Pioneering eDNA

Environmental DNA, or eDNA, uses genetic material from the environment – like soil or water—to detect and identify the presence of wildlife. Just as forensic teams look for human DNA to determine who was at the scene of a crime, scientists can use eDNA to see what species are present in a sampled area. Similar to humans shedding hair and skin cells; marine organisms shed DNA into the environment through skin cells, scales, or secretions.

What are the benefits of using eDNA in marine science?

eDNA provides a valuable window into our underwater world. A simple vial of water is used to determine a wide range of marine life at the time and place where the sample was taken. With continuous sampling, eDNA can show how biodiversity can vary across space and time.

Importantly, eDNA is a noninvasive sampling method. Traditionally, many fish biodiversity and abundance surveys utilize invasive methods that can kill or injure fish during sampling. While a valuable and effective methodology for scientific research, such surveys are not always ideal— especially when measuring vulnerable species or studying sensitive habitats such as eelgrass beds. eDNA avoids these risks.

In addition, uncommon, large, or fast species can often avoid surveys that use nets, lines, or trawls. Since eDNA is derived from a water sample, those potential biases are eliminated.

Our Executive Director, Ellen Pikitch, has written about the benefits of eDNA in a Perspective column published in the journal Science.

How are we using eDNA to further our scientific mission?

Coastal bays and estuaries are diverse, productive, and complex environments that are subject to a high level of human interference and are often negatively impacted by land-based pollution, overdevelopment, habitat loss, and overfishing. We have been studying and restoring a local Long Island estuary, Shinnecock Bay, for over ten years.

Part of our work involves understanding the biological communities within the bay. Through several methodologies, including eDNA, we are creating a baseline dataset of which species live in and use the bay, as well as determining seasonal and habitat utilization patterns.

We have seen the benefits of using eDNA already; for example, striped bass and several species of elasmobranchs are known to be abundant in the Shinnecock Bay ecosystem but are seldom caught in survey trawls. eDNA, however, consistently shows the presence of these species so that they are not overlooked in our biodiversity assessments.

We are also using eDNA for sampling in highly important, vulnerable environments where we are conducting restoration activities. This includes hard clam spawner sanctuaries, oyster reefs, and eelgrass beds that have all been part of the Shinnecock Bay Restoration Program and that we want to observe with minimal disturbance.

How does eDNA work?

The process of sampling, extracting, and analyzing eDNA takes several steps.

First, we collect a subsurface water sample at a predetermined location using a sterilized and labeled bottle. Each sample is kept on ice before being processed in the lab the following day. In the lab, we filter each water sample through a membrane that catches all of the material suspended in the water.

We then extract the DNA from the filters, separating it from the membrane and all the non-DNA material. We also measure concentration and purity to determine if the sample meets optimal standards and is free of contamination.

Finally, we send all our eDNA samples to a molecular analysis lab. There, a polymerous chain reaction, or PCR, is used to amplify pieces of DNA— in other words, to make many replicate copies. This amplification allows the biochemist to identify the DNA at the species level.

The results reveal which species were present at each sampling location, leading to a “biodiversity snapshot” around Shinnecock Bay over the course of a sampling season.