1887

Abstract

A Gram-reaction-negative, flexirubin-type-pigmented, rod-shaped, aerobic, non-motile bacterium, designated strain Z12, was isolated from a subsurface sediment sample. In a phylogenetic tree based on 16S rRNA gene sequences, strain Z12 formed a distinct clade with the members of the genus (<96.7 % sequence similarity). The G+C content of genomic DNA was 45.4 %. The major fatty acids of strain Z12 were iso-C, Cω6 and/or Cω7 (summed feature 3) and anteiso-C B and/or iso-C I (summed feature 4). The major respiratory quinone was MK-7 and the major polar lipid was phosphatidylethanolamine. On the basis of phenotypic, phylogenetic and genotypic features, strain Z12 is considered to represent a novel species, for which the name sp. nov., is proposed. The type strain is Z12 ( = JCM 30073 = CGMCC 1.12895).

Funding
This study was supported by the:
  • National Special Research Fund of China (Award GZHL20110317)
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.000025
2015-03-01
2024-05-04
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/65/3/827.html?itemId=/content/journal/ijsem/10.1099/ijs.0.000025&mimeType=html&fmt=ahah

References

  1. Baik K. S., Kim M. S., Kim E. M., Kim H. R., Seong C. N. ( 2007 ). Dyadobacter koreensis sp. nov., isolated from fresh water. . Int J Syst Evol Microbiol 57, 12271231. [View Article] [PubMed]
    [Google Scholar]
  2. Barrow G. I., Feltham R. K. A. (editors) ( 1993 ). Cowan and Steel’s Manual for the Identification of Medical Bacteria, , 3rd edn.. Cambridge:: Cambridge University Press;. [View Article]
    [Google Scholar]
  3. Bernardet J. F., Nakagawa Y., Holmes B. Subcommittee on the taxonomy of Flavobacterium and Cytophaga-like bacteria of the International Committee on Systematics of Prokaryotes ( 2002 ). Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. . Int J Syst Evol Microbiol 52, 10491070. [View Article] [PubMed]
    [Google Scholar]
  4. Chaturvedi P., Reddy G. S., Shivaji S. ( 2005 ). Dyadobacter hamtensis sp. nov., from Hamta glacier, located in the Himalayas, India. . Int J Syst Evol Microbiol 55, 21132117. [View Article] [PubMed]
    [Google Scholar]
  5. Chelius M. K., Triplett E. W. ( 2000 ). Dyadobacter fermentans gen. nov., sp. nov., a novel gram-negative bacterium isolated from surface-sterilized Zea mays stems. . Int J Syst Evol Microbiol 50, 751758. [View Article] [PubMed]
    [Google Scholar]
  6. Chen L., Jiang F., Xiao M., Dai J., Kan W., Fang C., Peng F. ( 2013 ). Dyadobacter arcticus sp. nov., isolated from Arctic soil. . Int J Syst Evol Microbiol 63, 16161620. [View Article] [PubMed]
    [Google Scholar]
  7. Chun J., Kang J. Y., Joung Y., Kim H., Joh K., Jahng K. Y. ( 2013 ). Dyadobacter jejuensis sp. nov., isolated from seawater. . Int J Syst Evol Microbiol 63, 17881792. [View Article] [PubMed]
    [Google Scholar]
  8. da Costa M. S., Albuquerque L., Nobre M., Wait R. ( 2011a ). The extraction and identification of respiratory lipoquinones of prokaryotes and their use in taxonomy. . Methods Microbiol 38, 197206. [View Article]
    [Google Scholar]
  9. da Costa M. S., Albuquerque L., Nobre M., Wait R. ( 2011b ). The identification of polar lipids in prokaryotes. . Methods Microbiol 38, 165181. [View Article]
    [Google Scholar]
  10. Dong Z., Guo X., Zhang X., Qiu F., Sun L., Gong H., Zhang F. ( 2007 ). Dyadobacter beijingensis sp. nov., isolated from the rhizosphere of turf grasses in China. . Int J Syst Evol Microbiol 57, 862865. [View Article] [PubMed]
    [Google Scholar]
  11. Felsenstein J. ( 1985 ). Confidence limits on phylogenies: an approach using the bootstrap. . Evolution 39, 783791. [View Article]
    [Google Scholar]
  12. Han L., Wu S. J., Qin C. Y., Zhu Y. H., Lu Z. Q., Xie B., Lv J. ( 2014 ). Hymenobacter qilianensis sp. nov., isolated from a subsurface sandstone sediment in the permafrost region of Qilian Mountains, China and emended description of the genus Hymenobacter . . Antonie van Leeuwenhoek 105, 971978. [View Article] [PubMed]
    [Google Scholar]
  13. Kim O. S., Cho Y. J., Lee K., Yoon S. H., Kim M., Na H., Park S. C., Jeon Y. S., Lee J. H. & other authors ( 2012 ). Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. . Int J Syst Evol Microbiol 62, 716721. [View Article] [PubMed]
    [Google Scholar]
  14. Kimura M. ( 1980 ). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. . J Mol Evol 16, 111120. [View Article] [PubMed]
