Data from: Impacts on microbial communities in sediment by aquaculture farming during one salmon cycle

In recent years, the salmon farming industry has grown significantly
worldwide, and in the Faroe Islands, it has become a major industry with
an annual production of over 94,000 tonnes, yielding 24% of the GDP.
According to environmental regulations, the ocean floor is monitored
during every production cycle at all farming sites, involving macrofaunal,
sensory, and chemical analyses. However, the impact of farming activity on
microorganisms in the Faroe Islands remains unknown. This study aimed to
assess the impact of Atlantic salmon farming on benthic microbial
communities, giving a better understanding of the effects on the
foundation of the benthic food web and to assess if these are more prone
to environmental impact than traditional macrofaunal biomonitoring.
Sediment cores were sampled along a transect from directly below the
salmon cages to a background reference site. The sampling occurred prior
to the release of salmon into the cages (‘before stocking’) and
immediately before the salmon were harvested (‘peak biomass’). The 16S
rRNA (V4-V5) gene was sequenced on an Illumina MiSeq from our sediment
samples at the surface, 3 cm, and 10 cm depth. Significant shifts in
microbial community composition were observed between ‘before stocking’
and ‘peak biomass’, as well as between different depth layers. Microbial
diversity increased with increasing distance from the cages and was at its
highest ‘before stocking’, indicating a significant impact of the salmon
farming on the microbial community structure. In contrast to the regularly
executed environmental monitoring, the results from this study showed an
impact on the sediments by the salmon farming, underlining the powerful
alternative of DNA-metabarcoding when biomonitoring an aquaculture area.