Persistence of Antibiotic Resistance Genes in Soil with Different Fertilization and Tillage Revealed By High Throughput qPCR and Sequencing.

Long-term effect of different fertilization and tillage on the residue of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in soil has not been reported. In the present study, soils from dryland and paddy fields with a 26 year history of either chemical fertilizer, manure, or no fertilization were investigated. Samples were tested using a qPCR array with 384 primer sets targeting ARGs and MGEs. Amplicons obtained from 48 primer sets targeting selected ARGs and MGEs, and the 16S rRNA gene were also sequenced. A positive correlation was observed between high throughput qPCR measurements and sequence abundance. Compared to the dryland soil, higher relative abundance of ARGs in the paddy soil was observed when no fertilizer was applied. Long term application of chemical fertilizer or manure generally increased the relative abundance of ARGs in the dryland soil. In contrast, the same treatments generally enhanced the dissipation of ARGs in the paddy soil. Long term application of manure increased the diversity of ARGs in both dryland soil and paddy soil. However, long term application of chemical fertilizer showed different influence; it increased the diversity of ARGs in the dryland soil but decreased the diversity of ARGs in the paddy soil. These results support that fertilizer application and changing the dryland to paddy field maybe used as a management strategy to reduce the persistence of ARGs in soil.