Using eDNA to Track Microbial and Meiofaunal Communities in the Environment Surrounding Coastal Finfish Aquaculture in Nova Scotia

Abstract

Finfish aquaculture has increased globally in recent years, leading to concerns about effects on the surrounding environment. Traditionally used biological environmental monitoring techniques are often time consuming and expensive, therefore eDNA has been investigated as an alternative method for monitoring the biological communities around aquaculture farms. The work described in this thesis looks at using three molecular techniques: amplicon sequencing, shotgun metagenomic sequencing, and qPCR to study eDNA in the sediment and water column around fish farms off the coast of Nova Scotia. Results from amplicon and shotgun metagenomic sequencing were able to show how sediment communities changed with farm production and fallowing, and also identify potential indicator taxa for organic loading. qPCR assays for Alexandrium sp. were able to confirm its presence in sediments, though further optimization is needed to produce reliable results. Overall, these results show the potential eDNA provides for monitoring the environment around finfish aquaculture sites.