High-density environmental DNA metabarcoding reveals fine-scale three-dimensional structure of a fish community in a semi-closed bay

Coastal fish communities are shaped by environmental factors in both horizontal and vertical dimensions, but the precise three-dimensional structure of these assemblages has been largely unexplored. To investigate this, researchers examined eDNA metabarcoding data collected at 100 sites across three depth levels in Maizuru Bay, a semi-enclosed bay in Japan.

This analysis, which involved 300 samples, identified 216 fish species, with species richness decreasing from 28.4 at the surface to 16.4 at the bottom. Notably, 33 species were found exclusively below the surface. The study revealed significant differences in fish assemblage composition across depth layers and horizontal positions within the bay.

Despite these factors being linked to assemblage composition, they collectively explained only 13.0% of the observed variation. The spatial position itself contributed 2.9% to this variation, which was greater than the contributions from depth (0.8%) and measured environmental variables (0.9%). This research underscores the importance of considering both horizontal and vertical dimensions when studying coastal fish biodiversity and underscores the need for comprehensive sampling strategies to accurately monitor marine ecosystems.