Environmental DNA (eDNA) analysis as a survey tool in natural spring and stock tank biomonitoring

Abstract

Recent research has shown the viability of environmental DNA (eDNA) in identifying the presence of organisms in freshwater ecosystems. Environmental DNA includes the DNA from an organism that is collected from environmental samples, instead of from the organism itself; by collecting water samples and analyzing this eDNA through metabarcoding techniques, the presence of species in a given ecosystem can be established. However, there is limited research indicating the feasibility of eDNA as a survey tool in water sources such as springs and stock tanks. Because of the scarcity of water in the high desert landscape of central Arizona, natural springs and man-made stock tanks, used as water sources for open range cattle, play an important role in the functioning of the ecosystem, and are a stopping point for many vertebrate species. Therefore, we address the question of whether eDNA analysis is a viable survey tool in monitoring vertebrate species presence in springs and stock tanks within the Prescott National Forest in the Arizona central highlands. Water samples were collected in 250 mL and 500 mL containers, and were filtered to capture fine particles and cells greater than 0.45 ?m. These particles were then amplified with universal primers for 16S sections, which are conserved in vertebrates as part of the rRNA gene. Current methodologies have shown that the 16S rRNA gene is effective in recognizing vertebrate DNA. The 16S rRNA metabarcoding technique used in this project detected the presence of species that are common to the Prescott National Forest, including species of bear, deer, and squirrel. Additionally, this eDNA metabarcoding technique detected the American bullfrog, which is an invasive species in the Southwestern United States. Our detection of the invasive American bullfrog represents a next step in better monitoring presence and removing the species from ecosystems throughout the region. Our results suggest eDNA metabarcoding is an effective tool in assessing species presence at natural springs and stock tanks, and should continue to be used for further research focused on biomonitoring in other water sources.