High-throughput DNA barcoding of oligochaetes to assess the biological quality of sediments in streams: validation of the method at large scale in Switzerland

Biological indices based on oligochaete communities are well suited to assess the biological quality of sediments in streams and lakes. However, the identification of oligochaetes based on their morphology is difficult and often impossible. This hinders the routine application of these indices. This problem is overcome by using DNA barcodes (short DNA sequences that are similar between individuals of the same species) for oligochaete identification. As part of the Synaqua project, we have developed a molecular oligochaete index based on high-throughput sequencing of genetically tagged specimens for assessing the biological sediment quality in streams and lakes. This molecular approach presents the advantage to know with precision the number of individuals of each species present in a sample and is therefore particularly well suited for environmental quality assessment.

In the OligoGen project, this molecular method is going to be validated at a large scale in streams in Switzerland. We will adapt this method for routine application and determine the optimal number of specimens to be sequenced per site. A technical guideline of this method will be proposed at the end of the project. In addition, we will continue to enrich the genetic database of Swiss aquatic oligochaetes.

In parallel, we will develop methods based on DNA metabarcoding. In DNA metabarcoding, all species of (a) particular organism group(s) present in environmental samples (e.g. water, sediments and sieved sediments) are identified. In particular, we will test the method of analyzing DNA extracted from ethanol preserving sieved sediment samples and investigate the possibility of using porewater (in fine/sandy sediments) as a vector of oligochaete DNA. We will test whether the porewater carries sufficient amounts of oligochaete-DNA to provide reliable information about the composition of the oligochaete community. 

Publications

Final report: OligoGen : Développement de méthodes oligochètes génétiques pour évaluer la qualité biologique des sédiments de cours d’eau
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Synthesis: OligoGen : Développement de méthodes oligochètes gé-nétiques pour évaluer la qualité biologique des sédi-ments de cours d’eau
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Literature 

Vivien, R., Holzmann, M., Werner, I., Pawlowski, J., Lafont, M., Ferrari, B.J.D. (2017) Cytochrome c oxidase barcodes for aquatic oligochaete identification: development of a Swiss reference database. PeerJ 5:e4122
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Vivien, R., Apothéloz-Perret-Gentil, L., Pawlowski, P., Werner, I., Ferrari, B.J.D. (2019) Testing different (e)DNA metabarcoding approaches to assess aquatic oligochaete diversity and the biological quality of sediments. Ecological Indicators 106: 105453
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Vivien, R., Apothéloz-Perret-Gentil, L., Pawlowski, P., Werner, I., Ferrari, B.J.D. (2020) High-throughput DNA barcoding of oligochaetes for abundance-based indices to assess the biological quality of sediments in streams and lakes. Scientific Reports 10, 2041
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