Environmental Engineering Research

Korean Society of Environmental Engineers (대한환경공학회)
권호 표지
DOI QR코드

DOI QR Code

Genetic Diversity and Molecular Phylogeny of Cyanobacteria from Sri Lanka Based on 16S rRNA Gene

  • Wanigatunge, R.P. (Institute of Fundamental Studies) ;
  • Magana-Arachchi, D.N. (Institute of Fundamental Studies) ;
  • Chandrasekharan, N.V. (Department of Chemistry, University of Colombo) ;
  • Kulasooriya, S.A. (Institute of Fundamental Studies)
  • Received : 2014.06.17
  • Accepted : 2014.11.22
  • Published : 2014.12.31
Download PDF
⟨ Previous Next ⟩

Abstract

The diversity of cyanobacteria in Sri Lanka was studied in different water reservoirs, paddy fields, brackish water and tsunami affected areas using light microcopy, 16S rRNA sequences, followed by phylogenetic analysis. Based on light microscopy, 24 genera were identified from environmental samples belonging to the orders Chroococcales, Oscillatoriales, Pleurocapsales and Nostocales. In cultures, 33 genera were identified from all five cyanobacterial orders, including Stigonematales. Based on 16S rRNA gene sequences and their morphology, two isolates were identified up to species level, 72 to genus level, one isolate up to family and 11 up to order level. Twelve isolates couldn't be assigned to any taxonomic level. The results of 16S rRNA gene sequences along with the phylogenetic analysis indicated that some cyanobacterial isolates could be accommodated to genus or order level. The 16S rRNA sequence analysis data in this study confirmed that order Nostocales and order Pleurocapsales cyanobacteria are monophyletic while orders Chroococcales, Oscillatoriales and Stigonematales cyanobacteria are polyphyletic. Polyphasic approach including the combination of light microscopy, cultures and the analysis of 16S rRNA gene sequences provide a promising approach to ascertain the diversity of cyanobacteria in different habitats.

