Diatoms are frequently used for water quality assessments; however, identification to species level is difficult, time-consuming and needs in-depth knowledge of the organisms under investigation, as nonhomoplastic species-specific morphological characters are scarce. We here investigate how identification methods based on DNA (metabarcoding using NGS platforms) perform in comparison to morphological diatom identification and propose a workflow to optimize diatom fresh water quality assessments. Diatom diversity at seven different sites along the course of the river system Odra and Lusatian Neisse from the source to the mouth is analysed with DNA and morphological methods, which are compared. The NGS technology almost always leads to a higher number of identified taxa (270 via NGS vs. 103 by light microscopy LM), whose presence could subsequently be verified by LM. The sequence-based approach allows for a much more graduated insight into the taxonomic diversity of the environmental samples. Taxa retrieval varies considerably throughout the river system, depending on species occurrences and the taxonomic depth of the reference databases. Mostly rare taxa from oligotrophic parts of the river systems are less well represented in the reference database used. A workflow for DNA-based NGS diatom identification is presented. 28 000 diatom sequences were evaluated. Our findings provide evidence that metabarcoding of diatoms via NGS sequencing of the V4 region (18S) has a great potential for water quality assessments and could complement and maybe even improve the identification via light microscopy.

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Diatom cultures of the G. parvulum species complex were established from seven different sites in the Faroe Islands, Sweden, Germany, Mexico and Korea, and were studied in detail. Eight morphodemes were identified which corresponded to the descriptions of the cosmopolitan taxon G. parvulum (Kützing) Kützing sensu lato: its nominate variety (var. parvulum), G. parvulum var. exilissimum Grunow and G. parvulum f. saprophilum Lange-Bertalot & Reichardt, G. [parvulum var.] lagenula Kützing plus four unidentifiable morphodemes. The concatenated analysis of the sequences of the markers 18SV4, rbcL, and ITS as well as morphological data resulted in a separation of four taxa based on their biogeography in Mexico, Korea, central Continental Europe and Northern Atlantic Europe. Mantel tests showed a significant correlation between molecular and geographical distances. The diagnoses of two taxa, G. parvulum sensu stricto, and G. lagenula, were emended, G. saprophilum elevated to species rank and epitypes designated. One species was newly described.