Jia‐Yi Zheng, Fang-Zhou Gao, Guang‐Guo Ying
Bacteria in the genus Acinetobacter are widespread in environmental systems. While some studies have raised concerns about health threats posed by environmental strains, others found their potential for bioremediation. This dual nature makes it valuable to resolve the genomic landscape of this genus. By conducting a large-scale meta-analysis of 1,253 river metagenomes, we demonstrated the prevalence of Acinetobacter in water and sediment, with species composition differing between the two habitats and A . lwoffii and A . tandoii being the most prevalent, respectively. We identified numerous species harboring resistance genes against 10 antibiotic classes, 22 biocide classes, and seven metals, together with genes related to 20 categories of virulence factors. Most species harbored genes associated with biogeochemical processes, and some encoded genes related to the degradation of persistent organic pollutants and hydrocarbons. We also recovered 296 metagenome-assembled genomes belonging to 38 species, 36 of which harbored resistance-related genes and ecological functional genes, suggesting potential links between resistance dissemination and ecological functions. Various metagenome-assembled genomes revealed metabolic, resistance, and other functional gene categories that were absent from currently available reference genomes, expanding the known genomic repertoire of multiple Acinetobacter species and highlighting the importance of environmental genomes for improving current reference collections. These findings highlight the ecological roles of Acinetobacter in rivers, but we should be aware of their health threats associated with antimicrobial resistance.