Algal and cyanobacterial diversity in saline rivers of the Elton Lake Basin (Russia) studied via light microscopy and next-generation sequencing

  • M. E. Ignatenko Institute for Cellular and Intracellular Symbiosis of the Ural Branch of the Russian Academy of Sciences
  • E. A. Selivanova Institute for Cellular and Intracellular Symbiosis of the Ural Branch of the Russian Academy of Sciences
  • Y. A. Khlopko Institute for Cellular and Intracellular Symbiosis of the Ural Branch of the Russian Academy of Sciences
  • Y. A. Khlopko Institute for Cellular and Intracellular Symbiosis of the Ural Branch of the Russian Academy of Sciences
  • T. N. Yatsenko-Stepanova Institute for Cellular and Intracellular Symbiosis of the Ural Branch of the Russian Academy of Sciences
Keywords: microalgae; Cyanobacteria; saline rivers; Elton; light microscopy; next-generation sequencing.


Naturally saline rivers are known in various regions of the world. Saline rivers with a salinity gradient from the source to the mouth are particularly interesting, because the range of salinity is the structure-forming factor of the hydrobiont assemblage. Such rivers are represented by saline rivers of the Elton Lake Basin in Volgograd region of Russia (the Bolshaya Samoroda River and the Malaya Samoroda River). Herein, we analyzed taxonomic structure and species diversity of microalgae and Cyanobacteria of the saline rivers flowing into the Elton Lake by light microscopy and next-generation sequencing. The differences and possible causes of inconsistencies in the results obtained by these methods are discussed. In total, 91 taxa of microorganisms were identified by integrated approach in the assemblages of microalgae and Cyanobacteria in the middle course of the Bolshaya Samoroda River, and 60 taxa – in the river mouth. The species diversity of those assemblages in the hypersaline Malaya Samoroda River was lower: 27 taxa from the middle course and 23 taxa from the mouth. Next-generation sequencing allowed us to refine and expand the list of microalgae taxa in the studied saline rivers due to detection of species which were hard to identify, low-abundance taxa, as well as extremely small-cell forms. Some discrepancies between the data obtained by light microscopy and next-generation sequencing indicate the advantage of simultaneous use of both methods for study of the algae communities. Such a comprehensive approach provides the most accurate and correct list of taxa added with the morphological descriptions and 18S rRNA and 16S rRNA partial sequences. Generally, 18 taxa have been recorded for the first time in the Bolshaya Samoroda River, belonging to the phyla Chlorophyta (Borodinellopsis sp., Chlorochytrium lemnae Cohn, Caespitella sp., Halochlorococcum sp., Tetraselmis cordiformis (H. J. Carter) F. Stein), Ochrophyta (Pseudocharaciopsis ovalis (Chodat) D. J. Hibberd, Characiopsis sp., Poterioochromonas stipitata Scherffel, Chrysolepidomonas sp.), Euglenozoa (Euglena bucharica I. Kisselev, Lepocinclis tripteris (Dujardin) B. Marin & Melkonian, Phacus orbicularis K. Hübner, P. parvulus G. A. Klebs), Cryptophyta (Hemiselmis cryptochromatica C. E. Lane & J. M. Archibald, Rhodomonas sp., Hanusia phi J. A. Deane), Haptophyta (Pavlova sp.), Cyanobacteria (Johanseninema constrictum (Szafer) Hasler, Dvorák & Poulícková). Seven taxa have been detected for the first time in the algal and cyanobacterial assemblages of the Malaya Samoroda River from the phyla Chlorophyta (Tetraselmis cordiformis, T. arnoldii (Proschkina-Lavrenko) R. E. Norris, Hori & Chihara, T. tetrathele (West) Butcher, Pyrobotrys elongatus Korshikov), Cryptophyta (Hanusia phi), and Cyanobacteria (Synechococcus elongatus (Nägeli) Nägeli, Oscillatoria simplicissima Gomont).


Afonina, E. Y., & Tashlykova, N. A. (2018). Plankton community and the relationship with the environment in saline lakes of Onon-Torey plain, Northeastern Mongolia. Saudi Journal of Biological Sciences, 25, 399–408.

Almutairi, A. W., & Toulibah, H. E. (2017). Effect of salinity and pH on fatty acid profile of the green algae Tetraselmis suecica. Journal of Petroleum and Environmental Biotechnology, 8(3), 1–6.

