In-field monitoring of airborne biodiversity using a passive sampler

The application of molecular techniques in analysing aerobiology and airborne environmental DNA (eDNA) has expanded rapidly in recent years, offering powerful tools for indirect detection of plant, animal, and microbial taxa at landscape scale. Monitoring shifts in plant communities in response to human activity or management actions is crucial to understand their impact on biodiversity. To date, most airborne DNA studies have focused on pollen and single species detection, overlooking a variety of aerobiological sources, including plant fragments. Consequently, surveying entire plant communities through DNA metabarcoding is increasingly utilised, as it has the potential to enhance detection accuracy and broaden ecological insights at a landscape scale.

Here, we present how a passive air sampler and DNA metabarcoding can be employed to characterise plant biodiversity by capturing aerobiological material. Samplers were deployed across woodland and grassland habitats, with weekly collections used to characterise local plant community composition and quantify temporal dynamics in species detection. Aerobiological material collected by the samplers were analysed using plant-targeted DNA markers and sequenced on the Oxford Nanopore Technologies MinION platform. To evaluate methodological robustness, a sampler was positioned adjacent to a standard pollen trap, enabling comparison of taxa recovered by molecular and morphological methods.

Temporal and spatial patterns revealed through traditional pollen microscopy were closely aligned with those obtained via our molecular workflow, with the DNA based method providing finer taxonomic resolution. Although three days of deployment yielded sufficient cellular material for aerobiological analysis, we recommend a minimum of six days to reliably capture full community composition. Overall, our results demonstrate that aerobiological DNA metabarcoding is a scalable and sensitive approach for characterising plant communities and provides a powerful compliment to existing biodiversity and pollen monitoring programmes.

Integrating environmental genomics with established, aerobiological surveillance methods offer substantial advantages, including the detection of non-pollen plant material and the early recognition of non-native or potentially invasive species. We see considerable potential in combining environmental genomics with existing airborne monitoring approaches. The portability of the MinION device enables metabarcoding directly at the point of sampling, reducing transport delays and minimizing sample degradation, and is especially valuable in biodiversity-rich but under-resourced areas, where timely aerobiological data can guide conservation decisions and support early detection of invasive species.