Environmental DNA: The next map of the ocean

Our map of the ocean is about to get an upgrade. For thousands of years, the ocean was marked by blank spots on the map, and phrases like Hic Sunt Dracones (“here be dragons”). Over time, mariners, explorers, and scientists have filled in these blank spots, from Ben Franklin’s mapping of the “Gulph Stream” to today’s detailed satellite images. When the first satellite images came back a few decades ago, it was like turning on a light in a dark room, showing us in crisp detail the swirling eddies and colorful blooms that elaborate the sea surface — features that had been invisible to us. Each time we get an update to the map, we can read and predict the ocean that much better.
There is still quite a lot of detail in the ocean that hasn’t been mapped, of course. The latest scientific development to give us new information is something called environmental DNA — or “eDNA” for short. It turns out that mapping the DNA that is in the ocean can reveal a lot about the inner workings of the currents and communities of critters that live there.
The idea is similar to how DNA is used in forensics. Fill a water bottle with a sample of the ocean and bring it to a lab to scan for DNA. Even a bottle that looks like it contains just clear seawater can have loads of information. The technology is getting simpler and cheaper, and soon this will be regular practice. So if DNA is used in forensics for solving crimes, what does ocean eDNA tell us?
Basically, eDNA is another problem-solving tool. For example, for decades people have been dealing with harmful and toxic microscopic species of phytoplankton, like the ones that cause red tides. Toxic blooms lead to shellfish closures, fish die-offs, and contaminated drinking water. Human development and climate change are making these blooms more common. With eDNA, we can get early warnings of red tides before they happen, helping with planning and mitigation. And we can detect newly arriving or invasive species before they get a foothold.

Nicholas Record, PhD, is a senior research scientist at Bigelow Laboratory for Ocean Sciences.

It’s possible to see traces of large animals as well, even in that same apparently clear bottle of seawater. As animals move about in the ocean, they constantly shed DNA. This can be either through shed scales or skin cells, or even in their feces. If you’ve ever swum in the ocean, you’ve left a trail of your own DNA behind you, to be swept up in the current — and you’ve also swallowed the DNA of whatever critters swam ahead of you. Reading the eDNA in a bottle of seawater can tell, for example, if there are endangered salmon or sturgeon in the area, even if we can’t find or catch any. The same goes for valuable species like elvers. It’s a way of tracking and mapping what would otherwise be invisible.
Scientists are already testing the conditions needed for eDNA to be used to detect the largest marine animals — whales. This could be particularly relevant in coastal Maine, where the presence or absence of right whales is a constant and controversial gap in knowledge. There are still some unanswered questions, such as how long can whale eDNA persist in ocean currents, and how far can it be transported? Once these questions are sorted out, it might soon be possible to map right whales — or map their absence — by filling bottles of water from the sides of boats.

A smartphone connected to the BioMeme Two3, a device that can be used to detect and identify DNA in the environment. Photo by P. Countway.

The technology is advancing fast, so fast, in fact, that it’s already smartphone -enabled. There’s a small device named the Two3, made by a company called BioMeme, that hooks directly into a smartphone. It’s about the size of a coffee mug, and it comes with kits that let users read different kinds of eDNA. Once this type of instrument is available off the shelf, water samples won’t need to be sent to labs. Anyone will be able to analyze eDNA right in the field.

Putting science like this into the hands of everyday people could be very powerful. Instead of reliance on government agencies or other monitoring organizations, the measurements and knowledge will be available to all, effectively “democratizing” the science. With all of these measurements, we’ll soon have another layer of the invisible details of the ocean mapped.

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