Aquaculture – ACENET

Predicting the Future of Fisheries

Ian Bradbury uses DNA technology to understand what aquatic species — whether Atlantic salmon, cod, crab or lobster to name just a few — Eastern Canada has and how they might respond to stressors such as climate change.

“We look at how things are adapted to the environment using genetic and genomic tools and then we use machine learning and climate models to look at how they might respond in the future,” explains Bradbury, a research scientist with the Department of Fisheries and Oceans and an adjunct professor at Dalhousie and Memorial Universities. (Genetics is the study of how genes work while genomics is the study and mapping of genomes, or the full set of genetic instructions for an organism.)

The goal is to be able to make projections in terms of the rate of change happening with a specific species, as well as how it will respond to climate change and how that might impact fisheries and other stakeholders using those resources in the future.

The classic example, he says, is Arctic char in Labrador, which is culturally important for Indigenous groups along the coast, ecologically important because it’s the dominant freshwater coastal fish species there and notable because it’s at the southern portion of its range in Labrador.

“So it would not be surprising that climate change might be pushing it northward,” Bradbury says. “And we’ve done a lot of work over the last couple of years, some of it using ACENET, to understand how Arctic char in Labrador and north of that, are adapted to their climate and then how climate change might affect that.”

Bradbury is building a baseline or map of genetic variation in Arctic char. His projections suggest that the Arctic char’s range will start moving north, meaning the southern portion of Labrador will no longer be suitable for char, which will have implications for the people living in the area and for the ecosystems that remain there.

Bradbury and his team need ACENET because genetic tools generate massive datasets — multiple terabytes in fact — and since data management and data analysis are most of what they do, they couldn’t do their work without ACENET.

“We don’t have access to the computational power that my students would need to do these sorts of analysis,” Bradbury says.

The students he supervises are sequencing the entire genomes of aquatic species and then analyzing them for differences among individuals and populations.

“We’re making associations with climate on a set, and we’re doing projections for future impacts,” Bradbury says.

While there are other options out there, he says, ACENET is particularly useful because it’s accessible to students. His research team includes students at all levels and postdocs at both Atlantic campuses.

Curbing Sea Lice in Salmon Farming

Gregor McEwan wants to help salmon farmers manage sea lice on their farms, and he’s using supercomputing to do it. It seems odd to think of research into aquatic life involving high-powered computing, but that’s what McEwan, a research scientist, is doing. He works under the supervision of Professor Crawford Revie in Revie’s lab in the Atlantic Veterinary College’s Department of Health Management at the University of Prince Edward Island. Salmon farming is an industry worth more than $16 billion worldwide, and Canada is the industry’s fourth-largest producer after Norway, Chile and Scotland. Farmed salmon is raised from eggs on land facilities and, when large enough, moved to cages in the sea. The fish are kept in the cages until they reach harvest weight — typically three to five kilograms. After that, they’re sent to processing plants to eventually become fillets available through retail. But often, in the sea cages, sea lice, among the most pervasive problems facing salmon farmers, invade. They attach to the salmon and feed off the fish’s mucus, flesh and blood, causing discomfort and reduced immunity for the salmon. “Usually, [due to immunity issues], they then get sick from something else, but enough sea lice will also kill the salmon,” McEwan says. “It’s a major issue for salmon farmers and they’re especially interested in using treatment methods they have — whether chemicals or mechanical treatments such as warm water baths — to solve it.” McEwan is trying to determine how they can use existing treatments most effectively and in what kind of patterns they should use them. “I build computer simulations to try out different strategies,” McEwan says. “It’s expensive to try them on the salmon farm in real time, so it makes sense to simulate them on computers.” To make the simulation work, he must set parameters — such as ‘how many lice are flowing on to the farm?’ — which is tricky. Such information is unknown because it’s not feasible to count lice in the open sea around each farm. “I take all the historical information I can get about the environment and the farmers’ weekly count records of sea lice on the salmon,” McEwan says. “I train the model with that information and extract the relevant parameters. I use machine-learning algorithms to get the correct parameters for the model. I can use the trend model to create predictions for the future. We can run scenarios where we say, ‘okay, what if this happens, or what if we use this kind of strategy?’” One of the things McEwan must consider is the ability of the lice to evolve a genetic resistance to the chemical treatments. For example, past research investigated the repercussions of wild salmon coming near the farm cages. Wild salmon carry lice, but McEwan’s discovered that, because their lice are genetically naïve to the chemical treatments, they bring what he calls a “genetic cleaner” to the equation. “Yes, you end up with a few more lice in the short term, but whatever treatments you’re using are more effective and work a lot longer because the genetic resistance is being cleaned out of the population,” he says. “It’s actually a net positive.” For McEwan’s simulations, ACENET’s resources are vital. His lab has powerful computers, but nothing on the scale of ACENET. He says without ACENET, everything he’s doing would take months instead of weeks. “We’d never be finished.”

A Crusade to Protect Crustaceans Against Climate Change

Fraser Clark is a man on a mollusc mission — or you could call it a crustacean crusade. The Dalhousie University animal science and aquaculture professor studies the immunology of crustaceans with a goal of understanding their health and what pathogens threaten them, particularly as East Coast waters warm, and the pH drops, as a result of climate change. He concentrates his research on the wild lobster, crab and shrimp fisheries, with a secondary focus on commercial shellfish, including scallops, oysters and mussels. “My work is on the health, disease and stress in these species,” Clark says. “I look at their immune response, their stress response and how they interact with pathogens.” His research aims to contribute to the health of the Atlantic Canadian fishery industry, helping fishers to have access to hardier and faster-growing products. “With the oysters, mussels and scallops, we find markers for disease and stress resilience, especially as it concerns the ocean’s response to climate change,” he says. When it comes to major wild fisheries, he says, only crustaceans remain. Lobster is the biggest, then crab and shrimp. “We’re finding some interesting differences between crustaceans in the same area, but I can’t say much about pathogens yet,” he says, stressing that none of the pathogens affects humans. “Some are new pathogens, some haven’t been studied before. We’re cataloguing what’s normal and what could come up the Eastern seaboard of the U.S. as waters warm. We know what’s down there, we know what’s up here and we’re able now to monitor it because we have baseline studies.” The differences in immune systems of crustaceans in the same habitat can be used as health-markers, something that currently doesn’t exist for crustaceans. Practically speaking, it’s useful to understand the immune systems of lobsters, for example, as they’re more valuable when alive. When they’re killed, cooked and processed, they are worth less on the market, but live ones that die before they’re sold aren’t worth anything at all, he notes. Surprisingly, he came to this work after doing a master’s in cancer research. “I didn’t feel I was having much of an impact in my local area,” says the Kensington, P.E.I.-born researcher. “So, I got involved in work at the Lobster Science Centre. Now there’s a local impact as I interact with fishers, industry, aquaculture associations and local governments. I can make a difference to their industry.” To do his work, Clark uses resources provided by Compute Canada. He uses its high-powered computing resources to sequence transcriptomes, which are similar to genomes. He then compares different immune genes in different species. He compares the different sequences and constructs models to see how closely related they are. “We’re really interested in how closely related the immune systems are of crab, lobster and shrimp all living in the same area,” he says. “They seem to get sick from different things even though they’ve all been growing in the same area for the last 150 million years.” To that end, the GenAp Galaxy web portal application hosted by Compute Canada has been helpful. “It allows biologists to use high-end computing resources without needing to do high-end coding,” he says. “As long as we understand the assumptions and limitations of the tests, we can get user-friendly data. My undergraduates and graduate students can learn to use these computing resources within days. It’s exceptionally helpful for biologists.”