Identification and molecular characterization of tropical cyanobacteria of the genus Nostoc, Calothrix, Tolypothrix and Scytonema (Nostocales: Nostocaceae), with possible biotechnological potential

Identification and molecular characterization of tropical cyanobacteria of the genus Nostoc, Calothrix, Tolypothrix and Scytonema (Nostocales: Nostocaceae), with possible biotechnological potential


  • Mariela Corrales Morales Universidad Nacional (UNA)
  • Karolina Villalobos Universidad Nacional (UNA)
  • Abad Rodríguez Rodríguez Universidad Nacional (UNA)
  • Nelson Muñoz Simón Universidad Nacional (UNA)
  • Rodolfo Umaña-Castro Universidad Nacional (UNA)



Cyanobacteria, 16S rRNA, rpoC1, characterization molecular, morphological identification, biotechnological potential


Cyanobacteria or “Blue-Green” algae comprise a diverse cluster of prokaryotic photoautotrophs that share a high morphological and molecular abundance. Biotechnological advances on nitrogen fixation, bioremediation, pharmaceutical and nutritional value have been developed. Traditional identification based on morphology has been the most common applied technique, but it may be inaccurate because of the phenotypic plasticity that those organisms present. For this reason, molecular techniques had become robust tools for taxonomic positioning of tropical cyanobacterial isolates, associated with morphology identification. This study focuses on the morphological identification and molecular characterization of cyanobacteria isolated in different tropical environments of Costa Rica, for biotechnological prospects. Strains were grown in BG0-11 media, photographed under light microscope and classified at genera level. Molecular identification was carried by PCR and sequencing using DNA-dependent RNA polymerase (rpoC1) and small-subunit ribosomal RNA (16S rRNA) gen primers. Subsequently, a phylogenetic positioning analysis was performed by MAFFTv.7 alignment and maximum likelihood by raxMLGUI. Based on phenotypic characteristics, four genera of Nostocales were identified: Calothrix sp., Tolypothrix sp., Scytonema sp. and Nostoc sp. Molecular analysis shows a taxonomic grouping that is consistent with the observed morphology, with the 16S rDNA gene yielding robust and stable results. The identified genera are known for their nitrogen fixation capability: Nostoc and Calothrix have been used in maintaining fertility and soil recovering studies. Nostoc is known for its nutritional properties and biofuel production; a characteristic shared by Tolypothrix as well. The last genera; Scytonema, it is known for its pharmacological properties. With the successful identification of cyanobacteria strains isolated from tropical environments, it is possible to continue the study of genes responsible for properties of biotechnological interest and to evaluate their potential, with future perspectives of application and biodiversity conservation.

Author Biographies

Mariela Corrales Morales, Universidad Nacional (UNA)

Laboratorio de Análisis Genómico, Escuela de Ciencias Biológicas, Universidad Nacional, Sede Omar Dengo, Heredia, Costa Rica

Karolina Villalobos, Universidad Nacional (UNA)

Laboratorio de Análisis Genómico, Escuela de Ciencias Biológicas, Universidad Nacional, Sede Omar Dengo, Heredia, Costa Rica

Abad Rodríguez Rodríguez, Universidad Nacional (UNA)

Laboratorio de Biotecnología de Microalgas, Escuela de Ciencias Biológicas, Universidad Nacional, Sede Omar Dengo, Heredia, Costa Rica

Nelson Muñoz Simón, Universidad Nacional (UNA)

Escuela de Ciencias Biológicas, Universidad Nacional, Sede Omar Dengo, Heredia, Costa Rica;

Rodolfo Umaña-Castro, Universidad Nacional (UNA)

Laboratorio de Análisis Genómico, Escuela de Ciencias Biológicas, Universidad Nacional, Sede Omar Dengo, Heredia, Costa Rica


Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990). Basic local alignment search tool. Journal of molecular biology, 215(3), 403-410.

Arima, H., Horiguchi, N., Takaichi, S., Kofuji, R., Ishida, K. I., Wada, K., & Sakamoto, T. (2012). Molecular genetic and chemotaxonomic characterization of the terrestrial cyanobacterium Nostoc commune and its neighboring species. FEMS microbiology ecology, 79(1), 34-45.

