The application of animal manure is a highly recommended traditional agricultural practice for soils of relatively low fertility. However, for the farmland purple soils that are widely distributed in the upper Yangtze River region, little knowledge has been established in previous studies about the changes in the antibiotic resistome upon manure amendment. In the present study, the impact of long-term pig manure slurry application on the occurrence of antibiotic resistance genes (ARGs) and bacterial community was assessed in arable calcareous purple soil using high-throughput quantitative polymerase chain reaction and Illumina sequencing. Four treatments, including a non-fertilization control (CK) and pig manure (OM), OM plus mineral N fertilizer (OMN) and OM plus mineral NPK fertilizer (OMNPK) treatments were investigated. Across all the soil samples receiving different treatments, a total of 139 unique ARGs and 6 mobile genetic element genes were detected, with multidrug and beta-lactam the two most dominant types of ARGs. The results of the principal coordinate analysis (PCoA) suggest that the profiles of soil ARGs in the two treatments of OM combined with mineral fertilizer(s) (i.e., OMN and OMNPK) were similar to those in the control treatment, while the soil receiving only pig manure application had a different pattern of ARGs from the soils in the other three treatments. A clear reduction of soil ARGs was observed in the OM treatment. Significant and positive relationships were found not only among ARGs but also between mobile genetic elements (MGEs) and ARGs. However, no significant relationships were detected between ARG patterns and bacterial community composition. These results imply that the long-term application of pig manure slurry to purple soil does not lead to the prevalence of ARGs; however, the potential for the horizontal transfer of ARGs in calcareous purple soil should not be ignored.
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