Unraveling the role of abundant and rare species in antibiotic resistance genes migration in soil-crops system under different fertilization regimes

Abstract

The microbiome plays a critical role in the dissemination of antibiotic resistance genes (ARGs) in the soil-crop system. Yet, how abundant/rare species distinctly contribute to the evolution of ARGs and their underlying mechanisms are still poorly understood. We investigated the distribution of ARGs in soils and crops under different fertilization and dissect the contributions of abundant/rare species to ARGs distribution and their ecological and metabolic mechanisms. Our results showed that recommended fertilizer amendments with biochar (RF-BC) or humic acid (RF-HA) significantly attenuated ARGs dissemination (p < 0.05), mainly by disrupting soil-to-crop transmission. For example, the relative abundances of ARGs such as Hpyl_rpoB_RIF, Saur_mupB_MUP, Sent_ramR, and Bpse_Omp38 decreased by 3.29∼76.19 % compared to other treatments. This was primarily attributed to BC/HA ability to enhance the contribution of rare species to ARGs distribution, mainly through niche preemption and competitive exclusion of ARG hosts. The RF-BC/RF-HA can alter microbial carbon metabolism, and the ‘fast carbon’ resources typically utilized by abundant species are converted into ‘slow carbon’ forms that support rare species, leading to an expansion of rare species niche occupation. Also, the RF-BC can alleviate cellular oxidative stress, thereby reducing ARGs proliferation, whereas no such effect was observed in HA. Additionally, RF-BC/RF-HA reduced the abundance of mobile genetic elements, with the relative abundances of tnpA-3 and tnpA(IS5) decreasing by 41.50∼81.10 % and 17.24∼70.92 %, respectively, which is directly associated with the reduction in soil ARG abundance. This study lays the groundwork for improving fertilization strategies to limit ARG spread and reduce related ecological and health risks.