AEI 8:371-386 (2016)  -  DOI:

Benthic monitoring of salmon farms in Norway using foraminiferal metabarcoding

Jan Pawlowski1,*, Philippe Esling1,2, Franck Lejzerowicz1, Tristan Cordier1, Joana A. Visco3, Catarina I. M. Martins4, Arne Kvalvik5, Knut Staven6, Tomas Cedhagen

1Department of Genetics and Evolution, University of Geneva, 1211 Geneva, Switzerland
2IRCAM, UMR 9912, Université Pierre et Marie Curie, 75005 Paris, France
3ID-Gene ecodiagnostics Ltd, 1228 Plan-les-Ouates, Switzerland
4Marine Harvest ASA, Bergen, 5035 Bergen, Norway
5Marine Harvest Norway, Region West,6004 Ã…lesund, Norway
6Marine Harvest Norway, Region Mid, 7777 Flatanger, Norway
7Department of Bioscience, Section of Aquatic Biology, University of Aarhus, 8000 Aarhus, Denmark
*Corresponding author:

ABSTRACT: 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.

KEY WORDS: Finfish farming · Biomonitoring · Environmental DNA · Next-generation sequencing · NGS · DNA barcoding · Foraminifera

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Cite this article as: Pawlowski J, Esling P, Lejzerowicz F, Cordier T and others (2016) Benthic monitoring of salmon farms in Norway using foraminiferal metabarcoding. Aquacult Environ Interact 8:371-386.

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