Guri Gledis, Ray Jessica Louise, Shelton Andrew Olaf, Kelly Ryan P, Præbel Kim, Andruszkiewicz Allan Elizabeth, Yoccoz Nigel, Johansen Torild, Wangensteen Owen S, Hanebrekke Tanja, Westgaard Jon-Ivar
Norwegian Institute of Marine Research Framsenteret Tromsø Norway.
Norwegian College of Fishery Science UiT the Arctic University of Norway Tromsø Norway.
Ecol Evol. 2024 Dec 11;14(12):e70678. doi: 10.1002/ece3.70678. eCollection 2024 Dec.
Environmental DNA (eDNA) detection employing quantitative PCR (qPCR) and droplet digital PCR (ddPCR) offers a non-invasive and efficient approach for monitoring aquatic organisms. Accurate and sensitive quantification of eDNA is crucial for tracking rare and invasive species and understanding the biodiversity abundance and distribution of aquatic organisms. This study compares the sensitivity and quantification precision of qPCR and ddPCR for eDNA surveys through Bayesian inference using latent parameters from both known concentration (standards) and environmental samples across three teleost fish species assays. The results show that ddPCR offers higher sensitivity and quantification precision, particularly at low DNA concentrations (< 1 copy/μL reaction), than qPCR. These findings highlight the superior performance of ddPCR for eDNA detection at low concentrations, guiding researchers towards more reliable methods for effective species monitoring. Additionally, this study indicates that a two-step (detection and concentration) model increased the precision of qPCR results, useful for enhancing the robustness of eDNA quantification. Furthermore, we investigated the lower limit of quantification for ddPCR, providing insights on how such limit can be extended, which could also be applied to qPCR.
采用定量聚合酶链反应（qPCR）和数字液滴聚合酶链反应（ddPCR）的环境DNA（eDNA）检测为监测水生生物提供了一种非侵入性的有效方法。准确、灵敏地定量eDNA对于追踪珍稀物种和入侵物种以及了解水生生物的生物多样性丰度和分布至关重要。本研究通过贝叶斯推断，利用来自三种硬骨鱼类检测的已知浓度（标准品）和环境样品的潜在参数，比较了qPCR和ddPCR在eDNA调查中的灵敏度和定量精度。结果表明，与qPCR相比，ddPCR具有更高的灵敏度和定量精度，尤其是在低DNA浓度（<1拷贝/μL反应）时。这些发现突出了ddPCR在低浓度eDNA检测方面的卓越性能，为研究人员提供了更可靠的有效物种监测方法。此外，本研究表明，两步（检测和浓度）模型提高了qPCR结果的精度，有助于增强eDNA定量的稳健性。此外，我们还研究了ddPCR的定量下限，为如何扩展该下限提供了见解，这也可应用于qPCR。
