1887

International Journal of Systematic and Evolutionary Microbiology

Volume 56, Issue 10

sp. nov., isolated from rice straw Free

Abstract

A facultatively chemolithoautotrophic, Gram-negative, aerobic, highly curved rod-shaped, non-motile, non-spore-forming bacterium, strain Jip08, was isolated from rice straw in Daejeon, South Korea. Strain Jip08 produced colourless colonies (1.0–1.5 mm) on R2A medium after 3 days. On the basis of 16S rRNA gene sequence similarity, strain Jip08 was shown to belong to the -2 subclass of the , and was most closely related to IAM 12100 (98.6 %), DSM 5895 (98.1 %), NCIMB 1785 (98.0 %), ATCC 25396 (96.6 %) and DM13 (95.8 %), all of which belong to the family . The genomic DNA G+C content of strain Jip08 was 69 mol%. Chemotaxonomic data [major ubiquinone, Q-10; major fatty acids, C isomer (summed feature of C 7/9/12), C cyclo 8 and C], 16S rRNA gene sequence analyses and some morphological and physiological features supported the affiliation of strain Jip08 to the genus . However, DNA–DNA hybridization data and some phenotypic properties showed that strain Jip08 could be distinguished from the single known species and represented a novel species, for which the name sp. nov. is proposed. The type strain is Jip08 (=KCTC 12212=NBRC 100963=IAM 15215).

  • Published Online:
© SGM
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.64093-0
2006-10-01
2020-01-18
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/56/10/2409.html?itemId=/content/journal/ijsem/10.1099/ijs.0.64093-0&mimeType=html&fmt=ahah

