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Canadian Aquaculture R&D Review 2009

Finfish - Salmon

Study to investigate protective effect of UV on fin abrasion

Now in its third year, a DFO co-funded study on the effects of ultra-violet radiation (UVR) on salmon fin abrasion is getting down to brass tacks. After two years of work with three strains of Pacific salmon, Dr. Max Bothwell of Environment Canada and Dr. Blair Holtby of DFO, will be narrowing their focus to one strain this year, and trying to determine the effect of stocking densities on a previously-demonstrated “protective” effect of UVR exposure in young salmonids.

The current work is being co-funded by DFO's Aquaculture Collaborative Research and Development Program (ACRDP) and Creative Salmon Company Ltd., a BC firm interested in improving the appearance and quality of chinook salmon for the high-end Japanese gourmet market.

A UVR paradox

Tank set-up at Sea Spring Hatchery. (Photo: Max Bothwell)

Juvenile Big Qualicum Chinook. (Photo: Max Bothwell)

UVR is a short- wavelength, high-energy component of natural sunlight that has long been demonstrated to have a variety of negative effects on living organisms. The current investigations began in 2007 when Max Bothwell decided to follow up on previous anecdotal observations of juvenile coho. Young fish reared indoors or under cover developed badly abraded fins, while those reared in open tanks outdoors or in shallow “free-run” flumes consistently did not. This went against conventional wisdom about the damaging effects of UV, a nagging paradox that could have important repercussions for hatchery operations. Preliminary work in flumes and Capilano troughs with populations of coho fry confirmed the protective effects of UV radiation and ruled out the involvement of pathogens.

The project began with Bothwell and his BC team performing UVR exposure trials on Big Qualicum chinook pre-smolts. They were astonished to find no measurable difference between exposed and sheltered populations, an indication that the previously noted “protective” effect of UVR on coho fins might be species- or strain-specific, dependent on timing, or due to unknown factors.

In 2008 the team ran expanded trials at the Sea Spring Hatchery in Chemainus, BC, using three different strains of salmon: Big Qualicum chinook, Big Qualicum coho and Yukon chinook. Tanks were covered with either UV-transparent or UV-opaque Plexiglass, and image analysis software was used to quantify fin damage. Both the Big Qualicum coho and the Yukon chinook showed significantly higher fin-fraying without UVR exposure. The Big Qualicum chinook continued to appear unaffected, regardless of exposure. With lower stocking densities in these trials, the effects were somewhat less pronounced than previous observations, but remained significant.

In this final year of the current ACRDP funding, work is underway at Sea Spring’s hatchery to investigate in more detail the effects of stocking densities and UV radiation with Yukon chinook, the strain that Creative Salmon is interested in developing for their Japanese markets. Bothwell also wants to study hormone responses mediated by the pineal glands of fish under different conditions, seeking a possible mechanism for the apparent protective effect of UVR on fin health.

Future studies would allow the team to relate protective response to gradients of UVR intensity, timing and duration, both indoors and outdoors, and identify the exact physiological mechanisms responsible for the protection from fin abrasion in UVR-exposed fish. This could translate into direct health benefits for hatcheries and improved product quality across the industry.

Downloading radiation exposure data in the field. (Photo: Max Bothwell)

Yukon chinook exposed to photoactive radiation (PAR) alone and to both PAR and ultraviolet radiation (UVR) show visible differences after five months. (Photo: Max Bothwell)

Duration: Jan ‘08 – Oct ’09.

Funded by: DFO-ACRDP. Co-funded by: Creative Salmon Co. Ltd.

Project team: Blair Holtby (DFO), Max Bothwell (Environment Canada), Ted Groves (Sea Spring Salmon Farm Ltd.), Jake Etzkorn (DFO)

Research team: Blair Holtby (DFO), Max Bothwell (Environment Canada), Ted. Groves (Sea Spring Salmon Farm Ltd.), Jake Etzkorn (DFO).

For information, contact: Blair Holtby (

Researchers identify genetic markers of the immune response to ISA

Infectious diseases present a significant economic burden to finfish aquaculture industries and there is concern that diseases may also negatively impact wild fish populations. Increasingly, genomic tools are being used to investigate diseases of fish and their causative agents and are beginning to provide scientists, clinicians and regulators with management options. Despite this, very little is known about the diseases and pathogens affecting Canadian finfish culture industries or adjacent wild populations.

(Photo: F. Leblanc)

Infectious salmon anemia virus (ISAV) is an important virus pathogen of salmonids and causes mass mortalities. It remains a recurrent problem in Eastern Canada and Maine since the initial epizootics of 1996.

