Finfish aquaculture has increased globally in recent years, raising concerns about the effect on the surrounding environment. Traditional biological monitoring techniques such as polychaete counts and percent coverage of the sulfur-oxidizing Beggiatoa sp. are often time-consuming and expensive, therefore eDNA is being investigated as an alternative method for monitoring the biological communities around aquaculture farms. A combined metabarcoding and metagenomic approach was used here to characterize the microbiota and meiofauna in sediments and water column samples collected around a fish farm off the coast of Nova Scotia. To provide a complete overview of the benthic and pelagic environments, changes in both sediment and water column communities were analyzed and compared to determine the main trends of the fallowing process at this specific finfish farm. Sampling for this study took place intermittently from July 2018 – November 2019 at the Cooke Aquaculture facility’s McNutt’s site outside of Shelburne, NS, which houses between 19-20 cages of Atlantic salmon (Salmo salar). During this time the farm was fallowed from approximately November 2018 – June 2019, allowing a separation of the samples into three categories: production cycle 1, mid-fallowing, and production cycle 2.
Results from metabarcoding showed that the water column community was influenced more by seasonal trends in temperature and water column mixing as opposed to the farm production cycle. nMDS plots showed that samples clustered tightly by sampling day regardless of the state of the farm, demonstrating a seasonality to both the prokaryotic and eukaryotic microbial communities. Given the farm site location, close to the open ocean, the strong seasonal cycle occurring in the water column was similar to what is observed for the microbial communities of the coastal North Atlantic Ocean. Unlike the water column, the beta diversity of benthic communities displayed significant differences between the 3 sample types (cage, buoy, barge), which showed a pattern connected to farm production as well as the location on the farm. Both the metabarcoding and metagenomics approaches tracked changes in the microbial and meiofaunal communities as the farm transitioned from production to fallowing, and into the subsequent production cycle. Potential indicator species of the sediment organic loading status were: Monhysterid nematode worms and sulfur metabolizing bacteria Sulfurovum and Desulfobacteraceae.