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Disrupting species identification: How using DNA barcoding and environmental DNA is changing the way scientists identify organisms in the field

This picturesque pond near Hamilton, Ontario is more than a pretty scene—it’s a natural habitat full of eDNA. With only a sample of water, Stantec and partners can tell what species reside—or don’t—in the aquatic environment. This non-invasive, efficient, and accurate method is expected to disrupt conventional sampling and provide leading-edge solutions for clients.

Barcodes are everywhere. They identify our computers at work, our groceries at the supermarket, and that snappy new shirt you bought last weekend. Barcodes make item identification quick and easy.

So why not use the same concept—quick and easy identification using technology—to identify species in nature? Like a barcode pulls a match from a database, could an organism’s DNA barcode be used to identify it from a crowd of similar species more accurately? These are the questions Environmental Services principal Mary Murdoch (Fredericton, New Brunswick) asked in 2012.

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She applied for and received Greenlight research funding, partnered with the University of Guelph’s Biodiversity Institute of Ontario (BIO), and went to work sampling DNA from benthic invertebrates (tiny organisms that live in bodies of water) as part of an environmental assessment for a client who operates a pulp mill in New Brunswick.

The scientists at BIO had already developed the DNA barcoding process, Mary applied it to Stantec projects. This partnership would become vitally important.

Conventional vs. barcode testing
For Mary’s project, biologist Joe Keene (Guelph, ON) used taxonomic morphology (the conventional method that matches physical features to known species), while BIO scientist Dr. Sarah Adamowicz used DNA barcoding (genomic matching), to identify species from a stream on a work site. Although matching physical features is currently the conventional method for species identification, it can sometimes be inaccurate—especially if species are similar visually, or if a species is missing parts and, as a result, looks like a different creature.

“A lot of our studies are rooted in understanding what particular species are present in a body of water,” Mary explains. “DNA barcoding is a new way of identifying species—it’s more objective than using physical features because it identifies a species by looking at its DNA.”

Specifically, Mary and the scientists at BIO look for a sequence of nucleotides within the genome to determine the DNA barcode. New barcodes—which are all matched to organisms using conventional methods—are added to BIO’s library on a weekly basis at the rate of one million per year. The library’s name? BOLD—the Barcode of Life Data system.

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Mary’s project contributed to the library, too. Of roughly 100 species represented in samples taken from the river system in question, Stantec and BIO both determined the species level for one third of the organisms. For another third, BIO got to an even lower taxonomic level. And for the remaining third, there was no record in the BOLD library—meaning the project provided the barcode sequences and the morphological match for these species and therefore added to the BOLD library.

“That was an important scientific contribution. We get recognized for that in their database because we’re able to say we provided the samples for the library records,” Mary explains, saying Stantec continues to regularly contribute to BOLD.

She adds, “The promise here is that DNA barcoding will allow us to identify species more quickly, more accurately, and less expensively in the future.”

Expanding to eDNA
So, what did Stantec’s initial Greenlight investment in Mary’s barcode DNA project return? An understanding of how to use the DNA barcode tool for similar studies.

“It allowed us to dip our feet in the water, essentially, and see if we wanted to swim. The pool is good,” Mary laughs. “A number of our staff have looked at these genomic tools and have started to pull them into projects.”

The next step? Testing for environmental DNA—or eDNA—in water. Mary explains that organisms shed cells (which include their DNA) into their environment. That environment can then be tested for the presence of DNA from the species scientists are studying. This way, scientists don’t need to directly capture or harm target species, they simply need to sample the environment in which they live and then look for their DNA in the sample. It’s also safer and more efficient for scientists in the field, not to mention more rapid.

The value of the eDNA method for confirming the presence or absence of a species is demonstrated alongside more conventional field methods, which is the direction the industry is now headed.

            Related Item: Read more on eDNA and environmental monitoring

Aquatic scientist Pam Reece (Sidney, BC), for example, is working with government and academic partners to use eDNA to survey remote watersheds for the presence of white sturgeon in British Columbia. This endangered and elusive fish lives in remote watersheds and large rivers, making conventional sampling difficult. Pam’s project will see if eDNA can be a more cost-effective and practical tool to confirm the presence of white sturgeon in remote areas.

“eDNA is an emerging tool for biodiversity assessment that will set us apart from our competition,” says Pam. “And it will get us working closely with influential project partners in government and academia.” 

