Acta Biologica Sibirica

Silica-scaled chrysophytes belong to the phylum Ochrophyta and the class Chrysophyceae (golden algae). This distinctive group comprises approximately 440 species of unicellular heterokont flagellates exhibiting diverse nutritional strategies, including autotrophy, mixotrophy, and heterotrophy. These organisms may occur singly or form colonies. They convert silicic acid dissolved in water into species-specific silica scales, ranging from 0.2 to 85 µm in size, which form a dynamic shell around the cell surface. The ultrastructure of these silica scales, observable through electron microscopy (EM), constitutes the primary taxonomic criterion for defining species among scale-bearing chrysophytes (Škaloud et al. 2013; Siver et al. 2015). As with other members of the class Chrysophyceae, scale-bearing chrysophytes possess the unique ability to form silica-based dormant structures known as stomatocysts endogenously, either at the end of their life cycle or in response to abrupt environmental changes (Sandgren 1981; Holen 2014). These stomatocysts are also species-specific (Duff et al. 1995; Bessudova et al. 2024a; 2025b; Firsova et al. 2026). To date, approximately 2000 different stomatocysts morphotypes have been described (Pang and Vijver 2021). However, only 38 morphotypes described in accordance with the recommendations of the International Group on the Description of Statospores (ISWG) have been linked to the species silica-scaled chrysophytes that produce them (Bessudova et al. 2024a-c; 2025b, c; Firsova et al. 2026). The formation of stomatocysts facilitates the successful colonization of different biotopes. Because these organisms can be identified by their individual scales, they are promising subjects for monitoring freshwaters, investigating biological diversity, and performing paleolimnological and biogeographic research. Two online databases have already been established for these purposes. One, entitled “Silica Secchi Disk” is available at: https://fmp.conncoll.edu/Silicasecchidisk/Center_Chrysophyte_Home_Page.html. This database focuses on silica-scaled chrysophytes found in North American waters and was developed under the supervision of Dr. Peter A. Siver at the Freshwater Ecology Laboratory of Connecticut College in North America. The second database, “Silica-scaled chrysophytes of Europe: distribution, morphology, and ecology,” is available at https://chrysophytes.eu/. This database was developed under the supervision of Pavel Škaloud in the Department of Botany at Charles University in Prague, Czech Republic. It contains records of silica-scaled chrysophytes found in European waters (Škaloud et al. 2013).

We have developed an online database documenting silica-scaled chrysophytes found in Siberian water bodies. It includes original micrographs, collection-site information, geographical coordinates linked to an online map, sampling dates, and key water parameters such as temperature, pH, and electrical conductivity.

The “Silica-scaled chrysophytes from Siberia” database was developed at the Limnological Institute of the Siberian Branch of the Russian Academy of Sciences in Irkutsk. It is implemented as a modern web application using the Next.js framework, the React library, and the TypeScript programming language. The data are stored in a PostgreSQL relational database and processed with the Prisma ORM.

The database compiles taxonomic data on genera and species, bibliographic references, physicochemical characteristics of the environment, the geographical coordinates of sampling stations, regional information, and species micrographs. The locations of recorded finds are visualized through an interactive map implemented with OpenLayers, an open-source JavaScript library.

The system comprises pages featuring catalogs of genera and species, reference lists, and sampling stations. The public application allows users to search the catalogs, view detailed profiles of individual species and genera, and access information about published sources and collection sites. Authorized users with administrator or editor privileges have access to tools for adding and deleting records, uploading and organizing images, and editing text blocks through a rich-text editor. The web application interface is available in both Russian and English.

The database contains scanning (SEM) and/or transmission (TEM) electron microscopy materials obtained from 30 published papers. Of these, 25 are copyrighted (Firsova et al. 2015; Bessudova et al. 2017; Bessudova and Likhoshway 2017; Bessudova et al. 2018a-c; 2019; 2020; 2021; 2022a, b; 2023a-g; 2024a, d; 2025a, b, d, e; Bashenkhaeva et al. 2025), while the remaining five were contributed by scientists who, at various times, studied silica-scaled chrysophytes in Siberian water bodies (Balonov and Kuzmina 1986; Kristiansen et al. 1997; Gusev 2016; Gusev et al. 2018; Gusev et al. 2022).

