Distinct Diversity, Assembly, and Co-Occurrence Patterns of the Prokaryotic Microbiome in Coral Ecosystems of the South China Sea

Coral reefs are among the most energetic marine ecosystems, taking a place in ecological balance. Microbes participate in the energy exchange in coral ecosystems, which may affect coral resistance and resilience. However, there is still a lack of understanding regarding the microbial structure between corals and seawater. In this study, microbial structure and interactions in coral and seawater were studied using quantitative PCR and high-throughput sequencing. We found that the abundance and diversity of microbes in corals were higher than those in seawater. Corals, as nonfluidic ecosystems, limited the dispersal of microbes, causing broader stochasticity in the ecological shaping process, whereas ecological drift and homogeneous selection were the most important assembly mechanisms in seawater. The microbial niche width was larger in the coral group than in the seawater group, indicating strong adaptability. A group of microbes (e.g., Caldilineaceae, Burkholderiaceae, and Nitrosopumilaceae) may become microbial indicators which differentiate seawater samples (e.g., SAR11 and SAR86 clades, Cryomorphaceae), which may be due to separated habitats and nutrition. Coral microbes may participate in nitrogen-metabolism to maintain a nitrogen limited microenvironment. Nodes linked in the coral co-occurrence network showed coexisting interactions and higher complexity based on the comparison of topological values. Collectively, significant differences in microbial fractions were demonstrated observed in terms of diversity, composition, co-occurrence patterns, assembly processes and predicted functions between coral and seawater samples, showing potential microbial interactions and providing in-depth insights into the metacommunity diversity in coral reef ecosystems.