marine drugs Article Antibacterial Activities of Bacteria Isolated from the Marine Sponges Isodictya compressa and Higginsia bidentifera Collected from Algoa Bay, South Africa RelebohileMatthewMatobole1,LeonardoJoaquimvanZyl1,*,ShirleyParker-Nance2,3, MichaelT.Davies-Coleman4andMarlaTrindade1 1 InstituteforMicrobialBiotechnologyandMetagenomics(IMBM),DepartmentofBiotechnology, UniversityoftheWesternCape,RobertSobukweRoad,Bellville7535,CapeTown,SouthAfrica; [email protected](R.M.M.);ituffi[email protected](M.T.) 2 DepartmentofZoology,NelsonMandelaMetropolitanUniversity,UniversityWay, PortElizabeth6031,SouthAfrica;[email protected] 3 SouthAfricanInstituteforAquaticBiodiversity(SAIAB),SomersetStreet,Grahamstown6139,SouthAfrica 4 DepartmentofChemistry,UniversityoftheWesternCape,RobertSobukweRoad,Bellville7535, CapeTown,SouthAfrica;[email protected] * Correspondence:[email protected];Tel.:+27-21-959-2325 AcademicEditor:KeithB.Glaser Received:8November2016;Accepted:30January2017;Published:17February2017 Abstract:Duetotheriseinmulti-drugresistantpathogensandotherdiseases,thereisrenewedinterest inmarinespongeendosymbiontsasarichsourceofnaturalproducts(NPs).TheSouthAfricanmarine environmentisrichinmarinebiotathatremainslargelyunexploredandmayrepresentanimportant sourceforthediscoveryofnovelNPs.Wefirstinvestigatedthebacterialdiversityassociatedwithfive SouthAfricanmarinesponges,whosemicrobialpopulationshadnotpreviouslybeeninvestigated, andselectthetwosponges(IsodictyacompressaandHigginsiabidentifera)withhighestspeciesrichness toculturebacteria. Byemploying33differentgrowthconditions415sponge-associatedbacterial isolateswereculturedandscreenedforantibacterialactivity. Thirty-fiveisolatesshowedantibacterial activity, twelve of which exhibited activity against the multi-drug resistant Escherichia coli 1699, implyingthatsomeofthebioactivecompoundscouldbenovel. Genomesequencingoftwoofthese isolatesconfirmedthattheyharbouruncharacterizedbiosyntheticpathwaysthatmayencodenovel chemicalstructures. Keywords: Isodictyacompressa;Higginsiabidentifera;naturalproducts;marinesponge;antimicrobial 1. Introduction The marine environment has been identified as a rich source of bioactive compounds with interesting chemical diversity, and in particular those produced by marine sponges [1]. Sponges belong to the phylum Porifera, and are some of the oldest metazoans on Earth [2,3]. There are fourclassesofmarinesponges,namelyCalcarea,Hexactinellida,HomoscleromorphaandDemospongiae withtheDemospongiaebeingmostabundant,representing83%ofdescribedspecies[4]. Thesefilter feedingsessileorganismsoccurprimarilyinmarineenvironmentswheretheysurviveunderimmense competitionandpredation[5–7]. Thereisevidencethatmanyofthepreviouslyidentifiedmarinespongesecondarymetabolites are of microbial origin [1,8–10]. Their ability to survive in this competitive environment could be due to their own adaptation, in addition to or perhaps because of the microbial communities Mar.Drugs2017,15,47;doi:10.3390/md15020047 www.mdpi.com/journal/marinedrugs Mar.Drugs2017,15,47 2of19 they harbor, which can account for up to 40% of the sponge’s wet weight [5,7,11]. Furthermore, these microbes are proven to produce medically relevant compounds including ecteinascidin-743 (Yondelis®), dolastatin-10 (Adcetris®) and halichondrin B (Halaven®) [12]. As a result, marine sponge-associated microbes are sought after for natural product discovery [13–16] due to their potentialfordeliveringnovelbioactivecompounds[17,18]. Ingeneral,thelargescaleproductionof microbial-derivedsecondarymetabolitesforstudyanduseishamperedbythelackofthesebacteriain culturecollections,eitherthroughaninabilitytoculturethemoridentifythemicrobesresponsiblefor producinganobservedbioactivity[19].Itisthereforeimportanttodeveloptechniquestocultivatethese marinespongesymbiontsinordertoaccessandexploittheirsecondarymetabolitecapabilities[20]. Theuseofnovelculturemedia,suchasveryminimalnutrientcontent[21],applicationofdiffusion