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dc.contributor.authorPeters, Lucy
dc.contributor.authorSpatharis, Sofie
dc.contributor.authorDario, Maria Augusta
dc.contributor.authorRoca, Inaki Javier Tomey
dc.contributor.authorKintner, Anna
dc.contributor.authorKanstad-Hanssen, Øyvind
dc.contributor.authorLlewellyn, Martin S.
dc.contributor.authorPræbel, Kim
dc.date.accessioned2019-03-08T12:50:38Z
dc.date.available2019-03-08T12:50:38Z
dc.date.issued2018-12-07
dc.description.abstractEnvironmental DNA (eDNA) metabarcoding is a relatively new monitoring tool featuring in an increasing number of applications such as the facilitation of the accurate and cost effective detection of species in environmental samples. eDNA monitoring is likely to have a major impact on the ability of salmonid aquaculture industry producers and their regulators to detect the presence and abundance of pathogens and other biological threats in the surrounding environment. However, for eDNA metabarcoding to develop into a useful bio-monitoring tool it is necessary to (a) validate that sequence datasets derived from amplification of metabarcoding markers reflect the true species’ identity, (b) test the sensitivity under different abundance levels and environmental noise and (c) establish a low-cost sequencing method to enable the bulk processing of field samples. In this study, we employed an elaborate experimental design whereby different combinations of five biological agents were crossed at three abundance levels and exposed to sterile pre-filtered and unfiltered seawater, prior to coarse filtering and then eDNA ultrafiltration of the resultant material. We then benchmarked the low-cost, scalable, Ion Torrent sequencing method against the current gold-standard Illumina platform for eDNA surveys in aquaculture. Based on amplicon-seq of the 18S SSU rDNA v9 region, we were able to identify two parasites (<i>Lepeophtheirus salmonis</i> and <i>Paramoeba perurans</i>) to species level, whereas the microalgae species <i>Prymnesium parvum</i>, <i>Pseudo-nitzschia seriata</i>, and <i>P. delicatissima</i> could be assigned correctly only to the genus level. Illumina and Ion Torrent provided near identical results in terms of community composition in our samples, whereas Ion Torrent was more sensitive in detecting species richness when the medium was unfiltered seawater. Both methods were able to reflect the difference in relative abundance between treatments in 4 out of 5 species when samples were exposed to the unfiltered seawater, despite the significant amount of background noise from both bacteria and eukaryotes. Our findings indicate that eDNA metabarcoding offers significant potential in the monitoring of species harmful to aquaculture and for this purpose, the low-cost Ion Torrent sequencing is as accurate as Illumina in determining differences in their relative abundance between samples.en_US
dc.description.sponsorshipWellcome Trust BBSRC The Faculty of Biosciences, Fisheries, and Economics, University of Tromsoen_US
dc.descriptionThe following article, Peters, L., Spatharis, S., Dario, M.A., Dwyer, T., Roca, I.J.T., Kintner, A., Kanstad-Hanssen, Ø., ... Præbel, K. (2018). Environmental DNA: A New Low-Cost Monitoring Tool for Pathogens in Salmonid Aquaculture. <i>Frontiers in Microbiology, 9</i>, can be accessed at <a href=https://doi.org/10.3389/fmicb.2018.03009> https://doi.org/10.3389/fmicb.2018.03009</a>.en_US
dc.identifier.citationPeters, L., Spatharis, S., Dario, M.A., Dwyer, T., Roca, I.J.T., Kintner, A., Kanstad-Hanssen, Ø., ... Præbel, K. (2018). Environmental DNA: A New Low-Cost Monitoring Tool for Pathogens in Salmonid Aquaculture. <i>Frontiers in Microbiology, 9</i>. https://doi.org/10.3389/fmicb.2018.03009en_US
dc.identifier.cristinIDFRIDAID 1641955
dc.identifier.doi10.3389/fmicb.2018.03009
dc.identifier.issn1664-302X
dc.identifier.urihttps://hdl.handle.net/10037/14914
dc.language.isoengen_US
dc.publisherFrontiers Mediaen_US
dc.relation.journalFrontiers in Microbiology
dc.rights.accessRightsopenAccessen_US
dc.subjectVDP::Agriculture and fishery disciplines: 900::Fisheries science: 920en_US
dc.subjectVDP::Landbruks- og Fiskerifag: 900::Fiskerifag: 920en_US
dc.subjectPseudo-nitzschia seriataen_US
dc.subjectPrymnesium parvumen_US
dc.subjectLepeophtheirus salmonisen_US
dc.subjectParamoeba peruransen_US
dc.subjectenvironmental DNA (eDNA)en_US
dc.subjectaquacultureen_US
dc.titleEnvironmental DNA: A New Low-Cost Monitoring Tool for Pathogens in Salmonid Aquacultureen_US
dc.typeJournal articleen_US
dc.typeTidsskriftartikkelen_US
dc.typePeer revieweden_US


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