Microbiota in monocultured Litopenaeus vannamei vs. polyculture with Trachinotus ovatus

The structures of the microbial community in the intestine, aquaculture water, and sediment of Litopenaeus vannamei, both in monoculture and mixed culture with Trachinotus ovatus, were analyzed by sequencing 16S rRNA amplicons. 1,120,500 valid reads were obtained from 21 samples, and 3,767 operational taxonomic units (OTUs) were classified. In the two culture modes, the abundance and diversity of bacterial in the sediment were significantly higher than in the L. vannamei intestine under the monoculture mode, in the water and intestines of L. vannamei and T. ovatus under the mix-culture mode (P 0.05). The dominant phyla in the sediment under two culture modes were Proteobacteria, Bacteroidetes, and Chloroflexi. The microbial community structure in the water and L. vannamei intestine were similar in both culture modes. The dominant phyla included Cyanobacteria, Proteobacteria, and Actinobacteria, with their abundances ranging from 80.88% to 97.10%. Proteobacteria was the dominant phylum in each group of samples, and the dominant genus in both culture modes was GpIIa. There was little difference in microbial community structures under the two culture modes; while the culture mode did not affect the core phyla/genera, there were differences in relative abundance. The experimental results provide a reference for the exploration of efficient and specific probiotic screening and microbial formulation techniques

Transcriptome analysis of <em>Marsupenaeus japonicus</em> hepatopancreas during WSSV persistent infection

White Spot Syndrome Virus (WSSV) can cause a large-scale death of cultured shrimp and significant damage to the shrimp farming industry. Marsupenaeus japonicus is one of the world's most important economically farmed shrimp. This study found that some M. japonicus survived the spontaneous outbreak of WSSV. Surprisingly, these virus-carrying shrimp showed no apparent illnesses or outbreaks of white spot disease in the subsequent cultivation, and their body size was substantially smaller than healthy shrimp, indicating a long-term fight between the host and the virus. To investigate this interesting phenomenon, we analyzed the transcriptomes of healthy shrimp and survived shrimp through the RNA-Seq platform, attempting to reveal the underlying molecular mechanism of the struggle between M. japonicus and WSSV. Transcriptional analysis showed that a total of 37,815 unigenes were assembled, with an average length of 1,193.34 bp and N50 of 2,049 bp. In the KEGG pathway, enrichment analysis of DEGs pathways related to immunity, biosynthesis, and growth metabolism was enriched, including pentose phosphate pathway, glycerophospholipid metabolism, fatty acid biosynthesis, Wnt signaling pathway, biosynthesis of amino acids, ascorbate, and aldarate metabolism. Our data showed a delicate balance between M. japonicus and WSSV infection: On the one hand, WSSV infection can cause host metabolism and biosynthesis disorders in the host, and the virus consumes a portion of the material and energy required for shrimp average growth and reproduction. If WSSV infection persisted for a long time, then the growth rate of M. japonicus decreased. On the other hand, the host can regulate immune defense to resist subsequent viral infection. This study reveals the underlying molecular mechanism of a long-term battle of M. japonicus against WSSV infection, providing novel insights for preventing WSSV persistent infection in M. japonicus and other farmed shrimp species

Metagenomic Analysis of Bacterial Communities and Antibiotic Resistance Genes in Penaeus monodon Biofloc-Based Aquaculture Environments

Biofloc technology (BFT) is one of the most promising technologies in global aquaculture for the purpose of improving water quality, waste treatment, and disease prevention in intensive aquaculture systems. However, characterization of the microbial species and antibiotic resistance potentially present in biofloc-based aquaculture environments is needed. In this study, we used high-throughput sequencing technology to comprehensively compare the bacterial communities in mariculture ponds of Penaeus monodon (P. monodon), by testing of water, biofloc, and intestine of P. monodon. Operational taxonomic units (OTUs) cluster analysis showed that the nine samples tested divided into 45 phyla and 457 genera. Proteobacteria was the dominant bacteria in water, biofloc and prawn intestine. In biofloc and intestine, the Ruegeria (2.23–6.31%) genus represented the largest proportion of bacteria, with Marivita (14.01–20.94%) the largest group in water. Microbial functional annotation revealed that in all the samples, genes encoding metabolism were predominant. The antibiotic resistance gene annotation showed the highest absolute abundance of patB, adeF, OXA-243, and Brucella_suis_mprF from Proteobacteria. PatB (11.33–15.01%), adeF (15.79–18.16%), OXA-243 (35.65%), and Brucella_suis_mprF (10.03%) showed the highest absolute abundance of antibiotic resistance genes in water, biofloc, and intestines, respectively. These findings may greatly increase our understanding of the characteristics of the microbiota of shrimp biofloc-based aquaculture systems and the complex interactions among shrimp, ambient microflora, and environmental variables. It provides a reference basis for policy on breeding, environmental safety, and maintaining food safety in the production of P. monodon