chambers[20,22]ormicroencapsulation[23],havesuccessfullyresultedintheisolationofpreviously unculturedmarinebacteria. SouthAfricahasauniquecoastlinethatisdominatedbytwomajorcurrentsystems: thecold BenguelacurrentandthewarmAgulhascurrent[24,25].Asaresultofthephysico-chemicaldifferences introducedbythetwocurrents,thecoastlinehasanexceptionallyrichandvariedmarinelifewhich remainslargelyunexplored. ThefewreportedstudiesperformedonSouthAfricanmarinesponges thus far do not take their associated microorganisms into account [26]. The latrunculid sponge, Tsitsikammafavus,endemictothecoastofSouthAfrica,representsoneofthefewspecimenswhose microbial diversity has been assessed and serves as an example of what South African sponges may have to offer [8]. Unique to this sponge is the production of pyrroloiminoquinones, known as tsitsikammamines, that mediate cytotoxicity through the cleavage of DNA due to inhibition of topoisomerase I [27] and it is thought that these secondary metabolites are of microbial origin [9]. TheSouthAfricancoastthereforerepresentsapotentiallyresourcefulenvironmentfortheexploration ofnovelbioactivecompounds. ThisstudyassessesthebacterialdiversityassociatedwithfiveSouthAfricanmarinesponges, namelyWaltherarndtiacaliculatum,Higginsiabidentifera,Isodictyacompressa,SpongiaandAxinellaspecies. AllfivespongesbelongtotheclassDemospongiae. TheHigginsiagenuswasfirstdescribedbyHigginin 1877duringascientificexpeditionaboardtheshipArgo,withthespeciesHigginsiabidentiferadescribed in1886andaccordingtotheWorldPoriferaDatabase,appearstobeendemictoSouthAfricancoastal waters[28,29]. IsodictyacompressawasfirstdescribedbyEsperin1794,whileWaltherarndtiacaliculatum was described by Kirkpatrick in 1903, both of which are endemic to South Africa [30–33] and the bacteriaassociatedwiththesethreemarinespongeshavenotbeeninvestigated. AxinellaandSpongia species have a global distribution and the microbial populations of some species of these sponge generahavebeenstudied[34–37]. Wefirstdeterminedthebacterialdiversityassociatedwiththese five sponges, then isolated bacteria from two of these and demonstrated their ability to produce antibacterialcompounds. HerewereportanewcollectionofSouthAfricanmarinesponge-associated bacteriathatshowantibacterialactivitywhensubjectedtoavarietyofcultureconditions. 2. MaterialsandMethods Unless otherwise specified, chemicals and reagents used in this study were supplied by SigmaAldrichChemicalCompany(Darmstadt,Germany),MerckChemicalandLaboratorySupplies (Darmstadt, Germany) and Kimix Chemical and Laboratory Supplies (Cape Town, South Africa). Theenzymes,DNAsizemarkersandpolymeraseswerepurchasedfromFermentasLifeSciencesLtd. (Vilnius,Lithuania). 2.1. SampleCollection Thefivemarinesponges(Waltherarndtiacaliculatum,PE05;Higginsiabidentifera,PE07;Isodictya compressa,PE09;anAxinellaspecies,PE11;andaSpongiaspeciesPE08)werecollectedinJanuaryand April2013inAlgoaBay,PortElizabeth,SouthAfrica(longitude34◦00.366Sandlatitude25◦43.209E; 15 ◦C), and kept on ice in sterile sea water. The sponge samples (Figure S1) were shipped to the Mar.Drugs2017,15,47 3of19 InstituteforMicrobialBiotechnologyandMetagenomics,CapeTown,wherethespongematerialwas storedat–20◦Cand–80◦Cin20%glyceroluntilfurtherprocessing. Voucherspecimensofallsponge samplesarehousedintheSouthAfricanInstituteforBiodiversity(SAIAB)inGrahamstown. 2.2. TerminalRestrictionFragmentLengthPolymorphism(T-RFLP)Analysis Thefivespongesampleswerethawedonanice/waterslurryandcutwithasterilebladeinto1g aliquotsforfurtherprocessing. TheUltraCleanSoilDNAIsolationkit(MOBIOLaboratories,Carlsbad, CA, USA) was used to isolate DNA according to the manufactures protocol. Metagenomic DNA (mDNA)wasfurtherpurifiedasdescribedbyLilesetal.