Keywords

References

  1. Beck C, Knoop H, Axmann IM, Steuer R. The diversity of cyanobacterial metabolism: genome analysis of multiple phototrophic microorganisms. BMC Genomics. 2012;13:56. https://doi.org/10.1186/1471-2164-13-56
  2. Scanlan D. Cyanobacteria: ecology, niche adaptation and genomics. Microbiology Today. 2001;28:128-130.
  3. Shih PM, Wu D, Latifi A, et al. Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing. Proc. Natl. Acad. Sci. USA. 2013;110:1053-1058. https://doi.org/10.1073/pnas.1217107110
  4. Dor I, Hornoff M. Salinity-temperature relations and morphotypes of a mixed population of coccoid cyanobacteria from a hot hypersaline pond in Israel. Marine Ecology. 1985;6:13-25. https://doi.org/10.1111/j.1439-0485.1985.tb00317.x
  5. Golubic S, Marcenko E. Ecologically induced convergent morphologies in blue-green algae of extreme environments. Schweiz. Z. Hydrol. 1965;27:207-217.
  6. Jungblut AD, Hawes I, Mountfort D, et al. Diversity within cyanobacterial mat communities in variable salinity meltwater ponds of McMurdo Ice Shelf, Antarctica. Environ. Microbiol. 2005;7:519-529. https://doi.org/10.1111/j.1462-2920.2005.00717.x
  7. Komarek J. Recent changes (2008) in cyanobacteria taxonomy based on a combination of molecular background with phenotype and ecological consequences (genus and species concept). Hydrobiologia. 2010;639:245-259. https://doi.org/10.1007/s10750-009-0031-3
  8. Stackebrand E, Goebel BM. Taxonomic Note: a for place for DNA-DNA reassociationand 16S rRNA sequence analysis in the present species definition in Bacteriology. Int. J. Syst. Evol. Micr. 1994;44:846-849. https://doi.org/10.1099/00207713-44-4-846
  9. Komarek J. Cyanobacterial Taxonomy: Current problems and prospects for the integration of traditional and molecular approaches. Algae. 2006;21:349-375. https://doi.org/10.4490/ALGAE.2006.21.4.349
  10. Abeywickrama BA, Abeywickrama L, Arulgnanam P. The Genera of the freshwater algae of Sri Lanka. UNSECO Man and the Biosphere National Committee for Sri Lanka, Special Publication 6. Colombo: National Science Council Sri Lanka; 1986. p. 103.
  11. Richerson PJ, Suchanek TH, Zierenberg RA, Osleger DA, Heyvaert AC, Slotton DG, Eagles-Smith CA, Vaughn CE. Anthropogenic stressors and changes in the Clear Lake ecosystem as recorded in sediment cores. Ecol. Appl. 2008;18:A257-A283. https://doi.org/10.1890/06-1458.1
  12. Hirimburegama W. Cyanobacteria in the Beira Lake polluted with urban waste. In: symposium on cyanobacteria toxins in water, Institute of Fundamental Studies; 1998; Kandy, Sri Lanka.
  13. Silva EIL, Wijeyaratne MJS. The occurrence of cyanobacteria in the reservoirs of the Mahaweli River basin in Sri Lanka. Sri Lanka J. Aquat. Sci. 1999;4:51-60.
  14. Jayatissa LP, Lawton LA, Cornish BJPA. Toxic cyanobacteria (blue-green algae) in fresh waters of Sri Lanka. In: Harmful Algae eds. Reguera B, Blanco J, Fernandez ML, Wyatt T, Intergovernmental Oceanographic Commission of UNESCO; 1998. p. 32-34.
  15. Jayatissa LP, Silva EIL, McElhiney J, Lawton LA. Occurrence of toxigenic cyanobacterial blooms in freshwaters of Sri Lanka. Syst. Appl. Microbiol. 2006;29:156-164. https://doi.org/10.1016/j.syapm.2005.07.007
  16. Magana-Arachchi DN, Wanigatunge RP, Jeyanandarajah P. Setting up a polymerase chain reaction assay for the detection of toxic cyanobacteria. J. Natl. Sci. Found. Sri. 2008;36:229-233.
  17. Magana-Arachchi D, Wanigatunge R, Liyanage M. Molecular characterization of cyanobacterial diversity in Lake Gregory, Sri Lanka. Chin. J. Oceanol. Limn. 2011;29:898-904. https://doi.org/10.1007/s00343-011-0519-3
  18. Castenholz RW, Waterbury JB. Group I. Cyanobacteria. In: JT Staley, MP Bryant, N Pfenning, JG Holt eds. Bergey's manual of systematic bacteriology, Vol. 3. Maryland: Williams and Wilkins Co.; 1989. p. 1710-1727.
  19. Boone DR, Castenholz RW. Bergey's Manual of Systematic Bacteriology. 2nd ed. New York: Springer-Verlag; 2001.
  20. Stanier RY, Kunisawa R, Mandel M, Cohen-Bazire G. Purification and properties of unicellular blue-green algae (Order Chroococcales). Bacteriological Rev. 1971;35:171-205.
  21. Allen MM, Stanier RY. Selective isolation of blue-green algae from water and soil. J. Gen. Microbiol. 1968;51:203-209. https://doi.org/10.1099/00221287-51-2-203
