Airborne environmental DNA for terrestrial vertebrate community monitoring

Abstract

Assessing and studying the distribution, ecology, diversity and movements of species is key in understanding environmental and anthropogenic effects on natural ecosystems. Although environmental DNA is rapidly becoming the tool of choice to assess biodiversity there are few eDNA sample types that effectively capture terrestrial vertebrate diversity and those that do can be laborious to collect, require special permits and contain PCR inhibitory substances, which can lead to detection failure. Thus there is an urgent need for novel environmental DNA approaches for efficient and cost-effective large-scale routine monitoring of terrestrial vertebrate diversity. Here we show that DNA metabarcoding of airborne environmental DNA filtered from air can be used to detect a wide range of local vertebrate taxa. We filtered air at three localities in Copenhagen Zoo, detecting mammal, bird, amphibian and reptile species present in the zoo or its immediate surroundings. Our study demonstrates that airDNA has the capacity to complement and extend existing terrestrial vertebrate monitoring methods and could form the cornerstone of programs to assess and monitor terrestrial communities, for example in future global next generation biomonitoring frameworks.

Toward quantitative metabarcoding

“…Over the past decade, rapid technological advances in the collection and analysis of trace genetic material from sampled environmental media (water (Ficetola et al 2008, Thomsen et al 2012), soil (Andersen et al 2012), feces (Pompanon et al 2012), or even air (Lynggaard et al 2022); hereafter environmental DNA [eDNA]) have opened new frontiers for environmental surveillance. Studies using eDNA have focused on diverse topics including monitoring biodiversity (Creer et al 2016), managing invasive species (Jerde et al 2013), characterizing diet (Deagle et al 2013), and supporting fisheries management (Fukaya et al 2021, Shelton et al 2022), in habitats from tropical forests (Lopes et al 2017) to the deep sea (Everett and Park 2018).…”

slendr: a framework for spatio-temporal population genomic simulations on geographic landscapes

“…However, many types of genomic resources distributed across space and time are represented by fragmentary mixtures of genomes from multiple species. This includes ancient microbiomes from human remains (Rasmussen et al , 2015), sedimentary DNA from permafrost, caves, or lake and marine cores (Willerslev et al , 2003; Parducci et al , 2017; Armbrecht et al , 2019; Vernot et al , 2021), and environmental DNA from water, soil, or air samples (Taberlet et al , 2012; Stat et al , 2017; Lynggaard et al , 2022). With future developments in SLiM, a fruitful avenue for slendr could include the simulation of spatio-temporal multi-species data.…”

How can academics contribute to biodiversity science?

“…Scientists have amazing new tools at their disposal. For example, we can monitor changes in forest cover on vast scales in near‐real time (Hoekman et al, 2020), and it may be possible to survey animal populations by sampling the air for the DNA they leave behind (Lynggaard et al, 2021; Stokstad, 2021). What remains is for us to find ingenious ways to use this information and these tools to make significant advances and, most importantly, to find the will to enact the needed change.…”