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Due to anthropogenic influences, habitat degradation and a continuous loss of biodiversity in freshwater ecosystems are occurring on a large scale, while these ecosystems constitute invaluable natural resources. Therefore, it is essential to study and monitor freshwater ecosystems to guide conservation efforts. Freshwater ecosystems are one of the less-studied fields in Georgia. Studies about the species distribution of many taxa and/or regions carried out during the last century have not been updated for decades. Here, we report the results of an environmental DNA ( eDNA ) metabarcoding exercise, based on samples collected from the Rioni River, a tributary to the Black Sea and a crucial aquatic ecosystem regionally and globally. The only comprehensive review of the fish of the Rioni River dates back to 1956. We compared the  eDNA -based taxonomic composition to the known faunal composition within the Rioni River and found that the  eDNA -based taxonomic coverage approached 75% of the expected total fish fauna. A number of new species occurrences were also found, including the first detection of three invasive alien species (   Carassius   gibelio   ,    Pseudorasbora   parva   ,    Rhinogobius   lindbergi   ) in the Rionis River Basin and a new country record of the ninespine stickleback (genus    Pungitius   ) for Georgia. In spite of the usefulness of the  eDNA  metabarcoding approach, the sparsity of the fish DNA barcode reference library for the region emerged as a limitation to this study. However, our findings still represent a great leap forward in updating fish status on the Rioni River and testing the effectiveness of the  eDNA  sampling for aquatic species.

﻿Fish diversity assessed by eDNA detection methods in the Rioni River

Fish diversity assessed by eDNA detection methods in the Rioni River