Monitoring the threatened Harttiella (Siluriformes, Loricariidae) with environmental DNA: A comparison between metabarcoding and targeted digital PCR

Environmental DNA has emerged as an efficient alternative to traditional sampling methods. A standard multispecies or a targeted single‐species approach can be used for analysing environmental DNA samples. The costs, benefits, and drawbacks associated with these two approaches are quite different. Here, a comparison between standard multispecies metabarcoding and targeted species assay using digital PCR (dPCR) for two threatened Harttiella species occurring in French Guiana (Harttiella lucifer and H. nsp. “Makwali”) was performed. Samples were collected in 11 sites of the upper Maroni River drainage basin and located in the Galbao mountain range, known to host the targeted species. The “Teleo” primer was used for the metabarcoding approach. To implement a new dPCR assay, specific primers and probes for the two targeted Harttiella species were developed. This targeted dPCR assay detected Harttiella in seven sites. All of these sites were also positive for metabarcoding detection, and the habitat characteristics were favourable for the species. This study demonstrated that both targeted (dPCR) and multispecies (metabarcoding) approaches can be used for the monitoring of the threatened H. lucifer and H. nsp. “Makwali” species. From a conservation point of view, we recommend to use the metabarcoding approach to update the spatial distribution of the species, while the dPCR method can be used for a temporal follow‐up of known Harttiella populations.