MONITORING – TRACKING THE CHANGES OF THE...
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MONITORING – TRACKING THE CHANGES OF THE SEAS Innova5ve monitoring tools: challenges and perspec5ves Chair: Roberto Danovaro, CONISMA DEVOTES Final Conference, 17 – 19 October 2016, Brussels PRESENTORS IN BLOCK 4 (15:45 – 17:30) Alessandro PorcheWa, University of Rome Tor Vergata Luis Felipe Ar5gas, Université du LiWoral Côte d'Opale Isabel Ferrera, Spanish Na5onal Council for Scien5fic Research Naiara Rodríguez-Ezpeleta, AZTI John Pearman, King Abdullah University of Science and Technology David Romain, The French Na5onal Centre for Scien5fic Research Next: Anne Chenouil, The French Na5onal Centre for Scien5fic Research Chris5an Wilson, OceanDTM
Transcript of MONITORING – TRACKING THE CHANGES OF THE...
MONITORING–TRACKINGTHECHANGESOFTHESEAS
Innova5vemonitoringtools:challengesandperspec5vesChair:RobertoDanovaro,CONISMA
DEVOTESFinalConference,17–19October2016,Brussels
PRESENTORSINBLOCK4(15:45–17:30)AlessandroPorcheWa,UniversityofRomeTorVergataLuisFelipeAr5gas,UniversitéduLiWoralCôted'OpaleIsabelFerrera,SpanishNa5onalCouncilforScien5ficResearchNaiaraRodríguez-Ezpeleta,AZTIJohnPearman,KingAbdullahUniversityofScienceandTechnologyDavidRomain,TheFrenchNa5onalCentreforScien5ficResearchNext:AnneChenouil,TheFrenchNa5onalCentreforScien5ficResearchChris5anWilson,OceanDTM
Comparingcommunitycomposi5oninASUs(ar5ficialsamplingunits)fromtheRedSeatotheBal5cSea
/AnneCHENUILetal.:Morphologyandmetabarcodingcomplementarity
DEVOTESfinalconference,MARINEBIODIVERSITY-THEKEYTOHEALTHYANDPRODUCTIVESEAS,17-19october2016,Brussels
AbigailE.Cahill,JohnK.Pearman,AngelBorja,LauraCaruga5,SusannaCarvalho,RobertoDanovaro,SarahDashfield,RomainDavid,Jean-PierreFéral,SergejOlenin,AndriusSiaulys,PaulSomerfield,AntoanetaTrayanova,MariaC.Uyarra
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Comparingcommunitycomposi5oninASUs
• THEGOAL
Setupmethodsforbiodiversitymonitoringthatarerepeatableinthelongterm
→Standardiza5onofsamplingmethods→Methodstodeterminecommunitycomposi5on(=dependingasliWleasleastpossibleonanexpertknowledge)
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Comparingcommunitycomposi5oninASUs
– Samplingdevice=ASUs(tobecomparedinnearfuturewithARMS,placedatthesamesites)
– Twomethodstoassesscommunitycomposi5on
- Visualtaxonomicaliden5fica5on- Metabarcoding
«Panscourers»
ASU
Afewmonthslater
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Comparingcommunitycomposi5oninASUs
Whatismetabarcoding?
- EnvironmentalSample: Mixtureoflivingorganisms
- Barcodingmolecule: DNAregion,variableenoughsothat
eachspecieshasitsownDNAsequence
Example1: 18SrRNA hugeReferenceDataBase(++usedforunicellulars)
Example2: COI hugeReferenceDataBaseformul5celularanimals
«Panscourers»
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Comparingcommunitycomposi5oninASUs
Whatismetabarcoding?
- EnvironmentalSample: Mixtureoflivingorganisms
- Barcodingmolecule: DNAregion,variableenoughsothat
eachspecieshasitsownDNAsequence
Example1: 18SrRNA hugeReferenceDataBase(++usedforunicellulars)
Example2: COI hugeReferenceDataBaseformul5celularanimals
- Obtainasetofsequencesfor1barcodingmolecule(orfew)
- EachDNAsequenceètaxonname(speciesorhigherlevel)ifinrefer.DB
ELSEèmoleculartaxon(mOTU)
«Panscourers»
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Comparingcommunitycomposi5oninASUs
Ostracods,Polychaetes,Bivalves,BriWlestars,…..
• Visualtaxonomicaliden5fica5on
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Comparingcommunitycomposi5oninASUs
Ostracods,Polychaetes,Bivalves,BriWlestars,…..
