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Methods to Investigate the Global Atmospheric Microbiome
Dommergue, A (Dommergue, Aurelien)1; Amato, P (Amato, Pierre)2; Tignat-Perrier, R (Tignat-Perrier, Romie)1,3; Magand, O (Magand, Olivier)1; Thollot, A (Thollot, Alban)1,3; Joly, M (Joly, Muriel)2; Bouvier, L (Bouvier, Laetitia)4; Sellegri, K (Sellegri, Karine)4; Vogel, T (Vogel, Timothy)3; Sonke, JE (Sonke, Jeroen E.)5; Jaffrezo, JL (Jaffrezo, Jean-Luc)1; Andrade, M (Andrade, Marcos)6,7; Moreno, I (Moreno, Isabel)6; Labuschagnea, C (Labuschagnea, Casper)8; Martina, L (Martina, Lynwill)8; Zhang, QG (Zhang, Qianggong)9; Larose, C (Larose, Catherine)3

The interplay between microbes and atmospheric physical and chemical conditions is an open field of research that can only be fully addressed using multidisciplinary approaches. The lack of coordinated efforts to gather data at representative temporal and spatial scales limits aerobiology to help understand large scale patterns of global microbial biodiversity and its causal relationships with the environmental context. This paper presents the sampling strategy and analytical protocols developed in order to integrate different fields of research such as microbiology, -omics biology, atmospheric chemistry, physics and meteorology to characterize atmospheric microbial life. These include control of chemical and microbial contaminations from sampling to analysis and identification of experimental procedures for characterizing airborne microbial biodiversity and its functioning from the atmospheric samples collected at remote sites from low cell density environments. We used high-volume sampling strategy to address both chemical and microbial composition of the atmosphere, because it can help overcome low aerosol and microbial cell concentrations. To account for contaminations, exposed and unexposed control filters were processed along with the samples. We present a method that allows for the extraction of chemical and biological data from the same quartz filters. We tested different sampling times, extraction kits and methods to optimize DNA yield from filters. Based on our results, we recommend supplementary sterilization steps to reduce filter contamination induced by handling and transport. These include manipulation under laminar flow hoods and UV sterilization. In terms of DNA extraction, we recommend a vortex step and a heating step to reduce binding to the quartz fibers of the filters. These steps have led to a 10-fold increase in DNA yield, allowing for downstream omics analysis of air samples. Based on our results, our method can be integrated into pre-existing long-term monitoring field protocols for the atmosphere both in terms of atmospheric chemistry and biology. We recommend using standardized air volumes and to develop standard operating protocols for field users to better control the operational quality.

Subject AreaMicrobiology
WOS IDWOS:000459260400001
Indexed BySCI
KeywordBiological Aerosol-particles Gaseous Elemental Mercury Source Apportionment Size Distribution Bacteria Variability Urban Troposphere Transport Site
WOS Research AreaMicrobiology
WOS SubjectMicrobiology
Cooperation Status国际
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Document Type期刊论文
Corresponding AuthorLabuschagnea, C (Labuschagnea, Casper)
Affiliation1.Univ Grenoble Aloes, Grenoble NP, CNRS, Inst Geosci Environm,IRD, Grenoble, France;
2.Univ Clermont Auvergne Sigma, UMR6096 CNRS, Inst Chim Clermont Ferrand, Clermont Ferrand, France;
3.Univ Lyon, Ecole Cent Lyon, Lab Ampere, CNRS UMR 5005,Environm Microbial Genom, Ecully, France;
4.Univ Clermont Auvergne, Lab Meteorol Phys LaMP, Clermont Ferrand, France;
5.Univ Toulouse, Inst Rech Dev, CNRS, Geosci Environm Toulouse, Toulouse, France;
6.Univ Mayor San Andres, Inst Phys Res, Lab Atmospher Phys, La Paz, Bolivia;
7.Univ Maryland, Dept Atmospher & Ocean Sci, College Pk, MD 20742 USA;
8.South African Weather Serv, Stellenbosch, South Africa;
9.Chinese Acad Sci, Inst Tibetan Plateau Res, Key Lab Tibetan Environm Changes & Land Surface P, Beijing, Peoples R China.
Recommended Citation
GB/T 7714
Dommergue, A ,Amato, P ,Tignat-Perrier, R ,et al. Methods to Investigate the Global Atmospheric Microbiome[J]. FRONTIERS IN MICROBIOLOGY,2019,10(0):243.
APA Dommergue, A .,Amato, P .,Tignat-Perrier, R .,Magand, O .,Thollot, A .,...&Larose, C .(2019).Methods to Investigate the Global Atmospheric Microbiome.FRONTIERS IN MICROBIOLOGY,10(0),243.
MLA Dommergue, A ,et al."Methods to Investigate the Global Atmospheric Microbiome".FRONTIERS IN MICROBIOLOGY 10.0(2019):243.
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