Accumulation and diversity of airborne, eukaryotic environmental DNA

Abstract

Environmental DNA (eDNA) metabarcoding is increasingly being implemented as a non-invasive and efficient approach for biodiversity research and monitoring across ecosystems. However, accurate detection of species with eDNA requires robust experimental designs as eDNA analysis carries a risk of contamination at every step of the fieldwork and laboratory processes. Several studies focus on rigorous laboratory procedures and processing of sequencing data, but surprisingly, little research investigates the process of background input of DNA in the field. For example, airborne DNA from localities outside the study area could potentially contaminate eDNA samples. Here, we use an experimental setup and eDNA metabarcoding to study the diversity and accumulation of airborne eukaryotic eDNA on exposed surfaces in the field. At two different natural locations, a coastal marine site and a terrestrial grassland site, we placed open containers each filled with 0.5 liters of water, which was then sampled at eight successive time points after exposure to the surroundings. We found an accumulation of detected species richness in the samples, which reached its maximum at the end of the experiment, 24 h after exposure. This result was consistent across both sites and across two markers (COI for eukaryotes and 12S for vertebrates). While many of the detected species were contaminants commonly found in eDNA studies, we also detected several other eukaryotic taxa. Most notable were metazoan species such as birds, fish, and insects, likely originating from airborne transport of eDNA. We also found that increasing the number of PCR cycles tended to have a positive impact on richness for the unfiltered reads but a negative impact on the richness after bioinformatic filtering. Our results add to the sparse evidence that metazoan eDNA can be transported by air, which have wide implications for eDNA research and calls for increased implementation of field control samples.