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Volume 58, Issue 11

sp. nov., from soil in Taiwan Free

Abstract

Among a large collection of Taiwanese soil isolates, a novel Gram-variable, rod-shaped, motile, endospore-forming bacterial strain, strain V10537, was subjected to a polyphasic study including 16S rRNA and gene sequence analysis, DNA–DNA hybridization experiments, cell wall peptidoglycan type, cellular fatty acid composition analysis and comparative phenotypic characterization. 16S rRNA gene sequence analysis indicated that the organism belonged to the genus . Strain V10537 possessed -diaminopimelic acid as the diagnostic diamino acid of the peptidoglycan. It contained menaquinone MK-7 as the predominant isoprenoid quinone and anteiso-C (53.6 %) and C (19.0 %) as the major fatty acids. Phylogenetically, the most closely related species to strain V10537 were , , , and , with 16S rRNA gene sequence similarities of 99.5, 98.8, 98.3, 98.2 and 98.1 % to the respective type strains. The gene sequence similarities between strain V10537 and these strains were 76.9–85.0 %. DNA–DNA hybridization experiments showed levels of relatedness of 8.5–45.6 % between strain V10537 and these strains. The DNA G+C content of strain V10537 was 46.7 mol%. Strain V10537 was clearly distinguishable from other species and thus represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is V10537 (=BCRC 17757 =DSM 19942).

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2008-11-01
2024-04-16
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References