Conventional sampling for the presence of white sturgeon can be a challenge…

Environmental scientist Dave Kikkert (Salt Lake City, UT) is also using Greenlight funding to develop, test, and use eDNA markers (similar to DNA barcoding), for the northern leatherside chub of Idaho, a near-threatened and notoriously hard to detect fish. Because the fish is small and often found only in a few places within a watershed, it can be hard to find using conventional sampling. He and his industry, government, and academic partners are planning a large sampling effort this season to develop a more comprehensive understanding of where the species lives, which will help protection efforts.

“We are in the early stages of working with this technology, and are partnering with research institutions and land management agencies. These partners have been very appreciative and impressed with the willingness of Stantec to put their own money and time into eDNA research,” says Dave. “In southern Idaho where my northern leatherside chub project took place, Greenlight has given us a great reputation with these agencies and institutions who see us more as a partner than a service provider.”

…and it’s the same challenge with the northern leatherside chub. With eDNA, scientists can sample water in a habitat to confirm the presence or absence of a species—a method that’s easier on the fish and faster for Stantec and our partners.

Disrupting the common lab
But there’s a challenge to overcome. As Mary, Pam, and Dave—along with other industry scientists—well know, it can take months for simple sample results to be returned from academic labs. So Stantec and BIO extended their partnership to help commercialize BIO’s research outcomes and develop a groundbreaking new tool for eDNA testing.

 “What we’re doing with Stantec is bringing the lab to the field,” says Mario Thomas, BIO’s chief executive officer.

Together, Stantec and BIO are developing and validating a handheld “pocket lab” device that tests eDNA samples on the spot. The device provides results to researchers in the field in a little over an hour and is connected to a mobile phone to send the results from the field to any Stantec location for future data management.  

“This changes everything,” says Mario. “In innovation lingo, this kind of advancement is called ‘disruptive.’ The device is going to disrupt the way biodiversity assessments and monitoring are done around the world. It’s more reliable, it’s fast, it’s less costly—it changes everything.”

Stantec’s vision and willingness to be an early adoptor of this new technology underscores what’s already a “very, very important relationship,” Mario added. “This is where the collaboration with Stantec becomes critical: we are a lab, we are researchers, we don’t have access to locations. Stantec, on an ongoing basis all over the world, carries out projects, has access to locations, and faces real-life challenges. This field validation is key.”

This technology samples eDNA in the field. Together, Stantec and BIO are developing a method where results from eDNA samples taken in the field are obtained in just a little over an hour and transmitted directly to Stantec associates back in the office.

The value of partnerships
Mary agrees with Mario about the vital nature of the Stantec-BIO partnership. In addition to advances with DNA barcoding, the BOLD library, eDNA, and the pocket lab, Mary says perhaps the most valuable outcome of the Greenlight project has been the development of partnerships with key contributors both within and outside of Stantec.

Those partners include the University of Victoria, the University of Alberta, and the Rocky Mountain Research Station (part of the U.S. Forest Service). And within the company, Mary now works with a team of scientists, each with their own eDNA project and their own industry, client, academic, and government partners. “Greenlight is a good return on partnerships, spawning new ideas, and creating opportunities and solutions for clients,” she says. “The program is a great way to use innovation for business development, to deepen our relationship with our communities, and to deliver tailored solutions to clients.”

Mary—and Stantec—will continue to take a leadership role in the industry with DNA Barcoding and eDNA solutions for clients. “We’re building on the work started in 2012 with the DNA barcode project, we’re adding to the BOLD library, and we’re applying these new technologies to more projects to really build our expertise in the use of these tools, build confidence with regulators, and help our clients become leaders in this field, too.”

Do you have an idea about using eDNA or DNA barcoding? Contact Mary, Pam, Dave, Marc, or Joe.

About Mary
With more than 20 years of experience in environmental consulting, Mary focuses her natural talents on environmental assessment and aquatic environmental effects monitoring for industrial, commercial, institutional, municipal, and infrastructure clients. Read more about Mary.

About this article
This article is part of an ongoing series focusing on the value Stantec’s Greenlight program brings to clients, communities, and employees. Through Greenlight, Stantec invests up to $2 million annually to fund employee ideas that benefit our clients, community, and Company. Greenlight is part of our Creativity & Innovation Program, which celebrates and encourages creativity and innovation at work and in our work. Check back soon for another story in our Greenlight series.

The promise here is that DNA barcoding will allow us to identify species more quickly, more accurately, and less expensively in the future.” – Mary Murdoch

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