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

Abstract Sequencing of environmental DNA (eDNA-seq) is an emergent new monitoring tool that promises to facilitate 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-seq to develop into a useful bio-monitoring tool it is necessary to (a) validate that sequence datasets derived from amplification of meta-barcoding markers reflect the true species’ identity and abundances in biological samples, and (b) establish a low-cost sequencing method to enable the bulk processing of environmental 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 pre-filtered and normal 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 eDNAseq detection in aquaculture. Based on amplicon-seq of the 18S SSU rDNA v9 region, we found that Illumina and Ion Torrent were equally good in identifying the two parasite species (Lepeophtheirus salmonis and Paramoeba perurans), 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 were also equally able to reflect 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 correct abundances of 4 out of 5 species in samples from unfiltered seawater, despite the significant amount of background noise from both bacteria and eukaryotes. Our findings indicate that eDNA-seq offers significant potential in the monitoring of species harmful to aquaculture and for this purpose, the low-cost Ion Torrent sequencing is equally as accurate as Illumina.