1887

Abstract

A Gram-stain-negative, strictly aerobic, non-motile, yellow, rod-shaped bacterium, designated strain E62-3, was isolated from soil of Enshi Grand Canyon, Hubei province, PR China. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain E62-3was most closely related to LNB2. Strain E62-3exhibited the highest 16S rRNA gene sequence similarity to YC7378(96.0 %), NL9(95.8 %), 469(95.7 %) and LNB2(95.5 %) within the family . The major fatty acids (>5 %) of strain E62-3 were Cω7, summed feature 3 (Cω7 and/or iso-C 2-OH), C and C 2-OH. The predominant respiratory quinone and polyamine were ubiquinone Q-10 and homospermidine, respectively. The predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine. The genomic DNA G+C content was 66.4 mol%. The genotypic, chemotaxonomic and phenotypic data revealed that the isolate represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is E62-3(=KCTC 42834=CCTCC AB 2015300).

Keyword(s): soil and Sphingomonas faucium
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.001064
2016-08-01
2021-08-01
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/66/8/2847.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.001064&mimeType=html&fmt=ahah

References

  1. 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]
  2. Busse H. J., Denner E. B., Buczolits S., Salkinoja-Salonen M., Bennasar A., Kämpfer P. 2003; Sphingomonas aurantiaca sp. nov., Sphingomonas aerolata sp. nov. and Sphingomonas faeni sp. nov., air- and dustborne and Antarctic, orange-pigmented, psychrotolerant bacteria, and emended description of the genus Sphingomonas . Int J Syst Evol Microbiol 53:1253–1260 [View Article][PubMed]
    [Google Scholar]
  3. Busse J., Auling G. 1988; Polyamine pattern as a chemotaxonomic marker within the Proteobacteria . Syst Appl Microbiol 11:1–8 [View Article]
    [Google Scholar]
  4. Cappuccino J. G., Sherman N. 2002 Microbiology: A Laboratory Manual, 6th Edn. Menlo Park. CA: Benjamin/Cummings;
    [Google Scholar]
  5. Chen H., Jogler M., Rohde M., Klenk H.-P., Busse H.-J., Tindall B. J., Sproer C., Overmann J. 2012a; 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]
    [Google Scholar]
  6. Chen F., Shi Z., Wang G. 2012b; Arenimonas metalli sp. nov., isolated from an iron mine. Int J Syst Evol Microbiol 62:1744–1749 [View Article]
    [Google Scholar]
  7. Chen H., Jogler M., Tindall B. J., Klenk H. P., Rohde M., Busse H. J., Overmann J. 2013; Sphingomonas starnbergensis sp. nov., isolated from a prealpine freshwater lake. Int J Syst Evol Microbiol 63:1017–1023 [View Article][PubMed]
    [Google Scholar]
  8. Collins M. D., Jones D. 1980; Lipids in the classification and identification of coryneform bacteria containing peptidoglycans based on 2, 4‐diaminobutyric acid. J Appl Bacteriol 48:459–470 [View Article]
    [Google Scholar]
  9. Dong X. Z., Cai M. Y. 2001 Determinative Manual for Routine Bacteriology Beijing: Scientific Press;
    [Google Scholar]
  10. Dussault H. P. 1955; An improved technique for staining red halophilic bacteria. J Bacteriol 70:484–485[PubMed]
    [Google Scholar]
  11. Fan H., Su C., Wang Y., Yao J., Zhao K., Wang Y., Wang G. 2008; Sedimentary arsenite-oxidizing and arsenate-reducing bacteria associated with high arsenic groundwater from Shanyin, Northwestern China. J Appl Microbiol 105:529–539 [View Article][PubMed]
    [Google Scholar]
  12. Felsenstein J. 1981; Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376 [View Article][PubMed]
    [Google Scholar]
  13. Felsenstein J. 1985; Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791 [View Article]
    [Google Scholar]
  14. Feng G. D., Yang S. Z., Wang Y. H., Zhang X. X., Zhao G. Z., Deng M. R., Zhu H. H. 2014; Description of a Gram-negative bacterium, Sphingomonas guangdongensis sp. nov. Int J Syst Evol Microbiol 64:1697–1702 [View Article][PubMed]
    [Google Scholar]
  15. Fitch W. M. 1971; Toward defining the course of evolution: minimum change for a tree topology. Syst Zool 20:406–416 [View Article]
    [Google Scholar]
  16. Kaur J., Kaur J., Niharika N., Lal R. 2012; Sphingomonas laterariae sp. nov., isolated from a hexachlorocyclohexane-contaminated dump site. Int J Syst Evol Microbiol 62:2891–2896 [View Article][PubMed]
    [Google Scholar]
  17. Kawahara K., Kuraishi H., Zähringer U. 1999; Chemical structure and function of glycosphingolipids of Sphingomonas spp and their distribution among members of the alpha-4 subclass of Proteobacteria . J Ind Microbiol Biotechnol 23:408–413 [View Article][PubMed]
    [Google Scholar]
  18. 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]
  19. Kim S. J., Moon J. Y., Lim J. M., Ahn J. H., Weon H. Y., Ahn T. Y., Kwon S. W. 2014; Sphingomonas aerophila sp. nov. and Sphingomonas naasensis sp. nov., isolated from air and soil, respectively. Int J Syst Evol Microbiol 64:926–932 [View Article][PubMed]
    [Google Scholar]
