Swiss Centre for Applied Ecotoxicology (Ecotox Centre), Eawag/EPFL, 1015, Lausanne, Switzerland.
Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.
PLoS One. 2016 Feb 11;11(2):e0148644. doi: 10.1371/journal.pone.0148644. eCollection 2016.
Aquatic oligochaetes are a common group of freshwater benthic invertebrates known to be very sensitive to environmental changes and currently used as bioindicators in some countries. However, more extensive application of oligochaetes for assessing the ecological quality of sediments in watercourses and lakes would require overcoming the difficulties related to morphology-based identification of oligochaetes species. This study tested the Next-Generation Sequencing (NGS) of a standard cytochrome c oxydase I (COI) barcode as a tool for the rapid assessment of oligochaete diversity in environmental samples, based on mixed specimen samples. To know the composition of each sample we Sanger sequenced every specimen present in these samples. Our study showed that a large majority of OTUs (Operational Taxonomic Unit) could be detected by NGS analyses. We also observed congruence between the NGS and specimen abundance data for several but not all OTUs. Because the differences in sequence abundance data were consistent across samples, we exploited these variations to empirically design correction factors. We showed that such factors increased the congruence between the values of oligochaetes-based indices inferred from the NGS and the Sanger-sequenced specimen data. The validation of these correction factors by further experimental studies will be needed for the adaptation and use of NGS technology in biomonitoring studies based on oligochaete communities.
水生寡毛类是一类常见的淡水底栖无脊椎动物，它们对环境变化非常敏感，目前已被一些国家用作生物指标。然而，要更广泛地将寡毛类用于评估河流和湖泊沉积物的生态质量，则需要克服基于形态学的寡毛类物种鉴定所带来的困难。本研究基于混合标本样本，测试了下一代测序（NGS）在快速评估环境样本中寡毛类多样性方面的应用，该研究以标准细胞色素 c 氧化酶 I（COI）条码作为工具。为了了解每个样本的组成，我们对这些样本中的每个标本进行了 Sanger 测序。我们的研究表明，大多数 OTUs（操作分类单元）都可以通过 NGS 分析检测到。我们还观察到 NGS 和标本丰度数据之间存在一致性，但不是所有 OTUs 都存在一致性。由于序列丰度数据在不同样本之间存在差异，我们利用这些变化来经验性地设计校正因子。我们表明，这些因子增加了从 NGS 和 Sanger 测序标本数据推断出的寡毛类生物指标值之间的一致性。需要通过进一步的实验研究来验证这些校正因子，以便在基于寡毛类群落的生物监测研究中适应和使用 NGS 技术。
