Insights into microbial contamination in paddy field ecology: matagenomic analysis of the abundances, diversity, and distribution of antibiotic resistance genes, virulence factors, and their potential bacterial hosts

Abstract

Rice cultivation, a vital component of agricultural production, often presents a "high-risk" environment for bacterial antibiotic resistance contamination. This study aims to compare the similarities and differences in antibiotic resistance genes, virulence factors, and the abundance of potential bacterial hosts in the rice cultivation environments of traditional monoculture, rice-frog co-culture, and rice-fish co-culture models. Samples of field water, field soil, and the intestinal contents of frogs or fish were collected from the rice cultivation bases of the three models. Metagenomic sequencing technology was used for analysis and comparison. At the phylum level of microbial communities, both Proteobacteria and Bacteroidetes were abundant in all three models. At the genus level, Acinetobacter, Massilia, and Enterococcus were the dominant genera in traditional cultivation, rice-frog co-culture, and rice-fish co-culture, respectively. In terms of antibiotic resistance, the models of traditional cultivation, rice-frog co-culture, and rice-fish co-culture respectively contained higher abundances of oleC, ropB2, and tetA(58). Plasmids significantly outnumbered transposons, insertion sequences, and integrons, suggesting that plasmids may be the primary carriers of horizontal gene transfer in paddy field environments. Network analysis revealed that the most complex correlations between ARGs, MGEs, and bacterial genera in the traditional model. Traditional cultivation had a high abundance of VFGs, with a significantly higher relative abundance of aggressive VFGs compared to defensive VFGs. Based on co-occurrence results, multiple subtypes of ARGs co-occurred with VFGs, and various bacteria were considered potential ARG hosts, indicating that the host bacteria of VFGs in traditional cultivation have a stronger offensive capability.