Baidouri Fouad El, Watts Alison W, Miller Jeffrey T, Kelly Muriel, Sevigny Joseph L, Gilbert Heather, Thomas W Kelley
Department of Civil & Environmental Engineering, University of New Hampshire, Durham, NH, 03824, USA.
Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, 03824, USA.
Sci Rep. 2025 Jan 7;15(1):1175. doi: 10.1038/s41598-025-85176-y.
Environmental DNA (eDNA) is revolutionizing how we investigate biodiversity in aquatic and terrestrial environments. It is increasingly used for detecting rare and invasive species, assessing biodiversity loss and monitoring fish communities, as it is considered a cost-effective and noninvasive approach. Some environments, however, can be challenging for eDNA analyses. Estuarine systems are highly productive, complex environments, but samples collected from these settings may exhibit PCR inhibition and a low fish read recovery. Here we present an approach for detecting fish in turbid, highly productive estuarine systems. The workflow includes bead-based extraction, inhibition removal, high fidelity and specificity DNA polymerase (Platinum SuperFi II) and multiplexing the universal MiFish primers. By applying this hybrid method to a variety of complex estuarine samples with known inhibition, we have more than doubled the number of recovered fish species while removing most of the off-target amplification.
环境DNA（eDNA）正在彻底改变我们调查水生和陆地环境中生物多样性的方式。它越来越多地用于检测珍稀和入侵物种、评估生物多样性丧失以及监测鱼类群落，因为它被认为是一种经济高效且非侵入性的方法。然而，有些环境对于eDNA分析来说可能具有挑战性。河口系统是高产且复杂的环境，但从这些环境中采集的样本可能会出现PCR抑制和鱼类读数回收率低的情况。在此，我们提出一种在浑浊、高产的河口系统中检测鱼类的方法。该工作流程包括基于磁珠的提取、抑制去除、高保真和特异性DNA聚合酶（Platinum SuperFi II）以及通用MiFish引物的多重化。通过将这种混合方法应用于各种已知具有抑制作用的复杂河口样本，我们在去除大部分非目标扩增的同时，使回收的鱼类物种数量增加了一倍多。
