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Abstract

Five strains of filamentous, sulfur-oxidizing bacteria were isolated from sulfur mats of different sulfide springs from various regions of the Northern Caucasus, Russia. A phylogenetic analysis based on 16S rRNA gene sequence comparison showed that all of the isolates are affiliated with the filamentous, colourless, sulfur-oxidizing bacteria of the genus within the and are closely related to . All strains are capable of growing heterotrophically, lithoautotrophically with thiosulfate or sulfide as the sole energy source and mixotrophically. Strains G1, G2, P and K2 are able to fix molecular nitrogen, but strain BL is not. Randomly amplified polymorphic DNA (RAPD)-PCR analysis was used to assess the level of genetic relationships among the isolates. The Nei and Li similarity index revealed high genetic similarity among strains G1, G2, P and K2 (above 75 %), indicating that they are closely related. In combination with physiological and morphological data, strains G1, G2, P and K2 can be considered as members of the same species. The lowest genetic similarity (approx. 20 %) was reached between strain BL and the other isolated strains. Strains BL and G1 shared 35 % DNA–DNA relatedness and showed 51 and 53 % relatedness, respectively, to ATCC 49749. On the basis of this polyphasic analysis, strains G1, G2, P and K2 represent a novel species within the genus , for which the name sp. nov. is proposed, with strain G1 (=DSM 21228 =VKM B-2520) as the type strain. In addition, strain BL represents a second novel species, sp. nov., with strain BL (=DSM 21227 =VKM B-2521) as the type strain.

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2009-12-01
2024-11-07
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References

