Shifts in Small Fish Community Caused by Coral Cover Variation at a Remote Reef in the South China Sea

Global coral reef fish biodiversity is undergoing a severe decline driven by both natural and anthropogenic disturbances. However, the biodiversity and ecological functions of small fishes have long been underestimated, mainly because small fishes are difficult to capture or to identify using underwater visual census (UVC). This study integrated environmental DNA (eDNA) metabarcoding and underwater visual census (UVC) to systematically survey the small fish community at Meiji reef, a region comprising two distinct habitats characterized by high coral cover (HC) and low coral cover (LC). A total of 149 small fish species were detected by the two methods combined, with eDNA identifying 132 species and UVC only 38. Species richness, Shannon index, and phylogenetic diversity of small fish are lower in LC, while functional diversity is higher in HC, suggesting that species retention is critical to maintaining ecosystem functions. Nevertheless, the overall decline in functional redundancy indicates a weakened buffering capacity and reduced resilience. Network analysis further revealed that HC areas exhibited denser node and connection structures and higher modularity. Correspondingly, the indicator species transitioned from Pomacentridae and Clupeidae in HC areas to benthic Blenniidae in LC areas, a taxonomic manifestation of ecosystem simplification resulting from the loss of structurally complex coral habitats. As coral cover decreased, the assembly mechanism of the small fish community shifted from a combination of environmental filtering and stochastic processes to stochastic dominance. Furthermore, significant interactions among eco-environmental factors and the biological community collectively shaped species distribution patterns, driving divergence in small fish community structures across regions. In summary, this study elucidates the mechanisms by which small fish communities respond to coral cover gradients at a fine habitat scale, providing essential insights into the ecological functions and environmental adaptability of small coral reef fish species.