eDNA Metabarcoding Reveals the Depth-Structured Variation of Coral Reef Fish

Global coral reef ecosystems face various levels of disturbance pressure. Understanding the depth-structured variation in coral reef fish communities can help us to better grasp and predict the adaptive changes of the ecosystem under different stressors. This study applied eDNA metabarcoding technology to analyze the spatial distribution of the coral reef fish at various depths (0 m, 5 m, 10 m, 15 m, 20 m, 30 m, 40 m, 50 m, and 60 m) within the Xisha Islands of China. The results indicated that the eDNA technology detected a total of 213 amplicon sequence variants (ASVs), including 33 species that were not identified using traditional methods. Herbivorous fish generally dominated in relative abundance across different depths. Moreover, the similarity among depth groups was largely absent, and significant differences existed in fish assemblages across depth gradients, consistent with the unique depth preferences of fish microhabitats. Importantly, our findings revealed distinct depth-structured variation among different functional groups of coral reef fish. Large carnivorous fish initially increased and then decreased along the depth gradient from 0 to 60 m, with a turning point around 20 m, while large herbivorous fish displayed the opposite trend. Small carnivorous and small herbivorous fish consistently declined along the same depth gradient. Additionally, the Margalef index (D) and Function richness (FRic) both displayed a consistent downward trend with increasing depth, while the Shannon–Wiener index (H′), Pielou index (J′), Quadratic entropy (RaoQ), Functional dispersion (FDis), and Functional evenness (FEve) initially increased and then decreased, peaking around 20 m. This study revealed that eDNA metabarcoding is an effective tool for evaluating coral reef fish biodiversity, community composition, and spatial distribution. It enhances our understanding of distribution dynamics and offers valuable insights for coral reef conservation and restoration efforts.