50Impactofspatialorganizationonanovelauxot

TheISMEJournal●ChristianZerfaß1,2●SongFeng3●RuthEichmann1●MunehiroAsally1,2●PatrickSchäfer1,2●OrkunSSoyer1,2Received:20October2017/Revised:31January2018/Accepted:7February2018©TheAuthor(s)2018.ThisarticleispublishedwithopenaccessAbstractAkeyprerequisitetoachieveadeeperunderstandingofmicrobialcommunitiesandtoengineersyntheticonesistoidentifytheindividualmetabolicinteractionsamongkeyspeciesandhowtheseinteractionsareaffectedbydifferentenvironmentalfactors.Decipheringthephysiologicalbasisofspecies–speciesandspecies–environmentinteractionsinspatiallyorganizedenvironmentsrequiresreductionistapproachesusingecologicallyandfunctionallyrelevantspecies.Tothisend,wefocushereonadefinedsystemtostudythemetabolicinteractionsinaspatialcontextamongtheplant-beneficialendophyticfungusSerendipitaindica,andthesoil-dwellingmodelbacteriumBacillussubtilis.FocusingonthegrowthdynamicsofS.indicaunderdefinedconditions,weidentifiedanauxotrophyinthisorganismforthiamine,whichisakeyco-factorforessentialreactionsinthecentralcarbonmetabolism.WefoundthatS.indicagrowthisrestoredinthiamine-freemedia,whenco-culturedwithB.subtilis.Thesuccessofthisauxotrophicinteraction,however,wasdependentonthespatialandtemporalorganizationofthesystem;thebeneficialimpactofB.subtiliswasonlyvisiblewhenitsinoculationwasseparatedfromthatofS.indicaeitherintimeorspace.Thesefindingsdescribeakeyauxotrophicinteractioninthesoilamongorganismsthatareshowntobeimportantforplantecosystemfunctioning,andpointtothepotentialimportanceofspatialandtemporalorganizationforthesuccessofauxotrophicinteractions.Thesepointscanbeparticularlyimportantforengineeringofminimalfunctionalsyntheticcommunitiesasplantseedtreatmentsandforverticalfarmingunderdefinedconditions.IntroductionHigher-levelfunctionsandpopulationdynamicswithinmicrobialcommunitiesareunderpinnedbytheinteractionsamongthecomposingspecieswithinthecommunityandtheirenvironment[1,2].Decipheringtheseinteractionsisaprerequisitetounderstandandmanagecomplexnaturalcommunities[3]andtoachievecommunity-levelsyntheticengineering[4–6].Tothisend,increasingnumbersofexperimentalstudiesand(meta)genomicsurveyshaveshownthatauxotrophicinteractions,involvingvitaminsandaminoacids,arewidespreadinmanymicrobialnaturalcommunities[2,7–10]andcanalsobeengineeredgeneti-callytocreatesyntheticcommunities[11–13].Specificauxotrophicinteractionsamongmicrobesareshowntoinfluenceecosystemfunctioning;forexample,infectionoutcomeswithinhigherorganisms[14],ecologicalpopu-lationdynamicsintheoceans[2],andthelevelofbiode-gradationoforganicmatterunderanoxicconditions[15,16].Ithasbeensuggestedthatauxotrophiescanresultfromreducedselectivepressuresformaintainingbiosynthesiscapabilitiesunderstablemetaboliteavailabilityduetoabioticorbioticsources[7,8].Thispropositionissupportedbytheobservedindependentevolutionofvitaminandaminoacidauxotrophiesindifferent,unrelatedtaxa[17,*PatrickSchä[e-mail]*[e-mail]1SchoolofLifeSciences,TheUniversityofWarwick,Coventry,CV47AL,UK2WarwickIntegrativeSyntheticBiologyCentre,TheUniversityofWarwick,Coventry,CV47AL,UK3LosAlamosNationalLaboratory,TheoreticalDivision(T-6),CenterforNonlinearStudies,LosAlamos,NM87545,USAElectronicsupplementarymaterialTheonlineversionofthisarticle()containssupplementarymaterial,whichisavailabletoauthorizedusers.1234567890();,:18],andpointstoadirectlinkagebetweenecologicaldynamicsandevolutionofauxotrophies[15].Thepossiblefluctuationsinmetaboliteavailabilitiesintimeandspacewouldbeexpectedtoimpactboththeemergenceofauxo-trophiesandthepopulationdynamicsofresultingauxo-trophicspecies.Forexample,inthemarineenvironment,wheretheobservedauxotrophiesrelatemostlytothelossofbiosynthesiscapacityforvitaminsandaminoacids,popu-lationdynamicsofauxotrophicspeciesarebelievedtobedirectlylinkedtothoseof“provider”species[2,7,19].Theecologicalinfluencesofauxotrophicspeciesoncommunitystructureandpopulationdynamicscanalsobeexertedbyabioticfluctuationsordirectlybytheabundancesandactionsofhigherorganismswithinthesystem.Theseecologicalinfluencesonmicrobialpopulationdynamicscanincreasesignificantlyinspatiallyorganizedsystems.Yet,thespatialcontextofmicrobialinteractionsisonlybeginningtobeappreciated[10,20–22].Consideringthateachspeciescandisplaymultiplemetabolicactionsandthatallofthesecanaffectacommonenvironment,itisnotclearifauxotrophicinteractionsarealwayssuccessfullyestablishedevenifgenetic/metaboliccomplementarityispresent.Forexample,metabolicinteractionsamonggeneticallyengineeredauxotrophicyeastareshowntorequireaninitialautonomousgrowthperiodtoestablish[10].Establishmentofthesemetabolicinteractionsmightalsoinvolvespatialfactorsincludingtheformationofmetabolicgradientsandspecificpopulationorganizationmightbeimportant[15,20–23].ThesespatialfactorscanincludeoxygenandpHgradients,asbothofthesecansignificantlychangeupongrowthofonespecies[24–27],andcandirectlyinfluenc