By Kimberly Bonvechio

In our Research Highlights blog series, we debut newly published fisheries research by our women of fisheries colleagues. If you have research you would like to highlight and share with our readers, submit a nomination form here!

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This Month’s Research Highlight:

Andres, Kara J., Timothy D. Lambert, David M. Lodge, Jose Andrés, and James R. Jackson. 2023. Combining sampling gear to optimally inventory species highlights the efficiency of eDNA metabarcoding. Environmental DNA 5:146-157.

There’s a lot of buzz these days around the use of environmental DNA – or eDNA – for managing and conserving our natural resources. 

For good reason. 

As natural resource agencies face increasingly large and complex problems, often with limited amounts of funding and staff to address them, they are looking to new ways to collect data over broad spatial and temporal scales in a time- and cost-efficient manner. That’s what makes the developing field of eDNA science, and its potential to increase our sampling capabilities, such an exciting frontier.  

So, what is eDNA? As organisms interact with each other and their environment, they release genetic material through things like excretions and shedding of tissues, and that material then accumulates in the air, water, and soil around them. This “extraneous” genetic information in the environment is what we refer to as eDNA. By taking environmental samples and analyzing the DNA present, scientists can gain information about what species are present without having to actually capture the organisms themselves. This can be especially helpful if the species is present in low abundance or isn’t susceptible to capture by current sampling gears. Although previous studies have shown that eDNA samples can be used to successfully detect fish species in aquatic environments, it’s not without its challenges and it’s still unclear how this technology can fit into our conventional sampling landscape. 

Dr. Kara Andres, currently a Postdoctoral Fellow at the Living Earth Collaborative at Washington University in St. Louis, Missouri, led recent efforts to help address some of these unknowns. She and her team used data from a fisheries long-term monitoring program at Oneida Lake, New York to determine the optimal combination of eDNA and conventional field sampling. Dr. Andres notes, “…because all gear types have pros and cons (that is, they differ in their sampling logistics, efficiency, and biases) we wanted to examine the efficiency of each survey approach independently and in combination. This allowed us to determine how to optimally allocate sampling effort/cost across different sampling gears to maximize survey efficiency.”

By the mere mention of “field work,” freshwater fisheries scientists would likely conjure up images of sampling with gears like electrofishing, fyke nets, and seines. Although the gear and manner of operation may differ, the general procedure is the same. Upon capture by the gear, the fisheries scientist identifies, counts, and records necessary information from the catch. Depending on the number of sites and samples, it can be a time-consuming and effort-intensive process. With eDNA sampling, on the other hand, fish sampling simply requires the collection of a water sample that is filtered for pieces of DNA. These pieces of DNA are then taken back to the laboratory where specific DNA sequences are amplified and the species identified. According to Dr. Andres and her team, it takes half the time or even less in person-hours of effort compared to other gears included in their study. 

Not only did the eDNA method outperform these other gears in terms of time- and cost-efficiency, but it also detected more fish species than all of the conventional sampling gears combined. Dr. Andres notes, “The biggest surprise to me was the sheer amount of information we collected in a single day of eDNA sampling versus an entire field season of conventional surveys.” This doesn’t mean eDNA can, nor should, replace these sampling gears, but rather that it can be an extremely valuable component of a monitoring program. Researchers found that some species were still missed with the eDNA method, and it wasn’t until eDNA data were combined with data from other sampling gears that they were able to maximize the number of species detected. Still, this can be a quick and efficient tool for gathering information on fishes, particularly from areas that aren’t easily sampled with other approaches.

Monitoring goals can vary widely, and although one day eDNA can be used for more than gathering species richness data, the technology isn’t quite there yet. Other information such as fish age and size can only be attained by collecting individuals with conventional gears. There are also some pretty big challenges that need to be overcome before eDNA can be used on a broadscale level. As summarized by Dr. Andres, “This is a developing field and we are still working on improvements to field and lab protocols, sequencing and processing, and reference databases. While these improvements are exciting and useful, we need to find a way to standardize eDNA sampling so that we can compare sites across time and space for use in monitoring. DNA-based monitoring approaches can also be inaccessible to scientists and managers that don’t have the facilities or materials required to shift away from conventional sampling approaches. For effective large-scale monitoring programs, we need to find a way to make these approaches feasible for more people.” 

There is still much work to be done, and Dr. Andres plans to continue developing this methodology and broaden its application for studying natural systems. Although her previous research has focused on fishes, she wants to expand her efforts to other taxonomic groups including invertebrates and bacteria. eDNA technology offers an opportunity to provide a much larger ecological picture than individual sampling gears that are most often designed to look at individual components in an ecosystem. 

The future of eDNA technology, with all of its potential applications, is definitely something to buzz about.

The full manuscript can be found or downloaded here:
doi.org/10.1002/edn3.366 (open access)