Phylogeny of the Order Bacillales inferred from 3’ 16S rDNA and 5’ 16S-23S ITS nucleotide sequences
Sabarimatou Yakoubou, Dong Xu, Jean-Charles Côté
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DOI: 10.4236/ns.2010.29121   PDF    HTML     5,303 Downloads   10,522 Views   Citations

Abstract

A short 220 bp sequence was used to study the taxonomic organization of the bacterial Order Bacillales. The nucleotide sequences of the 3’ end of the 16S rDNA and the 16S-23S Internal transcribed spacer (ITS) were determined for 32 Bacillales species and strains. The data for 40 additional Bacillales species and strains were retrieved directly from Genbank. Together, these 72 Bacillales species and strains encompassed eight families and 21 genera. The 220 bp se- quence used here covers a conserved 150 bp sequence located at the 3’ end of the 16S rDNA and a conserved 70 bp sequence located at the 5’ end of the 16S-23S ITS. A neighbor-joining phylogenetic tree was inferred from comparative analyses of all 72 nucleotide sequences. Eight major Groups were revealed. Each Group was sub-divided into sub-groups and branches. In general, the neighbor-joining tree presented here is in agreement with the currently accepted phylogeny of the Order Bacillales based on phenotypic and genotypic data. The use of this 220 bp sequence for phylogenetic analyses presents several advantages over the use of the entire 16S rRNA genes or the generation of extensive phenotypic and genotypic data. This 220 bp sequence contains 150 bp at the 3’ end of the 16S rDNA which allows discrimination among distantly related species and 70 bp at the 5’ end of the 16S-23S ITS which, owing to its higher percentage of nucleotide sequence divergence, adds discriminating power among closely related species from same genus and closely related genera from same family. The method is simple, rapid, suited to large screening programs and easily accessible to most laboratories.

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Yakoubou, S. , Xu, D. and Côté, J. (2010) Phylogeny of the Order Bacillales inferred from 3’ 16S rDNA and 5’ 16S-23S ITS nucleotide sequences. Natural Science, 2, 990-997. doi: 10.4236/ns.2010.29121.

Conflicts of Interest

The authors declare no conflicts of interest.

References

[1] Claus, D. and Berkeley, R.C.W. (1986) Genus Bacillus Cohn, 1872. In: Sneath, P.H.A., Mair, N.S., Sharpe, M.E. and J.G. Holt., Ed., Bergey’s Manual of Systematic Bac teriology, The Williams & Wilkins Co., Baltimore, 2, 11051139.
[2] Priest, F.G., Goodfellow, M. and Todd, C. (1988) A nu merical classification of the genus Bacillus. Journal of General Microbiology, 134(7), 18471882.
[3] Ash, C., Farrow, A.E., Wallbanks, S. and Collins, M.D. (1991) Phylogenetic heterogeneity of the genus Bacillus revealed by comparative analysis of smallsubunitriboso mal RNA sequences. Letters in Applied Microbiology, 13(4), 202206.
[4] Xu, D. and C?té, J.C. (2003) Phylogenetic relationships between Bacillus species and related genera inferred from comparison of 3’ end 16S rDNA and 5’ end 16S23S ITS nucleotide sequences. International Journal of System atic and Evolutionary Microbiology, 53, 695704.
[5] Ludwig, W., Schleifer, KH. and Whitman, W.B. (2009) Revised road map to the phylum Firmicutes. In: De Vos, P., et al. Eds., Bergey’s Manual of Systematic Bacteriology, 2nd Edition, The Firmicutes, SpringerVerlag, New York, 3, 117.
[6] Garrity, G.M., Bell, J.A. and Lilburn, T. (2005) The Re vised Road Map to the Manual. In: Brenner, D.J., Krieg, N.R., Staley, J.T. and Garrity, G.M., Eds., Bergey’s Manual of Systematic Bacteriology, 2nd Edition, The Proteobacteria, Part A, Introductory Essays. Springer, New York, 2, 159220.
[7] Sambrook, J. and Russell, D.W. (2001) Molecular Cloning: A Laboratory Manual. 3rd Edition, Cold Spring Harbor Laboratory Press, N.Y..
[8] Stephen, D., Jones, C. and Schofield, J.P. (1990) A rapid method for isolating high quality plasmid DNA suitable for DNA sequencing. Nucleic Acids Research, 18(24), 74637464
[9] Sanger, F., Nicklen, S. and Coulson, A.R. (1977) DNA sequencing with chaintermination inhibitors. Proceed ings of the National Academy of Sciences, USA, 74, 54635467.
[10] Saitou, N. and Nei, M. (1987) The neighborjoining method: A new method for reconstructing phylogenetic trees. Molecular Biology and Evolution, 4(4), 406425.
[11] Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positionsspecific gap penalties and weight matrix choice. Nucleic Acids Research, 22(22), 46734680.
[12] Kimura, M. (1980) A simple method for estimating evo lutionary rate of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution, 16(2), 111120.
[13] Page, R.D.M. (1996) TreeView: An application to display phylogenetic trees on personal computers. Computer Ap plication in the Biosciences, 12(4), 357358.
[14] Page, R.D.M. (2000) TreeView—tree drawing software for Apple Macintosh and Windows. http://taxonomy.zoology.gla.ac.uk/rod/treeview.html
[15] Lu, J., Nogi, Y. and Takami, H., (2001) Oceanobacillus iheyensis gen. nov., sp. nov., a deepsea extremely halotolerant and alkaliphilic species isolated from a depth of 1050 m on the Iheya Ridge. FEMS Microbiology Let ters, 205(2), 291297.
[16] Heyrman, J., Logan, N.A., Busse, H.J., Balcaen, A., Lebbe, L., et al. (2003) Virgibacillus carmonensis sp. nov., Virgibacillus necropolis sp. nov. and Virgibacillus picturae sp. nov., three novel species isolated from deteriorated mural paintings, transfer of the species of the genus Salibacillus to Virgibacillus, as Virgibacillus marismortui comb. nov. and Virgibacillus salexigens comb. nov., and emended description of the genus Virgibacillus. International Journal of Systematic and Evolutionary Microbio
[17] Zhilina, T.N., Garnova, E.S., Tourova, T.P., Kostrikina, N.A. and Zavarzin, G.A., (2001) AmAmphibacillus fer mentum sp. nov. and Amphibacillus tropicus sp. nov., new alkaliphilic, facultatively anaerobic, saccharolytic bacilli from Lake Magadi. Mikrobiologiya, in Russian, 70(6), 825837. English Translation: Microbiology, 70(6), 711722.
[18] Goto, K., Matsubara, H., Mochida, K., Matsumura, T., Hara, Y., et al. (2002) Alicyclobacillus herbarius sp. nov., a novel bacterium containing omegacycloheptane fatty acids, isolated from herbal tea. International Journal of Systematic and Evolutionary Microbiology, 52(1), 109 113.
[19] Yakoubou, S. and C?té, J.C. (2010) Phylogeny of γproteobacteria inferred from comparisons of 3’ end 16S rRNA gene and 5’ end 16S23S ITS nucleotide sequences. Natural Science, 2(6), 535543.

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