- Researchers tested a new self-preserving filter housing system that automatically preserves eDNA from water samples, while reducing the risk of DNA contamination and plastic waste.
- Scientists who use eDNA currently rely on cumbersome cold storage or liquid preservatives and single-use sampling equipment to preserve their eDNA samples, which are highly sensitive to degradation as well as contamination.
- The new system incorporates a hydrophilic plastic material in its filter housing that physically pulls water from the sample without having to add chemicals.
- In a six-month test, it allowed data collectors to preserve samples quickly and easily, at ambient temperature and with far reduced plastic waste, preventing degradation for weeks and with slightly higher amounts of captured DNA than a standard method.
When collecting a DNA sample from a species in the wild just isn’t possible — it’s elusive, it may disturb the animal, or a host of other reasons — field biologists often turn to collecting the next best thing: environmental DNA.
Known as eDNA, it comprises genetic material shed by animals and plants into the surrounding ecosystem through their skin, scales, feces or pollen, and has proved increasingly useful for identifying particularly aquatic species found at a given place.
Collecting and analyzing water or soil samples containing DNA of the organisms living in the area is quicker, easier and cheaper than traditional field DNA collection methods that require scientists to physically contact the animal or plant of interest and take a direct tissue sample from it.
Challenges in using eDNA
There is, however, a major drawback to the method: the eDNA in water is often dilute, so obtaining enough DNA of the target animal from water samples requires researchers to transport substantial amounts of water to a lab for analysis, which can cause the DNA to degrade over time.
To prevent degradation of the DNA during transport back to their labs, eDNA scientists tend to immediately filter out and preserve samples in the field. But the steps used in the preservation process, including transferring samples to cold storage or to ethanol or other chemical preservative, increase the risk of contamination of the DNA.
To mitigate that risk, eDNA field researchers have turned to single‐use filter housings that can immediately preserve eDNA samples on‐site, without their having to transport large volumes of water.
But what are sustainability-minded ecologists to do when the most effective data-collection method produces substantial plastic waste?
“Most of us got into ecology because we care about the ecosystems we study,” says researcher Austen Thomas. “The last thing we want to do is leave a legacy of plastic trash.”
Thomas led a group of researchers in Washington state, U.S., who developed a reusable filter housing that uses a partially biodegradable hydrophilic plastic, rather than chemicals or cold storage, to preserve eDNA samples. The hydrophilic (“water-loving”) property of the plastic means it pulls and absorbs water from the sample. They published details on the system and the results of a comparison of the new technique with a standard, chemical-based eDNA collection process.
A physical, rather than chemical, desiccant
“We started out simply looking for biodegradable plastics that could be molded into a filter housing, with the objective of reducing plastic waste,” Thomas, from the Smith-Root company, which develops technology for fisheries research, said in a statement. “That’s when we realized that some of the biodegradable compounds function by being highly hydrophilic.”
These compounds, the “secret” to creating a self-preserving eDNA filter, automatically preserved the collected eDNA by drying it out physically, rather than chemically. By physically pulling moisture from the sample, the desiccant material in the filter housing removed the need to use liquid chemicals and associated single-use plastic vials to preserve the eDNA.
The Smith-Root eDNA Sampler’s individual self‐preserving eDNA filter housings are packaged in resealable plastic bags that work with a ziplock-type of closure and can remain closed for weeks at ambient field temperature until the team is back at the lab. The process enables field teams to collect and transport many field samples without having to carry around cold-storage materials or liquid preservatives.
A team member first collects an eDNA sample from water by attaching the filter housing to a pump apparatus. A standard 47-millimeter (1.9-inch) membrane in the housing filters the water, which remains in the housing. The user then places the entire housing (still unopened) back into the resealable bag. The bag’s hydrophilic plastic then absorbs any remaining moisture in the housing container, preserving the eDNA captured on the filter membrane.
Back in the clean conditions of a laboratory, the team opens the filter housing via a pull tab and extracts the captured eDNA from the membrane.
For their study, the scientists compared the eDNA preservation capabilities of the self‐preserving hydrophilic filter housings to a standard ethanol preservation method using eDNA from two species, a New Zealand mudsnail (Potamopyrgus antipodarum) and a Columbia spotted frog (Rana luteiventris). They found that the new filter housings actually resulted in more amplified eDNA of the target species (in both cases) than the industry‐standard ethanol preservation method for sample collection, though both methods kept the eDNA from degrading over a six‐month testing period. These data suggest that the new method is at least an equally effective option for preserving eDNA captured in the field and storing the samples at low cost for up to six months.
Expanding the testing effort
The authors say in their paper their primary aim was to reduce the risk of eDNA contamination from handling of filters in the field and support the integration of eDNA into management or regulatory processes. By removing steps from the DNA preservation process, they suggest, the new system should enable field researchers to collect their samples in less time while using fewer forceps, buffers, vials, coolers and other materials.
“This really simplifies the eDNA sample collection process,” co-author Caren Goldberg, from Washington State University, said in the statement. “It also reduces the amount of time and training required for field staff to effectively collect eDNA samples.”
Streamlining the eDNA field sampling process, the researchers write in their paper, should help incorporate the efforts of non-expert (citizen scientist) data collectors into research programs. Some eDNA research studies already rely on citizen scientists and others who are new to the field or not professionally trained in field data collection.
To test the self-preserving filters across a broader range of locations and field conditions, the system’s developers have begun sending samples of the filters to eDNA researchers in various geographic regions. They encourage research groups interested in beta testing the new filters to contact them.
Citation
Thomas, A. C., Howard, J., Nguyen, P. L., Seimon, T. A., & Goldberg, C. S. (2018). ANDe™: A fully integrated environmental DNA sampling system. Methods in Ecology and Evolution, 9(6), 1379-1385. doi:10.1111/2041-210x.12994
FEEDBACK: Use this form to send a message to the editor of this post. If you want to post a public comment, you can do that at the bottom of the page.
