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

Abstract

Stygofauna are aquatic fauna that have evolved to live underground. The impacts of anthropogenic climate change, extraction and pollution on groundwater pose major threats to groundwater health, prompting the need for efficient and reliable means to detect and monitor stygofaunal communities. Conventional survey techniques for these species rely on morphological identification and can be biased, labour‐intensive and often indeterminate to lower taxonomic levels. By contrast, environmental DNA (eDNA)‐based methods have the potential to dramatically improve on existing stygofaunal survey methods in a large range of habitats and for all life stages, reducing the need for the destructive manual collection of often critically endangered species or for specialized taxonomic expertise. We compared eDNA and haul‐net samples collected in 2020 and 2021 from 19 groundwater bores and a cave on Barrow Island, northwest Western Australia, and assessed how sampling factors influenced the quality of eDNA detection of stygofauna. The two detection methods were complementary; eDNA metabarcoding was able to detect soft‐bodied taxa and fish often missed by nets, but only detected seven of the nine stygofaunal crustacean orders identified from haul‐net specimens. Our results also indicated that eDNA metabarcoding could detect 54%–100% of stygofauna from shallow‐water samples and 82%–90% from sediment samples. However, there was significant variation in stygofaunal diversity between sample years and sampling types. The findings of this study demonstrate that haul‐net sampling has a tendency to underestimate stygofaunal diversity and that eDNA metabarcoding of groundwater can substantially improve the efficiency of stygofaunal surveys.

Rapid detection of subterranean fauna from passive sampling of groundwater eDNA

“…However, this also introduces additional contamination risks from the equipment used for the nets. A previous study using actively filtered water samples found there was little difference in subterranean faunal richness between eDNA samples collected before and after net hauling (van der Heyde et al., 2023), but it is not confirmed that this would be the case for passive eDNA samples. Ideally, passive eDNA samplers could be deployed and collected at each bore for a few hours prior to net haul surveys being conducted.…”

“…van der Heyde et al, 2023), but it is not confirmed that this would be the case for passive eDNA samples. Ideally, passive eDNA samplersF I G U R E 3 Community composition of eukaryotes detected by eDNA metabarcoding of groundwater samples collected from Barrow Island and Bungaroo Creek.…”

“…Environmental DNA (eDNA) metabarcoding is a sensitive and widely used approach in terrestrial, marine, and aquatic biodiversity assessments with applications including, biosecurity (Kim et al., 2018), conservation (Harper et al., 2019), and cryptic taxa detection (Nester et al., 2020), with recent studies effectively using this method to assess subterranean biodiversity (Hashemzadeh Segherloo et al., 2022; van der Heyde et al., 2023; West et al., 2020). This tool uses whole and fragmented DNA shed into the environment, though scales, skin cells, saliva, feces, mucous, or other material (reviewed by Thomsen & Willerslev, 2015), which can then be extracted from a substrate (e.g.…”

“…Environmental DNA (eDNA) metabarcoding is a sensitive and widely used approach in terrestrial, marine, and aquatic biodiversity assessments with applications including, biosecurity (Kim et al, 2018), conservation (Harper et al, 2019), and cryptic taxa detection (Nester et al, 2020), with recent studies effectively using this method to assess subterranean biodiversity (Hashemzadeh Segherloo et al, 2022;van der Heyde et al, 2023;West et al, 2020).…”

“…Niches (i.e. stygofaunal, troglofaunal, non-subterranean taxon groups) were assigned to all metazoan taxa identified from OTU's aftervan der Heyde et al (2023). This allowed us to parse stygofaunal and troglofaunal taxa from nonsubterranean taxa.…”