Currently, black-odor river has received great attention in China. In this study, the micro-nano bubble technology (MBT) was used to mitigate the water pollution rapidly and continuously by increasing the concentration of dissolved oxygen (DO) in water. During treatment, the concentration of DO increased from 0.60 mg/L to over 5.00 mg/L, and the oxidation reduction potential (ORP) also changed from a negative value to over 100.00 mV after only five days aeration. High throughput pyrosequencing technology was employed to identify the microbial community structure. At genus level, the dominant bacteria were anaerobic and nutrient-loving microbes (e.g., Arcobacter sp
., Azonexus sp
., and Citrobacter sp.
) before, and the relative abundances of aerobic and functional microbes (e.g., Perlucidibaca sp.
, Pseudarcicella sp.
, Rhodoluna sp.
, and Sediminibacterium sp.
) were increased after treatment. Meanwhile, the water quality was significantly improved with about 50% removal ratios of chemical oxygen demand (CODCr
) and ammonia nitrogen (NH4+
-N). Canonical correspondence analysis (CCA) results showed that microbial community structure shaped by COD, DO, NH4+
-N, and TP, CCA1 and CCA2 explained 41.94% and 24.56% of total variances, respectively. Overall, the MBT could improve the water quality of urban black-odor river by raising the DO and activate the aerobic microbes.
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