High genetic diversity and variability of microbial communities in near-surface atmosphere of Crete island, Greece

Microorganisms are ubiquitous in the atmosphere with hundreds of taxa being identified in air samples collected around the world. Despite their importance on human and ecosystem health, the majority of air microbiological studies have been limited to cultivation-based methods that may not capture all of the microbial diversity in the air. The present study used pyrosequencing analysis of 16S rDNA fragments, in order to examine the short-term variability of microbial assemblage composition in near-surface atmosphere of two coastal cities of Crete island, eastern Mediterranean Sea. A diverse range of 16S rRNA genes was identified at both cities consisting of 17,720 different operation taxonomic units, 23 bacterial and 3 archaeal phyla, 93 orders and 204 families. A core microbiome containing members of Proteobacteria, Actinobacteria and Firmicutes was evidenced at both study sites, regardless the origin of transported air masses. Nevertheless, the local biodiversity profiles presented extensive differences at lower taxonomic level (i.e., species). A total of 7699 sequences were closely related to 101 strains that are commonly found in many different habitats, including agricultural soil, water, air, marine water and sediment, as well as human microbiome. Several of these strains were closely related to pathogens or putative pathogens, which can trigger infections, such as bacteremia and endocarditis to humans and blackleg disease in plants. The identified large differences in local biodiversity together with the presence of many pathogenic relatives demonstrate the significance of spatial variability in atmospheric biogeography and the importance to include airborne microbes in air quality studies.