The ecology of aboveground terrestrial eDNA: Its state, transport, and fate on aboveground surfaces

Abstract

Environmental DNA (eDNA) analysis has become a valuable tool for detecting aquatic and terrestrial species for monitoring efforts and site biodiversity assessments. However, if aboveground terrestrial eDNA surveys are to be widely adopted, it is necessary to first understand how terrestrial conditions affect the state, transport, and ultimate fate (or 'ecology') of terrestrially deposited eDNA. Many of the processes that affect the state, transport, and fate of eDNA in aquatic environments may not be applicable in aboveground systems, warranting an exploration of the terrestrial processes that likely do affect eDNA. Here we explore the ecology of aboveground terrestrial eDNA through a series of experiments evaluating the optimal filter pore size for intracellular eDNA collection, how eDNA is affected by rain events, and its degradation rate under different solar radiation conditions. We found that the captured concentration of intracellular eDNA was not significantly affected by an increase in filter pore size, suggesting there is a wide range of viable pore size options for targeting intracellular eDNA. We also found extracellular eDNA degrades more rapidly than intracellular forms when exposed to solar radiation, indicating the latter is a more viable target for collection. Finally, we identified that rainfall or mist will remove most terrestrial eDNA present on vegetation substrate. This study provides researchers and managers key insights into successfully designing and carrying out terrestrial eDNA surveys that maximize detection probability and minimize false positive results.

Terrestrial eDNA survey outperforms conventional approach for detecting an invasive pest insect within an agricultural ecosystem

“…Our finding that eDNA concentrations are positively related to visual counts extends knowledge of this phenomenon into a terrestrial system. It is also consistent with our expectations based on experiments using other eDNA capture methods on terrestrial surfaces (DLP, unpublished data) and based on what is known about the ecology of terrestrial eDNA (Valentin et al, 2020b). Small amounts of insect fecal matter remain detectable using eDNA for a week or more in the absence of significant rainfall (Valentin et al, 2020b).…”

“…The same advantages can also apply to eDNA sampled from terrestrial surfaces. The lanternfly assay we used can successfully detect quantities of genomic DNA as small as 0.4 femtograms (4 × 10 −7 ng; Valentin et al, 2020a), while insects moving through the environment leave a ‘trail’ of eDNA from fecal deposits that remains detectable for up to a week or more in the absence of rainfall (Valentin et al, 2020b). The spray aggregation technique we evaluated, along with other active terrestrial eDNA aggregation techniques (Valentin et al, 2018, 2020a), shares the advantage with aquatic studies of allowing the pooling of eDNA from variable amounts of substrates into fewer samples, thus increasing the potential power and reach of the tool.…”

“…While spraying, we also carefully inspected the vines visually, looking along stems and the upper and lower leaf surfaces for adult lanternflies or egg masses, and counting observed individuals within each plot. Environmental DNA from honeydew of related insects in the order Hemiptera can persist outdoors on foliage for ~4–8 d in the absence of rain, with a degradation rate of ~3%/hr (Valentin et al, 2020b). Therefore, unlike visual sampling, eDNA sampling was surveying for presence at the time of the survey and also up to a week prior.…”

Moving eDNA surveys onto land: Strategies for active eDNA aggregation to detect invasive forest insects

“…Several weeks later when we surveyed the site we found no indication of an active population via visual surveys, but we obtained positive eDNA results. Given the window of detectability for terrestrial eDNA is less than 1 week (Valentin, Kyle, Allen, Welbourne, & Lockwood, unpublished data) it is highly unlikely the L. delicatula DNA we detected came from the reported dead individual, indicating our result was attributed to live individuals present within the last week of our survey. This further demonstrates the power of eDNA surveys compared to visual ones.…”

Assessing the efficacy of eDNA metabarcoding for measuring microbial biodiversity within forest ecosystems

“…Next logical steps for the further study of the efficacy in using eDNA within throughfall as a biodiversity monitoring tool for terrestrial ecosystems ought to include the continued examination of addressing aforementioned biases and challenges 57,117 , and extending these methods to include the detection eukaryotes as well. Using field methodologies described here, or other standardized methods for sampling throughfall and stemflow 66,67,118 , one could simply modify the sample processing methods and sequencing primers.…”