  22. Desikachary TV. Cyanophyta. Indian Council for Agricultural Research, New Delhi. 1959;686.
  23. Waterbury JB, Stanier RY. Patterns of growth and development in pleurocapsalean cyanobacteria. Microbiol. Rev. 1978;42: 2-44.
  24. Komarek J, Anagnostidis K. Modern approach to the classification system of cyanophytes. 2-Chroocacales. Arch. Hydrobiol. Suppl. 1986;73:157-226.
  25. Holt JG, Krieg NR, Sneathm PHA, Staley JT, Williams ST (1994). Bergey's Manual of Determinative Bacteriology. 9th ed. Williams and Wilkins Co.; 1994.
  26. Komarek J, Anagnostidis K. Cyanoprokaryota. 1. Teil: Chroococcales. In: Ettle H. Gerloff J., Heynig H., Mollenhauer D. eds. Susswasserflora von Mitteleuropa, 19/1 bd. Jena: Gustav Fischer; 1998. p. 548-570.
  27. Komarek J, Anagnostidis K. Cyanoprokaryota 2. Teil: Oscillatoriales. In: H Ettl, J Gerloff, H Heynig, D Mollenhauer, et al. eds. Susswasserflora von Mitteleuropa, 19/2 bd. Berlin: Heidelberg; 2005. p. 759.
  28. Boom R, Sol CJ, Salimans MM, Jansen CL, Wertheim-van Dillen PM, van der Noordaa J. Rapid and simple method for purification of nucleic acids. J. Clin. Microbiol. 1990;28:495-503.
  29. Nubel U, Garcia-Pichel F, Muyzer G. PCR primers to amplify 16S rRNA genes from cyanobacteria. Appl. Environ. Microbiol. 1997;63:3327-3332.
  30. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl. Acid. S. 1999;41:95-98.
  31. Altschul SF, Madden TL, Schaffer AA, et al. Gapped Blast and PSI-Blast: A new generation of protein database search programs. Nucleic Acids Res. 1997;25:3389-3402. https://doi.org/10.1093/nar/25.17.3389
  32. Tamura K, Dudley J, Nei M, Kumar S. MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 2007;24:1596-1599. https://doi.org/10.1093/molbev/msm092
  33. Jukes TH, Cantor CR. Evolution of protein molecules. In: HN Munro eds. Mammalian Protein Metabolism. New York: Academic Press; 1969. p. 21-132.
  34. Saitou M, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 1987;4:406-425.
  35. Perera MBU, Yatigammana SK, Kulasooriya SA. Prevalence of toxigenic cyanobacteria in different climatic zones of Sri Lanka. In: International Symposium on Water Quality and Human Health: Challenges Ahead; 2012 March 22-23; Sri Lanka. 2012; p. 31-32.
  36. Silva EIL, Samaradiwakara SRMS. Limnology of Kandy Lake before the outbreak of a cyanobacteria bloom in May, 1999. III. phytoplankton composition and succession. Sri Lanka Journal of Aquatic Sciences. 2005;10:55-71. https://doi.org/10.4038/sljas.v10i0.7460
  37. Magana-Arachchi DN, Liyanage HM. Determination the presence of cyanotoxins in water reservoirs of Anuradhapura, using molecular and bioassay methods. J. Natl. Sci. Found. Sri. 2012;40:157-167.
  38. Perera MBU, Yatigammana SK, Kulasooriya SA, Athukorala NP. Distribution of C. raciborskii (A toxin producing cyanobacterium) in fresh water reservoirs. In: International Symposium on Water Quality and Human Health: Challenges Ahead; 2013 March 15-16; Sri Lanka.
  39. Srivastava AK, Bhargava P, Kumar A, Rai LC, Neilan BA. Molecular characterization and the effect of salinity on cyanobacterial diversity in the rice fields of Eastern Uttar Pradesh, India. Saline Syst. 2009;5;4. https://doi.org/10.1186/1746-1448-5-4
  40. Fernandez-Valiente E, Quesada A. A shallow water ecosystem: rice-fields. The relevance of cyanobacteria in the ecosystem. Limnetica. 2004;23:95-108.
  41. Song T, Martensson L, Eriksson T, Zheng W, Rasmussen U. Biodiversity and seasonal variation of the cyanobacterial assemblage in a rice paddy field in Fujian, China. FEMS Microbiol. Ecol. 2005;54:131-140. https://doi.org/10.1016/j.femsec.2005.03.008
  42. Kumari, Nidhi, Narayan OP, Rai LC. Cyanobacterial diversity shifts induced by butachlor in selected Indian rice fields in Eastern Uttar Pradesh and Western Bihar analyzed with PCR and DGGE. J. Microbiol. Biotechn. 2012;22:1-12. https://doi.org/10.4014/jmb.1106.06016
  43. Tajuddin N, Subramanian G. Cyanobacterial biodiversity and potential applications in biotechnology. Curr. Sci. India. 2005;89:47-57.
  44. Nagasathya A, Thajuddin N. Cyanobacterial diversity in the hypersaline environment of the saltpans of southeastern coast of India. Asian J. Plant Sci.. 2008;7:473-478. https://doi.org/10.3923/ajps.2008.473.478