This study is taking a genomic approach to the disease using DNA microchips to better understand the short and long term immune response of Atlantic salmon to ISAV and to identify genetic markers of this response. Validation of these genetic markers in vivo will provide tools to study disease and recovery from disease, resistance to clinical disease, or response to vaccination.

Duration: Jul ‘07 – Mar ’09.

Funded by: DFO-ACRDP. Co-funded by: New Brunswick Salmon Growers Association, DFO-GRDI.

Project team: Nellie Gagné (DFO), Mark Laflamme (DFO), Francis Leblanc (DFO), Kira Salonius (DFO), Nathalie Simard (DFO).

For information contact: Nellie Gagné (

Novel recombinant vaccine models against Infectious Salmon Anemia Virus (ISA)

Infectious salmon anemia virus (ISAV) is an important virus pathogen of salmonids and causes mass mortalities. It remains a recurrent problem in Eastern Canada and Maine since the initial epizootics of 1996.

Mélanie Roy (M.Sc candidate) preparing fish cells for plasmid transfection (Photo: N. Gagné)

Recombinant vaccines are based on the expression of synthetic DNA constructs encoding proteins from specific pathogens. Heat Shock Proteins (HSPs) are involved in protein conformation, chaperoning, shuffling, etc. Whenever a cell is stressed, HSPs are produced. When cells rupture, such as during viral infections, HSP-peptide complexes are released, and detected by specialized cells that present the antigenic peptide at their surface, thus activating the cytotoxic T cell response, as part of an effective immune response.

Researchers are taking a novel approach using recombinant ISAV protein subunits combined in vivo to fish HSPs. Various studies have demonstrated that antigenic recombinant peptides are more effective when combined with HSPs. In this approach, we will transfect fish cell lines with recombinant expression vectors. Once recombinant ISAV proteins are produced in these cells, necrosis (unplanned cell death) will be induced. Necrosis conditions will be selected such as to obtain the highest level of HSPs production before cell burst, and release of recombinant ISAV proteins associated with HSPs.

Duration: Jul ’07 – Mar ’09.

Funded by: DFO-ACRDP. Co-funded by: New Brunswick Salmon Growers Association, DFO-GRDI.

Project team: Nellie Gagné (DFO), Mark Laflamme (DFO), Mélanie Roy (MSc Student, U Moncton), Kira Salonius (DFO), Nathalie Simard (DFO)

For information contact: Nellie Gagné (

How do different strains of ISAV affect fish in the field?

Different strains of Infectious salmon anemia virus (ISAV) are associated with different pathogenicity in the field and in the laboratory. The apparent, but poorly elucidated disparity in virulence of ISAV strains confounds management decisions relating to infected fish. Laboratory studies show differences in mortality rates and onset, with some ISAV strains such as the HPR0 apparently posing little threat to the health of the fish, and strains such as the HPR4 posing considerable threat to infected fish.

While laboratory studies provide useful information, they are rarely an accurate representation of how the strains affect fish in the field. However field studies are often hampered by incomplete data sets, and confounding factors such as variables between sites and factors that can influence observed disease outside of the pathogen strain itself.

In the present study, the industry is making available detailed mortality data for ISAV infected and uninfected fish for two year classes of fish. Analysis of this data and other confounding factors will allow elucidation of the impact of different ISAV strains on fish in the field, helping inform fish health decisions regarding depopulation or eradication and disease control, and leading to intelligent and economical disease management.

Duration: Feb ’08 – May ’08.

Funded by: DFO-ACRDP. Co-funded by: Cooke Aquaculture Inc.

Project team: Nellie Gagné (DFO), Rachael Ritchie (RPC).

For information contact: Nellie Gagné ( Nellie.Gagné

ISA prevalence and sampling strategy in relation to outbreak stage and vaccination status

Hypothesized 3D Histogram of an ISAV outbreak. The frequency of infection is represented over time in function of the virus load (low values of PCR CT refer to high virus load, in red, when low values of PCR CT values refer to low virus load, in black). High infected fish (in red) are assumed to match with clinical mortality, and low infected fish are assumed to be apparently healthy fish

In 2005, a series of salmon cages were initiated in the New Brunswick aquaculture industry to explore vaccine efficacy in a randomized clinical field trial. In 2006, one of the study cages experienced a severe ISAV episode caused by the HPR4 virulent strain.

