41TheEcologicalRoleofVolatileandSolubleSec

ReviewTheEcologicalRoleofVolatileandSolubleSecondaryMetabolitesProducedbySoilBacteriaOlafTyc,,1ChunxuSong,1,3JeroenS.Dickschat,1,4MichielVos,2andPaolinaGarbeva1,*Therichdiversityofsecondarymetabolitesproducedbysoilbacteriahasbeenappreciatedforoveracentury,andadvancesinchemicalanalysisandgenomesequencingcontinuetogreatlyadvanceourunderstandingofthisbiochemicalcomplexity.However,wearejustatthebeginningofunderstandingthephysi-cochemicalpropertiesofbacterialmetabolites,thefactorsthatgoverntheirproductionandecologicalroles.Interspecificinteractionsandcompetitorsens-ingareamongthemainbioticfactorsaffectingtheproductionofbacterialsecondarymetabolites.Manysoilbacteriaproducebothvolatileandsolublecompounds.Incontrasttosolublecompounds,volatileorganiccompoundscandiffuseeasilythroughair-andgas-filledporesinthesoilandlikelyplayanimportantroleinlong-distancemicrobialinteractions.Inthisreviewweprovideanoverviewofthemostimportantsolubleandvolatileclassesofsecondarymetabolitesproducedbysoilbacteria,theirecologicalroles,andtheirpossiblesynergisticeffects.IntroductiontoSoilBacteriaSoilisahighlycomplex,heterogeneous,andnutrient-limitedenvironmentconsistingofanorganicmatrixwithliquidandgaseousporespossessingthehighestmicrobialdiversityonearth.Therhizosphere(seeGlossary),definedasthenarrowregionofsoilattachedtoplantrootsandinfluencedbyplantrootexudates,isahotspotofmicrobialinteractionsandactivities[1,2].Molecularphylogeneticanalysesrevealthatthesoilandrhizospherecancontainthousandsofuniquebacterialspeciespergram[3];however,todate,onlyasmallfractionofthesebacteriahasbeenculturedandstudiedfortheirabilitytoproducebioactivesecondarymetabolites.Culture-basedstudieshaverevealedthatevenasinglebacterialstraincanproduceavastarrayofsecondarymetabolitesencodedbycrypticgeneclustersthatarenottranscribedunderinvitroconditions.Secondarymetabolitesarenotdirectlyinvolvedinthegrowth,development,orreproductionoftheproducingbacteria,yettheymayplayimportantecologicalrolesintheinteractionswithotherorganisms.Bacterialsecondarymetabolitesoriginatefromafewclearlydefinedcompoundclassesviatheircorrespondingbiosyntheticpathways,butforeachcom-poundclassavariationofbuildingblocks,enzymaticmechanisms,andtailoringstepscanleadtoanextremelydiversearrayofchemicalstructures.Thisreviewprovidesashortdescriptionofthemainclassesofsolubleandvolatilesecondarymetabolitesproducedbysoilbacteria,andtheabioticandbioticenvironmentalfactorsaffectingtheproductionofthesesecondarymetabolites.WehighlighttheimportanceofinterspecificinteractionsandcompetitorsensingfortheproductionTrendsBacteriaproduceavastarrayofsec-ondarymetabolites,bothsolubleandvolatile,whichhavediverseandimpor-tantecologicalfunctions.Ithasbecomeincreasinglyclearthatsecondarymetaboliteproductionoftenistriggeredbyintra-andinterspecificinteractionsbetweensoilbacteria.Secondarymetabolitesmaybeusedasagentsofwarfareorasinfochem-icals,withvolatilecompoundspoten-tiallyactingoveragreaterspatialscalethansolublecompounds.Newanalyticaltechniquesaretrans-formingthestudyofsecondarymeta-bolitechemistry,physiology,andecology.1DepartmentofMicrobialEcology,NetherlandsInstituteofEcology(NIOO-KNAW),POBox50,6700AB,Wageningen,TheNetherlands2EuropeanCentreforEnvironmentandHumanHealth(ECEHH),UniversityofExeterMedicalSchool,PenrynCampusTR109FE,UK3UniversityofGroningen,Nijenborgh7,Groningen9747AG,TheNetherlands4UniversitätBonnKekulé-InstitutfürOrganischeChemieundBiochemieGerhard-Domagk-Straße1,53121Bonn,Germany*Correspondence:[e-mail](P.Garbeva).TIMI1402No.ofPages13TrendsinMicrobiology,MonthYear,Vol.xx,No.yy©2016ElsevierLtd.Allrightsreserved.TIMI1402No.ofPages13ofbothvolatileandsolublesecondarymetabolites,theirecologicalroles,andthepossiblesynergismbetweenvolatileandsolublecompounds,anewandvirtuallyunexploredarea.MainClassesofSecondaryMetabolitesProducedbySoilBacteriaSoilbacteriaproducealargeamountofsecondarymetaboliteswhichhavemanydifferentphysiochemicalandbiologicalproperties.Inthisarticlevolatileorganiccompoundsandsolublemetaboliteswillbedistinguished.Ontheonehand,volatileorganiccompoundsaresmallmolecules(300Da)belongingtodifferentchemicalclassesthatcanevaporateanddiffuseeasilythroughair-andwater-filledpores[4,5].Thesephysiochemicalpropertiesmakevolatilesidealcandidatemetabolitesforcooperationandcompetitionbetweensoilmicroorganismsthatdonotlivedirectlyadjacenttoeachother.Ontheotherhand,solublesecondarymetaboliteshaveahigherpolaritywhichmakesthemsolubleinwater.Theyactforshorterdistances,butusuallyexhibitstrongerbiologicalactivitiesastoxinsorantibiotics,asaconsequenceoftheirhighdegreeoffunctionalization.Here,wefirstsummarizethemainclassesofsecondarymetabolitesproducedbysoilbacteria,includingbothsolubleandvolatilecompounds(Figure[13_TD$DIFF]1;alsoseeTable[14_TD$DIFF]S1[15_TD$DIFF]inthesupplementalinformationonline),andgiveabriefintroductiontotheirbiosyntheticbackground.SolubleCompounds[2_TD$DIFF]Bacteriocinsareribosomallysynthesizedantimicrobialpeptidesproducedbybacteria.Theyexhibitactiv