[38]. TheNucleoSpin®GelandPCRClean-up kit(Macherey-Nagel,Düren,Germany)wasusedtoextractthemDNAfromtheagaroseplug. ThePCRreactionmixturetogenerateampliconsforT-RFLPwasasfollows: 1×PhusionDNA polymerase buffer, 0.2 mM dNTP mix, 0.5 µM of each forward primer E9F (5(cid:48)-GAGTTTGATCCT GGCTCAG-3(cid:48)) labelled at the 5(cid:48) end with fluorescein amidite (FAM) and reverse primer U1510R (5(cid:48)-GGTTACCTTGTTGTTACACTT-3(cid:48)),0.02U/µLofPhusionDNApolymerase(Fermentas,Lithuania), 100ngoftemplatemDNAandultraviolet(UV)treatedwater[39,40]. Thefollowingcyclingconditions wereused: initialdenaturationof98◦Cfor2minfollowedby35cyclesof98◦Cfor20s,54◦Cfor30s, 72◦Cfor1minandfinalelongationat72◦Cfor5min. Duplicateamplificationswereconductedfor eachsample,pooledandpurifiedusingtheNucleoSpin®GelandPCRClean-upkit(Macherey-Nagel). Amplicons(1µg)weredigestedin30µLvolumescontaining3µLof10×Tangobuffer,2µLofHhaI (10U/µL),4µLHaeIII(10U/µL),andUVtreatedwater. DigestionswereperformedinaBio-RadT100 ThermalCycler(Bio-Rad,Hercules,CA,USA)overnightat37◦C,followedbyinactivationat80◦C for20min. Capillaryelectrophoresisandanalysisofthefluorescentlylabelledterminalrestriction fragments(T-RFs)wascarriedoutonanautomatedABI3130XLgeneticanalyzer(AppliedBiosystems, FosterCity,CA,USA)bytheCentralAnalyticalFacilityattheUniversityofStellenbosch,SouthAfrica. The marker used for the analysis was GS500LIZ. T-RFLP profiles were analysed using freeware PeakScannerTMSoftwareVersion1.0(AppliedBiosystems). Peakheightwasusedtocharacterize uniqueT-RFs. Peaksshorterthan25bpandlargerthan1200bpwereexcludedfromfurtheranalysis. ValidpeakswereidentifiedandalignedusingtheonlineT-REXsoftware[41]tocreateanoperational taxonomicunit(OTU)datamatrix. Intheory, eachOTUrepresentsanindividualT-RFwhereone T-RFrepresentsonedistinctribotype[42]. Itshouldbenotedhoweverthat,onepeakmayrepresent twodifferentbacterialspeciesortwopeaksmaybeonebacterialspeciesdependingontherecognition siteofrestrictionenzymesonthe16SribosomalRNA(rRNA)genesequence[43–45]. TheOTUmatrix wasanalysedusingPrimer6,Version6.1.11(PrimerE,Plymouth,UK)softwareanddiversityindices forallthesamplesweredetermined. 2.3. BacterialCulturing Thawedspongematerial(1g)washomogenisedbygrindingwithasterilepestleandmortarin 9mLofsterileseawater. Thespongehomogenateswereseriallydilutedinsterileseawaterto10−6, andfromeachdilution,100µLaliquotswereplatedon23generalmedia(TableS1). Thefullculturing schemeisdepictedinFigureS2. Inaddition,aliquotsofthespongehomogenatesunderwentheat treatmenttoselectforendosporeformingbacteria[15]andtoinhibitthegrowthofGramnegativefast growingbacteria[46].TheheattreatmentprocesswasadaptedfromPhelanetal.(2012)[15]withminor modifications. Analiquotof100µLofthe10−1dilutionofthespongehomogenatewasincubatedat 80◦Cfor10minandseriallydilutedto10−6. Aliquotsof100µLwereasepticallyplatedonthreemedia ShivjiNutrientAgar(SNA),TrypticSoyAgar(TSA)andZobellAgar(ZBA).Liquidenrichmentwas usedtoselectforcyanobacteria[47]andnitrogenfixingbacteria[48]. Forliquidenrichmentcultures, 100µLofthe10−1dilutionsofthespongehomogenatewereaddedto9mLofAshby’sNitrogenFree Media(ANFA),MagMinSemi-SolidMedium(MMM)andBlueGreenAlgae(BG11)liquidmedia. Theliquidenrichmentcultureswereincubatedat15◦Cforuptosixweeksonashakerat150rpm. Subsequently,100µLoftheliquidenrichedcultureswereplatedonZBAplates,asZBAisoneofthe Mar.Drugs2017,15,47 4of19 richmediawhichcangenerallysupportproliferationofarangeofdifferentbacteria. Aftertheinitial isolations,threemediaGlucoseYeastMedia(GYM),TSAandZBAwereselectedasthe“standard/rich media”forroutineculturingandcharacterizationofthebacterialisolates. IsolatesfromTrypticase Soya Agar pH 4.5 (TS4), TSA and SNA, inclusive of those which underwent different treatments, wereculturedonTSA.IsolatesfromMediumAAgar(MAA),GYM,Modified172Fmedium(172), OatmealAgar(OMA),ActinomycesIsolationMedium(AIM),andPlanctomycetesMedium(PMM) alongwiththeirdifferenttreatmentswereculturedonGYM.Isolatesfromthethirteenothermedia withtheirrespectivetreatmentswerealsoculturedonZBA.Antibiotictreatedspongehomogenates