Pollen, fungi, and bacteria are the main microscopic biological entities present in outdoor air, causing allergy symptoms and disease transmission and having a significant role in atmosphere dynamics. Despite their relevance, a method for monitoring simultaneously these biological particles in metropolitan environments has not yet been developed. Here, we assessed the use of the Hirst-type spore trap to characterize the global airborne biota by high-throughput DNA sequencing, selecting regions of the 16S rRNA gene and internal transcribed spacer for the taxonomic assignment. We showed that aerobiological communities are well represented by this approach. The operational taxonomic units (OTUs) of two traps working synchronically compiled Ͼ87% of the total relative abundance for bacterial diversity collected in each sampler, Ͼ89% for fungi, and Ͼ97% for pollen. We found a good correspondence between traditional characterization by microscopy and genetic identification, obtaining more-accurate taxonomic assignments and detecting a greater diversity using the latter. We also demonstrated that DNA sequencing accurately detects differences in biodiversity between samples. We concluded that high-throughput DNA sequencing applied to aerobiological samples obtained with Hirst spore traps provides reliable results and can be easily implemented for monitoring prokaryotic and eukaryotic entities present in the air of urban areas.IMPORTANCE Detection, monitoring, and characterization of the wide diversity of biological entities present in the air are difficult tasks that require time and expertise in different disciplines. We have evaluated the use of the Hirst spore trap (an instrument broadly employed in aerobiological studies) to detect and identify these organisms by DNA-based analyses. Our results showed a consistent collection of DNA and a good concordance with traditional methods for identification, suggesting that these devices can be used as a tool for continuous monitoring of the airborne biodiversity, improving taxonomic resolution and characterization together. They are also suitable for acquiring novel DNA amplicon-based information in order to gain a better understanding of the biological particles present in a scarcely known environment such as the air.
Although many microorganisms are ubiquitously present in the air, airborne microbial communities have been much less characterized than those in soil or aquatic environments. Besides its ecological importance, detection and monitoring of the wide diversity of these aerosolized microorganisms (bacteria, viruses, fungi and pollen) is relevant for understanding allergy and disease outbreaks, especially in highly populated cities. In this study, we describe the simultaneous biodiversity of bacteria, fungi and plants present in the urban atmosphere of Madrid (Spain) along different seasonal periods, using DNA sequencing. Sampling in two different locations (downtown and peri-urban) we found that changes in the composition of each community are mainly driven by environmental factors, rather than by the features of the specific sampling microenvironments. While pollen particles are dominated by a few taxa characteristic of each season, bacteria and fungi show a high diversity but stable core communities along the year. The prokaryotic core is governed by soil and leaf surface bacteria, with predominance of Actinobacteria (Frankiales and Micrococcales) and Alphaproteobacteria (Sphingomonadales, Rhodobacterales, Rhizobiales and Acetobacterales). Fungal diversity is characterized by the steady presence of members of Capnodiales and Pleosporales. Pathogenic bacterial and fungal taxa were also detected across the year. We also correlated the airborne biodiversity with environmental variables. Air temperature has a strong influence on the community composition of bacteria, while pollen and fungi seasonal variations are mainly correlated with precipitation. Our results contribute to the characterization of airborne prokaryotic and eukaryotic communities in urban areas and show the suitability of this method for biosurveillance strategies.
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