Data from: Primer sets evaluation and sampling method assessment for the monitoring of fish communities in the North-western part of the Mediterranean Sea through eDNA metabarcoding

Environmental DNA (eDNA) metabarcoding appears to be a promising tool for
surveying fish communities. However, the effectiveness of this method
relies on primer set performance and on a robust sampling strategy. While
some studies have evaluated the efficiency of several primers for fish
detection, it has not yet been assessed in situ for the Mediterranean Sea.
In addition, mainly surface waters were sampled and no filter porosity
testing was performed. In this pilot study, our aim was to evaluate the
ability of six primer sets, targeting 12S rRNA (AcMDB07; MiFish; Tele04)
or 16S rRNA (Fish16S; Fish16SFD; Vert16S) loci, to detect fish species in
the Mediterranean Sea using a metabarcoding approach. We also assessed the
influence of sampling depth and filter pore size (0.45 µm versus 5 µm
filters). To achieve this, we developed a novel sampling strategy allowing
simultaneous surface and bottom filtration of large water volumes along
on-site the same transect. We found that 16S rRNA primer sets enabled more
fish taxa to be detected across each taxonomic level. The best combination
was Fish16S/Vert16S/AcMDB07, which recovered 95% of the 97 fish species
detected in our study. There were highly significant differences in
species composition between surface and bottom samples. Filters of 0.45 µm
led to the detection of significantly more fish species. Therefore, to
maximize fish detection in the studied area, we recommend to filter both
surface and bottom waters through 0.45 µm filters and to use a combination
of these three primer sets.