Vertebrate biodiversity in Italian river revealed through half a liter of sample

In a new study published in Water Biology and Security, researchers at the University of Florence and the University of Pisa revealed vertebrate biodiversity in Italian river through just half a liter of sample.

The team applied environmental DNA (eDNA) metabarcoding to the Serchio River basin in Tuscany, central Italy — an understudied river system with diverse habitats ranging from mountain streams to lowland reaches. Water samples were filtered at five strategic areas, and the genetic material naturally shed by organisms was extracted and sequenced. In total, 62 vertebrate taxa were identified across five classes — fish, amphibians, reptiles, birds and mammals — including protected species and invasive aliens.

eDNA vs. traditional methods

The researchers compared eDNA results with more than two years of conventional monitoring data, including visual transect surveys and electrofishing. “Across all areas, eDNA detected a higher number of species, including taxa not strictly tied to the river environment,” says corresponding author Gabriele Cananzi. “While traditional methods also picked up some unique species, eDNA proved superior overall in species detection.”

Main rivers hold more information than tributaries

A key finding was that the main river channels contained more eDNA diversity than smaller tributaries, suggesting that genetic material accumulates downstream. “This means future monitoring programmes could focus sampling effort on mainstem rivers to capture a more complete picture of basin-wide biodiversity with fewer sampling points,” explains Cananzi.

From invisible to visible

“Traditional monitoring methods are often invasive, require specialised expertise, and can lead to organism mortality,” says Cananzi. “eDNA metabarcoding offers a non-invasive alternative — from a single water sample, multiple vertebrate groups can be detected simultaneously, opening a new window for freshwater biodiversity monitoring.”

Notably, DNA traces of Lampetra (lamprey), a genus with no historical record in the Serchio basin, were detected, highlighting the method's sensitivity for rare and elusive species. “We also found a significant correlation between the number of European eel DNA reads and the number of dams between sampling sites and the estuary, suggesting that barriers shape eel distribution patterns,” adds Cananzi.

Contact the author:

Gabriele Cananzi, Department of Biology, University of Florence, Sesto Fiorentino, 50019, Italy gabrielecananzi@gmail.com

Funder:

This work was supported by the Cassa di Risparmio di Lucca, with the project “Quello che l'occhio non vede ma il DNA ambientale sì”.

Conflict of interest:

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

See the article:

Cananzi, G., Tatini, I., Li, T., Chemello, A., Zanantoni, L., Langeneck, J., Tricarico, E., Zuffi, M.A.L., Nocita, A., Chines, A., Serra, V., Petroni, G., 2026. Strategic eDNA metabarcoding sampling outperforms conventional monitoring methods and reveals spatial patterns of vertebrate biodiversity in a Mediterranean river basin. Water Biology and Security. https://doi.org/10.1016/j.watbs.2026.100715