Microscopic Manhunts for Sea Urchin DNA

By Zaie Nursey

This fall, I have had the opportunity to work in Senior Research Scientist Doug Rasher’s lab on developing a qPCR assay to detect green sea urchins in the water. The Gulf of Maine is a rich fishing ground and is home to many diverse ecosystems like kelp forests that are a habitat for many animals like cod, sea urchins, and baby fish.

In the 20th century, cod was overfished to the point of near extinction in the Gulf of Maine, which allowed green sea urchins to grow uncontrollably, devouring kelp forests and leaving them unable to support life. Soon afterwards, a lucrative urchin industry removed urchins from the gulf as well, allowing kelp to regrow. Surveys in 2018 show that even though there are a lot of urchin larvae and no known predators, researchers are not finding many adult urchins. This leads to the question: Where did all the urchins go and what is stopping their population from growing?

To search for the urchins, we use environmental DNA, or eDNA, to find out how many urchins are in a given water sample. eDNA is like looking for fingerprints at a crime scene. Similar to how humans leave behind DNA when we walk around, marine animals also leave DNA as they swim through the ocean. We can take a water sample and run qPCR (quantitative polymerase chain reactions) that can detect sea urchin DNA in our sample by amplifying a specific urchin gene and attaching a fluorescent molecule to it. We can quantify how much DNA is in a sample based on how brightly it glows. This allows us to figure out how many urchins are in a given area. 

Using this approach, we can drastically reduce the time and effort researchers need to spend collecting population data about the urchins and collect near real-time data about how urchin populations are changing around us. If we can track urchins in the Gulf, we can help figure out what is controlling their populations and keep the kelp forests healthy and able to sustain the amazing life that calls the Gulf of Maine home.

Postdoctoral Researcher Thew Suskiewicz prepares to deploy an urchin experiment in the Gulf of Maine. Photo credit: Rachel Kaplan

Zaie Nursey is a Colby College student in the 2020 Sea Change Semester Program at Bigelow Laboratory. This intensive experience provides an immersion in ocean research with an emphasis on hands-on, state-of-the-art methods and technologies.

Microscopic Manhunts for Sea Urchin DNA