Structural Analysis Based on 16S rDNA Sequences of Eight Strains of Leptospirillum ferriphilum from Acid Mine Drainage or Hot Spring

Abstract:

The correlations between the phylogenetic similarity and original geographical sites of L. ferriphilum were evaluated on the basis of 16S rDNA sequence analysis. Results indicated that all of L. ferriphilum strains in this work may be classified into three phylogenetic groups, and there were some certain links between phylogenic similarity and the mineralogical characteristics. Furthermore, structural analysis of 16S rDNA sequences suggested that nucleotide variables (signature sites) were not randomly distributed. Of 23 signature sites detected, 17 positions were found in the first 600 bp from 5' terminal except position 1020, 1022, 1023, 1147, 1155 and 1277. Interestingly, 13 positions of them were found in the V6 region. Thus, the secondary structure and minimal free energy were determined in the V6 region among strains of three phylogenetic groups. The above results may be very useful in helping to screen bioleaching microorganisms with great application prospect and discerning the microevolutionary mechanisms of species formation.

• Periodical: Advanced Materials Research (Volumes 550-553)
• Pages: 1128-1132
• DOI: https://doi.org/10.4028/www.scientific.net/AMR.550-553.1128
• Online since: July 2012
• Authors: Jian Gao, Jian Kang, Guan Zhou Qiu
• Keywords: 16S rDNA Sequence, L. ferriphilum, Secondary Structure, Signature Sites, Structural Analysis

References

[1] T. Rohwerder, T. Gehrke, K. Kinzler and W. Sand: Appl. Microbiol. Biotechnol. Vol. 63 (2003), p.239–248.

[2] D.B. Johnson, N. Okibe and K.B. Hallberg: J. Microbiol. Methods Vol. 60 (2005), p.299–313.

[3] D.E. Rawlings, H. Tributsch and G.S. Hansford: Microbiology Vol. 145 (1999), p.5–13.

[4] P.L. Bond, S.P. Smriga and J.F. Banfield: Appl. Environ. Microbiol. Vol. 66 (2000), p.3842–3849.

[5] G.W. Tyson, I. Lo, B.J. Baker, E.E. Allen, P. Hugenholtz and J.F. Banfield: Appl. Environ. Microbiol. Vol. 71(2005), p.6319–6324.

[6] N.J. Coram and D.E. Rawlings: Appl. Environ. Microbiol. Vol. 68 (2002), p.838–845.

[7] N.J. Coram, L.J. van Zyl and D.E. Rawlings: Appl. Environ. Microbiol. Vol. 71 (2005), p.7515–7522.

[8] P.H.M. Kinnunen and J.A. Puhakka: Process Biochem. Vol. 40 (2005), p.3536–3541.

[9] T.V. Ojumu, J. Petersen and G.S. Hansford: Hydrometallurgy Vol. 94 (2008), p.69–76.

[10] B. Ozkaya, E. Sahinkaya and P. Nurmi: Hydrometallurgy Vol. 88 (2007), p.67–74.

[11] I. M. Tuffin, S.B. Hector, S.M. Deane and D.E. Rawlings: Appl. Environ. Microbiol. Vol. 72 (2006), p.2247–2253.

[12] J. Gao, C.G. Zhang, X.L. Wu, H.H. Wang and G.Z. Qiu: Ann. Microbiol. Vol. 57 (2007), p.171–176.

[13] E.G. Porst: J. Am. Ceram. Soc. Vol. 28 (1945), p.62–64.

[14] H.Q. Yin, L.H. Cao, G. Z. Qiu, D. Z. Wang, L. Kellogg, J.Z. Zhou, X.X. Liu, Z.M. Dai, J.N. Ding and X.D. Liu: Arch. Microbiol. Vol. 189 (2008), pp.101-110.

[15] S. Kumar, J. Dudley, M. Nei and K. Tamura: Brief. bioinform. Vol. 9 (2008), p.299–306.

[16] D.H. Mathews, J. Sabina, M. Zuker and D.H. Turner: J. Mol. Biol. Vol. 288(1999), p.911–940.

[17] M.W. Gray, D. Sankoff and R.J. Cedergren: Nucleic Acids Res. Vol. 12 (1984), p.5837–5852.

[18] M. Nemati and S.T.L. Harrison: Miner. Eng. Vol. 13 (2000), p.19–24.

[19] I. Grigorii, T.P. Karavaiko, T.F. Turova, A.M. Lysenko, T.V. Kolganova, S.N. Ageeva, L.N. Muntyan and T.A. Pivovarova: Int. J. Syst. Evol. Microbiol. Vol. 53 (2003), p.113–119.

DOI: 10.1099/ijs.0.02319-0

[20] S.N. Ageeva, T.F. Kondrat'eva and G. I. Karavaiko: Mikrobiologiia Vol. 70 (2001), p.186–194.

[21] D.B. Johnson, S. Rolfe, K.B. Hallberg and E. Iversen: Environ. Microbiol. Vol. 3 (2001), p.630–637.

[22] B. Pettersson, G. Bölske, F. Thiaucourt, M. Uhlén and K.E. Johansson: J. Bacteriol. Vol. 180 (1998), p.2350–2358.