Evaluating environmental DNA metabarcoding as a survey tool for unionid mussel assessments

Freshwater mussels are a diverse group of bivalves that have >300 species found across North America. They play a key role in maintaining freshwater ecosystems through water filtration, nutrient cycling, habitat modification, and serving as food resources for other animals. However, many species in this group are on the brink of extinction, with ~1/3 of species considered endangered or threatened by the US federal government. Due to their ecological importance and their continuing population declines, the monitoring and management of unionid populations is of high priority. However, due to their rarity and the fact that unionids burrow into the benthic substrate, traditional visual surveys are time-consuming and require expert taxonomists. Therefore, novel methods to improve the efficiency and accuracy of surveys could be beneficial for population management.

Over the past decade, the analysis of aquatic environmental DNA (eDNA –genetic material released from urine, waste, mucus, or sloughed cells) has improved biological assessments by increasing species detection and unraveling patterns of biodiversity. Similar to criminal forensic analysis, eDNA surveys provide biologists an opportunity to survey biodiversity without ever actually observing or seeing the species being surveyed. This new survey method provides benefits for the monitoring of mussels by increasing detection probability, lowering survey costs, causing less obstruction and intrusion on the environment, and improving the ability to sample challenging and remote habitats. Stantec incorporated eDNA sampling to detect the entire mussel community upstream of the Six Mile Dam removal project on the Walhonding River (an Ohio River tributary) in Coshocton County near Warsaw, Ohio. The Walhonding River at the project site included a diverse mussel bed with the known presence of two federally-listed species (Plethobasus cyphyus and Theliderma cylindrica). Therefore, Stantec tested the applicability of eDNA methodology to detect this diverse mussel community, including the detection of listed species of regulatory importance.

Environmental DNA detected 22 of the 24 (91.67%) species that were found in the river with a traditional mussel survey, with the two absent species found as only single individuals within the sampling region. A species that was completely missed by a traditional survey was detected with eDNA (Potamilus alatus), along with hidden diversity within the genus Pyganodon. Both survey methods detected the presence of two federally listed species from multiple sampling cells (Plethobasus cyphyus and Theliderma cylindrica). Furthermore, eDNA provided similar estimates of relative mussel abundances across the sampling region. Estimates of mussel diversity were similar between the two methods. These results contribute to the growing knowledge of eDNA based biological assessments and provide valuable insight into comparing sampling effort and detection rates from conventional and eDNA survey methods. As eDNA collection can widen the traditional sampling season and improve the ability to sample difficult or dangerous environments, these results demonstrate the practicality of eDNA as a supplemental sampling method to describe diverse mussel communities and improve the detection of threatened and endangered species.

Read full article in Freshwater Biology.