Airborne Bacterial and Eukaryotic Community Structure across the United Kingdom Revealed by High-Throughput Sequencing

Abstract

Primary biological aerosols often include allergenic and pathogenic microorganisms posing potential risks to human health. Moreover, there are airborne plant and animal pathogens that may have ecological and economic impact. In this study, we used high-throughput sequencing techniques (Illumina, MiSeq) targeting the 16S rRNA genes of bacteria and the 18S rRNA genes of eukaryotes, to characterize airborne primary biological aerosols. We used a filtration system on the UK Facility for Airborne Atmospheric Measurements (FAAM) research aircraft to sample a range of primary biological aerosols across southern England overflying surface measurement sites from Chilbolton to Weybourne. We identified 30 to 60 bacterial operational taxonomic units (OTUs) and 108 to 224 eukaryotic OTUs per sample. Moreover, 16S rRNA gene sequencing identified significant numbers of genera that have not been found in atmospheric samples previously or only been described in limited number of atmospheric field studies, which are rather old or published in local journals. This includes the genera Gordonia, Lautropia, and Psychroglaciecola. Some of the bacterial genera found in this study include potential human pathogens, for example, Gordonia, Sphingomonas, Chryseobacterium, Morganella, Fusobacterium, and Streptococcus. 18S rRNA gene sequencing showed Cladosporium to be the major genus in all of the samples, which is a well-known allergen and often found in the atmosphere. There were also genetic signatures of potentially allergenic taxa; for example, Pleosporales, Phoma, and Brassicales. Although there was no significant clustering of bacterial and eukaryotic communities depending on the sampling location, we found meteorological factors explaining significant variations in the community composition. The findings in this study support the application of DNA-based sequencing technologies for atmospheric science studies in combination with complementary spectroscopic and microscopic techniques for improved identification of primary biological aerosols.

Seasonal Variability of the Airborne Eukaryotic Community Structure at a Coastal Site of the Central Mediterranean

“…Gusareva et al [ 1 ] also found that the plant-associated reads in the tropical air ecosystem collapsed at the level of Viridiplantae, according to 18S rRNA gene sequencing, but in this case the Fungi RA was on average more than 30 times greater than the mean Viridiplantae RA. Song et al [ 14 ] also applied 18S rRNA gene sequencing to PM samples collected across the United Kingdom, reporting that Fungi and Plantae (Phragmoplastophyta phylum) contributed on average 48.3% and 37.4%, respectively. Findings from our research, which are partially contrasting with those from the above-cited studies, may be ascribed to the strong dependence of the eukaryotic kingdom emission sources on the geographical characteristics of the monitoring region/country, and its corresponding atmospheric factors.…”

“…The phylum Microsporidia is a large group of eukaryotic obligate intracellular parasites that can only complete their life cycle within an infected eukaryotic host cell [ 26 ]. Ascomycota and Basidiomycota are the two largest fungal phyla, widespread in many environments, including the atmosphere [ 14 ], and were further analysed in this study since they were the most abundant and pervasive ones in the collected PM10 samples. The predominance of Ascomycota in airborne particles, as compared to Basidiomycota Fungi, was reported in many studies performed worldwide [ 16 , 25 , 27 ].…”

“…Abd Aziz et al [ 13 ] applied 16S rRNA gene sequencing to investigate the bacterial and fungal communities associated with PM2.5 mass concentrations both below and above the Korean air quality standard (36 μg m −3 ). Song et al [ 14 ] used high-throughput sequencing techniques, targeting the 16S rRNA of bacteria and the 18S rRNA genes of eukaryotes, so as to characterize airborne microorganisms across the United Kingdom and provide a review on airborne microbes that commonly originate from soil and water through liquid–air and soil–air interfaces. Furthermore, atmospheric factors regulating the airborne microbiome communities at the local and global levels can serve as microbial indicators of specific bioaerosol sources and seasonality, and need to be demonstrated in different environments.…”

Towards a UK Airborne Bioaerosol Climatology: Real-Time Monitoring Strategies for High Time Resolution Bioaerosol Classification and Quantification

“…The BIOARC project (Towards a UK Airborne Bioaerosol Climatology) aimed to evaluate the airborne concentrations of BioPM in the UK via targeted aircraft and groundbased sampling; early emerging results from the aircraft campaign were presented by Song et al [18] who demonstrated that Cladosporium was a major component in the boundary layer via PCR analysis. In this study, we present an overview and synthesis of the UKbased ground site UV-LIF bioaerosol spectrometer datasets collected during BIOARC.…”

“…Primary ice formation at temperatures warmer than −38 • C requires the presence of a catalyst ice nuclei (IN) particle via heterogeneous processes [14,15], where certain species of BioPM have been identified as potent IN in the critical −15 to 0 • C warm regime owing to the presence of ice nucleating proteins. Fungi such as Fusarium have displayed ice activity as warm as −3.5 • C [16], and such fungi have been observed in the upper atmosphere and free tropospheric cloud water samples [17][18][19]. Significantly, only small quantities (~0.01 L −1 ) of such warm temperature IN are needed to induce rapid mixed-phase cloud glaciation via secondary ice processes, resulting in reduced cloud lifetime and reflectivity, ultimately impacting the radiation budget [20].…”