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Environmental DNA is a reliable way to learn about migration from the twilight zone

Environmental DNA, or eDNA, gives researchers clues about which species are in that water–and their relative abundance. A WHOI-led study finds that changes in eDNA concentration reveals details of a creature’s movement to and from the ocean twilight zone. Natalie Renier © Woods Hole Oceanographic Institution

October 28, 2021

Woods Hole, MA — The mid-ocean “twilight zone” holds the key to several tantalizing questions about the marine food web and carbon-sequestering capacity of the ocean. But studying this vast and remote area is extremely difficult. Many inhabitants of the twilight zone are easily destroyed during sampling– or are quick to avoid any disturbance–so it’s difficult to sample them with traditional nets. Advances in acoustics have enabled more accurate estimates of biomass, but questions about the diversity and distribution of species within that biomass remain unanswered.

That knowledge gap is beginning to close, thanks to the genetic material—from scales, fecal pellets­, or bits of tissue–creatures shed as they move through the water. The resulting trail of environmental DNA, or eDNA, gives researchers clues about which species are in that water–and their relative abundance. In a paper published Thursday, October 28th in Scientific Reports, researchers at the Woods Hole Oceanographic Institution found that changes in the concentration of eDNA in the ocean accurately reflects the movement of creatures as they travel between the twilight zone and surface.

“A major finding of our paper is that the eDNA signal doesn’t go away immediately if the animal moves up or down in the water column,” said Elizabeth Andruszkiewicz Allan, a WHOI postdoctoral fellow during the study and currently a postdoc at the University of Washington. “That helps us answer some big questions we can’t answer with net tows or acoustic data. Which species are migrating? What percentage of them migrate each day? And who is an early or late migrator?”

Allan and co-author Weifeng “Gordon” Zhang, a WHOI physical oceanographer, utilized a computer model to simulate what happens to eDNA in the water column after it is shed by the host animal. They found that physical processes—currents, wind, and mixing—and settling of particles did not have a significant impact on the vertical distribution of the eDNA. In fact, most eDNA signals remained within 20 meters (66 feet) of where they were first shed, meaning that changes in eDNA concentration can reliably be used to determine where certain species live at different times of the day, the amount of time they spend at those depths, and the percentage of certain species that migrate from the twilight zone to the surface.

“Before this work, we couldn’t confidently say what happened to the eDNA shed by twilight zone species. But a very clear pattern showed up in the model, providing a baseline understanding of the concentration of eDNA between the surface and deep layers over time,” said Zhang. “With this new knowledge, field researchers will be able to target where they take the precious water samples so they can identify the migrating species and estimate the percentage of animals in each species group that migrate each day.”

As one of the first studies to model eDNA concentration, the researchers note that more field data is needed to help test the model. However, these promising results show just how useful eDNA can be for studying animal migration and carbon sequestration in difficult-to-access parts of the ocean like the twilight zone.

“These modeling results provide a foundation for which we’ll be able to more efficiently study the ecology of the ocean twilight zone,” said Annette Govindarajan, a WHOI molecular ecologist and co-author of the paper. “It sets up some experiments for future directions, some of which we’ve already started working on.”

This research was supported by the Woods Hole Oceanographic Institution’s Ocean Twilight Zone project, funded as part of The Audacious Project housed at TED.

About Woods Hole Oceanographic Institution:

The Woods Hole Oceanographic Institution (WHOI) is a private, non-profit organization on Cape Cod, Massachusetts, dedicated to marine research, engineering, and higher education. Established in 1930, its primary mission is to understand the ocean and its interaction with the Earth as a whole, and to communicate an understanding of the ocean’s role in the changing global environment. WHOI’s pioneering discoveries stem from an ideal combination of science and engineering—one that has made it one of the most trusted and technically advanced leaders in basic and applied ocean research and exploration anywhere. WHOI is known for its multidisciplinary approach, superior ship operations, and unparalleled deep-sea robotics capabilities. We play a leading role in ocean observation and operate the most extensive suite of data-gathering platforms in the world. Top scientists, engineers, and students collaborate on more than 800 concurrent projects worldwide—both above and below the waves—pushing the boundaries of knowledge and possibility. For more information, please visit