Periodic Reporting for period 1 - AIRDNA (Biodiversity is in the air – Biodiversity monitoring through the metabarcoding of air-borne eDNA)
Période du rapport: 2021-09-01 au 2023-08-31
Biodiversity is in decline due to human land use, exploitation, and climate change. To be able to counteract this alarming trend it is paramount to closely follow the state and trends of biodiversity at global scales. Because this is impossible with traditional monitoring, the last decade has seen a strong push for solutions to solve this challenge. In aquatic ecosystems the monitoring of species from the DNA they leave behind, so called ‘environmental DNA’ (eDNA) has emerged as one of the most powerful tools at our disposal. In terrestrial ecosystems, however, the power of eDNA for monitoring has so far been hampered by the local scale of the samples. The aim of this action was to advance airborne eDNA as a scalable tool for terrestrial biodiversity monitoring for organisms across the tree of life. This comprised (1) a comprehensive evaluation and benchmarking of aerosol sampling methods, (2) the exploration what biodiversity information was captured by filters of an established particulate matter monitoring networks used for public health and (3) an Investigation if the filter network could be used for early detection of an invasive forest pathogen Hymenoscyphus fraxineus, causing ash dieback.
Through these objectives, the project sought to overcome the limitations faced by terrestrial biological monitoring and open new avenues for scalable and efficient monitoring techniques, ultimately contributing to the preservation of biodiversity and ecosystem health.
Through these objectives, the project sought to overcome the limitations faced by terrestrial biological monitoring and open new avenues for scalable and efficient monitoring techniques, ultimately contributing to the preservation of biodiversity and ecosystem health.
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.
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.
Overall, this project lays the foundation for a new, globally scalable approach for terrestrial biomonitoring, leveraging new eDNA sampling methods and existing infrastructure. The sampler comparison was unique in its large scope, enabled through extensive collaborations across research groups at ETH Zürich and WSL. It will provide crucial data to guide future research in biodiversity monitoring and bio-surveillance in the emerging field of airborne environmental DNA research. The analysis of the filters from existing particulate matter monitoring stations showed that the filters captured DNA across the tree of life (DNA from Fungi, Bacteria and Vertebrates) and could play a valuable role for the bio surveillance and early detection of airborne pathogens. The method development which occurred as side-product of this two-year project resulted in the development of optimized, high-throughput, DNA extraction methods from large air filters for airborne eDNA from different taxonomic groups and in new PCR primers optimized for the amplification of arthropod DNA from air-samples which are significantly more specific than currently available Primers.
Taken together, the results from this action represent a significant step forward in the field of biodiversity monitoring and bio surveillance through airborne environmental DNA.
Taken together, the results from this action represent a significant step forward in the field of biodiversity monitoring and bio surveillance through airborne environmental DNA.