Avendaño, E. M., Pérez, R. M., & Rodríguez, G. S. (2014). Aislamiento, cultivo, viabilidad y evaluación de un consorcio cianobacteria-microalga como acondicionador de suelos. Medicina y Ciencias Biológicas, 35, 51.

Bohunická, M., Pietrasiak, N., Johansen, J. R., Gómez, E. B., Hauer, T., Gaysina, L. A., & Lukešová, A. (2015). Roholtiella, gen. nov. (Nostocales, Cyanobacteria) a tapering and branching cyanobacteria of the family

Nostocaceae. Phytotaxa, 197(2), 84-103.

Bultel-Poncé, V., Félix-Théodose, F., Sarthou, C., Ponge, J. F., & Bodo, B. (2004). New pigments from the terrestrial cyanobacterium Scytonema sp. collected on the Mitaraka Inselberg, French Guyana. Journal of natural products, 67(4), 678-681.

Castresana, J. (2002). Gblocks, v. 0.91b versión en línea disponible en: Cosultada el 18 de enero del 2017.

Cuevas, C., Goyenechea, I., & Iturbe U. (2007). La sistemática, base del conocimiento de la biodiversidad. A. Contreras Ramos (Ed.). UAEH, pp. 65

Darriba, D., Taboada, G. L., Doallo, R., & Posada, D. (2012). jModelTest 2: more models, new heuristics and parallel computing. Nature Methods, 9(8), 772.

De, P. K. (1939). The role of blue-green algae in nitrogen fixation in rice-fields. Proceedings of the Royal Society of London. Series B, Biological Sciences, 121-139.

Debnath, M., & Bhadury, P. (2016). Adaptive responses and arsenic transformation potential of diazotrophic Cyanobacteria isolated from rice fields of arsenic affected Bengal Delta Plain. Journal of Applied Phycology, 28(5), 2777-2792.

Desikachary, T. V. (1959). Cyanophyta. Indian Council of Agricultu¬ral Research, New Delhi, India. Monographs on Algae, pp. 686.

Dhar, D. W., Prasanna, R., Pabbi, S., & Vishwakarma, R. (2015). Significance of cyanobacteria as inoculants in agriculture. In Algal Biorefinery: An Integrated Approach, pp. 339-374.

Engene, N., Cameron, R., & Gerwick, W. H. (2010). 16S rRNA Gene heterogeneity in the filamentous marine cyanobacterial genus LYNGBYA1. Journal of Phycology, 46(3), 591-601.

Faldu, N., Patel, S., Vishwakarma, N. P., Singh, A. K., Patel, K., & Pandhi, N. (2014). Genetic diversity of marine and fresh water cyanobacteria from the Gujarat state of India. Advances in Bioscience and Biotechnology, 5(14), 1061.

Flores, E., López‐Lozano, A., & Herrero, A. (2015). Nitrogen Fixation in the Oxygenic Phototrophic Prokaryotes (Cyanobacteria): The Fight Against Oxygen. Biological Nitrogen Fixation, 879-890.

Galhano, V., De Figueiredo, D. R., Alves, A., Correia, A., Pereira, M. J., Gomes-Laranjo, J., & Peixoto, F. (2011). Morphological, biochemical and molecular characterization of Anabaena, Aphanizomenon and Nostoc strains (Cyanobacteria, Nostocales) isolated from Portuguese freshwater habitats. Hydrobiología, 663(1), 187-203.

Gugger, M., Lyra, C., Suominen, I., Tsitko, I., Humbert, J. F., Salkinoja-Salonen, M. S., & Sivonen, K. (2002). Cellular fatty acids as chemotaxonomic markers of the genera Anabaena, Aphanizomenon, Microcystis, Nostoc and Planktothrix (cyanobacteria). International Journal of Systematic and Evolutionary Microbiology, 52(3), 1007-1015.

Gupta, M., & Chaudhuri, A. N. (2016). Bioremediation of cadmium and lead and its effect on chlorophyll, enzymatic and non enzymatic antioxidants of cyanobacteria. International Journal of Scientific

Research, 4(6), 6-10.

