Unlocking mysteries from a single drop

Anything that lives in water leaves pieces of itself behind. Fragments of plants break off into the current. Fish leave trails of poop in their wake. Fur washes off a paddling beaver. A snail sheds mucus into the surrounding water. A drop of water contains a record of history—one told by the traces of tissue that living things leave behind.

These cells adrift in the water column contain genetic material (DNA), and scientists are increasingly looking to these traces as a rich source of data. Using sensitive detection methods, environmental DNA—or eDNA—can indicate what species were recently present in the ecosystem. This is helpful for a wide range of applications, from monitoring for indicators of water-borne pathogens to detecting elusive invasive species or species at risk.

Researchers from the University of Alberta’s School of Public Health aim to better understand microbial biological hazards present in our waterways.

Water, water, everywhere, but not enough samples

During warm summer months, many Albertans seek relaxation at the province’s lakes and rivers. But a brush with parasites can put a serious damper on the fun. Preventing water-borne disease is a key research interest for Patrick Hanington, an associate professor at the University of Alberta’s School of Public Health.

His team aims to better understand microbial biological hazards present in our waterways, such as swimmer’s itch, fecal bacteria and blue-green algae. eDNA has been a valuable tool for this research, enabling the tracking of microbes over space and time. But while his group has sophisticated tools at their disposal, getting sufficient samples to the lab is a significant hurdle.

“It’s really difficult for individual researchers like my group and I to go and get samples,” said Hanington, “and you need to have a certain frequency of sampling in order to get reliable information.”

Microbe populations can change quickly over time. A change in weather or water flow can dramatically impact the progression of an algae bloom or bacteria contamination. To understand whether a lake is safe to swim in or if a drinking source is contaminated, multiple samples need to be taken over time. To understand patterns at the provincial scale, sampling must be replicated across many distant waterbodies. This is a challenge for eDNA as samples must be processed within about 24 hours of collection. Collecting thousands of samples and driving them back to a centralized lab quickly becomes impossible.

Fortunately, researchers like Hanington are not the only ones interested in better monitoring. Many community members take keen interest in their local watersheds. Their motivations range from ensuring safe recreation and drinking water, to preventing the spread of invasive species, to conserving species at risk. While individuals and organizations conduct regular water sampling across the province, these groups often lack access to tools that could enable  the collection of more informative data—like eDNA.  If community members wanted to sample eDNA, they would need to somehow transport those samples to a university or other well-equipped institution. But what if there was a way to bring the lab to them? And what if, while pursuing their own questions, they could collect data on key microbial hazards, all from the same water sample?

“We envisioned that one way to expand the scope and scale of some of this water sampling was to involve community partners,” stated Hanington.

Putting high-tech tools in community members’ hands

A portable backpack sampling unit enables collection of water samples from even the most remote locations.

Community-based monitoring is not new, but typically involves relatively simple data collection. Where more advanced techniques are used, community members tend to lose the flexibility to pursue their own questions as they must operate under strict research protocols. eDNA is special in this regard. A single water sample has the power to answer many different questions, like what fish are present in the lake, or whether the lake has harmful levels of fecal bacteria. And because the DNA from multiple species can all be analyzed at the same time, an analysis performed by a community partner can be just as useful to Hanington and his team as one they collected themselves—even if they’re interested in different species. Supported by Alberta Innovates, Hanington leads a program to enable province-wide water monitoring by empowering community partners to sample eDNA.

Measuring eDNA involves a process known as qPCR (quantitative Polymerase Chain Reaction). First, the water is passed through a filter that catches any eDNA present in the sample. The filtered contents are then “washed” through a series of special buffer solutions, to purify and preserve the DNA. The purified DNA is then ready for analysis with a qPCR machine.

qPCR involves the use of special enzymes that make duplicate copies of select sequences of DNA. If even a single strand of the target DNA is present in the sample, the enzymes will rapidly duplicate it into millions or even billions of copies for easy detection. The number of copies produced indicates the quantity of the DNA sequence present in the original sample. qPCR is a powerful tool capable of detecting the tiniest traces of DNA, but it requires the careful preparation and purification of the samples while they are still fresh. To make this possible, Hanington’s team needed to train community members to properly collect and prepare samples on-site and, if interested, quantify the eDNA themselves using a portable qPCR machine.

“Part of our focus has been to understand how we can tweak the training to make sure they’re getting the best data they possibly can,” said Hanington. “People who get introduced to this technique; they have no idea of the small scale that they’re working at until they start doing it. You’re working with clear liquid that’s less than a drop of rain, basically.”

Once community partners are up and running, they have a great range of flexibility. The qPCR kits are portable and efficient, with partners able to collect and analyze a sample within a few hours. As the program has expanded, participants across the province are reliably collecting and quantifying eDNA out of their homes, their garages or even the back of their car. In the past year, almost 6,000 samples have been analyzed— an impossible feat for even a dedicated team of graduate students.

The program’s longest-running community partner, the Baptiste Lakes Stewardship Society, has used eDNA to narrow down drivers of blue-green algae blooms in their lakes.

“At first we thought it was sewage problems, but we ascertained that’s not the biggest issue,” recalled society president Dennis Irving. “The DNA monitoring has helped us narrow it down to some of the hotspot areas, and we will be doing some more testing this summer.”

Hanington believes the freedom of community members to pursue their own research interests is key to the program’s success.

“We have questions we want to answer, but we’re not restricting the community partners to our targets. It allows us to tailor projects to their needs,” stated Hanington.

