World Oceans Day – eDNAtec takes on challenge of monitoring marine biodiversity

To mark World Oceans Day on June 8th, eDNAtec, a Canadian specialist in environmental genomics, has announced that it has sequenced over six trillion DNA bases and made four million species-level detections from ocean and marine samples since its founding nine years ago. In so doing, eDNAtec is transforming the monitoring of biodiversity in the oceans and has made major contributions to six of UNESCO’s 10 Ocean Decade Challenges, including on protecting ecosystems, feeding the global population and unlocking ocean-based solutions to climate change.

“World Oceans Day’s mission is to catalyze action for healthy oceans,” says Dr. Mehrdad Hajibabaei, founder and chief scientific officer of eDNAtec. “At the core of this mission is an urgent need for capacity and scale to measure and monitor ocean health, especially when it comes to the vast biodiversity of the ocean. At eDNAtec, we are revolutionizing biodiversity detection and monitoring using cutting-edge genomic tools. We are working with all ocean sectors to help them in ocean stewardship and protection.”

eDNAtec is a pioneer in environmental DNA (eDNA) metabarcoding. Rather than collect physical specimens of all the organisms in a volume of ocean water, which is expensive, time-consuming and usually far from comprehensive, eDNA metabarcoding determines biodiversity by analyzing the DNA present in a small sample of water.

All organisms have a propensity for shedding biological material, and thus DNA, into their surrounding environment. A sample of ocean water will therefore contain DNA from all the organisms that have recently come into contact with it, from bacteria and plankton to fish and marine mammals, providing a comprehensive record of the biodiversity.

On expedition in the Baffin Bay in the Arctic in collaboration with Indigenous commercial fisheries, Nunavut Fisheries Association, to collect eDNA samples to support local fisheries development.

In practice, eDNA metabarcoding involves amplifying a particular gene that is possessed by all marine organisms but exists in slightly different forms in each species. Once amplified, all those different forms of the gene can be sequenced to determine what species they belong to, thus revealing the full range of species that have been in contact with the sample. eDNAtec has developed an innovative suite of workflows and standard operating procedures for conducting these analyses, which together form an ISO-certified process called EnviroSeqÒ.

This begins with collecting samples of ocean water, which are sent to eDNAtec’s laboratory – the Centre for Environmental Genomics Applications (CEGA). Here, the different forms of the gene are amplified by the polymerase chain reaction (PCR), using eDNAtec’s bespoke primers (synthetic strands of DNA with a sequence complementary to a common region on all forms of the target gene), and then sequenced with next-generation DNA sequencers. Finally, the data generated by the sequencers are interrogated by state-of-the-art informatics techniques to identify the different gene forms in the sample and the species they came from.

eDNAtec performs this eDNA metabarcoding service for clients in the oil and gas, fisheries, aquaculture, and offshore wind industries that want to know how their activities are impacting marine biodiversity, a growing regulatory requirement. This often comprises conducting an initial study to determine the baseline biodiversity in an ocean region and then monitoring how that biodiversity changes over time. It can also include detecting specific species of concern, whether unwanted pathogens and invasive species or rare, endangered species, and identifying bioindicator species, which can indicate the general health of a marine ecosystem.

Collecting water samples for eDNA analysis from a Niskin rosette water sampler in the South Atlantic.

Through its work with its various clients, encompassing over 170 projects in all the world’s oceans, eDNAtec has contributed to six of the 10 Ocean Decade Challenges set out by UNESCO’s Intergovernmental Oceanographic Commission. For example, its work with the Canadian government conducting baseline biodiversity surveys and monitoring for marine protected areas contributed to the ‘Protect and restore ecosystems and biodiversity’ challenge. Its work with the seafood sector on enhancing the efficiency and productivity of fisheries and aquaculture contributed to the ‘Sustainably feed the global population’ challenge. Its work with the energy sector on evaluating seagrass and mangrove ecosystems for carbon capture contributed to the ‘Unlock ocean-based solutions to climate change’ challenge.

eDNAtec sequencing team lead Emily Porter operates the Illumina NovaSeq 6000 ultra-high-throughput DNA sequencing platform.

eDNAtec also works closely with indigenous groups in Canada, including community engagement, capacity-building, and youth outreach and education. This is yet another aspect of eDNAtec’s ongoing efforts to use its technology and expertise to help protect the world’s oceans and sustain the blue economy.

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