The metabarcoding methods for studying the diversity of freshwater microalgae and routine biomonitoring are actively used in modern research. A lot of experience has been accumulated already, and many methodological questions have been solved (such as the influence of the methods and time of sample conservation, DNA extraction and bioinformatical processing). The reproducibility of the method has been tested and confirmed. However, one of the main problems—choosing a genetic marker for the study—still lacks a clear answer. We analyzed 70 publications and found out that studies on eukaryotic freshwater microalgae use 12 markers (different nuclear regions 18S and ITS and plastids rbcL, 23S and 16S). Each marker has its peculiarities; they amplify differently and have various levels of efficiency (variability) in different groups of algae. The V4 and V9 18S and rbcL regions are used most often. We concentrated especially on the studies that compare the results of using different markers and microscopy. We summarize the data on the primers for each region and on how the choice of a marker affects the taxonomic composition of a community.

Two new species of the genus Planothidium isolated from a river and hot spring in the Kamchatka Peninsula, Russia, are described on the basis of morphological and molecular data. These are P. tyushovii sp. nov. and P. dyakonovii sp. nov. The new species are characterised by the presence of a covered depression in the centre of the rapheless valve (i.e., a cavum). Comparison of the new species with closely related taxa is given and the phylogenetic relationships of the Planothidium frequentissimum species group are discussed.

Representatives of the Achnanthidium minutissimum complex have been studied from the Transbaikal region, Russia. The Transbaikal region is known for its unique algal flora and high levels of endemism. Despite the group of monoraphid diatoms being studied quite extensively in this region in recent years, only four species of Achnanthidium have been reported so far. Three new species are described based on LM and SEM microphotographs and molecular data: Achnanthidium baicalonanum sp. nov., A. obscurum sp. nov. and A. angustum sp. nov. Comparison with similar species is given. The new species differ from other species of the genus by valve shape, striae and areolae structure, shape of external distal raphe ends and central area. According to molecular data, the new species form separate branches within the A. minutissimum complex. Ecological preferences of the new species are examined. All of the new species are only known from the Transbaikal region. This study contributes to the understanding of Achnanthidium taxonomy and biogeography and will be an asset to future biomonitoring studies.

A total of 18 Humidophila strains isolated from soil samples from Cát Tiên National Park have been studied. Based on morphometric analysis and molecular data for the V4 18S rDNA and rbcL regions, we proposed the presence of four new species: H. vietnamica, H. paravietnamica, H. cattiensis, and H. concava. This is the first study that provides molecular data for such a large number of Humidophila strains. Furthermore, we encountered some Humidophila strains with clear morphological differences (which we assigned to several morphotypes) that cannot be separated using the selected genetic markers and cannot be attributed to phenotypic variations in one species; these require further study of their genetic structure. We also observed the opposite case, where in the absence of morphological differences, clear genetic differentiation is shown, which demonstrates the presence of cryptic taxa in our sample. The maximum differences for these strains were observed in the V4 18S rDNA region. Our results show that the effectiveness of commonly used genetic markers V4 18S rDNA and rbcL for separating species can vary greatly. Our study highlights the need to research different genetic markers and their use for proper species separation, as well as the genetic diversity of diatoms, and the need for further studies of intra- and interspecific genetic distances.

A new species of the genus Nupela, N. mongolica sp. nov., is described from Davaa Lake, Mongolia. The new species has been studied in LM, SEM and TEM, illustrating the unique structure of the areolae that is characteristic for this genus. According to the molecular analysis, N. mongolica sp. nov. forms an independent branch within the clade that includes other species of Nupela. The genus Nupela was originally placed in the suborder Neidiineae with an unclear position within the suborder due to its unique morphology; later it was included in the family Brachysiraceae despite the differences between Nupela and Brachysira. Molecular data show that strains of Nupela form a separate clade that is not closely related to other genera. Based on the distinct morphological structure of areolae in Nupela that is not present in any other pennate diatoms and the separate position of Nupela species on the phylogenetic tree, a new family Nupelaceae fam. nov. is suggested to accommodate this genus.

Two new species from the genus Planothidium are described from the Kamchatka Peninsula, Russia, based on morphological and molecular analysis: Planothidium piipii and P. novograblenovii. The new species are characterised by a horseshoe-shaped structure in the form of a sinus on the rapheless valve. Comparison with closely related species is provided; the new species are distinguished by various traits, including valve outline and dimensions, striation patterns, and sinus shape. According to molecular data, strains of the new species form a subclade within a clade that includes species of the Planothidium lanceolatum complex.