Identification of diatom species is based on morphological analysis of the siliceous frustules covering the cell. Frustules change due to natural processes in the cell size reduction cycle and may also be subject to teratological changes when exposed to environmental factors. The abnormal structure of valves may serve as an environmental pollution indicator, but an understanding of the morphogenesis mechanisms of different types of teratological changes is required. In this work, we evaluate the range of morphological changes in a monoclonal strain of Fragilaria sublanceolata-baikali that occurred during long-term cultivation. Cell ultrastructure and location of nucleus and chloroplasts during valve morphogenesis and interphase were investigated. It is known that diatom species with small cells have a reduced number of organelles, closely pressed against each other. Despite the reduction of F. sublanceolata-baikali cells to 4.5 mu m, the arrangement and size of organelles remain characteristic of a species with larger cells. For the first time, a complete change in all morphological features, including the reduction of apical fields and rimoportula, is shown. Specific deviations observed include a change of the valve shape from lanceolate to round, the changing of the central field position and displacement of areolar rows to one of the apical fields. We hypothesize that the formation of these teratologies could result from microtubule dysfunction or changes in gene expression potentially involved in valve morphogenesis. However, these dysfunctions are not related to mutagenesis and can be compensated for by Vegetative Cell Enlargement (VCE). Our results show the limits of morphological variability of the studied species and can be used to assess the effect of toxic substances in natural and experimental conditions.

The study of aquatic biodiversity in the context of ecosystem sustainability is of urgent research importance, with several existing knowledge gaps. Among the under-studied groups are silica-scaled chrysophytes. Their cells are covered with silica scales and bristles/spines, the species-specific structure of which can be distinguished only by electron microscopy. In June and August 2024, samples were collected from a broad aquatic system comprising the southern part of Lake Baikal and a cascade of four reservoirs formed after the construction of hydroelectric dams on the Angara River flowing from Lake Baikal. Using electron microscopy, we identified 45 species of silica-scaled chrysophytes in phytoplankton in 2024, and the overall checklist was expanded to 57, accounting for interannual differences. Clear differences in species composition and richness were observed both between seasons and among reservoirs. Approximately a quarter of the recorded species were heterotrophs, which do not contribute to primary production, whereas 44% were phototrophs and 31% mixotrophs, both groups contributing to the Si cycle and to primary production. Continuous monitoring of reservoirs is essential for understanding the processes shaping silica-scaled chrysophytes diversity and may serve as an additional criterion for assessing the sustainability and transformation of freshwater ecosystems.

Araphid diatoms of the genus Ulnaria are the dominant species in many freshwater ecosystems of Eurasia. Diatom populations are genetically heterogeneous and represent a combination of different genotypes. Genetic diversity is a necessary factor for adaptation to different environmental conditions and successful dispersal of species. We were analyzed the genetic diversity of the species Ulnaria danica and Ulnaria ulna using the example of monoclonal strains isolated from geographically distant water bodies of the continental part of Eurasia: Lake Ritsa, Lake Goluboe and Lake Baikal. Phylogenetic analysis of cox1 gene fragments of the studied strains demonstrated for the first time the heterogeneity of populations and the absence of geographic isolation for individual genotypes of the studied species. By analyzing the 18S rRNA marker genes, rbcL and cox1, the possibility of horizontal gene transfer between closely related species Fragilaria radians, Ulnaria acus, U. danica and U. ulna was established.

Psychrophilic pigment-forming strains, isolated from Lake Baikal and the Pokhabikha River, were studied. Based on culture-based, morphological, and biochemical properties, as well as the results of 16S rRNA gene sequence analysis, the studied bacteria were assigned to the genera Janthinobacterium and Iodobacter. The strains are able to form biofilms and produce violet pigment. When the pigments were extracted with methanol and identified by MALDI/TOF mass spectrometry, the pigments violacein and deoxyviolacein were identified.

