‘Environmental DNA’ Lets Scientists Probe Underwater Life

Tracking down marine life isn’t easy. Ocean scientists drag nets through the water to find the fish or plankton they are looking for, tag whales with harpoon-like devices, or scuba dive with an erase-proof whiteboard and hand counter to tally reef fish. That’s how you count creatures underwater. But an emerging technology called environmental DNA, or eDNA, is easing this time-consuming and expensive process for scientists by allowing them to grab water samples and check for DNA.

Each drop of seawater contains thousands of microorganisms, as well as bits of skin, mucus, and waste shed by passing fish and mammals. Using a robotic laboratory mounted on an underwater drone that filters and sequences the DNA that it finds, scientists and engineers can now identify marine life without coming back to shore. “You don’t need a big ship to collect your samples,” says Chris Scholin, executive director of the Monterey Bay Aquarium Research Institute, which is developing this new technology along with several other research groups across the US. “This has become portable and small enough to operate in real time on an autonomous underwater vehicle.”

Sampling remotely means that scientists might not have to go to sea in stormy weather to collect data, and can allow them to sample over a long period of time, instead of collecting information during a three- or four-week cruise. It also doesn’t require them to harvest the fish. Robotic vehicles recently traced the DNA of great white sharks congregating in the middle of the Pacific Ocean, tracked tropical fish along the Jersey Shore as they headed north to escape climate change, and found farm-raised fish genes while screening samples from New York Harbor.

This new technology is driven by the marriage of a device the size of a thumb drive called an Oxford Nanopore Minion sequencer to another recent invention, ocean-going autonomous vehicles (AUVs) that no longer take commands from ship or shore. These devices can follow environmental signals, such as temperature, salinity or the optical properties of plankton, just like a hound sniffing out an escaped convict’s trail. (Researchers use sonar to find plankton, the way an angler would use a fish finder.)

Photograph: Brian Keift/MBARI

Scholin’s colleagues at the research institute have also developed a new device that can be installed in a lake or freshwater stream to collect and analyze water samples hourly in an effort to give scientists a “DNA map” of fish populations along the coast. They are testing the eDNA sampler in the streams of Santa Cruz County, California, to detect spawning coho salmon and steelhead trout, as well as the spread of invasive striped bass and New Zealand mud snails. This experiment is wrapping up next month and the scientists’ data will be compared to hand counts by fisheries biologists.

Similar autonomous sampling technology is being used by several research teams to find out what’s living on tropical reefs, where scientists have placed multi-layer structures to attract the tiny organisms that call the reef home. The idea is to assess the diversity and density of “cryptic fauna”—the corals, sponges and soft-bodied animals that make up a big portion of the reef’s biodiversity—but are usually not counted by a census of marine life, says Allen Collins, director of NOAA’s National Systematics Lab and an adjunct curator at the Smithsonian Institution. Understanding the tiny animals that underlie the ecosystem is key to determining how well the whole system is faring. A collapse among an important yet overlooked animal—a type of shrimp, for example—might be a harbinger of problems among animals higher up the food chain.

A team of Australian marine biologists recently used remote eDNA samplers at an Indian Ocean coral reef as part of a population diversity study. Their goal was to identify new ranges for species that are facing climate change-driven pressures from rising temperatures and seawater acidity. Using the samplers, they found 376 kinds of fish and invertebrates over the study site, and that each reef had a different mix of marine life.

Experts say that these eDNA sampling techniques are improving quickly, but they still have a couple of drawbacks. DNA degrades in the water after only a few days, so samples collected by AUVs only provide a genetic snapshot of whatever passed by recently. Along coastal areas or near cities, scientists are also finding contamination from people. “The biggest monkey wrench is that we get human DNA almost everywhere,” says Mark Stoeckle, a senior research associate at Rockefeller University who has been using eDNA techniques to assess the health and diversity of underwater life in New York Harbor and along the New Jersey Shore. “And in New York Harbor, we get DNA of fish that people eat: Nile tilapia, branzino, barramundi.”

Photograph: Todd Walsh/MBARI

They also found a healthy amount of goldfish DNA. “It could be that there is a big goldfish population,” Stoeckle adds, “but it could also be people releasing goldfish.”

Stoeckle has been working with New Jersey state biologists to conduct DNA-based counts of commercial fish species by dropping one-liter bottles into the ocean at various depths and sampling the water inside. It’s part of a census of commercial species that has been ongoing since the 1960s, information that helps resource managers determine catch limits for local fishermen. But in addition to the target species, they are finding that some species of fish are moving north from their normal range along the coast of Florida and the Carolinas; they’re environmental refugees who are trying to escape increasing temperatures. The researchers found DNA from the gulf kingfish, which normally resides in the Chesapeake Bay and has never before been identified in New Jersey, as well as the Brazilian cownose ray, which is native to the Gulf of Mexico and has been unknown in northeastern waters.

Stoeckle says once some of the bugs can be worked out, eDNA sampling may soon prove to be a faster and cheaper way to assess the health of the marine ecosystem as humans increasingly rely on the ocean to provide more food and energy. “There’s a need to monitor the oceans more closely, because we are doing more in the ocean, such as building wind farms and pipelines and natural gas and oil extraction,” he says. “These are all things that may be beneficial economically, but we want to know what we are doing to the environment.”

More Great WIRED Stories

Read More