The original micrographs in the database were obtained from research performed between 2017 and 2026 in Siberian reservoirs, lakes and rivers. The study sites included the mouths of large and small rivers, bays, large and small lakes, and unnamed reservoirs. Specifically, the mouths of the following large rivers were examined: the Yenisei, Anabar, Olenek, Yana, Indigirka, Kolyma, Ob, Verkhnyaya Angara, Barguzin, Selenga, and Angara. The mouths of the small rivers include Temnik, Chikoy, Dzhizha, Irkut, Kuda, Kitoy, Belaya, and Ida. The large lakes are Baikal, Labynkyr, Bolshoe Toko, Vorota, Engelhardt, Taimyr, and Frolikha. Small lakes and unnamed water bodies include unnamed lakes in the Lower Yenisei basin, unnamed tundra lakes near the village of Tiksi, and unnamed lakes on Kotelny Island. The reservoirs are Khantayskoye, Kolymskoye, Irkutsk, Bratskoye, Ust-Ilimskoye, and Boguchanskoye.

Sampling for the early studies (through 2022) was performed with either a bathometer or a conventional container, collecting 1–1.3 L from the surface-water horizon. The samples were immediately fixed with Lugol’s solution. After settling and siphoning (concentration) (Utermöl 1958), they were prepared for EM analysis. In later studies (2022–2026), bathometric samples were filtered through 3-µm polyethylene terephthalate filters (Vladipor, Vladimir) using a filtration unit (Reatrek Filter, Obninsk). The material retained on the filter was rinsed off with 5 mL of the unfiltered sample, transferred to a 50-mL Falcon tube, and fixed with glutaraldehyde (final concentration, 2.5%), Lugol’s solution, or formaldehyde (final concentration, 3.7%–4%). The fixed samples were then processed for analysis using EM methods.

Samples were collected from the mouths of the Anabar, Olenek, Yana, Indigirka, and Kolyma rivers, as well as from unnamed tundra lakes near the village of Tiksi, using a plankton net with a mesh size of 15–30 µm. The samples were fixed with glutaraldehyde (final concentration, 2.5%), Lugol’s solution, or formaldehyde (final concentration, 3.7%–4%) and then prepared for EM.

For EM, 1 mL samples were transferred to 1.5 mL Eppendorf tubes and centrifuged in a MiniSpin centrifuge (Eppendorf, Germany) at a maximum speed of 13,400 rpm for 10 min. The supernatant was then removed by pipetting, and the precipitate was resuspended in distilled water and centrifuged three times. Next, 30% hydrogen peroxide (H₂O₂) was added to the washed precipitate, which was incubated in a thermostat at 80 °C for 2–4 h. The precipitate was then washed with distilled water to remove the H₂O₂ and centrifuged three additional times. Finally, the washed sample was prepared for examination by SEM or TEM.

For SEM examination, the washed precipitate (50 µL) was thoroughly mixed, and a drop was placed on an alcohol-pretreated SEM stub. The stub number was recorded in the work log. The sample was air-dried, sputter-coated with gold using an SCD 004 vacuum sputter coater (Balzers, Liechtenstein), and examined using a Quanta 200 scanning electron microscope (FEI Company, USA).

For TEM examination, the sample was deposited onto a prepared 3-mm-diameter mesh coated with a Formvar film substrate, dried at room temperature, and analyzed using a LEO 906E transmission electron microscope (Carl Zeiss, Germany).

As a result of research performed in the freshwaters, lakes and rivers of Eastern Siberia, an extensive information on silica-scaled chrysophytes has been compiled. This information needed to be cataloged and systematically organized to make it accessible to all interested users. To address this need, the database “Silica-scaled chrysophytes from Siberia” was developed and made available online at https://lin.irk.ru/chrysophytes-siberia. The database is designed to facilitate analysis of the distribution and ecology of silica-scaled chrysophytes in Siberian water bodies. The database contains distributional and ecological data based on more than 3,500 records extracted from 30 published papers. For each genus represented in the database, a concise description outlines its principal diagnostic features and the morphological terminology used for its silica elements, and is supplemented by a structural diagram. The taxa assigned to each genus are arranged alphabetically.

Each taxon entry includes links to the authors and the publication containing its original description, the original electron micrographs, discovery-site information with geographical coordinates linked to an online map, the sampling date, and key water parameters, including temperature, pH, and electrical conductivity (Fig. 1).