  1. Altschul, S. F., Madden, T. L., Schäffer, A. A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D. J.(1997). Gapped blast and psi-blast: a new generation of protein database search programs. Nucleic Acids Res 25, 3389–3402.[CrossRef] [Google Scholar]
  2. Armbruster, E. H.(1969). Improved technique for isolation and identification of Sphaerotilus. Appl Microbiol 17, 320–321. [Google Scholar]
  3. Aruga, S., Kamagata, Y., Kohno, T., Hanada, S., Nakamura, K. & Kanagawa, T.(2002). Characterization of filamentous Eikelboom type 021N bacteria and description of Thiothrix disciformis sp. nov. and Thiothrix flexilis sp. nov. Int J Syst Evol Microbiol 52, 1309–1316.[CrossRef] [Google Scholar]
  4. Ausubel, F. M., Brent, R., Kingston, R. E., Moore, D. D., Seidman, J. G., Smith, J. A. & Struhl, K. (editors)(1994).Current Protocols in Molecular Biology. New York: Wiley.
  5. Bej, A. K., Mahbubani, M. H., Dicesare, J. L. & Atlas, R. M.(1991). Polymerase chain reaction-gene probe detection of microorganisms by using filter-concentrated samples. Appl Environ Microbiol 57, 3529–3534. [Google Scholar]
  6. Blackwood, K. S., He, C., Gunton, J., Turenne, C. Y., Wolfe, J. & Kabani, A. M.(2000). Evaluation of recA sequences for identification of Mycobacterium species. J Clin Microbiol 38, 2846–2852. [Google Scholar]
  7. Chernousova, E. Yu., Akimov, V. N., Gridneva, E. V., Dubinina, G. A. & Grabovich, M. Yu.(2008). Phylogenetic in situ/ex situ analysis of a sulfur mat microbial community from a thermal sulfide spring in the North Caucasus. Mikrobiologiia 77, 255–260 (in Russian). [Google Scholar]
  8. 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]
  9. De Ley, J., Cattoir, H. & Reynaerts, A.(1970). The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 12, 133–142.[CrossRef] [Google Scholar]
  10. Fedorov, D. N., Ivanova, E. G., Doronina, N. V. & Trotsenko, Yu. A.(2008). A new system of degenerate-oligonucleotide primers for detection and amplification of nifHD genes. Mikrobiologiia 77, 286–288 (in Russian). [Google Scholar]
  11. Gerhardt, P., Murray, R. G. E., Costilow, R. N., Nester, E. W., Wood, W. A., Krieg, N. R. & Phillips, G. B. (editors)(1981).Manual of Methods for General Bacteriology. Washington, DC: American Society for Microbiology.
  12. Hampl, V., Pavlícek, A. & Flegr, J.(2001). Construction and bootstrap analysis of DNA fingerprinting-based phylogenetic trees with the freeware program FreeTree: application to trichomonad parasites. Int J Syst Evol Microbiol 51, 731–735.[CrossRef] [Google Scholar]
  13. Hatano, K. & Nishii, T.(1994). Taxonomic studies on Streptomyces violaceoruber group and related species based on gyrB sequences. IFO Res Commun 20, 83–91. [Google Scholar]
  14. Hill, J. E., Town, J. R. & Hemmingsen, S. M.(2006). Improved template representation in cpn60 PCR product libraries generated from complex templates by application of a specific mixture of PCR primers. Environ Microbiol 8, 741–746.[CrossRef] [Google Scholar]
  15. Howarth, R., Unz, R. F., Seviour, E. M., Seviour, R. J., Blackall, L. L., Pickup, R. W., Jones, J. G., Yaguchi, J. & Head, I. M.(1999). Phylogenetic relationships of filamentous sulfur bacteria (Thiothrix spp. and Eikelboom type 021N bacteria) isolated from wastewater-treatment plants and description of Thiothrix eikelboomii sp. nov., Thiothrix unzii sp. nov., Thiothrix fructosivorans sp. nov. and Thiothrix defluvii sp. nov. Int J Syst Bacteriol 49, 1817–1827.[CrossRef] [Google Scholar]
  16. Jian, W., Zhu, L. & Dong, X.(2001). New approach to phylogenetic analysis of the genus Bifidobacterium based on partial HSP60 gene sequences. Int J Syst Evol Microbiol 51, 1633–1638.[CrossRef] [Google Scholar]
  17. Jukes, T. H. & Cantor, C. R.(1969). Evolution of protein molecules. In Mammalian Protein Metabolism, vol. 3, pp. 21–132. Edited by H. N. Munro. New York: Academic Press.
  18. Kwok, A. Y., Su, S. C., Reynolds, R. P., Bay, S. J., Av-Gay, Y., Dovichi, N. J. & Chow, A. W.(1999). Species identification and phylogenetic relationships based on partial HSP60 gene sequences within the genus Staphylococcus. Int J Syst Bacteriol 49, 1181–1192.[CrossRef] [Google Scholar]
  19. Lane, D. G.(1991). In Nucleic Acid Techniques in Bacterial Systematics, pp. 115–175. Edited by E. Stackebrandt & M. Goodfellow. Chichester: Wiley.
  20. Larkin, J. M. & Shinabarger, D. L.(1983). Characterization of Thiothrix nivea. Int J Syst Bacteriol 33, 841–846.[CrossRef] [Google Scholar]
  21. Medlin, L., Elwood, H. J., Stickel, S. & Sogin, M. L.(1988). The characterization of enzymatically amplified eukaryotic 16S-like rRNA-coding regions. Gene 71, 491–499.[CrossRef] [Google Scholar]
  22. Nei, M. & Li, W. H.(1979). Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci U S A 76, 5269–5273.[CrossRef] [Google Scholar]
  23. Owen, R. J. & Lapage, S. P.(1976). The thermal denaturation of partly purified bacterial deoxyribonucleic acid and its taxonomic applications. J Appl Bacteriol 41, 335–340.[CrossRef] [Google Scholar]
  24. Rossetti, S., Blackall, L. L., Levantesi, C., Uccelletti, D. & Tandoi, V.(2003). Phylogenetic and physiological characterization of a heterotrophic, chemolithoautotrophic Thiothrix strain isolated from activated sludge. Int J Syst Evol Microbiol 53, 1271–1276.[CrossRef] [Google Scholar]
  25. Stead, D. E., Sellwood, J. E., Wilson, J. & Winey, I.(1992). Evaluation of a commercial microbial identification system based on fatty acid profiles for rapid, accurate identification of plant pathogenic bacteria. J Appl Bacteriol 72, 315–321.[CrossRef] [Google Scholar]
  26. Stewart, W. D. P., Fitzerald, G. P. & Burris, R. H.(1968). Acetylene reduction by nitrogen fixing blue-green algae. Arch Mikrobiol 62, 336–348.[CrossRef] [Google Scholar]
  27. Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F. & Higgins, D. G.(1997). The clustal_x windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25, 4876–4882.[CrossRef] [Google Scholar]
  28. Unz, R. F. & Head, I. M.(2005). Genus I. Thiothrix Winogradsky 1888, 39AL. In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 2, part B, pp. 131–142. Edited by D. J. Brenner, N. R. Krieg, J. T. Staley & G. M. Garrity. New York: Springer.
  29. Van de Peer, Y. & De Wachter, R.(1994).treecon for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment. Comput Appl Biosci 10, 569–570. [Google Scholar]
  30. Williams, T. M. & Unz, R. F.(1985). Filamentous sulfur bacteria of activated sludge: characterization of Thiothrix, Beggiatoa, and Eikelboom type 021N strains. Appl Environ Microbiol 49, 887–898. [Google Scholar]
  31. Yamamoto, S. & Harayama, S.(1998). Phylogenetic relationships of Pseudomonas putida strains deduced from the nucleotide sequences of gyrB, rpoD and 16S rRNA genes. Int J Syst Bacteriol 48, 813–819.[CrossRef] [Google Scholar]
  32. Yamamoto, S., Bouvet, P. J. M. & Harayama, S.(1999). Phylogenetic structure of the genus Acinetobacter based on gyrB sequences: comparison with the grouping by DNA–DNA hybridization. Int J Syst Bacteriol 49, 87–95.[CrossRef] [Google Scholar]
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RAPD patterns of newly isolated strains. Strains K2, G1 , P and G2 showed similar patterns. The pattern of strain BL is markedly different from those of the other strains. Lanes: 1, K2; 2, BL ; 3, G1 ; 4, P; 5, G2; M, markers (sizes indicated in bp).

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