Iteman, I., Rippka, R., de Marsac, N. T., & Herdman, M. (2002). rDNA analyses of planktonic heterocystous cyanobacteria, including members of the genera Anabaenopsis and Cyanospira. Microbiology, 148(2), 481-496.

Jensen, S., Petersen, B. O., Omarsdottir, S., Paulsen, B. S., Duus, J. Ø., & Olafsdottir, E. S. (2013). Structural characterisation of a complex heteroglycan from the cyanobacterium Nostoc commune. Carbohydrate polymers, 91(1), 370-376.

Kishore, K., & Bimal, R. (2010). Distribution of nitrogen‐fixing cyanobacteria (Nostocaceae) during rice cultivation in fertilized and unfertilized paddy fields. Nordic Journal of Botany, 28(1), 100-103.

Komárek, J., & Anagnostidis, K. (1989). Modern approach to the classification system of cyanophytes-4: Nostocales. Archives of Hydrobiology, Suppl. Algological Studies, 56, 247-345.

Komárek, J., & Anagnostidis, K. (1999). Cyanoprokaryota: I. Teil Chroococcales. Band 19/1, Sußwasserflora von Mitteleuropa, Gaustav Fischer Verlag, Jena. pp. 548.

Komárek, J., & Anagnostidis, K. (2005). Cya¬noprokaryota II. Teil Oscillatoriales, Band 19/2, Süßwasserflora von Mitteleuropa, Elsevier GmbH, Munchen. pp. 759.

Komarek, J., Sant’Anna, C. L., Bohunická, M., Mareš, J., Hentschke, G. S., Rigonato, J., & Fiore, M. F. (2014). Phenotype diversity and phylogeny of selected Scytonema-species (Cyanoprokaryota) from SE Brazil. Fottea, 13(2), 173-200.

Kumari, N., Srivastava, A. K., & Bhargava, P. (2009). Molecular approaches towards assessment of cyanobacterial biodiversity. African Journal of Biotechnology, 8(18), 4284-4298.

Lee, E., Ryan, U. M., Monis, P., McGregor, G. B., Bath, A., Gordon, C., & Paparini, A. (2014). Polyphasic identification of cyanobacterial isolates from Australia. Water Research, 59, 248-261.

Liao, H. F., Wu, T. J., Tai, J. L., Chi, M. C., & Lin, L. L. (2015). Immunomodulatory potential of the polysaccharide-rich extract from edible cyanobacterium Nostoc commune. Medical Sciences, 3(4), 112-123.

Lyra, C., Suomalainen, S., Gugger, M., Vezie, C., Sundman, P., Paulin, L., & Sivonen, K. (2001). Molecular characterization of planktic cyanobacteria of Anabaena, Aphanizomenon, Microcystis and Planktothrix genera. International Journal of Systematic and Evolutionary Microbiology, 51(2), 513-526.

Mouser, P. J., N’Guessan, A. L., Elifantz, H., Holmes, D. E., Williams, K. H., Wilkins, M. J. & Lovley, D. R. (2009). Influence of heterogeneous ammonium availability on bacterial community structure and the expression of nitrogen fixation and ammonium transporter genes during in situ bioremediation of uranium-contaminated groundwater. Environmental science & technology, 43(12), 4386-4392.

Porebski, S., Bailey, L. G., & Baum, B. R. (1997). Modification of a CTAB DNA extraction protocol for plants containing high polysaccharide and polyphenol components. Plant molecular biology reporter, 15(1), 8-15.

Prabakaran, P., & Ravindran, A. D. (2011). A comparative study on effective cell disruption methods for lipid extraction from microalgae. Letters in applied microbiology, 53(2), 150-154.

Prasanna, R., Sood, A., Ratha, S. K., & K Singh, P. (2013). Cyanobacteria as a “green” option for sustainable agriculture. Cyanobacteria: An Economic Perspective, pp. 145-166.

Quesada, A., & Vincent, W. F. (2012). Cyanobacteria in the cryosphere: snow, ice and extreme cold. In Ecology of cyanobacteria II. pp. 387-399.

