Is rice-crayfish co-culture a better aquaculture model: From the perspective of antibiotic resistome profiles

Aquaculture ecosystem is a hot-spot for antibiotic resistance genes (ARGs). Rice-crayfish co-culture was considered an eco-friendly aquaculture model and has been widely adopted in China. However, it is unclear whether rice-crayfish co-culture is one of the most eco-friendly models from the perspective of antibiotic resistance profiles. In this study, we evaluated the eco-friendliness of rice-crayfish co-culture, and compared this model with other aquaculture models, from the perspectives of antibiotics and ARG patterns, based on multi-omics and antibiotic profiles. Results showed that the nutrient levels, antibiotic concentrations, dominant microbial genera and ARG patterns in the rice-crayfish co-culture model were profoundly different from the other three aquaculture models (crab only aquaculture model, crayfish only aquaculture model, and crab-crayfish co-culture models). Specifically, the rice-crayfish co-culture model has significantly lower diversity of ARGs and lower potential risks of ARGs when compared to the other aquaculture models. Nutrient and antibiotic concentrations were the important environmental factors for shaping ARG patterns, but compared with environmental factors, the effects of mobile genes and bacteria community on the proliferation and transmission of ARGs were stronger. This study has deepened our understanding of ARGs in freshwater aquaculture ecosystem, and suggested that rice-crayfish co-culture model is a relatively eco-friendly aquaculture model when compared with the other aquaculture models.