
OligoNem – In situ methods using oligochaetes and nematodes for assessing sediment quality
Sediments play a critical role in biogeochemical cycling, and benthic processes support the base of aquatic food chains. However, sediments are often polluted and, as chemical sinks, can represent a risk for benthic communities. Even if no signs of pollution are apparent in the water column sediments can disturb the functioning of the ecosystem.It is therefore crucial to assess the sediment quality to assess the risk for aquatic ecosystems. Integrated methods for the evaluation of sediment quality do not only use physico-chemical and ecotoxicological analyses but also in situ indices that evaluate the diversity and sensitivity of macrobenthic communities. Nematodes and oligochaetes have been found to be most useful in this respect. To encourage the application of such indices the implementation of the French IOBS index for oligchaetes will be improved among other by using new DNA-based monitoring tools (e.g. barcoding) for their taxonomic identification. In addition, the possibility to implement the German NemaSPEAR index for nematodes in Switzerland will be explored.
Publications
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. https://doi.org/10.1038/s41598-020-58703-2Download Artikel [PDF, 1164 kb]
Vivien, R., Casado-Martinez, C., Lafont, M., Ferrari, B.J.D. (2020) Effect Thresholds of Metals in Stream Sediments Based on In Situ Oligochaete Communities. Environments 2020, 7, 31; doi:10.3390/environments7040031Download Artikel [PDF, 691 kb]
Vivien, R., Lafont, M., Ferrari, B.J.D. (2020) Assessment of abundance and community composition of benthic macroinvertebrates: recommendations for improved sampling, fixation and extraction of oligochaetes. Archives des Sciences, 71, 37-44Download Artikel [PDF, 726 kb]
Pesce, S., Ferrari, B.J.D. et al. (2019) Recommandations d’un collectif franco-suisse d’experts pour une meilleure évaluation de la qualité écotoxicologique des sédiments par l’étude des communautés benthiques. Sciences Eaux & Territoires 55, 1-9Download Artikel [PDF, 1876 kb]
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, 105453Download von Sciencedirect
Vivien, R., Lafont, M., Werner, I., Laluc, M., Ferrari, B.J.D. (2019) Assessment of the effects of wastewater treatment plant effluents on receiving streams using oligochaete communities of the porous matrix. Knowl. Manag. Aquat. Ecosyst. 2019, 420, 18Download Artikel [PDF, 361 kb]
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 https://doi.org/10.1007/s11356-018-2172-2Download at Springer
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.6050Download article [PDF, 232 kb]
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.4122Download article [PDF, 451 kb]
Vivien, R., Ferrari, B.J.D., Pawlowski, J. (2016) DNA barcoding of formalin‑fixed aquatic oligochaetes for biomonitoring. BMC Res Notes 9:342 DOI 10.1186/s13104-016-2140-1
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Vivien, R., Lejzerowicz, F., Pawlowski, J. (2016) Next-Generation Sequencing of Aquatic Oligochaetes: Comparison of Experimental Communities. PLoS ONE 11(2): e0148644
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Vivien, R., Lafont, M. (2015) Note faunistique sur les oligochètes aquatiques de la région genevoise et de Suisse. Revue suisse de Zoologie, 122:207-212
Download at Ville de Genève