Airborne Plant eDNA Reflects Local Biodiversity: A Multi-Method Assessment in a Botanical Garden

Airborne environmental DNA (eDNA) is emerging as a powerful tool for non-invasive assessment of terrestrial biodiversity. We evaluated the effectiveness of three analytical pipelines for characterizing plant diversity in a botanical greenhouse, with a particular focus on how particle size and sampling height influence detection. Air was sampled for up to four days using quartz filters, a 14-stage impactor, and a vertical filter stack. To assess methodological variability and identify optimal approach, three analytical pipelines were applied: (A) Illumina MiSeq amplicon sequencing with a QIIME-based workflow, and (B) Illumina NextSeq and (C) MinION shotgun sequencing processed with Kraken2.