Boldly going where no consultant has gone before: Using eDNA to monitor aquaculture

May 25, 2017 Marc Skinner

How a space-age technology can help solve our environmental challenges right here on earth


It may sound like something out of a “Star Trek” script but a new technology known as environmental DNA (aka eDNA) is far from science fiction. In fact, eDNA can help solve environmental monitoring challenges right here on earth.


Cages for fish farming in Montenegro

This newly emerging science allows extremely small traces of DNA—traces shed by organisms through bodily fluids, skin cells, or other secretions—to be detected in water and sediment samples without having to directly collect the organisms themselves. If you are trying to detect species that are rarely found in samples (think Species at Risk) or you need a sensitive system for an early warning system for microbial pathogens or parasites of concern, eDNA may be your solution.

So, how does this work? Maybe you’re interested in characterizing the benthic invertebrate community at your aquaculture site as part of your environmental monitoring plans. Normally you’d use sediment grabs, divers, or a remotely operated vehicle (ROV) to collect a sediment sample from the ocean bottom. Afterwards, you’d send those samples off to one of the few remaining traditional taxonomy labs and someone would manually identify and count all the critters in the sample under a microscope. In a few months, you’d receive your data.

Now, with eDNA techniques, you can use “batch sequencing” to quickly identify all these species based on their genomics. This rapid and sensitive tool can provide taxonomic identification results within days or weeks, as opposed to the months it currently takes to do it by eye under a microscope. Not only can eDNA give faster results from the lab but you also don’t need to spend as much time and effort sampling in the field. Since eDNA operates at the molecular level, it doesn’t require as much sample volume to get reliable data as with traditional sediment samples.

1 filter = jars of water
For water sampling, the efficiencies with eDNA are even greater. Traditionally you might collect many samples of multiple litres of water that are time consuming to collect and require much handling and processing effort. In contrast, eDNA water sampling is much faster and requires a fraction of the lab labour because you quickly filter large volumes of water. A single filter (smaller than your coffee filters at home) traps all the eDNA from the water you filter and is sent to the lab as your sample. This small eDNA filter replaces the copious jars of water from traditional sampling that would have to be stored and transported to the lab.

From detecting whether invasive species, like Asian carp in the Great Lakes, to confirming that the tuna in your sushi is really tuna, eDNA technology can help anyone who does or needs biological sampling. Every day, new advances are being made in lab methods and the hardware to sample eDNA. Our team at Stantec, and our collaborators, are helping develop and test handheld tools to allow species identifications in the field, eliminating the need to even send samples to the lab. Future R&D on integration into autonomous monitoring platforms will also allow more frequent sampling in remote areas and will better enable us to differentiate between natural fluctuations in the environment and impacts due to human activities.

Sci-fi science and the future
Even though I’m a scientist, I was never really a fan of sci-fi shows like “Star Trek.” But a quick Google search highlights how influential this television series was on a generation of scientists. The everyday tools of the 21st century—our smart phones, GPS, Bluetooth, iPads, and even automatic doors—were all once crazy futuristic contraptions only possible through the magic of Hollywood.

As I grew older, my marine biologist mind began to slowly appreciate the concept of a group of intrepid scientists and explorers packing all their best tech onto a ship to “boldly go where no man has gone before.” That’s how we’ve arrived at eDNA. From aquaculture monitoring to conserving biodiversity in the Amazon, eDNA technology can enable scientists to produce results using a fraction of the time and effort it traditionally takes to do their jobs with a molecular degree of certainty. It’s like Spock and Jacques Cousteau came together to solve environmental monitoring challenges. In my years as a grad student, I spent a lot of time and effort underwater collecting samples and back in the lab processing data.

I’m still not a sci-fi fan, but I do plan to use a lot more “Star Trek” in my life moving forward.


About the Author

Marc Skinner

Marc Skinner is a senior marine scientist and biostatistician involved in multiple ecosystem R&D initiatives. As a subject matter expert, Marc advises on and participates in environmental projects and research throughout North America.

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