NOW: Metagenomics are helping researchers understand and protect Canada’s freshwater supply: PrairieDNA, an environmental DNA (eDNA) project, launched this year to gain a greater understanding about the health and wellbeing of Canada’s lakes and river systems, while collaborating and partnering with Indigenous communities impacted by water quality issues.
Environmental DNA—often called eDNA—is transforming how scientists understand the natural world. Every living organism leaves behind tiny traces of genetic material in water, soil, or even air. By collecting and analyzing these fragments, researchers can detect subtle shifts in ecosystems. As the science of genomics continues its acceleration, eDNA is becoming a powerful tool for conservation, offering faster, less invasive, and more comprehensive monitoring than traditional methods.
eDNA lies at the heart of PrairieDNA, a Genome Canada and Genome Prairie-funded and administered project which launched in 2025. Dr. Eric Collins, Assistant Professor at the Clyton H. Riddell Faculty of Environment, Earth, and Resources at the University of Manitoba, leads the PrairieDNA project. Dr. Collins, who also leads another Genome Prairie-administered project, GENICE II, said PrairieDNA will seek to gain a greater understanding of the biodiversity among freshwater sources, mainly in Manitoba.
PrairieDNA will monitor water in places such as the Red River, Assiniboine River, the Brokenhead River, and Lake Winnipeg to understand its biodiversity and how that influences water quality,” said Collins in an interview from his Winnipeg office. “We’re collecting samples all over Manitoba and doing eDNA monitoring of those samples from natural waterways. So that’s lakes and rivers and streams, and we’re understanding the baseline biodiversity in those samples, how they change seasonally, how they change from stream to stream, and getting an idea of the total biodiversity.”
“The way we use genomics in this project is by collecting water samples and filtering all of the cells, extracting DNA from the filter, and then sequencing that using different genomic approaches. It will help us understand the diversity of life and the organisms present in the water. It will give the project a big picture view of what’s in the water and also very targeted, specific information to generate an accurate idea of the harm or the health of the water.”
“The project is heavily reliant on Oxford Nanopore DNA sequencing genomics tool for eDNA monitoring that will use a shotgun metagenomics for processing the data,” said Collins.
Shotgun metagenomics fragments all genetic material (DNA) from complex microbial communities and then sequences these pieces to reveal the full genomic content. The shotgun metagenomic approach provides deeper insights into diverse microbial ecosystems, which are common in eDNA studies.
University of Manitoba researchers collecting zooplankton in the south basin of Lake Winnipeg during the warmer months of 2025.
In addition to leveraging cutting-edge genomics technologies, PrairieDNA does not lack ambition and complexity. In addition to studying biodiversity, Collins indicated that the project will also examine human impacts on waterways and gather data on waterborne pathogens, which can pose health threats to communities.
“We’ll be studying nutrient inputs into Lake Winnipeg and their possible connection with harmful algae blooms, and our focus on pathogens will be mainly on municipal waters. We want to study water treatment systems and work with researchers who are looking at E coli and a variety of other organisms that are known to cause human harm.”
“PrairieDNA uses very sensitive techniques to find out where in the water treatment system the microbes are getting in.”
University of Manitoba students (l-r) Heather Canvin, Kiara Bocangel, and Chris Maher inspect a filter used to sample microbial eDNA from Lake Winnipeg.
At the same time, the project team will be monitoring and collecting samples, and an integral component of the project will involve strong collaborations with Indigenous leaders and communities in Manitoba and regions of Ontario.
“We had ongoing discussions and collaborations with several Indigenous communities in Manitoba and Ontario, and that formed the basis for the project,” said Collins.
“The project team is working with a number of Cree, Anishinaabe, and Métis communities in Manitoba and Ontario. It is important to understand how the data gathered from monitoring is appropriate for their needs. We want to provide these communities with useful data, perhaps via an internet portal or in translated language, so they can use the information and make decisions that best serve their people.”
“The project aims to increase monitoring capacity. We will provide training to a wide diversity of people to use eDNA tools and techniques, including Indigenous peoples.”
The PrairieDNA project is bringing together scientists and Indigenous communities to protect both people and the environment. Grounded in the understanding that human well-being is inseparable from the health of the land and water, the initiative recognizes that damage to ecosystems ultimately harms the communities that depend on them. By drawing on Indigenous knowledge and modern scientific tools, the project seeks to understand how deeply Prairie waterways and landscapes have been affected since settlement and what it will take to restore balance for future generations.
Collins said the relationships between researchers and communities started with a growing interest in human impacts on the environment, including the expansion of hydroelectric projects in Manitoba half a century ago.
“Many of the relationships with the project team and Indigenous communities were pre-existing. In Manitoba, we’re working in places like Split Lake, Cross Lake, and Broken Head, which are all along the Lake Winnipeg watershed. Previously, we had relationships with these places where water quality was an issue, much of it due to impacts from hydroelectric development on the Churchill and Nelson Rivers in the 1970s.
“The impacts of those hydro projects are still being felt, and so people who live along the watershed would like to know more about the growth of harmful algae blooms and mercury contamination. There are a lot of water quality issues in those communities, and they’re looking for ways to better understand what’s happening.”
Collins hopes that the technologies used by the PrairieDNA project team members will eventually be adapted and used in communities to monitor water supplies well into the future. That monitoring would include individuals from Indigenous communities, including young people interested in science.
“One of the models we’d like to develop is having students from those communities collect samples and then bring them to our labs. We would then teach them how to use the instrumentation and do all the techniques, and they then could take the data home to their communities.”
Collins indicated that, in addition to increasing interest in science among younger people, PrairieDNA will help further develop relationships and future partnerships with Indigenous people.
“Building relationships takes a long time, and there’s a lot of trust involved. I’ve had dozens of meetings with community members over the years. I know it will be easier to bring in new communities once you have established relationships in other places.”
“So there’s a natural growth in making these connections over time, but it’s really important that we continue these collaborations. So much of our future depends on the health and well-being of our environment and the people who live on the land.”
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Tony Bassett
Director of Communications
Genome Prairie
text/voice: 306.881.0255
email: tbassett@genomeprairie.ca
