Jump to ContentJump to Main Navigation
Show Summary Details
More options …


More options …
Volume 66, Issue 2


Rapid differentiation of phenotypically and genotypically similar Synechococcus elongatus strains by PCR fingerprinting.

Gangatharan Muralitharan
  • Department of Microbiology, School of Life Sciences, Bharathidasan University, Palkalaiperur, Tiruchirappalli, 620 024, Tamilnadu, India
  • Email
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Nooruddin Thajuddin
  • Department of Microbiology, School of Life Sciences, Bharathidasan University, Palkalaiperur, Tiruchirappalli, 620 024, Tamilnadu, India
  • Email
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
Published Online: 2011-02-20 | DOI: https://doi.org/10.2478/s11756-011-0003-8


PCR amplification techniques viz., repetitive DNA element PCR (REP-PCR), short tandemly repeated repetitive PCR (STRR-PCR) and arbitrarily primed PCR (RAPD-PCR) were used for the taxonomic discrimination among the strains of the unicellular cyanobacterium Synechococcus elongatus collected across the coastal regions of the Indian subcontinent. These strains showed similar phenotypic and genotypic characteristics. Data obtained from genomic fingerprinting were used to perform cluster analysis and demonstrated ability to differentiate strains at intra-specific level. Polymorphisms of different PCR amplification products can serve as strain-specific molecular fingerprints. In comparison with the STRR and RAPD, the REP primer set generates fingerprints of lower complexity, but still the phenogram clearly differentiated the strains. In conclusion, described PCR fingerprinting methods can be considered as promising tools for the differentiation at the strain level of cyanobacteria from the same species.

Keywords: Synechococcus elongatus; genetic diversity; PCR-fingerprinting; RAPD-PCR; REP-PCR; STRR-PCR

  • [1] Alberte R.S., Wood A.M., Kursar T.A. & Guillard R.R.L. 1984. Novel phycoerythrins in marine Synechococcus spp.: characterization, and evolutionary and ecological implications. Plant Physiol. 75: 732–739. http://dx.doi.org/10.1104/pp.75.3.732CrossrefGoogle Scholar

  • [2] Appuhamy S., Parton R., Coote J.G. & Gibb H.A. 1997. Genome fingerprinting of Haemophilus somnus by a combination of PCR methods. J. Clin. Microbiol. 35: 288–291. Google Scholar

  • [3] Armstrong J., Gibbs A., Peakall R. & Weiller G. 1994. The RAPDistance Package. ftp://life.anu.edu.au ( pub/molecular_biology_rapd_pack.exe. Google Scholar

  • [4] Castenholz R.W. & Waterbury J.B. 1989. Oxygenic photosynthetic bacteria. Group I. Cyanobacteria. Preface, pp. 1710–1727. In: Staley J.T., Bryant M.P., Pfennig N. & Holt J.G. (eds), Bergey’s Manual of Systematic Bacteriology, Vol 3, Williams & Wilkins, Baltimore. Google Scholar

  • [5] De Bruijn F.J. 1992. Use of repetitive (repetitive extragenic palindromic and enterobacterial repetitive intergenic consensus) sequences and the polymerase chain reaction to fingerprint the genomes of Rhizobium meliloti isolates and other soil bacteria. Appl. Environ. Microbiol. 58: 2180–2187. Google Scholar

  • [6] Georghiou P.R., Hamill R.J., Wright C.E., Versalovic J., Kowuth T., Watson D.A. & Lupski J.R. 1995. Molecular epidemiology of infections due to Enterobacter aerogens: identification of hospital-associated strains by molecular techniques. Clin. Infect. Dis. 20: 84–94. CrossrefGoogle Scholar

  • [7] Guevara R., Armesto J.J. & Caru M. 2002. Genetic diversity of Nostoc microsymbionts from Gunnera tinctoria revealed by PCR-STRR fingerprinting. Microb. Ecol. 44: 127–136. http://dx.doi.org/10.1007/s00248-002-1019-yCrossrefGoogle Scholar

  • [8] Herdman M., Castenholz R.W., Iteman I., Waterbury J.B. & Rippka R. 2001. Subsection I (Formerly Chroococcales Wettstein 1924, emend. Rippka et al., 1979), pp. 493–514. In: Boone D.R., Castenholz R.W. & Garrity G.M. (eds), Bergey’s Manual of Systematic Bacteriology, 2nd ed., Vol. 1, The archaea and the deeply branching and phototrophic bacteria, Springer Publishers, New York. Google Scholar

  • [9] Honda D., Yokota A. & Sugiyama J. 1999. Detection of seven major evolutionary lineages in cyanobacteria based on the 16S rRNA gene sequence analysis with new sequences of five marine Synechococcus strains. J. Mol. Evol. 48: 723–739. http://dx.doi.org/10.1007/PL00006517CrossrefGoogle Scholar

  • [10] Katayama T., Okamoto S., Narikawa R., Fujisawa T., Kawashima S. & Itoh M. 2002. Comprehensive analysis of tandem repeat sequences in cyanobacteria genome. Genome Inform. 13: 400–401. Google Scholar

