Detection of Charophyte Algae (Characeae) in Lakes Using Edna Metabarcoding

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Detection of charophyte algae (Characeae) and identification to species level is important for biodiversity conservation and ecological status assessment, and environmental DNA (eDNA) might enable fast and replicable species detection. The aims of our study were to evaluate the performance of the rbcL gene marker in detecting eDNA of Characeae and to compare the eDNA method with the results from traditional sampling. Characeae were sampled from two freshwater and two saline lakes in Serbia during spring, summer, and autumn 2023. In total, 7 species within 3 genera (Chara, Nitella and Nitellopsis) were detected by the traditional method, and species identity was confirmed using barcoding of the rbcL gene. Metabarcoding of eDNA detected 5 charophyte taxa, all from the genus Chara. C. canescens and C. contraria were detected to the species level by eDNA, while other taxa could be assigned to species groups only. The charophyte genera Nitella and Nitellopsis were not detected using eDNA approach, even though they were found by traditional methods. Our study confirms that it is possible to use eDNA metabarcoding to detect the presence of Characeae in lakes. It is, however, challenging to discriminate among different Chara species, and the overall agreement on presence and absence of taxa between traditional mapping and eDNA was 56% only, across four different lakes and three seasons.