Microbial communities and mobile genetic elements determine the variations of antibiotic resistance genes for a continuous year in the urban river deciphered by metagenome assembly

Abstract

Antibiotic resistance genes (ARGs) have become emerging environmental contaminants influenced by intricate regulatory factors. However, there is a lack of comprehensive studies on the evolution and distribution of ARGs over a full year in urban rivers, which serve as significant reservoirs of ARGs due to dynamic human activities. In this study, we conducted a 12-month metagenomic assembly to explore the microbial communities, ARGs, mobile genetic elements (MGEs) coexisting with ARGs, ARGs hosts, and the impact of environmental factors. Bacitracin (32%–47%) and multidrug (13%–24%) were detected throughout the year, constituting over 60% of the total abundance, making them the primary ARGs types. The assembly mechanisms of microbial communities and ARGs were primarily driven by stochastic processes. Integrase, IntI1, recombinase, and transposase were identified as the main MGEs coexisting with ARGs. Procrustes analysis revealed a significant structural association, indicating that the composition of host communities likely plays crucial roles in the seasonal composition and distribution of ARGs. Human pathogenic bacteria (HPBs) were identified in the summer, autumn, and winter, with Escherichia coli, Klebsiella pneumoniae, Acinetobacter lwoffii, and Burkholderiales bacterium being the primary HPBs. Mantle tests and PLS-PM equation analysis indicated that microbial communities and MGEs are the most critical factors determining the distribution and composition of ARGs in the river. Environmental factors (including water properties and nutrients) and ARGs hosts influence the evolution and abundance of ARGs by directly regulating microbial communities and MGEs. This study provides critical insights into risk assessment and management of ARGs in urban rivers.