Data from: Bottom trawling and multi-marker eDNA metabarcoding surveys reveal highly diverse vertebrate and crustacean communities: A case study in an urbanized subtropical estuary

Estuarine habitats serve as critical feeding and nursery grounds for many
aquatic species and support fisheries. However, monitoring these complex
ecosystems using conventional trawling methods is destructive, costly, and
labour-intensive. This study compared trawling and a multi-marker
environmental DNA (eDNA) metabarcoding approach to monitor marine
vertebrate and crustacean communities in an estuarine environment in
subtropical Hong Kong. We analysed 16 bottom trawl samples and the eDNA
from 32 two-litre water samples using primer sets specific to fishes and
mammals (MiFish-U, 12S-V5, and Berry-Fish) and decapod crustaceans
(MiDeca). We found that the eDNA approach detected more pelagic and
demersal fishes (237 vs. 106 in trawling) and elasmobranchs (6 vs. 3) than
trawling. The eDNA approach was also more effective than trawling in
detecting threatened vertebrates (16 vs. 4), including the Indo-Pacific
Finless Porpoise and the critically endangered Large Yellow Croaker. Among
the detected fish at species-level, 70 species were detected by both
approaches, 32 species were detected by trawling only, and 142 species
were detected by the eDNA approach only. Regarding crustaceans, the eDNA
approach detected slightly fewer decapods (61 vs. 77) and stomatopods (5
vs. 8) than trawl surveys. However, the eDNA approach could be enhanced
through the development of suitable decapod-specific primers and the
expansion of the local reference database. In addition, multivariate
analyses of the eDNA data revealed spatial patterns of fish and crustacean
assemblages that might associate with sediment loading, oxygen and
nutrient levels. Furthermore, there was a positive correlation between
eDNA read counts and trawl catch, but their correlation coefficient was
low. We conclude that eDNA metabarcoding can provide high-resolution
detection of species, composition, and unravel community-environment
relationships in estuarine ecosystems. Overall, integrating the
non-destructive eDNA approach can complement the conventional trawling
method for better-informed sustainable fishery management and
conservation.