Expanding the scope of official water monitoring programs

Beyond small-scale community partners, the program has fostered government partnerships, spurred by the COVID-19 pandemic. In 2020, some official monitoring programs were paused to limit travel and close contacts. University field research was also limited.

“We actually thought to ourselves, it’s really a perfect system for a situation like this, where there’s restricted sampling and it’s difficult for the traditional programs to work. If we have community partners who are already at these lakes collecting samples, there can be a lot less interaction between people,” said Hanington.

Hanington’s team partnered with Alberta Health to collect samples for their beach monitoring program by leveraging community volunteer networks. In the years since, the partnership has evolved into an effective pipeline for sample collection, involving the Alberta Lake Management Society’s LakeWatch volunteers. Beyond fostering lasting partnerships between the Government of Alberta and community partners, the beach monitoring program provided a unique scientific opportunity to validate community partner data.

“The program allowed us to have samples collected that were the exact same sample that was used as part of the official beach monitoring program,” said Hanington. “We could take the gold standard test done through the government testing facility, and compare that to our community partner qPCR data, all from the exact same water sample.”

What they found was energizing: 86 per cent of the time, data generated by the community partner is within 10 per cent of the gold standard. While expert monitoring programs are essential, the trial demonstrated community-based monitoring can generate reliable data and expand first-line surveillance over a much greater area.

“If a community member gets a positive, it allows you to target that location or region with the official program,” added Hanington.

Supporting conservation through invasive species detection

Alongside public health, eDNA-based tools can also support conservation. Early detection of invasive species enables intervention before they spread out of control. Whirling disease—caused by an invasive parasite that infects trout, whitefish and salmon—is a key concern in the southwest region of the province.

“In 2016, when whirling disease was detected in Johnson Lake, Alberta Innovates put us in touch with some of the people in Alberta Environment and Parks. We ended up working with them to design a qPCR test that could be used for environmental samples,” said Hanington.

As the provincial program has rolled back, Hanington has helped interested community partners take over the whirling disease monitoring. These partners in southern Alberta are now testing for whirling disease, zebra mussels and Chinese mystery snails.

“Invasive species and species at risk, such as bull trout, have really emerged as targets of interest with the groups we’re working with. And it’s really pulled us towards true eDNA-based monitoring where rather than looking for the organism in the water, you’re looking for DNA it has shed into the water,” stated Hanington.

Inspiring the next generation of Alberta’s water stewards

Community partners extract DNA from water samples they collected from Baptiste and Island Lake.

One of the most exciting outcomes to emerge from the program has been the involvement of Alberta students. During a teacher’s networking event, Alberta Innovates suggested that Inside Education, a natural resources education non-profit, connect with Hanington.

“Inside Education had worked with Alberta Innovates previously on lots of different projects,” recalled Kathryn Wagner, project manager for Inside Education. “We focus on bringing meaningful environmental education to Alberta classrooms and enriching the curriculum. Taking it the step beyond: what’s cool, what’s innovative, what’s happening on the ground?” Intrigued by the work of Hanington’s team, Wagner took a group of teachers to tour Hanington’s lab.

“He mentioned that a limiting factor is collecting water samples and getting the breadth of samples needed to answer key research questions,” said Wagner. “And I thought, ‘Oh, we’re out with students all the time! We work with schools all across the province.’ I thought, ‘I wonder if there’s a way to connect what we’re doing.’”

To test the feasibility of student involvement, Hanington brought a qPCR testing system to the 2016 Navigate Youth Water Leadership Summit in Canmore. Students in attendance were invited to extract DNA from water samples they had collected near their schools and analyze them for targets like cyanobacteria and fecal indicators.

“It really showed the proof of principle, that within a one-hour training session, we could talk to them about it and they could extract DNA and run a qPCR sample, and 20 minutes after the session is over the data is done,” recalled Hanington. “It’s quite easy and with even one person who knows what they’re doing, you can have the program run really smoothly.”

“We were just trying to test the waters—pun intended—to see how effective it was to teach students and have them extract the DNA,” recalled Wagner. “We had all the students bring water from their local water bodies to the summit in Canmore. They would say things like, ‘Oh wait, we can figure out what’s living in here?’”

This began a partnership between Hanington’s team and Inside Education to bring qPCR into the classroom. Participating schools would conduct water sampling and analyze their samples in the classroom, empowering students to investigate questions about their local watersheds. The program has since evolved into a lending library, where trained teachers can request access to a qPCR system through Inside Education.

Wagner remarked on the power of engaging students in the scientific community: “Knowledge transfer to young people—to let them know there’s really great work being done, that there’s good people working on it and sharing those stories that resonate broadly—schools are an awesome conduit for that. We often say, ‘Oh hey, you’re the future generation of leaders,’ but they’re the leaders now. We just need to engage with them.”

Next steps

For Hanington, new partners continue to join the community-based monitoring program. Currently, between 40–50 partners are participating. The school qPCR program is also set to expand when students return in the fall. In Hanington’s view, a key factor in the program’s success has been the strength of its partnerships.

“An awesome dimension of working with Alberta Innovates is that they’re so good at seeing the connection between the different projects they support—and even projects that they’re not able to support—and be able to link everyone together,” said Hanington.

As the program evolves and more partners engage, community members across the province are finding new opportunities to steward their local lakes, streams and rivers.

“It’s been pretty rewarding to have a partnership with Dr. Hanington. I think lots of the other lakes around here are jealous of us because we established that partnership,” joked community partner Dennis Irving. “He’s been just ace—and very patient in training us.”

Learn more about other projects we fund through the Water Innovation Program.

This article is part of Making Waves, an annual Alberta Innovates publication highlighting water solutions we support. You can read more stories from this issue below.