Fishing for DNA

Environmental scientists Jesse Ausubel and Mark Stoeckle have developed groundbreaking fish identification technology using DNA present in water


Imagine a glass of water holding an entire section of ocean. You can see all the fish that have passed through in the past day or two, swimming about right inside your cup.

A cup of seawater can tell us more than ever before, thanks to the work of Jesse Ausubel, director of Rockefeller University’s Program for the Human Environment, adjunct scientist at Woods Hole Oceanographic Institution, and longtime Vineyard Conservation Society science advisor. Mr. Ausubel and his colleague Mark Stoeckle, a senior research associate at the Program for the Human Environment, have pioneered a method for learning about species populations in the oceans simply through the collection of a glass of water. Something called environmental or extracellular DNA (eDNA) makes this possible. As animals move about in the water column, they shed DNA in all the same ways that humans do — skin, saliva, urine, fecal matter — and this is known as eDNA. “This information has always been available,” Mr. Ausubel explained. “Since the year 2000, we’ve known that there is DNA floating around in the water. That information wasn’t very useful because we didn’t have a reference library. I could sieve some DNA out of the water 15 years ago, but I couldn’t match it to anything.”

Essentially, without a library of DNA sequences to compare it with, there is no way to identify which DNA comes from which species. Mr. Ausubel co-founded the reference library that makes marine eDNA research possible. “I was involved in this big project called the Census of Marine Life from 2000 to 2010, and one of the things we did was obtain and sequence DNA for tens of thousands of different marine species,” Mr. Ausubel told the Times.

In order to amass this reference library of marine DNA, hundreds of scientists participated in over 500 expeditions to catch and identify sea creatures, collect their DNA, and sequence it. For his work with the Census of Marine Life, Mr. Ausubel was honored by French marine biologist Philippe Bouchet, who chose to name a type of lobster he discovered during this research Dinochelus ausubeli.

“It’s a whole new way of finding out what lives in and around the water,” explained Mr. Ausubel. “For thousands of years people have been interested in what lives in the water. To learn, people have used their eyes and nets. Starting around the 1950s and ’60s, people started using sonar ‘fish finders,’ which sometimes have acoustic signatures, but are otherwise unable to identify specific species.”

This is the niche for Mr. Ausubel’s scientific advancement. Environmental DNA enables both scientists and the average Joe to identify species in the water without having to observe or catch anything. You simply scoop up a cup of water, and send it off to a lab for DNA analysis. The lab uses a centrifuge to separate the DNA from the water, and uses short strands of each string, called primers, to match the strands to those in the Census of Marine Life database. Mr. Ausubel noted that environmental DNA tends to break down after a day or two, which means that this method offers very relevant information on the populations currently in an area. Surprisingly, the marginal cost for processing each water sample is only about $50, while the applications of this advancement are many, including studying migration and feeding patterns.

“My colleague Mark and I focus on vertebrates, like fish, but you could also focus on different primers to look at invertebrates, like turtles. If you were interested in squid and octopus — the cephalopods — you would need to use a different primer to seek out the relevant DNA,” Mr. Ausubel said.

Mr. Ausubel grew up summering on the Vineyard, and attributes his early love of the ocean to his Oak Bluffs childhood. He is still very much involved in local science, and has performed eDNA testing in the Tisbury Great Pond, Look’s Pond, and the Mill Pond. “It would be unique for the Vineyard to help pioneer some of the applications for this new technology. This is a useful tool to monitor ecological changes on Martha’s Vineyard, and the effect of interventions,” Mr. Ausubel said. He used the Mill Pond in West Tisbury as an example. “If you removed some of the dams and you wanted to monitor the changing ecology, this is an affordable, easy method to use. You could go and get a cup of water once a week from a couple of different spots and then analyze those. Over a year or two, you would see the change in the diversity of the animals. As of now, there are herring in the Tisbury Great Pond, but we didn’t get any herring in Look’s Pond. At one time there would have been herring there, and you could track their progress back into this run through their DNA.”

Going forward, Mr. Ausubel and Mr. Stoeckle are changing their focus a bit, from vertebrates to sharks and rays, to expand the scope of the project. Mr. Ausubel is also excited to explore the correlation between the amount of eDNA “reads,” essentially the number of strands in the water, and the population of species within the measurable vicinity. As he put it, “Amazingly, eDNA seems to correlate with abundance. If there are more pickerel, you’re going to get more pickerel DNA in the water.” Once this information is better understood, the opportunities for marine research advancement seem endless.

“It really is a revolution. It’s a bit like what happened in the 1990s with DNA in courtrooms,” Mr. Ausubel said. “This can really make a big difference.”