Metagenomic profiles of antibiotic resistance genes in paddy soils from South China

Overuse and arbitrary discarding of antibiotics have expanded antibiotic resistance reservoirs, from gut, waste water and activated sludge, to soil, freshwater and even the ocean. Based on the structured Antibiotic Resistance Genes Database and next generation sequencing, metagenomic analysis was used for the first time to detect and quantify antibiotic resistance genes (ARGs) in paddy soils from South China. A total of 16 types of ARGs were identified, corresponding to 110 ARG subtypes. The abundances and distribution pattern of ARGs in paddy soil were distinctively different from those in activated sludge and pristine deep ocean sediment, but close to those of sediment from human-impacted estuaries. Multidrug resistance genes were the most dominant type (38–47.5%) in all samples, and the ARGs detected encompassed the three major resistance mechanisms, among which extrusion by efflux pumps was predominant. Redundancy analysis (RDA) showed that pH was significantly correlated with the distribution of ARG subtypes (P < 0.05). Our results provided a broad spectrum profile of ARGs in paddy soil, indicating that ARGs are widespread in paddy soils of South China. Our results provided a wide spectrum profile of ARGs in paddy soil for the first time based on metagenomics. Graphical Abstract Figure. Our results provided a wide spectrum profile of ARGs in paddy soil for the first time based on metagenomics.