Preliminary results from these samples revealed that infected salmon are either highly or lowly infected with very few intermediate stages detected. This unexpected observation led to a hypothetical three dimensional model of the disease dynamic during the outbreak. This project is investigating the phenomena further.

Firstly, the model is being refined by further viral quantitative testing of this population. This is expected to provide a better comprehension of the disease dynamic which in turn will lead to an optimized surveillance program.

Secondly, the outbreak cage contained 7 different groups of Atlantic salmon vaccinated against different fish diseases including 3 groups vaccinated against ISAV and 4 groups not vaccinated against ISAV. Utilizing survival analysis statistical techniques is allowing for the simultaneous analysis of the prevalence and virus load distribution controlling for the vaccine group as well as other confounding factors. This kind of efficacy assessment, and the deeper understanding of the protective effect of the ISAV vaccine, will directly benefit the salmon culture industry.

Duration: Feb ’08 – Mar ’09.

Funded by: DFO-ACRDP. Co-funded by: Cooke Aquaculture Inc.

Project team: Nellie Gagné (DFO), Charles Caraguel (UPEI-AVC), Larry Hammell (UPEI-AVC), Carol McClure (UPEI-AVC), Mike Beattie (NB Department of Agriculture and Aquaculture), Larry Ingalls (Ocean Horizons Canada), Mike Szemerda (Cooke Aquaculture Inc)

For information contact: Nellie Gagné ( Nellie.Gagné

Efficacy of the APEX vaccine is tested under severe conditions

Infectious hematopoietic necrosis virus (IHNV) is an aquatic rhabdovirus that has had a devastating effect on the BC salmon aquaculture industry. In particular, Atlantic salmon are highly susceptible to this endemic pathogen at all life stages.

Efficacy of the APEX vaccine in Atlantic salmon subjected to an IHNV exposure simulating natural and/or elevated field challenges

To minimize the effects of IHNV, Novartis Animal Health Canada Inc. has developed a highly efficacious IHNV plasmid vaccine (APEX-IHN®) that is commercially available. Laboratory tests of the vaccine have revealed the vaccine to provide significant protection against lethal virus challenge. The efficacy observed in the laboratory setting has warranted the use of the vaccine in the field, however due to the lack of a natural field challenge it remains unclear as to the efficacy of the vaccine in an environmental outbreak.

This project will evaluate the effectiveness of the APEX vaccine under conditions that are equal to, or more severe than, a natural field challenge. This work is necessary for salmon farmers to better evaluate husbandry and disease management strategies.

Duration: Apr ‘07 – Oct ’07.

Funded by: DFO-ACRDP. Co-funded by: Marine Harvest, Novartis Animal Health Canada Inc.

Project team: Kyle Garver (DFO), Laura Hawley (DFO), Diane Morrison (Marine Harvest Canada Inc.), Todd Cook (Novartis Animal Health Canada Inc.), Allison MacKinnon (Novartis Animal Health Canada Inc.)

For information contact: Kyle Garver (

New rapid detection technique offers new tools to manage IHNV

The source of the infectious hematopoietic necrosis virus (IHNV) introduction to farmed salmon is unknown, but epidemiological investigations have identified sockeye salmon and herring as likely sources. Due to the potential devastating effect of IHNV on the economic sustainability of the BC salmon aquaculture industry, companies have developed biosecurity action plans for viral containment in the event of another outbreak. However, effectiveness of any containment plan depends on rapid diagnosis of the index case. Therefore, rapid and accurate diagnosis of IHNV is essential. The traditional method of diagnosing IHNV was through recognizing necrosis of cells grown in tissue culture – a technique requiring between 5 and 21 days for confirmation of virus.

Loading the qRT-PCR machine to begin a run.

Quantitative polymerase chain reaction (QPCR) is rapidly replacing more traditional methodologies as a diagnostic test. QPCR offers many advantages over other diagnostic techniques including a fast turn-around time as well as reduced frequency of false positives, increased sensitivity, low requirements for tissue and high sample through-put. This technology can also be employed in the detection of IHNV but must include an additional step owing to the fact that the genome of IHNV is composed of single-stranded, negative-sense RNA. Therefore, a reverse transcription step is required to convert genomic and messenger RNA (mRNA) to complementary DNA (cDNA). The research team is working on developing this type of assay for the detection of IHNV – a quantitative reverse transcription - qRT-PCR assay.

Duration: Apr ‘07 – Mar ’09.

Funded by: DFO-ACRDP. Co-funded by: BC Salmon Farmers Association, BC Centre for Aquatic Health Sciences

Project team: Kyle Garver (DFO), Valerie Funk (DFO), Zina Richmond (BC Centre for Aquatic Health Sciences (CAHS), Laura Hawley (DFO).

