Environmental DNA: a new low-cost monitoring tool for pathogens in salmonid aquaculture

Peters, L., Spatharis, S. , Dario, M. A., Dwyer, T., Roca, I. J.T., Kintner, A., Kanstad-Hanssen, Ø., Llewellyn, M. S. and Praebel, K. (2018) Environmental DNA: a new low-cost monitoring tool for pathogens in salmonid aquaculture. Frontiers in Microbiology, 9, 3009. (doi:10.3389/fmicb.2018.03009) (PMID:30581425) (PMCID:PMC6292926)

Peters, L., Spatharis, S. , Dario, M. A., Dwyer, T., Roca, I. J.T., Kintner, A., Kanstad-Hanssen, Ø., Llewellyn, M. S. and Praebel, K. (2018) Environmental DNA: a new low-cost monitoring tool for pathogens in salmonid aquaculture. Frontiers in Microbiology, 9, 3009. (doi:10.3389/fmicb.2018.03009) (PMID:30581425) (PMCID:PMC6292926)

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Abstract

Environmental 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 (Lepeophtheirus salmonis and Paramoeba perurans) to species level, whereas the microalgae species Prymnesium parvum, Pseudo-nitzschia seriata, and P. delicatissima 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.

Item Type:Articles
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Llewellyn, Dr Martin and Dwyer, Ms Toni and Spatharis, Dr Sofia
Authors: Peters, L., Spatharis, S., Dario, M. A., Dwyer, T., Roca, I. J.T., Kintner, A., Kanstad-Hanssen, Ø., Llewellyn, M. S., and Praebel, K.
College/School:College of Medical Veterinary and Life Sciences > Institute of Biodiversity Animal Health and Comparative Medicine
College of Medical Veterinary and Life Sciences > School of Life Sciences
Journal Name:Frontiers in Microbiology
Publisher:Frontiers
ISSN:1664-302X
ISSN (Online):1664-302X
Copyright Holders:Copyright © 2018 Peters, Spatharis, Dario, Dwyer, Roca, Kintner, Kanstad-Hanssen, Llewellyn and Praebel
First Published:First published in Frontiers in Microbiology 9: 3009
Publisher Policy:Reproduced under a Creative Commons License

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Project CodeAward NoProject NamePrincipal InvestigatorFunder's NameFunder RefLead Dept
632234Funding SchemesAnna DominiczakWellcome Trust (WELLCOTR)105614/Z/14/ZRI CARDIOVASCULAR & MEDICAL SCIENCES
726761A microbial basis for Atlantic Salmon energeticsMartin LlewellynBiotechnology and Biological Sciences Research Council (BBSRC)BB/P001203/1LS - ANIMAL BIOLOGY
720071RCUK-CONICYT Mucosal health and microbiota during sea lice parasitism: effect of oral delivery of immunomodulantsMartin LlewellynBiotechnology and Biological Sciences Research Council (BBSRC)BB/N024028/1LS - ANIMAL BIOLOGY