Scientific research on farmed salmon

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Science is the key to an environmentally sustainable aquaculture industry. In recent decades, Fisheries and Oceans Canada scientists and researchers have initiated or participated in an impressive number of research activities, some of which are listed below, related to all aspects of the salmon farming industry – from selective breeding to waste dispersion – as well as the health and safety of farmed salmon, fish feed, and the marine environment.


Within a three year study, researchers aim to determine the effect of rearing on the physiology and behaviour of smolt by comparing smolt captured in Fundy National Park reared in a saltwater facility (sea pens) with those reared in a freshwater facility (Mactaquac Biodiversity Facility) for future management applications.

Funded in part through the Aquaculture Innovation and Market Access Program, the Aquaculture Engineering Group inc. established a small finfish aquaculture operation in St. Mary’s Bay, Nova Scotia to test and demonstrate sustainable technologies for salmon farming. On the farm, the AEG Feeder provides stock with pulse-feeding capability, while AquaSonar technology and the AEG Feeder provide daily fish size updates. The AEG site management software application Neptune is also being used to evaluate daily smolt size data for superior feed management and market planning.

From 2004 to 2007, researchers in New Brunswick investigated the feasibility and cost-effectiveness of several potential early warning approaches for predicting harmful phytoplankton blooms at salmon farms. The study examined threshold concentrations of selected harmful phytoplankton species, spatial and temporal original of water (which could transport phytoplankton blooms) entering salmon farms, the effectiveness of a light sensor array for bloom detection, and the usefulness of satellite imagery for bloom detection.


Molecular mapping and gene microarray technology are being used by researchers to enhance molecular genetic capabilities for Chinook salmon. Investigation is focused on carotenoid pigment deposition in flesh as a major trait system, but also monitoring growth rate, survival, and age of maturation within the experiments.

Integrated multi-trophic aquaculture

The idea of growing finfish, shellfish, and marine plants together for the benefit of the environment and all three crops is known as integrated multi-trophic aquaculture or polyculture. Canadian researchers are studying various aspects of this model with the rearing of blue mussels and kelp near pre-established Atlantic salmon aquaculture sites in the Bay of Fundy. Research is also underway in British Columbia.



Genetic tools are being used by researchers to develop a strain of Northern Chinook Salmon for culture. Results from this study identified eight polymorphic microsatellite markers to enable a cost-effective analysis of northern BC and Yukon Chinook Salmon strains. These analyses indicated that although individual year classes had low diversity, the combined live broodstock (all year classes) and domesticated frozen milt inventory was as diverse as other domesticated strains.

A collaborative team of researchers is using genetic markers to determine which offspring produced by a disease-resistant family of Atlantic salmon have inherited the disease-resistant alleles. They are also testing whether genomic selection can improve growth rate in saltwater, rapid adaptation to seawater, disease resistance, and delayed sexual maturity more rapidly that the conventional breeding program currently used by a New Brunswick aquaculture company.

Canadian Aquaculture R&D Review 2013 article: “Performance selection and broodstock development program for Atlantic Salmon for use in commercial saltwater aquaculture production on the East Coast of Canada

A research project was coordinated in 2008 to transfer expertise in cryopreservation techniques for salmon milt to staff and technician training at the BC Centre for Aquatic Health Sciences in order to prepare for commercial application trials.

Researchers developed a cost-effective suite of 6-10 microsatellite loci (highly polymorphic co-dominant genetic markers) to estimate family relatedness among Chinook salmon individuals without tags. The research is part of an ongoing selective breeding program.

Between 2007 and 2010, a project was also undertaken to develop and apply a suite of variable genetic markers to cultured Coho Salmon for use in selective breeding programs.

A multi-disciplinary research team examined a number of hatchery production protocols in order to determine methods and techniques to improve handling of Atlantic Salmon eggs and increase survival of the eggs. As part of the study, mathematical models of embryonic development of the salmon were incorporated into a fish culturing computer program called WinSIRP.

Researchers in British Columbia conducted a series of tests to show that low oxygen levels have a direct impact on broodstock by increasing pre-spawning mortality, influencing the release of sex and stress hormones during the maturation process, and reducing egg production and viability. The adverse influence of high-water temperature during maturation, as well as carbon dioxide build-up in broodstock was also examined.

