Sub-inhibitory antibiotics reshape resistance dynamics in cyanobacteria-dominated waters

Cyanobacteria are competent hosts for antibiotic resistance genes, influencing the spread of bacterial resistance through their complex interactions within aquatic environments. However, the coevolution of antibiotic resistance between cyanobacteria and bacteria under sub-inhibitory antibiotic stresses remains unclear. To bridge this knowledge gap, we investigated the effects of Microcystis aeruginosa on modulating bacterial resistance evolution in aquatic ecosystems exposed to sub-inhibitory antibiotics. Results show that cyanobacteria reduced the abundance of antibiotic resistance bacteria (ARB) by 62% to 93% in antibiotic-free conditions and by up to 80 % under sub-inhibitory antibiotic concentrations. The concurrence of cyanobacteria and antibiotics significantly alter microbial community compositions, with Proteobacteria emerging as the dominant population (51%–66%) and Bacteroidota proliferating by 8.7-fold, alongside a significant enrichment of metabolism-related and pathogenic genes (p < 0.05). Redundancy analysis revealed that ARB prevalence was positively correlated with the abundances of Proteobacteria and Bacteroidota , but negatively correlated with Cyanobacteria . Our findings suggest that cyanobacteria may reduce the spread of bacterial resistance both in antibiotic-free and sub-inhibitory antibiotic environments, by reshaping population interactions. These insights are crucial for evaluating the risk of antibiotic-driven bacterial resistance spread in cyanobacteria-rich environments and are vital for the protection and assessment of aquatic environmental quality.