Metabarcoding with environmental DNA to identify wildlife species potentially attracted to uranium mine containment ponds as a water source in the arid southwest US

• Published in: Genome Vol. 60; no. 11; p. 955
• Main Authors: Klymus, Katy E, Richter, Catherine A, Thompson, Nathan L, Hinck, Jo Ellen
• Format: Journal Article
• Language: English
• Published: Ottawa Canadian Science Publishing NRC Research Press 01.11.2017
• Subjects: Acoustic surveying; Annual variations; Arid regions; Arid zones; Biodiversity; Canyons; Containment; Contaminants; Deoxyribonucleic acid; DNA; Environmental DNA; Environmental monitoring; Federal government; Food chains; Food contamination; Food webs; Genomics; Heavy metals; Markers; Mines; Phylogeny; Ponds; Radioisotopes; Risk assessment; rRNA 12S; rRNA 16S; Runoff; Seasonal variations; Species; Surface water; Taxa; Uranium; Water; Wildlife; Wildlife surveys; United States > US
• ISSN: 0831-2796; 1480-3321

Background: Development of new uranium mines in the Grand Canyon watershed in northern Arizona was restricted in 2009 by the federal government until studies assessing the potential impacts of radionuclide and heavy metal contamination could be completed. Water containment ponds at mines are designed to receive all surface run-off and contain elevated chemical concentrations. The ponds are also a constant water source in an arid region and could result in contaminant exposure to local food webs. To understand the heavy metal exposure pathways, we conducted environmental DNA (eDNA) metabarcoding in parallel with traditional biodiversity surveys via small mammal trapping and acoustic monitoring to identify wildlife using these water sources. With samples from surface water near active mines and mine containment ponds we employed a metabarcoding approach with 12S and 16S rRNA gene markers. Results: Using the 12S markers 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 Mexican free-tailed bat and the tiger salamander. Detection of the tiger salamander is of note because this species was not observed by the traditional biological survey techniques used. Due to low phylogenetic resolution of the 12S marker, most taxa were not identified down to species level. Using our 16S markers, we expect to improve our taxonomic resolution. We will compare our metabarcoding survey results with those from the traditional survey methods and also look at seasonal changes in species occurrence. Significance: As eDNA is quickly becoming a popular tool for wildlife surveys; we will discuss the advantages and limitations of this technique based on our experience. Ultimately this tool will enable us to better understand the overall biodiversity of the area and aid risk assessment of resuming new mining activities.