STREAM & DNA metabarcoding

STREAM & DNA metabarcoding
DNA metabarcoding is an emerging tool for monitoring present biodiversity. DNA metabarcoding uses bulk-benthos samples collected via the CABIN methods and gene sequencing linked to DNA/RNA barcode libraries to allow for faster, more complete profile of biodiversity content from very small samples.

STREAM & DNA metabarcoding

Key Takeaways:

  1. STREAM (Sequencing the Rivers for Environmental Assessment and Monitoring) is a community-based project that involves the collection of benthic macroinvertebrates from rivers across Canada to generate a better understanding of the health of river systems.
  2. The STREAM project is a validation project for the cutting-edge technology of DNA metabarcoding.
  3. DNA metabarcoding uses bulk-benthos samples collected via the CABIN methods and gene sequencing linked to DNA/RNA barcode libraries to allow for faster, more complete profile of biodiversity content from very small samples.

DNA metabarcoding is an emerging tool for monitoring present biodiversity. This is a made-in-Canada technology and now has the opportunity to move beyond proof of concept to demonstrating the possible.


This project uses a modified version of the Canadian Aquatic Biomonitoring Network (CABIN) protocol, developed by ECCC, to collect the benthics, which are the small animals on the bottom of streams. Benthic invertebrates are strong indicators of water quality since some are highly sensitive to pollutants and other changes that impact aquatic ecosystem health.

Living Lakes Canada trains and certifies interested organizations using the CABIN protocol adapted for STREAM and assists interested organizations in their first year of sampling, offering knowledge in site selection and monitoring, where appropriate. The organizations then commit to maintaining the project in later years, uploading results to the CABIN database and sharing data in open platforms.

Participants learn and build skills for stream health assessments, open sourced data inputs and access while using new, more cost-effective technology.


Originally Co-delivered by Living Lakes Canada, World Wildlife Fund-Canada, Environment and Climate Change Canada and University of Guelph, STREAM (Sequencing The Rivers for Environmental Assessment and Monitoring) is contributing to the better understanding of aquatic ecosystem health through the DNA metabarcoding of benthic macroinvertebrate samples collected across Canada. Currently the project is delivered by Living Lakes Canada and the University of Guelph, and continues to provide DNA metabarcoding that is potentially faster, more accurate and less expensive than morphological taxonomic identification given the greater capacity to analyze samples in bulk. It also has the potential to provide enhanced biodiversity information.

In 2019, the University of Guelph received a $2.6 million grant from Genome Canada to support DNA metabarcoding sample analysis of benthic macroinvertebrates for three years. The goal was to collect 1,500 samples in partnership with community-based water monitors across Canada and provide sample analysis for free, and provide training in the modified DNA-specific CABIN methods in 15 nationally distributed watersheds (5 watersheds per year from 2019-2021) based on data deficiencies and local capacity. The original project was extended for an additional year in 2022.

For 2023, Phase 2 of STREAM is continuing as a partnership between the Hajibabaei Lab at the University of Guelph’s Centre for Biodiversity Genomics, Living Lakes Canada and ECCC.

For more information, view the 2023 STREAM Information Handout.


Year 1 of the STREAM project focused on 5 priority watersheds: 

  • Columbia Basin, British Columbia
  • Skeena Basin, British Columbia
  • Peace/Athabasca, British Columbia
  • Bow Valley, Alberta
  • Sudbury,Ontario


Year 2 of the project was delayed due to COVID-19 public health restrictions, but focused on 2 additional priority watersheds: 

  • Upper Fraser-Nechako 
  • Upper South Saskatchewan 

We also supported Year 1 participants with collecting and shipping their Year 2 samples.


The following trainings took place in 2021 for Year 3:

  • Nelson, BC June 15-16
  • Rocky Mountain House, AB June 19-23
  • Kenora, ON August 6-9
  • Thunder Bay, ON August 9-13
  • Fort Nelson, BC August 25-29
  • Buick, BC August 30-September 3
  • Whitehorse, YT September 7-10
  • Ottawa, ON September 27-30
  • Invermere, BC October 11-15


For Year 4 of STREAM (2022), the following training courses took place:

  • Kimberley, BC, June 2-3
  • Fredericton, New Brunswick, June 14-17
  • Stó:lō First Nation, September 12-14


The 2018 field season, LLC was in the Liard, BC watershed in Northern B.C. (Canada's ninth largest watershed) working in partnership with the Dane Nan Yḗ Dāh Guardians to establish a biomonitoring program and host a two-day Program Manager/Field Tech CABIN field practicum.

There was also a training in the Skeena watershed, Smithers, BC for a Field Assistant level CABIN practicum in partnership with the Environmental Stewardship Initiative of BC.

The 2017 Field Season included:

  • Sunshine Coast Biomonitoring and eDNA Pilot Project
  • Central Ottawa Biomonitoring and eDNA Pilot Project


We are encouraging anyone interested in understanding the health of their river or stream system to contact us to learn more about the STREAM project. There are multiple levels of possible participation.

If you are interested in collaborating to support the understanding of Canada’s rivers health please email Living Lakes Canada Program Manager Raegan Mallinson:

See Raegan's profile.


To learn more about the program, look for the following recordings under Resources in the right hand column:

  • A film about the STREAM training with the Binche Whut'en First Nation in B.C. that was shortlisted in the 2021 Let's Talk About Water International Film Fest.
  • A film about the STREAM project that was released on March 22, 2020 for World Water Day.
  • A discussion about WWF-Canada's 2020 Watershed Reports and the role of STREAM hosted by WWF-Canada's Freshwater Specialist Catherine Paquette and Living Lakes Canada Program Manager Raegan Mallinson, that aired on November 9, 2020.
  • A three-part webinar hosted by Living Lakes Canada in spring 2021 to introduce the STREAM project to anyone interested in community-based water monitoring.



STREAM & DNA metabarcoding

Status - Active


Water Bodies
Rivers, Creeks and Streams
AlbertaBritish ColumbiaColumbia BasinNationalOntario
AcademiaCommunity groupsFirst NationsGovernment – Federal
Types of Work
CABINCitizen ScienceCommunity Based MonitoringDataMonitoringProtocol Development

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