1887

Abstract

A bacterial strain designated LYH-20 was isolated from a fish pond in Taiwan and characterized using a polyphasic taxonomy approach. Cells of strain LYH-20 were aerobic, Gram-stain-negative, non-motile, poly-β-hydroxybutyrate containing, showing straight and rod shaped that were covered by large capsules and formed yellow-coloured colonies. Growth occurred at 15–40 °C (optimum, 30 °C), with 0–1.0 % NaCl (optimum, 0–0.1 %) and at pH 5.0–9.0 (optimum, pH 8.0–9.0). According to a phylogenetic tree based on 16S rRNA gene sequence analysis, strain LYH-20 belonged to the genus and clustered with TNR-2, with which it shared the highest 16S rRNA gene sequence similarity (97.5 %). The major fatty acids (>10 %) of strain LYH-20 were Cω7 and C. The DNA G+C content was 67.5 mol%. The sole isoprenoid quinone was Q-10. The polyamines detected were spermidine, putrescine and homospermidine. The polar lipid profile consisted of a mixture of sphingoglycolipid, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol and three uncharacterized phospholipids. The DNA–DNA hybridization value for strain LYH-20 with TNR-2 was less than 35 %. Phenotypic characteristics of the novel strain also differed from those of the closest related species of the genus . On the basis of the genotypic, chemotaxonomic and phenotypic data, strain LYH-20 represents a novel species in the genus , for which the name sp. nov. is proposed. The type strain is LYH-20 (=BCRC 80911=LMG 29002=KCTC 42741).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.001511
2016-12-01
2021-08-01
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/66/12/5301.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.001511&mimeType=html&fmt=ahah