To improve the competitiveness of the Atlantic coast salmon aquaculture industry, a project was undertaken to supply farmers with access to disease-free ova as seedstock from the best strains. The disease-free ova were developed by applying land-based broodstock methods.


The release of nitrogenous wastes, principally ammonia, into the environment can have environmental, financial and regulatory implications. This project will explore how feed regimes designed to stimulate compensary growth (the increase in growth that occurs when an animal is fed at normal levels following a period of environmentally-induced slow growth) may be used to reduce nitrogen excretion into the environment during Chinook Salmon production.

Researchers evaluated the potential health benefit and growth effects in Atlantic Salmon fed with novel fish-feed formulations supplemented with specific by-products. DNA microarrays were used to measure the global gene expression response, as well as specific gene response to oxidative stress, inflammation, immunity, lipid and metabolism to try to identify the most promising marine by-products.

Between 2005 and 2008, a field trial was conducted to show that alternative diets using poultry fat, canola oil, or blends of these lipids to significantly replace fish oil and maintain adequate flesh levels of n-3 highly unsaturated fatty acids. The alternative diets indicated that contaminant concentrations can be decreased by up to 10 times, while maintaining the fatty acids known to have human health benefits. Subsequent research in this area was undertaken to develop a model to predict contaminant burden and fatty-acid content in farmed salmon based on the composition of their diets.

Researchers conducted a two-phased nutrition study on post-smolt Atlantic Salmon to dramatically reduce flesh concentrations of persistent organic pollutants to the lowest levels seen in wild salmon by feeding the fish diets based on plant and/or animal lipids and, in two cases, plant protein concentrates with contaminant-reduced fish oil. The second objective of the research was to re-instate flesh concentrations of fatty acids of importance for human health to levels observed in wild salmon

A four-month study confirmed that farmed Chinook Salmon derive significant benefits from astaxanthin being added to their feed, such as enhanced survival and antioxidant function. The study was designed mainly to draw comparisons between natural- and synthetic-source astaxanthin as flesh-pigmenting materials for post-smolt Chinook, looking at factors such as industry costs, as well as health and growth benefits, to respond to increasing demand from fish farmers for antioxidants derived from natural sources.

A nutrition study was undertaken to determine how the inclusion of different concentrations of canola oil (replacing anchovy oil) in the diets of spring Chinook Salmon affected the growth, health, ionoregulatory development, sea water tolerance, swimming performance, and whole body and lipid composition of the fish before and after transfer into sea water. The results indicated that canola oil was an excellent replacement for anchovy oil.

Two types of experimental fish protein hydrolysates (FPH) prepared from Pacific hake, along with two commercially prepared FPH’s, and a krill product were tested on juvenile Chinook Salmon over 35 days for their feed attractant qualities.

Grilse / Maturation

Early maturation of farmed fish results in lost production and higher costs to farmers.

A DFO-industry project team investigated the levels of melatonin observed in salmon under natural lighting photoperiods in the Bay of Fundy region and under manipulated photoperiods through the use of artificial lighting. The research sought to determine the effectiveness of lighting regimes in reducing melatonin levels and to give insight on how grilse rates might be further reduced. An economic benefit analysis of the improved growth and delayed maturation due to the use of an artificial photoperiod showed savings of up to $100,000 per cage.

Research was undertaken to develop and standardize a simple, cost-effective assay for measuring levels of insulin-like growth factor and the level of grilsification in Atlantic Salmon. As part of the project, growth factor levels were also studied in production fish several months before harvest, as well as in broodstock fish, to assess the application of the assay for predicting grilse before the on-set of early maturity.


Beginning in 2004, a three-phased project sought to inform the amendment of British Columbia’s aquaculture waste control regulations regarding farm sites located over hard-seabed substrates. In phase one, video imagery was recommended as the most effective tool for operational monitoring. Phase two reviewed marine environmental video monitoring methods, developed video data interpretation and classification protocols, and conducted field survey trials. Phase three involved working with stakeholders and regulators to amend the regulations.

