Production of axenic cultures of diatoms is a highly relevant task, as these widespread organisms are objects of research in different fields of biology, from ecology to whole‐genome studies, and promising as producers of various organic molecules, including biologically active substances. However, culturing of diatoms isolated from natural communities is accompanied by the development of associated microorganisms. We propose a procedure for establishing an axenic culture of the freshwater diatom Synedra asus subsp. radians (Kütz.) Skabitsch. from Lake Baikal. Such a culture has been produced and maintained by subculturing in our laboratory. The procedure involves filtration (to remove free bacteria), detergent treatment (to remove microorganisms associated with diatom frustules), selection of effective antibiotics and their concentrations nontoxic for diatoms (by the disk diffusion method), cell treatment with the selected antibiotic (ciprofloxacin), repeated filtration, and monoclonal culturing of diatom cells. Axenity of the culture was verified microscopically (after DAPI staining) and by molecular biological methods.

Pyrosequencing of amplicons V3-V4 of the 16S rRNA gene of 30 samples from the photic layer across the three basins of Lake Baikal has revealed 44 958 sequences of the domain Bacteria. The most representative phylums among all classified sequences in the samples were Actinobacteria, Bacteroidetes, Verrucomicrobia, Proteobacteria, Acidobacteria, and Cyanobacteria. As much as 38.5% of the total number of sequences has been determined to the level of genus. The taxonomic composition of bacterial communities was similar regardless of some differences in the composition and abundance of spring phytoplankton. Closely related or identical sequences of bacteria inhabiting the epilimnion of other lakes worldwide have been discovered for most sequences. This confirms the similarity of microbial communities in freshwater ecosystems.

Phytoplankton and bacterioplankton play a key role in carbon cycling of aquatic ecosystems. In this study, we found that co-occurrence patterns between different types of phytoplankton, bacterioplankton, and environmental parameters in Lake Baikal during spring were different over the course of three consecutive years. The composition of phytoplankton and bacterial communities was investigated using microscopy and 16S rRNA gene pyrosequencing, respectively. Non-metric multidimensional scaling (NMDS) revealed a relationship between the structure of phytoplankton and bacterial communities and temperature, location, and sampling year. Associations of bacteria with diatoms, green microalgae, chrysophyte, and cryptophyte were identified using microscopy. Cluster analysis revealed similar correlation patterns between phytoplankton abundance, number of attached bacteria, ratio of bacteria per phytoplankton cell and environmental parameters. Positive and negative correlations between different species of phytoplankton, heterotrophic bacteria and environmental parameters may indicate mutualistic or competitive relationships between microorganisms and their preferences to the environment.