SYNAQUA –  Genetic Biomonitoring of Aquatic Ecosystems

SYNAQUA – Genetic Biomonitoring of Aquatic Ecosystems

In the Interreg project SYNAQUA (SYNérgie transfrontalière pour la bio-surveillance et la préservation des écosystèmes  AQUAtiques) project partners from Switzerland and France seek to establish genetic methods for the biomonitoring of surface waters. This innovative approach relies on the taxonomic determination of bioindicator organisms based not on their morphology, but directly on their DNA. A new high-throughput method for analysing environmental DNA allows for developping robust and reliable tools to calculate molecular indices and assess ecological water quality. Thereby established methods for biomonitoring will be optimised.

The project SYNAQUA has its focus on two groups of bioindicator organisms, diatoms and oligochaetes, which for the first time will be used together. Both groups of organisms are currently used for biomonitoring in Switzerland and in France. Diatoms are tiny freshwater algae and show a contamination with nutrients and organic contaminants. Oligochaetes are benthic invertebrates that develop in sediments and therefore are used as indicators for sediment quality. The following points will be considered:

  • Validation of the molecular method
  • Development of a standardised DNA index for assessing surface water quality. The approach will be tested in French and Swiss rivers and in the shore areas of Lake Geneva.
  • Raising awareness in professionals and the public for the advantages of environmental genomics
  • Improvement of the efficiency of environmental protection

Workshop Synthesis

Strategy for Successful Integration of eDNA-based Methods in Aquatic Monitoring

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All results of SYNAQUA are available online.


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.
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Vivien, R., Apothéloz-Perret-Gentil, L., Pawlowski, J., 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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Lefrançois, E., Apothéloz-Perret-Gentil, L., Blancher, P., Botreau, S., Chardon, C., Crepin, L., Cordier, T., Cordonier, A., Domaizon, I., Ferrari, B.J.D., Guéguen, J., Hustache, J.-C., Jacas, L., Jacquet, S., Lacroix, S., Mazenq, A.-L., Pawlowska, A., Perney, P., Pawlowski, J., Rimet, F., Rubin, J.-F., Trevisan, D., Vivien, R., Bouchez, A. (2018) Development and implementation of eco-genomic tools for aquatic ecosystem biomonitoring: the SYNAQUA French-Swiss program. Environmental Science and Pollution Research
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Vivien, R., Werner, I., Ferrari, B.J.D. (2018) Simultaneous preservation of the DNA quality, the community composition and the density of freshwater oligochaetes for the development of genetically based biological indices. PeerJ, DOI 10.7717/peerj.6050
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Vivien, R., Holzmann, M., Werner, I., Pawlowski, J., Lafont, M. and Ferrari, B.J.D. (2017) Cytochrome c oxidase barcodes for aquatic oligochaete identification: development of a Swiss reference database. PeerJ, DOI 10.7717/peerj.4122
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