University of Strasbourg, Laboratoire Image Ville Environnement, UMR 7362 CNRS, Strasbourg, France.
Namur Molecular Tech, CHU UCL Namur, Yvoir, Belgium.
Sci Total Environ. 2024 Dec 1;954:176200. doi: 10.1016/j.scitotenv.2024.176200. Epub 2024 Sep 14.
While environmental DNA (eDNA) metabarcoding holds promise as a holistic approach to assess vegetation changes and community composition across diverse spatial and temporal scales, systematic investigations of its efficacy compared to conventional field surveys remain scarce in the literature. The present study explores the differences in plant diversity recovered from field surveys and captured with a multi-marker eDNA metabarcoding approach (two nrDNA ITS1 and ITS2, and two cpDNA rbcL and trnL) from river water samples. The eDNA metabarcoding approach retrieved 46 aquatic plants (hydrophytes and helophytes) and 245 terrestrial plants, compared to 24 and 127 species identified from field surveys. On average, eDNA samples collected immediately downstream of the survey sites recovered 43 % and 39 % of the aquatic and terrestrial species observed, respectively. Discrepancies were explained by differences in taxonomic resolution, the stochasticity of the retrieval of rare and elusive species, and the presence of reference sequences. We found a significant positive correlation between spatial and community distances at scales ranging from 2 to 9 km and identified turnover as the driving force of these differences. Metabarcoding demonstrated sensitivity to community changes and both approaches converge on a similar community structure. Interestingly, eDNA samples collected immediately upstream of the survey sites exhibited significant species overlap with the downstream samples (c. 100 m apart). Overall, our results demonstrate that within-site species mismatches between the methods are nonnegligible, and they question the use of eDNA for generating complete species lists at scales comparable to our field surveys (< 100-m transects). However, with adequate sampling and a multi-marker metabarcoding approach, eDNA has the potential to approximate catchment gamma diversity with less sampling effort than conventional surveys.
虽然环境 DNA（eDNA）宏条形码作为一种整体方法来评估不同时空尺度的植被变化和群落组成具有很大的前景，但在文献中，与传统实地调查相比，其功效的系统研究仍然很少。本研究探讨了从实地调查中回收的植物多样性与通过多标记 eDNA 宏条形码方法（两个 nrDNA ITS1 和 ITS2，以及两个 cpDNA rbcL 和 trnL）从河水样本中捕获的植物多样性之间的差异。与从实地调查中鉴定的 24 种和 127 种相比，eDNA 宏条形码方法共检索到 46 种水生植物（水生植物和沼生植物）和 245 种陆生植物。平均而言，在调查点下游采集的 eDNA 样本分别回收了观察到的水生和陆生物种的 43%和 39%。差异可以通过分类分辨率的差异、稀有和难以捉摸的物种检索的随机性以及参考序列的存在来解释。我们发现，在 2 至 9 公里的范围内，空间和群落距离之间存在显著的正相关关系，并确定物种更替是这些差异的驱动因素。宏条形码对群落变化具有敏感性，两种方法都收敛于相似的群落结构。有趣的是，在调查点上游采集的 eDNA 样本与下游样本（相距约 100 米）存在显著的物种重叠。总体而言，我们的结果表明，两种方法之间的站点内物种不匹配不可忽略，并且它们质疑在与我们的实地调查（<100 米的横截）可比的规模上使用 eDNA 生成完整的物种列表的用途。然而，通过适当的采样和多标记宏条形码方法，eDNA 具有以比传统调查更少的采样努力来近似集水区 gamma 多样性的潜力。
