Swiss Centre for Applied Ecotoxicology (Ecotox Centre), Lausanne/Dübendorf, Switzerland.
Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.
Sci Rep. 2020 Feb 6;10(1):2041. doi: 10.1038/s41598-020-58703-2.
Aquatic oligochaete communities are valuable indicators of the biological quality of sediments in streams and lakes, but identification of specimens to the species level based on morphological features requires solid expertise in taxonomy and is possible only for a fraction of specimens present in a sample. The identification of aquatic oligochaetes using DNA barcodes would facilitate their use in biomonitoring and allow a wider use of this taxonomic group for ecological diagnoses. Previous approaches based on DNA metabarcoding of samples composed of total sediments or pools of specimens have been proposed for assessing the biological quality of ecosystems, but such methods do not provide precise information on species abundance, which limits the value of resulting ecological diagnoses. Here, we tested how a DNA barcoding approach based on high-throughput sequencing of sorted and genetically tagged specimens performed to assess oligochaete species diversity and abundance and the biological quality of sediments in streams and lakes. We applied both molecular and morphological approaches at 13 sites in Swiss streams and at 7 sites in Lake Geneva. We genetically identified 33 or 66 specimens per site. For both approaches, we used the same index calculations. We found that the ecological diagnoses derived from the genetic approach matched well with those of the morphological approach and that the genetic identification of only 33 specimens per site provided enough ecological information for correctly estimating the biological quality of sediments in streams and lakes.
水生寡毛类动物群落是溪流和湖泊底泥生物质量的有价值指示物，但基于形态特征将标本鉴定到物种水平需要坚实的分类学专业知识，而且仅适用于样本中存在的一小部分标本。使用 DNA 条码鉴定水生寡毛类动物将有助于它们在生物监测中的应用，并允许更广泛地将这个分类群用于生态诊断。以前提出的基于总沉积物或标本池的 DNA metabarcoding 样本的方法已经被用于评估生态系统的生物质量，但这些方法不能提供关于物种丰度的精确信息，这限制了由此产生的生态诊断的价值。在这里，我们测试了基于高通量测序对分类和遗传标记标本的 DNA 条码方法在评估溪流和湖泊中寡毛类动物物种多样性和丰度以及底泥生物质量方面的表现。我们在瑞士的 13 个溪流地点和日内瓦湖的 7 个地点应用了分子和形态学方法。我们在每个地点都遗传鉴定了 33 或 66 个标本。对于这两种方法，我们都使用了相同的指数计算。我们发现，遗传方法得出的生态诊断与形态学方法得出的诊断非常吻合，并且每个地点仅鉴定 33 个标本就提供了足够的生态信息，可以正确估计溪流和湖泊底泥的生物质量。
