Spatiotemporal patterns of airborne microbial communities in forest and grassland ecosystems

The atmosphere harbors a diverse and dynamic reservoir of microorganisms, yet their distribution in the atmosphere and response to environmental variation remains a subject of ongoing investigation. In this study, we compared airborne bacterial and fungal communities at subalpine forest (NWT) and steppe grassland (CPER) sites, over diel, vertical, and seasonal gradients. Air samples were collected at three heights over 4 months at NWT with concurrent sampling at CPER during two of those months. Fungal communities exhibited greater site-specific variability and sensitivity to environmental factors than bacterial communities, particularly at NWT, where vertical stratification and diel cycles significantly structured microbial diversity. In comparison, bacterial communities were temporally dynamic but showed weaker responses to local environmental conditions and minimal site-level differences. This may indicate broader dispersal and a ubiquitous set of bacterial taxa. Environmental drivers, such as atmospheric moisture and air pressure, strongly influenced microbial beta-diversity at NWT, while air temperature and wind speed impacted diversity at CPER, again highlighting ecosystem-specific responses. Despite compositional differences, a subset of shared bacterial and fungal ASVs was consistently detected across sites, with most shared ASVs detected at greater heights at NWT. This, along with wind patterns moving eastward from NWT toward CPER, indicates potential atmospheric transport between sites, with taxa dispersal being filtered by height. These results underscore the role of ecosystem structure, meteorological conditions, and air mass movement in shaping the aerobiome and suggest that airborne microbial communities are shaped by both local emission and long-range atmospheric transport processes.IMPORTANCEUnderstanding the drivers of airborne microbial community structure is essential for predicting microbial dispersal, ecosystem connectivity, and responses to environmental change. This study reveals that atmospheric fungal and bacterial communities are shaped by distinct ecological and environmental factors, with fungi exhibiting stronger site-specific responses and vertical stratification than bacteria. The contrasting patterns between subalpine forest and grassland ecosystems underscore how local conditions influence microbial diversity and transport potential. Importantly, the detection of shared taxa, especially at greater sampling heights, suggests that atmospheric transport may connect distant ecosystems and that certain taxa are ubiquitous. These findings highlight the complexity of the aerobiome and its sensitivity to spatial and temporal dynamics, providing new insights into microbial distribution and the role of the atmosphere in microbial exchange across landscapes.