References

  1. Beveridge T. J., Lawrence J. R., Murray R. G. E. 2007; Sampling and staining for light microscopy. In Methods for General and Molecular Bacteriology, 3rd edn. pp. 19–33 Edited by Beveridge T. J., Breznak J. A., Marzluf G. A., Schmidt T. M., Snyder L. R. Washington, DC: American Society for Microbiology;
    [Google Scholar]
  2. Bowman J. P. 2000; Description of Cellulophaga algicola sp. nov., isolated from the surfaces of Antarctic algae, and reclassification of Cytophaga uliginosa (ZoBell and Upham 1944) Reichenbach 1989 as Cellulophaga uliginosa comb. nov. Int J Syst Evol Microbiol 50:1861–1868 [View Article][PubMed]
    [Google Scholar]
  3. Breznak J. A., Costilow R. N. 2007; Physicochemical factors in growth. In Methods for General and Molecular Bacteriology, 3rd edn. pp 309–329 Edited by Beveridge T. J., Breznak J. A., Marzluf G. A., Schmidt T. M., Snyder L. R. Washington, DC: American Society for Microbiology;
    [Google Scholar]
  4. Busse J., Auling G. 1988; Polyamine pattern as a chemotaxonomic marker within the Proteobacteria . Syst Appl Microbiol 11:1–8 [View Article]
    [Google Scholar]
  5. 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]
  6. Chang S. C., Wang J. T., Vandamme P., Hwang J. H., Chang P. S., Chen W. M. 2004; Chitinimonas taiwanensis gen. nov., sp. nov., a novel chitinolytic bacterium isolated from a freshwater pond for shrimp culture. Syst Appl Microbiol 27:43–49 [View Article][PubMed]
    [Google Scholar]
  7. Chen W. M., Laevens S., Lee T. M., Coenye T., De Vos P., Mergeay M., Vandamme P. 2001; Ralstonia taiwanensis sp. nov., isolated from root nodules of Mimosa species and sputum of a cystic fibrosis patient. Int J Syst Evol Microbiol 51:1729–1735 [View Article][PubMed]
    [Google Scholar]
  8. Chen H., Jogler M., Rohde M., Klenk H. P., Busse H. J., Tindall B. J., Spröer C., Overmann J. 2012; Reclassification and emended description of Caulobacter leidyi as Sphingomonas leidyi comb. nov., and emendation of the genus Sphingomonas . Int J Syst Evol Microbiol 62:2835–2843 [View Article][PubMed]
    [Google Scholar]
  9. Cole J. R., Wang Q., Cardenas E., Fish J., Chai B., Farris R. J., Kulam-Syed-Mohideen A. S., McGarrell D. M., Marsh T. et al. 2009; The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 37:D141–D145 [View Article][PubMed]
    [Google Scholar]
  10. Collins M. D. 1994; Isoprenoid quinones. In Chemical Methods in Prokaryotic Systematics pp. 265–309 Edited by Goodfellow M., O’Donnell A. G. Chichester: Wiley;
    [Google Scholar]
  11. Embley T. M., Wait R. 1994; Structural lipids of eubacteria. In Chemical Methods in Prokaryotic Systematics pp. 121–161 Edited by Goodfellow M., O’Donnell A. G. Chichester: Wiley;
    [Google Scholar]
  12. 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 [View Article]
    [Google Scholar]
  13. Felsenstein J. 1981; Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376 [View Article][PubMed]
    [Google Scholar]
  14. Felsenstein J. 1993; PHYLIP (Phylogeny Inference Package), Version 3.5c. Distributed by the Author. Department of Genome Sciences University of Washington Seattle, USA:
  15. 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]
  16. Hamana K., Sakamoto A., Tachiyanagi S., Terauchi E., Takeuchi M. 2003; Polyamine profiles of some members of the alpha subclass of the class Proteobacteria: polyamine analysis of twenty recently described genera. Microbiol Cult Collect 19:13–21
    [Google Scholar]
  17. 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]
  18. Kim J. H., Kim S. H., Kim K. H., Lee P. C. 2015; Sphingomonas lacus sp. nov., an astaxanthin-dideoxyglycoside-producing species isolated from soil near a pond. Int J Syst Evol Microbiol 65:2824–2830 [View Article][PubMed]
    [Google Scholar]
  19. Kimura M. 1983 The Neutral Theory of Molecular Evolution Cambridge: Cambridge University Press; [CrossRef]
    [Google Scholar]
  20. Kluge A. G., Farris J. S. 1969; Quantitative phyletics and the evolution of anurans. Syst Zool 18:1–32 [View Article]
    [Google Scholar]
  21. Kumar S., Stecher G., Tamura K. 2016; mega7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874 [View Article][PubMed]
    [Google Scholar]
  22. Lányí B. 1987; Classical and rapid identification methods for medically important bacteria. Methods Microbiol 19:1–67 [CrossRef]
    [Google Scholar]
  23. Margesin R., Zhang D. C., Busse H. J. 2012; Sphingomonas alpina sp. nov., a psychrophilic bacterium isolated from alpine soil. Int J Syst Evol Microbiol 62:1558–1563 [View Article][PubMed]
