Agung Setia Batubara, Muliari Muliari, Binari Manurung, Khairiza Lubis, Firman M. Nur, Afrizal Bigman Silitonga, Yusrizal Akmal, Mustaqim Mustaqim, Siti Maulizar, Irfannur Irfannur
Lake Toba, the world's largest volcanic caldera and a designated UNESCO Global Geopark, is facing significant threats, yet a definitive ichthyofaunal census remains unavailable through traditional methods. This study aimed to assess the fish species composition and status, particularly focusing on the prevalence of non-native species, using environmental DNA (eDNA) metabarcoding. Water samples were collected from five strategic locations in Lake Toba during August–September 2025, and eDNA was analyzed using the MiFish primers targeting the mitochondrial 12S rRNA gene. The eDNA analysis successfully identified 23 fish species, categorizing 19 species as confirmed detection (82.61%) and 4 as unconfirmed taxa, 17.39%). The results revealed a dominance in relative read abundance by 11 introduced species against only 8 native species. The study recorded two new introduced fish species for the lake: Gambusia affinis and Trichopodus pectoralis. Furthermore, the analysis provided taxonomic clarity for the Mystacoleucus genus, confirming the conspecific nature of M. padangensis and M. marginatus. While the high proportion of confirmed detections supports eDNA as a reliable monitoring tool, the occurrence of unconfirmed taxa, including the repeated detection of Rhinogobius similis, highlights the need for careful bioinformatic filtering and further ecological validation. In conclusion, this eDNA study provides the first molecular inventory of Lake Toba's fish fauna, indicating that introduced species may be an important ecological factor influencing native fish populations. These findings highlight the potential need for conservation attention to support declining native fish populations and maintain the biodiversity of this globally significant geopark. © 2026 European Regional Centre for Ecohydrology of the Polish Academy of Sciences
Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Negeri Medan, Medan, 20221, Indonesia; Department of Marine Science, Faculty of Agriculture, Universitas Malikussaleh, Aceh Utara, Indonesia; Research Center for Biosystematics and Evolution, National Research and Innovation Agency (BRIN), Cibinong, 16911, Indonesia; Department of Aquaculture, Faculty of Agriculture, Universitas Almuslim, Bireuen, Indonesia; Graduate Program of Biology, Faculty of Biology, Universitas Gadjah Mada, Yogjakarta, Indonesia