Diatoms are a group of unicellular eukaryotes that are essential primary producers in aquatic ecosystems. The dynamic nature of their habitat necessitates a quick and specific response to various stresses. However, the molecular mechanisms of their physiological adaptations are still underexplored. In this work, we study the response of the cosmopolitan freshwater diatom Ulnaria acus (Bacillariophyceae, Fragilariophycidae, Licmophorales, Ulnariaceae, Ulnaria) in relation to a range of stress factors, namely silica deficiency, prolonged cultivation, and interaction with an algicidal bacterium. Fluorescent staining and light microscopy were used to determine the physiological state of cells under these stresses. To explore molecular reactions, we studied the genes involved in the stress response—type III metacaspase (MC), metacaspase-like proteases (MCP), death-specific protein (DSP), delta-1-pyrroline-5-carboxylate dehydrogenase (ALDH12), and glutathione synthetase (GSHS). We have described the structure of these genes, analyzed the predicted amino acid sequences, and measured their expression dynamics in vitro using qRT-PCR. We demonstrated that the expression of UaMC1, UaMC3, and UaDSP increased during the first five days of silicon starvation. On the seventh day, it was replaced with the expression of UaMC2, UaGSHS, and UaALDH. After 45 days of culture, cells stopped growing, and the expression of UaMC1, UaMC2, UaGSHS, and UaDSP increased. Exposure to an algicidal bacterial filtrate induced a higher expression of UaMC1 and UaGSHS. Thus, we can conclude that these proteins are involved in diatoms’ adaptions to environmental changes. Further, these data show that the molecular adaptation mechanisms in diatoms depend on the nature and exposure duration of a stress factor.

In the context of global climate changes, it is important to assess the sustainability perspective of aquatic ecosystems based on marker organisms. In this work, we analyzed seasonal dynamics of silica-scaled chrysophytes in freshwater communicating environments which have considerable differences in water temperature between two ecosystems: the deep and cold oligotrophic Lake Baikal versus the shallower and warmer downstream Irkutsk Reservoir having mesotrophic features. During three seasons of the open water period of 2023, 38 species of silica-scaled chrysophytes were observed at 17 stations using scanning and transmission microscopy. The distribution of silica-scaled chrysophytes was shown to correlate with the water temperature. The greatest species richness was observed in the spring season in a large bay of the Irkutsk Reservoir (23 species), the smallest in the cold spring waters of Southern Baikal (up to 7 species). Widespread species living in Southern Baikal continued to grow in warmer waters of the reservoir. Using the example of silica-scaled chrysophytes, the stability of the high-latitudinal freshwater ecosystems affected by climate change is discussed. Continuous increment of the water temperature can lead to an increased abundance of widespread species and the displacement of psychrophilic species, affecting the overall biodiversity in such ecosystems.

On a model natural object, the Lake Baikal–Angara River–Irkutsk Reservoir (IR), we studied changes in the qualitative and quantitative characteristics of phytoplankton communities over three seasons in 2023 depending on seasonal changes in habitat parameters. Of the 151 identified taxa, Chrysophyta (57), Chlorophyta (41) and Bacillariophyta (24) predominated in diversity. Over the entire observation period, the highest values of total biomass and total abundance were detected in the IR in June (hydrological spring) at a water temperature of 10.0–12.7 °C, and the lowest in August, despite the fact that the water warmed up to 20 °C. No mass blooms of Cyanobacteria were observed. Statistical analysis of species abundance profiles revealed that phytoplankton community structure varied across time and space. The direct effect of cold lake waters on the structure of phytoplankton in the reservoir was observed only in early June. In summer and autumn, the structures of phytoplankton in the lake and in the reservoir differed, even at the same water temperature. Low concentrations of phosphates and nitrates, high species diversity, the presence of cold-water species and species with a wide range of temperature preferences formed a dynamic spatiotemporal structure of IR phytoplankton, distinct from other temperate reservoirs, including Lake Baikal. The results obtained are important for understanding the mechanisms of formation of the flora of artificial reservoirs of temperate latitudes and for their monitoring, taking into account seasonal dynamics and the context of global climate warming.

Studying correlations between phytoplankton communities and environmental factors is critical for understanding how aquatic ecosystems function. The high sensitivity of phytoplankton to changes in these factors makes it possible to control the state of the ecosystem of water bodies. Artificial lakes often demonstrate increased trophic status, inducing changes in phytoplankton structure. In this paper, we studied phytoplankton in June 2023 (hydrological spring) in two ecosystems, South Baikal and the Irkutsk Reservoir, that are connected by a water course but have different environmental parameters. The gradient of environmental parameters from the lake towards the reservoir revealed peculiarities in the distribution of some microalgae species. Microscopy and statistical analysis showed that water temperature was the most important factor affecting the structure of the communities. The warmer water of the reservoir, in contrast to the lake, demonstrated a twofold increase in species number, abundance, and biomass. Downstream from the reservoir, we observed a succession in the dominating Baikal species complex, its supplementation, and replacement with other species typical of the summer period and Baikal bays. The trophic status of the reservoir during the study may be described as oligotrophic, with local traits of mesotrophicity; its water refers to Class I and Class II and may be qualified as clean.

