Environmental DNA: A New Low-Cost Monitoring Tool for Pathogens in Salmonid Aquaculture

Overview
TitleEnvironmental DNA: A New Low-Cost Monitoring Tool for Pathogens in Salmonid Aquaculture
AuthorsPeters L, Spatharis S, Dario MA, Dwyer T, Roca IJT, Kintner A, Kanstad-Hanssen Ø, Llewellyn MS, Praebel K
TypeJournal Article
Journal NameFrontiers in microbiology
Volume9
IssueN/A
Year2018
Page(s)3009
CitationPeters L, Spatharis S, Dario MA, Dwyer T, Roca IJT, Kintner A, Kanstad-Hanssen Ø, Llewellyn MS, Praebel K. Environmental DNA: A New Low-Cost Monitoring Tool for Pathogens in Salmonid Aquaculture. Frontiers in microbiology. 2018; 9:3009.

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 (

Properties
Additional details for this publication include:
Property NameValue
Journal CountrySwitzerland
Publication TypeJournal Article
Language Abbreng
LanguageEnglish
Elocation10.3389/fmicb.2018.03009
DOI10.3389/fmicb.2018.03009
Journal AbbreviationFront Microbiol
Publication Date2018
pISSN1664-302X
ISSN1664-302X
Publication ModelElectronic-eCollection
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PMID: PMID:30581425