Detection of freshwater mussels (Unionidae) using environmental DNA in riverine systems

Abstract

Environmental DNA (eDNA) methods are being developed for use in conservation biology to improve upon conventional species survey techniques. Validation of eDNA methods in different environmental contexts is required if they are to be widely adopted. One potential application of eDNA methods is for the detection of freshwater mussels (Bivalvia: Unionidae), which are among the most imperiled species in North America. Conventional unionid survey methods are highly invasive and can be difficult to conduct due to issues with morphological identification and their cryptic use of habitat. eDNA methods can potentially provide a non‐invasive, extremely specific, and highly sensitive alternative. Here, we examine the effectiveness of eDNA methods at detecting an imperiled unionid, the wavy‐rayed lampmussel (Lampsilis fasciola), in lotic systems with moderate discharge. We developed a novel qPCR assay for the detection of L. fasciola eDNA, which included a custom internal positive control to check for PCR inhibition. We used different experimental densities of caged L. fasciola specimens as a point source of eDNA within two rivers of the Grand River watershed in Southern Ontario. Sampling occurred at set distances downstream of the cage using purpose‐built sampling equipment. Detection was obtained at the cage (i.e., point of eDNA shedding) but not downstream at distances ≥10 m during stream discharges of approximately 1,632–2,332 L/s. The results indicate that eDNA is diluted rapidly in rivers with moderate discharge and that high‐resolution spatial sampling efforts may be necessary to obtain meaningful eDNA‐based distribution data of unionids, and other sessile organisms, present at low density in lotic systems.

Metabarcoding assays for the detection of freshwater mussels (Unionida) with environmental DNA

“…Species accumulation curves also show that most sites were not adequately sampled. The presence of PCR inhibitors is a potential factor that can lower species detection (Gasparini et al., 2020; Jane et al., 2015; McKee et al., 2015); however, we found no evidence of inhibition in our samples in qPCR tests prior to sequencing. Given the lack of inhibition and the substantially smaller volume processed per site relative to other studies, sampling effort likely led to our lower species detections.…”

“…In conclusion, our work adds to the growing literature which points to the suitability of eDNA analyses for monitoring mussel populations (Belle et al., 2019; Cho et al., 2016; Currier et al., 2018; Gasparini et al., 2020; Prié et al., 2020). The study verified two Unionida‐specific metabarcoding assays suitable for freshwater mussel monitoring through eDNA sampling.…”

“…The two main strategies for species detection from eDNA are a targeted approach using PCR amplification from species‐specific primers and a multispecies approach known as metabarcoding, which involves high‐throughput sequencing of all the products of amplification from “universal” primers developed for a taxon of interest. Analysis of eDNA has been suggested as an additional tool for monitoring mussels, especially rare and endangered species (Cho et al., 2016; Gasparini et al., 2020; Prié et al., 2020). Monitoring of mussels with eDNA offers advantages of being less labor‐intensive, less invasive for the organisms and their habitat, and potentially detecting cryptic individuals or life stages, or animals living in inaccessible habitats (Stoeckle et al., 2016).…”

Pathway to Increase Standards and Competency of eDNA Surveys (PISCeS)—Advancing collaboration and standardization efforts in the field of eDNA

“…Other suggested approaches to test for inhibition presented here are by spiking the eDNA samples with an artificial positive control (gBlock) (Roux et al., 2020) and by using an IntegritE‐DNA TM test (Hobbs et al., 2020). The most common and overall successful approach to remove inhibitors is by diluting the problematic samples (Gasparini et al., 2020; Skinner et al., 2020; Thomas et al., 2019). Although there are ways of dealing with PCR inhibition, an important issue remains which is the variability in inhibition among sampling sites and seasons.…”

Environmental DNA is effective in detecting the federally threatened Louisiana Pinesnake (Pituophis ruthveni)

“…Over the past decade, the utility of eDNA analysis has grown rapidly, and its efficacy has been demonstrated from freshwater, marine, subterranean, terrestrial, and airborne samples (e.g., Franklin et al., 2019; Harper et al., 2020; Johnson, Cox, & Barnes, 2019; Niemiller et al., 2018; Thomsen et al., 2012). Since eDNA analysis was first applied to macrobiota (Ficetola et al., 2008), it has become an important conservation and management tool that is capable of detecting both invasive and imperiled species at low abundances in numerous contexts (e.g., Gasparini, Crookes, Prosser, & Hanner, 2020; Goldberg, Strickler, & Fremier, 2018; Kessler, Ash, Barratt, Larson, & Davis, 2020; de Souza, Godwin, Renshaw, & Larson, 2016; Tréguier et al., 2014; Valentin et al., 2020; Wacker et al., 2019).…”