In order to explore the microbial community structure in different functional areas of recirculating aquaculture system, as well as to understand the relationship between environmental factors and the microbial community, microbial community structure in recirculating aquaculture system was analyzed by using high-throughput sequencing with 16S rRNA in this study. The results showed that Proteobacteria and Bacteroidetes were the most dominant phyla in overall system, the compositions of dominant genera were quite different in different areas of system, while the relative abundances of Vibrio in whole system were both exceeding 1%. α-diversity (Shannon, ACE and chao1) of samples collected from biofilter and Rapana venosa pond were highest, and that in abalone pond and natural seawater were lowest. Non-metric multi-dimensional scaling (NMDS) analysis showed the system areas possessed distinctive distances of microbial communities except samples between biofilter and culture pond inlet. The removal rates of ammonia nitrogen and nitrite nitrogen from biofilter to the inlet of culture pond were 8.77% and 45.12%, respectively. The concentrations of nitrate nitrogen maintained a high level in the whole system (148.50~200.47 mg/L). There was no significant correlations between environmental factors and microbial community structure, temperature and nitrite nitrogen had relatively stronger effects on microbial community structure. This study provides a reference for the design improvement and daily management of recirculating aquaculture system in the next step.
