Metabarcoding of Environmental DNA Samples to Explore the Use of Uranium Mine Containment Ponds as a Water Source for Wildlife

Abstract

Understanding how anthropogenic impacts on the landscape affect wildlife requires a knowledge of community assemblages. Species surveys are the first step in assessing community structure, and recent molecular applications such as metabarcoding and environmental DNA analyses have been proposed as an additional and complementary wildlife survey method. Here, we test eDNA metabarcoding as a survey tool to examine the potential use of uranium mine containment ponds as water sources by wildlife. We tested samples from surface water near mines and from one mine containment pond using two markers, 12S and 16S rRNA gene amplicons, to survey for vertebrate species. We recovered large numbers of sequence reads from taxa expected to be in the area and from less common or hard to observe taxa such as the tiger salamander and gray fox. Detection of these two species is of note because they were not observed in a previous species assessment, and tiger salamander DNA was found in the mine containment pond sample. We also found that sample concentration by centrifugation was a more efficient and more feasible method than filtration in these highly turbid surface waters. Ultimately, the use of eDNA metabarcoding could allow for a better understanding of the area's overall biodiversity and community composition as well as aid current ecotoxicological risk assessment work.

Limitations of current knowledge about the ecology of Grey Foxes hamper conservation efforts

“…Most studies that reported relative abundance (RAB) for this species used camera traps (n= 14), track and scat transects (n= 6), or track plots (n= 3). Hair snares (Downey et al 2007), observations by archery deer hunters (Cooper et al 2012), and environmental DNA (eDNA, Klymus et al 2017) were each reported detecting Grey Foxes by a single study.…”

Environmental DNA (eDNA) metabarcoding of pond water as a tool to survey conservation and management priority mammals

“…This suggests that concentrated samples can contaminate negative controls during metabarcoding. Negative controls at each stage of metabarcoding can identify contaminant introduction (Klymus, Richter, Thompson, & Hinck, 2017;Ushio et al, 2017), but contaminants in these controls can amplify exponentially with no competition affecting inferences (Harper et al, 2018). Innovative approaches are needed to mitigate metabarcoding contamination, such as false positive estimation using occupancy models (Ficetola et al, 2015) or sequencing thresholds, i.e.…”

Airborne eDNA Reflects Human Activity and Seasonal Changes on a Landscape Scale

“…Sun et al (2019) used eDNA metabarcoding to understand Dipteria and other organism populations in human caused roadside stormwater ponds. Additionally, Klymus et al (2017) examined how anthropogenic uranium containment ponds impacted the biodiversity of vertebrate species. Early applications also include monitoring of the re-introduction of Rhine sculpin (Cottus rhenanus) into its native range (Hempel et al, 2020) and at-risk, pre-restoration coral community monitoring (Nichols and Marko 2019).…”