Distinct bacterial and eukaryotic communities reflect the specificity of different coral reefs in the South China Sea

The microbial composition of surrounding waters is crucial for the health of coral reefs and holds significant value for understanding the complexity and environmental adaptability of coral reef ecosystems. This study reveals the spatial heterogeneity and diversity characteristics of bacterial and eukaryotic communities in different coral reef regions of the South China Sea. Chao and Shannon indices showed significant differences (p < 0.05) in diversity of bacterial and eukaryotic communities across different coral reefs. PCoA (principal coordinate analysis) indicates significant differences in community composition among regions, highlighting the crucial role of coral reef environmental heterogeneity on microbial community. NST (normalized stochasticity ratio) analysis indicates that community assembly in coral reef areas is more influenced by ecological stochastic processes. Major bacterial groups include Proteobacteria, Cyanobacteria, and Bacteroidota, while dominant eukaryotic groups include Dinophyceae, Apicomplexa, Bacillariophyta, Florideophyceae, Mamiellophyceae, Syndiniales, Prasino-Clade-VII, and Ascomycota, each showing significant abundance differences across coral reef regions (p < 0.05). High abundance of Rhodobacterales and Flavobacteriales are detected in all coral reef waters. Correlation analysis indicates that temperature, pH, and salinity are important factors affecting the bacterial and eukaryotic communities. This study reveals the spatial heterogeneity of microbial communities in coral reef regions of South China Sea and underscores the significant impact of marine environmental heterogeneity on community structure.