DNA Metabarcoding Reveals Hidden Biodiversity
Genomicist Mehrdad Hajibabaei empowers Canadian communities to monitor bioindicator species in their local freshwater ecosystems.
Hannah joined The Scientist as an assistant editor in 2023. She earned her PhD in neuroscience from the University of Washington in 2017 and completed the Dalla Lana Fellowship in Global Journalism in 2020.
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Healthy freshwater ecosystems are crucial for supporting wildlife and supplying humans with necessities like food, water, energy, and transportation. Despite this, there is a remarkable lack of data on the status of many waterways, especially in large, sparsely populated countries like Canada.
The citizen science project Sequencing The Rivers for Environmental Assessment and Monitoring (STREAM), led by Mehrdad Hajibabaei at the University of Guelph, aims to close these data gaps through partnerships with communities across the country. In STREAM, community members collect samples of river sediment and send them to the Hajibabaei laboratory, where researchers analyze the diversity of bottom-dwelling invertebrates and certain types of microalgae as bioindicators of ecosystem health.1
Historically, this would have required extensive evaluation by highly trained taxonomists painstakingly sorting one miniscule species from another under the microscope. To streamline this process, Hajibabaei and his team use DNA metabarcoding. After extracting DNA from the substrate samples, they amplify and sequence specific sections of the genome that are highly variable between species. Then, using the bioinformatics pipeline MetaWorks, they compare these identifying “barcodes” to a DNA reference library to determine which species are present.
Researchers can use these data for large-scale projects, like investigating the role of biodiversity in ecosystem function or the effect of climate change on freshwater species. They also use the data to answer questions about local ecosystem health posed by the community, such as whether a problematic invasive species is present, or whether restoration efforts are having the desired effects.
“We are basically democratizing access to biodiversity data,” said Hajibabaei. “Biodiversity is vast, but a lot of it is too small for us to see. The technologies that we have now will allow us to see that biodiversity through the lens of DNA, and let anyone, anywhere, access that information… hopefully leading towards a society that values biodiversity more.”
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- Robinson CV et al. Ecol Indic. 2022;145:109603.