Fragilaria and Ulnaria are two closely related diatom genera for which the delimitation and circumscription of several species is unclear. We studied strains isolated from Lake Baikal and compared them with the species from freshwater reservoirs in Europe and Asia using phylogenetic and species delimitation methods, microscopy and interclonal crossing experiments. The results of the phylogenetic analyses of the fragments of rbcL and 18S rRNA genes revealed that baikalian F. radians clade was independent from the representatives of the genus from other localities. Among Ulnaria we found the following 18S rRNA phylogenetic tree groups at species level: U. acus, U. ulna and U. danica. Genetic distance between genera varied between 3.9–10.2% substitutions in rbcL gene and 3.2–11.5% in 18S rRNA. The boundary between intraspecies and interspecies polymorphism for studied species of Ulnaria and Fragilaria in these marker genes was around 0.8% substitutions. Morphometric characters of individual strains showed their variability and division into F. radians, U. acus and U. ulna together with U. danica. Strains of U. acus and U. danica from different localities of Europe and Asia were sexually compatible inside the species. Sexual reproduction has never been observed in monoclonal cultures, either between this species or with strains of the Fragilaria.

In an aquatic ecosystem, the supply of nutrients is essential for the biogeochemical cycle, and it affects the taxonomic composition of the microbial communities. Here, by using high-throughput sequencing (HTS) of the 16S and 18S rRNA gene fragments, we compared free-living (FL) and particle-associated (PA) bacterial communities and microeukaryotic communities in the areas with different nutrient intakes in freshwater Lake Baikal during the ice-covered and summer periods. Samples were taken at the inflow of the Selenga River, which is the main tributary of the lake, and at several established coastal research stations. The metabolic potential of the bacterial communities was predicted using PICRUSt. Differences were found in both FL and PA communities of the river mouth compared to the photic zone of the lake. The composition of FL communities was significantly different between the sampling sites in the ice-covered period, which is most likely influenced by different hydrochemical conditions. In contrast, the PA communities were more similar during the ice-covered period, but they changed considerably from spring to summer and their diversity increased. The diversity of the microeukaryotic communities also increased in summer, which may have contributed to the increase in bacterial diversity. In co-occurrence networks analysis, the number of interconnected bacterial OTUs in FL exceeded those for PA. The FL communities were dominated by Actinobacteriota, while the major PA OTUs belonged to a mixed cluster, which were mainly assigned to the phyla Bacteroidota and Verrucomicrobiota. As a result, PA communities were enriched in pathways responsible for the metabolism of sulfur, fucose, cellulose and urea. Our results confirm the difference between the FL and PA bacterial communities in Lake Baikal. These results also highlight the complex pattern of interactions between bacteria and microeukaryotes in a natural freshwater ecosystem across spatial and temporal scales.

Hydroelectric dams create new ecosystems such as reservoirs. Several hydroelectric dams forming shallow reservoirs were built on the Angara River flowing out of Lake Baikal. The first of them in downstream Angara is Irkutsk Reservoir, with several shallow bays. Since silica-scaled chrysophytes are effective bioindicators for aquatic ecosystems, this paper aimed to determine their distribution, taxonomic structure and species richness in South Baikal and Irkutsk Reservoir, which have different environmental parameters. Thirty-one species were found using scanning and transmission electron microscopy. Only seven of them inhabited South Baikal in June 2023 at 3.66–4.51 °C and pH 7.80–8.24, with Chrysosphaerella baicalensis, Spiniferomonas trioralis f. cuspidata and Mallomonas alpina being prevalent. Only one species (M. alpina) was dominant in Irkutsk Reservoir at all stations at a water temperature of 5.33–11.55 °C and pH 8.10–8.52, alongside three other abundant species, Synura cf. glabra, Mallomonas acaroides and M. crassisquama. The maximum number of species (23) was found in a shallow bay of the reservoir at maximal values of temperature (11.5 °C) and pH (8.57) and minimal values of phosphate and nitrate concentrations during the study. The enrichment of Irkutsk Reservoir in species of silica-scaled chrysophytes was due both to cosmopolitan widespread and polyzonal species as well as to rare boreal, arctic–boreal, and unknown, possibly new species.

