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Although the microbial ecology of aquaculture systems is receiving increasing attention, the composition and controlling factors of aquaculture microbes has yet to be determined. This study explored the bacterial community present in water, sediment and intestine samples from an aquaculture site using high-throughput sequencing. The correlation between this bacterial community and environmental factors provides a reference for the environmental regulation of aquaculture sites. The dominant bacteria recorded from sediment, water, and intestine samples were Proteobacteria, Bacteroidetes, Cyanobacteria, Acidobacteria, Actinobacteria, and Firmicutes. Approximately 72.5% and 48.2% OTUs (operational taxonomic units) from the intestines of 17 cultured species were identical to those present in sediment and water samples, respectively. This finding indicated that sediment and water are major sources of intestinal microbes. Welch's t-test test found that the dominant microbial taxa differed significantly among sediment, water, and intestine samples, and that each of these environments has unique dominant microbial taxa that are closely related to their habitats. Principal component analysis showed that sediment, water, and intestine samples collected at different sites were clustered together and similar environments exhibited similar microbial community structures. This research examined the relationship between the intestinal microbes of multiple cultured organisms and the culture environment. Canonical correlation analysis revealed that environmental parameters, such as pH, COD, temperature, salinity, nitrite, and nitrate regulate the composition of microbial community structures. Nitrites and nitrates were significantly positively correlated to potential pathogens, such as Vibrio, Photobacterium, Tenacibaculum, and Mycobacterium, thereby providing a scientific theoretical basis for water quality regulation and disease prevention in aquaculture sites.

Some diatom species cause red tides under eutrophic conditions, but little is known about their impact on the ecological structure of coastal systems. In this study, the effects of diatom red tides on the bacterial and eukaryotic communities in aquaculture systems were analyzed using high-throughput sequencing. The correlation between these communities and environmental factors was also analyzed. Principal coordinate analysis (PCoA) and non-metric multidimensional scaling (NMDS) showed that there were significant differences in the microbiome in red tide ponds and normal ponds (p