Geographical and Environmental Factors Differentially Shape Planktonic Microbial Community Assembly and Resistomes Composition in Urban Rivers

ABSTRACT Global urbanization accelerates pollution challenges in urban rivers, including increased transmission of bacterial antibiotic resistance genes (ARGs), severely threatening the health of aquatic ecosystems and human health. Yet, systematic knowledge of differences in distribution and community assembly patterns of bacterial resistance across urban rivers at a continental scale is still insufficient. In this study, we conducted extensive sampling in nine representative urban rivers across China. We used amplicon and shotgun metagenomic sequencing, state‐of‐the‐art bioinformatics, and multivariate statistics to investigate distribution patterns and community assembly mechanisms of planktonic microbiomes (i.e., bacterioplankton and planktonic microeukaryotes), including their resistomes, i.e., ARGs and metal resistance genes (MRGs). Geographical and environmental factors played a pivotal role in shaping distribution patterns of planktonic microbiomes vs. resistomes in the studied urban rivers. Phylogenetic‐bin‐based null model analysis (iCAMP) indicated that planktonic microbiomes, dominated by dispersal limitation and drift, tend toward spatial heterogeneity. In contrast, planktonic resistomes, driven by deterministic processes, display more similar distribution patterns. Cross‐validated Mantel tests revealed that geographical factors (i.e., geographic distance) were the primary regulators of planktonic microbial community assembly, while environmental factors (i.e., temperature) control assembly processes of planktonic resistomes. Our findings provide crucial insights into the mechanisms driving the biogeographical distribution and community assembly of planktonic microbial entities in urban rivers at a continental scale, offering valuable implications for mitigating and managing the spread of ARGs from the environment to humans.