1887

Abstract

Two novel polysaccharide-degrading bacteria (strains DCY03 and DCY04) were isolated from a soil sample of a ginseng field in the Republic of Korea and were identified as representing members of the genus on the basis of phenotypic characteristics and phylogenetic inference based on 16S rRNA gene sequences. Cells of the two isolates were Gram-positive, spore-forming, non-motile, straight rods. Based on DNA–DNA relatedness data, the strains were considered to belong to the same species. The DNA G+C content ranged from 56.6 to 57.0 mol%. The predominant cellular fatty acid was anteiso-C (63.8–62.8 %). Levels of 16S rRNA gene sequence similarity between the two novel isolates and the type strains of recognized species were 91.4–96.5 %. Strains DCY03 and DCY04 could clearly be distinguished from phylogenetically closely related species on the basis of DNA–DNA relatedness data and phenotypic characteristics. Therefore, on the basis of these data, the two isolates are considered to represent a novel species of the genus , for which the name sp. nov. is proposed. The type strain is DCY03 (=KCTC 13010=LMG 23604).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.64533-0
2007-01-01
2020-01-27
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/57/1/146.html?itemId=/content/journal/ijsem/10.1099/ijs.0.64533-0&mimeType=html&fmt=ahah

References

  1. An, D.-S., Im, W.-T., Yang, H.-C., Kang, M.-S., Kim, K.-K., Jin, L., Kim, M.-K. & Lee, S.-T. ( 2005; ). Cellulomonas terrae sp. nov., a cellulolytic and xylanolytic bacterium isolated from soil. Int J Syst Evol Microbiol 55, 1705–1709.[CrossRef]
    [Google Scholar]
  2. Atlas, R. M. ( 1993; ). Handbook of Microbiological Media, pp. 196, 843. Edited by L. C. Parks. Boca Raton, FL: CRC Press.
  3. Buck, J. D. ( 1982; ). Nonstaining (KOH) method for determination of Gram reactions of marine bacteria. Appl Environ Microbiol 44, 992–993.
    [Google Scholar]
  4. Chung, Y. R., Kim, C. H., Hwang, I. & Chun, J. ( 2000; ). Paenibacillus koreensis sp. nov., a new species that produces an iturin-like antifungal compound. Int J Syst Evol Microbiol 50, 1495–1500.[CrossRef]
    [Google Scholar]
  5. Daane, L. L., Harjono, I., Barns, S. M., Launen, L. A., Palleroni, N. J. & Haggblom, M. M. ( 2002; ). PAH-degradation by Paenibacillus spp. and description of Paenibacillus naphthalenovorans sp. nov., a naphthalene-degrading bacterium from the rhizosphere of salt marsh plants. Int J Syst Evol Microbiol 52, 131–139.
    [Google Scholar]
  6. Ezaki, T., Hashimoto, Y. & Yabuuchi, E. ( 1989; ). Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in micro-dilution 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]
  7. Felsenstein, J. ( 1985; ). Confidence limit on phylogenies: an approach using the bootstrap. Evolution 39, 783–791.[CrossRef]
    [Google Scholar]
  8. 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]
  9. Hall, T. A. ( 1999; ). bioedit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41, 95–98.
    [Google Scholar]
  10. Heyndrickx, M., Vandemeulebroecke, K., Scheldeman, P., Hoste, B., Kersters, K., De Vos, P., Logan, N. A., Aziz, A. M., Ali, N. & Berkeley, R. C. ( 1995; ). Paenibacillus (formerly Bacillus) gordonae (Pichinoty et al. 1986) Ash et al. 1994 is a later subjective synonym of Paenibacillus (formerly Bacillus) validus (Nakamura 1984) Ash et al. 1994: emended description of P. validus. Int J Syst Bacteriol 45, 661–669.[CrossRef]
    [Google Scholar]
  11. Kang, M.-S., Im, W.-T., Ten, L. N. & Lee, S.-T. ( 2003; ). Isolation and diversity of bacteria having extracellular degrading enzymes of xylan and/or amylose and/or cellulose. In Proceedings of the International Meeting of the Federation of Korean Microbiological Societies 2003, abstract B4022, p. 165. Seoul: The Microbiological Society of Korea.
  12. Kim, D. S., Bae, C.-Y., Jeon, J.-J., Chun, S.-J., Oh, H. W., Hong, S. G., Baek, K.-S., Moon, E. Y. & Bae, K. S. ( 2004; ). Paenibacillus elgii sp. nov., with broad antimicrobial activity. Int J Syst Evol Microbiol 54, 2031–2035.[CrossRef]
    [Google Scholar]
  13. Kim, M. K., Im, W.-T., Ohta, H., Lee, M. & Lee, S.-T. ( 2005; ). Sphingopyxis granuli sp. nov., a β-glucosidase producing bacterium in the family Sphingomonadaceae in α-4 subclass of the Proteobacteria. J Microbiol 43, 152–157.