werepreparedbyadding20µg/mLofstreptomycin[49]tothehomogenate. Thehomogenateswere agitatedonashaker(150rpm)for1hatroomtemperature. Thespongehomogenateswerecentrifuged at 11,000× g for 3 min and the supernatant was discarded. Sterile sea water (1 mL) was used to re-suspendthepelletandthesuspensionwasseriallydilutedto10−6. Aliquotsof100µLofthe10−1to 10−6dilutionswereplatedoneightmedia(OMA,OMA+NaCl(1.8%wt/vol),AIM,GYM,172,MAA, YeastExtract-MaltExtract(YEME)andStarchCaseinNitrateAgar(SCN))containingcyclohexamide (100µg/mL)andnalidixicacid(50µg/mL)[50]. Allplateswereincubatedat15◦Cforuptofour weeks. Colonies were examined and picked on a daily basis selecting for colonies with different morphologies(shape,colour,texture,andsize). 2.4. AntimicrobialScreening Themarinesponge-associatedisolateswerescreened,usingagaroverlayassays,forantibacterial activityagainsttheGram-positivestrainsMycobacteriumsmegmatisLR222,BacilluscereusATCC10702, StaphylococcusepidermidisATCC14990andtheGramnegativestrainsPseudomonasputidaATCC27853 andthemultidrugresistantEscherichiacoli1699(Cubist,Lexington,MA,USA).Isolateswerecultivated onfour media (ZBA,GYM,TSAand ActivatedCharcoalMedium (ACM))fortwoweeks atroom temperature. On the day prior to carrying out the overlay assays, the test strains were cultured overnightin10mLLuriaBroth(LB)at37◦Cwithaerationat250rpm. Toensurethatapproximately thesameconcentrationofcells(usingopticaldensitymeasurements,OD )werepresentinthesloppy 600 agar,thefollowingformulaewereusedtocalculatethevolumeofculturetoaddto6mLofsloppy agar (LB): OD × X µL = 4 (for E. coli). OD × X µL =160 (for other test strains). The sloppy 600 600 agarcontainingtheteststrainswaspouredoverthemarineisolategrowth,incubatedat30◦Cand examinedforzonesofinhibitionafter16handagainafter48h. For induction of antimicrobial activities, a one-strain-many-active-compounds (OSMAC) approach was followed. A total of 29 isolates were selected; 12 that gave hits against the panel ofteststrainsintheoverlayassaysandanadditional17isolatesthatdidnotshowantibacterialactivity inthefirstroundofscreening(TableS2). Amatrixincorporatingthefollowinggrowthmodificationsor treatmentswasdeveloped: heatorcoldshocktreatment,co-culturingwithsponge-associatedbacteria, andvaryingcarbon(mannitol,succinicacidandstarchat5mM)andnitrogen(NH ClorNaNO at 4 3 0.02%w/v)sourcesorphosphateconcentrations(KH PO at0.1µMor0.5mM).Thebasemedium 2 4 employedwasaminimalmediacontainingperliter: 18gNaCl,2gMgCl ,0.525gKCl,0.075gCaCl 2 and2.38gHEPESbuffer. Theexperimentwassetupina96-wellformatonlargepetridishplates (20mm × 150mm). Themethodofplatingin96-wellformatwassimilartothatdescribedin[51] withsomemodification. Singlecoloniesfromtheselectedisolateswereinoculatedinto96-wellplates containing70µLsterilewaterineachwell,andshakenat100rpmonashakerfor10minatroom temperature(RT).Cultureswerethenplatedasepticallyonthedifferentmatrixmediausinga96-pin hedgehogandallowedtogrowfor2weeksatRT.Theorderofinoculationofisolateswasinterchanged betweenisolatesthatgavepositivehitsonstandardmediuminthefirstroundofscreeningandthose whichdidnot. Allisolateswereinoculatedintriplicateoneach96-wellplateandthereforelocated atdifferentpositionsresultingindifferentneighboringisolateswhichresultedinaco-culturesetup (FigureS3). Onthedaypriortoperformingoverlays,coldandheatshocktreatmentswerecarried out. Theheatshockmethodusedwasadaptedfrom[52]withminorchanges. Heatshockplateswere Mar.Drugs2017,15,47 5of19 incubatedfor1hat42◦C,whereascoldshocktreatmentwascarriedoutat4◦Cfor1h. Theheat andcoldshocktreatmentswererepeatedonthedayoftheantibioticoverlayassay. Thedaypriorto carryingouttheoverlayassay,singlecoloniesofeachoftheteststrainswasinoculatedintoLuriaBroth (10mL)andthecultureswereincubatedat37◦Covernightwhileshakingat250rpm. Theoptical density(OD )oftheculturesweredeterminedafterwhichtheyweredilutedtoachievethesame 600 overallconcentrationofcells. Anoverlayassaysimilartothatdescribedabovewascarriedoutusing 24mLofagarforthelargeformatplates(20mm×150mm). 