Methods to investigate the global atmospheric microbiome

Aurelien Dommergue, Pierre Amato, Romie Tignat-Perrier, Olivier Magand, Alban Thollot, Muriel Joly, Laetitia Bouvier, Karine Sellegri, Timothy Vogel, Jeroen E. Sonke, Jean Luc Jaffrezo, Marcos Andrade, Isabel Moreno, Casper Labuschagne, Lynwill Martin, Qianggong Zhang, Catherine Larose

Research output: Contribution to journalArticlepeer-review

34 Scopus citations

Abstract

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.

Original languageEnglish
Article number243
JournalFrontiers in Microbiology
Volume10
Issue numberFEB
DOIs
StatePublished - 2019

Bibliographical note

Funding Information:
This program is funded by ANR-15-CE01-0002 – INHALE. RT-P’s doctoral grant is funded by Région Auvergne – Rhöne Alpes. Part of the analytical equipment was supported at IGE by the AirOSol platform within Labex OSUG@2020 (ANR10 LABX56). AD and QZ were also supported by the program CAMPUS France program XU GUANGQI (38718ZC INHALE_NAMCO). Financial support for AMS, DMC and Villum field campaigns was provided by the French Polar Institute IPEV (programs 1028 and 399).

Publisher Copyright:
© 2007 - 2019 Frontiers Media S.A. All Rights Reserved.

Keywords

  • Aerobiology
  • Aerosols
  • Atmosphere
  • Biogeography
  • Methods
  • Microorganisms biodiversity
  • Protocols

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