Passive sampling reveals composition of airborne bacteria and fungi across five East African cities

Airborne microbes significantly influence environmental processes and human exposure, yet they remain poorly characterized in Africa. This study presents a regional survey of airborne bacterial and fungal communities across 10 sites in five East African countries: Burundi, the Democratic Republic of the Congo, Kenya, Rwanda, and Tanzania. Polyurethane foam passive air samplers (PUF-PASs) were deployed concurrently, and airborne bacterial and fungal communities were characterized using 16S rRNA gene and ITS amplicon sequencing. Genus-level analyses identified both bacterial taxa (Massilia, Sphingomonas, Pseudomonas, Bacillus, and Kocuria) and fungal genera (Cladosporium, Alternaria, Aspergillus, Curvularia, and Penicillium) that are commonly detected in outdoor air and urban atmospheric environments. Beta-diversity analysis revealed no significant country-level differences in bacterial communities (ANOSIM (R = -0.045, p = 0.597)), while fungal communities exhibited significant differences among countries (ANOSIM (R = 0.652, p = 0.002)). Cross-border comparisons showed that nearby sites within 10 km did not consistently share similar microbial profiles. These findings indicate a broadly shared regional bacterial aerobiome, with more pronounced spatial structuring among fungal communities. This study serves as a proof-of-concept demonstration that PUF-PASs can be used to characterize airborne microbial communities in East Africa, while highlighting the need for future bioaerosol research with enhanced temporal replication and broader spatial coverage to support long-term public health surveillance in the African region.