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

Abstract

Groundwater is the physically largest freshwater ecosystem, yet one of the least explored habitats on earth, both because of accessing difficulties and the scarcity of the organisms inhabiting it. Here, we demonstrate how a two-fold approach provides complementary information on the occurrence and diversity of groundwater amphipods. Firstly, we used a citizen science approach in collaboration with municipal water providers who sampled groundwater organisms in their spring catchment boxes over multiple weeks, followed by DNA barcoding. Secondly, we collected four 10 L water samples at each site, in one sampling event, for environmental DNA (eDNA) metabarcoding. We found that citizen science was very effective in describing the distribution and abundance of groundwater amphipods. Although the single time-point of eDNA sampling did not detect as many amphipods, it allowed the assessment of the entire groundwater community, including microorganisms. By combining both methods, we found different amphipod species co-occurring with distinct sequences from the eDNA-metabarcoding dataset, representing mainly micro-eukaryotic species. We also found a distinct correlation between the diversity of amphipods and the overall biodiversity of groundwater organisms detected by eDNA at each site. We thus suggest that these approaches can be used to get a better understanding of subterranean biodiversity.

Pronounced changes of subterranean biodiversity patterns along a Late Pleistocene glaciation gradient

“…The groundwater amphipods were sorted and 2106 specimens were identified to species level using genetic barcoding (see the Supporting information for specimen list including sequences and Genbank accession numbers). We used records from Altermatt et al (2019) and identified new specimens using the laboratory protocol and taxonomic assignment method from Alther et al (2021) and Couton et al (2023), and individuals were barcoded by sequencing the Folmer fragment of the mtDNA COI gene (Folmer et al 1994). The primers LCO1490‐JJ and HCO2198‐JJ (Astrin and Stüben 2008) were used to amplify a 658 bp long fragment.…”

“…Most data were collected by drinking water providers as part of a highly structured and representative citizen science program (Alther et al 2021, Studer et al 2022, Schneider et al 2023, in which 906 sampling sites were systematically sampled, providing presence-absence data. At each sampling site (spring catchment box with unique coordinates), organisms were filtered from the raw groundwater using filter nets attached to inlet pipes and from the overflow basin using a small hand net (for the detailed sampling protocol see Alther et al 2021, Couton et al 2023. Repeated samples were collected for many sites.…”

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).…”

“…(2021), Couton, Studer, et al. (2023) and Raghavan et al. (2023) employed participatory approaches to raise awareness on aquatic subterranean fauna, in projects that also led to the discovery of new species (amphipod genus Niphargus and catfish Horaglanis populi ) and new information on the distribution and abundance of subterranean species.…”