4 min read
Aug 21, 2024
Dr. Eily Allan is a research scientist at the University of Washington’s (UW) School of Marine and Environmental Affairs and Chief Scientist of the eDNA Collaborative who studies the transport of marine mammal DNA in the environment. Dr. Kim Parsons is a research geneticist who leads the Molecular Genetics Team for the US National Oceanic and Atmospheric Administration’s Northwest Fisheries Science Center (NOAA) in Seattle, USA. In a partnership between UW and NOAA, Allan and Parsons’ teams are uncovering how environmental DNA (eDNA) travels over space and time in marine waters, so they can better monitor and detect large marine mammals like whales and dolphins (cetaceans) in the eastern Pacific Northwest.
Traveling long distances from coastal to offshore habitats, cetaceans pose an interesting challenge for researchers who need to collect data where these animals spend most of their time: at depth. To overcome the common challenges of collecting eDNA at depth, Allan and Parsons have collaborated with Ocean Diagnostics to collect eDNA in the Pacific Northwest’s Hood Canal fjord using the company’s innovative depth sampling technology called Ascension.
“Having the opportunity to work with an instrument like Ascension that allows us to sample at depth from a small boat is really a game changer for us,” says Allan. Parsons adds, “Especially collecting multiple samples at each of those depths.”
While eDNA depth sampling can be conducted from large vessels using instruments like Niskin bottles and rosettes, the methods are limited and often require winch systems and trained personnel. Sampling schedules and locations are often dictated by the ship’s existing survey routes instead of the scientists’ targeted sampling needs, and many coastal datasets are also lacking because large ships are too big to explore near-shore habitats.
In June 2024, the UW and NOAA teams deployed Ascension from a 24-foot aluminum boat within the waters of Hood Canal. While Ascension was being deployed and filtering at depth, filtered surface samples were simultaneously collected at each of the stations.
Allan states, “Not needing a winch or a big boat, a lot of operators like myself and Kim can go out on a boat with small crews and hand deploy (Ascension) down to 200 meters and grab water samples. (Ascension) is easily deployed by non-trained or little-trained personnel on any type of platform.”
Parsons, who has deployed Niskin samplers from a similar boat to collect one sample at one depth, explains, “Having the carousel of filters on Ascension allowed us to deploy it once, trigger it at two different depths and collect multiple samples at each depth. That allowed us to collect biological replicates, something that is super challenging when we're collecting eDNA samples but is really informative.”
When looking for rare target species, researchers must minimize the amount of time between collecting and filtering the water and submerging the filter into preservative. Niskin sampling requires post-sampling filtration either on board the vessel or back in a lab. Both options take time and expose the samples to potential contamination making the data less reliable. Ascension provides in-situ filtration at each sample depth which reduces potential sources of contamination throughout the entire process.
“When we're moving water, we need to have clean bottles. The person that's grabbing the water needs to be cleaned. Everything must be very, very clean. (Ascension) really reduces the workload if we can filter within the environment we deploy,” shares Allan.
With Ascension providing real time data updates every second, Allan and Parsons felt confident in the instrument’s volumes and CTD data. The modular design, filter housing preparation, filter protection and collection of negative controls further enhanced confidence in data reliability.
“Just knowing how the design of the carousel rotates around the pump and that everything's being triggered at a predetermined depth, I feel like we could detect contamination and trace it back to the source, and that's important,” Parsons illustrates.
She continues, “The real time flow rate and depth data is also important because it allowed us to monitor how the instrument was sitting in the water column and make corrections during filtration and between samples. It gave us confidence in the moment and for the future samples coming off the back end.”
The cost of depth sampling with even one ship is a huge expense that can pose another research barrier, even though depth samples from each station is of high scientific value.
“The per-use cost (for Ascension) is really low because all we're doing is reloading filters and those filters are like $1 each,” claims Allan.
What really drew Allan and Parsons to the instrument was ability to use a filter that was directly comparable their other protocols and sampling methods. This compatibility, along with real-time data monitoring, automation and the instrument’s modular design hit home.
Parsons reveals, “We can incorporate the data generated from samples collected with Ascension into our existing data stream from our other samples because we're using the same filters, same water volume and the same lab protocols.”
Ascension’s easy-to-use interface was another draw to the instrument. Allan expresses, “Some of the other instruments we work with are so complicated that we could never program them ourselves which is prohibitive because if we want to make one little change, we can't do it on the fly. She continues, "(Ascension’s) interface is really helpful. Not needing a software engineer was a high (priority) on our list.”
To capture the environmental DNA needed to better monitor cetaceans, an instrument is needed that is versatile enough to be used from a variety of platforms where the user can choose where to deploy it and at what depths.
“It's always going to be challenging to get the spatial coverage that we want if it requires us to be sitting at or moving between stations,” Allan emphasizes.
Now equipped with three Ascensions, UW and NOAA plan to deploy an instrument from a series of fixed installations to increase the spatial coverage and collect more samples at a finer scale in the next sampling round.
Working with oceanographers on modeling in the Hood Canal fjord where there is a lot of vertical mixing of the water column, and leveraging the initial big-picture data collected with Ascension in summer 2024, the team will next attempt to discover whether surface water provides a different signal in terms of time and distance from the mammal than at depth, so they can better determine the ideal depth for eDNA sampling for such rare and mobile target species.
Allan concludes, “The best place to look for information is going to be at depth. Ascension is really one of the only ways that we can get our hands on those deeper samples given the platforms of opportunity available to us for this project.”
Contact us to learn more about Ascension, read more stories, or subscribe to our newsletter (below) for more technology and collaboration stories!