Antibiotic resistance genes and their links with bacteria and environmental factors in three predominant freshwater aquaculture modes

Rapid development of aquaculture industry and increasing demand of various inputs (especially antibiotics), are suspected to promote the occurrence and spread of ARGs in aquaculture related environments. However, the occurrences of ARGs under different freshwater aquaculture practices are rarely known. Here, we investigated the seasonal profiles of the main ARGs, intI1 and bacteria in waters from three kinds of predominant freshwater aquaculture practices around the Honghu Lake (China), as well as their co-occurrences and interrelationships with antibiotics, heavy metals and general water quality. The results indicate that quinolone resistance genes (qnrB), tetracycline resistance genes (tetB and tetX) and sulfonamide resistance genes (sul1 and sul2) were the top five predominant ARGs with seasonal variations of abundance. Fish ponds were of the highest absolute abun-dances of tested ARGs than the other two modes. Crayfish ponds and their adjacent ditches shared similar ARGs profile. Different subtypes of ARGs belonging to the same class of resistance were varied in abundances. Some bacteria were predicted to carry different ARGs, which indicating multi-antibiotic resistances. Moreover, the combined environmental factors (antibiotics, heavy metals and water quality) partially shaped the profiles of ARGs and bacteria composition. Overall, this study provides new comprehensive understanding on the charac-terization of ARGs contamination in different freshwater aquaculture practices from the perspectives of envi-ronmental chemistry, microbiology and ecology. The results would benefit the optimization of aquaculture practices toward environmental integrity and sustainability.

Automated summary

The study investigated seasonal profiles of main antibiotic resistance genes (ARGs) and bacteria in waters from three predominant freshwater aquaculture practices near Honghu Lake in China. Results showed that fish ponds had the highest absolute abundances of tested ARGs, while crayfish ponds and adjacent ditches had similar ARGs profiles. Some bacteria were predicted to carry different ARGs, indicating multi-antibiotic resistances. Environmental factors partially shaped the profiles of ARGs and bacteria composition.