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Research Vessel Docks at Exploratorium, Dives into eDNA

Research Vessel Docks at Exploratorium, Dives into eDNA

Before heading to explore the depths of the California coastline and the underwater paradise of the Channel Islands, the Exploration Vessel Nautilus and its crew took a break: the 211-foot-long ship docked at the Exploratorium.

(Photo: Gayle Laird/Exploratorium)

On June 21 and 22, the Nautilus was anchored at the end of our pier, and museum staff were able to take a tour of the vessel. The ship, which uses sonar technology and remotely-operated vehicles (ROVs) to map and sample the ocean floor, has 31 scientists and 17 crew members. It is led by Robert Ballard, President of the Ocean Exploration Trust, and is known for livestreaming its explorations and chatting with members of the public who are on shore.   

The Nautilus had just finished a research cruise along the Cascadia Subduction Zone when it arrived at the Exploratorium. The cruise studied methane seep habitats from southern British Columbia to northern California.

In the process, scientists on the Nautilus collected water samples they hope will allow them to identify what types of deep-water coral are present in the region. 

The approach is known as environmental DNA. It requires scientists to collect a water sample, filter out the cells, and then analyze their DNA in order to determine what types of organisms are present in the water. Effectively, it means learning what species live in an area without ever having to see them or collect physical samples. 

Special cylindrical bottles are attached to Hercules, one of two ROVs on the Nautilus. Called Niskin bottles, they are open on both ends. After Hercules is in the water, the ROV pilot triggers one or more of the bottles to shut, trapping a water sample inside. Scientists later filter and analyze the sample. (Photo: Gayle Laird/Exploratorium)

While eDNA has been used to identity and monitor freshwater species and ocean microbes, such as plankton, its use on non-microbial marine life, such as coral, is more limited.

Unlike plankton, which floats in the ocean, coral is anchored. Scientists on board the Nautilus hope that by collecting water samples in deep-sea coral environments, they can capture and analyze cells shed by the organisms. The Cascadia cruise was their first attempt.

“If we can get it to work, it provides a non-invasive way to get a good profile,” said Meredith Everett, a post-doctoral researcher with the Northwest Fisheries Science Center and the lead scientist working on the Nautilus’ eDNA sampling project.

The technique also makes sampling faster since one water sample can be used to identify multiple species.

The work required the help of the Nautilus’ two ROVs, Argus and Hercules. Hercules, whose features include two arms that can be manipulated to collect samples, is attached to Argus by a nearly 100-foot tether. While Argus is sometimes used alone to survey a broad area, when paired with Hercules, it acts as a light source and keeps watch of the more nimble ROV.

Hercules collected 30 samples on the Cascadia cruise, and the Nautilus has continued collecting samples since leaving the Exploratorium and resuming its summer research season.

Everett, who was on board for the cruise, has brought the samples back to her lab in Seattle for analysis. To some extent, she knows what she’s looking for: Hercules also took some physical coral samples, and the scientists were able to see about 15 types of coral using the ROV’s camera. In the weeks to come, Everett will continue to work on extracting and studying DNA from the samples.

The Nautilus is currently in the middle of its Channel Island exploration. Next, it will travel down to the Southern California Margin to map unexplored areas of the sea floor before returning to the Exploratorium on August 17. You can also join us throughout the summer for live chats with the scientist and educators on board the Nautilus.