  45. Chatchawan T, Peerapornpisal Y, Komarek J. Diversity of cyanobacteria in man-made solar saltern, Petchaburi Province, Thailand- a pilot study. Fottea. 2011;11:203-214.
  46. Nubel U, Garcia-Pichel F, Clavero E, Muyzer G. Matching molecular diversity and ecophysiology of benthic cyanobacteria and diatoms in communities along a salinity gradient. Environ. Microbiol. 2000;2:217-226. https://doi.org/10.1046/j.1462-2920.2000.00094.x
  47. Garcia-Pichel F, Lopez-Cortes A, Nubel U. Phylogenetic and morphological diversity of cyanobacteria in soil desert crusts from the Colorado plateau. Appl. Environ. Microb. 2001;67:1902-1910. https://doi.org/10.1128/AEM.67.4.1902-1910.2001
  48. Boutte C, Komarkova J, Grubisi S, et al. A polyphasic approach to assess the cyanobacterial diversity of summer samples from Czech reservoirs. Algol. Stud.. 2005;117:177-195. https://doi.org/10.1127/1864-1318/2005/0117-0177
  49. Magana-Arachchi DN, Wanigatunge RP. First report of genus Chroococcidiopsis (cyanobacteria) from Sri Lanka: a potential threat to human health. J. Natl. Sci. Found. 2013;41:65-68.
  50. Seo PS, Yokota A. The phylogenetic relationships of cyanobacteria inferred from 16S rRNA, gyrB, rpoC1 and rpoD1 gene sequences. J. Gen. Appl. Microbiol. 2003;49:191-203. https://doi.org/10.2323/jgam.49.191
  51. Otsuka S, Suda S, Li R, Watanabe M, Oyaizu H, Matsumoto S, Watanabe MM. Characterization of morphospecies and strains of the genus Microcystis (Cyanobacteria) for a reconsideration of species classification. Phycol. Res. 1999;47:189-197. https://doi.org/10.1111/j.1440-1835.1999.tb00298.x
  52. Ishida K, Cao Y, Hasegawa M, Okada N, Hara Y. The origin of chlorarachniophyte plastids, as inferred from phylogenetic comparisons of amino acid sequences of EF-Tu. J. Mol. Evol. 1997;45:682-687. https://doi.org/10.1007/PL00006272
  53. Marquardt J, Palinska KA. Genotypic and phenotypic diversity of cyanobacteria assigned to the genus Phormidium (Oscillatoriales) from different habitats and geographical sites. Arch. Microbiol. 2007;187:397-413. https://doi.org/10.1007/s00203-006-0204-7
  54. Otsuka S, Suda S, Li R, Matsumoto S, Watanabe MM. Morphological variability of colonies of Microcystis morphospecies in culture. J. Gen. Appl. Microbio.. 2000;46:39-50. https://doi.org/10.2323/jgam.46.39
  55. Gugger MF, Hoffmann L. Polyphyly of true branching cyanobacteria (Stigonematales). Int. J. Syst. Evol. Micr. 2004;54:349-357. https://doi.org/10.1099/ijs.0.02744-0
  56. Ishida T, Watanabe MM, Sugiyama J, Yokota A. Evidence for polyphyletic origin of the members of the orders of Oscillatoriales and Pleurocapsales as determined by 16S rDNA analysis. FEMS Microbiol. Lett. 2001;201:79-82. https://doi.org/10.1111/j.1574-6968.2001.tb10736.x
  57. Schirrmeister BE, Antonelli A, Bagheri HC. The origin of multicellularity in cyanobacteria. BMC Evol. Biol. 2011;11:45. https://doi.org/10.1186/1471-2148-11-45
  58. Turner S. Molecular systematics of oxygenic photosynthetic bacteria. Plant Syst. Evol. 1997;11:13-52. https://doi.org/10.1007/978-3-7091-6542-3_2
  59. Palinska KA, Liesack W, Rhiel E, Krumbein WE. Phenotype variability of identical genotypes: the need for a combined cyanobacterial taxonomy demonstrated on Merismopedia-like isolates. Arch. Microbiol. 1996;166:224-233. https://doi.org/10.1007/s002030050378
  60. Janse I, Meima M, Edwin W, Kardinaal A, Zwart G. High-resolution differentiation of cyanobacteria by using rRNA-internal transcribed spacer denaturing gradient gel electrophoresis. Appl. Environ. Microb. 2003;69:6634-6643. https://doi.org/10.1128/AEM.69.11.6634-6643.2003
  61. Wilmotte A, Turner S, Van de Peer Y, Pace NR. Taxonomic study of marine Oscillatoriacean strains (cyanobacteria) with narrow trichomes. II. Nucleotide sequence analysis of the 16S ribosomal RNA. J. Phycol. 1992;28:828-838. https://doi.org/10.1111/j.0022-3646.1992.00828.x

Cited by

  1. Cyanobacterial diversity in the algal–bacterial consortia from Subarctic regions: new insights from the rock baths at White Sea Coast pp.1573-5117, 2018, https://doi.org/10.1007/s10750-018-3844-0
  2. First record of cyanobacteria species: Cephalothrix komarekiana, from tropical Asia vol.26, pp.2, 2014, https://doi.org/10.4491/eer.2020.040