A novel passive airborne eDNA approach for scalable terrestrial biodiversity monitoring
Data files
Mar 30, 2026 version files 625.49 MB
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Nutshell_ALLDATA.xlsx
111.02 KB
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Raw_data_12S.zip
244.73 MB
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Raw_data_16S.zip
380.64 MB
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README.md
3.72 KB
Abstract
Terrestrial biodiversity’s rapid decline demands expansion of high-resolution biomonitoring to support science-based policy. Environmental DNA (eDNA) analysis has proven effective in aquatic systems but remains underexplored for terrestrial habitats, partly due to point-source sampling bias and difficulty in upscaling. Air has emerged as a promising substrate, yet most studies use active samplers which tend to be expensive, bulky, and require power, potentially hindering broad deployment. We present a newly developed, inexpensive, reusable, and easy-to-use passive approach (Nutshell eDNA sampler) to capture eDNA suspended in air across time (6-96 hours) within Rotterdam Zoo, the Netherlands. Its performance was compared to two commonly-used active airborne eDNA samplers for vertebrate diversity detection. In total, 88 species were detected, including 24 zoo residents. The Nutshell eDNA sampler was the most effective at detecting zoo residents, surpassing active samplers in species richness within 48 hours and continuing to accumulate new species beyond 96 hours, including detections of both patchy and singleton signals. It also detected the furthest species signal (515m). Zoo airborne eDNA further demonstrated a positive correlation to species total biomass, suggesting larger vertebrates or populations release proportionately more DNA into the air. Our findings indicate that for long, unsupervised biomonitoring, passive airborne eDNA sampling presents a promising approach for assessing vertebrate communities and putatively reduces detection noise in stochastic air eDNA signals due to its signal integration. While deeper investigations into airborne eDNA sampling strategies are needed, passive methods can offer a much needed logistically flexible, low-maintenance approach compared to short-burst collection strategies employed by many active samplers.
All sequences are in FastQ files. The first number of each file corresponds to sampling week (1,2,3), the second number corresponds to site (1,2,3,4,5,6; with site 6 being the indoor exhibit building and sites 1-5 being the outdoor sampling locations, lat/long info found within Jager et al. 2026 manuscript), and the last number corresponds to deployment time of the passive Nutshell eDNA sampler (6, 24, 48, 72, 96 hours). When noted, the names of the active samplers correspond to Coriolis Micro (COR), Pollensniffer (PS), otherwise each sample corresponds to the Nutshell eDNA sampler. Postive Controls (POS; harbor porpoise, Phocoena phocoena) and Negative Controls (NEG) are also included.
Two folders are available, Raw_data_12S.zip for our 12S marker (12S05 forward /12S05 reverse), and Raw_data_16S.zip for our 16S marker (16Smam1/16Smam2). Libraries were sequenced at Macrogen Europe (Netherlands) on an Illumina MiSeq (v3 chemistry, 150 bp paired-end), targeting 50,000 reads per sample.
Data available are in files Raw Sequences_ 12S and Raw Sequences_16S. Metadata files (including taxanomic ID) can be found in the affiliated excel file (Nutshell_ALLDATA).
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README: “Nutshell_ALLDATA.xlsx”
7 sheets in total
Metadata – this sheet contains information pertaining to Sample (Week-location-deploymenthour-marker); Technique (Nuthsell eDNA,Coriolis Micro, Pollensniffer); Week (1,2,3); Location (1,2,3,4,5,6; Location 6 = indoor & 1-5 = outdoor); Timpoint (deployment duration; 6,24,48,72,96 hours); Average Temperature (Celcius); Total Precipitation (mm); Average wind speed (m/s); Average wind speed (km/h)
Read counts per ASV per sample – this sheet contains information on the DNA sequence identifications, labeled “ASV_ID” with a corresponding number (column a), followed by which sample (columns B-DW) contained those ASV’s. Each column (B-DW) name corresponds to Week-Site-hour-barcode marker). The barcode marker was either 12S (12S05 forward /12S05 reverse) or 16S(16Smam1/16Smam2) for which all raw sequences are located in the affiliated folders. Numbers within cells are the number of individual sequence reads.
Taxonomy – ASV-ID (corresponds to ASV number if “Read counts per ASV per sample”), followed by affiliated taxonomic identification (LCA – least common ancestor; Kingdom, Phylum, Class, Order, Family, Genus, Species).
Read counts per bodymass – Each row described the identified zoo species, number of sequencing reads (read counts), number of individuals of that species housed or displayed at the Rotterdam Zoo, the average body mass per individual and the total mass of the entire population of that species at the zoo during the time of sampling. Total mass has been log transformed and each source for average body mass is indicated through a URL.
Accuracy File – per air eDNA technique (Nutshell, pollensniffer, Coriolis micro), outdoor location (1-5), this sheet gives the proportion of species detected within the average range (distance) per technique. Average distance per technique can be found in Jager et al. 2026.
Dist. of detecteions per sample – information on air eDNA sampler (technique), week (1,2,3), Location (1-6), Timepoint (sampling duration in hours), and the individual zoo species ID’s. Numbers within cells represent the distance (meters) from enclosure centroid (based on google earth) to sampler.
Distance of detections (m) - this describes the distance (m) to each sampler (location; 1-6) as an average across weeks, based on each zoo species.