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Dust coming from the large deserts on Earth, such as the Sahara, can travel long distances and be dispersed over thousands of square kilometers. Remote dust deposition rates are increasing as a consequence of global change and may represent a mechanism for intercontinental microbial dispersal. Remote oligotrophic alpine lakes are particularly sensitive to dust inputs and can serve as sentinels of airborne microbial transport and the ecological consequences of accelerated intercontinental microbial migration. In this study, we applied high-throughput sequencing techniques (16S rRNA amplicon pyrosequencing) to characterize the microbial communities of atmospheric deposition collected in the Central Pyrenees (NE Spain) along three years. Additionally, bacteria from soils in Mauritania and from the air-water interface of high altitude Pyrenean lakes were also examined. Communities in aerosol deposition varied in time with a strong seasonal component of interannual similarity. Communities from the same season tended to resemble more each other than those from different seasons. Samples from disparate dates, in turn, slightly tended to have more dissimilar microbial assemblages (i.e., temporal distance decay), overall suggesting that atmospheric deposition may influence sink habitats in a temporally predictable manner. The three habitats examined (soil, deposition, and air-water interface) harbored distinct microbial communities, although airborne samples collected in the Pyrenees during Saharan dust outbreaks were closer to Mauritian soil samples than those collected during no Saharan dust episodes. The three habitats shared c.a. 1.4% of the total number of microbial sequences in the dataset. Such successful immigrants were spread in different bacterial classes. Overall, this study suggests that local and regional features may generate global trends in the dynamics and distribution of airborne microbial assemblages, and that the diversity of viable cells in the high atmosphere is likely higher than previously expected., (Copyright © 2014 Elsevier B.V. All rights reserved.)