Rajaniemi, P., Hrouzek, P., Kaštovska, K., Willame, R., Rantala, A.,

Hoffmann, L. & Sivonen, K. (2005). Phylogenetic and morphological evaluation of the genera Anabaena, Aphanizomenon, Trichormus and Nostoc (Nostocales, Cyanobacteria). International Journal of Systematic and Evolutionary Microbiology, 55(1), 11-26.

Rambaut, A. (2009). FigTree v1.4 2012–2014: Tree Figure Drawing Tool. Disponible en línea: Consultada el 19 de enero del 2017.

Rinkel, B. E., & Manoylov, K. M. (2014). Calothrix an evaluation of fresh water species in United States rivers and streams, their distribution and preliminary ecological findings. Proceedings of the academy of natural sciences of Philadelphia, 163(1), 43-59.

Sant'Anna, C. L., Azevedo, M. T. P., Fiore, M. F., Lorenzi, A. S., Kaštovský, J., & Komárek, J. (2011). Subgeneric diversity of Brasilonema (Cyanobacteria, Scytonemataceae). Brazilian Journal of Botany, 34(1), 51-62.

Seo, P. S., & Yokota, A. (2003). The phylogenetic relationships of cyanobacteria inferred from 16S rRNA, gyrB, rpoC1 and rpoD1 gene sequences. The Journal of general and applied microbiology, 49(3), 191-203.

Sharma, N. K. (2015). From natural to human-impacted ecosystems: rationale to investigate the impact of urbanization on cyanobacterial diversity in soils. Biodiversity and Conservation, 24(4), 1007-1015.

Sihvonen, L. M., Lyra, C., Fewer, D. P., Rajaniemi-Wacklin, P., Lehtimäki, J. M., Wahlsten, M., & Sivonen, K. (2007). Strains of the cyanobacterial genera Calothrix and Rivularia isolated from the Baltic Sea display cryptic diversity and are distantly related to Gloeotrichia and Tolypothrix. FEMS microbiology ecology, 61(1), 74-84.

Silva, P. G., & de Jesús S. H. (2013). Biomass production of Tolypothrix tenuis as a basic component of a cyanobacterial biofertilizer. Journal of applied phycology, 25(6), 1729-1736.

Singh, S. P., Kumari, S., Rastogi, R. P., Sinha, R., & Sinha, R. P. (2010). Photoprotective and biotechnological potentials of cyanobacterial sheath pigment, scytonemin. African Journal of Biotechnology, 9(5), 580-588.

Singh, S. P., Pathak, J., & Sinha, R. P. (2017). Cyanobacterial factories for the production of green energy and value-added products: An integrated approach for economic viability. Renewable and Sustainable Energy Reviews, 69, 578-595.

Stamatakis, A., Ludwig, T., & Meier, H. (2005). RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics, 21(4), 456-463.

Teneva, I., Stoyanov, P., Mladenov, R., & Dzhambazov, B. (2012). Molecular and phylogenetic characterization of two species of the genus Nostoc (Cyanobacteria) based on the cpcB-IGS-cpcA locus of the phycocyanin operon. Journal of Bioscience and Biotechnology, 1(1), 9-19.

Thajuddin, N., & Subramanian, G. (2010). Cyanobacterial biodiversity and potential applications in biotechnology. Current Science, 89(1), 47-57

Wilmotte, A., and M. Herdman. 2001. Phylogenetic relationships among cyanobacteria based on 16S rRNA sequences, pp. 487–493. In D. R.

Boone and R. W. Castenholz (ed.), Bergey’s manual of systematic bacteriology, vol. 1. Springer, New York, N.Y.

Zhen, Z., Liu, J., Rensing, C., Yan, C., & Zhang, Y. (2017). Effects of two different high-fidelity DNA polymerases on genetic analysis of the cyanobacterial community structure in a subtropical deep freshwater reservoir. Archives of Microbiology, 199(1), 125-134.



How to Cite

Corrales Morales, M., Villalobos, K., Rodríguez Rodríguez, A., Muñoz Simón, N., & Umaña-Castro, R. (2017). Identification and molecular characterization of tropical cyanobacteria of the genus Nostoc, Calothrix, Tolypothrix and Scytonema (Nostocales: Nostocaceae), with possible biotechnological potential. UNED Research Journal, 9(2).