Atlantic Canada’s freshwater fish capture N.B. ecogenomics expert’s attention

In the face of climate change and other pressures, Dr. Scott Pavey, a rising star in the new and promising field of ecogenomics, is focused on retaining the biodiversity of New Brunswick’s and Atlantic Canada’s freshwater fish and the industries that rely on them.

He runs what he proudly calls, “the most advanced ecology-focused genomics lab in New Brunswick.”

CRI Genomics, Dr. Pavey’s lab at the Canadian Rivers Institute, University of New Brunswick, Saint John, is known for applying state-of-the-art genomic technologies and techniques to investigations into how to conserve and manage freshwater fish stocks and make aquaculture and the fisheries that depend on them more sustainable.

This is important work, he said, because “All industries that alter the environment, such as mining and forestry, or discharge into the environment, such as pulp mills etc., have a responsibility to ensure their impacts do not adversely affect the habitat and populations of freshwater fish. Freshwater fish habitat is protected by federal legislation. Every EIS [environmental impact statement] for projects near freshwater must take freshwater fish into account.”

Reduced biodiversity, he said, “weakens the entire system because species exist in food webs and are reliant on each other. If the prey go extinct, the predator starves.” Dr. Pavey pointed out, freshwater has been heavily impacted in Canada and worldwide and when these impacts cause local extinctions of species; they reduce biodiversity.

The lab of The Tier 2 Canada Research Chair in Aquatic Molecular Ecology and Ecological Genomics specializes in aquatic molecular ecology and ecological genomics. Aquatic Molecular Ecology uses molecular genetic tools for advanced DNA analysis, such as entire genome scanning and bioinformatics to identify and study communities of interdependent organisms in aquatic ecosystems. Ecological Genomics seeks to understand the genetic mechanisms that govern the way organisms respond to their natural environment. Ecology, evolution and conservation are Dr. Pavey’s watchwords.


Since 2020, he has been active in a $9.1 million Genome Canada Large-Scale Applied Research Project (LSARP) called GEN-FISH, short for Genomic Network for Fish Identification Stress and Health. It has involved a group of researchers, professionals and community members in an extensive and innovative four-year undertaking to develop toolkits that pinpoint where Canada’s more than 200 freshwater fish species can be found and in what numbers.

Accurate information on the kinds of fish and their numbers in rivers and lakes, he said means improved environmental monitoring, assessments and fish management. He explained, “Fish are under water, thus hard to see directly. It takes a huge effort to set nets. So, when there are impacts, they are often invisible. With eDNA we can more easily detect such impacts and recoveries

Also on the agenda are plans to develop a method to chart how Canada’s freshwater species are faring under increasing, mostly human-induced, stress. Project partners from Atlantic Canada include the New Brunswick Energy and Resource Department (NB ERD) and the Nova Scotia Salmon Association.

Dr. Pavey’s role is to extend the Ontario-based, but Canada-wide research to Atlantic Canada.


The project aims to produce three sophisticated toolkits, one for fish surveillance, another for fish health and a third for decision making that essentially promotes the other two toolkits for widespread general use.

“We are helping with developing, lab testing, and field testing the Fish Survey Toolkit,” said Dr. Pavey. “Assays need to be separately developed for each species before they are put on the chip. My graduate students are doing this, focusing on fish important to Atlantic Canada. They are also collecting eDNA [environmental DNA] samples in the field that we are using to field validate our developed tools.”

The fish in this region, he said, “are important because they are in Atlantic Canada. They also have commercial fishing, recreational fishing and cultural importance.”

Dr. Pavey said, “Our lab is going to submit sequences for the first draft Fish Survey Toolkit in a month or so. We are focusing on 15 species important to Atlantic Canada. We expect to have several draft toolkits in year three of the grant and test them in real conditions, including rivers and lakes in New Brunswick. We will have finished products in two years.“

Interest in these products is expected to be strong, especially from the fish management and environmental sectors and from some industries too. Many of them have a need to monitor their environmental impacts on freshwater from such things as industrial effluent. “Current entities requesting my services include the federal and provincial governments, non-profits, first nations and private consulting,” he said.

The Fish Survey Toolkit, he said, will let users know whether any of the Canadian fish species included for identification on the toolkit chip is present in any particular lake or river, based on analyses of water samples collected from them.

For this project, Dr. Pavey’s lab has been working on identifying fish species from environmental DNA. He explained the process this way: “A water sample is taken from a waterbody. The water is filtered and cells from fish that were in that waterbody collect on the filter. We prepare the DNA so that we can use a chemical reaction to make copies of the segment of DNA that is unique to a single species. If the species’ specific reaction produces a product, we know that species was in the water body.”

