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We collected inhalable airborne microbiota of PM2.5 in Guangzhou from March 5th to 10th, 2016, during a continuous wet weather. The mean PM2.5 concentration (95.04 μg/m3) was higher than the class II Chinese National Ambient Air Quality Standard (75 μg/m3) and the WHO guideline value (25 μg/m3). Furthermore, the highest PM2.5 concentration was obtained on March 5th, the second on March 7th, and the lowest on March 9th due to rain (Figure 1). Considering that 16s rDNA sequencing requires a high concentration of DNA extract from samples, we selected samples that were collected on March 5th and 7th for subsequent study. Although the PM2.5 concentrations of the samples collected on March 6th and 8th were higher than standard, their quality and quantity of extracted DNA did not suffice for further sequencing. The three filters collected daily were combined into one specimen, labeled Sample 1 and Sample 2. There is evidence that the PM2.5 concentration is positively correlated with the concentration of microorganisms and has no significant influence on the abundances and community of microbial[23]. The above results suggested that the PM2.5 pollution in Guangzhou was heavier and the samples we collected were significant.
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The taxonomic composition distribution (phylum, order, class, family, genus level) of each sample is shown in Figure 2. Proteobacteria, Bacteroidetes, Actinobacteria, Cyanobacteria, and Firmicutes were the most common bacterial phyla in all PM2.5 samples (each sequencing sample contained three filter membranes collected at the same time), with average relative abundances of 62.54%, 18.06%, 5.89%, 5.66%, and 4.50%, respectively (Figure 2A). Gammaproteobacteria, Betaproteobacteria, Saprospirae, Alphaproteobacteria, and Actinobacteria were the dominant bacteria classes with average relative abundances of 28.55%, 20.46%, 14.66%, 13.15%, and 5.62%, respectively (Figure 2B). In order classification level, the most abundant orders were Xanthomonadales (22.93%), Burkholderiales (20.15%), Saprospiraes (14.66%), Actinomycetales (5.55%), and Streptophyta (4.31%) (Figure 2C). At the family level, Xanthomonadaceae, Comamonadaceae, and Chitinophagaceae represented more than 55% of the total OTUs with percentages ranging from 14% to 23% (Figure 2D). From the largest to smallest, the genera were Stenotrophomonas, Chitinophaga, and Brevundimonas. However, the genus level had more than 30% unclassified genera (Figure 2E).
Figure 2. Relative abundance maps of bacterium. (A) Phylum classification level histogram, (B) Class classification level histogram, (C) Order classification level histogram, (D) Family classification level histogram, and (E) Genus classification level histogram. At the Phylum level, all species were used to draw the histogram. The species with abundance was less than 0.5% in all samples were classified into ‘others’ in other ranks.
The airborne bacteria in both samples contained both gram-positive and gram-negative bacteria. Gram-negative Stenotrophomonas (23.57%) was the most dominant genus. The Gram-positive bacteria found were Lactobacillus, Rothia, and Corynebacterium.
The detailed classifications of the genera noted in both samples are presented in Table 1. Mann-Whitney U test results showed that there was no obvious difference between both samples (P > 0.05). Overall, the dominant airborne bacteria genera that were detected in both samples were Stenotrophomonas, Chitinophaga, Brevundimonas, Sediminibacterium, Acinetobacter, Pseudomonas, and Sphingomonas (relative abundance > 1%), which accounted for more than 40% of the total airborne bacteria. In details, the dominant bacterial genera in Sample 1 were Stenotrophomonas (23.57%), Chitinophaga (13.36%), Brevundimonas (2.79%), Sediminibacterium (2.31%), Acinetobacter (1.21%), Sphingomonas (1.13%), Paracossus (1.04%), Lactobacillus (1.02%), and Pseudomonas (1.02%). For Sample 2, the dominant bacterial genera were Stenotrophomonas (21.30%), Chitinophaga (10.90%), Brevundimonas (2.47%), Sediminibacterium (1.94%), Pseudomonas (1.94%), Acinetobacter (1.72%), Janthinobacterium (1.35%), Sphingomonas (1.30%), and Chryseobacterium (1.09%). From the results, it is obvious that diverse microorganisms are present in Guangzhou PM2.5.
