The idea that you can raise a bottle of seawater from 600 meters below the surface and discover evidence of creatures you have never once seen through a camera lens is subtly amazing. No video. No tangible sample. Just bits of genetic material floating like biological confetti in the chilly darkness. That’s what environmental DNA is all about, and NOAA recently made a lot of it public.
In collaboration with the Smithsonian National Museum of Natural History, the Northern Gulf Institute, and NOAA’s Atlantic Oceanographic and Meteorological Laboratory, NOAA Ocean Exploration published its first publicly available eDNA datasets in April. These datasets were collected from expeditions conducted aboard the NOAA Ship Okeanos Explorer between 2021 and 2023. It’s difficult to comprehend the numbers alone: 229,913 occurrence records from Atlantic and Pacific waters at depths greater than 200 meters. The National Center for Biotechnology Information has received the raw sequences. The Ocean Biodiversity Information System provides organism identifications. This data is now accessible to anyone, anywhere.
It’s important to consider how this differs from the way deep-sea science has historically operated. For many years, the two main sources of information that scientists had about the deep ocean were what ROV cameras were able to capture and what nets were able to retrieve. Both have clear limitations. Things are missed by cameras. Smaller, faster, or more delicate organisms are often completely eliminated by nets, which also harm delicate habitats. Another issue is that closely related species that appear almost identical on video can be difficult to distinguish from one another without the kind of detail that footage seldom offers. A lot of this is avoided by eDNA. Every organism that shed skin, mucus, or waste in the surrounding water, sometimes hours or days earlier, is present in trace amounts in a water sample. Seldom seen on camera is the barreleye fish, Macropinna microstoma, one of those truly bizarre-looking deep-sea creatures with transparent, rotating eyes. However, eDNA from Okeanos expeditions indicates that it has been present the entire time, albeit in the dark.
In 2021, NOAA made eDNA collection a high-priority exploration variable and integrated it into regular Okeanos Explorer operations. The ship’s remotely operated Deep Discoverer vehicle was used to gather samples at depth, and they were subsequently filtered in a wet lab on board. After that, AOML researchers created a processing pipeline especially to manage the volume of data, which had actually been a bottleneck in the field because gathering eDNA is one thing, but interpreting it at scale is quite another. For the metabarcoding analysis, three genetic markers—12S, 18S (V4), and COI—were employed. These markers target distinct taxonomic groups and provide a more comprehensive picture of biodiversity than any one marker could.
What can be found in this dataset is remarkable. proof of fish, marine mammals, invertebrates, and microorganisms. Previous visual observations from previous Okeanos dives were confirmed by a few organisms. Some, like that barreleye fish, had never been seen up close during these expeditions. Since other organizations, independent researchers, and conservationists worldwide now have access to the raw sequences and can use their own analytical tools on them, it might take years to fully understand what these datasets ultimately reveal. There are no limitations on use, including commercial applications, because the data has been made available under a CC0 1.0 public domain waiver.
Similar to how satellite imaging revolutionized atmospheric research, there is a feeling in ocean science circles that eDNA is nearing a turning point. The method is less invasive than trawling, more affordable than long-term ROV operations, and increasingly capable of identifying organisms of a wide variety of sizes and taxa. Standardizing collection procedures, creating repeatable workflows, and making the output readable for researchers who weren’t on the ship when the samples were taken have always been the challenging aspects of the data pipeline. This release is a genuine attempt to address that issue; it is based on Darwin Core Archive formatting and distributed via globally accessible repositories.
It’s difficult to ignore the timing. A standardized, publicly accessible baseline of what inhabits these waters is crucial for reasons far beyond pure science, given the renewed public and governmental interest in both biodiversity monitoring and deep-sea resource management. A water sample taken 200 meters below the Atlantic can teach fisheries regulators, marine spatial planners, and even astrobiologists who are starting to consider how we might find life in alien oceans. All NOAA did was provide a starting point.