Potential effects on wild fish and shellfish and/or the freshwater environment

Using high-definition videos and still photos along constant depth contours for a distance up to 1 kilometer from farm net pens, researchers sought to identify methods for monitoring, quantifying, and evaluating potential impacts to hard-bottom substrates to inform ecosystem-based environmental regulation and decision making.

Researchers are reviewing existing regional reports that sought to identify and map sensitive fishery areas in southwest New Brunswick in relation to aquaculture in the 1990s and early 2000s. The purpose of this review is to complete two draft technical reports on approaches to aquaculture site monitoring in relation to habitat suitability and sensitivity for invertebrate resources.

A team of researchers set out to produce a series of two-dimensional GIS-based maps to describe: the spatial distribution of aquaculture sites; potential zones of aquaculture impact; disease plumes from salmon farms; and the distribution of major fishery resources and activities in the coastal zone of southwest New Brunswick. The maps were expected to determine site-specific and cumulative overlaps between aquaculture sites and their zones of potential influence with respect to disease and waste dispersion with major resources and harvesting activities.

“Groundtruthing” techniques were used by researchers on a former aquaculture site to identify distinct regions of seafloor. The techniques may provide a steering tool for sampling designs associated with benthic monitoring programs.

The presence of an aquaculture cage site under study did not appear to displace harbour porpoise from the Bay of Fundy are except during short intervals when high disturbance activities such as food delivery by barge or cage clearing took place.


To investigate the fate of wastes associated with fish farming and the potential influences on benthic communities at sites on the south coast of Newfoundland, a three-year study to validate DEPOMOD was initiated in 2010. Data was collected using sediment traps along transects extending from an Atlantic Salmon farm and a rainbow trout farm. Model predictions will be compared to the observed organic flux.

A multi-year investigation was undertaken to determine whether natural carotenoid pigments, astaxanthin and canthaxanthin, added to salmon feed may be found in wild species living near salmon cage sites. Initial results showed that canthaxanthin can be detected in the reproductive and digestive tissues of several species (crab, lobster, sea urchins). However, this pigment was not detected in the same species collected four to six kilometers away from the sites. The pigment astaxanthin, by contrast, was found at low levels in all samples, both near and far from the cages. While these pigments have not been shown to harm wild species sampled, the study of canthaxanthin’s distribution through the ecosystem may provide a valuable tool to objectively evaluate how aquaculture activities interact with the environment.

Predicting the dispersal of feed pellets and fecal waste through the use of hydrodynamic modeling is necessary to estimate the benthic zone of influence surrounding farm systems. It also helps with site selection and provides research and monitoring tools for regulating the aquaculture industry. In order to accurately validate the hydrodynamic models, researchers carried out lab flume experiments to determine traction thresholds and transport rates of various feed and fecal matter.

Drawing mini slo-corer (Photo: G. Morton)
Drawing mini slo-corer (Photo: G. Morton)

New tools for parameterizing the erodibility of aquaculture wastes and their associated contaminants were developed by a research team for use in predictive models and as far-field indicators.

To identify a reliable and precise method of tracking the fate of aquaculture wastes, studies in British Columbia and New Brunswick looked at stable isotopes, trace elements (copper and zinc), pigments, pesticides, antibiotics, and secondary effects on wild populations.

Researchers evaluated the effectiveness of DEPOMOD and dissolved oxygen models as cause and effect tools for relating farm production waste to benthic deposition and oxygen depletion in the vicinity of fish farms within the macro-tidal environment of the Bay of Fundy.

A trial to evaluate the efficacy of using an airlift feed collector to collect and re-suspend uneaten food pellets back to salmon cages in Newfoundland, as well as the effect of this technique on fish performance and feed conversion, was conducted between 2007 and 2009. The trial was part of an overall evaluation of the environmental effects of reduced feed wastage on the seabed under salmon cages.

Example of the aquaculture waste impact model DEPOMOD simulation showing the predicted footprint of deposition (g Carbon/m2/d) beneath and around a hypothetical fish farm site.

