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Journal Articles Aquaculture Environment Interactions Year : 2016

Benthic monitoring of salmon farms in Norway using foraminiferal metabarcoding


The rapid growth of the salmon industry necessitates the development of fast and accurate tools to assess its environmental impact. Macrobenthic monitoring is commonly used to measure the impact of organic enrichment associated with salmon farm activities. However, classical benthic monitoring can hardly answer the rapidly growing demand because the morphological identification of macro-invertebrates is time-consuming, expensive and requires taxonomic expertise. Environmental DNA (eDNA) metabarcoding of meiofauna-sized organisms, such as Foraminifera, was proposed to overcome the drawbacks of macrofauna-based benthic monitoring. Here, we tested the application of foraminiferal metabarcoding to benthic monitoring of salmon farms in Norway. We analysed 140 samples of eDNA and environmental RNA (eRNA) extracted from surface sediment samples collected at 4 salmon farming sites in Norway. We sequenced the variable region 37f of the 18S rRNA gene specific to Foraminifera. We compared our data to the results of macrofaunal surveys of the same sites and tested the congruence between various diversity indices inferred from metabarcoding and morphological data. The results of our study confirm the usefulness of Foraminifera as bioindicators of organic enrichment associated with salmon farming. The foraminiferal diversity increased with the distance to fish cages, and metabarcoding provides an assessment of the ecological quality comparable to the morphological analyses. The foraminiferal metabarcoding approach appears to be a promising alternative to classical benthic monitoring, providing a solution to the morpho-taxonomic bottleneck of macrofaunal surveys.
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Origin : Publication funded by an institution

Dates and versions

hal-01341949 , version 1 (05-07-2016)


Attribution - CC BY 4.0



Jan Pawlowski, Philippe Esling, Franck Lejzerowicz, Tristan Cordier, Joana A. Visco, et al.. Benthic monitoring of salmon farms in Norway using foraminiferal metabarcoding . Aquaculture Environment Interactions, 2016, 8, pp.371-386. ⟨10.3354/aei00182⟩. ⟨hal-01341949⟩
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