References

  1. An, D.-S., Im, W.-T., Yang, H.-C. & Lee, S.-T. ( 2006; ). Shinella granuli gen. nov., sp. nov., and proposal of the reclassification of Zoogloea ramigera ATCC 19623 as Shinella zoogloeoides sp. nov. Int J Syst Evol Microbiol 56, 443–448.[CrossRef]
    [Google Scholar]
  2. Aslam, Z., Im, W. T., Kim, M. K. & Lee, S.-T. ( 2005a; ). Flavobacterium granuli sp. nov., isolated from granules used in a wastewater treatment plant. Int J Syst Evol Microbiol 55, 747–751.[CrossRef]
    [Google Scholar]
  3. Aslam, Z., Im, W.-T., Ten, L. N. & Lee, S.-T. ( 2005b; ). Phenylobacterium koreense sp. nov., isolated from South Korea. Int J Syst Evol Microbiol 55, 2001–2005.[CrossRef]
    [Google Scholar]
  4. Atlas, R. M. ( 1993; ). Handbook of Microbiological Media. Edited by L. C. Parks. Boca Raton, FL: CRC Press.
  5. Bae, H.-S., Im, W.-T. & Lee, S.-T. ( 2005; ). Lysobacter concretionis sp. nov., isolated from anaerobic granules in an upflow anaerobic sludge blanket reactor. Int J Syst Evol Microbiol 55, 1155–1161.[CrossRef]
    [Google Scholar]
  6. Beijerinck, M. W. ( 1904; ). Phénomènes de réduction produits par les microbes. Arch Neerland Sci Ex Nat 9, 131–157.
     [Google Scholar]
  7. Buck, J. D. ( 1982; ). Nonstaining (KOH) method for determination of Gram reactions of marine bacteria. Appl Environ Microbiol 44, 992–993.
     [Google Scholar]
  8. Collins, M. D. & Jones, D. ( 1981; ). Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiol Rev 45, 316–354.
     [Google Scholar]
  9. Doronina, N. V., Braus-Strohmeyer, S. A., Leisinger, T. & Trotsenko, Y. A. ( 1995; ). Isolation and characterization of a new facultatively methylotrophic bacterium: description of Methylorhabdus multivorans gen. nov., sp. nov. Syst Appl Microbiol 18, 92–98.[CrossRef]
    [Google Scholar]
  10. Dreyfus, B., Garcia, J. L. & Gillis, M. ( 1988; ). Characterization of Azorhizobium caulinodans gen. nov., sp. nov., a stem-nodulating nitrogen-fixing bacterium isolated from Sesbania rostrata. Int J Syst Bacteriol 38, 89–98.[CrossRef]
    [Google Scholar]
  11. 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]
  12. Felsenstein, J. ( 1985; ). Confidence limit on phylogenies: an approach using the bootstrap. Evolution 39, 783–791.[CrossRef]
    [Google Scholar]
  13. 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]
  14. 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]
  15. Im, W.-T., Kang, M.-S., Park, H.-Y., Kim, M.-K. & Lee, S.-T. ( 2003; ). Culturable bacterial strain's diversity of environmental samples. In Proceedings of the International Meeting of the Federation of Korean Microbiological Societies, abstract B4023, p. 165. Seoul: Federation of Korean Microbiological Societies.
  16. Kelly, D. P. & Wood, A. P. ( 2000; ). Reclassification of some species of Thiobacillus to the newly designated genera Acidithiobacillus gen. nov., Halothiobacillus gen. nov. and Thermithiobacillus gen. nov. Int J Syst Evol Microbiol 50, 511–516.[CrossRef]
    [Google Scholar]
  17. Kelly, D. P., McDonald, I. R. & Wood, A. P. ( 2000; ). Proposal for the reclassification of Thiobacillus novellus as Starkeya novella gen. nov., comb. nov., in the α-subclass of the Proteobacteria. Int J Syst Evol Microbiol 50, 1797–1802.
     [Google Scholar]
  18. 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]
  19. Kimura, M. ( 1983; ). The Neutral Theory of Molecular Evolution. Cambridge: Cambridge University Press.
  20. 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]
  21. La, H.-J., Im, W.-T., Ten, L. N., Kang, M.-S., Shin, D.-Y. & Lee, S.-T. ( 2005; ). Paracoccus koreensis sp. nov., isolated from anaerobic granules in an upflow anaerobic sludge blanket (UASB) reactor. Int J Syst Evol Microbiol 55, 1657–1660.[CrossRef]
    [Google Scholar]
  22. Lewin, R. A. & Lounsbery, D. M. ( 1969; ). Isolation, cultivation and characterization of flexibacteria. J Gen Microbiol 58, 145–170.[CrossRef]
    [Google Scholar]
  23. Lingens, F., Blecher, R., Blecher, H., Blobel, F., Eberspächer, J., Fröhner, C., Görisch, H., Görisch, H. & Layh, G. ( 1985; ). Phenylobacterium immobile gen. nov., sp. nov., a Gram-negative bacterium that degrades the herbicide chloridazon. Int J Syst Bacteriol 35, 26–39.[CrossRef]
    [Google Scholar]
  24. 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]
  25. Quan, Z.-X., Im, W.-T. & Lee, S.-T. ( 2006; ). Azonexus caeni sp. nov., a denitrifying bacterium isolated from sludge of a wastewater treatment plant. Int J Syst Evol Microbiol 56, 1043–1046.[CrossRef]
    [Google Scholar]
  26. Raj, H. D. ( 1983; ). Proposal for Ancylobacter gen. nov. as a substitute for the bacterial genus Microcyclus Ørskov 1928. Int J Syst Bacteriol 33, 397–398.[CrossRef]
    [Google Scholar]
  27. Saitou, N. & Nei, M. ( 1987; ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425.
     [Google Scholar]
  28. Sasser, M. ( 1990; ). Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids. MIDI Technical Note 101. Newark, DE: MIDI.
  29. Shin, Y. K., Lee, J.-S., Chun, C. O., Kim, H.-J. & Park, Y.-H. ( 1996; ). Isoprenoid quinone profiles of the Leclercia adecarboxylata KCTC 1036T. J Microbiol Biotechnol 6, 68–69.
     [Google Scholar]
  30. 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]
  31. 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]
  32. 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]
  33. Vasil'eva, L. V., Lafitskaya, T. N. & Namsaraev, B. B. ( 1979; ). New genus of budding bacteria Angulomicrobium tetraedrale having radially symmetrical cells. Mikrobiologiia 48, 1033–1039 (in Russian; English translation pp. 843–849).
     [Google Scholar]
  34. Wayne, L. G., Brenner, D. J., Colwell, R. R. & 9 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]
  35. Xin, Y. H., Zhou, Y. G., Zhou, H. L. & Chen, W. X. ( 2004; ). Ancylobacter rudongensis sp. nov., isolated from roots of Spartina anglica. Int J Syst Evol Microbiol 54, 385–388.[CrossRef]
    [Google Scholar]
  36. Yang, D.-C., Im, W.-T., Kim, M. K. & Lee, S.-T. ( 2005; ). Pseudoxanthomonas koreensis sp. nov. and Pseudoxanthomonas daejeonensis sp. nov. Int J Syst Evol Microbiol 55, 787–791.[CrossRef]
    [Google Scholar]
  37. Yang, D.-C., Im, W.-T., Kim, M. K., Ohta, H. & Lee, S.-T. ( 2006a; ). Sphingomonas soli sp. nov., a β-glucosidase-producing bacterium in the family Sphingomonadaceae in the α-4 subgroup of the Proteobacteria. Int J Syst Evol Microbiol 56, 703–707.[CrossRef]
    [Google Scholar]
  38. Yang, H.-C., Im, W.-T., Kang, M. S., Shin, D.-Y. & Lee, S.-T. ( 2006b; ). Stenotrophomonas koreensis sp. nov., isolated from compost in South Korea. Int J Syst Evol Microbiol 56, 81–84.[CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.64093-0
Loading
Starkeya koreensis sp. nov., isolated from rice straw
Int J Syst Evol Microbiol 56, 2409 (2006); https://doi.org/10.1099/ijs.0.64093-0
/content/journal/ijsem/10.1099/ijs.0.64093-0
/content/journal/ijsem/10.1099/ijs.0.64093-0
Loading

Data & Media loading...

Supplements

vol. , part 10, pp. 2409-2414

A comparison of selected characteristics of strain Jip08 and IAM 12100 . [PDF](44 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