A project undertaken during 2004 and 2005 successfully demonstrated the utility of the waste model DEPOMOD in predicting the effect of marine cage finfish farms on near-field seabed conditions. A second project was undertaken between 2005 and 2007 to: further validate the model at different sites; determine waste feed rates; assess carbon concentration in feed and fecal material; investigate the importance of re-suspension processes; and determine cage movement due to currents and winds.

Researchers assessed the effects of varying levels of organic enrichment associated with aquaculture activities on benthic meiofaunal assemblages in a sub-tidal setting across a range of ocean bottom substrates within the Broughton Archipelago. Certain meiofaunal groups, such as kinorhynchs, crustaceans, and polychaetes showed sharp declines in abundance with increasing free sulfide concentration, while other groups, such as nematodes and foraminifera, showed a general decline.

Scientists examined how different feed pellets react to different water flows to try to populate a chart or matrix of what different sizes and types of fish-feed pellets do once they have passed through the fish pens and settled on the ocean floor. The resulting matrix of predictions would then be used in conjunction with the farm-footprint modeling system, DEPOMOD.

Research in the Bay d’Espoir area of Newfoundland was undertaken to establish the infrastructure and foundation for an oceanography program to collect and model physical environmental data. Information collected will be used to map the environmental parameters and potential zones of influence for future use in establishing production management areas.


Researchers are presently engaged in a project that seeks to answer the question of mating success between farmed mature Atlantic Salmon and wild spawners from Newfoundland river stocks. As part of the research, fertilization rates and gamete quality will be assessed in both farmed and wild mature fish and crosses will be completed to evaluate fertilization and hatch rates. The effect of water quality will also be tested to better understand the potential reproductive effect of salmon escapes from local farms on wild spawners in their natural environment.


The Aquaculture Innovation and Market Access Program provided funding to Shorelink Enterprises for the development of an innovative, environmentally friendly, efficient, economically viable, and modular anti-fouling technology for fish pen nets. The Aquamax Net Manager is a transportable net cleaning system moved by vessel or barge from aquaculture site to aquaculture site, which does not require cage nets to be removed from the water for cleaning.

Animal health

This four-year study aims to determine the necessary background information needed to access what role, if any, salmon farming play as a source of pathogens for wild juvenile salmon.

Researchers are examining the effects of reduced oxygen (natural and culture-induced inshore hypoxia) on Atlantic Salmon growth and immune system functions

A two-year study conducted in vitro and in vivo experiments on farmed salmon in Newfoundland to learn more about fish immunity and physiology during environmental stressors such as hypoxia.

Clinical field trials were conducted on Atlantic cod and Atlantic Salmon injected with vaccines to provide industry with information on growth, survival, and carcass characteristics so they could critically evaluate the potential for adverse effects of adjuvants contained in different vaccines.

Infectious Salmon Anemia Virus (ISAv)

A hypothetical three-dimensional model of the ISA disease dynamic was refined by researchers by conducting additional viral quantitative testing on salmon infected by the HPR4 strain of the virus in 2006. A better understanding of the disease dynamic is expected to inform an optimized surveillance program.

A multi-disciplinary team of researchers proposed a novel approach for vaccines using recombinant ISA virus protein subunits combined in vivo to fish heat shock proteins. Heat shock proteins are abundant in cells and one of their functions is to present antigenic peptides to the immune cells to trigger an immune response. Complementary research also sought to develop a novel form of vaccine based on the RNA interference mechanism, which works by transfecting fish cells with small RNA molecules that act as guides in targeting and destroying pathogens. In addition, research is being undertaken between 2009 and 2013 to test a plasmid construct expressing ISA virus protein subunits combined to a heat shock protein binding sequences, as well as a novel RNA interference-based vaccine.

Scientists used a genomic approach to better understand the diversity of ISA virus and to relate this diversity to responses for infection, the development of disease, and the recovery from (or resistance to) clinical disease. Subsequent research used DNA microchips to better understand the short- and long-term immune response of Atlantic Salmon to ISA and to identify genetic markers of this response. In addition, DNA microarray and ‘quantitative real-time polymerase chain reaction’ assays were used to study the global gene expression responses of naturally immunized Atlantic Salmon during the course of a new infection with a highly virulent ISA virus isolate.

