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

Abstract

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.

The effect of “Fishery-PV Integration” on Penaeus monodon culture and Micro-ecological environment

“…Our results indicated that Proteobacteria, Actinobacteriota, and Bacteroidota were the predominant phylum in water, effluent, and shrimp intestines, consistent with the levels found in the freshwater and marine cultured environment of P. vannamei (Fan, et al, 2019), freshwater crab aquaculture environments (Fang, et al, 2019), and P. monodon biofloc-based aquaculture environments (Chen, et al, 2022). It is important to understand the bacterial groups with competitive advantages in shrimp intestines and the surrounding environments of cultured animals for the screening of probiotics in aquaculture.…”

“…In addition, PV panels can provide power to cold chain logistics warehouses, thus promoting the development of fisheries. Currently, amplicon and metagenomic sequencing have been widely applied to study the microflora of aquaculture environments, including traditional white shrimp ponds (Zhang, et al, 2019), higher-place white shrimp ponds (He, et al, 2020), and biofloc-based aquaculture ponds (Chen, et al, 2022), etc. Therefore, to explore the practicability of the "Fishery-PV Integration" farming model, the present study cultured P. monodon in the "Fishery-PV Integration" engineering culture system and used metagenomic sequencing and 16S rRNA gene sequencing technologies to compare the composition, function, and ARGs profiles of bacterial communities in shrimp intestines, water, and effluent.…”

The effect of “Fishery-PV Integration” on Penaeus monodon culture and research on the micro-ecological environment

“…As a new aquaculture model, it is necessary to evaluate the security and ecological impact of the "Fishery-PV Integration" pond by analyzing its ARGs. In the current study, the relative abundance of total ARGs in the "Fishery-PV Integration" pond was about 0.49-4.27 × 10 −4 ppm, which was lower than the relative abundance of ARGs in P. monodon biofloc culture (2.46-5.82×10 -4 ppm) (Chen et al, 2022) and coastal industrial mariculture systems (0.27-4.55×10 -4 ppm) (Wang et al, 2018). Furthermore, a total of 123 ARGs were identified in the "Fishery-PV Integration" ponds, significantly lower than the number found in biofloc culture ponds (483 ARGs) (Chen et al, 2022) and freshwater shrimp culture ponds (229 ARGs) (Zhao et al, 2018), indicating that "Fishery-PV Integration" culture ponds are less easily enriched by ARGs than are other aquaculture ponds and thus are safer in terms of public health.…”

“…In the current study, the relative abundance of total ARGs in the "Fishery-PV Integration" pond was about 0.49-4.27 × 10 −4 ppm, which was lower than the relative abundance of ARGs in P. monodon biofloc culture (2.46-5.82×10 -4 ppm) (Chen et al, 2022) and coastal industrial mariculture systems (0.27-4.55×10 -4 ppm) (Wang et al, 2018). Furthermore, a total of 123 ARGs were identified in the "Fishery-PV Integration" ponds, significantly lower than the number found in biofloc culture ponds (483 ARGs) (Chen et al, 2022) and freshwater shrimp culture ponds (229 ARGs) (Zhao et al, 2018), indicating that "Fishery-PV Integration" culture ponds are less easily enriched by ARGs than are other aquaculture ponds and thus are safer in terms of public health. Recent studies have found that ARGs in aquaculture will eventually enter the human body after long-term enrichment along with the cycle of matter and food chain transmission, causing harm to human health (Wright et al, 2013;Dong et al, 2021).…”

“…Although the fi sh-light in g complem ent ary has considerable potential for development, basic research on its micro-ecological environment and cultured organisms is still lacking. Currently, amplicon and metagenomic sequencing have been widely applied to study the microflora of aquaculture environments, including traditional white shrimp ponds (Zhang et al, 2019), higher-place white shrimp ponds (He et al, 2020), and biofloc-based aquaculture ponds (Chen et al, 2022). This present study cultures P. monodon in the "Fishery-PV Integration" engineering culture system, using metagenomic sequencing and 16S rRNA gene sequencing technologies to compare the composition, function, and ARGs profiles of bacterial communities in shrimp intestines, water, and effluent.…”