1887

Abstract

A novel Gram-staining-negative, aerobic and rod-shaped strain designated 541 was isolated from surface-sterilized root tissue of maize, collected from the Fangshan District of Beijing, People’s Republic of China, and was subjected to a taxonomic study using a polyphasic approach. According to a phylogenetic tree based on 16S rRNA gene sequences, strain 541 represented a member of the genus and clustered with DSM 19645, with which it shared the highest 16S rRNA gene sequence similarity (98.8 %). The predominant respiratory quinone was ubiquinone-10 (Q-10), the major polyamine was sym-homospermidine and the major cellular fatty acids were Cω7 (50.9 %), C (22.0 %) and C 2-OH (11.4 %). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine and sphingoglycolipid. The DNA G+C content was 64.7 mol%. DNA–DNA relatedness between strain 541 and its closest phylogenetic relative DSM 19645 was 50.8 %. The results of physiological and biochemical tests and the differences in the fatty acid profiles allowed a clear phenotypic differentiation of strain 541 from closely related species of the genus Strain 541 represents a novel species within the genus , for which the name sp. nov. is proposed, with the type strain 541 (=CGMCC 1.15008=DSM 100587).

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2016-09-01
2020-01-23
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References

  1. 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]
  2. Bligh E. G., Dyer W. J.. 1959; A rapid method of total lipid extraction and purification. Can J Biochem Physiol37:911–917 [CrossRef][PubMed]
    [Google Scholar]
  3. Breznak J. A., Costilow R. N.. 2007; Physicochemical factors in growth. In Methods for General and Molecular Bacteriology, 3rd edn. pp309–329 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 H.-J., Bunka S., Hensel A., Lubitz W.. 1997; Discrimination of members of the family Pasteurellaceae based on polyamine patterns. Int J Syst Bacteriol47:698–708 [CrossRef]
    [Google Scholar]
  5. 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]
  6. 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]
  7. Collins M., Jones D.. 1980; Lipids in the classification and identification of coryneform bacteria containing peptidoglycans based on 2,4-diaminobutyric acid. J Appl Microbiol48:459–470
    [Google Scholar]
  8. Collins M. D.. 1985; Isoprenoid quinone analysis in classification and identification. In Chemical Methods in Bacterial Systematics pp267–287 Edited by Goodfellow M., Minnikin D. E.. London: Academic Press;
    [Google Scholar]
  9. Consden R., Gordon A. H.. 1948; Effect of salt on partition chromatograms. Nature162:180–181 [CrossRef][PubMed]
    [Google Scholar]
  10. 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]
  11. Delory G. E., King E. J.. 1945; A sodium carbonate-bicarbonate buffer for alkaline phosphatases. Biochem J39:245 [CrossRef][PubMed]
    [Google Scholar]
  12. Dong X., Xin Y., Jian W., Liu X., Ling D.. 2000; Bifidobacterium thermacidophilum sp. nov., isolated from an anaerobic digester. Int J Syst Evol Microbiol50:119–125 [CrossRef][PubMed]
    [Google Scholar]
  13. Felsenstein J.. 1981; Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol17:368–376 [CrossRef][PubMed]
    [Google Scholar]
  14. Huang H. D., Wang W., Ma T., Li G. Q., Liang F. L., Liu R. L.. 2009; Sphingomonas sanxanigenens sp. nov., isolated from soil. Int J Syst Evol Microbiol59:719–723 [CrossRef][PubMed]
    [Google Scholar]
  15. Kämpfer P., Busse H. J., McInroy J. A., Glaeser S. P.. 2015; Sphingomonas zeae sp. nov., isolated from the stem of Zea mays. Int J Syst Evol Microbiol65:2542–2548 [CrossRef][PubMed]
    [Google Scholar]
  16. Kates M.. 1896; Techniques in Lipidology. In Isolation, Analysis and Identification of Lipids, 2nd edn. pp.232–254 Edited by Burdon R. H., Van Knippenberg P. H.. Amsterdam: Elsevier;
    [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 Microbiol62:716––721 [CrossRef][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 Microbiol65:2824–2830 [CrossRef][PubMed]
    [Google Scholar]
