Applicability of diatom metabarcoding in the ecological status assessment of Hungarian lotic and soda pan habitats

[Display omitted] •Diatoms are used as bioindicators in ecological status assessment of aquatic ecosystems.•Testing metabarcoding on running waters and soda pans compared to morphology.•Significant correlation in community composition, environmental drivers and indices.•Discrepancies mainly due to reference database incompleteness.•Metabarcoding can not replace morphological identification in present form. Diatoms are widely applied in the ecological status assessment of aquatic ecosystems using indices calculated from pollution sensitivity and indicator values of species. Traditional, morphology-based identification of species requires in-depth taxonomic knowledge and expertise. Identifying taxa according to their barcode sequences obtained with high-throughput sequencing (metabarcoding) would be a promising alternative. In this pilot study, we tested the applicability of metabarcoding of benthic diatom assemblages for the ecological status assessment of Hungarian water bodies, comparing its performance to that of morphology-based identification of species. The barcode region of the rbcL gene was investigated in samples from running waters with various trophic states and unique lentic habitats, namely soda pans. For running waters, the Specific Pollution Sensitivity Index (IPS) and for soda pans the H index and the Indice Biologique Diatomées (IBD) were calculated from the morphology- and sequence-based abundances. The ecological quality ratio was determined for running waters. Overall, more infrageneric taxa were found with microscopy than with metabarcoding in the lotic and lentic samples. The correspondence between taxon lists detected by the two methods was relatively low but increased considerably in the case of morphologically dominant taxa. Community composition based on microscopy and DNA sequence analysis showed a significant correlation and was determined by the same main environmental drivers. Morphology-based indices strongly correlated with sequence-based indices. Both aspects indicated the same ecological status class for more than half of the lotic samples. In other cases, a status shift from good to moderate was frequent, a phenomenon that could prove problematic because the Water Framework Directive prescribes intervention for waters with a moderate or worse status. Considering discrepancies between the results obtained with microscopy and metabarcoding, using both methods in parallel could be proposed until the reference database has bee