Prokaryotic Communities Vary with Cultivation Modes of Shrimp (Litopenaeus vannamei)

In response to the growing market demand for Litopenaeus vannamei, a variety of single-species, high-density, intensive, and high-yield aquaculture modes have arisen. These aquacultural systems are teeming with microorganisms, which play roles in water quality and host health. To uncover the prokaryotic community composition across cultivation modes, we investigated the prokaryotic community composition at two fractionated sizes in the water of three culture modes of Litopenaeus vannamei, including high-level pond culture, biofloc technology (BFT), and pond culture. The 16S rRNA gene high-throughput sequencing results indicated that the taxa particularly enriched by high-level pond culture modes were mainly Deltaproteobacteria, while Alpha- and Gammaproteobacteria and Flavobacteria were enriched in the BFT culture modes. The pond culture enriched Bacteroidetes, Sphingobacteriia, Actinobacteria, and Cyanobacteria. PCoA analysis showed that for the pond samples, there were significant differences in the community composition compared with the samples from the other two modes. However, the high-level pond and biofloc samples showed similar community compositions. Furthermore, Canonical Correspondence Analysis (CCA) and Variance Partitioning Analysis (VPA) revealed that NH₄⁺-N, salinity (Sal), and NO₃^--N were key factors affecting the aquaculture communities.