Data from: Environmental monitoring through protist NGS metabarcoding: assessing the impact of fish farming on benthic foraminifera communities

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 demands highly trained specialists and is extremely
time-consuming and costly, what makes 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 (NGS) of environmental DNA and RNA
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 Scotland. We investigated the
foraminiferal diversity based on ribosomal minibarcode sequences generated
by the Illumina NGS 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
alpha diversity loss in strongly impacted sites, especially visible in the
RNA data. We also detected some candidate bioindicator foraminiferal
species. Based on this proof-of-concept study, we conclude that NGS
metabarcoding using foraminifera and other protists has considerable
potential to become a new tool for surveying the impact of aquaculture and
other industrial activities in the marine environment.