Validation of the Hirst-Type Spore Trap for Simultaneous Monitoring of Prokaryotic and Eukaryotic Biodiversities in Urban Air Samples by Next-Generation Sequencing

• Published in: Applied and environmental microbiology 2017-07, Vol.83 (13)
• Main Authors: Núñez, Andrés, Amo de Paz, Guillermo, Ferencova, Zuzana, Rastrojo, Alberto, Guantes, Raúl, García, Ana M, Alcamí, Antonio, Gutiérrez-Bustillo, A Montserrat, Moreno, Diego A
• Format: Article
• Language: English
• Subjects: Air - analysis; Air Microbiology; Allergies; Bacteria; Bacteria - classification; Bacteria - genetics; Bacteria - isolation & purification; Biodiversity; Biomonitoring; Biota; Cities; Deoxyribonucleic acid; Disease transmission; DNA; DNA sequencing; Eukaryota - classification; Eukaryota - genetics; Eukaryota - isolation & purification; Eukaryotes; Fungi; Fungi - classification; Fungi - genetics; Fungi - isolation & purification; High-Throughput Nucleotide Sequencing - methods; Microbial Ecology; Microscopy; Phylogeny; Pollen; Pollen - genetics; Prokaryotes; Relative abundance; Ribonucleic acid; RNA; rRNA 16S; Seasons; Spacer; Spore traps; Spores, Fungal - classification; Spores, Fungal - genetics; Spores, Fungal - isolation & purification; Urban areas; Validation studies
• ISSN: 0099-2240; 1098-5336
• DOI: 10.1128/aem.00472-17

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 >87% of the total relative abundance for bacterial diversity collected in each sampler, >89% for fungi, and >97% 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. 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.