Metagenomic insights into antibiotic resistome in a paddy field soil marked by fertilization patterns

Abstract

Novel fertilizers have emerged as viable alternatives to conventional fertilizers, effectively enhancing agricultural productivity–especially in paddy soils. However, their application may introduce emerging contaminants including antibiotic resistance genes (ARGs). In this study, we systematically evaluated the impacts of three types of fertilizers–conventional chemical (CC), organic-inorganic composite (OI), and slow- and controlled-release (SC) fertilizers–on soil fertility, microbial communities, and ARGs in paddy fields of Xiong'an New Area, China. SC had the greatest effect on soil fertility, increasing nitrogen, phosphorus, and organic matter levels by 5.25 %–23.15 %. The abundance of ARGs varied with different treatments. Higher levels of ARGs, at 0.28 copies per 16S rRNA gene copy, were found in the surface soils of the CC and OI treatments, whereas lower levels, at 0.26 copies per 16S rRNA gene copy, were observed in the rhizosphere soil of the OI treatment. OI showed the highest abundance of top five subclasses ARGs in rhizosphere soil, indicating enhanced risk of ARG generation, especially in the rhizosphere. Additionally, OI resulted in higher microbial diversities, with key genera including Streptomyces (4.3 %–5.2 %), Bradyrhizobium (2.4 %–2.9 %), and Sphingomonas (2.1 %–2.7 %) showing positive correlattions with most ARGs. Redundancy analysis, network plots, and Mantel test indicated that nutrients explained 58.45 % of the variation in ARGs followed by soil properties. This study demonstrates that SC fertilizers represent a promising alternative for sustainable agriculture, effectively enhancing soil fertility while minimizing ARG dissemination risks. Our findings underscore the importance of implementing stringent contaminant management protocols when substituting conventional fertilizers with novel alternatives.