    [Google Scholar]
  14. Kimura, M. ( 1983; ). The Neutral Theory of Molecular Evolution. Cambridge: Cambridge University Press.
  15. Komagata, K. & Suzuki, K. I. ( 1987; ). Lipid and cell wall analysis in bacterial systematics. Methods Microbiol 19, 161–207.
    [Google Scholar]
  16. Kouker, G. & Jaeger, K.-E. ( 1987; ). Specific and sensitive plate assay for bacterial lipase. Appl Environ Microbiol 53, 211–213.
    [Google Scholar]
  17. Kumar, S., Tamura, K. & Nei, M. ( 2004; ). mega3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5, 150–163.[CrossRef]
    [Google Scholar]
  18. Kuroshima, K.-I., Sakane, T., Takata, R. & Yokota, A. ( 1996; ). Bacillus ehimensis sp. nov. and Bacillus chitinolyticus sp. nov., new chitinolytic members of the genus Bacillus. Int J Syst Bacteriol 46, 76–80.[CrossRef]
    [Google Scholar]
  19. Mesbah, M., Premachandran, U. & Whitman, W. B. ( 1989; ). Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 39, 159–167.[CrossRef]
    [Google Scholar]
  20. Oshima, H., Miyazaki, R., Ohe, Y., Hayashi, H., Kawamura, K. & Kikuyama, S. ( 2002; ). Isolation and sequence of a novel amphibian pancreatic chitinase. Comp Biochem Physiol Part B Biochem Mol Biol 132, 381–388.[CrossRef]
    [Google Scholar]
  21. Rivas, R., Mateos, P. F., Martínez-Molina, E. & Velázquez, E. ( 2005a; ). Paenibacillus xylanilyticus sp. nov., an airborne xylanolytic bacterium. Int J Syst Evol Microbiol 55, 405–408.[CrossRef]
    [Google Scholar]
  22. Rivas, R., Mateos, P. F., Martínez-Molina, E. & Velázquez, E. ( 2005b; ). Paenibacillus phyllosphaerae sp. nov., a xylanolytic bacterium isolated from phyllosphere of Phoenix dactylifera. Int J Syst Evol Microbiol 55, 743–746.[CrossRef]
    [Google Scholar]
  23. Rivas, R., Gutiérrez, C., Abril, A., Mateos, P. F., Martínez-Molina, E., Ventosa, A. & Velázquez, E. ( 2005c; ). Paenibacillus rhizosphaerae sp. nov., isolated from the rhizosphere of Cicer arietinum. Int J Syst Evol Microbiol 55, 1305–1309.[CrossRef]
    [Google Scholar]
  24. Saitou, N. & Nei, M. ( 1987; ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425.
    [Google Scholar]
  25. 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]
  26. Sasser, M. ( 1990; ). Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids. MIDI Technical Note 101. Newark, DE: MIDI.
  27. Schleifer, K. H. & Kandler, O. ( 1972; ). Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 36, 407–477.
    [Google Scholar]
  28. Shida, O., Takagi, H., Kadowaki, K., Nakamura, L. K. & Komagata, K. ( 1997; ). 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]
  29. 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]
  30. Sutherland, I. W. ( 1999; ). Polysaccharases for microbial exopolysaccharides. Carbohydr Polym 38, 319–328.[CrossRef]
    [Google Scholar]
  31. 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]
  32. Ten, L. N., Im, W.-T., Kim, M.-K., Kang, M.-S. & Lee, S.-T. ( 2004; ). Development of a plate technique for screening of polysaccharide-degrading microorganisms by using a mixture of insoluble chromogenic substrates. J Microbiol Methods 56, 375–382.[CrossRef]
    [Google Scholar]
  33. Terra, W. R. & Ferreira, C. ( 1994; ). Insect digestive enzymes: properties, compartmentalization and function. Comp Biochem Physiol Part B Biochem Mol Biol 109, 1–62.[CrossRef]
    [Google Scholar]
  34. 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 24, 4876–4882.
    [Google Scholar]
  35. 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]
  36. Yoon, J.-H., Seo, W.-T., Shin, Y. K., Kho, Y. H., Kang, K. H. & Park, Y.-H. ( 2002; ). Paenibacillus chinjuensis sp. nov., a novel exopolysaccharide-producing bacterium. Int J Syst Evol Microbiol 52, 415–421.
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.64533-0
Loading
/content/journal/ijsem/10.1099/ijs.0.64533-0
Loading

Data & Media loading...

Supplements

Transmission electron micrographs of cells of strains DCY03 and DCY04. [PDF](51 KB)

PDF

Expanded phylogenetic tree based on 16S rRNA gene sequences showing the relationship of sp. nov. to other species of the genus [PDF](22 KB)

PDF

Most cited articles

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