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 prime..., Sampling strategy
This study was conducted over a two-day period (03/05/2022 - 04/05/2022) in the Marine Protected Area (MPA) of Cap Roux, located in the North-western part of the Mediterranean Sea, between Cannes and Saint-Raphael, France. Established in 2003, it covers an area of 450 ha spanning from the shoreline to the 100 m isobath. All types of fishing are prohibited but permanent surveillance is lacking. The habitats within the MPA consist of typical ecosystems of the Mediterranean Sea such as Posidonia oceanica meadows, rocky and coralligenous reefs. We have chosen this study area due to its high species richness, making it an ideal sampling location to test our metabarcoding strategy.
For this study, we have developed a novel sampling strategy allowing the simultaneous filtration of surface and bottom water. Two transects of approximately 1.3 km in length were designed, inside the MPA, crossing several habitats to allow the detection of a broad range of species . Along these tr..., , # 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

[https://doi.org/10.5061/dryad.612jm648m](https://doi.org/10.5061/dryad.612jm648m)

Raw sequence data for each primer, were analysed using the suite of OBITools programs ([https://pythonhosted.org/OBITools/welcome.html](https://pythonhosted.org/OBITools/welcome.html); Boyer et al., 2016) and the SumaClust clustering tool (Mercier et al., 2013). The script is provided with the data description (methods paragraph)

## Description of the data and file structure

Raw data description:

Library AOYG-150 contains sequences obtained using AcMDB07 primer set
Library AOYG-160 contains sequences obtained using Fish16FD primer set
Library AOYG-147 contains sequences obtained using Fish16S primer set
Library AOYG-158 contains sequences obtained using Tele03 primer set
Library AOYG-159 contains sequences obtained using Tele04 pr...