For information contact: Kyle Garver (

Melatonin assay improves photoperiod regimes to reduce grilsification

Photoperiod plays a significant role in the development and maturation of salmon. Alterations in the natural photoperiod can accelerate or decelerate smoltification or reproductive maturation. By appropriately manipulating photoperiod, spawning times can be controlled to allow for the production of out-of-season smolts, and grilse rates can be reduced during grow out allowing enhanced growth and greater insurance of quality marketable product.

Sampling salmon cage with controlled photoperiod.

The way in which photoperiod is perceived by salmon and how signals are relayed to systems which control sexual maturation is not clearly understood. But evidence suggests that melatonin, produced by the pineal gland, may be a significant mediator of the photoperiod effects. In salmon, melatonin levels rise during dark hours and drop during light hours. Since melatonin levels appear to help communicate day/night lengths to salmon, monitoring its levels would be an effective way to measure the efficiency and accuracy of artificial lighting systems in lengthening light hours in a 24 hour day.

The project team is investigating 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. Melatonin levels are correlated with grilse rates, fish weight, water temperatures, family/stock origin and light intensity measurements. The data from these investigations should indicate the effectiveness of the lighting regimes being used in reducing melatonin levels and give insight on how grilse rates might be further reduced.

Duration: Jul ‘07 – Mar ’09.

Funded by: DFO-ACRDP. Co-funded by: Cooke Aquaculture

Project team: Brian Glebe (DFO), Keng Pee Ang (Cooke Aquaculture)

For information contact: Brian Glebe (

Monitoring in Fortune Bay assesses the risk of hypoxia in Atlantic salmon

Salmon cages - Spyglass I / Spyglass II

Aquaculture is expanding rapidly in Fortune Bay and specific sites have experienced low dissolved oxygen in the past. Real time biological and environmental monitoring of the area is vitally important. Water currents, oxygen, temperature, and salinity are being monitored at sites where low dissolved oxygen has been observed as well as sites that have not seen such events.

In addition, Newfoundland weather produces significant environmental effects impacting fish. Determining stress levels and immune responses of cultured fish are essential tools for improving productivity and fish health. In vitro and in vivo experiments will be conducted on salmon to investigate health status of farmed fish under environmental stressors such as hypoxia through evaluation of fish immunity and physiology using flow cytometry and real-time PCR. Laboratory trials are being conducted at the Northwest Atlantic Fisheries Centre. Field sampling of fish is being conducted in collaboration with the industry partner to examine any physiological and/or immunological changes in fish during episodes of hypoxia.

Duration: Apr ‘08 – Mar ’10.

Funded by: DFO-ACRDP. Co-funded by: Northern Harvest Sea Farms.

Project team: Dounia Hamoutene (DFO), Gehan Mabrouk (DFO), Dwight Drover (DFO), Lynn Lush (DFO), Fred Page (DFO), Doug and Jennifer Caines (Northern Harvest Sea Farms)

For information contact: Dounia Hamoutene (

Flesh quality of farmed salmon enhanced through diet formulation modelling

A multidisciplinary team of researchers with expertise in nutrition, contaminants, health and aquaculture science is developing a model to predict contaminant burden and fatty acid content in farmed salmon based on the composition of contaminants and lipid profiles in the corresponding fish diets.

Farmed salmon are fed alternate diets and contaminant bioaccumulation is examined as a function of fish size, feeding practices and growth characteristics. The levels of the target contaminants (PCDDs, PCDFs, PCBs, PBDEs, and 20 Organochlorine [OC] pesticides) are measured in the flesh of a wide range of farmed Atlantic salmon of all sizes fed three different composition diets.

Concurrently, the research team is examining the impact of the alternate feeds on the profiles of the omega-3 unsaturated fatty acids in the flesh of the target species. The bioaccumulation behavior of the target contaminants and the profiles of the fatty acids are then modeled. The model is calibrated according to the findings of this study. The intent is to use the model developed from this study to predict contaminant burden and fatty acid content in farmed salmon based on the composition of contaminants and lipid profiles in the corresponding fish diets.

Duration: Jul ‘08 – Mar ’10.

Funded by: DFO-ACRDP. Co-funded by: Cook Aquaculture, National Research Council of Canada.

Project team: Michael G.Ikonomou (DFO), Keng Pee Ang (Cooke Aquaculture), Santosh P. Lall (NRC IMB).