-ClasslevelID:simple,thusreliableButthepersonmustdis5nguishanostracodfromamollusc…-Itisaquan5ta5vemethod:specimencounts/class
• Visualtaxonomicaliden5fica5on
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Comparingcommunitycomposi5oninASUs
• Metabarcoding
1DNAextrac5onofmixedanimals/phylum/ASU
EquimolarmixtureofDNAofallphyla
HiFiPCRamplifica5onoftheCOIbarcodingfragment(313bp)
Ampliconlibrary+Illuminasequencing
PlatormorIndustry
Bioinforma5cs
SpeciesComposi5on
(notquan5ta5ve)
Sta5s5cs,tests,…
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Comparingcommunitycomposi5oninASUs
• Metabarcoding
1DNAextrac5onofmixedanimals/phylum/ASU
EquimolarmixtureofDNAofallphyla
HiFiPCRamplifica5onoftheCOIbarcodingfragment(313bp)
Ampliconlibrary+Illuminasequencing
PlatormorIndustry
Bioinforma5cs
SpeciesComposi5on
(notquan5ta5ve)
Thismethoddoesnotgivetherela5vefrequencyoftaxa
Sta5s5cs,tests,…
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Comparingcommunitycomposi5oninASUs
IneachSea:3loca5ons(about10-40kmapart)
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Comparingcommunitycomposi5oninASUs
Ineachsea:3loca5onsIneachloca5on:3ARMSUnderwater:from12to18months
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Comparingcommunitycomposi5oninASUs
• Results
– Minimum: 120 specimens/ASU RedSea– Maximum: 9800 specimens/ASU BlackSea
– SometaxaarepoorlyrecoveredinmolecularOTUsdespitetheirabundance(e.g.My#lusmussels)(falsenega5ves)
– …butalsosome(lowfrequency)falseposi5ves(PCRcontamina5ons)
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Comparingcommunitycomposi5oninASUs
Numberofspecimens
EachdotisoneASU Sea
Mass(g)
low
low
high
high
Morphologydata
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Comparingcommunitycomposi5oninASUs
Numberofspecimens
EachdotisoneASU Sea
Mass(g)
low
low
high
high
• Differencesamongseas
• Variabilitywithinseas
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Comparingcommunitycomposi5oninASUs
Morphology(class)
mOTU=metabarcoding
high
high
low
low
MorphologyvsMolecular
(1-∑pi2)
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Comparingcommunitycomposi5oninASUs
o Significantdifferen5a5onamongseas
o Highdiscrimina5ngpowerof
mOTUs(metabarcoding)
mOTU=metabarcoding
Morphology(class)
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Comparingcommunitycomposi5oninASUs
• Themainoutcomeso Morphologicaliden5fica5on,attheclasslevel,waseasilyand
reliablydonebyasinglepersonforverydifferentenvironments.
o Metabarcodingdoesnotmimictradi5onaltaxonomybutprovidescomparableresults,andwithhigherdiscrimina5on.
o Weshallanalysetheinfluenceofenvironmentalfactorsonthisdataset(thoughnotideallydesignedforthis)
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Comparingcommunitycomposi5oninASUs
o Morphologyandmetabarcodingareverycomplementary
Possibleimprovement:metabarcodingmethod,nearlyquan5ta5ve,notbasedonPCR:captureprobes(promisingpublishedstudies,nouniversalprobesetyet)
Morphology(class)
Metabarcoding
Taxonomicexper5se
Lowrequirement Norequirementatall
Quan5ta5vetaxarepresenta5on
Excellent(counts,biomass)
UnreliablewhenPCR-based(butseebelow)
Possibilityofup-scaling?
Restricted Good
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Comparingcommunitycomposi5oninASUs
o Morphologyandmetabarcodingareverycomplementary
Possibleimprovement:metabarcodingmethod,nearlyquan5ta5ve,notbasedonPCR:captureprobes(promisingpublishedstudies,nouniversalprobesetyet)
Morphology(class)
Metabarcoding
Taxonomicexper5se
Lowrequirement Norequirementatall
Quan5ta5vetaxarepresenta5on
Excellent(counts,biomass)
UnreliablewhenPCR-based(butseebelow)
Possibilityofup-scaling?
Restricted Good
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Comparingcommunitycomposi5oninASUs
• Themainchallengesforthefuture
• Assessnaturalvariabilityofcommunitycomposi5on• Relatevaria5onsincommunitycomposi5ontopressuresorenvironmentalchanges
èAnalysemuchmoreASUswithineachsea-moreloca5ons(varyingenvironmentalcondi5ons)-temporalsampling
