Environmental DNA detection and quantification of invasive red-eared sliders,Trachemy scripta elegans, in ponds and the influence of water quality

Abstract

Environmental DNA (eDNA) is a powerful tool for monitoring the distribution of aquatic macro-organisms. However, environmental factors, including the water temperature and water quality, can affect the inhibition and/or degradation of eDNA, which complicates accurate estimations of eDNA concentrations and the detection of the presence/absence of species in natural habitats. Further very few eDNA studies have been conducted for reptiles, especially with respect to estimating their biomass and/or abundances. Here we examined the relationship between the visually-observed number of red-eared sliders (Trachemys scripta elegans) and eDNA concentrations across 100 ponds. Additionally, we evaluated the effect of water quality on red-eared slider eDNA concentration in these ponds. We found that there was a significant positive correlation between the observed number of red-eared sliders and the eDNA concentration in the ponds. On comparing various water quality indicators, including dissolved nitrogen, dissolved phosphorous, organic matter, and chlorophyll a (Chl. a), we found that only Chl. a had a negative correlation with the red-eared slider eDNA concentration, while we did not find any inhibition in the quantitative PCR. We conclude that concentrations of eDNA can potentially be used for estimating the abundance of the red-eared slider. Additionally, Chl. a might indirectly influence the degradation of eDNA through the microorganisms bonded to the phytoplankton in the ponds, as microbial activity is thought to decrease eDNA persistence.

A Model and Simulation of the Influence of Temperature and Amplicon Length on Environmental DNA Degradation Rates: A Meta-Analysis Approach

“…Environmental DNA (eDNA) methods are innovative methods developed for monitoring macroorganisms, especially aquatic species (Ficetola et al, 2008;Minamoto et al, 2012;Taberlet et al, 2012;Takahara et al, 2012;Ushio et al, 2018;Kakuda et al, 2019;Tsuji et al, 2019). The eDNA method is used to investigate species distribution.…”

Water pre-filtration methods to improve environmental DNA detection by real-time PCR and metabarcoding

“…Most eDNA studies that use a filtration approach have been conducted in marine or freshwater systems, where water appears to be non-turbid at the time of collection [15][16][17][18]. This is owing to the unique set of challenges that turbid water poses when detecting eDNA, such as the clogging of filters and the presence of PCR inhibitors [19][20][21]. Previous studies have utilised extraction kits-which come with anti-inhibitory washes-various pore sizes, membrane types, and pre-filtration steps to prevent filter clogging [22][23][24][25].…”

A review of applications of environmental DNA for reptile conservation and management

“…Fediajevaite et al ( 2021 ) recognized that this may partially reflect research effort, as reptile studies were the second least represented in the meta‐analysis. Of the studies reviewed here, only 22% compared eDNA methods and traditional surveying (with temporal overlap between the two methods), with mixed results: three found eDNA and traditional survey detections were comparable (Akre et al, 2019 ; Kakuda et al, 2019 ; Kucherenko et al, 2018 ), three found eDNA outperformed traditional surveys (Feist et al, 2018 ; Matthias et al, 2021 ; Raemy & Ursenbacher, 2018 ), and two found that traditional surveys outperformed eDNA (Ratsch et al, 2020 ; Rose et al, 2019 ). These studies were not able to be directly compared to conclude whether eDNA outperforms traditional surveying due to substantial variation in sample methods, design, and reporting metrics.…”