Integrating DNA metabarcoding and morphological analysis improves marine zooplankton biodiversity assessment

Marine copepod communities play crucial roles in ocean ecosystems. However, their accurate assessment remains challenging due to taxonomic complexities. This study combines morphological and DNA metabarcoding approaches to evaluate copepod diversity and community structure in the northern East China Sea. Zooplankton samples were collected from 10 stations along a coastal-offshore gradient in August 2019. Morphological analysis identified 34 species from 25 genera, while DNA metabarcoding detected 31 species from 20 genera. Both methods revealed distinct coastal and offshore assemblages, with Paracalanus parvus s.l. as the dominant species across all stations. A significant positive correlation was found between morphology-based individual counts and metabarcoding sequence reads (Spearman's Rho = 0.58, p < 0.001), improving at the genus level (Rho = 0.70, p < 0.001). Redundancy analysis revealed that salinity, temperature, and phytoplankton density significantly influenced copepod distribution. Although both approaches captured similar broad-scale patterns, they provided complementary insights into community structure. Morphological identification was more effective for detecting Cyclopoida diversity, whereas DNA metabarcoding had greater sensitivity for specific Calanoid species. This study underscores the value of integrating traditional and molecular methods for marine biodiversity assessment, especially in the context of global environmental changes.