For information contact: Michael Ikonomou (

Use of genetic markers indicates family-level differences in coho growth performance

Coho in rearing tank / Coho fillets

Family selection methods are powerful approaches for improving the performance of agricultural species. Modern methods of analysis now enable tracking parents and offspring to families using microsatellite and other molecular genetic marker based systems. Development of a suite of variable genetic markers therefore can significantly enhance breeding programs. This project is developing and applying these genetic markers to cultured coho salmon.

Some of these variable markers have been mapped to chromosomal regions associated with loci (quantitative trait loci QTLs) controlling traits of interest which enhance performance in other species. Analysis of the genetic basis of growth in coho salmon and rainbow trout show that this trait is largely controlled by additive genetic variance, making it likely that controls of growth rate will be found in these two species using family analyses of phenotypic variation and molecular genetics.

Recent research has shown that QTL marker loci identified in one salmonid species are often associated with control of the same trait in other salmonids. The team is developing markers associated with QTLs originally developed de novo in rainbow trout, Arctic char and Atlantic salmon, and applying them to coho salmon production populations to assess whether family-level differences in performance exist, and to assess whether specific markers are associated with growth performance.

Aquaculture broodstock can become bottlenecked due to a lack of novel genetic material being introduced over a period of several generations. Researchers in this project have introduced new genetic variation from wild strains into a domesticated coho salmon stock, and are currently assessing the effects on growth performance under aquaculture conditions. Genetic marker-based determination of families within this production population is being used for this analysis.

Duration: Nov ‘07 – Sep ’10.

Funded by: DFO-ACRDP. Co-funded by: Tri-Gen Fish Improvement Ltd.

Project team: Ruth Withler (DFO), Tri-Gen Fish Improvement Ltd.

For information contact: Ruth Withler (

Coho in polyculture with wasabi

Eggs subdivided for fertilization in breeding program

Airlift feed collector reduces feed loss and environmental impact of salmon farming in Newfoundland

Feed wastage from Atlantic salmon cage sites on the south cost of Newfoundland can be costly and it is important to evaluate and reduce the economic and environmental impact. Investigators in this project are determining the amount of actual feed wasted at different feeding times and the pattern of such wastage during each meal. They are also examining the nutritional losses of the wasted pellets and their disintegration pattern.

A trial to evaluate the efficacy of using an airlift feed collector to collect and re-suspend the uneaten pellets back to the cages is being conducted. The effect of this technique on fish performance and feed conversion ratios is also being investigated. In addition, the team is conducting an evaluation of the environmental effects of the reduced feed wastage on the sea bed under the cages.

Duration: Jun ‘07 – Mar ’09.

Funded by: DFO-ACRDP. Co-funded by: Natures Sea Farms Inc.

Project team: Atef A.H. Mansour (DFO), Gehan Mabrouk (DFO), Elizabeth Barlow (NL DFA)

For information contact: Atef Mansour (

New Brunswick team developing novel vaccine technologies

A research group in New Brunswick is working on a truly novel form of vaccine for salmonids. Farmed Atlantic salmon are susceptible to a variety of pathogens from bacterial or viral origins. To date, only a few commercial vaccines are available, and of these, many have less than the desired efficacies. Many of these vaccines are based on attenuated or killed pathogens. More modern vaccines are based on recombinant DNA technologies. Such vaccines “pre-expose” the fish to non-virulent versions of the pathogen, with the goal of boosting the immune response if an actual infection should occur.

This team, however, is developing a novel form of vaccine based on the RNA interference (RNAi) mechanism. The mechanism works by transfecting fish cells with small RNA molecules. These molecules act as guides that target and destroy pathogenic mRNAs by using the fish’s RNAi system. The fish RNAi system is active in natural populations of fish, where it functions to regulate gene expression, and protect fish from certain infectious diseases.

Work in this project is focused on manipulating this system to specifically protect fish from pathogens that are problematic to the salmon aquaculture industry. The project is initially developing a vaccine against the Infectious Salmon Anemia Virus, but the researchers believe this system can be easily adaptable to many other pathogens.

Duration: Sep ‘08 – Apr ’09.

Funded by: DFO. Co-funded by: U Moncton.

Project team: Mark Laflamme (DFO), Nellie Gagné (DFO), Chanel Losier (Undergraduate student, U Moncton)

For information contact: Mark Laflamme (

Aquaculture Engineering Group establishes Nova Scotia operation to demonstrate eco-friendly solutions

Aquaculture Engineering Group Inc. (AEG) is establishing a small finfish aquaculture operation in St. Mary’s Bay, Nova Scotia to demonstrate sustainable technologies for salmon farming. The company plans to raise Atlantic salmon on the site through the early smolt stage of a grow-out cycle (60-300 g).

