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Volume 66, Issue 9

sp. nov., isolated from forest soil, and emended description of the genus Coenye 2000 Free

Abstract

A Gram-staining-negative, facultatively aerobic, white-colony-forming bacterium, designated strain SE-S21, was isolated from forest soil of Jeju Island in Korea. Cells were motile rods with a single polar flagellum, showing catalase- and oxidase-positive reactions. Growth was observed at 10–40 °C (optimum, 30 °C), pH 4.0–10.0 (optimum, pH 7.0–7.5) and with 0–4.0 % (w/v) NaCl (optimum, 0–2 %). Only ubiquinone-8 was detected as the isoprenoid quinone, and C, C cyclo, Cω8 cyclo and summed feature 2 (comprising C aldehyde and/or unknown) were found to be the major fatty acids. Phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, an unknown aminophospholipid, an unknown aminolipid and an unknown lipid were detected as the major polar lipids. Putrescine and 2-hydroxyputrescine were the predominant polyamines. The DNA G+C content was 61.0 mol%. Phylogenetic analyses based on 16S rRNA and DNA gyrase B gene sequences revealed that strain SE-S21 formed a phyletic lineage within the genus . Strain SE-S21 was most closely related to KOx and CCUG 38742 with 98.8 % and 98.7 % 16S rRNA gene sequence similarities, respectively. However, the DNA–DNA relatedness values between strain SE-S21 and the type strains of and were 26.6±5.7 % and 20.5±3.7 %, respectively. On the basis of phenotypic, chemotaxonomic and molecular features, strain SE-S21 clearly represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is SE-S21 (=KACC 18127=JCM 30137). An emended description of the genus is also proposed.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): forest soil , new taxa , Pandoraea terrae and Taxonomy
© 2016 IUMS
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2016-09-01
2024-10-03
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References