    [Google Scholar]
  15. Kishino H., Hasegawa M. ( 1989 ). Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea. . J Mol Evol 29, 170179. [View Article] [PubMed]
    [Google Scholar]
  16. Lee M., Woo S. G., Park J., Yoo S. A. ( 2010 ). Dyadobacter soli sp. nov., a starch-degrading bacterium isolated from farm soil. . Int J Syst Evol Microbiol 60, 25772582. [View Article] [PubMed]
    [Google Scholar]
  17. Liu Q. M., Im W. T., Lee M., Yang D. C., Lee S. T. ( 2006 ). Dyadobacter ginsengisoli sp. nov., isolated from soil of a ginseng field. . Int J Syst Evol Microbiol 56, 19391944. [View Article] [PubMed]
    [Google Scholar]
  18. 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, 159167. [View Article]
    [Google Scholar]
  19. Minnikin D. E., O’Donnell A. G., Goodfellow M., Alderson G., Athalye M., Schaal A., Parlett J. H. ( 1984 ). An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. . J Microbiol Methods 2, 233241. [View Article]
    [Google Scholar]
  20. Murray R., Doetsch R. N., Robinow C. F. ( 1994 ). Determinative and cytological light microscopy. . In Methods for General and Molecular Bacteriology, pp. 2141. Edited by Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R. . Washington, DC:: American Society for Microbiology;.
    [Google Scholar]
  21. Reasoner D. J., Geldreich E. E. ( 1985 ). A new medium for the enumeration and subculture of bacteria from potable water. . Appl Environ Microbiol 49, 17.[PubMed]
    [Google Scholar]
  22. Reddy G. S., Garcia-Pichel F. ( 2005 ). Dyadobacter crusticola sp. nov., from biological soil crusts in the Colorado Plateau, USA, and an emended description of the genus Dyadobacter Chelius and Triplett 2000. . Int J Syst Evol Microbiol 55, 12951299. [View Article] [PubMed]
    [Google Scholar]
  23. Saitou N., Nei M. ( 1987 ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. . Mol Biol Evol 4, 406425.[PubMed]
    [Google Scholar]
  24. Sasser M. ( 1990 ). Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. Netwark, DE:: MIDI Inc;.
    [Google Scholar]
  25. Shen L., Liu Y., Yao T., Wang N., Xu B., Jiao N., Liu H., Zhou Y., Liu X., Wang Y. ( 2013 ). Dyadobacter tibetensis sp. nov., isolated from glacial ice core. . Int J Syst Evol Microbiol 63, 36363639. [View Article] [PubMed]
    [Google Scholar]
  26. Smibert R. M., Krieg N. R. ( 1994 ). Phenotypic characterization. . In Methods for General and Molecular Bacteriology, pp. 607654. Edited by Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R. . Washington, DC:: American Society for Microbiology;.
    [Google Scholar]
  27. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S. ( 2011 ). mega5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. . Mol Biol Evol 28, 27312739. [View Article] [PubMed]
    [Google Scholar]
  28. Tang Y., Dai J., Zhang L., Mo Z., Wang Y., Li Y., Ji S., Fang C., Zheng C. ( 2009 ). Dyadobacter alkalitolerans sp. nov., isolated from desert sand. . Int J Syst Evol Microbiol 59, 6064. [View Article] [PubMed]
    [Google Scholar]
  29. Thompson J. D., Higgins D. G., Gibson T. J. ( 1994 ). clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. . Nucleic Acids Res 22, 46734680. [View Article] [PubMed]
    [Google Scholar]
  30. Weeks O. B. ( 1981 ). Preliminary studies of the pigments of Flavobacterium breve NCTC 11099 and Flavobacterium odoratum NCTC 11036. . In The Flavobacterium–Cytophaga Group, pp. 108114. Edited by Reichenbach H., Weeks O. B. . Weinheim:: Gesellschaft für Biotechnologische Forshung;.
    [Google Scholar]
  31. Zhang D. C., Liu H. C., Xin Y. H., Zhou Y. G., Schinner F., Margesin R. ( 2010 ). Dyadobacter psychrophilus sp. nov., a psychrophilic bacterium isolated from soil. . Int J Syst Evol Microbiol 60, 16401643. [View Article] [PubMed]
    [Google Scholar]
  32. Zhang R. G., Tan X., Zhao X. M., Deng J., Lv J. ( 2014 ). Moheibacter sediminis gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from sediment, and emended descriptions of Empedobacter brevis, Wautersiella falsenii and Weeksella virosa . . Int J Syst Evol Microbiol 64, 14811487. [View Article] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.000025
Loading
/content/journal/ijsem/10.1099/ijs.0.000025
Loading

Data & Media loading...

Supplements

Supplementary Data

PDF
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