Project: Environmental DNA


Environmental DNA (eDNA) uses a small seawater sample to simultaneously monitor the abundance of fishes, invertebrates and marine mammals without seeing or capturing them.

More and more, natural and anthropogenic pressures are impacting marine ecosystem health over large scales—both spatial and temporal. The eDNA project aims to develop a faster, cheaper and more sensitive approach for measuring how these impacts may change biological baselines and initiate shifts in community composition and diversity over time. Developing eDNA techniques allows for streamlined sampling of species and ecosystems worldwide, putting the evidence on the table for the relevant agencies, parties and the public to consider for more informed and transparent decision-making.

The eDNA team is also working with the multi-institute MBON project to contribute their findings to a greater understanding of how biodiversity interconnects with ecosystem sciences.


A crew launches multiple instruments to take ocean measurements and collect water samples for the eDNA project.  Photo Credit: Jesse Port.

Project Updates

The Center’s Environmental DNA (eDNA) project, is a collaborative research effort that has international and national-scale implications. Last year, the Center was awarded $830,000 out of a larger $7 million Marine Biodiversity Observation Network (MBON) grant to develop and test innovative genetic sampling techniques. As part of this 5-year grant, our MBARI and Stanford scientists are working with the National Oceanic and Atmospheric Administration and the University of South Florida to incorporate eDNA monitoring into a demonstration Marine Biodiversity Observation Network that includes the Monterey Bay, Florida Keys and Flower Garden Banks National Marine Sanctuaries. Recent field research featuring researchers from the Hopkins Marine Station and its Marine Life Observatory compared visual survey data with eDNA from kelp forest water samples to groundtruth the use of eDNA as a tool for measuring biodiversity. Results indicate that eDNA data can identify the same species as visual surveys and could help revolutionize marine wildlife and biodiversity monitoring and management by making species identification much less time consuming and less expensive.

In addition, the Center’s eDNA team continue to develop and test eDNA technology as a future tool to inform ecosystem monitoring and management needs. For example, in experiments conducted at the Tuna Research Conservation Center at Hopkins Marine Station with Dr. Barb Block, the eDNA team successfully designed assays that distinguished differences in the shedding and persistence rates of the eDNA of anchovies, sardines and mackerel, three commercially and ecologically important fish species along the California coast. The results of our experiments indicate that the shedding and decay rates for anchovy and sardines by biomass are similar and an order of magnitude higher than for mackerel. We also found that anchovy, sardine and mackerel DNA persisted on the order of days, suggesting eDNA is a promising tool for efficiently and effectively tracking fish in marine waters.

The team also scaled up our bioinformatics pipeline last year to enable processing of larger sequence data files, and, using facilities at the Monterey Bay Aquarium, studied whether eDNA sampling methods could be used to profile the diet of cookie-cutter sharks through gut content sampling.

Another collaboration between the Center, the Monterey Bay Aquarium, the Hopkins Marine Station, and Stanford enabled COS staff to break new ground in using eDNA for biodiversity sampling. After testing the potential of eDNA to sample multiple species simultaneously in a tank at the Monterey Bay Aquarium, the eDNA team conducted a similar study in the wild kelp forest. The results published in Molecular Ecology (Port et al. 2015) were comparable to visual surveys done by SCUBA divers and hold great promise.

In May 2016, the COS team spent 27 days aboard the NOAA vessel, Rueben Lasker, collecting over 400 water samples along the entire Monterey Bay National Marine Sanctuary, spanning from Gulf of the Farallones to Cambria. These collections have allowed us to optimize our methods, improving eDNA as a monitoring tool and resulting in standard operating procedures that are public to any group interested in conducting marine eDNA studies today.

In September 2016, the COS and Monterey Bay Aquarium Research Institute (MBARI) eDNA team spent 10 days aboard the R/V Western Flyer to continue eDNA sample collections for the Monterey Bay Long Term Monitoring Program, the results of which are adding to our understanding of the biodiversity and community dynamics in Monterey Bay over the last decade. We are currently processing this historical sample set from 2008 to 2016 and preliminary eDNA findings are reflecting trends seen in fisheries landings data. Recently, former COS Early Career Fellow, Ryan Kelly, and current COS Early Career Fellow, Collin Closek, along with others published a comparative study enumerating biodiversity via physical observations vs. the efficacy of different genetic markers for eDNA detection (Kelly et. al, 2017). Our eDNA work is currently funded by BOEM, NASA, and NOAA as part of the Marine Biodiversity Observation Network (MBON). The eDNA holds great promise for bringing us closer to management-relevant technology and methods.

Center for Ocean Solutions eDNA Team:
Project Leads: Larry Crowder (science director) Alexandria Boehm (affiliated researcher and member of science advisory committee)
Early Career Fellows: Collin Closek (early career fellow)