Environmental monitoring through protist next‐generation sequencing metabarcoding: assessing the impact of fish farming on benthic foraminifera communities

<jats:title>Abstract</jats:title><jats:p>The measurement of species diversity represents a powerful tool for assessing the impacts of human activities on marine ecosystems. Traditionally, the impact of fish farming on the coastal environment is evaluated by monitoring the dynamics of macrobenthic infaunal populations. However, taxonomic sorting and morphology‐based identification of the macrobenthos demand highly trained specialists and are extremely time‐consuming and costly, making it unsuitable for large‐scale biomonitoring efforts involving numerous samples. Here, we propose to alleviate this laborious task by developing protist metabarcoding tools based on next‐generation sequencing (<jats:styled-content style="fixed-case">NGS</jats:styled-content>) of environmental <jats:styled-content style="fixed-case">DNA</jats:styled-content> and <jats:styled-content style="fixed-case">RNA</jats:styled-content> extracted from sediment samples. In this study, we analysed the response of benthic foraminiferal communities to the variation of environmental gradients associated with salmon farms in <jats:styled-content style="fixed-case">S</jats:styled-content>cotland. We investigated the foraminiferal diversity based on ribosomal minibarcode sequences generated by the <jats:styled-content style="fixed-case">I</jats:styled-content>llumina <jats:styled-content style="fixed-case">NGS</jats:styled-content> technology. We compared the molecular data with morphospecies counts and with environmental gradients, including distance to cages and redox used as a proxy for sediment oxygenation. Our study revealed high variations between foraminiferal communities collected in the vicinity of fish farms and at distant locations. We found evidence for species richness decrease in impacted sites, especially visible in the <jats:styled-content style="fixed-case">RNA</jats:styled-content> data. We also detected some candidate bioindicator foraminiferal species. Based on this proof‐of‐concept study, we conclude that <jats:styled-content style="fixed-case">NGS</jats:styled-content> metabarcoding using foraminifera and other protists has potential to become a new tool for surveying the impact of aquaculture and other industrial activities in the marine environment.</jats:p>