Abstract. Ulnaria a us is a cosmopolitan freshwater diatom. As a rule, diatom populations represent a combination of different genotypes. In early study, using a fragment of the rbcL gene of U. acus strains isolated from geographically distant regions, no significant genetic differences were found in the populations of this species. In this paper, we analyzed 41 strains isolated from different regions of Eurasia. Based on the analysis of the 18S rRNA gene fragment, it was shown that all strains form a single clade consisting of U. acus. Phylogenetic analysis of cox1 genes revealed that Eurasian strains of U. acus form three clades. Strains of U. acus from Lake Ritsa (Abkhazia) and Lake Matano (Indonesia) are not heterogeneous. Strains of U. acus isolated from Lake Baikal (Russia) and the r. Erdre (France) contained two clades and we can suggest that the genetic structure of the populations of this species is heterogeneous. All studied populations are conspecific taking into account their sexual compatibility of at least two generations.

Although under-ice microbial communities are subject to a cold environment, low concentrations of nutrients, and a lack of light, they nevertheless take an active part in biogeochemical cycles. However, we still lack an understanding of how high their diversity is and how these communities are distributed during the long-term ice-cover period. Here, we assessed for the first time the composition and distribution of microbial communities during the ice-cover period in two subarctic lakes (Labynkyr and Vorota) located in the area of the lowest temperature in the Northern Hemisphere. The diversity distribution and abundance of main bacterial taxa as well as the composition of microalgae varied by time and habitat. The 16S rRNA gene sequencing method revealed, in general, a high diversity of bacterial communities where Proteobacteria (~ 45%) and Actinobacteria (~ 21%) prevailed. There were significant differences between the communities of the lakes: Chthoniobacteraceae , Moraxellaceae , and Pirellulaceae were abundant in Lake Labynkyr, while Cyanobiaceae , Oligoflexales , Ilumatobacteraceae , and Methylacidiphilaceae were more abundant in Lake Vorota. The most abundant families were evenly distributed in April, May, and June their contribution was different in different habitats. In April, Moraxellaceae and Ilumatobacteraceae were the most abundant in the water column, while Sphingomonadaceae was abundant both in water column and on the ice bottom. In May, the abundance of Comamonadaceae increased and reached the maximum in June, while Cyanobiaceae , Oxalobacteraceae , and Pirellulaceae followed . We found a correlation of the structure of bacterial communities with snow thickness, pH, N min concentration, and conductivity. We isolated psychrophilic heterotrophic bacteria both from dominating and minor taxa of the communities studied. This allowed for specifying their ecological function in the under-ice communities. These findings will advance our knowledge of the under-ice microbial life.

Diatoms are capable of accumulating substantial amounts of triacylglycerides in their cells, which differ in the composition of fatty acids depending on the conditions of cultivation, making them attractive subjects in biotechnology. In the present study, we characterized the structural features of lipid bodies in the diatom Entomoneis cf. paludosa (W. Smith) Reimer strain 8.0727-B and revealed the peculiarities of fatty acid composition in cultures during the stationary and exponential growth phases. Laser scanning confocal microscopy revealed an increased number of lipid bodies in the cytoplasm during the stationary phase of culture growth. Electron microscopy of ultrathin sections showed that an extreme increase in the number and size of plastoglobules in the cells occurs in the stationary phase of culture growth. The gas chromatography with mass spectrometric detection method revealed differences in the fatty acid composition depending on the growth phase. The studied strain can be recommended as a source of hexadecanoic and octadecanoic fatty acids from the culture during the stationary growth phase, as well as eicosapentaenoic fatty acid from the culture during the exponential growth phase.

