Profiles of tetracycline resistance genes in paddy soils with three different organic fertilizer applications

The rapid expansion of organic rice cultivation areas have been accompanied by increased application of organic fertilizers. The high prevalence of soil antibiotic resistance caused by organic fertilizer application poses a severe threat to the agricultural and soil ecosystems. To date, research efforts and understanding of the effects and mechanism of action of the various organic fertilizers on antibiotic resistance in paddy soils remain poorly investigated. Tetracycline resistance genes (TRGs, including tetB, tetC, tetL, tetZ, tetM, tetO, tetT, and tetX), class 1 integron-integrase gene (intI1) and bacterial communities were characterized using quantitative-PCR and Illumina MiSeq sequencing, in paddy soils exposed to inorganic fertilizer (NPK), animal-derived organic fertilizer (AOF, composted swine and/or chicken manure), plant-derived organic fertilizer (POF, rapeseed cake and/or astragalus) and commercial organic fertilizer (COF, composted of animal manure mix with crop residues) applications. Compared with NPK, AOF applications significantly increased the relative abundance of TRGs, which was predominantly expressed in the increase of the relative abundance of tetC, tetM, tetO, tetT, and tetX, while POF and COF had no significant effect on the relative abundance of TRGs. Principal coordinate analysis revealed that AOF and POF significantly altered bacterial communities in paddy soils relative to NPK, while COF had no significant change of bacterial communities. Variation partitioning analysis indicated that soil physicochemical properties were the decisive factors for the changes of TRGs in organic paddy fields. Furthermore, redundancy analysis and the Mantel test showed that TRG profiles in AOF applied paddy soils were strongly influenced by electrical conductivity (EC). Total nitrogen (TN) and organic matter (OM) affected the distribution of TRGs in COF and POF applied paddy soils through a different mechanism. This study provides insights into the impacts of different types of organic fertilizer on the profiles of TRGs in paddy soils. [Display omitted] •The effect of different organic fertilizers on TRG profiles in paddy fields was compared.•AOF prefers to enrich ribosomal protection proteins and enzymatic modification genes.•EC was the primary factor in the changes of TRGs in AOF applied paddy soils.•TRG profiles in POF and COF applied paddy soils was associated with TN and OM.