AEG is developing and demonstrating a number of its advanced solutions through this project. The AEG Feeder provides stock with pulse feeding capability compared with the meal feeding approach that is now standard in the industry. The AquaSonar technology and the onboard AEG Feeder integrate the fish sizing program to allow daily fish size updates from permanently mounted AquaSonar units. The AEG site management software application Neptune is being applied to evaluate daily smolt size data for superior feed management and market planning.

A submersible HDPE collar is being developed for use with the innovative AEG Containment System. Logistics mitigation strategies, possible only while using integratedAEG Solutions to enhance overall farm management and productivity, are being refined.

Aquaculture Engineering Group Inc. was incorporated in November 2002 to develop equipment and management solutions that address current industry technology shortcomings.

Duration: Aug ‘08 – Dec ’10.

Funded by: DFO-AIMAP. Co-funded by: NS DFA, ACOA, NRC-IRAP, Skretting Canada, Marine Systems International.

Project team: Chris Bridger (AEG), Phillip Dobson (AEG), Wade Landry (AEG), Dave Hoar (Motion Design), Skretting Canada, Motion Design, Marine Systems International, Future Nets & Supplies, Aquatic Sensing Technologies Limited, Huntsman Marine Science Centre.

For information contact: Chris Bridger (


Researchers use DNA chips to uncover immune response to ISAV isolates

Infectious salmon anemia virus (ISAV) affects salmon in Atlantic Canada. In earlier research by the team, controlled challenges were conducted using an ISAV HPR2 (non-virulent) isolate and low levels of fish mortality were observed. The team hypothesized that the surviving fish had developed immunity against ISAV and would resist exposure to virulent ISAV isolates. This hypothesis was supported by a high survival rate of these fish following a re-challenge with an ISAV HPR4 isolate (virulent type). Further work with various rearing conditions and exposure regiments is being done in this project to confirm these results.

Although a variety of factors may be implicated, it seems the apparent variability in virulence between the various ISAV isolates is linked to the HPR type. The viral mechanisms leading either to fish death or survival and resistance are not well understood at the immune or molecular levels. In order to gain further understanding of these mechanisms, the research team is using 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 ISAV.

The results of this project are expected be useful in many areas of fish health such as novel vaccine development, the evaluation of isolate virulence, fish selection for resistance to disease, and others.

Duration: Apr ‘08 – Mar ’11.

Funded by: DFO-GRDI.

Project Team: Nellie Gagné (DFO), Mark Laflamme (DFO), Brian Glebe (DFO)

For information contact: Nellie Gagné (

Oceanographic study supports salmon production management in Newfoundland

The province of Newfoundland is experiencing a significant influx of investment in salmonid farming. The increasing biomass, the growing number of companies, the diversity of production strategies, and the concentration of farm sites, particularly in outer Bay d’Espoir, are challenging the management of biosecurity and sustainability of salmon farming on the south coast of Newfoundland.

The lack of data and full understanding of the oceanography of the outer Bay d’Espoir area precludes establishment of scientifically validated production and management areas to guide site licensing, production planning, and sustainable management of the industry. The problem is particularly acute in this area because company production plans will result in overlapping year-classes in the area in 2009.

This project is establishing the infrastructure and the foundation for Newfoundland to be able to carry out an oceanography program to collect and model the physical environmental data - currents, dissolved oxygen, temperature, and salinity – and map the environmental parameters and potential zones of influence that will be used to establish production management areas.

Duration: Sep ‘08 – Mar ’09.

Funded by: DFO-PARR.

Project team: Gehan Mabrouk (DFO), Geoff Perry (DFO), Dave Senciall (DFO), Fred Page (DFO), Peter J. Cranford (DFO), Dwight Drover (DFO), Randy Losier (DFO), Thomas Puestow (MUN C-CORE), Darrell Green (NAIA)

For information contact: Gehan Mabrouk (

Rapid IHN detection technique piloted in BC project

In British Columbia, infectious hematopoietic necrosis virus (IHNV) is the most economically significant viral pathogen of salmonids. Since the introduction of Atlantic salmon to the BC coast in the mid 1980’s, there have been two serious outbreaks of IHN in farmed Atlantic salmon. The estimated economic loss resulting from both combined outbreaks was $40 million in inventory representing $200 million in lost sales. Due to the potential devastating effect of IHNV on the economic sustainability of the BC salmon aquaculture industry, companies have developed biosecurity action plans in the event of another outbreak. However, the effectiveness of any such plan depends on rapid diagnosis.