2.5. DNASequencingandPhylogeneticAnalysis For16SrRNAidentificationofthebioactiveisolates,genomicDNAextractionwasperformed usingtheGeneJETGenomicDNAPurificationKit(ThermoScientific,Waltham,MA,USA).Asingle colony was inoculated in 10 mL TSA broth or 1⁄4 strength ZBA broth and incubated on a shaker (150rpm)atroomtemperaturefor2to5daysdependingongrowthrate. DNAextractionwascarried outaccordingtothemanufacturer’sinstructionsforGram-negativebacteria. Minormodifications were made for Gram-positive bacteria where 200 µL of lysis buffer (25 mM Tris-HCl pH8, 50 mM glucose,10mMEDTAand25mg/mLlysozyme)wasaddedtothepelletedbacterialcellsandthe solutionswereincubatedat37◦Cfor30min.Thereafterthemanufacturer’sinstructionswerefollowed. PCRamplificationwasperformedin50µLvolumeswhichconsistedof1×DreamTaqbuffer,0.2mM ofdNTPmix,1µMofeachofthereverseandforwardprimers,100ngtemplateDNA,1.25UDreamTaq DNApolymerase(Fermentas),andsteriledistilledwater. TheuniversalprimersE9FandU1510Rwere usedtoamplifythe16SrRNAgenesequencesofthemarinesponge-associatedbacteria. Thefollowing cyclingconditionswereused: initialdenaturation95◦Cfor5min,35cyclesof95◦Cfor45s,55◦Cfor 45s,72◦Cforoneandahalfminandfinalelongationof72◦Cfor10min. TheDNAsequencedeterminationofpurified16SrRNAgeneproductswerecarriedoutbythe CentralAnalyticalFacilityatStellenboschUniversityusinganABIPRISM377automatedsequencer (Applied Biosystems). The data from the sequencing unit was processed using Chromas Pro 1.5a software (Technelysium, South Brisbane, QLD, Australia) for alignment and manual editing of sequences. The neighbor-joining phylogenetic tree was constructed using MEGA 7 software [53]. Bootstraptestswereperformed1000times. 2.6. GenomeSequencing WholegenomesequencingofPE09-72andPE09-221wasperformedatthesequencingfacility withintheInstituteforMicrobialBiotechnologyandMetagenomics,UniversityoftheWesternCape, SouthAfrica. GenomicDNAwaspreparedusingstandardphenol:chloroformextraction. Sequencing librarieswerepreparedusingtheIlluminaNexteraXTlibraryprepkitaccordingtothemanufacturer’s instructions and sequencing was performed using the Illumina MiSeq Reagent kit V3 (Illumina, SanDiego,CA,Country)whichincludeda10%phiXV3spike[54]. Thisresultedin2×300basepair (bp)pairedendreads(forwardandreverse). AnalysisofthesequencedatawascarriedoutusingCLC Genomicsversion7.5.1(CLC,Aarhus,Denmark). RawreadswerereferenceassembledtophiXV3 genomeusedinthesequencingreactionforqualitycontrol. Unmappedreadsweremappedtothe humangenometoremoveanycontaminatingsequences. Adenovoassemblywascarriedouton theremainingunmappedreadsusingdefaultparameters. Basicanalysisoftheassembledcontigs were carried out using the RAST server [55] and BLAST analysis against the NCBI database [56]. ThegenomeshavebeendepositedintheGenbankdatabaseunderaccessionnumbersMIJA00000000 andMIJB00000000forPE09-72andPE09-221respectively. Mar.Drugs2017,15,47 6of19 3. ResultsandDiscussion 3.1. BacterialDiversityAnalysisandCulturingofMarineSponge-AssociatedBacteria Fivesponges(PE05,PE07,PE08,PE09,PE11)wereinvestigatedfortheirbacterialdiversity,using 16S rRNA based T-RFLP analysis to identify those with highest diversity and unique operational taxonomicunits(OTUs)toimprovethechanceofisolatingnovelbacteria. T-RFLPprofilesrevealed thattherewasatotalof179OTUsfromthefivemarinesponges,90ofwhichwereunique(Figure1). StudieshaveclassifiedmicrobialOTUsaseitherspeciesspecificOTUs(definedasOTUsuniquetoa certainspoMnagr.e Dsrupgse 2c0i1e7,s 1)5,o 4r7 spongespecificOTUs(definedasOTUsfoundinspongesbut6 onf o18t foundin otherenvironments)[57,58]. Notably,fiveoftheOTUsweresharedamongallfivespongesindicating other environments) [57,58]. Notably, five of the OTUs were shared among all five sponges indicating thattherepthreats tehnet raetpirveeseOntTatUivse OcoTuUlsd cobuelds bpeo snpgonegsep sepcecifiificc [[5599,6,600].] . Figure 1. Venn diagram of species specific and