Fine-scale differences in eukaryotic communities inside and outside salmon aquaculture cages revealed by eDNA metabarcoding

Abstract

Aquaculture impacts on marine benthic ecosystems are widely recognized and monitored. However, little is known about the community changes occurring in the water masses surrounding aquaculture sites. In the present study, we studied the eukaryotic communities inside and outside salmonid aquaculture cages through time to assess the community changes in the neighbouring waters of the farm. Water samples were taken biweekly over five months during the production phase from inside the cages and from nearby points located North and South of the salmon farm. Eukaryotic communities were analyzed by eDNA metabarcoding of the partial COI Leray-XT fragment. The results showed that eukaryotic communities inside the cages were significantly different from those in the outside environment, with communities inside the cages having higher diversity values and more indicator species associated with them. This is likely explained by the appearance of fouling species that colonize the artificial structures, but also by other species that are attracted to the cages by other means. Moreover, these effects were highly localized inside the cages, as the communities identified outside the cages, both North and South, had very similar eukaryotic composition at each point in time. Overall, the eukaryotic communities, both inside and outside the cages, showed similar temporal fluctuations through the summer months, with diversity peaks occurring at the end of July, beginning of September, and in the beginning of November, with the latter showing the highest Shannon diversity and richness values. Hence, our study suggests that seasonality, together with salmonid aquaculture, are the main drivers of eukaryotic community structure in surface waters surrounding the farm.

Maximizing sampling efficiency to detect differences in fish community composition using environmental DNA metabarcoding in subarctic fjords

“…Many studies have now confirmed the strengths of eDNA metabarcoding for local detection of species and, thus community composition inference (Hansen et al, 2018). Similarly to analogous studies (Cilleros et al, 2019; Fraija‐Fernández et al, 2020; Jeunen, Knapp, et al, 2019; Jo et al, 2019; Larson et al, 2022; Li et al, 2021; Turon et al, 2022), our eDNA metabarcoding study confirm that fish community composition and biodiversity patterns can be reliably estimated using this approach.…”

High resolution longitudinal molecular and morphological tracking of planktonic threats to salmon aquaculture: new candidates and old players

“…Custom demultiplexing of internal and external barcodes was undertaken using a combination of flexbar (Dodt et al, 2012; Renaud et al, 2015) and deML (Renaud et al, 2015). Operational taxonomic units OTUs were identified and assigned to taxonomy from demultiplexed samples using the MJOLNIR pipeline (https://github.com/uit-metabarcoding/MJOLNIR) as in (Turon et al, 2022). MJOLNIR implements a variety of programs from the OBITOOLS package (Boyer et al, 2016) for sequence preprocessing and taxonomic assignment as well as VSEARCH (Rognes et al, 2016) and SWARM (Mahé et al, 2022) for chimera detection and OTU clustering respectively.…”

Environmental DNA as a Tool for Better Understanding the Distribution, Abundance, And Health of Atlantic Salmon and Pacific Salmon

“…These investigations consistently found evidence that benthic microbial diversity, as measured from eDNA metabarcoding of bacteria and other organisms, is inversely related to organic enrichment and other impacts from aquaculture. Another investigation used eDNA metabarcoding to assess the eukaryotic communities within salmon pens off the coast or Norway relative to the nearby marine environment (Turon et al 2022). In contrast to observed trends in benthic microbial diversity, researchers found evidence that eukaryotic eDNA diversity was higher in water samples collected within salmon pens relative to those collected outside.…”

“…In contrast to observed trends in benthic microbial diversity, researchers found evidence that eukaryotic eDNA diversity was higher in water samples collected within salmon pens relative to those collected outside. This finding was attributed, at least partially, to the colonization of aquaculture structures by various taxa, such as brown algae and jellyfish (Turon et al 2022).…”