  1. Ash, C., Farrow, J. A. E., Wallbanks, S. & Collins, M. D.(1991). Phylogenetic heterogeneity of the genus Bacillus revealed by comparative analysis of small-subunit-ribosomal RNA sequences. Lett Appl Microbiol 13, 202–206. [Google Scholar]
  2. Ash, C., Priest, F. G. & Collins, M. D.(1993). Molecular identification of rRNA group 3 bacilli (Ash, Farrow, Wallbanks and Collins) using a PCR probe test. Proposal for the creation of a new genus Paenibacillus. Antonie Van Leeuwenhoek 64, 253–260. [Google Scholar]
  3. Barrow, G. I. & Feltham, R. K. A.(1993).Cowan and Steel's Manual for the Identification of Medical Bacteria, 3rd edn. Cambridge: Cambridge University Press.
  4. Cámara, B., Strömpl, C., Verbarg, S., Spröer, C., Pieper, D.-H. & Tindall, B.-J.(2007).Pseudomonas reinekei sp. nov., Pseudomonas moorei sp. nov. and Pseudomonas mohnii sp. nov., novel species capable of degrading chlorosalicylates or isopimaric acid. Int J Syst Evol Microbiol 57, 923–931.[CrossRef] [Google Scholar]
  5. Chern, L.-L., Stackebrandt, E., Lee, S.-F., Lee, F.-L., Chen, J.-K. & Fu, H.-M.(2004).Chitinibacter tainanensis gen. nov., sp. nov., a chitin-degrading aerobe from soil in Taiwan. Int J Syst Evol Microbiol 54, 1387–1391.[CrossRef] [Google Scholar]
  6. Chun, J., Lee, J. H., Jung, Y., Kim, M., Kim, S., Kim, B. K. & Lim, Y. W.(2007). EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. Int J Syst Evol Microbiol 57, 2259–2261.[CrossRef] [Google Scholar]
  7. Collins, M. D. & Jones, D.(1981). A note on the separation of natural mixtures of bacterial ubiquinones using reverse-phase partition thin-layer chromatography and high performance liquid chromatography. J Appl Bacteriol 51, 129–134.[CrossRef] [Google Scholar]
  8. Ezaki, T., Hashimoto, Y. & Yabuuchi, E.(1989). Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 39, 224–229.[CrossRef] [Google Scholar]
  9. Felsenstein, J.(1981). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17, 368–376.[CrossRef] [Google Scholar]
  10. Felsenstein, J.(2007).phylip (phylogeny inference package), version 3.67. Distributed by the author. Department of Genome Sciences and Department of Biology, University of Washington, Seattle, USA.
  11. Fitch, W. M.(1971). Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20, 406–416.[CrossRef] [Google Scholar]
  12. Garrity, G. M. & Holt, J. G.(2001). Taxonomic outline of the Archaea and Bacteria. In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 1, pp. 155–166. Edited by D. R. Boone, R. W. Castenholz & G. M. Garrity. New York: Springer.
  13. Hasegawa, T., Takizawa, M. & Tanida, S.(1983). A rapid analysis for chemical grouping of aerobic Actinomycetes. J Gen Appl Microbiol 29, 319–322.[CrossRef] [Google Scholar]
  14. Kämpfer, P., Buczolits, S., Albrecht, A., Busse, H.-J. & Stackebrandt, E.(2003). Towards a standardized format for the description of a novel species (of an established genus): Ochrobactrum gallinifaecis sp. nov. Int J Syst Evol Microbiol 53, 893–896.[CrossRef] [Google Scholar]
  15. Kimura, M.(1980). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16, 111–120.[CrossRef] [Google Scholar]
  16. Komagata, K. & Suzuki, K.(1987). Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 19, 161–207. [Google Scholar]
  17. Rivas, R., Mateos, P. F., Martínez-Molina, E. & Velázquez, E.(2005).Paenibacillus xylanilyticus sp. nov., an airborne xylanolytic bacterium. Int J Syst Evol Microbiol 55, 405–408.[CrossRef] [Google Scholar]
  18. Saitou, N. & Nei, M.(1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425. [Google Scholar]
  19. Sánchez, M. M., Fritze, D., Blanco, A., Spröer, C., Tindall, B. J., Schumann, P., Kroppenstedt, R. M., Diaz, P. & Pastor, F. I. J.(2005).Paenibacillus barcinonensis sp. nov., a xylanase-producing bacterium isolated from a rice field in the Ebro River delta. Int J Syst Evol Microbiol 55, 935–939.[CrossRef] [Google Scholar]
  20. Shida, O., Takagi, H., Kadowaki, K. & Komagata, K.(1996). Proposal for two new genera, Brevibacillus gen. nov. and Aneurinibacillus gen. nov. Int J Syst Bacteriol 46, 939–946.[CrossRef] [Google Scholar]
  21. Shida, O., Takagi, H., Kadowaki, K., Nakamura, L. K. & Komagata, K.(1997a). Transfer of Bacillus alginolyticus, Bacillus chondroitinus, Bacillus curdlanolyticus, Bacillus glucanolyticus, Bacillus kobensis, and Bacillus thiaminolyticus to the genus Paenibacillus and emended description of the genus Paenibacillus. Int J Syst Bacteriol 47, 289–298.[CrossRef] [Google Scholar]
  22. Shida, O., Takagi, H., Kadowaki, K., Nakamura, L. K. & Komagata, K.(1997b). Emended description of Paenibacillus amylolyticus and description of Paenibacillus illinoisensis sp. nov. and Paenibacillus chibensis sp. nov. Int J Syst Bacteriol 47, 299–306.[CrossRef] [Google Scholar]
  23. Stackebrandt, E. & Goebel, B. M.(1994). Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44, 846–849.[CrossRef] [Google Scholar]
  24. Stackebrandt, E., Frederiksen, W., Garrity, G. M., Grimont, P. A. D., Kämpfer, P., Maiden, M. C. J., Nesme, X., Rosselló-Mora, R., Swings, J. & other authors(2002). Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 52, 1043–1047.[CrossRef] [Google Scholar]
  25. Tai, C.-J., Kuo, H.-P., Lee, F.-L., Chen, H.-K., Yokota, A. & Lo, C.-C.(2006).Chryseobacterium taiwanense sp. nov., isolated from soil in Taiwan. Int J Syst Evol Microbiol 56, 1771–1776.[CrossRef] [Google Scholar]
  26. Takeda, M., Suzuki, I. & Koizumi, J.(2005).Paenibacillus hodogayensis sp. nov., capable of degrading the polysaccharide produced by Sphaerotilus natans. Int J Syst Evol Microbiol 55, 737–741.[CrossRef] [Google Scholar]
  27. Tamaoka, J. & Komagata, K.(1984). Determination of DNA base composition by reversed-phase high-performance liquid chromatography. FEMS Microbiol Lett 25, 125–128.[CrossRef] [Google Scholar]
  28. Tamura, K., Dudley, J., Nei, M. & Kumar, S.(2007).mega4: molecular evolutionary genetics analysis (mega) software version 4.0. Mol Biol Evol 24, 1596–1599.[CrossRef] [Google Scholar]
  29. 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]
  30. Vandamme, P., Pot, B., Gillis, M., De Vos, P., Kersters, K. & Swings, J.(1996). Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol Rev 60, 407–438. [Google Scholar]
  31. Wang, L.-T., Lee, F.-L., Tai, C.-J. & Kasai, H.(2007). Comparison of gyrB gene sequences, 16S rRNA gene sequences and DNA–DNA hybridization in the Bacillus subtilis group. Int J Syst Evol Microbiol 57, 1846–1850.[CrossRef] [Google Scholar]
  32. Wayne, L. G., Brenner, D. J., Colwell, R. R., Grimont, P. A. D., Kandler, O., Krichevsky, M. I., Moore, L. H., Moore, W. E. C., Murray, R. G. E. & other authors(1987). International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37, 463–464.[CrossRef] [Google Scholar]
  33. Yamamoto, S. & Harayama, S.(1995). PCR amplification and direct sequencing of gyrB genes with universal primers and their application to the detection and taxonomic analysis of Pseudomonas putida strains. Appl Environ Microbiol 61, 1104–1109. [Google Scholar]
  34. Yamamoto, S., Bouvet, P. J. & Harayama, S.(1999). Phylogenetic structures 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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Paenibacillus taichungensis sp. nov., from soil in Taiwan
Int J Syst Evol Microbiol 58, 2640 (2008); https://doi.org/10.1099/ijs.0.65776-0
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vol. , part 11, pp. 2640 - 2645

Maximum-parsimony (Fig. S1) and maximum-likelihood (Fig. S2) trees based on 16S rRNA gene sequences of strains.

Maximum-parsimony (Fig. S3) and maximum-likelihood (Fig. S4) trees based on gene sequences of strains.

[PDF file of Supplementary Figs S1-S4](27 KB)

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