1887

Abstract

In order to assess the potential of several molecular targets for the identification, typing and traceability of cyanobacteria in freshwater reservoirs, molecular techniques were applied to 118 cyanobacterial isolates mostly sourced from Portuguese freshwater reservoirs and representative of three orders of cyanobacteria: Chroococcales (54), Oscillatoriales (15) and Nostocales (49). The isolates were previously identified by morphological methods and subsequently characterized by composite hierarchical cluster analysis of STRR and LTRR (short and long tandemly repeated repetitive sequences) PCR fingerprinting profiles. Representative isolates were selected from each cluster and their molecular identification, at the species level, was obtained or confirmed by phylogenetic positioning using 16S rRNA gene and phylogenies. A highly congruent association was observed between STTR- and LTRR-based clusters and taxonomic affiliation, revealing the usefulness of such PCR fingerprinting profiles for the identification of cyanobacteria. Composite analysis of hierarchical clustering of M13 and ERIC PCR fingerprints also appeared suitable for strain typing and traceability within a reservoir, indicating its potential for use in cyanobacterial monitoring, as a quality management control. Based on Simpson () and Shannon–Wiener (′) indices a high diversity was observed within all species, with showing the lowest diversity values (=0.83; ′=0.88) and the highest ones (=′=0.99). A diagnostic key based on 16S-ARDRA, ITS amplification and ITS-ARDRA for identification purposes is also presented.

Loading

Article metrics loading...

/content/journal/micro/10.1099/mic.0.022848-0
2009-02-01
2021-05-08
Loading full text...

Full text loading...

/deliver/fulltext/micro/155/2/642.html?itemId=/content/journal/micro/10.1099/mic.0.022848-0&mimeType=html&fmt=ahah

