Detection of charophyte algae (Characeae) in lakes using eDNA metabarcoding

Summary

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 7 charophyte taxa, 6 from the genus Chara and Nitellopsis obtusa. C. canescens was detected to the species level by eDNA, while other taxa could be assigned to species groups within the genus Chara only. The charophyte genus Nitella was not detected using eDNA metabarcoding, even though it was found by traditional methods. Our study confirms that it is possible to use eDNA metabarcoding to detect the presence of Characeae in lakes. The overall agreement on the presence and absence of taxa between traditional mapping and eDNA was 80,5%, across four different lakes and three seasons. The rbcL marker, however, cannot discriminate all Characeae to species level, limiting its use for biodiversity monitoring or ecological status assessment.