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.

We studied the morphology, ultrastructure, and phylogeny of eight soil diatom strains assigned to the Pinnularia genus. Six of these strains, identified by us as new species, are described for the first time. We provide a comprehensive comparison with related species and include ecological data. Molecular phylogeny reconstruction using 18S rDNA and rbcL affiliates the new strains with different subclades within Pinnularia, including ‘borealis’, ‘grunowii’ and ‘stomatophora’. We also studied the fatty acid profiles in connection with the emerging biotechnological value of diatoms as a source of lipids. Stearic (36.0–64.4%), palmitic (20.1–30.4%), and palmitoleic (up to 20.8%) acids were the dominant fatty acids in the algae cultured on Waris-H + Si medium. High yields of saturated and monounsaturated fatty acids position the novel Pinnularia strains as a promising feedstock for biofuel production.

Seven Pinnularia species from the Transbaikal area, Russia, are described as new for science. These are P. baicalgenkalii, P. baicalflexuosa, P. microfrauenbergiana, P. pergrunowii, P. siberiosinistra, P. baicalodivergens, and P. baicalislandica. All species are described by original LM and SEM microphotographs and molecular phylogeny. We provide comparisons between the taxa and document variability in the features found in the species. The number of Pinnularia species in the Transbaikal area is the largest number of species of the genus anywhere in the world.

A new species, Cryptomonas tropica sp. nov., is described from Cat Tien National Park (Vietnam) based on morphological and molecular data. Strains of the new species were isolated from soil, which is an unusual environment for photosynthetic cryptomonads. This species has elliptical cells in ventral view and a single plastid notched into several irregular lobes without microscopically visible pyrenoids. Phylogenetic relationships inferred from nuclear-encoded SSU, LSU, ITS2 rDNA and psbA cpDNA show that the new species forms an independent branch on the phylogenetic tree of the genus Cryptomonas. In all phylogenetic analyses, this lineage was sister to clades containing other small-celled, pyrenoid-less species: Cryptomonas erosa, C. parmana, C. macilenta, C. obovoidea and C. commutata. C. tropica has been observed in two distant localities in Cat Tien National Park.