References

  1. Baker P. 1991; Identification of Common Noxious Cyanobacteria Part I – Nostocales : Urban Water Research Association of Australia. Research Report no: 29
    [Google Scholar]
  2. Baker P. 1992; Identification of Common Noxious Cyanobacteria Part II – Chroococales Oscillatoriales : Urban Water Research Association of Australia. Research Report no: 46
    [Google Scholar]
  3. Bourrelly P. 1970 Les Algues d'Eau Douce: Les Algues Bleus et Rouges, Les Eugléniens, Peridiniens, et Cryptomonadines Paris: N. Boubée & Cie;
    [Google Scholar]
  4. Bruno L., Billi D., Albertano P., Urzi C. 2006; Genetic characterization of epilithic cyanobacteria and their associated bacteria. Geomicrobiol J 23:293–299
    [Google Scholar]
  5. Castenholz R. W. 2001; Phylum BX. Cyanobacteria. . In Bergey's Manual of Systematic Bacteriology , 2nd edn. vol. 1, pp 473–599 Edited by Boone D. R., Castenholz R. W., Garrity G. M. New York: Springer;
  6. Cavalier-Smith T. 2002; The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification. Int J Syst Evol Microbiol 52:7–76
    [Google Scholar]
  7. Choi G. G., Bae M. S., Ahn C. Y., Oh H. M. 2008; Induction of axenic culture of Arthrospira ( Spirulina ) platensis based on antibiotic sensitivity of contaminating bacteria. Biotechnol Lett 30:87–92
    [Google Scholar]
  8. Gkelis S., Rajaniemi P., Vardaka E., Moustaka-Gouni M., Lanaras T., Sivonen K. 2005; Limnothrix redekei (Van Goor) Meffert (Cyanobacteria) strains from Lake Kastoria, Greece form a separate phylogenetic group. Microb Ecol 49:176–182
    [Google Scholar]
  9. Gugger M. F., Hoffmann L. 2004; Polyphyly of true branching cyanobacteria (Stigonematales. Int J Syst Evol Microbiol 54:349–357
    [Google Scholar]
  10. Gugger M., Lyra C., Henriksen P., Couté A., Humbert J., Sivonen K. 2002; Phylogenetic comparison of the cyanobacterial genera Anabaena and Aphanizomenon . Int J Syst Evol Microbiol 52:1867–1880
    [Google Scholar]
  11. Huelsenbeck J. P., Ronquist F. R. 2001; MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics 17:754–755
    [Google Scholar]
  12. Huey B., Hall J. 1989; Hypervariable DNA fingerprinting in Escherichia coli : minisatellite probe from bacteriophage M13. J Bacteriol 171:2528–2532
    [Google Scholar]
  13. Hunter P. R., Gaston M. A. 1988; Numerical index of the discriminatory ability of typing systems: an application of Simpson's index of diversity. J Clin Microbiol 26:2465–2466
    [Google Scholar]
  14. Ishida T., Watanabe M. M., Sugiyama J., Yokota A. 2001; Evidence for polyphyletic origin of the members of the orders of Oscillatoriales and Pleurocapsales as determined by 16S rDNA analysis. FEMS Microbiol Lett 201:79–82
    [Google Scholar]
  15. Iteman I., Rippka R., Tandeau de Marsac N., Herdman M. 2002; rDNA analyses of planktonic heterocystous cyanobacteria, including members of the genera Anabaenopsis and Cyanospira . Microbiology 148:481–496
    [Google Scholar]
  16. Joyner J. J., Litaker R. W., Paerl H. W. 2008; Morphological and genetic evidence that the cyanobacterium Lyngbya wollei (Farlow ex Gomont) Spexiale and Dyck encompasses at least two species. Appl Environ Microbiol 74:3710–3717
    [Google Scholar]
  17. Kaneko T., Sato S., Kotani H., Tanaka A., Asamizu E., Nakamura Y., Miyajima N., Hirosawa M., Sugiura M. other authors 1996; Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC 6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions. DNA Res 3:109–136
    [Google Scholar]
  18. Kaneko T., Nakamura Y., Wolk C. P., Kuritz T., Sasamoto S., Watanabe A., Iriguchi A., Ishikama K., Kawashima K. other authors 2001; Complete genomic sequence of the filamentous nitrogen-fixing cyanobacterium Anabaena sp. strain PCC 7120. DNA Res 8:205–213
    [Google Scholar]
  19. Komárek J., Anagnostidis K. 1986; Modern approach to the classification system of Cyanophytes; 2; Chroococcales. Algol Stud 43:157–226
    [Google Scholar]
  20. Komárek J., Anagnostidis K. 1989; Modern approach to the classification system of Cyanophytes. 4. Nostocales. Algol Stud 56:247–345
    [Google Scholar]
  21. Kondo R., Yoshida T., Yusi Y., Hiroishi S. 2000; DNA–DNA reassociation among a bloom-forming cyanobacterial genus, Microcystis . Int J Syst Evol Microbiol 50:767–770
    [Google Scholar]
  22. 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]
  23. Litvaitis M. K. 2002; A molecular test of cyanobacterial phylogeny: inferences from constraint analyses. Hydrobiologia 468:135–145
    [Google Scholar]
  24. Lu W., Evans H., McColl S. M., Saunders V. A. 1997; Identification of cyanobacteria by polymorphisms of PCR-amplified ribosomal DNA spacer region. FEMS Microbiol Lett 153:141–149
    [Google Scholar]
  25. Lyra C., Hantula J., Vainio E., Rapala J., Rouhiainen L., Sivonen K. 1997; Characterization of cyanobacteria by SDS-PAGE of whole-cell proteins and PCR/RFLP of the 16S rRNA gene. Arch Microbiol 168:176–184
    [Google Scholar]
  26. 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. Int J Syst Evol Microbiol 51:513–526
    [Google Scholar]
  27. Lyra C., Laamanen M., Lehtimäki J. M., Surakka A., Sivonen K. 2005; Benthic cyanobacteria of the genus Nodularia are non-toxic, without gas vacuoles, able to glide and genetically more diverse than planktonic Nodularia . Int J Syst Evol Microbiol 55:555–568
    [Google Scholar]
  28. Marquardt J., Palinska K. A. 2007; Genotypic and phenotypic diversity of cyanobacteria assigned to the genus Phormidium (Oscillatoriales) from different habitats and geographical sites. Arch Microbiol 187:397–413
    [Google Scholar]
  29. Masepohl B., Görlitz K., Böhme H. 1996; Long tandemly repeated repetitive (LTRR) sequences in the filamentous cyanobacterium Anabaena sp. PCC 7120. Biochim Biophys Acta; 130726–30