  20. Kimura M. 1980; A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120 [View Article][PubMed]
    [Google Scholar]
  21. Kroppenstedt R. M. 1985; Fatty acid and menaquinone analysis of actinomycetes and related organisms. In Chemical Methods in Bacterial Systematics (Society for Applied Bacteriology Technical Series No. 20) pp. 173–199 Edited by Goodfellow M., Minnikin D. E. London: Academic Press;
    [Google Scholar]
  22. Lanyi B. 1987; Classical and rapid identification methods for medically important bacteria. Methods Microbiol 19:1–67 [CrossRef]
    [Google Scholar]
  23. Lee J. S., Shin Y. K., Yoon J. H., Takeuchi M., Pyun Y. R., Park Y. H. 2001; Sphingomonas aquatilis sp. nov., Sphingomonas koreensis sp. nov., and Sphingomonas taejonensis sp. nov., yellow-pigmented bacteria isolated from natural mineral water. Int J Syst Evol Microbiol 51:1491–1498 [View Article][PubMed]
    [Google Scholar]
  24. Lin S. Y., Shen F. T., Lai W. A., Zhu Z. L., Chen W. M., Chou J. H., Lin Z. Y., Young C. C. 2012; Sphingomonas formosensis sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium isolated from agricultural soil. Int J Syst Evol Microbiol 62:1581–1586 [View Article][PubMed]
    [Google Scholar]
  25. Maruyama T., Park H. D., Ozawa K., Tanaka Y., Sumino T., Hamana K., Hiraishi A., Kato K. 2006; Sphingosinicella microcystinivorans gen. nov., sp. nov., a microcystin-degrading bacterium. Int J Syst Evol Microbiol 56:85–89 [View Article][PubMed]
    [Google Scholar]
  26. 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 Evol Microbiol 39:159–167 [View Article]
    [Google Scholar]
  27. 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 2:233–241 [View Article]
    [Google Scholar]
  28. Reichenbach H. 1992; The order Cytophagales . In The Prokaryotes, 2nd edn. vol. 4 pp. 3631–3675Edited by Balows A., Trüper H. G., Dworkin M., Harder W., Schleifer K. H. New York: Springer; [CrossRef]
    [Google Scholar]
  29. Romanenko L. A., Uchino M., Frolova G. M., Tanaka N., Kalinovskaya N. L., Latyshev N., Mikhailov V. V. 2007; Sphingomonas molluscorum sp. nov., a novel marine isolate with antimicrobial activity. J Microbiol Methods 57:358–363 [View Article]
    [Google Scholar]
  30. 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]
  31. Sasser M. 1990; Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Technical Note 101 Newark, DE: MIDI Inc;
    [Google Scholar]
  32. Smibert R. M., Krieg N. R. 1994; Phenotypic characterization. In Methods for General and Molecular Bacteriology607–654 Edited by Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R. Washington, DC: American Society for Microbiology;
    [Google Scholar]
  33. Son H. M., Yang J. E., Park Y., Han C. K., Kim S. G., Kook M., Yi T. H. 2013; Sphingomonas kyungheensis sp. nov., a bacterium with ginsenoside-converting activity isolated from soil of a ginseng field. Int J Syst Evol Microbiol 63:3848–3853 [View Article][PubMed]
    [Google Scholar]
  34. 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]
  35. 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 28:2731–2739 [View Article][PubMed]
    [Google Scholar]
  36. 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]
  37. Uchida H., Hamana K., Miyazaki M., Yoshida T., Nogi Y. 2012; Parasphingopyxis lamellibrachiae gen. nov., sp. nov., isolated from a marine annelid worm. Int J Syst Evol Microbiol 62:2224–2228 [View Article][PubMed]
    [Google Scholar]
  38. Wei S., Wang T., Liu H., Zhang C., Guo J., Wang Q., Liang K., Zhang Z. 2015; Sphingomonas hengshuiensis sp. nov., isolated from Hengshui Lake Wetland Reserve of China. Int J Syst Evol Microbiol 65:4644–4649 [CrossRef]
    [Google Scholar]
  39. Xu P., Li W. J., Tang S. K., Zhang Y. Q., Chen G. Z., Chen H. H., Xu L. H., Jiang C. L. 2005; Naxibacter alkalitolerans gen. nov., sp. nov., a novel member of the family ‘Oxalobacteraceae’ isolated from China. Int J Syst Evol Microbiol 55:1149–1153 [View Article][PubMed]
    [Google Scholar]
  40. Yabuuchi E., Yano I., Oyaizu H., Hashimoto Y., Ezaki T., Yamamoto H. 1990; Proposals of Sphingomonas paucimobilis gen. nov. and comb. nov., 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]
  41. 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]
  42. Yasir M., Aslam Z., Song G. C., Jeon C. O., Chung Y. R. 2010; Sphingosinicella vermicomposti sp. nov., isolated from vermicompost, and emended description of the genus Sphingosinicella . Int J Syst Evol Microbiol 60:580–584 [View Article][PubMed]
    [Google Scholar]
  43. Zhang Y. Q., Chen Y. G., Li W. J., Tian X. P., Xu L. H., Jiang C. L. 2005; Sphingomonas yunnanensis sp. nov., a novel gram-negative bacterium from a contaminated plate. Int J Syst Evol Microbiol 55:2361–2364 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.001064
Loading
/content/journal/ijsem/10.1099/ijsem.0.001064
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