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Based on long-term systematic sampling, information is currently limited regarding the impacts of different air pollution levels on variations of bacteria, fungi and ammonia-oxidizing microorganisms (AOMs) in fine particulate matter (PM 2.5), especially their interactions. Here, PM 2.5 samples were weekly collected at different air pollution levels in Beijing, China during one-year period. Microbial composition was profiled using Illumina sequencing, and their interactions were further investigated to reveal the hub genera with network analysis. Diversity of bacteria and fungi showed obvious seasonal variations, and the heavy- or severe-pollution levels mainly affected the diversity and composition of bacteria, but not fungi. While, the community structure of both bacteria and fungi was influenced by the combination of air pollution levels and seasons. The most abundant bacterial genera and some genera with highest abundance in heavy- or severe-pollution days were the hub bacteria in PM 2.5. Whereas, only the dominant fungi in light-pollution days in winter were the hub fungi in PM 2.5. The complex positive correlations of bacterial or fungal pathogens would aggravate the air pollution effects on human health, despite of their low relative abundances. Moreover, the strong co-occurrence and co-exclusion patterns of bacteria and fungi in PM 2.5 were identified. Furthermore, the hub environmental factors (e.g., relative humidity and atmospheric pressure) may play central roles in the distributions of bacteria and fungi, including pathogens. Importantly, AOMs showed significant co-occurrence patterns with the main bacterial and fungal genera and potential pathogens, providing possible microbiological evidences for controlling ammonia emissions to effectively reduce PM 2.5 pollution. These results highlighted the more obvious air pollution impacts on bacteria than fungi, and the complex bacterial-fungal interactions, as well as the important roles of AOMs in airborne microbial interactions webs, improving our understanding of bioaerosols in PM 2.5. Image 1 • H or S-pollution levels significantly affected variations in bacteria, but not fungi. • Abundant bacteria were also hub bacteria in PM 2.5 , but it was not true for fungi. • Complex interactions of pathogens would aggravate haze impacts on human health. • Strong co-occurrence and co-exclusion patterns of bacteria and fungi were observed. • AOMs were positively related to dominant bacteria and fungi, as well as pathogens. Interactions among bacteria, fungi, AOMs and environmental variables at different air-pollution levels provide new insight into the bioaerosols in PM 2.5 in Beijing, China. [ABSTRACT FROM AUTHOR]