shared operational taxonomic units (OTUs) (at genus Figure1.Vleenvenl) dini athger asemlecotefds mpaerciniees spsopnegceisfi. candsharedoperationaltaxonomicunits(OTUs)(atgenus level)intheselectedmarinesponges. The Simpson index of the bacterial species from PE05 and the PE11 was the least even, indicating the presence of more dominating OTUs in these samples, while the other sponges had a more even TheSimpsonindexofthebacterialspeciesfromPE05andthePE11wastheleasteven,indicating distribution of species abundance (Table 1). PE07 and PE09 yielded the most OTUs with 43 and 44 the presenrceespoecftimveloyr eandd ohmadi nthaet ihniggheOstT eUvesnnienss.t hAeltsheousgahm sepelmesin,gwly hloiwle, tthhee OoTtUhse rfrosmp othneg perseshenatd a more even distrisbtuudtyio wneroe fsimspilearc tioe sthea bnuumnbdearsn ocfe T‐(RTFaLbPl‐eba1se)d. OPTEU0s 7repaonrdtedP fEro0m9 oythieerl dsteuddietsh wehemreo 4s5t aOndT Us with 32 OTUs were identified in Hymeniacidon heliophila and 36 and 22 OTUs were identified in Haliclona 43 and 44 respectively and had the highest evenness. Although seemingly low, the OTUs from tubifera depending on the restriction enzymes used [61]. PE09 had the highest number of species thepresentstudyweresimilartothenumbersofT-RFLP-basedOTUsreportedfromotherstudies specific OTUs (14) with the second highest being PE05 with 11 OTUs. Although PE07 had the second where45anhidgh3e2st OnuTmUbserw oefr OeTidUes notnifilye tdhriene Hwyerme esnpieaccifiidco tno hthelisio spahmilpalea nwdhi3ch6 iannddica2te2dO thTaUt fsewweerr eH.i dentified inHaliclonabidteunbtiiffeerraa‐spdeecpifiecn OdTinUgs woneret hiesorlaetsetdr ifcrtoimon theen zsaymmplees. uGsiveedn [t6h1e ].hiPghEe0r 9dhivaedrsittyh eanhdi gehveenst number representation of species present in both PE07 and PE09, as well as the uniqueness of PE09 profiles ofspeciesspecificOTUs(14)withthesecondhighestbeingPE05with11OTUs. AlthoughPE07had and the representative nature of PE07, these were selected for bacterial isolation studies. the second highest number of OTUs only three were specific to this sample which indicated that fewerH.bidentifera-speciTfiacblOe 1T. UDisvewrsietyr eindisicoelsa otfe tdhe fsrpoonmget‐ahsesosciaamtedp mleic.roGbiiavl epnoptuhlaetiohnisg. herdiversityandeven representationSoamfpsplee IcDie spreseMntariinneb SoptohnPgeE I0D7andPES0p9e,caiess wSpeelclifaics OthTeUusniqSu enes1s −o λf PE09profiles andtherepresenPtaEt0i5v enatureofPWE. 0ca7l,ictuhlaetsuemwereselectedforb1a1cterialisolat3io6 nstu0.d69i2e3s. PE07 H. bidentifera 3 43 0.9388 PTEa0b8l e1.DSipvoenrgsiait (yspionndgiica)e sspo. f0t0h1eRSsApoSPnNge -associatedm7 icrobialpopu2l4a tion0s..8514 PE09 I. compressa 14 44 0.9306 PE11 Axiinella sp. 007RSASPN 7 32 0.7706 SampleID MarineSpongeID SpeciesSpecificOTUs S 1−λ Index: species richness (S) = OTUs; Simpson index (1 − λ) = evenness. PE05 W.caliculatum 11 36 0.6923 PE07 A total of 415 uniquHe b.abcitdeerniatli fceoralonies, as judged by their morp3hology (size, shap4e3, colour a0n.9d3 88 PEte0x8ture), wereS ipsoonlagteiad (fsrpoomn gthiae) twspo. s0p0o1nRgSe AsaSmPpNles with PE09 yieldi7ng 273 isolates and2 1442 bacte0r.i8al5 14 PEis0o9lates from PE07, respecIt.ivceolmy.p Trheses faewest number of isolates were1 o4btained from sam4p4les grow0in.9g3 06 PEin1 1liquid enrichmeAnxt iimneeldliausmp .a0n0d7 fRroSmA SthPeN heat treated medium, w7hich yielded 5 an3d2 12 isola0t.e7s7 06 respectively. This could be due to the selectivity in the liquid enrichment medium which was meant Index:speciesrichness(S)=OTUs;Simpsonindex(1−λ)=evenness. to select for nitrogen fixing bacteria. In the case of heat treatment, the low viable microbial numbers post treatment indicate that the number of spore‐forming bacteria are low in these marine sponges or that sporulation had not been induced in spore formers at the time of harvest [15]. The antibiotic Mar.Drugs2017,15,47 7of19 