Diatom metabarcoding as a tool to assess the water quality of two large tributaries of the Danube River

• The benthic community in the Sava River was predominantly colonized by pennate diatoms. • In the benthic community in the Tisa River centric diatoms were predominant. • rbcL marker provided a comprehensive view of the diatom community. • Presence/absence of taxa assessed with rbcL to assess water quality of large lowland rivers proved more similar to morphological identification. This study examines the effectiveness of digital microscopic and molecular analysis ( rbcL and 18S markers) in assessing diatom community composition and water quality in two international rivers (Sava and Tisa rivers). Also, two different approaches were applied for calculating diatom indices: based on the relative abundance of taxa and the presence/absence of taxa. The rbcL marker showed up as a more suitable choice for providing a comprehensive view of the diatom community compared to 18S, which can be partly attributed to variations in the coverage of reference databases. Furthermore, both morphological and molecular analysis pointed out statistically different ecological statuses of investigated rivers. Diatom indices derived from molecular data indicated one or two classes of lower ecological status than those based on morphological analysis. However, the average diatom indices derived from molecular presence/absence data were higher than those based on the relative abundance of taxa. After summarizing all the results, we can recommend using the rbcL marker with taxa presence/absence data for routine monitoring of large lowland rivers.