December 6th, 2024

Ancient Cores from an Ocean Canyon

DNA analysis of sediment cores offers researchers a 14,000-year window into a deep-sea ecosystem.

Taking a sediment core a thousand meters below the surface of the ocean can be a tricky business. But once you have a core, the material contained within it can tell a fascinating story about the inhabitants of ancient ecosystems and environmental change. Researchers are increasingly enthusiastic about examining marine sediment cores to decipher the ways that deep-sea ecosystems have altered over thousands of years.

The critical tool is environmental DNA (eDNA) analysis. This is a non-invasive method that captures DNA from environmental samples—whether seawater, soil, or marine sediment—to detect what organisms were living in the ecosystem. A subset of eDNA is sedimentary ancient DNA (sedaDNA). The sedaDNA approach is now being used to help researchers understand biodiversity shifts in specific ocean locations over time. 

Marine canyons are biodiversity hotspots, where organisms have adapted to the unique conditions of the deep sea. Barkley Canyon, located off the coast of southern Vancouver Island, reaches depths of up to 2,000 meters. The area is a popular destination for deep-sea research due to its steep coral cliffs and rich array of marine life.  

Cooper Stacey, a marine geologist with Natural Resources Canada, has worked to extract marine sediment cores from Barkley Canyon that are as much as two meters in length. Researchers Linda Rutledge and Danielle Grant at the Hakai Institute Ancient DNA Laboratory on Quadra Island are studying some of these cores, enabling them to begin to reconstruct Barkley Canyon ecosystems—all the way back to the Pleistocene-Holocene transition that occurred 11,000–14,000 years ago. 

Ancient Cores from an Ocean Canyon

A piston corer used for sediment sampling is deployed by a technician off the Vector, a Canadian Coast Guard hydrographic survey vessel. In Barkley Sound, the core sampling rig is smaller, and known as a gravity corer. Photo courtesy NRCAN

So far they have detected ancient genomic signals for harmful algal blooms (HABs), including a bioluminescent dinoflagellate called a sea sparkle; a type of Pacific jellyfish called sea nettle; bony and cartilaginous fish; and coastal ferns—the latter potentially hinting at a way that terrestrial materials made their way into this deep ocean canyon. 

“Canyons are also of interest to sedaDNA work because they accumulate organic matter from nearby and more distant regions of the ocean, including the shallows,” says Rutledge. “The results can provide a broad view of biodiversity that is not only site-specific.”

One concern for scientists is that certain technologies, such as the use of X-rays, might affect the quality of the DNA they are trying to sequence. X-rays are routinely used in marine geology to assess the density and composition of sediment cores, and Hakai Institute researchers are testing to see whether they impact biodiversity estimates.

If X-rays are found to leave DNA undamaged, that means that the many archived and X-rayed marine sediment cores stored in global repositories could continue to be used for sedaDNA work. Updates coming soon!