For the comparative experiment of aerosol samplers (1) we collected air samples at eight locations in Switzerland using six active and two passive air sampling devices. The air samplers differed in their collection method and the amount of air captured varied by two orders of magnitudes. We successfully extracted DNA and amplified marker genes from plants, insects, vertebrates, and fungi across all sampler types. We found that DNA concentration varied significantly between different sampling methods, with higher concentration for samplers that capture larger air volumes. However, preliminary results suggest that there was no direct correlation between the volume of air sampled or DNA concentration and species richness. In contrast, longer sampling durations did result in the detection of a greater number of species, suggesting that sampling time might be more relevant than sample volume.
The high throughput analysis of the filter obtained from existing air filter stations required the development of new DNA extraction protocols. During this project, we designed and validated a high-throughput extraction protocol using magnetic beads on a liquid handler. The protocol development revealed a fundamental trade-off between extracting extra-organismal DNA from animals and intracellular DNA from organisms with hard cell walls, such as bacteria and fungi. Taking this into account, we developed a dual lysis protocol allowing the simultaneous extraction of airborne DNA for organisms across the tree of life. Using this protocol, we successfully extracted DNA from Bacteria, Fungi and Vertebrates from the filters collected by the particulate matter monitoring stations. In total, we extracted >1400 filters from a ten-year time-series. While the DNA extraction could be completed within the timespan of the project, the downstream analyses are still underway. Preliminary results from single-species assays targeting the detection of Hymenoscyphus fraxineus showed positive detection for 21 out of 23 station-years analyzed so far, showing great potential for the existing particulate matter monitoring stations to play a role bio surveillance in urban areas.