Lab technician, Kristin Mulholland, pipetting with precision (Photo: BC CAHS)

The traditional method of diagnosing IHNV was through recognizing necrosis of cells grown in tissue culture – a technique requiring between 5 and 21 days for confirmation of virus. Quantitative PCR (QPCR) is rapidly replacing more traditional methodologies as a diagnostic test. QPCR offers many advantages over other diagnostic techniques including a fast turn-around time, increased sensitivity, and high sample through-put. The BC Centre for Aquatic Health Sciences (BC CAHS) is piloting the application of the rapid detection for salmon farms in BC.

Located in Campbell River, BC CAHS operates as a fourth pillar organization bringing together industry, academics and government researchers to drive innovation.

Duration: Jul ‘08 – Jan ’09.

Funded by: DFO-AIMAP. Co-funded by: BC Salmon Farming Industry.

Project team: Linda Sams (BC CAHS), Sonja Saksida (BC CAHS), Valerie Funk (BC CAHS), Kevin G. Butterworth (UBC-CAER)

For information contact: Linda Sams (

BC project implements new cryopreservation technology for aquaculture

Cryopreservation of milt or sperm from fish is a new technology in the aquaculture industry. This is in contrast to cattle breeding where artificial insemination (AI) with frozen semen has been essential for breeding progress since 1965. Today advances in technology have reached a level where cryopreservation can be exploited commercially. Cryopreservation of milt can increase the number of offspring from genetically superior males, and speed up the breeding process. For production of commercial eggs, frozen milt increases the possibilities of varied production techniques and increased operational efficiencies.

Mike Anderson of New Zealand King Salmon looking under the microscope for activity of sperm after the milt was brought out of the cryopreserved state. (Photo: BC CAHS)

The BC Centre for Aquatic Health Sciences (BC CAHS) is coordinating a project to import expertise in cryopreservation techniques from New Zealand King Salmon and transfer those techniques through staff and technician training and through pilot, commercial application. With a focus on sustainable farming practices, New Zealand King Salmon has built a reputation for one of the finest salmon stock breeding programs in the world and uniquely avoids the use of chemicals or vaccines in supporting the pristine advantages of its grow-out environment in the Marlborough Sounds.

This project brings together BC salmon farming companies working through their membership with the BC Salmon Farmers Association (BCSFA).

Duration: Sep ‘08 – Nov ’08.

Funded by: DFO-AIMAP. Co-funded by: BCSFA and Member companies, New Zealand King Salmon, BC CAHS.

Project team: Linda Sams (BC CAHS), BCSFA, Michael David Anderson (New Zealand King Salmon), Karl James French (New Zealand King Salmon).

For information contact: Linda Sams (

Juvenile coho monitoring project

Researchers prepare a seine net along the shores of Discovery Passage (Photo: BC CAHS)

A collaborative research partnership is monitoring phytoplankton and zooplankton levels in the Northern Georgia Strait to determine optimal release dates for the improved survival of juvenile, enhanced coho. The collaboration is being facilitated by the BC Centre for Aquatic Health Sciences (BC CAHS) in partnership with the BC Ministry of Environment (BC MOE) – Marine Division, DFO Quinsam Hatchery, A-Tlegay Fisheries, Ritchie Foundation, Campbell River Foundation, Campbell River Lodge, and the City of Campbell River.

At the Quinsam Hatchery, as well as other hatcheries on the BC coast, survival of enhanced coho has dropped from highs of 8-10% in the 1980’s to less than 1% today. Many factors are contributing to this decline including changes in magnitude and timing of ocean productivity (i.e., plankton blooms) likely related to global climate change.

Researchers are analyzing plankton levels in the stomach contents of captured coho. They will use this data to adapt the timing of release such that the juvenile fish enter seawater when food is at maximum availability. The development of this project will lead to a long-term monitoring program that will help guide the release time of enhanced coho in this area. The full report is available on the BC CAHS website

Duration: Jan ’07 – Oct ‘07

Funded by and Project team from: BC CAHS, BC MOE – Marine Division, DFO Quinsam Hatchery, A-Tlegay Fisheries, Ritchie Foundation, Campbell River Foundation, Campbell River Lodge, City of Campbell River

For information contact: Linda Sams (


Researchers use amoebae to study furunculosis

Furunculosis is an infectious disease occurring particularly in farmed trout and salmon. The disease is caused by the Aeromonas salmonicida bacteria. A growing number of strains of A. salmonicida are resistant to multiple antibiotics. This compromises the ability to overcome future infections caused by this bacterium.