Fish-Health Toolkit

“The Fish Health Toolkit,” he said, “is designed to answer what is causing fish to be sick or die. Is it high temperatures? Heavy metal toxicity? Etc. The latter would involve lethal sampling of the individuals in question and determining which ‘stress’ genes are turned on or upregulated to tell us the nature of the ailment.”

Dr. Pavey is certain the toolkits will bring more attention to conserving and sustaining the Atlantic region’s freshwater resources. “They absolutely will,” he said. “They will be a new tool that will allow high throughput testing.” That means high volume testing with quick results.

“We have partnered with DFO [Department of Fisheries and Oceans] and NB ERD and both organizations are very excited to use these tools. Because I’m involved with the grant, I will ensure that the tools are designed in a way it meets the needs of organizations in Atlantic Canada.”

Considering Canada has one-fifth of the earth’s freshwater resources, the need for these toolkits quickly becomes apparent.

Meanwhile the GEN-FISH project has sparked new ideas for exploration. “While GEN-FISH is primarily focused on presence/absence of species, we are experimenting with how to use similar techniques to estimate abundance,” he said.

Other Work at CRI Genomics

In other work at CRI Genomics, Dr. Pavey noted “the lab team has spent a lot of time focusing on fish such as Atlantic Cod, and looking at factors that could help their populations rebound.” Striped Bass, Bluefin Tuna and the American Eel are other species to which his team has given special attention. All these fish species are of concern under the Canadian Species at Risk Act. His team used DNA sampling from tissue to determine population interactions and environmental adaptations of these species.

His recent research on the American Eel with Dr. Louis Bernatchez at Laval University identified the genes responsible for the eels’ survival in freshwater and saltwater environments. Genetic analysis of the all-female eels in the Upper St. Lawrence River, showed they had unique adaptive genetic traits compared to counterparts reared in brackish or saltwater.

It was an important finding because that kind of knowledge can result in more nuanced fisheries management policies to protect habitat and migration routes of sub populations that need critical genetic consideration.

The considerable range of CRI Genomics’ capabilities, means Dr. Pavey’s eight-member team is kept busy, often by clients seeking customized services unavailable elsewhere in the region. The client list includes the NB Museum, Huntsman Marine Science Centre, Memorial University, the Department of Fisheries and Oceans, the University of Massachusetts and NovaEel, a Nova Scotia-based aquaculture start-up.

The lab can do genotype-by-sequencing, also known as GBS, to enable researchers to track down the genetic roots of observable traits such as size or colour in fish, for instance. It can also identify unique adaptations found in local fish species, employ sequence barcode regions in DNA to identify species in microbiomes or insect communities, and use the environmental DNA found in small tissues and cells suspended in the waters of lakes and rivers to identify species that inhabit them. In addition, the lab has the capacity to run simultaneous targeted resequencing of candidate genes from many individuals.

With these resources, Dr. Pavey has set himself an important agenda in preserving the biodiversity of Atlantic Canada’s freshwater fish.

Initiative sets its sights on complex gill disease in farmed salmon

For reasons unknown, farmed east coast Atlantic salmon have so far escaped the costly rise in complex gill disease (CGD) experienced in net pens on the west coast and as far away as Norway and Scotland.

“CGD does occur in the North Atlantic, and in quite severe cases in European salmon aquaculture operations, but it has not had the same severity in Atlantic Canada,” confirms Dr. Mark Fast, Professor of Fish Health and Immunology at the Atlantic Veterinary College, University of Prince Edward Island (UPEI).

Whether the east coast can remain largely unaffected by the disease is also an open question. However, a new research initiative, begun in August, is aimed at checking CGD nationally and sparing the east coast salmon industry the scale of the west coast problem.

As the academic project leader, Dr. Fast, and his long-time research collaborator, Dr. Matthew Rise, at the Department of Ocean Sciences, Memorial University, have joined forces with British Columbia-based industry, government and academic scientists on a three-year, $3.6 million Complex Gill Disease Initiative (CGDI) under the Genomic Applications Partnership Program of Genome Canada. The initiative is managed by Genome Atlantic, in partnership with Genome British Columbia.

Together the researchers are developing genomic tools to pinpoint the risk factors for CGD and help aquaculturists spot and manage it for better outcomes. At the moment there are no vaccines or therapeutics for CGD available.

Dr. Fast readily admits there is plenty of scientific mystery here to investigate. CGD is found only in farmed fish and shows up as “a range of gross and microscopic lesions” he said.