Researchers also worked to determine the virulence differences between ISA virus strains so that: rapid economical and improved assays for the differential strains in routine surveillance programs could be developed; and intelligent and cost-effective management of the disease could occur. In 2008, researchers analyzed detailed mortality data for ISA-infected and uninfected fish for two year-classes of fish to learn more about the impact of different ISA virus strains on fish in the field and to help inform fish health decisions. Complementary research also used salmon DNA chips to study the immune response and global gene expression patterns in fish following exposure to either HPR2- or HPR4-type isolates of ISA virus.

Infectious hematopoietic necrosis virus

Scientists at the Pacific Biological Station established IHN virus challenge models and developed ultra-filtration methodologies that allow for the concentration of viruses from large volumes of water to facilitate the determination of the minimum infectious dose as well as viral shedding rates. Using these established methods, research was undertaken to provide quantitative estimates of these parameters for Atlantic Salmon post-smolts under controlled experimental conditions. Based on results, the study team will begin to establish a viral dispersal model and assess transmission risk of IHN virus in Atlantic Salmon net pen aquaculture.

The effectiveness of the APEX-IHN® vaccine was evaluated under conditions equal to, or more severe than, a natural field challenge to inform the disease management strategies and husbandry practices of salmon farmers.

The BC Centre for Aquatic Health Sciences piloted the application of rapid detection diagnostic methods (quantitative polymerase chain reaction) for salmon farms in British Columbia.

Epidemiological investigations have been useful in identifying potential mechanisms of IHN virus transmission and have led to implementation of effective IHN biocontainment strategies on farm sites. But to interrupt the disease cycle, vaccines are required in addition to existing good fish health management practice tools. Researchers thus tested the efficacy and duration of protection of an inactivate IHN vaccine administered in combination with a multivalent bacteria vaccine routinely used by the industry.

A multi-disciplinary team also tested the reliability of the 'reverse transcriptase polymerase chain reaction' assay for IHN virus detection to determine its utility for shorter diagnosis time, which would permit earlier management changes to reduce the spread of disease. Complementary research in this area was undertaken to develop a 'quantitative reverse transcription polymerase chain reaction' assay as quantitative methodologies as a diagnostic test are replacing more traditional methodologies.

Research on the genetic factors which influence the resistance of various salmon species to IHN indicated that differences in IHN susceptibility in salmon may result from species-specific differences in the ability to prevent the virus from entering host cells, rather than the overall strength of immune response.

Loma salmonae (gill parasite)

ELISA, an enzyme-linked immunosorbant assay, was developed by researchers to use as a diagnostic tool for the detection and quantification of Loma salmonae infection in Chinook Salmon. This technology uses highly sensitive and specific antibodies for pathogen detection. Between 2010 and 2013, the state of development of ELISA assays for the detection of antibodies against other viral pathogens, such as ISA and viral hemorrhagic septicemia will also be evaluated for future use.

Researchers worked to develop a recombinant subunit vaccine for Loma salmonae by generating a subtractive cDNA library using both infected and uninfected gill tissue and then, using the library to identify parasite proteins most likely to provide immunity.


Between 2004 and 2006, field trials to the Bay d’Espoir strain of Aeromonas salmonicida subpecies were undertaken at salmon farms in the Newfoundland area using the results of laboratory studies conducted in 2003 and 2004.

Sea lice

Sea lice infection is an animal health issue for both wild and farmed salmon. Numerous research activities have been undertaken by researchers to understand sea lice, their relationship to the marine environment and fish, and the treatments and methods used to reduce their abundance near wild and farmed salmon species.

Product quality

Without ultra-violet radiation exposure, salmon show higher fin-fraying. A team of researchers studied the effects of stocking densities and UV-radiation with various species of Chinook over a three-year period, as well as possible mechanism for the apparent protective effect of UV-radiations on fin health.

Findings from extensive research on the presence of environmental contaminants in the flesh of three species of farmed salmon and five species of wild salmon from coastal BC indicated that current levels of major contaminants in both wild and farmed species are below the recommended levels of concern for human health.

Kudoa thyrsites

While k. thyrsites does not pose fish health risks, this intramuscular parasite affects product quality by causing pitting and softening of fish muscle tissue after harvest.

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