Arora, M., Anil, A. C., Leliaert, F., Delany, J., & Mesbahi, E. (2013). Tetraselmis indica (Chlorodendrophyceae, Chlorophyta), a new species isolated from salt pans in Goa, India. European Journal of Phycology, 48(1), 61–78.

Bel’kova, N. L., Dzyuba, E. V., Sukhanova, E. V., & Khanaeva, T. A. (2008). Adaptaciya metodov molekulyarno-geneticheskogo analiza dlya izucheniya mikroorganizmov, associirovannyh s rybami [Adaptation of molecular genetic methods to study microorganisms associated with fish]. Inland Water Biology, 1(2), 192–195 (in Russian).

Belevich, T. A., Ilyash, L. V., Milyutina, I. A., Logacheva, M. D., Goryunov, D. V., & Troitsky, A. V. (2015). Metagenomika pikovodoroslej Belogo morya: Pervye dannye [Metagenomic analyses of White Sea picoalgae: First data]. Biochemistry, 80(11), 1514–1521 (in Russian).

Burkova, T. N. (2016). Taksonomicheskaya harakteristika fitoplanktona vysokomineralizovannoj reki Bol’shaya Smorogda (Priel’ton’e) [Taxonomic characteristics of phytoplankton river Big Smorogda with high-mineral waters (Lake Elton’s plain)]. Samarskaya Luka: Problems of regional and global ecology, 25(1), 131–138 (in Russian).

Burkova, T. N. (2012). Fitoplankton mineralizovannoj reki Malaya Samoroda (ozero Elton) [Phytoplankton of the saline River Malaya Smorogda (Lake Elton)]. Materials of the reports of the II All-Russian Scientific Conference with international participation “Small rivers: Ecological state and prospects of development”. Cheboksary, 70–74 (in Russian).

Burkova, T. N. (2015). Aal’goflora planktona vysokomineralizovannoj reki Bol’shaya Smorogda (Priel’ton’e) [Algae flora of saline plankton of the River Bolshaya Smorogda (Lake Elton)]. Proceedings of the Samara Scientific Center, 17(4), 745–748 (in Russian).

Deane, J., Hill, D., Brett, S., & McFadden, G. (1998). Hanusia phi gen. et sp. nov. (Cryptophyceae): Characterization of ‘Cryptomonas sp. Φ’. European Journal of Phycology, 33(2), 149–154.

Edgar, R. C. (2013). UPARSE: Highly accurate OTU sequences from microbial amplicon reads. Nature Methods, 10, 996–998.

Gao, W., Chen, Z., Li, Y., Pan, Y., Zhu, J., Guo, S., Hu, L., & Huang, J. (2018). Bioassessment of a drinking water reservoir using plankton: High throughput sequencing vs. traditional morphological method. Water, 10(1), 82.

Gorokhova, O. G. (2018). Al’goflora rek bassejna gipergalinnogo ozera Elton [Flora algae rivers tributaries salt Lake Elton]. In: Environmental problems of large river basins – 6”. Materials of the international conference. Pp. 81–83 (in Russian).

Gorokhova, O. G., & Zinchenko, T. D. (2014). Fitoplankton vysokomineralizovannyh rek Priel’ton’ya [Phytoplankton of the highly mineralized rivers of the Lake Elton basin]. Proceedings of the Samara scientific center, Russian Academy of Sciences, 16(5), 1715–1721 (in Russian).

Gorokhova, O. G., & Zinchenko, T. D. (2016). Raznoobrazie i struktura soobshchestv fitoplanktona vysokomingeralizovannyh rek bassejna ozera El’ton [Diversity and structure of phytoplankton communities in highly mineralized rivers of the Lake Elton basin]. Water: Chemistry and Ecology, 11, 58–65 (in Russian).

Groendahl, S., Kahlert, M., & Fink, P. (2017). The best of both worlds: A combined approach for analyzing microalgal diversity via metabarcoding and morphology-based methods. PLoS One, 12(2), e0172808.

Guiry, M. D., & Guiry, G. M. (2021). AlgaeBase. World-wide electronic publication, National University of Ireland, Galway.

