Exploring Deepwater Ecosystems with eDNA

Between September 23-27, 2019, a team of ocean scientists and engineers from WHOI and Lehigh University used NOAA's research vessel Manta and the newly developed autonomous underwater vehicle (AUV) Mesobot to collect environmental DNA (eDNA) in order to explore the biodiversity of deepwater ecosystems near Flower Garden Banks National Marine Sanctuary in the Northwestern Gulf of Mexico. eDNA, short for environmental DNA, is the genetic material that organisms leave behind in the water column. As with forensic science, marine species are able to be identified by the invisible signs of their presence constantly being left in the environment.

As part of the Ocean Twilight Zone Project, WHOI researchers Dr. Annette Govindarajan and Dr. Dana Yoerger developed a novel pumping and filtering system mounted on the Mesobot to collect eDNA from seawater while at depth. The system filtered more than 700 liters of water per dive through six independent pairs of filters. The expedition included five dives, totaling nearly 15 hours in the water, reaching depths of over 365 meters (1,200 feet) and produced a total of 42 samples from the vehicle.

Justin Fujii prepares to launch Mesobot equipped with a high-volume eDNA sampler into the Gulf of Mexico. (Allison Albritton)

Back in the laboratories of Dr. Santiago Herrera and Dr. Govindarajan, researchers are using modern gene-sequencing technologies to identify coral, fish, and invertebrate species found in the deep benthic and pelagic Gulf. Dr. Herrera and Dr. McDermott, in collaboration with Dr. Andrea Quattrini (Smithsonian Institution), Dr. Erik Cordes (Temple University), and Dr. Catherine McFadden (Harvey Mudd College), are also investigating how varying ocean conditions, including temperature, oxygenation, and pH, affect the stability and persistence of eDNA in the deep ocean. Generating a model to estimate how long eDNA remains in the water column will provide an important framework for marine scientists around the world to use eDNA as an accurate means for studying the biodiversity of deepwater ecosystems. The results from this eDNA research will be directly applicable to the management and conservation of areas currently being considered for protection as part of the proposed expansion of Flower Garden Banks National Marine Sanctuary.