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“Fishery-photovoltaic (PV) Integration” is a novel aquaculture model that provides enormous potential for aquaculture development. However, research on the aquaculture environment and organisms under the “Fishery-PV Integration” mode is presently sparse. This study investigated Penaeus monodon as a model, studying the growth rates of shrimp, water quality conditions, and the micro-ecological environment. After 105 days of rearing, P. monodon (initial weight of 0.006 ± 0.001 g) reached an average body weight of 11.69 ± 0.92 g. The water quality was stable (C(NH4+) ≤ 1.57 mg/L) during the experimental period. The 16S rRNA gene sequencing results showed that bacterial community structures were significantly distinct among water, effluent and intestinal environments, with a closer relationship between the microbiotas in effluent and water. The dominant phyla present in shrimp intestines, water, and effluent were Proteobacteria, Actinobacteriota, and Bacteroidota. Likewise, Ralstonia, Candidatus Aquiluna, and Vibrio were the dominant genus in the three groups. The relative abundance of Vibrio as a common opportunistic pathogen for shrimp was relatively low, which is beneficial to promote the healthy growth of shrimp. The function of the “Fishery-PV Integration” microbiota was investigated using metagenomic technology. Results showed that microorganisms played an essential role in regulating intestinal amino acids, carbohydrate, and energy metabolisms. Antibiotic resistance genes (ARGs) data indicate that tetH, QnrVC6 and tetX were dominated ARGs in the intestine. At the same time, the ARGs with the highest relative abundance in the water and effluent groups were MexL and adeF. Notably, only 123 ARGs were identified within the “Fishery-PV Integration” pond. This outcome is significantly lower than other studies, indicating that shrimp cultured in the “Fishery-PV Integration” pond had a higher level of food safety. The current study describes the characteristics of the microflora and ARGs distribution in the “Fishery-PV Integration” pond for the first time, providing fundamental information for formulating management strategies for the whole microflora to maintain the health of shrimp.

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.