Development of a lake genetic index based on chironomids and oligochaetes

A biological index based on the structure of chironomid and oligochaete communities has been developed to assess the biological quality of sediments in lakes and in particular their trophic state (degree of oxygenation). However, it is difficult and often impossible to identify chironomids and oligochaetes to species level based on their morphology. This obstacle could be overcome by identifying chironomids and oligochaetes using DNA barcodes. 

As part of the Synaqua project, we developed a molecular oligochaete index based on high-throughput sequencing of genetically tagged specimens to assess the biological quality of river and lake sediments. This molecular approach has the advantage of precisely determining the number of individuals of each species present in a sample and is therefore particularly well suited for assessing the quality of natural environments. 

The aim of this project is to test whether the approach developed as part of the Synaqua project could be transposed to chironomids and to develop a lake genetic index based on high-throughput sequencing of genetically tagged specimens of chironomids and oligochaetes communities. In addition, a database of DNA barcode sequences of chironomids present in Swiss lakes will be initiated.

Publications

Lods-Crozet, B., Chevalley, P.-A. (2016) Evolution du zoobenthos profond du Léman, Rapp. Comm. int. prot. eaux Léman contre pollut., Campagne 2015, 132-141

Vivien, R., Apothéloz-Perret-Gentil, L., Pawlowski, J., Werner, I., Lafont, M., & 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 (8 pp.). doi.org/10.1038/s41598-020-58703-2 , Institutional Repository