Vertical profiling of airborne microbial communities across the atmospheric boundary layer

Aerobiological studies have traditionally focused on near-surface sampling and horizontal biogeographic patterns, while vertical microbial structuring within the atmospheric boundary layer (ABL) remains poorly characterized. This knowledge gap is largely due to logistical constraints, including limited accessibility, the need for aerial platforms, and technological challenges in collecting sufficient biomass over short sampling periods.

Here, we present an integrated approach to investigate airborne microbial communities across different levels of the ABL in a coastal Antarctic environment. Microbial samples were collected simultaneously at lower and higher atmospheric levels using aerial and ground-based platforms, and microbial community composition and abundance, as well as morphometry were analysed using metabarcoding and microscopy-based techniques. The study was conducted at a low-orography coastal site in Antarctic Peninsula, what is representative of air masses from the Southern Ocean, and supported by atmospheric observations and air-mass trajectory analyses.

Our results reveal a clear vertical differentiation in airborne microbial communities. Air sampled at higher atmospheric levels showed microbial communities with reduced diversity and distinct taxonomic signatures compared to those closer to the surface, consistent with selective processes acting during vertical transport and atmospheric residence. Samples from near-surface showed comparatively more homogeneous communities, reflecting strong mixing of local biological sources, whereas communities from higher-altitude samples exhibited greater variability among the samples, influenced by broader-scale atmospheric transport. Despite these differences, partial overlap in community composition between atmospheric layers suggests vertical connectivity within the ABL. Variations in microbial abundance and morphometric cell characteristics further support the role of atmospheric structure and stability in shaping airborne microbial assemblages.