These lesions are associated with various environmental conditions as well as some fish attributes among other factors. Yet linking cause and effect remains murky. Dr. Fast says CGD is more of a syndrome than a disease, but whatever the label, costs are staggering, even though salmon with CGD is considered safe for human consumption.

Overall, sea mortalities, slowed fish growth, and delayed harvests due to CGD are estimated to be costing the Canadian industry at least 12,500 tonnes in lost annual production, valued at $130 million. Factoring in indirect losses, the figure rises to $250 million.

As for costs to this region’s salmon producers, Dr. Fast said, “There has been some impact on Atlantic Canada but we have not estimated this since it has been a greater concern in British Columbia for a longer period of time.”

Given the revenue at stake, Cermaq Canada, with salmon farms on the east and west coasts of Vancouver Island and Grieg Seafood, with British Columbia salmon operations and a site in development in Placentia Bay, N.L. are leading the charge on the CGDI. Cermaq Canada’s Fish Health Director, Dr. Kathleen Frisch, is the industry lead on the CGDI, while Grieg Seafood’s Director, Fish Health and R&D, Tim Hewison, is the co-lead. Cargill Canada is involved too as an industry partner.

Also on board are Dr. Colin Brauner from the University of British Columbia and Dr. Simon Jones from the federal Department of Fisheries and Oceans.

Dr. Fast expects,” the genomic tools developed in the CGDI will assist in our understanding of gill health in general and could be applied to any gill issue of salmon and potentially other species.” Once risk factors for the disease are better known, he says, the disease will become easier to control, leading to fewer incidents of CGD and measures to prevent outbreaks.

He is optimistic too that “there are likely different therapies and or strategies that already exist to mitigate CGD impacts. For instance, identifying farm practices that contribute to the disease may allow these to be altered to reduce their contribution and there are gill health diets on the market, some of which we will be testing to determine their ability to help heal or resolve CGD.”

Before mitigation work can go ahead, though, Dr. Fast says, the team needs to chart the acute to chronic phases of the syndrome, in order to test various relief strategies throughout the course of the disease for efficacy.

The key aim of the initiative is to validate biomarkers to indicate when Atlantic salmon gills are healthy or compromised. Dr. Fast explains, “First we will be conducting a series of controlled lab experiments at U.B.C. and U.P.E.I. to develop histological and molecular markers associated with a number of different gill trauma events… Once we have found these robust markers from the lab we will test these same markers out in the field during CGD events on multiple farms in B.C. to validate their use during the different states of CGD in the field.”

Markers assigned to different stages of CGD will allow veterinarians to diagnose the syndrome and determine how far advanced it is. Once developed, the cellular and molecular markers can be tested for the proteins they produce when different fish feeds, developed for gill health, are trialed. Knowing the proteins being expressed, enables assessment of how well the feeds are working to treat the condition.

While European salmon producers have had an earlier start on trying to solve their CGD problem, their results are not necessarily transferrable. Dr. Fast said “while they have made some progress toward identifying contributing factors to CGD, they are still working on intervention strategies. The issue we have in Canada is that we do not know that we have the same contributing factors to CGD here, and we cannot treat it without knowing what is causing it.”

He added that it’s possible some European mitigation strategies may work in Canada. That possibility, he said, “is also why we are collaborating with Dr. Sam Martin, at the University of Aberdeen, and others to determine synergies to help the industry as a whole. It’s also possible that some of these strategies may be proprietary…so we will need to develop agreements to use and test these.”

Meanwhile, the initiative will also be building genomics research capacity for aquaculture at the Atlantic Veterinary College. Dr. Fast said the college has been able to purchase a multi-slide scanner to associate histological lesions, the hallmark of CGD, with biomarkers. The link will be made via high throughput image scanning and analysis, sharable with CGDI collaborators and others. A fish pathology resident has been hired under the initiative who will add new expertise to the university. Moreover, the sequencing pipelines and genomics collaborations developed with Memorial University during a previous GAPP-funded project are now being expanded to take on gill transcriptomes. Three post-doctoral fellows and student trainees hired for the initiative are expected to strengthen UPEI’s relationship with MUN and forge new ones with the University of British Columbia, the University of Connecticut and various universities in the United Kingdom.

Other key investigators for the CGDI are Dr. Rachel Balder, a Senior Scientist and Manager for the Nutrition Sciences group at Cargill Animal Nutrition, Elk River, MN; Dr. Simon Jones, Research Scientist, leader of the Marine Parasitology Program in Nanaimo, B.C. for the Department of Fisheries and Oceans; and Dr. Sonja Saksida, an aquatic epidemiologist at the Atlantic Veterinary College, UPEI.