The amoeba is used in evaluation of the bacteria’s virulence. Each of the wells contains a different strain of bacteria (black). Strains in which the amoeba cannot grow (no white areas) are virulent. (Photo: Laboratoire Charette)

One solution to this problem involves the creation of compounds to complement the antibiotics and thus decrease the infectious nature of the bacteria. Development of these anti-infection agents requires, as a first step, better understanding the virulent behaviour of the bacteria and thus finding molecular targets suitable for developing these anti-infection agents. Repeated confrontations between bacteria and host are necessary for this kind of study.

For ethical, economic and practical reasons, it is difficult to do this while using the living fish as the host. Here, the research team is studying the virulence of A. salmonicidausing a substitute host, the amoeba Dictyostelium discoideum. The objective is to define the infectious nature of A. salmonicida and propose new approaches to treat infections caused by this bacterium.

Duration: Mar ’08 – ongoing.

Funded by: U Laval. Co-Funded by: RAQ, AUCC.

Project team: Steve Charette (U Laval), Rana Daher (M.Sc Student, U Laval), Geneviève Filion (U Laval), Michael Reith (NRC-IMB)

For information contact: Steve Charette (


Hard seabed monitoring project progresses to support new waste control regulations in BC

In British Columbia many finfish aquaculture operations are sited over hard seabed substrates, where conventional soft seabed sampling techniques (sediment grabs and cores) cannot be used to sample benthic communities. Most of these sites have higher currents and little accumulation of natural sediments. Hard seabed biological communities differ from soft seabed communities as they are dominated by attached or mobile epibenthic organisms rather than infaunal organisms.

For hard seabeds the current Finfish Aquaculture Waste Control Regulation (FAWCR) lacks standard protocols for field survey data interpretation and analysis. In addition, performance standards (e.g., the level and type of community change deemed to be unacceptable) have not been defined. A three-phase project, beginning in 2003, has now concluded its third phase.

In Phase 1 video imagery was recommended as the most effective tool for operational monitoring. Phase 2 reviewed marine environmental video monitoring methods and monitoring parameters, developed video data interpretation and classification protocols, and conducted ROV field survey and classification trials. Phase 3 of this project involved working with stakeholders and regulators to amend the regulations.

Duration: Jan ‘04 – Oct ‘08

Funded by: BCARDC-AE. Co-Funded by: BCMoE, BCMAL, DFO

Project team: Brian Emmett (Archipelago Marine Research), Pam Thuringer (Archipelago Marine Research), Sarah Cook (Archipelago Marine Research), Jon Chamberlain (DFO), Jason Dunham (DFO), Barb Cannon (Creative Salmon Ltd)., Dave Stirling (Mainstream Canada), Sharon Dedominicis (Marine Harvest Canada), Mia Parker (Grieg Seafood BC Ltd), Norm Penton (BCSFA), Bill Harrower (BCMAL), March Klaver (DFO), Kerra Hoyseth (DFO) Bernie Taekema (BCMoE)

For information contact: Brian Emmett (

Molecular genetic capabilities to improve strains of Chinook salmon in BC

Chinook salmon farming in British Columbia has been underway for more than 20 years and remains an important industry that provides significant commercial and social benefit to the Province. The future success of salmon farming, as with all agricultural activities, depends upon continual application of science. In particular, application of emerging genomic methodologies has significant potential to facilitate the development and improvement of salmon strains in BC.

Mature red and white Chinook salmon (Photo: R. Devlin)

For example, developing a molecular genetic map for Chinook salmon will allow the identification of genes involved in commercially important traits which can facilitate marker-assisted breeding programs. Similarly, application of microarray technology (large-scale gene expression analysis) has large potential for its ability to detect important genetic differences between strains of salmon with different phenotypic traits.

Molecular mapping and gene microarray technology are being utilized in this project 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 these experiments.

Start-End: Jul ‘08 – Jul ’12.

Funded by: DFO-ACRDP. Co-funded by: Yellow Island Aquaculture Ltd.

Project team: Robert Devlin (DFO), Wendy Tymchuk (DFO), Ann and John Heath (YIAL), Dan Heath (University of Windsor), Willie Davidson (Simon Fraser University), Dag Inge Vage (CiGene, Norway).

For information contact: Robert Devlin (

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