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Data from: Variability of the atmospheric PM10 microbiome in three climatic regions of France

Cite this dataset

Samaké, Abdoulaye et al. (2020). Data from: Variability of the atmospheric PM10 microbiome in three climatic regions of France [Dataset]. Dryad.


Air pollution is a major public-health concern and it is recognized that particulate matter causes damage to human health through oxidative-stress, being responsible for several million premature deaths worldwide each year. Recent findings showed that, airborne microorganisms/spores can modulate aerosol toxicity by altering the oxidative potential of PM10. Primary Biogenic Organic Aerosols (PBOA) appears to be produced by only few genera of microorganisms, emitted by surrounding vegetation in the case of a regionally-homogeneous field site. This study presents the first comprehensive description of the structure and main sources of airborne microbial communities associated with the temporal trends in PM10 SC concentrations at 3 French sites, under different climates. By combining sugar chemistry and DNA Metabarcoding approaches, we intended to identify PM10-associated microbial communities and their main sources at three climatically different sampling-sites in France during summer 2018. This study accounted also for the interannual variability of the structure of summer airborne microbial community associated with PM10-SC concentrations during a consecutive 2-year survey at one site. Our results showed that the temporal evolutions of SC in PM10 in the three sites are associated with the abundance of only few specific airborne fungal and bacterial taxa. These taxa differ significantly between the 3 climatic regions studied. The structure of microbial communities associated with PM10 SC concentrations during a consecutive 2-year survey remained stable in the rural area. The atmospheric concentration levels of PM10 SC-species vary significantly between the 3 studied sites, but with no clear difference according to site typology (rural vs urban), suggesting that SC emissions are more related to regional climatic characteristics. The overall microbial beta diversity in PM10 samples is significantly different from that of the main vegetation around the studied urban sites. This indicates that airborne microorganisms at such urban sites do not originate only from the immediate surrounding vegetation, which is contrasting with observations at the scale of a regionally homogeneous rural site made in 2017. These results improve our understanding of the spatial behavior of tracers of PBOA emission sources, which need to be better characterized to further implement this important OM-mass fraction into CTM models.


obitools commands used in the analysis of data

This file contains the obitools commands used to manipulate sequence reads, filter sequences, and assign taxonomy

obitools commands.txt

Usage notes

Database of MOTUs and sequences

Bacterial and fungal community compositions were surveyed using respectively the Bact02 and Fung02 primer pairs. This files contain different type of samples for two consecutive years: letter 'A' corresponds to aerosols sampled in summer 2017, while 'P' corresponds to those collected in summer 2018. 'S' indicates soil samples collected during summer 2017. Letters 'F' and 'X' corresponds to leaf samples.

P1 to P20 correspond to aerosols collected at Marseille site; P21 to P36 corresponds those collected at OPE sit; P37 to P60 indicate aerosols collected at Grenoble site. 

Letters 'FM', 'X1 to X3' correspond to leaf samples collected at Marseille site; Letters 'FG' correspond to leaf samples collected at Grenoble site.