Department of Biology, Tennessee Technological University, 1100N. Dixie Ave., Cookeville, TN, 38505, USA.
Department of Biology, Centre College, 600 W Walnut St., Danville, KY, 40422, USA.
Mol Ecol Resour. 2017 Nov;17(6):1223-1230. doi: 10.1111/1755-0998.12667. Epub 2017 Apr 11.
Environmental DNA (eDNA) can be used as an assessment tool to detect populations of threatened species and provide fine-scale data required to make management decisions. The objectives of this project were to use quantitative PCR (qPCR) to: (i) detect spiked salamander DNA in soil, (ii) quantify eDNA degradation over time, (iii) determine detectability of salamander eDNA in a terrestrial environment using soil, faeces, and skin swabs, (iv) detect salamander eDNA in a mesocosm experiment. Salamander eDNA was positively detected in 100% of skin swabs and 66% of faecal samples and concentrations did not differ between the two sources. However, eDNA was not detected in soil samples collected from directly underneath wild-caught living salamanders. Salamander genomic DNA (gDNA) was detected in all qPCR reactions when spiked into soil at 10.0, 5.0, and 1.0 ng/g soil and spike concentration had a significant effect on detected concentrations. Only 33% of samples showed recoverable eDNA when spiked with 0.25 ng/g soil, which was the low end of eDNA detection. To determine the rate of eDNA degradation, gDNA (1 ng/g soil) was spiked into soil and quantified over seven days. Salamander eDNA concentrations decreased across days, but eDNA was still amplifiable at day 7. Salamander eDNA was detected in two of 182 mesocosm soil samples over 12 weeks (n = 52 control samples; n = 65 presence samples; n = 65 eviction samples). The discrepancy in detection success between experiments indicates the potential challenges for this method to be used as a monitoring technique for small-bodied wild terrestrial salamander populations.
环境 DNA (eDNA) 可用作评估工具，以检测受威胁物种的种群，并提供做出管理决策所需的精细尺度数据。本项目的目的是使用定量 PCR (qPCR)：(i) 检测土壤中添加的蝾螈 DNA，(ii) 随时间量化 eDNA 降解，(iii) 确定使用土壤、粪便和皮肤拭子在陆地环境中检测蝾螈 eDNA 的可检测性，(iv) 在中观实验中检测蝾螈 eDNA。蝾螈 eDNA 在 100%的皮肤拭子和 66%的粪便样本中均被阳性检测到，且两种来源的浓度没有差异。然而，从直接从野生捕获的活体蝾螈下收集的土壤样本中未检测到蝾螈 eDNA。当将蝾螈基因组 DNA (gDNA) 以 10.0、5.0 和 1.0 ng/g 土壤的浓度添加到土壤中时，所有 qPCR 反应中均检测到 gDNA，且添加浓度对检测浓度有显著影响。当以 0.25 ng/g 土壤的浓度添加时，只有 33%的样本显示可回收的 eDNA，这是 eDNA 检测的下限。为了确定 eDNA 降解的速率，将 gDNA（1 ng/g 土壤）添加到土壤中并在七天内进行定量。随着天数的增加，蝾螈 eDNA 浓度下降，但在第 7 天仍可扩增。在 12 周的时间内（n = 52 个对照样本；n = 65 个存在样本；n = 65 个逐出样本），在两个中观实验土壤样本中检测到蝾螈 eDNA。实验之间检测成功率的差异表明，该方法用作小体型野生陆地蝾螈种群监测技术存在潜在挑战。
