Biodiversity and Evolutionary Biology Department, Museo Nacional de Ciencias Naturales, CSIC, José Gutiérrez Abascal, Madrid, Spain.
Consultores en Biología de la Conservación S.L., Daoiz, Madrid, Spain.
PLoS One. 2023 Oct 30;18(10):e0283088. doi: 10.1371/journal.pone.0283088. eCollection 2023.
Environmental DNA (eDNA) metabarcoding has been increasingly used to monitor the community assemblages of a wide variety of organisms. Here, we test the efficacy of eDNA metabarcoding to assess the composition of Iberian freshwater fishes, one of the most endangered groups of vertebrates in Spain. For this purpose, we sampled 12 sampling sites throughout one of Spain's largest basins, the Duero, which is home to approximately 70% of the genera and 30% of the primary freshwater fish in Spain. We sampled these sampling sites in the summer by using electrofishing, a traditional sampling method, and eDNA metabarcoding of river water samples using the mitochondrial 12S rRNA gene (12S) as a marker. We also resampled four of these sampling sites in autumn by eDNA. We compared the results obtained through eDNA metabarcoding with those of electrofishing surveys (ones conducted for the present study and past ones) and assessed the suitability of 12S as an eDNA metabarcoding marker for this group of freshwater fishes. We found that the 12S fragment, analysed for 25 Iberian species, showed sufficient taxonomic resolution to be useful for eDNA approaches, and even showed population-level differences in the studied populations across the tissue samples for Achondrostoma arcasii. In most cases, a greater number of species was detected through eDNA metabarcoding than through electrofishing. Based on our results, eDNA metabarcoding is a powerful tool to study the freshwater fish composition in the Iberian Peninsula and to unmask cryptic diversity. However, we highlight the need to generate a local genetic database for 12S gene for such studies and to interpret the results with caution when studying only mitochondrial DNA. Finally, our survey shows that the high detection sensitivity of eDNA metabarcoding and the non-invasiveness of this method allows it to act as a detection system for species of low abundance, such as early invasive species or species in population decline, two key aspects of conservation management of Spanish freshwater fishes.
环境 DNA（eDNA）代谢组学已被越来越多地用于监测各种生物群落的组成。在这里，我们测试了 eDNA 代谢组学评估伊比利亚淡水鱼类组成的功效，伊比利亚淡水鱼类是西班牙最濒危的脊椎动物之一。为此，我们在西班牙最大的流域之一杜罗河（Duero）的 12 个采样点进行了采样，该流域是西班牙约 70%的属和 30%的主要淡水鱼的家园。我们在夏季通过电捕鱼（一种传统的采样方法）和河流水样的 eDNA 代谢组学（以线粒体 12S rRNA 基因（12S）作为标记）在这些采样点进行了采样。我们还在秋季通过 eDNA 对其中的四个采样点进行了重采样。我们将通过 eDNA 代谢组学获得的结果与电捕鱼调查（本研究和过去进行的调查）的结果进行了比较，并评估了 12S 作为该组淡水鱼类 eDNA 代谢组学标记的适宜性。我们发现，在所分析的 25 种伊比利亚物种中，12S 片段具有足够的分类分辨率，可用于 eDNA 方法，甚至在阿孔斯特罗马·阿卡西（Achondrostoma arcasii）的研究种群中，在组织样本中显示出种群水平的差异。在大多数情况下，通过 eDNA 代谢组学检测到的物种数量多于电捕鱼。根据我们的结果，eDNA 代谢组学是研究伊比利亚半岛淡水鱼类组成和揭示隐匿多样性的有力工具。但是，我们强调需要为 12S 基因生成本地遗传数据库，并在仅研究线粒体 DNA 时谨慎解释结果。最后，我们的调查表明，eDNA 代谢组学的高检测灵敏度和该方法的非侵入性使其可以作为低丰度物种的检测系统，例如早期入侵物种或种群减少的物种，这是西班牙淡水鱼类保护管理的两个关键方面。
