23Seasonalandecohydrologicalregulationofacti

TheISMEJournalfluxesintemperaterainforestsoilDavidJ.Levy-Booth1,2●IanJ.W.Giesbrecht2,3●ColleenT.E.Kellogg1,2●ThierryJ.Heger4●DavidV.D’Amore5●PatrickJ.Keeling6●StevenJ.Hallam1●WilliamW.Mohn1Received:9February2018/Revised:12October2018/Accepted:3December2018©InternationalSocietyforMicrobialEcology2018AbstractThePacificcoastaltemperaterainforest(PCTR)isaglobalhot-spotforcarboncyclingandexport.YettheinfluenceofmicroorganismsoncarboncyclingprocessesinPCTRsoilispoorlycharacterized.WedevelopedandtestedaconceptualmodelofseasonalmicrobialcarboncyclinginPCTRsoilthroughintegrationofgeochemistry,micro-meteorology,andeukaryoticandprokaryoticribosomalamplicon(rRNA)sequencingfrom216soilDNAandRNAlibraries.SoilmoistureandpHincreasedduringthewetseason,withsignificantcorrelationtonetCO2fluxinpeatbogandnetCH4fluxinbogforestsoil.FungalsuccessioninthesesiteswascharacterizedbytheapparentturnoverofArchaeorhizomycetesphylotypesaccountingfor41%ofITSlibraries.Anaerobicprokaryotes,includingSyntrophobacteraceaeandMethanomicrobiaincreasedinrRNAlibrariesduringthewetseason.PutativelyactivepopulationsofthesephylotypesandtheirbiogeochemicalmarkergenesforsulfateandCH4cycling,respectively,werepositivelycorrelatedfollowingrRNAandmetatranscriptomicnetworkanalysis.ThelatterphylotypewaspositivelycorrelatedtoCH4fluxes(r=0.46,p0.0001).Phylotypefunctionalassignmentsweresupportedbymetatranscriptomicanalysis.Weproposethatactivemicrobialpopulationsrespondprimarilytochangesinhydrology,pH,andnutrientavailability.Theincreasedmicrobialcarbonexportobservedoverwintermayhaveramificationsforclimate–soilfeedbacksinthePCTR.IntroductionSoilsofthePacificcoastaltemperaterainforest(PCTR)ofNorthAmericasequestergloballyimportantamountsofcarbon(~198–900MgCha−1)[1]andcontributesomeofthehighestratesofdissolvedorganiccarbon(DOC)exporttocoastalmarginsintheworld(10.5–29.9gCm−2y−1)[2].SoilCH4fluxesinthePCTRrangefromuptake(0.05–0.55mgCm−2h−1)inuplandforeststostrongemissions(0–1.08mgCm−2h−1)fromombrotrophicpeatbogs[3].Microbialcommunitiesregulatetheflowofcarbonthroughcoastalecosystemsviadecompositionofplantbiomass[4,5],yetthecontrolsonmicrobialcarboncyclinginhydricsoils,suchthoseinthePCTR,arelittleunderstood.Nutrientlimitation,lowO2,andacidicsoilinthePCTRrestrictorganicmatterdegradation[6].Thecarbohydrate-activeenzymes(CAZy)database[7]canfacilitateinvesti-gationofcarboncyclinginsoilcommunities[8,9],andrevealtheflowofcarbonandenergythroughpeatlandsfrombiopolymerdegradationtoC1metabolism[10].*[e-mail]1DepartmentofMicrobiology&Immunology,LifeSciencesInstitute,UniversityofBritishColumbia,Vancouver,BC,Canada2HakaiInstitute,TulaFoundation,HeriotBay,BC,Canada3SchoolofResourceandEnvironmentalManagement,SimonFraserUniversity,Burnaby,BC,Canada4TheUniversityofAppliedSciencesWesternSwitzerland,CHANGINS,Delémont,Switzerland5U.S.DepartmentofAgriculture,ForestService,PacificNorthwestResearchStation,Juneau,Alaska,USA6DepartmentofBotany,UniversityofBritishColumbia,Vancouver,BritishColumbia,CanadaSupplementaryinformationTheonlineversionofthisarticle()containssupplementarymaterial,whichisavailabletoauthorizedusers.1234567890();,:1234567890();,:Itremainstobeseenhowenvironmentalconditionsindistinctseasonsandecohydrologicalclassesaffectsmicro-bialorganicmatterdegradationandcarboncycling.Anaerobicmetabolicpathwaysplayamajorroleinthemineralizationoforganiccarboninwaterloggedsoils.AnaerobicdegradationintheseenvironmentscanovercomethermodynamiclimitationsthroughthemaintenanceoflowH2concentrationsbycouplingfermentationbysulfate-reducingbacteria(SRB)tothereductionCO2toCH4byhydrogenotrophicmethanogens[11,12].Thissyntrophicinteractionisamajorcomponentofmetabolisminanaerobicbogsoil[13],whichmaybestimulatedbywinterprecipitationinthePCTR.Quantifyingcarbonbalanceduetotheseprocessesisimperativeforreconcilingannualterrestrialcarbonbudgets.Quantifyingactivemicrobialpopulationscanrevealhowcommunitiesrespondtochangingenvironmentalconditionsandcontributetonutrientcycles.However,limitationsofmethodsofassessingactivemicrobialgroupsmustbeaddressed.SufficientmRNAisdifficulttoextractandpurifyfromhigh-organicsoils.RibosomalRNA(rRNA)canberecoveredusinghigh-throughputmethods,butcellularconcentrationisnotwellcorrelatedwithgrowthratesinmixedcommunities[14].Further,dormantcellscancontaindetectablerRNA[15].Yet,rRNAanalysiscanpotentiallyreducebiasduetodeadordormantcells[16].Asribosomeconcentrationindicatespotentialforproteinsynthesisandthuscellularactivity,theanalysisofrRNAmayprovideecologically-meaningfulinsightsintodynamicsofputativelyactivemicrobialcommunitymembers[10,17–19].Tocharacterizeinsitutotal(DNAlibraries)andputa-tivelyactive(rRNAlibraries)microorganismsandtheirroleinDOC,CO2,andCH4cyclingandexportwesequencedampliconsofarchaealandbacterial16SrRNA,fungalITS,andeukaryotic18SrRNA(focusedonsoilprotists).Metatranscriptomics(mRNA)validatedphyl