Distribution of tetracycline resistance genes within an organic fertilizer-amended soil–rice continuum

The transmission of antibiotic resistance genes (ARGs) to humans through the consumption of plants grown in manure-amended soils is a critical concern. However, the effect of manure application on the profiles of tetracycline resistance genes (TRGs) within the soil–rice continuum remains unclear. In this study, tetracycline (TC) content, bacterial communities, abundance of 8 TRGs, and class 1 integron (intI1) were characterized using high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS), Illumina sequencing, and quantitative PCR (qPCR) in rhizosphere soils, roots, and grains of rice exposed to pig manure (PM), rapeseed cake (RC), and chemical fertilizer (CF), respectively. Our findings indicate that the type of sample was the primary determinant of TRGs abundance variation within the soil-rice continuum, with a consistent decline from rhizosphere soils to roots to grains. Furthermore, fertilization type significantly influenced TRGs abundance, with the highest levels observed in PM treatment. TetZ and tetX were predominant, constituting over 90% of total TRGs abundance across all samples. In addition, the mechanism of TRGs profile formation varies with sample types. Bacterial communities-TC content-intI1 interactions determined the change in TRGs abundance in rhizosphere soils, and bacterial communities constituted the most important factor affecting TRGs abundance within the roots. However, bacterial communities and/or intI1 poorly explained the change in TRGs abundance within the grains. Our study attempts to explore the underlying mechanism for the profiles of TRGs in soil–rice continuums exposed to manure, as well as provides a theoretical basis for controlling the spread of endogenous antibiotic resistance within rice grown in soil receiving pig manure.