1887

Abstract

A Gram-staining-negative, non-motile, orange-coloured and rod-shaped aerobic bacterium, designated W18RD, was isolated from the alpine meadow soil of the Tibetan plateau. Phylogenetic analysis based on 16S rRNA gene sequences positioned strain W18RD as a representative of a novel species under the genus which was most closely related to DSM 13665 with a sequence similarity level of 97.14 %. Meanwhile, it also had a high level of sequence similarity with DSM 25432 (96.51 %), CGMCC 1.10206 (96.43 %) and DSM 24164 (96.26 %). The G+C content of the genomic DNA of the type strain W18RD was 66.4mol%. DNA–DNA relatedness for the type strain W18RD with respect to its closest phylogenetic relative DSM 13665was 21.54±1.2 %. Major cellular fatty acids in strain W18RD were C 7 and/or C 6 (48.12 %), C 7 and/or C 6 (21.98 %) and C 2-OH (14.93 %), with ubiquinone-10 (Q-10) as the predominant respiratory quinone. The polar lipid profile of the strain consisted of phosphatidylethanolamine, phosphatidylglycerol, sphingoglycolipid, phosphatidylcholine, diphosphatidylglycerol and two unknown lipids. Based on the evidence from a combination of phenotypic, taxonomic and phylogenetic analyses, strain W18RD represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is W18RD (=CGMCC 1.15645=DSM 103336).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.001346
2016-10-01
2020-01-29
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/66/10/4269.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.001346&mimeType=html&fmt=ahah

