How Environmental DNA Can Support the Aquaculture Industry

Published in the Cold Harvester, Newfoundland Aquaculture Magazine, Summer 2022

The sampling of environmental DNA (eDNA) is proving a game changer for ocean industries, including aquaculture.

All organisms shed into the environment traces of their DNA, which serve as reliable identifiers of species. The eDNA in one water sample can reveal a large quantity of data about the variety and number of organisms present, including even the smallest microbes.

eDNAtec is a Newfoundland-based company on the forefront of the rapidly growing eDNA technology field. Using advanced sequencing technologies and computer programs, they can sequence and identify any species from environmental samples such as water, soil or even air.

Typically, aquaculture stocks are monitored for pathogens using biological samples that are taken routinely or when there are changes in the health of animals. The use of eDNA can discover these pathogens even before they become apparent in the fish themselves. 

“There’s a range of pathogenic species, including viruses, bacteria, parasites and even algae blooms,” said Nicole Fahner, Associate Director of the Centre for Environmental Genomics Applications (CEGA) within eDNAtec. “With eDNA monitoring, you don’t need to collect the fish to detect the pathogenic or potentially pathogenic species. We can design a monitoring program that includes DNA references to all pathogens of interest, then monitor over time and watch for changes that might be an early warning of problems.”

Any aquaculture monitoring program would be designed and calibrated to the organisms of interest in the water column and the benthic environment. Water and benthic samples might be taken inside the pen, directly outside it and some distance away, as a control.  

“Pathogen detection through comprehensive eDNA monitoring helps to create a healthier ecosystem, which results in a better environment to raise fish stocks and that has a benefit for the whole ecological community,” Fahner said. “Importantly, eDNA sampling can be completed in a fraction of the time required for conventional monitoring, is highly cost effective and reveals an order of magnitude more species.”

EDNAtec established its CEGA facility as a centre of excellence to advance environmental genomics technologies for real world applications. 

“CEGA is a one-of-a-kind R&D centre with high throughput sequencing platforms and specialized data analysis tools that are completely dedicated to environmental genomics applications,” said Mark Ploughman, Senior Advisor, Sustainability, with eDNAtec. “We are one of the few eDNA labs certified to the ISO 9001:2015 standard of Quality Management System. We have developed the EnviroSeq® end-to-end standard operating procedure, hardened and tested through hundreds of genomics projects around the world. We have the latest technology, including the Illumina MiSeq and NovaSeq 6000 sequencing platforms. Last but not least, we have the people, including pioneers who were pivotal in the development of eDNA technologies along with some of the brightest young scientists in the industry.”For more information, please visit

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