marine fish eDNA metabarcoding

Accurate and cost-effective approaches are desired for efficient and sustained long-term biodiversity monitoring. Environmental DNA (eDNA) metabarcoding is a relatively recent genetic method that is becoming a species-monitoring tool. Still, its ability to reveal key aspects of biodiversity beyond richness and to elucidate species spatial dynamics, especially across depth in coastal ecosystems, remains poorly assessed. One critical aspect is the performance and reliability of eDNA metabarcoding, which requires testing against high-effort traditional survey methods in relevant ecological and geographical environments. We evaluated the performance of eDNA metabarcoding for monitoring the fish community associated with a port terminal on the central coast of Peru. At the terminal, a long-term monitoring program (BMAP) has gathered 12 years of continuous fish data using fisheries gears (nets and hooks) coupled with visual identification and barcoding. Water samples were collected and filtered in from the infrastructure and adjacent areas, and eDNA metabarcoding was performed using MiFish-U/E primers, which target a region of the 12S rRNA gene. We compared taxonomic, functional, and phylogenetic diversity estimates and the spatial distribution (horizontal and vertical) obtained from BMAP surveys and eDNA metabarcoding.