Effects of bioturbation on environmental DNA migration through soil media

Abstract

Extracting and identifying genetic material from environmental media (i.e. water and soil) presents a unique opportunity for researchers to assess biotic diversity and ecosystem health with increased speed and decreased cost as compared to traditional methods (e.g. trapping). The heterogeneity of soil mineralogy, spatial and temporal variations however present unique challenges to sampling and interpreting results. Specifically, fate/transport of genetic material in the terrestrial environment represents a substantial data gap. Here we investigate to what degree, benthic fauna transport genetic material through soil. Using the red worm (Eisenia fetida), we investigate how natural movement through artificial soil affect the transport of genetic material. All experiments were run in Frabill® Habitat® II worm systems with approximately 5 cm depth of artificial soil. We selected an “exotic” source of DNA not expected to be present in soil, zebrafish (Danio rerio) tissue. Experiment groups contained homogenized zebrafish tissue placed in a defined location combined with a varying number of worms (10, 30 or 50 worms per experimental group). Experimental groups comprised two controls and three treatment groups (representing different worm biomass) in triplicate. A total of 210 soil samples were randomly collected over the course of 15 days to investigate the degree of genetic transfer, and the rate of detection. Positive detections were identified in 14% - 38% of samples across treatment groups, with an overall detection rate of 25%. These findings highlight two important issues when utilizing environmental DNA for biologic assessments. First, benthic fauna are capable of redistributing genetic material through a soil matrix. Second, despite a defined sample container and abundance of worm biomass, as many as 86% of the samples were negative. This has substantial implications for researchers and managers who wish to interpret environmental DNA results from terrestrial systems. Studies such as these will aid in future study protocol design and sample collection methodology.

The state, transport, and fate of aboveground terrestrial arthropod eDNA

“…These processes can elevate or reduce detection probability by either increasing the effective sampling area or diluting the eDNA beyond detection, respectively (Schultz & Lance, 2015). Transportation of eDNA deposited within soil is not as well understood beyond recognition that eDNA is unlikely to move laterally through the soil substrate (Taberlet et al, 2018) (though see Prosser & Hedgpeth, 2018). Given water appears to be a dominant transport mechanism for eDNA, we posit that arthropod eDNA deposited on vegetative surfaces will be predominately transported by weather events like rainfall, transferring it to the soil where it may percolate through the soil column for unknown distances (Figure 1).…”

Predicting global numbers of teleomorphic ascomycetes

“…The fungal diversity estimate increases with the advent of more uncultured fungi and fungi from environmental samples. Environmental DNA (meta-DNA) can be genetic material acquired directly from environmental samples, such as soil, sediment, water and others devoid of any clear signs of biological material is an effective, safe and quick standardized sampling method (Prosser and Hedgpeth 2018). The development of advanced molecular techniques such as high-throughput sequencing has greatly contributed in identification of undescribed species (Barnes and Turner 2015).…”

Monitoring schistosomiasis and sanitation interventions—The potential of environmental DNA

“…For both eDNA and eRNA, the environmental processes that will affect their movement and decay within the environment should also be noted. Studies into the spatial and temporal fate of eDNA in aquatic environments (Harrison, Sunday, & Rogers, 2019) and soil (Prosser & Hedgpeth, 2018) in relation to biodiversity have been carried out but there are still knowledge gaps of the fate of eDNA in tropical ecosystems (reviewed in the context of fecal indicator bacteria (Rochelle-Newall, Nguyen, Le, Sengtaheuanghoung, & Ribolzi, 2015).…”