Abstract
Effective biodiversity survey methods are crucial to monitor ecosystems threatened by climatic fluctuations and anthropogenic pressures. Here we advance methods for collecting a novel source of biodiversity data – airborne environmental DNA (eDNA), and investigate whether it yields habitat- and season-specific signatures of terrestrial vertebrate communities. Using custom-made, portable, and low-budget samplers, we sampled airborne eDNA in three protected nature areas across Denmark spanning different nature types and seasons. We show that coarse grade air filters, larger filter area, increased airflow rate, and dry storage of filters at -20 °C yield detections of higher numbers of vertebrate taxa with more consistent detections of communities across samples. Further, we find that detected vertebrate communities are characteristic of the sampled nature types and seasons. Collectively, these refinements enable effective monitoring of terrestrial vertebrate biodiversity using portable and low-budget air samplers.
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First national survey of terrestrial biodiversity using airborne eDNA
Airborne eDNA captures three decades of ecosystem biodiversity
Shotgun sequencing of airborne eDNA achieves rapid assessment of whole biomes, population genetics and genomic variation
Data availability
Demultiplexed sequences are submitted to Short Read Archive (SRA) in the GenBank (Experiment 1: 16Smam – BioProject ID = PRJNA1437738, BirT – BioProject ID = PRJNA1437538; Experiment 2: 16Smam – BioProject ID = PRJNA1437745, BirT – BioProject ID = PRJNA1437753; Experiment 3: 16Smam – BioProject IDs = PRJNA1437761 (first three replicates) and PRJNA1437768 (last three replicates), BirT – BioProject IDs = PRJNA1437771 (first three replicates) and PRJNA1437774 (last three replicates). Raw sequences (multiplexed samples) and bioinformatic pipeline (including nucleotide tags, primer sequences and a document for connecting primers and tags to sample PCR replicates) are submitted to Zeneodo data repository: 10.5281/zenodo.1564004351. Curated OTU tables are submitted to Global Biodiversity Information Facility’s (GBIF) online metabarcoding repository: Experiment 1 (BirT: https://doi.org/10.15468/g4x26w, 16Smam: https://doi.org/10.15468/tgj6ua), Experiment 2 (BirT: https://doi.org/10.15468/tu8sg4, 16Smam: https://doi.org/10.15468/2j5228) and Experiment 3 (BirT: https://doi.org/10.15468/wmqecd, 16Smam: https://doi.org/10.15468/ghtjpd).
Code availability
Data analysis code is available in GitHub: https://github.com/Kbodawatta/Airborne_eDNA_Methods_Paper.
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Acknowledgements
This work was funded by the Carlsberg Foundation Semper Ardens: Accelerate grant (CF21-0411) awarded to Kristine Bohmann. C.L. was supported by a research grant from VILLUM FONDEN (grant no. VIL41390). We thank The Danish Nature Agency for permission to conduct fieldwork at Kalvebod Fælled and Aage V. Jensen Naturfonden for permission to conduct fieldwork in Æbelø and Lille Vildmose. We thank Sanne Frederiksen, Thomas Holst Christensen, Jacob Heilmann-Clausen, and Timothy Cutajar for facilitating our fieldwork. Further, we thank Binia De Cahsan Westbury for habitat illustrations and Tina Blumensaadt Brand, Pernille Vibeke Selmer Olsen, Lasse Vinner, and Julie Bitz-Thorsen for assistance and discussions regarding lab work and sequencing.
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K.H.B., A.M.M., C.L., and K.B. developed the idea. K.H.B. and A.M.M. carried out the field sampling. K.H.B. conducted laboratory analyses. K.H.B., A.M.M., J.A.R., M.S.J., C.L., and K.B. developed the methodology. K.H.B. conducted data processing and statistical analyses. L.H. and T.F. consulted with bioinformatic and statistical analyses. K.H.B., C.L., and K.B. wrote the initial draft. All authors contributed to editing the manuscript.
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The authors declare the following competing interests: M.S.J. is Chief Science Officer at Rensair, a company working with indoor air quality, air filters and sensors, in addition to being Chief Science Officer at Devlabs, a company making environmental sensors. There are no commercial connections between these companies and the research described in this publication.
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Communications Biology thanks Fabian Roger, Anish Kirtane and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Primary Handling Editor: Michele Repetto. A peer review file is available.
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Bodawatta, K.H., Madsen, A.l.M., Holman, L.E. et al. Advancing airborne eDNA sampling methods for monitoring diverse terrestrial vertebrate communities.
Commun Biol (2026). https://doi.org/10.1038/s42003-026-09950-y
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DOI: https://doi.org/10.1038/s42003-026-09950-y
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