  • [11] Kumar S., Tamura K. & Nei M. 2004. MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Brief. Bioinform. 5: 150–163. http://dx.doi.org/10.1093/bib/5.2.150CrossrefGoogle Scholar

  • [12] Laloui W., Palinska K.A., Rippka R., Partensky F., Tandeau de Marsac N., Herdman M. & Iteman I. 2002. Genotyping of axenic and non-axenic isolates of the genus Prochlorococcus and the OMF-’Synechococcus’ clade by size, sequence analysis or RFLP of the Internal Transcribed Spacer of the ribosomal operon. Microbiology 148: 453–465. Google Scholar

  • [13] Lupski J.R. & Weinstock G.M. 1992. Short, interspersed repetitive DNA sequences in prokaryotic genomes. J. Bacteriol. 174: 4525–4529. Google Scholar

  • [14] Ma Y., Jiao N.J. & Zeng Y.H. 2004. Natural community structure of cyanobacteria in the South China Sea as revealed by rpoC1 gene sequence analysis. Lett. Appl. Microbiol. 39: 353–358. http://dx.doi.org/10.1111/j.1472-765X.2004.01588.xGoogle Scholar

  • [15] Mazel D., Houmard J., Castets A.M. & Tandeau de Marsac N. 1990. Highly repetitive DNA sequences in cyanobacterial genomes. J. Bacteriol. 172: 2755–2761. Google Scholar

  • [16] Muralitharan G. & Thajuddin N. 2008. Evidence on the presence of tRNAfmet group I introns in the marine cyanobacterium Synechococcus elongatus. J. Microbiol. Biotechnol. 18: 23–27. Google Scholar

  • [17] Nei M. & Li W.H. 1979. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc. Natl. Acad. Sci. USA, 76: 5269–5273. http://dx.doi.org/10.1073/pnas.76.10.5269CrossrefGoogle Scholar

  • [18] Neilan B.A. 1995. Identification and phylogenetic analysis of toxigenic cyanobacteria by multiplex randomly amplified polymorphic DNA PCR. Appl. Environ. Microbiol. 61: 2286–2291. Google Scholar

  • [19] Ong L.J. & Glazer A.N. 1987. R-phycocyanin II, a new phycocyanin occurring in marine Synechococcus species: identification of the terminal energy acceptor bilin in phycocyanins. J. Biol. Chem. 262: 6323–6327. Google Scholar

  • [20] Palenik B. 2001. Chromatic adaptation in marine Synechococcus strains. Appl. Environ. Microbiol. 67: 991–994. http://dx.doi.org/10.1128/AEM.67.2.991-994.2001CrossrefGoogle Scholar

  • [21] Prabina B.J., Kumar K. & Kannaiyan S. 2005. DNA amplification fingerprinting as a tool for checking genetic purity of strains in the cyanobacterial inoculum. World J. Microbiol. Biotechnol. 21: 629–634. http://dx.doi.org/10.1007/s11274-004-3566-5CrossrefGoogle Scholar

  • [22] Rasmussen U. & Svenning M. 1998. Fingerprinting of cyanobacteria based on PCR with primers derived from short and long tandemly repeated repetitive sequences. Appl. Environ. Microbiol. 64: 265–272. Google Scholar

  • [23] Rippka R., Deruelles J., Waterbury J.B., Herdmann M. & Stanier Y. 1979. Generic assignments, strain histories and properties of pure cultures of cyanobacteria. J. Gen. Microbiol. 111: 1–61. CrossrefGoogle Scholar

  • [24] Robertson B.R., Tezuka N. & Watanabe M.M. 2001. Phylogenetic analyses of Synechococcus strains (cyanobacteria) using sequences of 16S rDNA and part of the phycocyanin operon revealed multiple evolutionary lines and reflects phycobilin content. Int. J. Syst. Evol. Microbiol. 51: 861–871. CrossrefGoogle Scholar

  • [25] Rouhiainen L., Sivonen K., Buikema W.J. & Haselkorn R. 1995. Characterization of toxin-producing cyanobacteria by using an oligonucleotide probe containing a randomly repeated heptamer. J. Bacteriol. 177: 6021–6026. Google Scholar

  • [26] Selvakumar G. & Gopalaswamy G. 2008. PCR based fingerprinting of Westiellopsis cultures with short tandemly repeated repetitive (STRR) and highly iterated palindrome (HIP) sequences. Biologia 63: 283–288. http://dx.doi.org/10.2478/s11756-008-0065-4Web of ScienceCrossrefGoogle Scholar

  • [27] Sood A., Prasanna R., Prasanna B.M. & Singh P.A. 2008. Genetic diversity among and within cultured cyanobionts of diverse species of Azolla. Folia Microbiol. 53: 35–43. http://dx.doi.org/10.1007/s12223-008-0005-2Web of ScienceCrossrefGoogle Scholar