  19. Komagata K., Suzuki K.. 1988; Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol19:161–207[CrossRef]
    [Google Scholar]
  20. Kosako Y., Yabuuchi E., Naka T., Fujiwara N., Kobayashi K.. 2000; Proposal of Sphingomonadaceae fam. nov., consisting of Sphingomonas Yabuuchi, et al. 1990, Erythrobacter Shiba and Shimidu 1982, Erythromicrobium Yurkov, et al. 1994, Porphyrobacter Fuerst, et al. 1993, Zymomonas Kluyver and van Niel 1936, and Sandaracinobacter Yurkov et al. 1997, with the type genus Sphingomonas Yabuuchi et al. 1990. Microbiol Immunol44:563–575[CrossRef]
    [Google Scholar]
  21. Lane D. J.. 1991; 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematic pp115–175 Edited by Stackerandt E., Goodfellow M.. Chichester: Wiley;
    [Google Scholar]
  22. Lee K. B., Liu C. T., Anzai Y., Kim H., Aono T., Oyaizu H.. 2005; The hierarchical system of the Alphaproteobacteria: description of Hyphomonadaceae fam. nov., Xanthobacteraceae fam. nov. and Erythrobacteraceae fam. nov. Int J Syst Evol Microbiol55:1907–1919 [CrossRef][PubMed]
    [Google Scholar]
  23. Liu Q., Liu H. C., Zhang J. L., Zhou Y. G., Xin Y. H.. 2015; Sphingomonas psychrolutea sp. nov., a psychrotolerant bacterium isolated from glacier ice. Int J Syst Evol Microbiol65:2955–2959 [CrossRef][PubMed]
    [Google Scholar]
  24. Liu Y., Yao S., Lee Y. J., Cao Y., Zhai L., Zhang X., Su J., Ge Y., Kim S. G., Cheng C.. 2015; Sphingomonas morindae sp. nov., isolated from Noni (Morinda citrifolia L.) branch. Int J Syst Evol Microbiol65:2817–2823 [CrossRef][PubMed]
    [Google Scholar]
  25. Marmur J.. 1961; A procedure for the isolation of DNA from micro-organisms. J Mol Biol3:208–218[CrossRef]
    [Google Scholar]
  26. Marmur J., Doty P. 1962; Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature. J Mol Biol5:109–118 [CrossRef][PubMed]
    [Google Scholar]
  27. Miller J. H.. 1972; Experiments in Molecular Genetics Cold Spring Harbour, NY: Cold Spring Harbour Laboratory Press;
    [Google Scholar]
  28. Minnikin D. E., O'Donnell A. G., Goodfellow M., Alderson G., Athalye M., Schaal A., Parlett J. H., O’Donnell A.. 1984; An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Meth2:233–241 [CrossRef]
    [Google Scholar]
  29. Rzhetsky A., Nei M.. 1992; Statistical properties of the ordinary least-squares, generalized least-squares, and minimum-evolution methods of phylogenetic inference. J Mol Evol35:367–375 [CrossRef][PubMed]
    [Google Scholar]
  30. Rzhetsky A., Nei M.. 1993; Theoretical foundation of the minimum-evolution method of phylogenetic inference. Mol Biol Evol10:1073–1095[PubMed]
    [Google Scholar]
  31. Saitou N., Nei M.. 1987; The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol4:406–425[PubMed]
    [Google Scholar]
  32. Sasser M.. 1990; Identification of bacteria by gas chromatography of cellular fatty acids MIDI Technical Note 101 Newark. DE: MIDI Inc;
    [Google Scholar]
  33. Takeuchi M., Kawai F., Shimada Y., Yokota A.. 1993; Taxonomic study of polyethylene glycol-utilizing bacteria: emended description of the genus Sphingomonas and new descriptions of Sphingomonas macrogoltabidus sp. nov., Sphingomonas sanguis sp. nov. and Sphingomonas terrae sp. nov. Syst Appl Microbiol16:227–238 [CrossRef]
    [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 Microbiol51:1405–1417 [CrossRef][PubMed]
    [Google Scholar]
  35. Tamura K., Stecher G., Peterson D., Filipski A., Kumar S.. 2013; mega6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol30:2725–2729[CrossRef]
    [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 Res25:4876–4882 [CrossRef][PubMed]
    [Google Scholar]
  37. 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]
  38. Wu C., Lu X., Qin M., Wang Y., Ruan J.. 1989; The analysis of menaquinone compound in microbial cells by HPLC. Microbiology16:176–178
    [Google Scholar]
  39. 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]
  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 Microbiol52:1485–1496 [CrossRef][PubMed]
    [Google Scholar]
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