4 — Using Environmental DNA to Observe Life in the Ocean

Mark Stoeckle is Senior Research Associate in the Program for the Human Environment at The Rockefeller University. Dr. Stoeckle’s research applies information from DNA to better understand the natural world.

He helped organize the early meetings that laid the foundation for DNA barcoding, a standardized method for identifying species from DNA. His current work is developing methods for analyzing DNA in seawater, called environmental DNA or eDNA, to help count fish and other ocean life.


Thank you for this invitation. This is a very interesting group. I am a research scientist at Rockefeller University. I use eDNA to count fish and it’s given me a different perspective on what’s in the water. Our object of research is a glass of water or a bottle of water. We analyze eDNA using modern techniques—the little bits of eDNA that are floating in the water—and from that we can learn what animals are nearby. We’re starting to learn how we can not only know if they’re there, but how many of them there are.

Seawater contains DNA from nearby animals. This is called environmental DNA, or eDNA for short. eDNA in a 500 mL seawater sample can reveal dozens of fish species. 

The method starts with collecting water—a 500 milliliter juice bottle is enough water to get the kind of information we’re looking at. Then we filter it to concentrate any particles that are floating in the water. Those particles include what you can think of as dandruff of animals—bits of cells that they shed as they’re going through the water.

eDNA is from cells and bits of cells shed from body surfaces, sort of a kind of dandruff. You can trap these cell particles by filtering the water through a very small pore size filter.

We take those particles, we purify eDNA from that, and then we sequence it. Out of the sequencing machine we get a report of not only the different sequences that are in there, but how many copies there are, so we match those sequences to a genetic library in the same way you would match sequences from a crime scene. If we get more reads, as they’re called, or copies of eDNA of the species, that generally means there are more of that fish. In this sample we got more reads of the menhaden than we got of black sea bass. The eDNA that’s in the water lasts a few days until it’s lost, through degradation and dispersal, and this means it’s really telling us what animals are nearby or were nearby very recently.

Here is the material from one liter of water. It contains all the particles that are floating in the water—including sediment, bacterial, algae, as well as the cells containing eDNA.

New York City is surrounded by fish—that is one of the things I’ve come to appreciate. This is us collecting water in the East River, throwing a bucket in the water. This is the 59th Street Bridge, and out of this one sample we got a dozen species. And over here is a bar graph showing you the number of reads for each of these species: for menhaden we had a lot of reads; we think that means it’s more abundant than the conger eel, for which we just had a few reads.

Collecting water from the East River near the 59th ST Bridge. We tie a rope to a bucket and toss it in.

I am a naturalist. I pay a lot of attention to what’s around us. I was surprised by all the different fish, or at least DNA of fish, that we have in the East River. Some you may know if you are a fisherman, like black sea bass and striped bass, and some you may not know, like oyster toadfish and conger eel—those were completely new to me.

You can use eDNA to see if the environment is getting better or worse. We went to the Gowanus Canal in Brooklyn. It was a Superfund site, and not very long ago was one of the most polluted areas in NYC. The city and the federal government have done a lot to clean it up—there’s a flushing system that brings a lot more water through. We went out with the Gowanus Dredgers, which is a non-profit group; they take canoe trips on the Gowanus canal. (I recommend it if you’re in New York City.)

Getting ready for canoe tour of Gowanus Canal, a once famously polluted waterway. The tour is organized by Gowanus Dredgers. 

We collected bottles of water and we got more than 20 different species of fish from DNA. You may be able to see, up here, almost all of it was this one fish, Atlantic Silverside, and we could actually see these—I saw these in the water. They are in very large schools; you can even tell they were there just from the canoe. But you get a lot more diversity of fish.

Collecting water at the fishing pier at Coney Island. eDNA reveals how the community of fish species differs between Coney Island, East River, and Gowanus Canal.

When you go to different places, you get different DNA, and we can see DNA change; we can see fish migrating just like birds migrate. This is a project done with high school students Victor Shahov and Thomas Poku. We went and took the subway out to Coney Island every week starting in March, and continued in April, May, June, July, and August.

Fish species detected at Coney Island by eDNA. Water samples were collected weekly starting in March (M) and continuing through August (A).  Each column is a weekly sample, and black indicates that species was detected,

Each column is a different week and if it’s black that means that species was detected. In March and April, there are not very many species—we did get winter flounder, which is a cold water species—and then, as the water warms up, we get a lot more different species here. What I can say from doing this is there are many fish you won’t find in the East River but you do find at Coney Island. For example, this is a smooth dogfish (which is a small shark), and these are cownose ray, bullnose ray, and bottlenose dolphin (there are dolphins out in New York harbor and you can take tours and see them). So we’re excited. This may be a way to not just to monitor fish but also marine animals. Why are we excited about DNA? The traditional methods of counting fish are costly, they’re time and capital intensive, they need special equipment and trained personnel. This is a marine trawl survey. You’ve got a lot of people here; you’ve got big equipment; they have to be experts; they have to identify the fish right away, so they can go on to the next trawl.

This is a lot of work, so we don’t actually do a lot of measurements of what’s in the ocean. eDNA gives us a relatively low-cost, harmless-to-the-environment technology that we can use to add to our knowledge. It’s much easier to collect water than it is to put one of these big nets in the water. A little bit of water tells you a lot—it’s a remarkably powerful technology—so the number of fish species we get out of one liter of water is more than the number of fish species you catch if you drag a trawl that goes through 60 million liters of water. 60 million liters of water is enough to fill a football field, up to the goalpost. Fish are very patchy, but the DNA from the fishes are spread around. We can take advantage of that by doing our water sampling. We have good evidence it’s telling us really what is actually there. This is a comparison of eDNA results to trawl results from January, June, August, and November for four different species. You can see the month that windowpane flounder is abundant by eDNA is also the month that it’s abundant by trawl. For smooth dogfish, again the abundance is very similar by the eDNA as it is by trawl. (Fish have different months that they’re abundant; they’re like birds or other kinds of animals.)

Another comparison to the trawl is to compare the eDNA reads to the trawl weight in a certain single month. The species that are most abundant by trawl—clearnose skate, striped sea robin, and bullnose ray—are also most abundant by the eDNA. And the ones that are least abundant by the trawl—lined seahorse, hogchoker, and red cornetfish—are also the least abundant by eDNA. So we think it’s giving us good information and can improve our knowledge of what’s going on in the ocean—and the reason we need better technology is we’re doing a lot to the ocean, and some of the things we’re doing may be helping but several of them may be hurting, and we need a way to monitor that. Obviously fishing has big impacts; there’s a lot more interest in agriculture. This is oil and gas exploration. There’s a tremendous push to put wind farms off the coast.

Being able to understand what’s happening to the fish and populations with these is going to be important. Obviously, we want to know about changes with weather and climate. Are conservation areas working? We have marine protected areas, just like we have natural parks, but we don’t really have an easy way to know if it is helping that we set up these restricted areas and if our restoration efforts are working. These are high school students with the Billion Oyster Project in New York City, trying to restore oysters to New York harbor, and eDNA may be a way to monitor if that is working.

This is a lab that grows coral and uses them to repopulate coral reefs. eDNA will certainly be useful for research and exploration; the ocean is unknown and a lot of it has never been visited by a person or any machine that we would make.

So DNA, just by collecting water, is going to augment what we do, including in areas that are very difficult to access, like the deep ocean. There’s a lot of DNA when you go in the water—of the animals that live there—and we can learn a lot from that. This is the research team I work with, colleagues of mine at Monmouth University and at Rockefeller; and I’ll add that this work is supported by the New Jersey Department of Environmental Protection. Thank you.