Groundwater environmental DNA metabarcoding reveals hidden diversity and reflects land‐use and geology

Abstract

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Integrating citizen science and environmental DNA metabarcoding to study biodiversity of groundwater amphipods in Switzerland

“…Specifically, it was unclear if the scarcity of organisms collected (with often only one to very few individuals sampled despite high sampling efforts) was an indication of the actual low abundances of macro-invertebrates or if the sampling method was missing out local occurrences. Moreover, the citizen science approach does not allow the study of microorganisms, the main component of groundwater communities 27 .…”

“…One promising approach to the study of groundwater organisms is the use of environmental DNA (eDNA), where organisms’ occurrence is derived through the presence of their DNA in water or soil samples 19 – 21 . Several studies have already investigated the potential of eDNA for groundwater 22 , either by using species-specific techniques to detect one or a few organisms (e.g., 23 , 24 ), or by applying a metabarcoding approach to get a description of whole communities (e.g., 25 – 27 ). The application of a molecular method is particularly adapted for studying the variety of groundwater cryptic species.…”

“…Moreover, using water as a sampling medium is ideal to overcome the accessibility issue, as water can be pumped or captured directly where it naturally flows out of the ground. Several limitations, however, can hamper the use of eDNA in groundwater, such as the lack of reference sequences in public databases for taxonomic assignments in metabarcoding approaches 25 , 27 , or the lack of suitable primers for groundwater organisms 22 . Moreover, eDNA does not provide phenotypic information (e.g., sex, life-stage), and does not allow the description of new species, which generally depends on the availability of actual specimens for morphological description and designing a type specimen.…”

Groundwater is a hidden global keystone ecosystem

“…(2020)) to assess diversity of, and map the distributions of, species (Takahashi et al., 2023). First applications of eDNA to groundwater systems have been promising, recovering vast biodiversity hitherto mostly undocumented (Alther et al., 2021; Couton, Hürlemann, et al., 2023; Couton, Studer, et al., 2023; Saccò, Guzik, et al., 2022; van der Heyde et al., 2023). For selected taxa such as subterranean salamanders and cavefish, bioacoustics, the study of animal sounds, can be used to not only detect species, but also inform on their welfare and behaviour (Hyacinthe et al., 2019; Mcloughlin et al., 2019).…”

Effective conservation of subterranean‐roosting bats

“…Threats to subterranean ecosystems are escalating and affecting species and populations at different scales Mammola et al, 2022;Wynne et al, 2021). Globally, climate change is altering microclimatic conditions in subterranean environments (Mammola, Piano, et al, 2019;, whereas broad-scale habitat change at the surface, including urbanization and deforestation, affects the quality of habitats underneath (Couton et al, 2023;Whitten, 2009). At regional and local scales, factors such as diseases (e.g., white-nose syndrome [WNS]) (Hoyt et al, 2021), overexploitation (e.g., tourism, guano harvesting, hunting for bushmeat and trade), and direct habitat destruction and alteration (e.g., mining) (Chaber et al, 2021;Ferreira et al, 2022;Frick et al, 2020;Furey & Racey, 2016;Piano et al, 2022) all can result in local population declines of subterranean biota, including subterranean-roosting bats.…”