A comparison of bacterial community structure in seawater pond with shrimp, crab, and shellfish cultures and in non-cultured pond in Ganyu, Eastern China

The aim of this study was to gain an understanding of the effects of mariculture on the bacterial communities in a co-culture pond, which is a popular culture model for shrimp, crab, and shellfish along the eastern coast of China. Six seawater samples were collected from a pond with cultures of shrimp, crab, and shellfish, and six other samples were collected from a non-cultured pond (control). The diversity of the bacterial communities in the samples was examined using the MiSeq desktop sequencer (Illumina) to amplify and sequence the V4-V5 region of the 16S ribosomal DNA analysis. The Meta-Stat computer program was used to assess the differences in the two communities. The sequences produced from all 12 samples were categorized into 1533 unique phylotypes, including 30 phyla, 81 classes, 270 families, and 414 genera. The top five dominant communities in the culture pond were Proteobacteria, Chloroflexi, Actinobacteria, Firmicutes, and Acidobacteria, while Proteobacteria, Planctomycetes, Bacteroidetes, Actinobacteria, and Cyanobacteria were the dominant communities in the control pond. Higher abundance was observed in the culture pond at the phylum, class, and genus levels, and the same result was also observed in the rarefaction curves. Elusimicrobia, Fibrobacteres, Fusobacteria, Tenericutes, MVP-21, SM2F11, and WCHB1-60 were present, whereas Deferribacteres and Lentisphaerae, as well as the candidate divisions BRC1, OD1, and OP11, disappeared from the culture pond. Moreover, abundant phylotypes (Aeromonadaceae, Pseudomonadaceae, Enterobacteriaceae, Bradyrhizobiaceae, Clostridiaceae, and Xanthomonadaceae) were present in the culture pond, but only rarely present in the control pond. These results suggest that mariculture contributed to the change in bacterial communities in the culture pond compared with the non-culture pond. Proteobacteria was the most dominant community in both ponds, but the second most dominant community was Planctomycetes in the control pond and Chloroflexi in the culture pond. Seven new phyla were observed, but five phyla disappeared in the culture pond. The disease- or metabolism-related members of the bacterial communities, namely, Aeromonadaceae, Pseudomonadaceae, Enterobacteriaceae, and Xanthomonadaceae, were abundant phylotypes in the culture pond. Our results contribute to an improved understanding of the establishment and maintenance of the bacterial community structure in a complex aquaculture ecosystem and may have practical applications in terms of improving seawater quality and early disease warning in this popular mariculture model in China.