Benthic monitoring of salmon farms in Norway using foraminiferal metabarcoding

J Pawlowski,T Cordier,K Staven,A Kvalvik,P Esling,T Cedhagen,Ja Visco,Cim Martins,F Lejzerowicz

doi:10.3354/aei00182

J Pawlowski, T Cordier + Show 7 more

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https://doi.org/10.3354/aei00182

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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, clas- sical benthic monitoring can hardly answer the rapidly growing demand because the morpholog- ical 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 diver- sity 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.

Highlights

By 2030, aquaculture is projected to supply over 60% of fish destined for direct human consumption (World Bank 2013)
We tested the accuracy of foraminiferal metabarcoding as an alternative to macrofaunal benthic monitoring in Norway. To achieve this objective, (1) we used molecular data to describe the Pawlowski et al.: DNA-based benthic monitoring communities of benthic Foraminifera living in the vicinity of salmon farms; (2) we analysed the changes of foraminiferal communities inferred from metabarcoding data in relation to environmental gradients; and (3) we evaluated the potential congruence between diversity metrics of foraminiferal metabarcoding data and benthic macrofaunal indices
We investigated the potential correlation between different foraminiferal diversity indices (S, SN, H ’, Chao) and the 4 standard indices based on benthic macrofaunal analysis commonly used in Norway (H ’, NSI, NQI1, NQI2)

Summary

INTRODUCTION

By 2030, aquaculture is projected to supply over 60% of fish destined for direct human consumption (World Bank 2013). We used both DNA- and RNAbased metabarcoding to investigate the impact of organic enrichment associated with salmon farming on the diversity of benthic Foraminifera in Scotland and New Zealand. We tested the accuracy of foraminiferal metabarcoding as an alternative to macrofaunal benthic monitoring in Norway To achieve this objective, (1) we used molecular data to describe the Pawlowski et al.: DNA-based benthic monitoring communities of benthic Foraminifera living in the vicinity of salmon farms; (2) we analysed the changes of foraminiferal communities inferred from metabarcoding data in relation to environmental gradients (distance to cages); and (3) we evaluated the potential congruence between diversity metrics of foraminiferal metabarcoding data and benthic macrofaunal indices. The species identification, counting and calculation of macrofaunal indices was done by Havbrukstjenesten AS (West region) and Akvaplan-niva AS (Central region)

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