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Aquaculture pond is a complex ecosystem where the microorganisms in the sediments, in the animal intestinal tract and in water interact with each other to influence the water quality and health of aquatic animals. In order to understand the spatial distribution and relationship of microbial communities in intensively farmed genetically improved farmed tilapia (GIFT, Oreochromis niloticus), 454 high-throughput pyrosequencing was applied to analyse the 16S rRNA gene of bacteria in intensive GIFT ponds in Wuxi City, Jiangsu Province, China. A total of 72 747 initial sequences were obtained from four depths of pond water, from tilapia large intestines and from pond sediment. The most common phylum in all samples was Proteobacteria, Actinobacteria and Cyanobacteria were the most abundant in water, Fusobacteria and Firmicutes in the large intestine and Chloroflexi in sediment samples. The sediment microbial community structure was comparatively similar to that of the tilapia large intestine. The microbial communities from different water depths were somewhat similar, especially the three most shallow samples, although the abundance of Actinobacteria gradually decreased with increased water depth. This data offer a preliminary exploration of the response mechanisms of the bacterial communities to aquafarming and contributes to the understanding of the status of bacterial communities of tilapia pond systems during the peak period of breeding from the aspect of their spatial distributions.

Bacterial community compositions in the surface sediment of tilapia ponds and their responses to pond characteristics or seasonal variations were investigated. For that, three ponds with different stocking densities were selected to collect the samples. And the method of Illumina high-throughput sequencing was used to amplify the bacterial 16S rRNA genes. A total of 662, 876 valid reads and 5649 operational taxonomic units were obtained. Further analysis showed that the dominant phyla in all three ponds were Proteobacteria, Bacteroidetes, Chloroflexi, and Acidobacteria. The phyla Planctomycetes, Firmicutes, Chlorobi, and Spirochaetae were also relatively abundant. Among the eight phyla, the abundances of only Proteobacteria, Bacteroidetes, Firmicutes, and Spirochaetae were affected by seasonal variations, while seven of these (with the exception of Acidobacteria) were affected by pond differences. A comprehensive analysis of the richness and diversity of the bacterial 16S rRNA gene, and of the similarity in bacterial community composition in sediment also showed that the communities in tilapia pond sediment were shaped more by pond differences than by seasonal variations. Linear discriminant analysis further indicated that the influences of pond characteristics on sediment bacterial communities might be related to feed coefficients and stocking densities of genetically improved farmed tilapia (GIFT).

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