    [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 [View Article]
    [Google Scholar]
  25. Murray R. G. E., Doetsch R. N., Robinow C. F. 1994; Determinative and cytological light microscopy. In Methods for General and Molecular Bacteriology pp. 21–41 Edited by Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R. Washington, DC: American Society for Microbiology;
    [Google Scholar]
  26. Nokhal T. H., Schlegel H. G. 1983; Taxonomic study of Paracoccus denitrificans . Int J Syst Bacteriol 33:26–37 [View Article]
    [Google Scholar]
  27. Powers E. M. 1995; Efficacy of the Ryu nonstaining KOH technique for rapidly determining gram reactions of food-borne and waterborne bacteria and yeasts. Appl Environ Microbiol 61:3756–3758[PubMed]
    [Google Scholar]
  28. Saitou N., Nei M. 1987; The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425[PubMed]
    [Google Scholar]
  29. Sasser M. 1990 Identification of bacteria by gas chromatography of cellular fatty acids MIDI Technical Note 101 Newark, DE: MIDI Inc;
    [Google Scholar]
  30. Schlegel H. G., Lafferty R., Krauss I. 1970; The isolation of mutants not accumulating poly-β-hydroxybutyric acid. Arch Mikrobiol 71:283–294 [View Article]
    [Google Scholar]
  31. Sheu S. Y., Chen Y. L., Chen W. M. 2015; Sphingomonas fonticola sp. nov., isolated from spring water. Int J Syst Evol Microbiol 65:4495–4502 [View Article][PubMed]
    [Google Scholar]
  32. Spiekermann P., Rehm B. H., Kalscheuer R., Baumeister D., Steinbüchel A. 1999; A sensitive, viable-colony staining method using Nile red for direct screening of bacteria that accumulate polyhydroxyalkanoic acids and other lipid storage compounds. Arch Microbiol 171:73–80 [View Article][PubMed]
    [Google Scholar]
  33. Takeuchi M., Hamana K., Hiraishi A. 2001; Proposal of the genus Sphingomonas sensu stricto and three new genera, Sphingobium, Novosphingobium and Sphingopyxis, on the basis of phylogenetic and chemotaxonomic analyses. Int J Syst Evol Microbiol 51:1405–1417 [View Article][PubMed]
    [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 25:4876–4882 [View Article][PubMed]
    [Google Scholar]
  35. Tindall B. J., Sikorski J., Smibert R. A., Krieg N. R. 2007; Phenotypic characterization and the principles of comparative systematics. In Methods for General and Molecular Bacteriology, 3rd edn. pp. 330–393 Edited by Beveridge T. J., Breznak J. A., Marzluf G. A., Schmidt T. M., Snyder L. R. Washington, DC: American Society for Microbiology;
    [Google Scholar]
  36. Wayne L. G., Brenner D. J., Colwell R. R., Grimont P. A. D., Kandler O., Krichevsky M., Moore L. H., Moore W. E. C., Murray R. G. E. et al. 1987; International committee on systematic bacteriology. report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Microbiol 37:463–464 [CrossRef]
    [Google Scholar]
  37. Wen C. M., Tseng C. S., Cheng C. Y., Li Y. K. 2002; Purification, characterization and cloning of a chitinase from Bacillus sp. NCTU2. Biotechnol Appl Biochem 35:213–219 [View Article][PubMed]
    [Google Scholar]
  38. Yabuuchi E., Yano I., Oyaizu H., Hashimoto Y., Ezaki T., Yamamoto H. 1990; Proposals of Sphingomonas paucimobilis gen. nov. and comb. nov., Sphingomonas parapaucimobilis sp. nov., Sphingomonas yanoikuyae sp. nov., Sphingomonas adhaesiva sp. nov., Sphingomonas capsulata comb. nov., and two genospecies of the genus Sphingomonas . Microbiol Immunol 34:99–119 [View Article][PubMed]
    [Google Scholar]
  39. Yabuuchi E., Kosako Y. 2005; Order IV Sphingomonadales ord. nov. In Bergey’s Manual of Systematic Bacteriology, 2nd edn. vol. 2 pp. 230–233 Edited by Brenner D. J., Krieg N. R., Staley J. R., Garrity G. M. New York: Springer;
    [Google Scholar]
  40. Yabuuchi E., Kosako Y., Fujiwara N., Naka T., Matsunaga I., Ogura H., Kobayashi K. 2002; Emendation of the genus Sphingomonas Yabuuchi et al. 1990 and junior objective synonymy of the species of three genera, Sphingobium, Novosphingobium and Sphingopyxis, in conjunction with Blastomonas ursincola . Int J Syst Evol Microbiol 52:1485–1496 [View Article][PubMed]
    [Google Scholar]
  41. Zhang J. Y., Liu X. Y., Liu S. J. 2010; Sphingomonas changbaiensis sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 60:790–795 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.001511
Loading
/content/journal/ijsem/10.1099/ijsem.0.001511
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most cited this month Most Cited RSS feed

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