Atotalof415uniquebacterialcolonies,asjudgedbytheirmorphology(size,shape,colourand texture),wereisolatedfromthetwospongesampleswithPE09yielding273isolatesand142bacterial isolatesfromPE07,respectively. Thefewestnumberofisolateswereobtainedfromsamplesgrowing in liquid enrichment medium and from the heat treated medium, which yielded 5 and 12 isolates respectively. Thiscouldbeduetotheselectivityintheliquidenrichmentmediumwhichwasmeant toselectfornitrogenfixingbacteria. Inthecaseofheattreatment,thelowviablemicrobialnumbers posttreatmentindicatethatthenumberofspore-formingbacteriaarelowinthesemarinesponges ortMhaar.t Dsrpuogsr 2u0l1a7t, i1o5,n 47h adnotbeeninducedinsporeformersatthetimeofharvest[15]. Thean7 toifb 1i8o tic treatmentyielded37isolateswhilethenon-treatedmediumresultedin361bacterialisolates. GYM treatment yielded 37 isolates while the non‐treated medium resulted in 361 bacterial isolates. GYM wasthemediumwhichresultedinthehighestnumberofbacterialisolates(40)whichaccountedfor was the medium which resulted in the highest number of bacterial isolates (40) which accounted for 10%ofthetotalisolates. AIMandZBAresultedin39(10%)and37(9%)isolatesrespectively(Figure2). 10% of the total isolates. AIM and ZBA resulted in 39 (10%) and 37 (9%) isolates respectively (Figure ThemediumwhichresultedinthefewestbacterialisolateswereMMMandSeawaterAgar(SWA)since 2). The medium which resulted in the fewest bacterial isolates were MMM and Seawater Agar (SWA) eachcontributedonlyonebacterialisolate. Bothmediadiscouragegrowthoffastgrowingbacteria since each contributed only one bacterial isolate. Both media discourage growth of fast growing thubsarcetesruialt itnhgusi nrefseuwlteinrgn iunm febweresr onfummbicerrosb oifa lmisicorloabteiasl. isolates. Figure 2: Total number (and percentage) of bacterial isolates cultured from the marine sponge Figure2.Totalnumber(andpercentage)ofbacterialisolatesculturedfromthemarinespongesamples samples PE07 and PE09 per medium type. The number shown inside each pie section indicates the PE07andPE09permediumtype.Thenumbershowninsideeachpiesectionindicatestherawnumber raw number of isolates from that medium type. Only 1 isolate was recorded from MMM and SWA ofisolatesfromthatmediumtype.Only1isolatewasrecordedfromMMMandSWArespectively. respectively. 3.2. AntimicrobialScreeningandInduction 3.2. Antimicrobial Screening and Induction TheantibacterialpropertiesofmicrobialisolatesfromPE07andPE09wereinvestigatedinan The antibacterial properties of microbial isolates from PE07 and PE09 were investigated in an agaargaorv oervlearylaays assasyaya gaagianisntstfi fviveet etesstts sttrraaiinnss ((TTaabbllee 22)).. MMoosstt iissoolalatetes soonnlyl yshsohwowede da naanrraorwro wspescpteructmru m ofaocf taivctiitvyi,tyb,e bineginagc aticvtievea gaagianinststo onnlyly oonnee tteesstt ssttrraaiinn wwhheenn ccuultluturerded ono nstsatnadnadradr mdemdeiad (iZaB(ZAB, AGY,GMY, M, TSATSaAn danAd CAMCM).)H. oHwoweveevre,ri, siosloaltaetessP PEE0077-‐77,, PPEE0077-‐114444,, PPEE0077‐-220077, ,PPEE090‐98-78,7 P,EP0E90‐190-150 a5nadn PdEP09E‐0191-91 19 disdpilsapylaeydeadc aticvtiivtyitya gaagianinststt wtwooo orrm moorree tteesstt ssttrraaiinnss.. NNoottaabblyly, ,PPEE007‐77- 7anadn dPEP0E90‐191-191 o9nolyn ldyisdpilsapyleady ed actaivcittiyviatyg aaignasitnGstr aGmr-apmo‐spitoisvietivtees ttesstrt asintrsa,inwsh, iwlehPilEe0 7P-E10474‐,1P44E,0 7P-E20077‐2a0n7d aPnEd0 9P-E10059‐h1a05d ahcatdiv iatcytiavgitayi nst botahgaGinrasmt b-optohs iGtirvaema‐npdosGitrivaem a-nndeg Gatriavme‐tneesgtasttirvaein tse.stM sotrsatinasc.t iMviotystw aactsivreitcyo wrdaesd raecgoaridnesdt Ba.gcaeirnesuts Bw. ith 17oceurteuosf w32itsht r1a7i nosust hoofw 32in sgtraacitnisv isthyoawgianign satctthivisityte astgastinrasitn t,hwis htielset ssetvraeinn,i swohlailtee ssegvaevne iascotliavtietsy gaagvaei nst theahctiigvhitlyy aangatiibnisott ticher ehsiigsthalnyt aEn.tciboiloit1i6c9 r9es(irsetsainstta En.t ctooli5 126k9n9 o(wrensisatnatnitb