  30. 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]
  31. Neilan B. A. 2002; The molecular evolution and DNA profiling of toxic cyanobacteria. Curr Issues Mol Biol 4:1–11
    [Google Scholar]
  32. Nilsson M., Bergman B., Rasmussen U. 2000; Cyanobacterial diversity in geographically related and distant host plants of the genus Gunnera . Arch Microbiol 173:97–102
    [Google Scholar]
  33. Nübel U., Garcial-Pichel F., Muyzer G. 1997; PCR primers to amplify 16S rRNA genes from Cyanobacteria. Appl Environ Microbiol 63:3327–3332
    [Google Scholar]
  34. Otsuka S., Suda S., Shibata S., Oyaizu H., Matsumoto S., Watanabe M. M. 2001; A proposal for the unification of five species of the cyanobacterial genus Microcystis Kützing ex Lemmermann 1907 under the rules of the bacteriological code. Int J Syst Evol Microbiol 51:873–879
    [Google Scholar]
  35. Pitcher D., Saunders N., Owen R. 1989; Rapid extraction of bacterial DNA with guanidium thyocinate. Lett Appl Microbiol 8:151–156
    [Google Scholar]
  36. Prasanna R., Kumar R., Sood A., Prasanna B. M., Singh P. K. 2006; Morphological, physiochemical and molecular characterization of Anabaena strains. Microbiol Res 161:187–202
    [Google Scholar]
  37. Priest F., Austin B. 1993; Classification. In Modern Bacterial Taxonomy , 2nd edn. pp 1–13 London: Chapman & Hall;
  38. Rajaniemi P., Hrouzek P., Kastovska K., Willame R., Rantala A., Hoffmann L., Komarek J., Sivonen K. 2005; Phylogenetic and morphological evaluation of the genera Anabaena , Aphanizomenon , Trichormus and Nostoc (Nostocales, Cyanobacteria. Int J Syst Evol Microbiol 55:11–26
    [Google Scholar]
  39. Rasmussen U., Svenning M. 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]
  40. 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 reveal multiple evolutionary lines and reflect phycobilin content. Int J Syst Evol Microbiol 51:861–871
    [Google Scholar]
  41. Rocap G., Distel D. L., Waterbury J. B., Chisholm S. W. 2002; Resolution of Prochlorococcus and Synechococcus ecotypes by using 16S–23S ribosomal DNA internal transcribed spacer sequences. Appl Environ Microbiol 68:1180–1191
    [Google Scholar]
  42. Rudi K., Skulberg O. M., Larsen F., Jakobsen K. S. 1997; Strain characterization and classification of oxyphotobacteria in clone cultures on the basis of 16S rRNA sequences from the variable regions V6, V7, and V8. Appl Environ Microbiol 63:2593–2599
    [Google Scholar]
  43. Saker M. L., Nogueira I. C. G., Vasconcelos V. M., Neilan B. A., Eaglesham G. H., Pereira P. 2003; First report and toxicological assessment of the cyanobacterium Cylindrospermopsis raciborskii from Portuguese freshwaters. Ecotoxicol Environ Saf 55:243–250
    [Google Scholar]
  44. Seo P. S., Yokota A. 2003; The phylogenetic relationships of cyanobacteria inferred from 16S rRNA, gyrB , rpoC1 and rpoD1 gene sequences. J Gen Appl Microbiol 49:191–203
    [Google Scholar]
  45. Skulberg R., Skulberg O. M. 1990 Forskning med Algekulturer NIVAs Kultursampling av Alger ( Research with Algal Cultures. NIVA's Culture Collection of Algae Oslo, Norway: Norsk Institutt for Vannforskning;
    [Google Scholar]
  46. Sneath P. H. A., Johnson R. 1972; The influence on numerical taxonomic similarities of errors in microbiological tests. J Gen Microbiol 72:377–392
    [Google Scholar]
  47. Suda S., Watanabe M. M., Otsuka S., Mahakahant A., Yongmanitchai W., Norpartnaraporn N., Liu Y., Day J. G. 2002; Taxonomic revision of water-bloom-forming species of oscillatorioid cyanobacteria. Int J Syst Evol Microbiol 52:1577–1595
    [Google Scholar]
  48. Swofford D. L. 2003 paup. Phylogenetic analysis using parsimony (and other methods). Version 4.0b10 Sinauer Associates; Sunderland, Massachusetts:
    [Google Scholar]
  49. Teaumroong N., Innok S., Chunleuchanon S., Boonkerd N. 2002; Diversity of nitrogen-fixing cyanobacteria under various ecosystems of Thailand. I. Morphology, physiology and genetic diversity. World J Microbiol Biotechnol 18:673–682
    [Google Scholar]
  50. Valério E., Pereira P., Saker M. L., Franca S., Tenreiro R. 2005; Molecular characterization of Cylindrospermopsis raciborskii strains isolated from Portuguese freshwaters. Harmful Algae 4:1044–1052
    [Google Scholar]
  51. van Belkum A., Scherer S., van Alphen L., Verbrugh H. 1998; Short-sequence DNA repeats in prokaryotic genomes. Microbiol Mol Biol Rev 62:275–293
    [Google Scholar]
  52. 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
    [Google Scholar]
  53. Vincze T., Posfai J., Roberts R. J. 2003; NEBcutter: a program to cleave DNA with restriction enzymes. Nucleic Acids Res 31:3688–3691
    [Google Scholar]
  54. West N. J., Adams D. G. 1997; Phenotypic and genotypic comparison of symbiotic and free-living cyanobacteria from a single field site. Appl Environ Microbiol 63:4479–4484
    [Google Scholar]
  55. 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
    [Google Scholar]
  56. Zar J. H. 1996 Biostatistical Analysis , 3rd edn. Upper Saddle River, NJ: Prentice-Hall International;
  57. Zheng W. 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
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/mic.0.022848-0
Loading
/content/journal/micro/10.1099/mic.0.022848-0
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Supplementary material 2

PDF

Supplementary material 3

PDF

Supplementary material 4

PDF

Supplementary material 5

PDF

Supplementary material 6

PDF

Supplementary material 7

PDF

Supplementary material 8

PDF

Supplementary material 9

PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error