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Environmental DNA metabarcoding as an efficient tool to monitor freshwater systems in northwestern Italy

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Abstract

Freshwater ecosystems are experiencing one of the highest rates of biodiversity decline among extant ecosystems. To inform effective conservation actions, it is imperative to develop reliable monitoring techniques to assess the species richness of freshwater communities. In this study, we applied for the first time an eDNA metabarcoding assay on six watercourses in Liguria, northwestern Italy. Our first aim was to validate this method as a reliable monitoring tool for Ligurian fish communities. To reach this goal, we compared the results of the eDNA-based sampling with those obtained from two electrofishing campaigns carried out during the same season. The eDNA-based approach yielded congruent results with electrofishing data and showed a slightly higher resolution since it was able to detect two threatened species that were not detected by traditional monitoring. Just one species that eluded eDNA detection was electrofished instead. Thanks to a multi-marker metabarcoding approach, we were also able to detect other vertebrate species living in, or associated with, the sampled watercourses, such as aquatic birds and amphibians. Overall, our results confirmed that aquatic eDNA assay proves to be a valuable tool to monitor freshwater-related systems and to inform efficient management and protection schemes for such habitats.

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Data availability

The detailed workflow and all scripts used in this study are available at the GitHub page: https://github.com/giorgiastaffoni/STREAM. Raw reads have been deposited in the NCBI Short Read Archive (BioProject accession ID:  PRJNA1175355; SRA accession numbers: from SRX26441509 to SRX26441596).

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Acknowledgements

We thank Livia Tolve and Giacomo Chini for their help in sampling work. We also thank Chiara Natali and Chiara Vergata for their support in lab work. We are grateful to Stefano Cannicci for his useful comments on the manuscript.

Funding

This work was supported by the LIGURIA REGIONAL AUTHORITY (Italy) through Grant Number G55J19000450007 of the Biodiv’Connect program of the European Interreg Biodiv’ALP France-Italy ALCOTRA 2014-2020 project. The authors acknowledge the support by the Italian Ministry of University and Research through the NATIONAL BIODIVERSITY FUTURE CENTER (NBFC), part of the National Recovery and Resilience Plan, Mission 4, Component 2, Investment 1.4, Project CN00000033.

Author information

Author notes

  1. Lorenzo Ballini and Giorgia Staffoni have contributed equally to this work.

Authors and Affiliations

  1. Department of Biology, University of Florence, Via Madonna del Piano 6, 50019, Sesto Fiorentino, FI, Italy

    Lorenzo Ballini, Giorgia Staffoni, Davide Nespoli, Alessio Iannucci & Sara Fratini

  2. ARPAL, Regional Agency for the Protection of the Ligurian Environment, Via Bombrini 8, 16149, Genoa, Italy

    Dario Ottonello

  3. Department of Environment, Land and Infrastructure Engineering (DIATI), Polytechnic of Turin, Corso Duca degli Abruzzi 24, 10129, Turin, Italy

    Alessandro Candiotto, Simone Forte & Paolo Vezza

Authors
  1. Lorenzo Ballini
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  2. Giorgia Staffoni
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  3. Davide Nespoli
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  4. Dario Ottonello
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  5. Alessandro Candiotto
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  6. Simone Forte
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  7. Paolo Vezza
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  8. Alessio Iannucci
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  9. Sara Fratini
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Contributions

Lorenzo Ballini, Giorgia Staffoni, Alessio Iannucci, and Sara Fratini wrote the manuscript. Sara Fratini and Alessio Iannucci conceptualized and designed the study. Lorenzo Ballini collected the eDNA samples. Dario Ottonello, Alessandro Candiotto, Simone Forte, and Paolo Vezza conducted the electrofishing survey. Lorenzo Ballini, Alessio Iannucci, and Sara Fratini performed lab work and provided lab support. Giorgia Staffoni ran the bioinformatics analysis, with the support of Davide Nespoli. All authors read and approved the final version of the manuscript.

Corresponding author

Correspondence to Alessio Iannucci.

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Ballini, L., Staffoni, G., Nespoli, D. et al. Environmental DNA metabarcoding as an efficient tool to monitor freshwater systems in northwestern Italy. Hydrobiologia 852, 791–803 (2025). https://doi.org/10.1007/s10750-024-05723-y

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  • DOI: https://doi.org/10.1007/s10750-024-05723-y

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