Simplified, Portable and Cost‐Efficient Airborne eDNA Metabarcoding to Expand Tropical Biodiversity Assessments

ABSTRACT Aquatic environmental DNA (eDNA) analysis has been widely established as a sensitive and non‐invasive species detection tool for global biodiversity monitoring. In contrast, the uptake of airborne eDNA has been constrained by the absence of robust, high‐throughput samplers suited to humid tropical settings. We present a simplified, portable, and cost‐efficient active air sampler that injects air into a liquid collection medium, shifting airborne eDNA from stationary, resource‐heavy set‐ups to field‐deployable, scalable workflows. Using a greenhouse vertebrate mock community to test the sensitivity of our approach, airborne eDNA sampling recovered most taxa present, with high detection rates for birds, mammals, and reptiles. An optimized collection buffer increased sequencing yield by about one fourth over sterile water. To subsequently assess its application in biodiversity research and conservation science, we tested its functionality in the Chocó‐Andean montane forests of northern South America, using a tree‐of‐life metabarcoding approach as part of ongoing biodiversity surveys to inform the establishment of a protected area network. While aquatic eDNA detected hundreds of vertebrates and thousands of arthropods and embryophytes, airborne eDNA recovered slightly lower OTU richness. Airborne sampling was particularly effective for mammals, whereas aquatic sampling recovered more actinopterid, amphibian, and avian OTUs. Overlap in species detection between methods was low, highlighting the complementarity of airborne and aquatic eDNA‐based species assessments. By integrating accessibility, portability, and scalability, our approach broadens the applicability of airborne eDNA, where combining airborne and aquatic eDNA metabarcoding can rapidly deliver broad‐scale biodiversity data to support conservation planning in megadiverse yet resource‐limited regions.