  1. Anandham R., Indiragandhi P., Kwon S. W., Sa T. M., Jeon C. O., Kim Y. K., Jee H. J. 2010; Pandoraea thiooxydans sp. nov., a facultatively chemolithotrophic, thiosulfate-oxidizing bacterium isolated from rhizosphere soils of sesame (Sesamum indicum L.). Int J Syst Evol Microbiol 60:21–26 [View Article][PubMed]
     [Google Scholar]
  2. Busse H. -J., Bunka S., Hensel A., Lubitz W. 1997; Discrimination of members of the family Pasteurellaceae based on polyamine patterns. Int J Syst Bacteriol 47:698–708 [View Article]
     [Google Scholar]
  3. Chang H. W., Nam Y. D., Jung M. Y., Kim K. H., Roh S. W., Kim M. S., Jeon C. O., Yoon J. H., Bae J. W. 2008; Statistical superiority of genome-probing microarrays as genomic DNA–DNA hybridization in revealing the bacterial phylogenetic relationship compared to conventional methods. J Microbiol Methods 75:523–530 [View Article][PubMed]
     [Google Scholar]
  4. Coenye T., Falsen E., Hoste B., Ohlén M., Goris J., Govan J. R., Gillis M., Vandamme P. 2000; Description of Pandoraea gen. nov. with Pandoraea apista sp. nov., Pandoraea pulmonicola sp. nov., Pandoraea pnomenusa sp. nov., Pandoraea sputorum sp. nov. and Pandoraea norimbergensis comb. nov. Int J Syst Evol Microbiol 50:887–899 [View Article][PubMed]
     [Google Scholar]
  5. Coenye T., LiPuma J. J. 2002; Use of the gyrB gene for the identification of Pandoraea species. FEMS Microbiol Lett 208:15–19 [View Article][PubMed]
     [Google Scholar]
  6. Daneshvar M. I., Hollis D. G., Steigerwalt A. G., Whitney A. M., Spangler L., Douglas M. P., Jordan J. G., MacGregor J. P., Hill B. C. et al. 2001; Assignment of CDC weak oxidizer group 2 (WO-2) to the genus Pandoraea and characterization of three new Pandoraea genomospecies. J Clin Microbiol 39:1819–1826 [View Article][PubMed]
     [Google Scholar]
  7. Felsenstein J. 2002; phylip (phylogeny inference package), version 3.6a. WA, USA: Seattle: Department of genetics, University of Washington;
  8. Gomori G. 1955; Preparation of buffers for use in enzyme studies. In Methods in Enzymology vol. 1 , pp. 138–146 Edited by Colowick S. P., Kaplan N. O. New York: Academic press;
     [Google Scholar]
  9. Gonzalez J. M., Saiz-Jimenez C. 2002; A fluorimetric method for the estimation of G+C mol% content in microorganisms by thermal denaturation temperature. Environ Microbiol 4:770–773[PubMed] [CrossRef]
     [Google Scholar]
  10. Kim M., Oh H. S., Park S. C., Chun J. 2014; Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 64:346–351 [View Article][PubMed]
     [Google Scholar]
  11. Kim O. S., Cho Y. J., Lee K., Yoon S. H., Kim M., Na H., Park S. C., Jeon Y. S., Lee J. H. et al. 2012; Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62:716–721 [View Article][PubMed]
     [Google Scholar]
  12. Komagata K., Suzuki K. 1987; Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 19:161–208 [CrossRef]
     [Google Scholar]
  13. Lányí B. 1987; Classical and rapid identification methods for medically important bacteria. Methods Microbiol 19:1–67 [CrossRef]
     [Google Scholar]
  14. Lee S. H., Shim J. K., Kim J. M., Choi H. K., Jeon C. O. 2011; Henriciella litoralis sp. nov., isolated from a tidal flat, transfer of Maribaculum marinum Lai et al. 2009 to the genus Henriciella as Henriciella aquimarina nom. nov. and emended description of the genus Henriciella. Int J Syst Evol Microbiol 61:722–727 [View Article][PubMed]
     [Google Scholar]
  15. Lee H. J., Jeong S. E., Cho M. S., Kim S., Lee S. S., Lee B. H., Jeon C. O. 2014; Flavihumibacter solisilvae sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 64:2897–2901 [View Article][PubMed]
     [Google Scholar]
  16. Minnikin D. E., Patel P. V., Alshamaony L., Goodfellow M. 1977; Polar Lipid Composition in the Classification of Nocardia and Related Bacteria. Int J Syst Bacteriol 27:104–117 [View Article]
     [Google Scholar]
  17. Nawrocki E. P., Eddy S. R. 2007; Query-dependent banding (QDB) for faster RNA similarity searches. PLoS Comput Biol 3:e56 [View Article][PubMed]
     [Google Scholar]
  18. Sahin N., Tani A., Kotan R., Sedlácek I., Kimbara K., Tamer A. U. 2011; Pandoraea oxalativorans sp. nov., Pandoraea faecigallinarum sp. nov. and Pandoraea vervacti sp. nov., isolated from oxalate-enriched culture. Int J Syst Evol Microbiol 61:2247–2253 [View Article][PubMed]
     [Google Scholar]
  19. Sasser M. 1990 Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids MIDI Technical Note 101 Newark, DE: MIDI Inc;
     [Google Scholar]
  20. Smibert R. M., Krieg N. R. 1994; Phenotypic characterization. In Methods for General and Molecular Bacteriology , pp. 607–654 Edited by Gerhardt P. Washington, DC: American Society for Microbiology;
     [Google Scholar]
  21. Stackebrandt E., Frederiksen W., Garrity G. M., Grimont P. A., Kämpfer P., Maiden M. C., Nesme X., Rosselló-Mora R., Swings J. et al. 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 [View Article][PubMed]
     [Google Scholar]
  22. Stackebrandt E., Ebers J. 2006; Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 33:152–155
     [Google Scholar]
  23. Stamatakis A., Ott M., Ludwig T. 2005; "RAxML-OMP: An efficient program for phylogenetic inference on SMPs". In Proceedings of 8th International Conference on Parallel Computing Technologies (PaCT2005), Lecture Notes in Computer Science vol. 3506 pp. 288–302 Springer Verlag;
     [Google Scholar]
  24. Tabacchioni S., Ferri L., Manno G., Mentasti M., Cocchi P., Campana S., Ravenni N., Taccetti G., Dalmastri C. et al. 2008; Use of the gyrB gene to discriminate among species of the Burkholderia cepacia complex. FEMS Microbiol Lett 281:175–182 [View Article][PubMed]
     [Google Scholar]
  25. 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 22:4673–4680 [View Article][PubMed]
     [Google Scholar]
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Pandoraea terrae sp. nov., isolated from forest soil, and emended description of the genus Pandoraea Coenye et al. 2000
Int J Syst Evol Microbiol 66, 3524 (2016); https://doi.org/10.1099/ijsem.0.001229
/content/journal/ijsem/10.1099/ijsem.0.001229
/content/journal/ijsem/10.1099/ijsem.0.001229
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