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The feasibility of using bacterial community profiling with next-generation DNA sequencing to assess temporal and spatial environmental disturbances from finfish aquaculture in the Bay of Fundy



Figure 1. Photograph of remotely operated vehicle (ROV) used for sampling benthic bacteria

Changes to marine habitats from organic loading associated with finfish aquaculture activities is reflected in the species diversity and the physiological traits of the resident organisms, ranging from bacteria to large mobile marine animals. At the time of the study, Aquaculture Management had indicated that its management threshold for organic loading impacts from aquaculture is no greater than a 50% biodiversity loss. This is measured using proxy indicators of the benthic sediment oxic state via sulfides.

This project tested the concept that benthic conditions can be easily and cost-effectively monitored via bacterial population diversity using the latest DNA sequencing technology. This technology is beginning to be adopted internationally and setting new standards for environmental monitoring. If this technique can detect benthic biodiversity changes associated with aquaculture activities, it could be applicable to all bottom types, in all depths of water. The approach obtains samples from the very surface layers of the sediment where the turnover of bacteria can be very rapid and will allow a view of the current environmental conditions of the bottom. This hypothesis was tested in the Bay of Fundy to develop an understanding of the spatial and temporal limitations of this technique.


Bacterial community profiling, using DNA screening, showed distinct patterns of bacterial communities between Atlantic Salmon farms and reference sites in the Bay of Fundy, New Brunswick. The spatial pattern of bacterial communities was consistent with what is known about the dispersion of organic wastes and their contribution to the oxygen levels on the seafloor. Anaerobic bacteria, which tend to thrive in anoxic and hypoxic environments, were denser near aquaculture activities compared to reference sites.

Differences in the bacterial community and the biological activity of bacteria in the seabed were also detected between seasons (September and January). The decline in the bacterial community between September and January was likely reflecting the much lower temperatures and reduction in overall productivity.

The use of ATP to assess biological activity of the seabed was also very successful. There was a rapid and significant decline in ATP along a transect away from the farm and biological activity appeared to reach normal levels by 50 m. There was also a decline in the biological activity between September and January.

This study successfully demonstrated that bacteria could be effectively sampled and easily identified in a timely manner to provide information on biological impacts to marine ecosystems in relation to aquaculture. It brought a much-needed biological component into the assessment toolbox and provided a large amount of data that can be used for different management applications ranging from ecosystem impacts from anthropogenic activities, to fish health to climate change.


Frühe, L., Dully, V., Forster, D., Keeley, N.B., Laroche, O., Pochon, X., Robinson, S.M.C., Wilding, T., Stoeck, T. 2021. Global trends of benthic bacterial diversity and community composition along organic enrichment gradients of salmon farms. Frontiers in Microbiology 12:637811. doi: 10.3389/fmicb.2021.637811

Program Name

Program for Aquaculture Regulatory Research (PARR)


2016 - 2017

Principal Investigator

Shawn Robinson
Research Scientist, Fisheries and Oceans Canada, St. Andrews Biological Station, Maritimes Region

Team Member

Ben Forward, New Brunswick Research and Productivity Council

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