  • [28] Thajuddin, N. & Muralitharan G. 2008. Applications of PCR based fingerprinting in the phylogeny of marine cyanobacteria. Indian Hydrobiol. 11: 25–41. Google Scholar

  • [29] Thajuddin N. & Subramanian G. 1992. Survey of Cyanobacterial flora of the southern east coast of India. Bot. Mar. 35: 305–311. http://dx.doi.org/10.1515/botm.1992.35.4.305CrossrefGoogle Scholar

  • [30] Toledo G. & Palenik B. 1997. Synechococcus diversity in the California Current as seen by RNA polymerase (rpoC1) gene sequences of isolated strains. Appl. Environ. Microbiol. 63: 4298–4303. Google Scholar

  • [31] Toledo G., Palenik B. & Brahamsha B. 1999. Swimming marine Synechococcus strains with widely different photosynthetic pigment ratios form a monophyletic group. Appl. Environ. Microbiol. 65: 5247–5251. Google Scholar

  • [32] Urbach E., Scanlan D.J., Distel D.L., Waterbury J.B. & Chisholm S.W. 1998. Rapid diversification of marine picophytoplankton with dissimilar light-harvesting structures inferred from sequences of Prochlorococcus and Synechococcus (cyanobacteria). J. Mol. Evol. 46: 188–201. http://dx.doi.org/10.1007/PL00006294CrossrefGoogle Scholar

  • [33] van Coppenhole B., Watanabe I., van Hove C., Second G., Huang N. & McCouch S.R. 1993. Genetic diversity and phylogeny analysis of Azolla based on DNA amplification by arbitrary primers. Genome 36: 686–693. http://dx.doi.org/10.1139/g93-092CrossrefGoogle Scholar

  • [34] Versalovic J., Koeuth T. & Lupski J.R. 1991. Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting of bacterial genomes. Nucleic Acids Res. 19: 6823–6831. http://dx.doi.org/10.1093/nar/19.24.6823CrossrefGoogle Scholar

  • [35] Waterbury J.B. & Rippka R. 1989. Subsection I. Order Chroococcales Wettstein 1924, emend. Rippka et al., 1979, pp. 1728–1746. In: Staley J.T., Bryant M.P., Pfennig N. & Holt J.G. (eds), Bergey’s Manual of Systematic Bacteriology, Vol 3, Williams & Wilkins, Baltimore. Google Scholar

  • [36] Waterbury J.B., Watson S.W., Valois F.W. & Franks D.G. 1986. Biological and ecological characterization of marine unicellular cyanobacterium Synechococcus. Can. Bul. Fish. Aquat. Sci. 214: 71–120. Google Scholar

  • [37] Waterbury J.B., Willey J.M., Franks D.G., Valois F.W. & Watson S.W. 1985. A cyanobacterium capable of swimming motility. Science 230: 71–120. http://dx.doi.org/10.1126/science.230.4721.74CrossrefGoogle Scholar

  • [38] West N.J. & Adams D.G. 1997. Phenotypic and genotypic comparison of symbiotic and free living cyanobacteria from single field site. Appl. Environ. Microbiol. 63: 4479–4484. Google Scholar

  • [39] Wilson K.M., Schembri M.A., Baker P.D. & Saint C.P. 2000. Molecular characterization of the toxic cyanobacterium Cylindrospermopsis raciborskii and design of a species specific PCR. Appl. Environ. Microbiol. 66: 332–338. http://dx.doi.org/10.1128/AEM.66.1.332-338.2000CrossrefGoogle Scholar

  • [40] Zheng W., Nilsson M., Bergman B. & Rasmussen U. 1999. Genetic diversity and classification of cyanobacteria in different Azolla species by the use of PCR fingerprinting. Theor. Appl. Genet. 99: 1187–1193. http://dx.doi.org/10.1007/s001220051323CrossrefGoogle Scholar

  • [41] Zheng W., Song T., Bao X., Bergman B. & Rasmussen U. 2002. High cyanobacterial diversity in coralloid roots of cycads revealed by PCR fingerprinting. FEMS Microbiol. Ecol. 40: 215–222. http://dx.doi.org/10.1111/j.1574-6941.2002.tb00954.xCrossrefGoogle Scholar

About the article

Published Online: 2011-02-20

Published in Print: 2011-04-01

Citation Information: Biologia, Volume 66, Issue 2, Pages 238–243, ISSN (Online) 1336-9563, ISSN (Print) 0006-3088, DOI: https://doi.org/10.2478/s11756-011-0003-8.

Export Citation

© 2011 Slovak Academy of Sciences. This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License. BY-NC-ND 3.0

Citing Articles

Here you can find all Crossref-listed publications in which this article is cited. If you would like to receive automatic email messages as soon as this article is cited in other publications, simply activate the “Citation Alert” on the top of this page.

Cara L. Fiore, Krista Longnecker, Melissa C. Kido Soule, and Elizabeth B. Kujawinski
Environmental Microbiology, 2015, Volume 17, Number 10, Page 3949

Comments (0)

Please log in or register to comment.
Log in