Gusakov V. A. (2019). Donnaya mejofauna vysokomineralizovannyh rek prirodnogo parka “El’tonskij” (Rossiya) [Bottom meiofauna of highly mineralised rivers in the Eltonsky Nature Park (Russia)]. Nature Conservation Research, 4(1), 37–63 (in Russian).

Gutiérrez-Cánovas, C., Arribas, P., Naselli-Flores, L., Bennas, N., Finocchiaro, M., Millán, A., & Velasco, J. (2019). Evaluating anthropogenic impacts on naturally stressed ecosystems: Revisiting river classifications and biomonitoring metrics along salinity gradients. Science of the Total Environment, 658, 912–921.

Hašler, P., Dvořak, P., Johansen, J., Kitner M., Ondřej, V., & Pouličkova, A. (2012). Morphological and molecular study of epipelic filamentous genera Phormidium, Microcoleus and Geitlerinema (Oscillatoriales, Cyanophyta/Cyanobacteria). Fottea, a Journal of the Czech Phycological Society, 12(2), 341–356.

Heidelberg, K. B., Nelson, W. C., Holm, J. B., Eisenkolb, N., Andrade, K., & Emerson, J. B. (2013). Characterization of eukaryotic microbial diversity in hypersaline Lake Tyrrell, Australia. Frontiers in Microbiology, 4, 115.

Ishika, T., Bahri, P. A., Laird, D. W., & Moheimani, N. R. (2018). The effect of gradual increase in salinity on the biomass productivity and biochemical composition of several marine, halotolerant, and halophilic microalgae. Journal of Applied Phycology, 30, 1453–1464.

Kim, K. M., Park, J.-H., Bhattacharya, D., & Yoon, H. S. (2014). Applications of next-generation sequencing to unravelling the evolutionary history of algae. International Journal of Systematic and Evolutionary Microbiology, 64, 333–345.

Klindworth, A., Pruesse, E., Schweer, T., Peplies, J., Quast, C., Horn, M., & Glöckner, F. O. (2013). Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Research, 41(1), e1.

Komárek, J., Kaštovský, J., Mareš, J., & Johansen, J. R. (2014). Taxonomic classification of cyanoprokaryotes (cyanobacterial genera) 2014, using a polyphasic approach. Preslia, 86, 295–335.

Krakhmalny, A. F. (2011). Dinofitovye vodorosli Ukrainy (Illyustrirovannyj opredelitel’) [Dinophyta of Ukraine (Illustrated book for identification)]. Alterpres, Kiev (in Russian).

Krammer, K., & Lange-Bertalot, H. (1986). Bacillariophyceae. 1. Teil: Naviculaceae. Süßwasserflora von Mitteleuropa 2/1. Gustav Fisher Verlag, Jena (in German).

Krammer, K., & Lange-Bertalot, H. (1988). Bacillariophyceae. 2. Teil: Bacillariaceae, Epithemiaceae, Surirellaceae. Süßwasserflora von Mitteleuropa 2/2. Gustav Fisher Verlag, Jena (in German).

Krammer, K., & Lange-Bertalot, H. (1991a). Bacillariophyceae. 3. Teil: Centrales, Fragilariaceae, Eunotiaceae. Süßwasserflora von Mitteleuropa 2/3. Gustav Fischer Verlag, Stuttgart; Jena (in German).

Krammer, K., & Lange-Bertalot, H. (1991b). Bacillariophyceae. 4. Teil: Achnanthaceae, kritische Ergänzungen zu Navicula (Lineolatae) und Gomphonema. Gesamtliteraturverzeichnis. Süßwasserflora von Mitteleuropa 2/4. Gustav Fischer Verlag, Stuttgart (in German).

Kulikovskiy, M. S., Gusev, E. S., Andreeva, S. A., & Annenkova, N. V. (2014). Phylogenetic position of the diatom genus Geissleria Lange-Bertalot et Metzeltin and description of two new species from Siberian mountain lakes. Phytotaxa, 177(2), 249–260.

Lentendu, G., Wubet, T., Chatzinotas, A., Wilhelm, C., Buscot, F., & Schlegel, M. (2014). Effects of long-term differential fertilization on eukaryotic microbial communities in an arable soil: A multiple barcoding approach. Molecular Ecology, 23(13), 3341–3355.

Lin, G., Chai, J., Yuan, S., Mai, C., Cai, L., Murphy, R. W., Zhou, W., & Luo, J. (2016). VennPainter: A tool for the comparison and identification of candidate genes based on Venn diagrams. PLoS One, 11(4), e0154315.

