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

Abstract

Freshwater unionid mussels are a taxa‐rich group of bivalves that play a critical role in maintaining freshwater ecosystems, but are heavily imperilled due to anthropogenic influences. Environmental DNA (eDNA) provides potential benefits for the monitoring of unionids through higher detection sensitivity, lower costs, less intrusion on the environment, and added advantages for sampling challenging and remote habitats. We compare an extensive mussel rescue survey conducted as part of the demolition of a dam with the detection of mussels using eDNA metabarcoding. The unique mussel rescue survey provided a rare opportunity for an in‐depth analysis of unionid eDNA detection across both small sampling cells and a large sampling region. Environmental DNA detected 22 of the 24 (91.67%) species sampled in the rescue survey, with the two absent species found as only single individuals. A species missed by the rescue survey was detected with eDNA (Potamilus alatus), along with hidden cryptic 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, and eDNA successfully detected the two federally listed species present. 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 metabarcoding as a supplemental sampling method to describe diverse mussel communities and improve the detection of threatened and endangered species.

Molecular identity crisis: environmental DNA metabarcoding meets traditional taxonomy—assessing biodiversity and freshwater mussel populations (Unionidae) in Alabama

“…Our objective was to evaluate the use of eDNA as a sampling technique for a well-studied assemblage of freshwater mussels in the biologically diverse Sipsey River system in the southeastern USA. Four recent studies have demonstrated the effectiveness of metabarcoding to identify freshwater mussel species in France, Switzerland, Italy, Morocco ( Prié et al, 2021 ), Virginia, USA ( Klymus et al, 2021 ), Ontario, Canada ( Coghlan et al, 2021 ), and Ohio, USA ( Marshall et al, 2022 ). However, these studies describe a range of agreement of species detection from eDNA compared with traditional surveys ranging from 40% to 58% agreement in Virginia/Tennessee ( Klymus et al, 2021 ) to 92% in Ohio ( Marshall et al, 2022 ).…”

“…Four recent studies have demonstrated the effectiveness of metabarcoding to identify freshwater mussel species in France, Switzerland, Italy, Morocco ( Prié et al, 2021 ), Virginia, USA ( Klymus et al, 2021 ), Ontario, Canada ( Coghlan et al, 2021 ), and Ohio, USA ( Marshall et al, 2022 ). However, these studies describe a range of agreement of species detection from eDNA compared with traditional surveys ranging from 40% to 58% agreement in Virginia/Tennessee ( Klymus et al, 2021 ) to 92% in Ohio ( Marshall et al, 2022 ). Similarly, our eDNA results were broadly consistent with the data from traditional quadrat-based field surveys, although both community eDNA and conventional sampling detected some species that the other method did not.…”

“…It might be possible to obtain greater yields from turbid water with a sequential filtering strategy by passing water through filters of decreasing pore size, which has been demonstrated as an effective method to overcome volume limitations while reducing pore size in recent qPCR studies ( e.g ., Turner et al, 2014 ; Moushomi et al, 2019 ; Cooper et al, 2021 ). Among multispecies mussel eDNA studies, a range of water volumes have been sampled, typically targeting 0.5 to 1 L ( Coghlan et al, 2021 ; Marshall et al, 2022 , this study), but range from 0.045 to 30 L ( Klymus et al, 2021 ; Prié et al, 2021 ). Optimizing sample volume and filter pore sizes will be necessary for improved multi species eDNA detection in turbid waters.…”

“…Fewer freshwater mussel studies have used metabarcoding methods, which can detect multiple species with a single sample, while also identifying other taxonomic groups including host fishes. Several recent studies have demonstrated the utility of metabarcoding to describe and compare mussel diversity in riverine systems, although some challenges remain ( Coghlan et al, 2021 ; Klymus et al, 2021 ; Prié et al, 2021 ; Marshall et al, 2022 ). For this study, we developed a microfluidic metabarcoding array that targets a wide range of species that are known to be present in a diverse southeastern USA stream, the Sipsey River, Alabama.…”

Dead‐end hollow fiber ultrafiltration capture of environmental DNA for freshwater mussel (Unionidae) species detection with metabarcoding

“…Early freshwater mussel eDNA studies primarily used species‐specific assays, although more recently, studies have emerged using metabarcoding approaches to identify unionid mussel communities (Coghlan et al, 2021; Klymus et al, 2021; Marshall et al, 2022; Prié et al, 2021). These metabarcoding studies have included development of multiple metabarcoding primers and have demonstrated that high proportions of the known mussel community can be detected using eDNA (e.g., >80% (Coghlan et al, 2021) and 91% (Marshall et al, 2022)). Both species‐specific and metabarcoding approaches face similar challenges, including the need for numerous field samples and replicates to obtain sufficient detection rates when typical eDNA filtering approaches are employed (Marshall et al, 2022).…”