Sierra Nevada sweep: metagenomic measurements of bioaerosols vertically distributed across the troposphere

Abstract

To explore how airborne microbial patterns change with height above the Earth's surface, we flew NASA's C-20A aircraft on two consecutive days in June 2018 along identical flight paths over the US Sierra Nevada mountain range at four different altitudes ranging from 10,000 ft to 40,000 ft. Bioaerosols were analyzed by metagenomic DnA sequencing and traditional culturing methods to characterize the composition and diversity of atmospheric samples compared to experimental controls. The relative abundance of taxa changed significantly at each altitude sampled, and the diversity profile shifted across the two sampling days, revealing a regional atmospheric microbiome that is dynamically changing. the most proportionally abundant microbial genera were Mycobacterium and Achromobacter at 10,000 ft; Stenotrophomonas and Achromobacter at 20,000 ft; Delftia and Pseudoperonospora at 30,000 ft; and Alcaligenes and Penicillium at 40,000 ft. Culturebased detections also identified viable Bacillus zhangzhouensis, Bacillus pumilus, and Bacillus spp. in the upper troposphere. to estimate bioaerosol dispersal, we developed a human exposure likelihood model (7-day forecast) using general aerosol characteristics and measured meteorological conditions. By coupling metagenomics to a predictive atmospheric model, we aim to set the stage for field campaigns that monitor global bioaerosol emissions and impacts. Aerosols (mostly desert dust, black carbon and ocean spray) regularly disperse across the Pacific Ocean with springtime atmospheric winds-in fact, models suggest that as much as 64 Teragrams of Asian aerosols can be transported to North America annually 1. Past studies have reported microorganisms co-transported with globally-dispersed aerosols, and that both DNA signatures and viable cells can be detected in air masses 2-4. For example, thousands of taxonomic signatures were measured in springtime Asian dust plumes delivering free tropospheric bioaerosols to an alpine research station in central Oregon 3. In a separate flight project surveying airborne microorganisms in the western region of the United States, several taxa were found to be enriched in the upper atmosphere, including bacterial families Lachnospiraceae, Ruminococcaceae and Erysipelotrichaceae 2. Despite harsh conditions in the atmosphere, viable bacterial isolates were recovered from the same study 2 , including Bacillus sp., Micrococcus sp., Arthrobacter sp. and Staphylococcus sp. Previous aerobiology campaigns using aircraft were flown at single altitudes in order to refine collection methods and demonstrate some of the first measurements of an atmospheric microbiome 2,5-7. To date, there are only a few studies that have examined microbiological changes across a vertical gradient in Earth's troposphere 8-10. More studies using advanced genomic techniques such as shotgun metagenomic sequencing will be essential to formulating predictive models of bioaerosols and how the atmospheric microbiome is influenced by meteorological

Vertical stratification of the air microbiome in the lower troposphere

“…Early interest in airborne microbial organisms is attributed to the works and writing of Louis Pasteur in 1865 (3), with subsequent assessments of airborne microorganisms relying on microscopic and cultivationbased methods (4,5). Attempts to analyze the microbial content of the vertical air column date back to the early 20th century when aviation pioneers such as Charles Lindberg conducted the Skyhook experiments (6)(7)(8)(9)(10). Other vertical experimental designs resorted to air sampling on mountains with high elevation (11)(12)(13), low-height sampling at research towers (14), or meteorological balloons (15).…”

The hop downy mildew pathogen Pseudoperonospora humuli

“…humuli is presumed to be highly dispersible by wind based on dispersal characteristics of the sister species P . cubensis (Jaing et al, 2020; Ojiambo et al, 2015). However, models for prediction of long‐distance dispersal have not been developed for P .…”

Identifying optimal bioinformatics protocols for aerosol microbial community data

“…However, bioaerosol metagenomic and transcriptomic techniques have been developed (Jiang et al, 2015) and successfully applied in a handful of very recent studies. (Amato et al, 2019;Amato et al, 2017;Jaing et al, 2020). Jaing et al (2020) performed metagenomic sequencing on bioaerosols above the Sierra Nevada mountains in the US and obtained 5,000,000 reads, although only 640,000 were successfully assigned at the genus level.…”

“…(Amato et al, 2019;Amato et al, 2017;Jaing et al, 2020). Jaing et al (2020) performed metagenomic sequencing on bioaerosols above the Sierra Nevada mountains in the US and obtained 5,000,000 reads, although only 640,000 were successfully assigned at the genus level. Transcriptomics on microbial communities in clouds has been performed for rRNA genes (Amato et al, 2017) and untargeted amplification has been applied to full cloud metagenomes and transcriptomes to compensate for low biomass (Amato et al, 2019).…”