In preparation for whole-genome sequencing, the axenic culture for two strains of a freshwater diatom Fragilaria radians were produced. Although their axenicity was controlled for the cultures’ entire lifetime, the published genomic assembly was later found to contain a large amount of bacterial sequences. Using various in silico analyses of whole genome read libraries and 16S rRNA sequencing of culture samples, we reconstruct the history of the contamination and document the failures of various axenicity control methods. This knowledge is used to discuss how these failures could have been avoided, and to provide guidelines for future works on axenic diatom cultures.

. In our earlier work, multiple diatom protein-coding genes were found to consist of long repeats, in some cases even including several copies of the entire protein within a single open reading frame. 28 of them were amplified and sequenced from Fragilaria radians total DNA, thus proving that they are not assembly or annotation artifacts. Out of these 28, 16 were successfully sequenced from cDNA of the same species, confirming their expression and, hypothetically, functionality. Much like the original set of unvalidated sequences, this group shows little functional and structural specificity. Most duplications are shared with other diatom species, implying either multiple independent duplications an ancient duplication event and vertical inheritance.

Diatoms from the extreme cold habitats in northern areas of East Siberia are still poorly studied. Ecological significance of the lakes of the Pole of Cold of the Northern Hemisphere consists in their pristine environment characterized by special environmental factors, such as the long ice cover period, low temperatures, short vegetative period, low photosynthetically active radiation, deficiency of nutrients. Such water systems can thus be used as sensitive indicators of environmental changes. The diatom Ulnaria ulna (Nitzsch) Compere from the genus Ulnaria (Kutzing) Compere is wide-spread in fresh and brackish waters of the world, both in plankton and in benthos, which raises questions about the actual distribution of this species and the presence of cryptic species hidden under this name. In this study, monoclonal cultures of Ulnaria were isolated from epilithic micro-phytobenthos collected in Lake Labynkyr, located in the northern Pole of Cold region in the Sakha Republic (Yakutia), and were investigated in detail by light and scanning electron microscopy and phylogenetic analysis of the rbcL gene fragments. Cells in culture were able to attach to the substrate with mucilage strands secreted through the pore fields of both valves at one end of the cell. The results of the morphometric and phylogenetic analyses enabled to identify the isolated clones as Ulnaria pilum Kulikovskiy & Lange-Bertalot and showed that species morhoplogical variability is larger than originally described.

Formation of diatom siliceous cell walls occurs inside the cells and depends on the availability of silicon from the environment. In the current work we have studied the valve morphogenesis of a freshwater pennate diatom Ulnaria danica in a laboratory culture synchronized by silica starvation and absence of light. Approximate timelines were established for the initiation of valve synthesis and formation of its major components. It was shown that the silicon surge uptake takes place, e.g. silicon concentration in the medium reduces during the first 30 minutes after the addition of silicon to a synchronized culture. During the formation of main valve elements, intracellular silicon pool is lower than it is after the end of synchronization, returning to the original level only 90 minutes after the addition of silica and beginning of the morphogenesis.

Silicon transporters (SIT) are the proteins, which capture silicic acid in the aquatic environment and direct it across the plasmalemma to the cytoplasm of diatoms. Diatoms utilize silicic acid to build species-specific ornamented exoskeletons and make a significant contribution to the global silica cycle, estimated at 240 ±40 Tmol a year. Recently SaSIT genes of the freshwater araphid pennate diatom Synedra acus subsp. radians are found to be present in the genome as a cluster of two structural genes (SaSIT-TD and SaSIT-TRI) encoding several concatenated copies of a SIT protein each. These structural genes could potentially be transformed into “mature” SIT proteins by means of posttranslational proteolytic cleavage. In the present study, we discovered three similar structural SuSIT genes in the genome of a closely related freshwater diatom Synedra ulna subsp. danica. Structural gene SuSIT1 is identical to structural gene SuSIT2, and the two are connected by a non-coding nucleotide DNA sequence. All the putative “mature” SITs contain conserved amino acid motifs, which are believed to be important in silicon transport. The data obtained suggest that the predicted “mature” SIT proteins may be the minimal units necessary for the transport of silicon is S. ulna subsp. danica. The comparative analysis of all available multi-SITs has allowed us to detect two conservative motifs YQXDXVYL and DXDID, located between the “mature” proteins. Aspartic acid-rich DXDID motif can, in our opinion, serve as a proteolysis site during the multi-SIT cleavage. The narrow distribution of the distances between CMLD and DXDID motifs can serve as additional evidence to the conservation of their function.