Study on the Microflora Structure in a Litopenaeus vannamei–Sinonovacula constricta Tandem-Culture Model Based on High-Throughput Sequencing under Different Culture Densities

Abstract

In this study, we evaluated the intestinal contents of Pacific whiteleg shrimp (Litopenaeus vannamei), the visceral mass of razor clams (Sinonovacula constricta) and the water columns and the substrate sediments in different culture-density groups in a L. vannamei–S. constricta tandem-culture model by high-throughput sequencing of the 16S rRNA gene. The results show that the culture density affected the bacterial floral structure of the water columns, substrate sediment and razor-clam gut masses without making significant differences in the bacterial flora structure of the shrimp gut; the Shannon diversity indexes of the bacterial communities in the substrate sediment, shrimp gut and razor-clam gut masses were not significantly different among the density groups, and the Shannon diversity index of the bacterial communities in the water column was higher in the group with higher culture densities; at the phylum level, the dominant bacteria common to the shrimp guts, razor-clam visceral mass, water columns and substrate sediment were Proteobacteria and Bacteroidetes; Chloroflexi was the dominant bacterium specific to the substrate sediment; and Firmicutes was the dominant bacterium specific to the shrimp gut and razor-clam gut mass. We used national standards (GB 17378.4-2007, China) to evaluate the content of water-quality factors through the environmental factors and the genus-level correlation analysis of bacterial flora that follow: the dominant bacterium in the water column, uncultured_bacterium_f_Rhodobacteraceae, was negatively correlated with PO43−-P; the dominant bacteria in the substrate sediments, uncultured_bacterium_f_Anaerolineaceae and Woeseia, were significantly and negatively correlated with DO; and the dominant bacteria Lactococcus spp. in the razor-clam gut mass and the shrimp intestines were positively correlated with DO. These results show that culture density directly affects water-quality factors, which in turn affect the culture environment and the composition structure of the bacterial flora in a cultured organism.