Functional metagenomic analysis of dust-associated microbiomes above the Red Sea

Abstract

Atmospheric transport is a major vector for the long-range transport of microbial communities, maintaining connectivity among them and delivering functionally important microbes, such as pathogens. Though the taxonomic diversity of aeolian microorganisms is well characterized, the genomic functional traits underpinning their survival during atmospheric transport are poorly characterized. Here we use functional metagenomics of dust samples collected on the Global Dust Belt to initiate a Gene Catalogue of Aeolian Microbiome (GCAM) and explore microbial genetic traits enabling a successful aeolian lifestyle in Aeolian microbial communities. The GCAM reported here, derived from ten aeolian microbial metagenomes, includes a total of 2,370,956 non-redundant coding DNA sequences, corresponding to a yield of ~31 × 106 predicted genes per Tera base-pair of DNA sequenced for the aeolian samples sequenced. Two-thirds of the cataloged genes were assigned to bacteria, followed by eukaryotes (5.4%), archaea (1.1%), and viruses (0.69%). Genes encoding proteins involved in repairing UV-induced DNA damage and aerosolization of cells were ubiquitous across samples, and appear as fundamental requirements for the aeolian lifestyle, while genes coding for other important functions supporting the aeolian lifestyle (chemotaxis, aerotaxis, germination, thermal resistance, sporulation, and biofilm formation) varied among the communities sampled.

Microbial functional signature in the atmospheric boundary layer

“…These genes associated with global stress-related functions are likely acquired during sporulation formation and certainly do not result from adaptation of fungi in air. When studying genes coding more specific proteins that are not associated with spore resistance, such as lipoate synthase and chromosome plasmid partitioning protein ParA, which might play a role in oxidative stress (Allary et al, 2007;Bunik, 2003) and are more generally found in stress resistance and adaptability of microorganisms (Shoeb et al, 2012;Zhang et al, 2018), they were occasionally found in relatively high concentrations in air samples (Fig. S3).…”

“…Given that cultivable organisms represent about 1 % of the entire microbial community (Vartoukian et al, 2010), culture-independent techniques and especially metagenomic studies applied to atmospheric microbiology have the potential to provide additional information on the selection and genetic adaptation of airborne microorganisms. However, to our knowledge, only five metagenomic studies on airborne microbial communities at one or two specific sites per study exist (Aalismail et al, 2019;Cao et al, 2014;Gusareva et al, 2019;Yooseph et al, 2013). Metagenomic investigations of complex microbial communities in many ecosystems (for example, soil, seawa-Published by Copernicus Publications on behalf of the European Geosciences Union.…”

Microbial functional signature in the atmospheric boundary layer

“…microorganisms. However, to our knowledge, only five metagenomic studies on airborne microbial communities at one or two specific sites per study exist (Aalismail et al, 2019;Amato et al, 2019;Cao et al, 2014;Gusareva et al, 2019;Yooseph et al, 2013). Metagenomic investigations of complex microbial communities in many ecosystems (for example, soil, seawater, lakes, feces, sludge) have provided evidence that microorganism functional signatures reflect the abiotic conditions of their environment, with different relative abundances of specific microbial functional classes (Delmont et al, 2011;Li et al, 2019;Tringe et al, 2005;Xie et al, 2011).…”

Microbial Ecology of the Planetary Boundary Layer

“…Moreover, airborne microbial activity-related investigations have been mainly carried out on microorganisms isolated from cloud water where chemical species are in solution. Although a high diversity in functional genes has been revealed from planetary boundary layer microbial metagenomes [135,136], (Tignat-Perrier et al, in revision), the significance of planetary boundary layer microbial activity on atmospheric chemistry remains unknown.…”