References

  1. Altenburger P., Kämpfer P., Makristathis A., Lubitz W., Busse H.-J.. 1996; Classification of bacteria isolated from a medieval wall painting. J Biotechnol47:39–52 [CrossRef]
    [Google Scholar]
  2. An D.-S., Liu Q.-M., Lee H.-G., Jung M.-S., Kim S.-C., Lee S.-T., Im W.-T.. 2013; Sphingomonas ginsengisoli sp. nov. and Sphingomonas sediminicola sp. nov. Int J Syst Evol Microbiol63:496–501 [CrossRef][PubMed]
    [Google Scholar]
  3. Anzai Y., Kim H., Park J.-Y., Wakabayashi H., Oyaizu H.. 2000; Phylogenetic affiliation of the pseudomonads based on 16S rRNA sequence. Int J Syst Evol Microbiol50:1563–1589 [CrossRef][PubMed]
    [Google Scholar]
  4. 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 Microbiol53:1253–1260 [CrossRef][PubMed]
    [Google Scholar]
  5. 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 Microbiol62:2835–2843 [CrossRef][PubMed]
    [Google Scholar]
  6. De Ley J., Cattoir H., Reynaerts A.. 1970; The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem12:133–142 [CrossRef][PubMed]
    [Google Scholar]
  7. Embley T. M.. 1991; The linear PCR reaction: a simple and robust method for sequencing amplified rRNA genes. Lett Appl Microbiol13:171–174 [CrossRef][PubMed]
    [Google Scholar]
  8. 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 Microbiol64:1697–1702 [CrossRef][PubMed]
    [Google Scholar]
  9. Gu Z., Liu Y., Shen L., Liu X., Xiao N., Jiao N., Liu H., Zhou Y., Zhang S.. 2015; Hafnia psychrotolerans sp. nov., isolated from lake water. Int J Syst Evol Microbiol65:971–974 [CrossRef][PubMed]
    [Google Scholar]
  10. 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 Collect19:13–21
    [Google Scholar]
  11. Hiraishi A., Ueda Y., Ishihara J.. 1998; Quinone profiling of bacterial communities in natural and synthetic sewage activated sludge for enhanced phosphate removal. Appl Environ Microbiol64:992–998[PubMed]
    [Google Scholar]
  12. Huang H. Y., Li J., Zhao G. Z., Zhu W. Y., Yang L. L., Tang H. Y., Xu L. H., Li W. J.. 2012; Sphingomonas endophytica sp. nov., isolated from Artemisia annua L. Int J Syst Evol Microbiol62:1576–1580 [CrossRef][PubMed]
    [Google Scholar]
  13. Huss V. A., Festl H., Schleifer K. H.. 1983; Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. Syst Appl Microbiol4:184–192 [CrossRef][PubMed]
    [Google Scholar]
  14. Jin X.-F., Kim J.-K., Liu Q.-M., Kang M.-S., He D., Jin F.-X., Kim S.-C., Im W.-T.. 2013; Sphingomonas ginsenosidivorax sp. nov with the ability to transform ginsenosides. A Van Leeuw J Microb103:1359–1367[CrossRef]
    [Google Scholar]
  15. Kaur J., Kaur J., Niharika N., Lal R.. 2012; Sphingomonas laterariae sp. nov., isolated from a hexachlorocyclohexane-contaminated dump site. Int J Syst Evol Microbiol62:2891–2896 [CrossRef][PubMed]
    [Google Scholar]
  16. 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 Microbiol62:716–721 [CrossRef][PubMed]
    [Google Scholar]
  17. Kim M., Oh H.-S., Park S.-C., Chun J.. 2014a; Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol64:346–351 [CrossRef]
    [Google Scholar]
  18. Kim S.-J., Moon J.-Y., Lim J.-M., Ahn J. H., Weon H.-Y., Ahn T.-Y., Kwon S.-W.. 2014b; Sphingomonas aerophila sp. nov. and Sphingomonas naasensis sp. nov., isolated from air and soil, respectively. Int J Syst Evol Microbiol64:926–932 [CrossRef]
    [Google Scholar]
  19. 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 Microbiol65:2824–2830 [CrossRef][PubMed]
    [Google Scholar]
  20. Lee J., Sperandio V., Frantz D. E., Longgood J., Camilli A., Phillips M. A., Michael A. J.. 2009; An alternative polyamine biosynthetic pathway is widespread in bacteria and essential for biofilm formation in Vibrio cholerae. J Biol Chem284:9899–9907 [CrossRef][PubMed]
    [Google Scholar]
  21. 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 Microbiol62:1581–1586 [CrossRef][PubMed]
    [Google Scholar]
  22. Liu B., Pop M.. 2009; ARDB—antibiotic resistance genes database. Nucleic Acids Res37:D443–D447[CrossRef]
    [Google Scholar]
  23. Marmur J.. 1961; A procedure for the isolation of deoxyribonucleic acid from micro-organisms. J Mol Bio3:208–218 [CrossRef]
    [Google Scholar]
  24. Nigam A., Jit S., Lal R.. 2010; Sphingomonas histidinilytica sp. nov., isolated from a hexachlorocyclohexane dump site. Int J Syst Evol Microbiol60:1038–1043 [CrossRef][PubMed]
    [Google Scholar]
  25. Romano I., Lama L., Nicolaus B., Poli A., Gambacorta A., Giordano A.. 2006; Halomonas alkaliphila sp. nov., a novel halotolerant alkaliphilic bacterium isolated from a salt pool in Campania (Italy). J Gen Appl Microbiol52:339–348 [CrossRef][PubMed]
    [Google Scholar]
  26. Smibert R. M., Krieg N. R.. 1994; Phenotypic characterization. In Methods for General and Molecular Bacteriology , pp.607–654 Edited by Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R.. Washington, DC: American Society for Microbiology;
    [Google Scholar]
  27. 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 Microbiol51:1405–1417 [CrossRef][PubMed]
    [Google Scholar]
  28. 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 and evol28:2731–2739 [CrossRef]
    [Google Scholar]
  29. Tindall B. J.. 1990; Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol lett66:199–202 [CrossRef]
    [Google Scholar]
  30. Wayne L. G., Brenner D. J., Colwell R. R., Grimont P. A. D., Kandler O., Krichevsky M. I., 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 Bacteriol37:463–464[CrossRef]
    [Google Scholar]
  31. Wittich R. M., Busse H. J., Kämpfer P., Macedo A. J., Tiirola M., Wieser M., Abraham W. R.. 2007; Sphingomonas fennica sp. nov. and Sphingomonas haloaromaticamans sp. nov., outliers of the genus Sphingomonas. Int J Syst Evol Microbiol57:1740–1746 [CrossRef][PubMed]
    [Google Scholar]
  32. 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]
  33. 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 Immunol34:99–119 [CrossRef][PubMed]
    [Google Scholar]
  34. 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 Microbiol52:1485–1496 [CrossRef][PubMed]
    [Google Scholar]
  35. Zhu L., Si M., Li C., Xin K., Chen C., Shi X., Huang R., Zhao L., Shen X., Zhang L.. 2015; Sphingomonas gei sp. nov., isolated from roots of Geum aleppicum. Int J Syst Evol Microbiol65:1160–1166 [CrossRef][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.001346
Loading
/content/journal/ijsem/10.1099/ijsem.0.001346
Loading

Data & Media loading...

Supplements

Supplementary File 1

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