Characterization of airborne microbial communities at a high-elevation site and their potential to act as atmospheric ice nuclei

Abstract

Bacteria and fungi are ubiquitous in the atmosphere. The diversity and abundance of airborne microbes may be strongly influenced by atmospheric conditions or even influence atmospheric conditions themselves by acting as ice nucleators. However, few comprehensive studies have described the diversity and dynamics of airborne bacteria and fungi based on culture-independent techniques. We document atmospheric microbial abundance, community composition, and ice nucleation at a high-elevation site in northwestern Colorado. We used a standard small-subunit rRNA gene Sanger sequencing approach for total microbial community analysis and a bacteria-specific 16S rRNA bar-coded pyrosequencing approach (4,864 sequences total). During the 2-week collection period, total microbial abundances were relatively constant, ranging from 9.6 x 10(5) to 6.6 x 10(6) cells m(-3) of air, and the diversity and composition of the airborne microbial communities were also relatively static. Bacteria and fungi were nearly equivalent, and members of the proteobacterial groups Burkholderiales and Moraxellaceae (particularly the genus Psychrobacter) were dominant. These taxa were not always the most abundant in freshly fallen snow samples collected at this site. Although there was minimal variability in microbial abundances and composition within the atmosphere, the number of biological ice nuclei increased significantly during periods of high relative humidity. However, these changes in ice nuclei numbers were not associated with changes in the relative abundances of the most commonly studied ice-nucleating bacteria.

FIG. 1.

Total APS particle counts, total microbial abundance, and total number of ice nuclei observed in clear and cloudy skies and in replicate snow samples. (A) The left y axis shows APS particle counts (gray bars) (P = 0.09 for clear versus cloudy) and DAPI counts (DNA-containing particles) (black bars) (P = 0.47 for clear versus cloudy) for samples collected in clear air, cloudy air, and from fresh snow. The right y axis shows the number of IN observed per volume of air or melted snow (white bars) (P = 0.05 between cloudy and clear). The air samples are in units of particles or IN m⁻³ of air, while the snow samples are in units of particles or IN per liter of snow melt. There were no statistics run between the air and snow samples, as the units cannot be compared, and there were no total particle measurements, as the APS instrument was only used for atmospheric aerosols. (B) Relationship between the mean relative humidity during each of the air sampling periods and the total number of ice nuclei m⁻³ of air.

FIG. 2.

Coarse level taxonomic description of the nine air samples and two snow samples. The numbers in parentheses represent the total number of sequenced clones from each sample (E < 1e⁻¹⁰⁰) that were nonchimeric with an E value of <1e⁻¹⁰⁰. Refer to Table 1 for a complete description of each sample ID listed on the x axis.

FIG. 3.

Composition of the fungal communities as determined using full-length Sanger sequencing. Numbers in parentheses indicate the number of sequences obtained from each sample. Refer to Table 1 for a complete description of each sample listed on the x axis.

FIG. 4.

Rarefaction curves at the 99%, 97%, and 95% sequence similarity levels. Curves shown are from the most diverse (sample ID 4-4.CL.N; solid lines) and least diverse (sample ID 3-24.CL.D; dashed lines) of the nine airborne bacterial samples.

FIG. 5.

Most abundant bacterial groups identified using bar-coded pyrosequencing. Numbers in parentheses indicate the number of sequences obtained from each sample (E < 1e⁻¹⁰⁰) that were nonchimeric with an E value of <1e⁻¹⁰⁰ from a single tagged pyrosequencing run. Refer to Table 1 for a complete description of each sample ID listed on the x axis. Proteobacterial groups are designated by the Greek symbols α, β, and γ.

FIG. 6.

Nonmetric multidimensional scaling plot of the UniFrac distance matrix from the tagged pyrosequence bacterial data set. These plots compress the multidimensional UniFrac distance matrix to two dimensions. (A) Air and snow data. Stress value, 0.01. (B) Data for air only; IDs correspond to the IDs listed in Table 1. Stress value, 0.07.

FIG. 7.

Phylogenetic distribution of representative full-length Sanger sequences that have similarities to the 16S rRNA gene of known ice-nucleating bacteria. Sequences were aligned using the Greengenes NAST aligner, and the maximum-likelihood tree was made using RAxML-7.0.4. A Streptomyces sequence was used as the outgroup. Each Sanger sequence is represented by its sample ID (see Table 1 for sample descriptions).