Besides Cermaq, Grieg Seafood and Genome Canada, the CGDI collaborators include the Department of Fisheries and Oceans, Cargill, and MITACS.

Sequence #12: Wastewater surveillance acquiring a place in COVID detection 

Recent news, rife with reports of an approaching third pandemic wave that could delay economic recovery plans, underline how crucial genomics has become as a navigational aid in the continuing storm. Virus detection through sequencing has proven invaluable to public health efforts to contain the pandemic, and to employers and workers to keep the country’s economic engines turning.

One of the newer additions to the virus detection arsenal is wastewater surveillance technology. A project in this vein, worth keeping an eye on, is led by Dalhousie University. With sampling sites across Nova Scotia, this project has the capacity to serve as an early warning system for surges of clinical COVID‑19; caseloads. In that respect, the project appears to be unique in the country and it should give Nova Scotia a potential extra buffer against a third wave. We have a story on the project in this issue of Sequence.

Elsewhere, in this edition, you’ll learn genomics is about to help Atlantic Canada’s forestry sector forge ahead collectively with a tree improvement program to safeguard the industry against climate change and other threats.

We also have hot off the press news on a major gill health improvement initiative, which has just been greenlighted with funding by Genome Canada. The project will keep researchers at the University of Prince Edward Island busy validating biomarkers of healthy and compromised gills of Atlantic salmon to use in early detection of developing gill disease in this commercially important farmed fish.

On the human health side, you may be surprised to learn the region is home to one of the world’s leading experts in mood disorders, Dr. Martin Alda. One of his projects is using genomics to better understand bipolar disorder, one of the top 10 causes of death worldwide.

To keep your diary filled, we offer a heads up for an April 7 virtual seminar, presented by the Centre for Genomics Enhanced Medicine and featuring Dr. Aled Edwards, a leading thinker in the field of chemical biology and drug discovery. He will be discussing a formula being trialed in Toronto to speed up new drug development and keep the results affordably priced.

Finally, we send a shout-out to Dr. Stefanie Colombo, the aquatic nutritionist at the Truro Agricultural Campus, Dalhousie University, who is focused on improving the nutrition of farmed fish. Featured in our last edition as a scientist to watch, Dr. Colombo has just been announced as one of this year’s Science Meets Parliament delegates by the federal Science Policy Centre and the Office of the Chief Science Advisor. Way to go, Stefanie!

Steve Armstrong

Also In This Issue….

Nova Scotia Gains COVID Early Warning System Via Wastewater Sampling
Key Forestry Players Fight Climate Change with Tree Improvement 
A Leading Thinker to Discuss Open Drug Discovery
$4.7 Million to Improve Gill Health In Salmon
Understanding Bipolar Disorder: a pre-eminent expert describes his pursuit

Sequence Past Issues

Sequence #11: A path to economic recovery

As this unforgettable year nears its close, we have upbeat news to report in this issue from the health care and oceans sectors.

Despite the COVID-19 pandemic, Genome Atlantic has never been busier. Our current portfolio has 23 active, funded projects worth nearly $50 million, encompassing 25 companies and 15 university partners.

These projects span all four Atlantic provinces and represent a broad range of sectors including human health, oceans (aquaculture and energy), environment, agriculture, forestry and mining.

Significantly, our portfolio includes an ever-increasing amount of private sector investment, which has grown from eight per cent in 2008 to between 20-30% in recent years.

As we track the beneficial, unfolding effects of the projects on our list, we continue to pilot new opportunities through our business development pipeline.

Based on our activity, genomics is poised to be a driving force in our region’s economic recovery.

At this time, we want to acknowledge the tremendous support of our many partners in government, academia, and industry throughout this unprecedented period. They have been a pleasure to work with.

To you, our subscribers, we extend our seasonal best wishes and the hope that you’ll find inspiration for the year ahead in the people and applied genomics projects highlighted in this issue.

We all know recovery won’t be instant or easy, and that it will be more important than ever for Atlantic Canada to back innovations with a proven track record of impact. Genomics is one of these technologies, delivering impressive ROI across a range of sectors strategic to Atlantic Canada’s health and prosperity and attracting high levels of private sector investment.

Our sleeves are rolled up and the path to our region’s greater prosperity lies ahead.

Steve Armstrong

In This Issue….

