Taking eDNA underground: factors affecting eDNA detection of subterranean fauna in groundwater

Dr Mieke Van Der Heyde¹, Nicole White¹, Paul  Nevill¹, Andrew Austin^2,3, Michelle Guzik^2,3

¹Trace and Environmental DNA Laboratory, Curtin University, Bentley, Australia, ²South Australia Museum, Adelaide, Australia, ³Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, The University of Adelaide, Adelaide, Australia

Abstract:

The subterranean fauna comprises ancient taxon groups (>40 million years), which are predominantly short-range endemics that are found in aquatic (stygofauna) or terrestrial (troglofauna) underground habitats. Because of their small size and cryptic appearance, detecting and distinguishing subterranean fauna by morphology alone is extremely difficult. Despite considerable research in the last decade, much of the subterranean fauna of Australia remains poorly known.  Environmental DNA (eDNA)-based methods have real potential to dramatically improve on existing species detection approaches because they can be applied to detect subterranean fauna in a large range of habitats and at all life stages of species, without requiring specialized taxonomic expertise. We have investigated factors that may influence eDNA detection of subterranean fauna for biodiversity surveys and the possible methodical approaches to examining this: efficient and effective monitoring including depth of sampling, sample type (water or sediment), and physicochemical properties of the water. Samples were collected from 17 groundwater wells on an island northwest of WA, and subterranean fauna were collected and identified in the field to provide a morphological comparison. Our results indicate greater subterranean fauna diversity could be detected from shallow water samples with higher dissolved oxygen content, compared to deeper samples or sediment. Additionally, the comparison between morphological and eDNA based assessment revealed greater diversity using DNA; however, assays were biased against certain taxa. Overall, eDNA methods can greatly improve survey of subterranean fauna, but further development of sampling protocols and eDNA assays is required.

Biography:

Mieke is currently a Research Associate with the Trace and Environmental DNA (TrEnD) Laboratory. Her research focus is developing and applying eDNA methods to monitor terrestrial and subterrestrial ecosystems. Mieke completed her PhD in 2020 with the ARC Centre for Mine Site Restoration (CMSR) and the TrEnD Labs. Her research focussed on the application of eDNA surveys to monitor soil microbes, vertebrates, invertebrates, and plants during mine site restoration. In late 2020, Mieke started her post-doc position at Curtin studying underground communities living in the groundwater (stygofauna).