Environmental DNA Research in the Northeast

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Environmental DNA (eDNA) is loose genetic material shed by organisms in mucus, feces, or tissue particles. It can be collected from seawater with simple tools—even just a bucket.

Extracted DNA can then be compared to sequences in reference libraries, such as GenBank. This allows us to identify individual species or entire marine communities that shed the material where we collected it.

This approach can also reveal predators and prey by extracting DNA from the feces of marine mammals or the stomachs of marine animals. This innovative technology is a game-changer for improving assessments of ecosystems, habitat, and fishery stocks.

eDNA Surveys and Marine Development

NOAA Fisheries works to maintain biodiversity in a busy ocean where there are many human activities. One element of this commitment includes mitigating the effects of offshore wind energy development on our resource surveys. We can sample ocean water for eDNA in places and at times when other fishery survey methods, like trawl surveys, are harder to use.

Adding eDNA Sampling to Ecosystem Monitoring Surveys

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We are assisting with a larger effort to plan our next-generation resource surveys. A major component of the plan is to add eDNA sampling to our Ecosystem Monitoring Surveys. This will focus on fixed stations where Niskin bottles on a rosette are deployed to collect seawater from various depths. Through detailed documentation of eDNA biodiversity, we can provide information on community composition and its change in marine fishes and mammals in a changing sea.

Sampling in the Southern New England Energy Development Area

We work with our center's Passive Acoustic Monitoring Branch on this survey. Every 5 months we deploy and retrieve hydrophones that are listening for large marine mammals, concurrent with eDNA water sampling. We hope to use eDNA to understand changes in fish and marine mammal species diversity in the area. Meanwhile, we will compare eDNA detections and acoustic detections of sound-producing marine mammals and maybe even fish.

Bottom Trawl Survey

We take eDNA water samples during our center’s well-established bottom trawl surveys. Through comparing eDNA detections and trawl catch, we can better understand the pros and cons of each method. We also examine how to use eDNA data to help enhance bottom trawl surveys.

Habitat Assessments

GoPro Aquaculture Project

Shellfish aquaculture produces food, creates economic opportunities in coastal areas, and enhances natural harvests. To foster successful, responsible, and sustainable aquaculture, we need to understand how aquaculture gear may interact with marine ecosystems.

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Off-bottom, tiered oyster cages are an increasingly popular way to culture large numbers of oysters on a small footprint. These cages create complex structures that can attract fish and other animals seeking food, shelter, and refuge from water currents or predators. Because of the cages' structure, they can function like naturally occurring rock reefs, providing beneficial habitat to ecologically and economically important fish and invertebrates.

As part of this project we collect water around the cages for eDNA analysis to help us understand how this type of aquaculture affects the waters and sea life at the site. The method we use combines DNA-based species identification with sequencing millions of copies of DNA in the environment simultaneously, to characterize the fish communities associated with oyster cages and rock reefs.

National Seamount Surveys

The Northeast Canyons and Seamount Marine National Monument is a relatively undisturbed oceanic habitat. In 2024, collaborating with marine scientist Peter Auster at Mystic Aquarium/University of Connecticut, we applied eDNA metabarcoding on samples collected from this pristine environment to better understand biodiversity within the monument.

Environmental Protection Agency Historic Remediation Site

We collaborate with U.S. Environmental Protection Agency scientists to collect eDNA samples from a subarea within HARS, a dredged material ocean dumping site off southern New Jersey. Through comparing diversity matrices at dumping sites and control sites, we evaluate potential ecological impacts dredged materials have on benthic and pelagic fishes.

Trophic Dynamics

We apply eDNA metabarcoding to samples beyond seawater. For example, we have used it to identify prey by analyzing feces from seals and gut contents from squid. The high sensitivity of the eDNA method allows us to identify prey species that may have been missed by morphological identification.

For example fishermen have landed a few fish in the Gulf of Maine that have the body shape of haddock and also some characteristics of Atlantic cod. They are referred to as "coddock" in the fishing industry. Our analyses could determine if these are indeed individuals with mixed DNA of cod and haddock.

For more information, contact Christopher Powers