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


Couton, Marjorie; Studer, Angela; Hürlemann, Samuel; Locher, Nadine; Knüsel, Mara; Alther, Roman; Altermatt, Florian (2023). Integrating citizen science and environmental DNA metabarcoding to study biodiversity of groundwater amphipods in Switzerland. Scientific Reports, 13(1):18097.

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.

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.

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Additional indexing

Item Type:Journal Article, refereed, original work
Communities & Collections:07 Faculty of Science > Institute of Evolutionary Biology and Environmental Studies
08 Research Priority Programs > Global Change and Biodiversity
Dewey Decimal Classification:570 Life sciences; biology
590 Animals (Zoology)
Scopus Subject Areas:Health Sciences > Multidisciplinary
Uncontrolled Keywords:Multidisciplinary
Language:English
Date:23 October 2023
Deposited On:12 Jan 2024 11:23
Last Modified:30 Jun 2024 01:36
Publisher:Nature Publishing Group
ISSN:2045-2322
OA Status:Gold
Free access at:Publisher DOI. An embargo period may apply.
Publisher DOI:https://doi.org/10.1038/s41598-023-44908-8
PubMed ID:37872363
Project Information:
  • : FunderSchweizer Nationalfonds
  • : Grant ID31003A_173074
  • : Project TitleRiverDNA: uncovering fundamental biodiversity in riverine systems using environmental DNA
  • : FunderUniversität Zürich
  • : Grant IDURPP-Global Change & Biodiversity
  • : Project TitleToward a better integration of evolution and community ecology Team Members
  • : Project Websitehttps://www.gcb.uzh.ch/en/Research/Phase-II-Projects/Landscapes/Project-2-Florian-Altermatt.html
  • : FunderBundesamt für Umwelt
  • : Grant IDBAFU /FOEN
  • : Project Title
  • : FunderFachverband für Gas, Wärme und Wasser
  • : Grant IDSVGW/SSIGE
  • : Project Title
  • Content: Published Version
  • Language: English
  • Licence: Creative Commons: Attribution 4.0 International (CC BY 4.0)