Liu, Y., Yao, T., Jiao, N., Kang, S., Xu, B., Zeng, Y., Huang, S., & Liu, X. (2009). Bacterial diversity in the snow over Tibetan Plateau Glaciers. Extremophiles, 13, 411–423.

Manoylov, K. M. (2014). Taxonomic identification of algae (morphological and molecular): Species concepts, methodologies, and their implications for ecological bioassessment. Journal of Phycology, 50, 409–424.

Manoylov, K. M., France, Y. E., Geletu, A., & Dominy, J. N. (Jr.). (2016). Algal community membership of estuarine mudflats from the savannah river, United States. Journal of Marine Science and Engineering, 4(1), 11.

Masyuk, N. P., & Lilitskaya, G. G. (2006). Chlorodendrophyceae class. nov. (Chlorophyta, Viridiplantae) in the flora of Ukraine. II. The Genus Tetraselmis F. Stein. Ukjrainskii Botanicheskii Jurnal, 63(6), 741–758 (in Ukrainian).

Masyuk, N. P., Posudin, Y. I., & Lilitskaya, G. G. (2007). Fotodvizhzenie kletok Dunaliella Teod. (Dunaliellales, Chlorophyceae, Viridiplantae) [Photomovement of Dunaliella Teod. cells (Dunaliellales, Chlorophyceae, Viridiplantae)]. Kiev (in Russian).

Medlin, L. K. (2018). Mini review: Diatom species as seen through a molecular window. Brazilian Journal of Botany, 41, 457–469.

Millán, A., Velasco, J., Gutiérrez-Cánovas, C., Arribas, P., Picazo, F., Sánchez-Fernández, D., & Abellán, P. (2011). Mediterranean saline streams in Southeast Spain: What do we know? Journal of Arid Environments, 75, 1352–1359.

Mohammadi, M., Kazeroni, N., & Baboli, M. J. (2015). Fatty acid composition of the marine micro alga Tetraselmis chuii Butcher in response to culture conditions. Journal of Algal Biomass Utilization, 6(2), 49–55.

Oliveira, M. C., Repetti, S. I., Iha, C., Jackson, C. J., Díaz-Tapia, P., Lubiana, K. M. F., Cassano, V., Costa, J. F., Cremen, M. C. M., Marcelino, V. R., & Verbruggen, H. (2018). High-throughput sequencing for algal systematic. European Journal of Phycology, 53(3), 256–272.

Orfeo, O. (1999). Sedimentological characteristics of small rivers with loessic headwaters in the Chaco, South America. Quaternary International, 62, 69–74.

Palinska, K. A., Vogt, J. C., & Surosz, W. (2018). Biodiversity analysis of the unique geothermal microbial ecosystem of the Blue Lagoon (Iceland) using next-generation sequencing (NGS). Hydrobiologia, 811, 93–102.

Pawlowski, J., Kelly-Quinn, M., Altermatt, F., Apothéloz-Perret-Gentil, L., Beja, P., Boggero, A., Borja, A., Bouchez, A., Cordier, T., Domaizon, I., Feio, M. J., Filipe, A. F., Fornaroli, R., Graf, W., Herder, J., Hoorn, B., Jones, J. I., Sagova-Mareckova, M., Moritz, C., Barquín, J., Piggott, J. J., Pinna, M., Rimet, F., Rinkevich, B., Sousa-Santos, C., Specchia, V., Trobajo, R., Vasselon, V., Vitecek, S., Zimmerman, J., Weigand, A., Leese, F., & Kahlert, M. (2018). The future of biotic indices in the ecogenomic era: Integrating (e)DNA metabarcoding in biological assessment of aquatic ecosystems. Science of the Total Environment, 637–638, 1295–1310.

Rivera, S. F., Vasselon, V., Ballorain, K., Carpentier, A., Wetzel, C. E., Ector, L., Bouchez, A., & Rimet, F. (2018a). DNA metabarcoding and microscopic analyses of sea turtles’ biofilms: Complementary to understand turtle behavior. PLoS One, 13(4), e0195770.

Rivera, S. F., Vasselon, V., Jacquet, S., Bouchez, A., Ariztegui, D., & Rimet, F. (2018b). Metabarcoding of lake benthic diatoms: From structure assemblages to ecological assessment. Hydrobiologia, 807, 37–51.