itoot 5ic2s )k.nIotwwna saanltsiobinootitcesd). tIht awtanso ne also noted that none of the isolates displayed antibacterial activity on more than two growth media, suggesting inducible genes or pathways. It is also important to note that all isolates grew to some degree on the media used and lack of activity is not due to the inability of the isolate(s) to grow. Mar.Drugs2017,15,47 8of19 oftheisolatesdisplayedantibacterialactivityonmorethantwogrowthmedia,suggestinginducible genesorpathways. Itisalsoimportanttonotethatallisolatesgrewtosomedegreeonthemediaused andlackofactivityisnotduetotheinabilityoftheisolate(s)togrow. Table2.Antibacterialactivitiesagainstteststrainsinstandardmedium. TestStrains Isolate GramNegative GramPositive E.coli1699 P.putida M.smegmatis B.cereus S.epidermidis PE07-5 GYM GYM ZBA PE07-7 TSA,ZBA TSA,ZBA PE07-86 TSA PE07-105 GYM PE07-133 GYM PE07-143 TSA,ZBA PE07-144 GYM GYM PE07-172 TSA PE07-200 GYM PE07-201 GYM PE07-204 GYM PE07-207 GYM GYM PE09-7 TSA PE09-73 ACM PE09-87 GYM GYM GYM PE09-100 ZBA PE09-105 GYM,TSA TSA,GYM TSA PE09-108 GYM PE09-110 ZBA PE09-119 ZBA,GYM TSA,ZBA ACM,TSA PE09-124 ACM PE09-140 ACM PE09-142 ACM PE09-168 ACM PE09-197 ACM PE09-210 ACM PE09-213 ACM PE09-221 ZBA PE09-228 ACM PE09-229 ACM PE09-235 ACM PE09-266 ZBA Totalhits 7 5 8 17 6 Tofurtherinduceantimicrobialactivities, anOSMACapproachwastakenforasubsetofthe isolates. Fromscreening29microbialisolatesinthematrixof36culture/treatmentconditionsand co-culture,sixisolatesshowedinducedantibacterialactivities(Table3). Mostnotably,isolatePE09-72 producedactivityagainstallteststrainsinmannitolcontainingmedium,especiallywiththeaddition of heat shock, whereas only one activity was produced with succinic acid as the carbon source. Thisindicatesthatthepathway(s)responsiblefortheactivitiesarelikelysubjecttocarboncatabolite repression(CCR)[62]. Althoughnomediumcompositioninducedactivitiesagainstallteststrains, some medium compositions (NH Cl-LP, NH Cl-HP and NaNO -HP) induced activity in PE09-72 4 4 3 againstfouroftheteststrainswhenmannitolwasusedascarbonsourceandthecultureheatshocked. Differential antimicrobial activities were observed in relation to the media the isolates were culturedon. Forinstance,theisolatePE07-5showedantibacterialactivitiesagainstE.coli1699and M. smegmatis in GYM medium and only against B. cereus on ZBA medium. This is a well-known phenomenonregardingmicrobialsecondarymetaboliteproduction[8,63]. Mar.Drugs2017,15,47 9of19 Mar. Drugs 2017, 15, 47 9 of 18 Table3.Antibacterialactivitiesofsixselectedsponge-associatedisolatesundermatrixscreeningconditions.Threeoftheisolatesdidnotdisplayactivityintheinitial scTreaebnlein 3g. ,Awnhtiebraecatsertihael aoctthiverititehsr eoef issiox lsaetelescdteidd .spRoTn:gReo‐oasmsoTceiamtepde irsaotluartees( 2u7nd◦Cer) ;mHaStr:iHx esacrteSehnoincgk ctroenadtimtioennst.( 4T2hr◦eCe )o;fC tSh:eC iosoldlastehso dckidt rneoatt mdiesnptla(y4 a◦cCti)v.ity in the initial screening, whereas the other three isolates did. RT: Room Temperature (27 °C); HS: Heat Shock treatment (42 °C); CS: Cold shock treatment (4 °C). None‐Active in Primary Screening Active in Primary Screening PE07‐103 PE09‐55 PE09‐72 PE07‐105 PE09‐140 PE09‐229 TSA Standard GYM media ZBA ACM NH4Cl‐LP NH4Cl‐HP RT NaNO3‐LP m NaNO3‐HP u di NH4Cl‐LP e m NH4Cl‐HP nitol HS NaNO3‐LP n NaNO3‐HP a M NH4Cl‐LP NH4Cl‐HP CS NaNO3‐LP NaNO3‐HP NH4Cl‐LP NH4Cl‐HP RT m NaNO3‐LP diu NaNO3‐HP me NH4Cl‐LP d NH4Cl‐HP ci HS c a NaNO3‐LP cini NaNO3‐HP uc NH4Cl‐LP S NH4Cl‐HP CS NaNO3‐LP NaNO3‐HP Mar.Drugs2017,15,47 10of19 Mar. Drugs 2017, 15, 47 Table3.Cont. 10 of 18 None-Active in Primary Screening Active in Primary Screening PE07-103 PE09-55 PE09-72 PE07-105 PE09-140 PE09-229 NH4Cl-LP NH4Cl-HP RT NaNO3-LP m NaNO3-HP diu NH4Cl-LP me HS NH4Cl-HP h NaNO3-LP c Star NaNO3-HP NH4Cl-LP NH4Cl-HP CS NaNO3-LP NaNO3-HP Key Test Strain Colour E. coli1699 M. smegmatis P. putida B. cereus S. epidermidis