Environmental DNA Metabarcoding for Marine Biodiversity Monitoring: Species Detection Concordance With Traditional Trawl Surveys Across 24 Temperate and Tropical Sites

This study investigates concordance between eDNA metabarcoding species detection and traditional bottom trawl survey catch across 24 temperate and tropical marine sites spanning five ocean regions within the context of marine biology and environmental genomics, an area of growing scientific importance given its implications for cost-effective fisheries stock assessment, biodiversity monitoring network design, and CITES-listed species surveillance in data-poor oceanic regions. Using paired eDNA water sampling (n=3 replicates, 1-L, 0.2 um Sterivex filter) and bottom trawl at 24 sites with 12S rRNA and COI PCR amplicon metabarcoding (Illumina MiSeq 2x300 bp) against FishBase and BOLD reference libraries, we examine fish shedding cellular DNA into water column via mucus, feces, and degraded cells that persists 12-48 hours, enabling sensitive non-invasive detection of species present at low density below trawl catchability threshold in 24 sites x 3 eDNA replicates + 1 trawl per site = 72 eDNA samples and 24 trawl hauls; eDNA detected 848 unique ASVs mapping to 284 named fish species across sites drawn from 24 sites spanning 5 ocean regions: NW Atlantic (n=6), Pacific (n=6), Indian Ocean (n=4), Mediterranean (n=4), Caribbean (n=4) at 20-150 m depth. Results indicate that overall eDNA-trawl Sorensen concordance is 0.72 across 24 sites with eDNA detecting 28.4% additional species absent from trawl (low-density species, cryptic species) and trawl detecting 14.2% additional species not in eDNA (deep benthic species with low water column eDNA shed) (p < 0.001), with Sorensen 0.72; eDNA unique detections 28.4%; trawl unique 14.2% as the primary quantitative benchmark. Concordance between primary and confirmatory measurement approaches exceeded 93%, validating the analytical framework. These findings contribute empirically to marine biology and environmental genomics and carry actionable implications for the design of programs and policies targeting cost-effective fisheries stock assessment, biodiversity monitoring network design, and CITES-listed species surveillance in data-poor oceanic regions.