Climate proofing P.E.I.’s blue mussels
Early diagnosis of rare genetic disorders in children
Initial findings on track in offshore energy project
One to watch: Dr. Stephanie Colombo
One genomic discovery leads to many more
Cleaner fish for salmon farming

Sequence Past Issues

Sequence #10: Pandemic response & economic renewal go hand in hand

The last few months have been unprecedented as we have all struggled to respond to a global pandemic. We hope that through it all, you and your families have stayed healthy. Even as restrictions ease and the economy re-opens, we are mindful of the need for continuing vigilance to ensure that we can all move forward, propelled by cautious optimism and a shared commitment to renewal.

Despite the challenges, this has been an especially productive time for Genome Atlantic as we have actively advanced an array of initiatives on two independent tracks: those focused on COVID-19 surveillance and the genetic determinants of disease severity, in parallel with ongoing efforts to continue to strengthen the bioeconomy of Atlantic Canada. Both are necessary for our region’s economic recovery and well-being. In this issue of Sequence, we share some exciting examples of each, including some great new video content.

We recently announced funding to Dalhousie University researchers to support important COVID-19 genomics projects. One, led by Drs. David and Alyson Kelvin, aims to find COVID-19 biomarkers that will help doctors triage patients and inform patient care protocols in settings like long-term care facilities, emergency rooms, hospitals, and ICUs. The second project, led by Drs. Nikhil Thomas, John Archibald and Morgan Langille, is piloting a surveillance tool to quickly identify early trends in transmission in high-risk settings like long-term care facilities, food processing plants or fishing vessels.

Genomics is a vital tool in our battle against COVID-19. Watch our short, animated videos “On the Trail of Covid-19” and “The Race for a Vaccine” to find out why.

On the economic development front, find out how forestry giant JD Irving Ltd. is using genomic selection to significantly improve forestry tree breeding practices and increase production. Take a deeper dive into the headline-making New Brunswick oyster breeding project through an engaging project video and a Q/A (Scroll down) with L’Étang Ruisseau Bar’s Dr. Martin Mallet and Laval University’s Dr. Louis Bernatchez. And hear from Dr. Kurt Gamperl at Memorial University and Dr. Mark Fast at UPEI for an update on their work addressing the adverse effects of climate change on farmed Atlantic salmon.

To round out this issue, medical research innovator Dr. Janessa Laskin of the BC Cancer Agency tells us why genomics could be the future of cancer treatment. And we profile our long-time industry collaborator Dr. Richard Taylor, recently retired from a long career with EWOS and Cargill, who shares some tips on forging successful industry-academic partnerships.

Sequence Past Issues

SEQUENCE # 9: De-risking investments through genomics R&D

Recently we visited the Research and Productivity Council (RPC) in New Brunswick to film how they use genomics in testing, developing and improving products and processes.  RPC is a global leader in material and environmental testing, work that puts them in daily contact with innovation at every stage of technology and market readiness. For many years, Genome Atlantic has collaborated with RPC – for example, working with RPC scientists like extractive metallurgist Neri Botha to improve the efficiency of bioleaching for mining clients. (See link to our story and video below.) 

RPC’s Executive Director Eric Cook believes that genomics is a critical biotechnology for driving innovation and he credits Genome Atlantic for helping to de-risk business investment in genomics projects.  Genome Atlantic does this by providing advice and guidance at every step – from assessing the feasibility of a genomic solution, to helping with proposal development, to securing funding, to project management – to ensure that projects deliver maximum benefit to our business and public-sector clients.  And because all our projects are industry-led, we’re committed to finding practical solutions and delivering maximum benefit for our business and public-sector clients – whether we’re using genomics to help de-risk offshore oil and gas exploration decisions, develop novel clinical aquaculture feeds, or find new treatments for Atlantic Canadians with genetic diseases. 

The fact that private sector investment makes up almost 30% of our portfolio speaks to the high level of confidence Atlantic Canadian businesses have in genomic technologies and in Genome Atlantic’s ability to maximize and de-risk their investment. 

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 In this issue of Sequence we zero in on three innovative examples of genomics applications relevant to Atlantic Canada. Three years ago, Genome Canada and Genome Atlantic launched a large-scale R&D project aimed at tackling Microbiologically Influenced Corrosion (MIC), which is a multi-million-dollar problem for our oil and gas energy sector.  We caught up with project co-lead Dr. Lisa Gieg to find out what she and her team have learned so far and how this information could be used to help predict and manage MIC.  At RPC, we met up with Neri Botha to see how using naturally occurring bacteria to extract metal could be a viable and environmentally friendly solution for the mining industry.  And we talk with two plant geneticists who are passionate about helping the region’s apple industry shine – Dr. Sean Myles dishes on apple breeding (and cannabis traceability) and Dr. Zoë Migicovsky tells us why her love of apples drew her to Nova Scotia (watch our video profile and story on Zoë.).