Table 1. Distribution of bacteria at the genera level during March in Guangzhou
Phylum Class Order Family Genus Sample 1 Sample 2 P value Proteobacteria Gammaproteobacteria Pseudomonadales Moraxellaceae Acinetobacter G− 1.21 1.72 0.70 Gammaproteobacteria Enterobacteriales Enterobacteriaceae Escherichia G− 0.14 0.71 − Gammaproteobacteria Pseudomonadales Pseudomonadaceae Pseudomonas G− 1.02 1.94 0.40 Gammaproteobacteria Xanthomonadales Xanthomonadaceae Stenotrophomonas G− 23.57 21.30 1.00 Alphaproteobacteria Rhizobiales Bradyrhizobiaceae Bradyrhizobium G− 0.77 0.64 − Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas G− 1.13 1.30 0.73 Alpha Proteobacteria Caulobacterales Caulobacteraceae Brevundimonas G− 2.79 2.47 − Alpha Proteobacteria Rhodobacterales Rhodobacteraceae Rubellimicrobium G− 0.93 0.88 0.86 Alphaproteobacteria Sphingomonadales Sphingomonadaceae Kaistobacter G− 0.70 0.70 0.89 Betaproteobacteria Burkholderiales Oxalobacteraceae Janthinobacterium G− 0.44 1.35 0.40 Bacteroidetes Flavobacteria Flavobacteriales Flavobacteriaceae Chryseobacterium G− 0.31 1.09 0.13 Sphingobacteriia Sphingobacteriales Chitinophagaceae Chitinophaga G− 13.36 10.90 − NA NA NA Sediminibacterium G− 2.31 1.94 − Actinobacteria NA Actinomycetales Corynebacteriaceae Corynebacterium G+ 0.26 0.50 1.00 Actinobacteria Actinomycetales Micrococcaceae Rothia G+ 0.34 0.65 − Deinococcus-Thermus Deinococci Deinococcales Deinococcaceae Deinococcus G− 0.62 0.81 0.97 Firmicutes Bacilli Lactobacillales Lactobacillaceae Lactobacillus G+ 1.02 0.28 0.13 Arthropoda Insecta Lepidoptera Cossidae Paracossus 1.04 0.93 0.49 Unclassified 35.69 37.39 0.45 Others (< 0.5%) 12.35 12.51 0.18 -
A bacterial phylogeny tree was used to reveal the relationships between bacteria, in order to identify the prokaryotic species and estimate their phylogenetic distance. The length of the branch represents the difference of their evolutionary distance. Thus, as species evolution distance move closer, the distance in species phylogeny tree becomes shorter. The average bootstrap values for the sample 1 and sample 2 trees were 76.50% and 78.10%, respectively. Additionally, more than 80% of the branches in each tree exhibited bootstrap values > 70%. The phylogeny tree presented 15 phyla; Acidobacteria, Acitinobacteria, Armatimonadetes, Bacteroidetes, Chlamydiae, Chloroflexi, Cyanobacteria, Firmicutes, Fusobacteria, Planctomycetes, Proteobacteria, Spirochaetes, Tenerioutes, Thermi, and Verrucomicrobia (Figure 3). The above results indicated that Guangzhou PM2.5 carries a variety of bacteria, a span multiple phylum.
doi: 10.3967/bes2020.042
Distribution of Microbiota in Fine Particulate Matter Particles in Guangzhou, China
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Abstract:
Objective High PM2.5 concentration is the main feature of increasing haze in developing states, but information on its microbial composition remains very limited. This study aimed to determine the composition of microbiota in PM2.5 in Guangzhou, a city located in the tropics in China. Methods In Guangzhou, from March 5th to 10th, 2016, PM2.5 was collected in middle volume air samplers for 23 h daily. The 16S rDNA V4 region of the PM2.5 sample extracted DNA was investigated using high-throughput sequence. Results Among the Guangzhou samples, Proteobacteria, Bacteroidetes, Firmicutes, Cyanobacteria, and Actinobacteria were the dominant microbiota accounting for more than 90% of the total microbiota, and Stenotrophomonas was the dominant gram-negative bacteria, accounting for 21.30%–23.57%. We examined the difference in bacterial distribution of PM2.5 between Beijing and Guangzhou at the genus level; Stenotrophomonas was found in both studies, but Escherichia was only detected in Guangzhou. Conclusion In conclusion, the diversity and specificity of microbial components in Guangzhou PM2.5 were studied, which may provide a basis for future pathogenicity research in the tropics. -
Key words:
- PM2.5 /
- Microbiota /
- Guangzhou /
- Diversity
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Figure 2. Relative abundance maps of bacterium. (A) Phylum classification level histogram, (B) Class classification level histogram, (C) Order classification level histogram, (D) Family classification level histogram, and (E) Genus classification level histogram. At the Phylum level, all species were used to draw the histogram. The species with abundance was less than 0.5% in all samples were classified into ‘others’ in other ranks.
Table 1. Distribution of bacteria at the genera level during March in Guangzhou
Phylum Class Order Family Genus Sample 1 Sample 2 P value Proteobacteria Gammaproteobacteria Pseudomonadales Moraxellaceae Acinetobacter G− 1.21 1.72 0.70 Gammaproteobacteria Enterobacteriales Enterobacteriaceae Escherichia G− 0.14 0.71 − Gammaproteobacteria Pseudomonadales Pseudomonadaceae Pseudomonas G− 1.02 1.94 0.40 Gammaproteobacteria Xanthomonadales Xanthomonadaceae Stenotrophomonas G− 23.57 21.30 1.00 Alphaproteobacteria Rhizobiales Bradyrhizobiaceae Bradyrhizobium G− 0.77 0.64 − Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas G− 1.13 1.30 0.73 Alpha Proteobacteria Caulobacterales Caulobacteraceae Brevundimonas G− 2.79 2.47 − Alpha Proteobacteria Rhodobacterales Rhodobacteraceae Rubellimicrobium G− 0.93 0.88 0.86 Alphaproteobacteria Sphingomonadales Sphingomonadaceae Kaistobacter G− 0.70 0.70 0.89 Betaproteobacteria Burkholderiales Oxalobacteraceae Janthinobacterium G− 0.44 1.35 0.40 Bacteroidetes Flavobacteria Flavobacteriales Flavobacteriaceae Chryseobacterium G− 0.31 1.09 0.13 Sphingobacteriia Sphingobacteriales Chitinophagaceae Chitinophaga G− 13.36 10.90 − NA NA NA Sediminibacterium G− 2.31 1.94 − Actinobacteria NA Actinomycetales Corynebacteriaceae Corynebacterium G+ 0.26 0.50 1.00 Actinobacteria Actinomycetales Micrococcaceae Rothia G+ 0.34 0.65 − Deinococcus-Thermus Deinococci Deinococcales Deinococcaceae Deinococcus G− 0.62 0.81 0.97 Firmicutes Bacilli Lactobacillales Lactobacillaceae Lactobacillus G+ 1.02 0.28 0.13 Arthropoda Insecta Lepidoptera Cossidae Paracossus 1.04 0.93 0.49 Unclassified 35.69 37.39 0.45 Others (< 0.5%) 12.35 12.51 0.18 -
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