Aquaculture Industry Identifies New Possibilities in eDNA

Every time a shark swims by, a blade of kelp sways in the water, or a tiny copepod poops, it leaves behind traces of DNA. These floating bits of genetic code, called environmental DNA, enable scientists to monitor the distribution and abundance of different species — even those just passing through or too rare or small to easily observe.

The Maine-eDNA project was a five-year, multi-institutional effort, led by Bigelow Laboratory and University of Maine, to unlock the full potential of that eDNA. Though the project officially wrapped up last year, researchers are continuing to unravel their findings and take the work in new, exciting directions.

As a newly minted research scientist at Bigelow Laboratory, Robin Sleith is leveraging the lessons learned and partnerships made through Maine-eDNA for important management challenges on the Maine coast, from monitoring harmful algae blooms in public waterways to, more recently, optimizing aquaculture operations.

“In a lot of these instances, things that started within Maine-eDNA have turned into sustaining grants that build off the larger effort and take it in new directions, which was always our hope for the project,” Sleith said.

For example, he and Senior Research Scientist Dave Emerson were recently awarded $200,000 from the Maine Coastal and Marine Climate Action Fund to continue developing an eDNA database in partnership with Midcoast Conservancy, University of Maine, and the Sipayik Environmental Department. The database will contain eDNA data — across seasons and years — from Maine’s freshwater lakes to the coast.

“We’re putting together what will be one of the largest and most comprehensive eDNA datasets out there,” Sleith said. “Grants often require data to be publicly available, but there isn’t always a mandate to make it user friendly. We want to build something such that anyone who is interested can work with our data, find value in it, and perhaps find exciting new applications for it.”

That user-first mentality, Sleith said, is at the heart of several industry partnerships that have grown out of Maine-eDNA.

For the last several years, for example, he’s worked with Mook Sea Farm to develop methods to identify bacterial pathogens that could affect Mook’s oyster hatchery operations. Funded by the USDA Sustainable Agriculture Research and Extension program, the team is developing tools that are durable for the field, retain the accuracy of a lab-based test, and cater to Mook’s particular needs.

“Aquaculture farmers are working on a timescale of hours to days, so they need to know right away that a batch of seed or a food source is infected,” Sleith said. “Getting these tools to be as rapid as possible is going to be key.”

Now, Sleith and other Bigelow Laboratory scientists like Senior Research Scientist Nichole Price, are turning the power of eDNA to the rapidly growing kelp industry. The hope is to develop simple molecular tests that can differentiate between different kelp species and detect species of interest.

“EDNA tools are like molecular tweezers where you can pick out a single organism and say how much of it is in a sample, no matter what else is in there,” Sleith said. “Once we have those tools for something like sugar kelp in the Gulf of Maine, we’ll be able to use that knowledge to build the right ‘tweezers’ for other species of interest in other regions.”

With support from the Builders Initiative, they’re also working to understand how kelp breaks down in sediments on the ocean floor to assess the potential of buried kelp for storing excess carbon absorbed from the atmosphere. Sleith’s role is to create eDNA tools that can accurately quantify how much kelp is in sediment samples, which will be essential information for farmers trying to access carbon credits down the road. With user-friendly tests, farmers will also be able to determine when their crop starts to break down over the course of the season to help them optimize harvesting.

“From the farmer's perspective, we’re interested in understanding if there are aspects of operations that can be optimized by using the power of eDNA,” Sleith said. “We want to develop tools that will help farmers, whether that’s in shellfish or seaweed, make the best decisions for their businesses and customers.”

Photo Captions:

Photo 1: Research Scientist Robin Sleith helps out during a tour with Maine Oyster Company, a leading aquaculture business in the state that also opened their dock to the Maine-eDNA team for sampling (Credit: Sydney Greenlee).

Photo 2: Senior Research Associate Brittney Honisch collects kelp for research supported by the Builders Initiative (Credit: Robin Sleith).