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Article

Environmental DNA Metabarcoding as a Tool for Fast Fish Assessment in Post-Cleanup Activities: Example from Two Urban Lakes in Zagreb, Croatia

by
Matej Vucić
1,*,†,
Thomas Baudry
2,3,†,
Dušan Jelić
4,
Ana Galov
1,
Željko Pavlinec
5,
Lana Jelić
6,
Biljana Janev Hutinec
6,
Göran Klobučar
1,
Goran Slivšek
7 and
Frédéric Grandjean
2
1
Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, HR-10000 Zagreb, Croatia
2
Laboratoire Ecologie et Biologie des Interactions, Université de Poitiers, UMR CNRS 7267, Equipe Ecologie Evolution Symbiose, 86000 Poitiers, France
3
Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, HR-10000 Zagreb, Croatia
4
BIOTA Ltd., Maksimirska Cesta 129/5, HR-10000 Zagreb, Croatia
5
Aquarium Pula Ltd., Verudela 33, HR-52100 Pula, Croatia
6
Public Institution for Management of Natural Values of City of Zagreb—Zagreb City Nature, Maksimirski perivoj 1, HR-10000 Zagreb, Croatia
7
Centre for Applied Bioanthropology, Institute for Anthropological Research, Gajeva ulica 32, HR-10000 Zagreb, Croatia
*
Author to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Fishes 2025, 10(8), 375; https://doi.org/10.3390/fishes10080375
Submission received: 13 June 2025 / Revised: 17 July 2025 / Accepted: 24 July 2025 / Published: 4 August 2025
(This article belongs to the Special Issue Mapping and Monitoring Aquatic Biodiversity in Hotspot Habitat Areas Using Environmental DNA (eDNA))
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Abstract

This study evaluated the effectiveness of eDNA metabarcoding in assessing fish communities in two urban lakes (First Lake and Second Lake) in Zagreb, Croatia, following IAS removal. Water samples were collected in April and June 2024 and analyzed using MiFish primers targeting the 12S rRNA gene. The results indicated that the cleanup efforts were largely successful, as several IAS previously recorded in these lakes were not detected (Ameiurus melas, Lepomis gibbosus, and Hypophthalmichthys spp.). However, some others persisted in low relative abundances, such as grass carp (Ctenopharyngodon idella), topmouth gudgeon (Pseudorasbora parva), and prussian/crucian carp (Carassius sp.). Species composition differed between lakes, with common carp (Cyprinus carpio) dominating Maksimir First Lake, while chub (Squalius cephalus) was prevalent in Maksimir Second Lake. Unexpected eDNA signals from salmonid and exotic species suggest potential input from upstream sources, human activity, or the nearby Zoo Garden. These findings underscore the utility of eDNA metabarcoding in biodiversity monitoring and highlight the need for continuous surveillance and adaptive management strategies to ensure long-term IAS control.
Keywords: invasive species; eDNA; management; removal; urban ecosystem invasive species; eDNA; management; removal; urban ecosystem

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MDPI and ACS Style

Vucić, M.; Baudry, T.; Jelić, D.; Galov, A.; Pavlinec, Ž.; Jelić, L.; Hutinec, B.J.; Klobučar, G.; Slivšek, G.; Grandjean, F. Environmental DNA Metabarcoding as a Tool for Fast Fish Assessment in Post-Cleanup Activities: Example from Two Urban Lakes in Zagreb, Croatia. Fishes 2025, 10, 375. https://doi.org/10.3390/fishes10080375

AMA Style

Vucić M, Baudry T, Jelić D, Galov A, Pavlinec Ž, Jelić L, Hutinec BJ, Klobučar G, Slivšek G, Grandjean F. Environmental DNA Metabarcoding as a Tool for Fast Fish Assessment in Post-Cleanup Activities: Example from Two Urban Lakes in Zagreb, Croatia. Fishes. 2025; 10(8):375. https://doi.org/10.3390/fishes10080375

Chicago/Turabian Style

Vucić, Matej, Thomas Baudry, Dušan Jelić, Ana Galov, Željko Pavlinec, Lana Jelić, Biljana Janev Hutinec, Göran Klobučar, Goran Slivšek, and Frédéric Grandjean. 2025. "Environmental DNA Metabarcoding as a Tool for Fast Fish Assessment in Post-Cleanup Activities: Example from Two Urban Lakes in Zagreb, Croatia" Fishes 10, no. 8: 375. https://doi.org/10.3390/fishes10080375

APA Style

Vucić, M., Baudry, T., Jelić, D., Galov, A., Pavlinec, Ž., Jelić, L., Hutinec, B. J., Klobučar, G., Slivšek, G., & Grandjean, F. (2025). Environmental DNA Metabarcoding as a Tool for Fast Fish Assessment in Post-Cleanup Activities: Example from Two Urban Lakes in Zagreb, Croatia. Fishes, 10(8), 375. https://doi.org/10.3390/fishes10080375

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