Airborne Bacterial Communities of PM2.5 in Beijing-Tianjin-Hebei Megalopolis, China as Revealed by Illumina MiSeq Sequencing: A Case Study

Abstract

Bacteria are ubiquitous and abundant in the atmosphere and some of them are potential pathogens known to cause diseases or allergies in humans. However, the quantities and compositions of total airborne bacterial community and their relationships with environmental factors remain poorly investigated. Here, a case study of the total airborne bacteria of PM 2.5 collected at six cities in Beijing-Tianjin-Hebei (BTH) megalopolis, China were profiled using quantitative polymerase chain reaction (qPCR) and Illumina MiSeq (PE300) sequencing. qPCR results showed the high abundance of total airborne bacteria of PM 2.5 in BTH, ranging from 4.82 × 10 4 ± 1.58 × 10 3 to 2.64 × 10 5 ± 9.63 × 10 4 cell m -3 air, and averaged 1.19 × 10 5 cell m -3 air. The six PM 2.5 samples were classified into three groups. Proteobacteria, Cyanobacteria, Actinobacteria and Firmicutes were the four dominant phyla of PM 2.5 . 18 common potential pathogens with extremely low percentage (3.61%) were observed, which were dominated by Enterococcus faecium and Escherichia coli. Plants and soil are probably the main sources of bacteria in PM 2.5 , as suggested by the high percentages of Chloroplast, plant-associated bacteria (e.g., Rhizobiales and Sphingomonadales) and soil-inhabiting bacteria (e.g., Burkholderiales and Pseudomonadales). Variation partitioning analysis (VPA) indicated that the atmospheric pollutants explained the most of the variation (31.90%) in community structure of PM 2.5 , followed by meteorological conditions (15.73%) and the chemical compositions of PM 2.5 (11.32%). The case study furthers our understanding of the diversity and composition of airborne bacterial communities of PM 2.5 in BTH, and also identified the main factors shaping the bacterial communities.

Fungi diversity in PM<sub>2. 5</sub> and PM<sub>1</sub> at the summit of Mt. Tai: abundance, size distribution, and seasonal variation

“…To determine the fungal biomass, we performed qPCR (Gao et al, 2017a;Yamaguchi et al, 2016;Lee et al, 2010) using a CFX96 real-time PCR detection system (Bio-Rad, Hercules, CA, USA) in 25 µL reaction mixtures containing 12.5 µL TransStart Green qPCR SuperMix, 1 µL ITS3-KYO2 (5 -GATGAAGAACGYAGYRAA-3 ), 1 µL ITS4 (5 -TCCTCCGCTTATTGATATGC-3 ), 5 µL sample DNA, and 5.5 µL double-distilled H 2 O. The amplification followed a three-step PCR for fungal ITS regions: 40 cycles of denaturation at 95 • C for 30 s, primer annealing at 52 • C for 30 s, and extension at 72 • C for 30 s. A standard curve was created using tenfold dilution series of fungal ITS region plasmids.…”

“…During 2013During , 2014During , and 2015, serious air pollution events associated with the inadequate use of clean energy in the transport, domestic, and industrial sectors affected northern China, which includes several areas with severe air pollution, namely Beijing, Tianjin, Shijiazhuang, Jinan, and Qingdao. Most researchers focus their attention on the case study of bacterial abundance and diversity (Gao et al, 2014(Gao et al, , 2017aXu, et al, 2017a;Wei et al, 2017). The various physical, chemical, and biological factors caused by the severe haze or dust episodes may cause shifts in the bacterial community structure.…”

acp-2017-204-RC1-Response to Reviewer #1

“…During 2013During , 2014During , and 2015, serious air pollution events associated with the inadequate use of clean energy in the transport, domestic, and industrial sectors affected northern China, which includes several areas with severe air pollution, namely Beijing, Tian-jin, Shijiazhuang, Jinan, and Qingdao. Most researchers focus their attention on the case study of bacterial abundance and diversity (Gao et al, 2014(Gao et al, , 2017aXu, et al, 2017a;Wei et al, 2017). The various physical, chemical, and biological factors caused by the severe haze or dust episodes may cause shifts in the bacterial community structure.…”

Variation of Bacterial and Fungal Community Structures in PM2.5 Collected during the 2014 APEC Summit Periods

“…PM 2.5 components such as organic carbon, elemental carbon, sulfates, nitrates, and geological material have been studied in different cities and regions (Xiu et al, 2015;Zhao et al, 2016;Zhan et al, 2016). However, few studies have explored the biological fraction of PM 2.5 including bacteria, fungi, pollen, viruses, spores, and cell debris (Cao et al, 2014;Li et al, 2015;Yan et al, 2016;Gao et al, 2017). The identification of bacteria and fungi in aerosol particles through culture-based methods and clone library sequencing has been documented (Stoeck et al, 2007;Fahlgren et al, 2010;Haas et al, 2013Haas et al, , 2014Tarigan et al, 2017), but these results do not realistically reflect the microbial community composition and diversity due to the limitation of cultivatable microorganisms and number of constructed clones in an aerosol sample (Amann et al, 1995;Nocker et al, 2007).…”

“…Subsequently, correlation between various factors and cultivable bacteria or fungi during haze and non-haze days in Beijing have been studied (Gao et al, 2015b;Gao et al, 2016) with increasing focus on the species composition and dynamics of bioaerosol particles (Wei et al, 2016). Recently, high-throughput sequencing technology based on the rRNA gene of microorganisms and metagenomes are being used to survey the composition and diversity of microbial communities in atmospheric particles (Nonnenmann et al, 2010;Bowers et al, 2011a;Cao et al, 2014;Gao et al, 2017). However, there is little information regarding the transformation in the biological components of the PM 2.5 in relation to different pollution levels.…”