Currently, the online database includes records for 151 described species and intraspecific taxa representing seven genera: Chrysosphaerella (7 species), Spiniferomonas (18), Paraphysomonas (15), Lepidochromonas (13), Polylepidomonas (1), Mallomonas (62), and Synura (35). The database also contains information on 43 potentially new species whose silica scales differ from those of previously described species, although insufficient material is available for their complete characterization. Of these, 11 species belong to the genus Mallomonas, 10 to Synura, 15 to Paraphysomonas, 3 to Lepidochromonas, 2 to Spiniferomonas, and 2 to Chrysosphaerella. These records further highlight the significant potential diversity of silica-scaled chrysophytes inhabiting Siberian water bodies. In the future, these specimens may help characterize the species more comprehensively and advance studies of their ecology and biogeography. Among the potentially new species are unique specimens, including Mallomonas sp. 8 from the subglacial samples of Lake Baikal. Its posterior scales bear a feature unique within the genus: an opening at the base of the dome. Only two of the approximately 250 species known worldwide exhibit this distinctive ultrastructural feature, including the extant species Mallomonas paludosa Fott and the fossil M. aperturae Siver, described from sedimentary rocks dating to the Middle Eocene (approximately 47.8 Ma) (Siver 2018).

The database contains original electron micrographs of most species, acquired using both SEM and TEM. Because these complementary techniques reveal different aspects of morphology, their combined use provides the most comprehensive view of scale ultrastructure (Fig. 1). The micrographs presented depict scales, bristles, or spines. For most species, the micrographs show cells, whereas for 12 species they show stomatocysts: Chrysosphaerella baikalensis Popovskaya (Stomatocyst 507 Firsova et Bessudova 2024), C. coronacircumspina Wujek et Kristiansen (Stomatocyst 156 Zeeb et Smol 1993), Spiniferomonas abrupta Nielsen (Stomatocyst 513 Firsova et Bessudova 2025) (Fig. 1), S. minuta Nicholls (Stomatocyst 331 Firsova et Likhoshway 2006), S. septispina Nicholls (Stomatocyst 302 (Firsova 2006) Firsova et Bessudova 2024), S. bourrellyi Takahashi (Stomatocyst 180 Zeeb et Smol 1993), S. trioralis Takahashi (Stomatocyst 111 Zeeb et al. 1990), Paraphysomonas corynephora Preisig et Hibberd (Stomatocyst 52 (Duff et Smol 1991) Duff et al. 1995), P. circumvallata Thomsen (Stomatocyst 514 Firsova et Bessudova 2026), Mallomonas akrokomos Ruttner (Stomatocyst 118 Zeeb et al. 1990), M. crassisquama (Asmund) Fott, and Mallomonas sp. 5 (Stomatocyst 166 Zeeb et Smol 1993). Identifying known stomatocyst morphotypes, or discovering new ones and correlating them with the species that produce them, enables their use in monitoring modern water bodies and as paleoindicators for reconstructing the geological past. Moreover, stomatocyst morphotypes may provide an additional criterion for defining species of silica-scaled chrysophytes.

The location data identify the water body from which the samples were collected, the station number for large water bodies, and the corresponding geographical coordinates. Based on the sampling stations, the online database contains records for 256 locations and 234 unique station coordinates (Fig. 2).

The sampling date is essential for monitoring and investigating seasonal and interannual changes in the region’s water bodies.

The selection of three key water parameters (temperature, pH, and electrical conductivity) was based on laboratory and field studies demonstrating the particular sensitivity of silica-scaled chrysophytes to these characteristics (Gutowski 1989; Siver and Hamer 1989; 1992; Cumming et al. 1992; Siver and Lott 2010; 2012; Hyatt et al. 2010). Gradients in these parameters play an important role in determining species distributions in the environment (Siver and Lott 2010; 2012; Siver 2015; Bessudova et al. 2024d).

The online database is freely available to all interested researchers seeking information on the distribution and ecological ranges of these species across Siberian reservoirs, lakes and rivers. It will support monitoring, paleolimnological and biogeographic research, biodiversity studies, and investigations into the processes shaping biodiversity.

The microscopy studies were performed at the Electron Microscopy Center of the Shared Research Facilities “Ultramicroanalysis” of the Limnological Institute, https://www.lin.irk.ru/copp/, accessed on 5 March 2025. The study was supported by the Ministry of Science and Higher Education of the Russian Federation in the frames of Agreements FWSR-2026-0001 project, theme No. 1023032700153-7.6.17.