Saadaoui, I., Ghazal, G. A., Bounnit, T., Khulaifi, F. A., Jabri, H. A., & Potts, M. (2016). Evidence of thermo and halotolerant Nannochloris isolate suitable for biodiesel production in Qatar Culture Collection of Cyanobacteria and Microalgae. Algal Research, 14, 39–47.

Selivanova, E. A., Ignatenko, M. E., Yatsenko-Stepanova, T. N., & Plotnikov, A. O. (2019). Diatom assemblages of the brackish Bolshaya Samoroda River (Russia) studied via light microscopy and DNA metabarcoding. Protistology, 13(4), 215–235.

Shitikov, V. K., Rosenberg, G. S., & Zinchenko, T. D. (2003). Kolichestvennaya gidroekologiya: Metody sistemnoj identifikacii [Quantitative hydroecology: Methods of system identification]. IEWB RAS, Togliatti (in Russian).

Skarlato, S. O., & Telesh, I. V. (2017). Razvitie koncepcii maksimal’nogo raznoobraziya protistov v zone kriticheskoj solenosti vody [Development of the concept of maximum diversity of protists in the zone of critical salinity of water]. Biology of the Sea, 43(1), 3–14 (in Russian).

Solovchenko, A. E., Selivanova, E. A., Chekanov, K. A., Sidorov, R. A., Nemtseva, N. V., & Lobakova, E. S. (2015). Indukciya vtorichnogo karotinogeneza u novyh galofil’nyh mikrovodoroslej iz roda Dunaliella (Chlorophyceae) [Induction of secondary carotenogenesis in new halophile microalgae from genus Dunaliella (Chlorophyceae). Biochemistry, 80, 1508–1513 (in Russian).

Telesh, I., Schubert, H., & Skarlato, S. (2013). Life in the salinity gradient: Discovering mechanisms behind a new biodiversity pattern. Estuarine, Coastal and Shelf Science, 135, 317–327.

Tsarenko, P. M. (1990). Opredelitel’ hlorokokkovyh vodoroslej Ukrainskoj SSR [Determinant of Сhlorococcal algae of the Ukrainian SSR]. Naukova Dumka, Kiev (in Russian).

Vasser, S. P., Kondratyeva, N. V., Masyuk, N. P., Palamar-Mordvintseva, G. M., Vetrova, Z. I., Kordyum, E. L., Moshkova, N. A., Prikhodkova, L. P., Kovalenko, O. V., Stupina, V. V., Tsarenko, P. M., Junger, V. P., Radchenko, M. I., Vinogradova, O. N., Bukhtiyarova, L. N., & Razumna, L. F. (1989). Vodorosli. Spravochnik [Algae. Guide]. Naukova Dumka, Kiev (in Russian).

Wangensteen, O. S., Palacín, C., Guardiola, M., & Turon, X. (2018). DNA metabarcoding of littoral hardbottom communities: High diversity and database gaps revealed by two molecular markers. PeerJ, 6, e4705.

Yatsenko-Stepanova, T. N., Ignatenko, M. E., Nemtseva, N. V., & Gorokhova, O. G. (2015). Avtotrofnye mikroorganizmy ust’evyh uchastkov vodotokov sistemy ozera El’ton [Autotrophic microorganisms of the mouth parts of the watercourses in the system of Lake Elton]. Arid Ecosystems, 21(2), 47–54 (in Russian).

Zhan, A., Hulak, M., Sylvester, F., Huang, X., Adebayo, A. A., Abbott, C. L., Adamowicz, S. J., Heath, D. D., Cristescu, M. E., & MacIsaac, H. J. (2013). High sensitivity of 454 pyrosequencing for detection of rare species in aquatic communities. Methods in Ecology and Evolution, 4, 558–565.

Zhang, J., Kobert, K., Flouri, T., & Stamatakis, A. (2014). PEAR: A fast and accurate illumina paired-end read merger. Bioinformatics, 30(5), 614–620.

Zinchenko, T. D., Golovatyuk, L. V., Abrosimova, E. V., & Popchenko, T. V. (2017). Macrozoobenthos in saline rivers in the Lake Elton Basin: Spatial and temporal dynamics. Inland Water Biology, 10(4), 384–398.


Most read articles by the same author(s)