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Abstract

Strain Ndbn-20, a Gram-staining-negative, non-spore-forming bacterium, was isolated from compost of plant litter. The strain was able to degrade dicamba. Phylogenetic analysis based on 16S rRNA gene sequences indicated that Ndbn-20represented a member of the family of the and showed high sequence similarities to SP1 (98.8 %), RW1 (97.9 %), 382 (97.7 %) and UM2 (97.7 %). However, the strain showed low DNA sequence relatedness with SP1 (45.6±1.9 %), RW1 (33.5±2.3 %), UM2 (39.4±3.6 %) and 382 (42.1±4.1 %). Ndbn-20 possessed Q-10 as the predominant ubiquinone, spermidine as the major polyamine, and summed feature 8 (comprising Cω7/Cω6), summed feature 3 (comprising Cω7/Cω6), Cω6, C and C2-OH as the major fatty acids (>5 % of the total). The profile of polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, glycolipid, sphingoglycolipid, phosphatidyldimethylethanolamine and phosphatidylglycerol. The DNA G+C content was 65.4 mol%. Based on a polyphasic taxonomic analysis, strain Ndbn-20 is proposed to represent a novel species of the genus , with the proposed name of sp. nov. The type strain is Ndbn-20 (=CCTCC AB 2016143=KACC 18661).

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2016-09-01
2022-01-21
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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 J., Auling G. 1988; Polyamine pattern as a chemotaxonomic marker within the Proteobacteria . SystAppl Microbiol 11:1–8 [View Article]
    [Google Scholar]
  3. 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]
  4. Chun J., Lee J. H., Jung Y., Kim M., Kim S., Kim B. K., Lim Y. W. 2007; EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. Int J Syst Evol Microbiol 57:2259–2261 [View Article][PubMed]
    [Google Scholar]
  5. Collins M. D., Pirouz T., Goodfellow M., Minnikin D. E. 1977; Distribution of menaquinones in Actinomycetes and Corynebacteria . J Gen Microbiol 100:221–230 [View Article][PubMed]
    [Google Scholar]
  6. 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]
  7. Felsenstein J. 1981; Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376 [View Article][PubMed]
    [Google Scholar]
  8. Felsenstein J. 1985; Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791 [View Article]
    [Google Scholar]
  9. Fitch W. M. 1971; Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406–416 [View Article]
    [Google Scholar]
  10. Francis I. M., Jochimsen K. N., De Vos P., van Bruggen A. H. 2014; Reclassification of rhizosphere bacteria including strains causing corky root of lettuce and proposal of Rhizorhapis suberifaciens gen. nov., comb. nov., Sphingobium mellinum sp. nov., Sphingobium xanthum sp. nov. and Rhizorhabdus argentea gen. nov., sp. nov. Int J Syst Evol Microbiol 64:1340–1350 [View Article][PubMed]
    [Google Scholar]
  11. Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R. 1994 Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology;
    [Google Scholar]
  12. Kim M., Kang O., Zhang Y., Ren L., Chang X., Jiang F., Fang C., Zheng C., Peng F. 2016; Sphingoaurantiacus polygranulatus gen. nov., sp. nov., isolated from high-Arctic tundra soil, and emended descriptions of the genera Sandarakinorhabdus, Polymorphobacter and Rhizorhabdus and the species Sandarakinorhabdus limnophila,Rhizorhabdus argentea and Sphingomonas wittichii . Int J Syst Evol Microbiol 66:91–100 [View Article][PubMed]
    [Google Scholar]
  13. Lane D. L. 1991; 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics pp 115–175 Edited by Stackebrandt E. R., Goodfellow M. Chichester: Wiley;
    [Google Scholar]
  14. Mccarthy A. J., Cross T. 1984; A taxonomic study of Thermomonospora and other monosporic Actinomycetes . Microbiology SGM 130:5–25 [View Article]
    [Google Scholar]
  15. 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]
  16. Nigam A., Jit S., Lal R. 2010; Sphingomonas histidinilytica sp. nov., isolated from a hexachlorocyclohexane dump site. Int J Syst Evol Microbiol 60:1038–1043 [View Article][PubMed]
    [Google Scholar]
  17. 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]
  18. Sambrook J., Russell D. W. 2001 Molecular Cloning: A Laboratory Manual, 3rd edn.. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press;
    [Google Scholar]
  19. Sasser M. 1990; Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids. MIDI Technical Note 101. Newark, DE: MIDI Inc;
  20. 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]
  21. 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]
  22. Tindall B. J. 1990; Lipid composition of Halobacterium lacusprofundi . FEMS Microbiol Letts 66:199–202 [View Article]
    [Google Scholar]
  23. Wayne L. G., Brenner D., Colwell R. R., Grimont P. A. D., Kandler O., Krichevsky M. I., Moore L., Moore W. E. C., Murray R. G. E. et al. 1987; Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464 [CrossRef]
    [Google Scholar]
  24. Yabuuchi E., Yamamoto H., Terakubo S., Okamura N., Naka T., Fujiwara N., Kobayashi K., Kosako Y., Hiraishi A. 2001; Proposal of Sphingomonas wittichii sp. nov. for strain RW1T, known as a dibenzo-p-dioxin metabolizer. Int J Syst Evol Microbiol 51:281–292 [View Article][PubMed]
    [Google Scholar]
  25. Yao L., Jia X., Zhao J., Cao Q., Xie X., Yu L., He J., Tao Q. 2015; Degradation of the herbicide dicamba by two sphingomonads via different O-demethylation mechanisms. Int Biodeterior Biodegrad 104:324–332 [View Article]
    [Google Scholar]
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