Performance evaluation of high-volume electret filter air samplers in aerosol microbiome research
Year: 2020
Type: article
Abstract: BACKGROUND: Reliable identification and quantification of bioaerosols is fundamental in aerosol microbiome research, highlighting the importance of using sampling equipment with well-defined performance characteristics. Following advances in sequencing technology, shotgun metagenomic sequencing (SMS) of environmental samples is now possible. However, SMS of air samples is challenging due to low biomass, but with the use of high-volume air samplers sufficient DNA yields can be obtained. Here we investigate the sampling performance and comparability of two hand-portable, battery-operated, high-volume electret filter air samplers, SASS 3100 and ACD-200 Bobcat, previously used in SMS-based aerosol microbiome research. RESULTS: SASS and Bobcat consistently delivered end-to-end sampling efficiencies > 80% during the aerosol chamber evaluation, demonstrating both as effective high-volume air samplers capable of retaining quantitative associations. Filter recovery efficiencies were investigated with manual and sampler-specific semi-automated extraction procedures. Bobcat semi-automated extraction showed reduced efficiency compared to manual extraction. Bobcat tended towards higher sampling efficiencies compared to SASS when combined with manual extraction. To evaluate real-world sampling performance, side-by-side SASS and Bobcat sampling was done in a semi-suburban outdoor environment and subway stations. SMS-based microbiome profiles revealed that highly abundant bacterial species had similar representation across samplers. While alpha diversity did not vary for the two samplers, beta diversity analyses showed significant within-pair variation in subway samples. Certain species were found to be captured only by one of the two samplers, particularly in subway samples. CONCLUSIONS: SASS and Bobcat were both found capable of collecting sufficient aerosol biomass amounts for SMS, even at sampling times down to 30 min. Bobcat semi-automated filter extraction was shown to be less effective than manual filter extraction. For the most abundant species the samplers were comparable, but systematic sampler-specific differences were observed at species level. This suggests that studies conducted with these highly similar air samplers can be compared in a meaningful way, but it would not be recommended to combine samples from the two samplers in joint analyses. The outcome of this work contributes to improved selection of sampling equipment for use in SMS-based aerosol microbiome research and highlights the importance of acknowledging bias introduced by sampling equipment and sample recovery procedures.
Source: Environmental Microbiome
Language: English
Subfield: Health, Toxicology and Mutagenesis
Field: Environmental Science
Domain: Physical Sciences
Open Access status: gold
Estimated APC paid: $1,825
Funders: Bill and Melinda Gates Foundation, Alfred P. Sloan Foundation, Vallee Foundation, WorldQuant Foundation, Norwegian Sequencing Centre, Universitetet i Oslo, Norges Forskningsråd, National Institutes of Health, National Institute of Mental Health, National Institute of Allergy and Infectious Diseases, National Institute of Neurological Disorders and Stroke, National Institute of Biomedical Imaging and Bioengineering
Awards: Mapping the RNA modification N6-methyladenosine during Zika virus infection, G4198848887, Community Research Education and Engagement for Data Science (CREEDS), The Spatiotemporal Landscape of the Human Brain Epitranscriptome, Joan & Sanford I. Weill Medical College of Cornell University - to monitor the spread of antimicrobial resistance by generating a global map of bacterial species, resistance genes and markers, and modified bases..., Research - Weill Cornell Medical College (2015), Epigenome Interactions in Complex Neurogenetic Disorders
OpenAlex ID: W3045954288