Environmental microbial communities typically exhibit unbalanced distribution, characterized by a few abundant species coexisting with a multitude of rare species. However, few attentions were paid to the abundant and rare taxa in airborne microbial community. Here, we explored the distribution pattern, assembly mechanisms, and ecological roles of airborne bacterial and fungal communities, including pathogens. Daily sampling was conducted over a one-month period in Nanchang, China. Our results found out the uneven distribution of airborne microbial community. Compared with rare taxa, abundant taxa, exhibited broader niche widths, more ubiquitous distribution and stronger correlations with environmental factors. Stochastic processes dominated the assembly of abundant taxa, whereas deterministic processes governed the assembly of rare taxa. Air pollutants (PM2.5, PM10, NO2, etc.) were identified as key factors regulating the assembly of bacterial subcommunities, but had no significant influence on that of fungal subcommunities. Co-occurrence network analysis indicated that abundant species played a more critical role in maintaining the community stability in the atmosphere. Potential pathogens were mainly distributed in abundant taxa. Notably, dominant pathogens like Staphylococcus aureus (0.62 %) and Nigrospora sps. (15.72 %) were unpredicted by neutral community model and showed strong correlations with environmental factors. Overall, our findings provide insights into the ecological mechanisms structuring airborne microbial communities, with particular implications for understanding pathogenic microorganisms.
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