Language selection


Temporal assessment of organic loading from finfish aquaculture on hard bottom communities in Newfoundland



Fisheries and Oceans Canada (DFO) developed and implemented the Aquaculture Activities Regulations (AAR) to clarify conditions under which aquaculture operators may treat their fish for disease and parasites, as well as deposit organic matter (i.e., uneaten feed and faeces). These regulations permit aquaculture operators to deposit organic matter and treatments within certain restrictions while avoiding, minimizing, and mitigating potential impacts of aquaculture on fish habitat and on commercial, recreational and Aboriginal fisheries. In support of the AAR, there is a need to evaluate monitoring standards and protocols for biochemical oxygen demanding (BOD) deposits (i.e., organic matter) in locations where it is not possible to collect sediment samples (i.e., hard-bottom substrates). So far, research findings had suggested that video (i.e., visual) monitoring should be the primary tool for environmental assessment; however, a better understanding of its limitations is necessary.
To assess the impacts from unconsumed fish feed and fish faeces on the benthic community, video monitoring data was validated with information on the benthic community. Samples of the waste that builds up under finfish farm net-pens was collected and analyzed for changes in fauna and flora, and specifically for the presence or absence of indicator species (i.e., Polychaete worms and bacterial mats) known to occur near finfish farms. The study also evaluated the use of remote video survey methods (ROVs) for monitoring benthic impacts, based on the protocol used in British Columbia. The results from this study support the development of science advice on the best practices for monitoring the effects of finfish aquaculture on the hard bottom benthic community.


Finfish aquaculture production was associated with the presence of bacterial mats and opportunistic polychaetes, two performance indicators that can be visually detected and are not found at reference sites. Bacterial community composition was determined via 16S rRNA gene sequencing under a hard-bottom aquaculture site in Newfoundland. Flocculent matter was composed of the genera Spirochaeta (12%), Prolixibacter (5.6%) and Marinifilum (4.6%). Bacterial mats were not composed of Beggiatoa as hypothesized, but instead were dominated by the genera Prevotella (21%), Odoribacter (20%), Spirochaeta (15%), and Meniscus (11%). In addition, bacterial composition analysis revealed four clusters, three of which (defined as "recently disturbed," "intermediate impact," and "high impact") differed markedly from a fourth "low impact" cluster that contained far-field samples collected >500 m from cages. Samples within the high impact group were most often collected directly under cages, whereas those in the intermediate impact group were mainly sampled from 20 to 40 m from cages. Large scale phylum shifts and a decline in bacterial diversity were observed in the high impact cluster, indicating significant ecological change. Samples from sites of different fallow duration were found in the high impact cluster, indicating incomplete recovery, even after 35 months of fallowing. Our results suggested that effects can be accurately tracked using bacterial community profiles or specific biomarkers. In addition to the identification of bacteria, our results showed that the chemical signature of the samples confirms that copper (Cu), zinc (Zn), calcium (Ca) and phosphorus (P) present around fish cages, are direct markers of aquaculture wastes. Persistence of two pyrethroids, one avermectin, and one antibiotic in grab samples showed a potentially lasting association between these chemicals and the organic matter from fish feed and wastes, even after 2 years. Overall, the concentrations measured did not indicate a direct lethal toxicity on marine organisms (as per studies described in literature) except for Zn. Nevertheless, the long-term persistence of a flocculent mixture rich in chemicals and the lack of information on sublethal and synergistic effects on hard-bottom communities calls for caution and additional studies.


Verhoeven J., Dufour S., Salvo F., Hamoutene D., 2016. The bacterial community composition of flocculent matter under a salmonid aquaculture site in Newfoundland, Canada. Aquaculture Environmental Interactions 8:637-646 - DOI:

Hamoutene, D., F. Salvo, S. Egli, A. Modir-Rousta, R. Knight, G. Perry, C. Bottaro and S. Dufour. Measurement of Aquaculture Chemotherapeutants in Flocculent Matter Collected at a Hard-Bottom Dominated Finfish Site on the South Coast of Newfoundland (Canada) After Two Years of Fallow. Frontiers in Marine Science 5 (2018): 228.

Verhoeven J.T.P., Salvo F., Knight R., Hamoutene D., Dufour S.C., 2018. Temporal Bacterial Surveillance of Salmon Aquaculture Sites Indicates a Long Lasting Benthic Impact With Minimal Recovery. Front. Microbiol. 9:3054. DOI:

Program Name

Program for Aquaculture Regulatory Research (PARR)


2015 - 2018

Principal Investigator(s)

Dounia Hamoutene
Research Scientist, Aquaculture Section, Northwest Atlantic Fisheries Centre
80 East White Hills Road, St. John’s, Newfoundland and Labrador

Team Member(s)

Flora Salvo

Pierre Goulet

Dwight Drover

Kimberly Burt

Jon Grant, Department of Oceanography, Dalhousie University

Jeffrey Barrell, Department of Oceanography, Dalhousie University

Suzanne Dufour, Memorial University of Newfoundland

Robert Sweeney, Sweeney International Marine Corp. and SIMCorp Marine Environmental

Date modified: