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Atmospheric transport is critical to dispersal of microorganisms between habitats and this 52 underpins resilience in terrestrial and marine ecosystems globally. A key unresolved question 53 is whether microorganisms assemble to form a taxonomically distinct, geographically 54 variable, and functionally adapted atmospheric microbiota. Here we characterised inter-55 continental patterns of microbial taxonomic and functional diversity in air within and above 56 the atmospheric boundary layer and in underlying soils for 596 globally sourced samples. 57 Bacterial and fungal assemblages in air were taxonomically structured and deviated 58 significantly from purely stochastic assembly. Patterns differed with location and reflected 59 underlying surface cover and environmental filtering. Source-tracking indicated a complex 60 recruitment process involving local soils plus globally distributed inputs from drylands and 61 the phyllosphere. Assemblages displayed stress-response and metabolic traits relevant to 62 survival in air, and taxonomic and functional diversity were correlated with macroclimate and 63 atmospheric variables. Our findings highlight complexity in the atmospheric microbiota that 64 is key to understanding regional and global ecosystem connectivity. 65