthemajorityofitssoilmicrobeswerenewtoscience.“Weknowsurprisinglylittleaboutthesoilmicrobiome,”saysFierer.Thisisparticularlytrueforsub-SaharanAfrica.SouthAfrica,ascientificleaderintheregion,hasalonghistoryofsoilscience,butuntilnow,itsresearchershavefocusedonsoilchemistryratherthansoilmicrobes.Anunderstandingofthesoilmicrobiomeanditseffectoncropsisespeciallyrelevantnowbecausemicrobialcommunitiesareexpectedtobeaffectedbyclimatechange.FundedbytheUSAgencyforInternationalDevelopment(USAID),theAfricanprojectwilltakesamplesinSouthAfrica,Namibia,Botswana,Zimbabwe,Mozambique,Zambia,Kenya,Ethiopia,Côted’Ivoire,andNigeria.Thegoalofthethree-yearinitiativeistocreateabroadsurveyofsoilchemistryandmicrobiologyacrossarangeofregionsandclimates.Itsresearchers,ledbyCowan,willuseclimate,topographyandgeologytochoose1,000samplelocationsmostlikelytocapturethemaximumdiversity.Ateachpoint,scien-tistswillrecorddataaboutthearea,includingtemperatureandaltitude,andtakephotosofthesiteaswellasdiggingthesamples,whichtheywillsendbacktoCowan’slabinSouthAfrica.Eachcountryisresponsibleforitsownsamplecollectionusingastandardizedmethod.Cowan’steam,incollaborationwithresearcherssentfrompartnercountries,willextracttheDNAfromthesamples — andamplifyandsequencesectionscontainingspe-cificDNAtagsthatmarkthemoutasbacteria.Theresearchersexpecttofindunknownbac-terialgenomesaswellasknownones.Intheproject’snextphase,theywilllookatsoilfungi.Therearepracticalchallengesahead.ZimbabweisunderUSsanctionsandnoteli-gibleforUSAIDsupport,soCowanmustfindalternativefundingtoundertakesamplingthere.Andtheprojectmayrunupagainstanti-biopiracylegislation,whichrestrictsthemove-mentofsamplesacrossborders.“Ifitprovestobeimpossibletogetalltheappropriatepermitsfrompartnernations,we’lljusthavetoleavethemout,”saysCowan.Theproject“representsakeysteptochartingthediversityofthesoilmicrobiomeandmap-pingthehiddenbiodiversityfoundbelowground”,saysFierer.Althoughvaluableforcreatingabaselineforfurtherstudies,thesekindsofdatacanprovideonlyasuperficialunderstandingofthemicrobiome,notesplantmolecularbiologistSimonaRadutoiuatAarhusUniversityinDenmark.Herworkinvolvesin-depthstudiesofhowsoilbacte-riainteractwithplants,whichisnecessarytounderstandtheroleofmicrobesinplanthealth.“Thisisaverygoodinitiative,”shesays,“butisastartandshouldbecontinued,improvedandsustained.”“Theresolutionisnotgreat,”acknowledgesCowan,“butthenoveltyisenormous.”Headds:“Wedon’thavetheresourcestodothecoverageandanalysesthatwouldtaketheprojecttoamoresophisticatedlevel.”HehopesthattheprojectwilldevelopasmoreAfricanscientistsaretrainedtoper-formmicrobiomeanalyses,allowingmoresamplestobetakenandahigherresolutionofsampling.“Weknowourpartnersarestrug-glingtobuildcutting-edgelabs,”hesays.“Wecan’thelpthembuildtheirlaboratories,butwecanbringstudentsheretotraintheminthepracticalities.”■ECOLOGYMappingAfrica’ssoilmicrobiomeSub-Saharanprojectcouldonedayhelpecosystemsresistclimatechangeandimproveagriculture.Anecosystem’sabilitytosupportcropsisaffectedbythebacteriaandfungiinthesoil.“Weknowsurprisinglylittleaboutthesoilmicrobiome.”152|NATURE|VOL539|10NOVEMBER2016INFOCUSNEWS©2016MacmillanPublishersLimited,partofSpringerNature.Allrightsreserved.