Temporal Dynamics of Airborne Bacterial and Fungal Communities in Megacity Shanghai: Diel Asynchrony, Environmental Drivers, and Cold Front Perturbations

Atmospheric bacteria and fungi are key components of urban bioaerosols, and their community structures are closely related to urban air quality, bioaerosol concentration, and environmental driving factors. However, the temporal dynamics and environmental drivers of bacterial and fungal community structures remain poorly characterized in megacities such as Shanghai, China. From November 2024 to November 2025, we conducted a year-long, cross-seasonal bioaerosol sampling and high-throughput DNA sequencing campaign to investigate the seasonal and diel variations, environmental covariation, and meteorological responses of atmospheric bacteria and fungi in Shanghai. The results show that seasonal transitions cannot significantly alter the α-diversity of bacterial or fungal communities, but significantly shift their community compositions, exhibiting a stronger differentiation for fungi than bacteria (PERMANOVA R² = 0.133 vs. 0.054, p = 0.001). At the diel scale, bacterial communities exhibit weak diurnal variation, whereas fungal communities display significantly higher nocturnal Chao1 richness and Shannon diversity, along with distinct compositional separation. Cladosporium and Alternaria are enriched during the day, while saprotrophic basidiomycetes such as Irpex and Trametes are more abundant at night. Fungal composition covaries most strongly with meteorological gradients governed by boundary layer height, clear-sky surface downward solar radiation, temperature, relative humidity, atmospheric pressure and visibility, whereas bacterial–environment associations are weaker. The Relative Exposure-Relevant Proportion (RERP), dominated by Cladosporium and Alternaria, is higher during daytime and negatively associated with relative humidity (β = −0.23, q = 0.001). During a strong cold-air event, bacterial communities shifted rapidly following immediate air mass replacement and high wind shear before stabilizing, whereas fungal communities underwent a more gradual and cumulative turnover. The RERP also elevated during this event, accompanied by a greater contribution from Talaromyces. These findings reveal contrasting dynamics between airborne bacteria and fungi under both background and transient synoptic disturbances, providing crucial observational insights for bioaerosol modeling and risk prediction in urban environments.