Short-term deep-sea cage culture of Trachinotus ovatus increases mobility of antibiotic-resistance genes

Antibiotic resistance genes (ARGs) have been extensively studied in offshore mariculture areas, yet their profiles in deep-sea cage culture environments remain largely unexplored. In this study, the proliferation, hosts and spread risks of ARGs before and after deep-sea cage mariculture activities were investigated, employing environmental parameter measurements, metagenomic assembly, and binning approaches. Our results showed that following aquaculture activity, the abundances of fosmidomycin- (an antibiotic targeting the MEP pathway), MLS (Macrolides, lincosamides, streptogramines), phenicol-, and triclosan-related ARGs decreased, while diaminopyrimidine- (interfere with the folic acid metabolism of bacteria), rifamycin-, aminoglycoside- (prevent bacterial protein synthesis), multidrug-, and mupirocin-related ARGs increased, thereby increasing the likelihood of microorganisms acquiring resistance. The hosts of these ARGs were classified into 38 classes across 19 phyla, with Gammaproteobacteria accounting for over 36.29 % of all ARG hosts, and Alphaproteobacteria contributing an additional 16.9 %. This information can guide us in targeting specific types of microorganisms for controlling particular ARGs. Certain ARGs were predominantly located on plasmids, indicating enhanced mobility and an increased risk of horizontal gene transfer. Additionally, the presence of plasmids, viruses, or mobile genetic elements in aquaculture-affected water showed a general increase, further highlighting the environmental risk of ARG spread. Overall, this study deepens our understanding of the environmental impacts of deep-sea cage aquaculture.