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A Glimpse of the Ocean’s Twilight Zone Through Environmental DNA

To most people the Twilight Zone evokes memories of Rod Serling’s iconic TV series of the 1950s and 1960s, or the less tantalizing recent reboot. But the Twilight Zone project at the Woods Hole Oceanographic Institution isn’t a peek at William Shatner seeing a monster on an airplane’s wing or Billy Mumy turning an annoying adult into a jack-in-the-box.

The twilight zone is a layer of the ocean that encircles the planet, from about 200 to 1,000 meters (650 to 3,300 feet) deep. It’s also called the mesopelagic or midwater region. The zone is cold and dark, with flashes from bioluminescent organisms that shield them from predators. Pressure reaches 1,500 pounds per square inch. The biomass of fish in the twilight zone may exceed that of the rest of the ocean – but we know little about their distribution.

Residents of the twilight zone range from tiny bacteria and plankton, to fish, crustaceans, squid, and all sorts of gooey variations on the animal theme, like jellyfish and comb jellies. Quadrillions of bristlemouth fish, named for their spiny teeth, live in the zone. And we don’t even know how many species have yet to be described. The animals in the twilight zone support the vast food web, moving carbon from the surface to the depths, regulating climate.

From the depths of the twilight zone animals swim upward in search of food during the dark hours, diving deeper when the sun comes out to avoid predators. These diurnal movements appeared to U.S. Navy sonar operators during World War II as the seafloor undulating. “Theirs is the largest animal migration on the planet, and it happens every 24 hours, sweeping across the world’s oceans in a massive living wave,” according to the program’s website.

The cold, dark depths are challenging for humans to mine for signs of life. The slightest disturbance sends animals fleeing, and some organisms are so soft that they melt away when hauled up in nets or sampling containers.

To investigate the scene without disturbing the life, researchers from the Twilight Zone project are collecting environmental DNA – aka eDNA – and using computer modeling to conduct a census of sorts, deducing the goings on from the distribution of DNA from excrement, shed skin and scales, and other bits of the nucleic acid that waft off bodies. The patterns of DNA distribution and concentration provide clues to the abundance, movement, and migration of species. The work appears in Scientific Reports.

The simulation model considers two sizes of eDNA. Large particles ranging from tens of microns (a millionth of a meter) to a millimeter include fecal pellets, tissue chunks, and eggs and sperm. Small particles down to a tenth of a micron come from the big ones. The model considers movements that are part of an animal’s behavior; attributes of the eDNA like settling and degradation; and physical influences such as mixing and horizontal movement.

I was able to envision these experiments by vividly recalling the view of the back end of a hippopotamus at the hippoquarium exhibit at the Detroit zoo. The animal defecated, and then revved up his tail like a giant pinwheel, spinning the excrement in wide circles. But the DNA of the deep, according to the model of oceanic eDNA, doesn’t appear to be quite so kinetic.

“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. 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?” said first author Elizabeth Andruszkiewicz Allan in a news release.

Physical processes like currents, wind, and mixing, as well as settling of the material, didn’t much influence the vertical distribution of the eDNA, which tended to stay within 20 meters (66 feet) of the source. That means that the eDNA pattern can reveal where certain species live at different times of day, the duration of time spent at particular depths, and the percentage of a species’ members that migrate from the twilight zone to the surface during a day.

“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 team member and oceanographer Weifeng 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,” he added.

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