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Abstract

A Gram-stain-negative, strictly aerobic bacterium, designated R1-4, was isolated from soil from a military shooting range in the Republic of Korea. Cells were non-motile short rods, oxidase-positive and catalase-negative. Growth of R1-4 was observed at 15–45 °C (optimum, 30 °C) and pH 6.0–9.0 (optimum, pH 7.0). R1-4 contained summed feature 8 (comprising C18 : 1ω7c/C18  : 1ω6c), summed feature 3 (comprising C16 : 1ω7c/C16  : 1ω6c), cyclo-C19 : 0ω8c and C16 : 0 as the major fatty acids and ubiquinone-10 as the sole isoprenoid quinone. Phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, sphingoglycolipid, phosphatidylcholine, an unknown glycolipid and four unknown lipids were detected as polar lipids. The major polyamine was spermidine. The G+C content of the genomic DNA was 64.4 mol%. The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that R1-4 formed a tight phylogenetic lineage with Novosphingobium sediminicola HU1-AH51 within the genus Novosphingobium . R1-4 was most closely related to N. sediminicola HU1-AH51 with a 98.8 % 16S rRNA gene sequence similarity. The DNA–DNA relatedness between R1-4 and the type strain of N. sediminicola was 37.8±4.2 %. On the basis of phenotypic, chemotaxonomic and molecular properties, it is clear that R1-4 represents a novel species of the genus Novosphingobium , for which the name Novosphingobium humi sp. nov. is proposed. The type strain is R1-4 (=KACC 19094=JCM 31879).

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2017-08-22
2019-10-20
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References

  1. Takeuchi M, Hamana K, Hiraishi A. 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 2001;51:1405–1417 [CrossRef][PubMed]
    [Google Scholar]
  2. Kämpfer P, Martin K, Mcinroy JA, Glaeser SP. Proposal of Novosphingobium rhizosphaerae sp. nov., isolated from the rhizosphere. Int J Syst Evol Microbiol 2015;65:195–200 [CrossRef][PubMed]
    [Google Scholar]
  3. Sheu SY, Liu LP, Chen WM. Novosphingobium bradum sp. nov., isolated from a spring. Int J Syst Evol Microbiol 2016;66:5083–5090 [CrossRef][PubMed]
    [Google Scholar]
  4. Chaudhary DK, Kim J. Novosphingobium naphthae sp. nov., from oil-contaminated soil. Int J Syst Evol Microbiol 2016;66:3170–3176 [CrossRef][PubMed]
    [Google Scholar]
  5. Baek SH, Lim JH, Jin L, Lee HG, Lee ST. Novosphingobium sediminicola sp. nov. isolated from freshwater sediment. Int J Syst Evol Microbiol 2011;61:2464–2468 [CrossRef][PubMed]
    [Google Scholar]
  6. Ngo HT, Trinh H, Kim JH, Yang JE, Won KH et al. Novosphingobium lotistagni sp. nov., isolated from a lotus pond. Int J Syst Evol Microbiol 2016;66:4729–4734 [CrossRef][PubMed]
    [Google Scholar]
  7. Zhang L, Gao JS, Kim SG, Zhang CW, Jiang JQ et al. Novosphingobium oryzae sp. nov., a potential plant-promoting endophytic bacterium isolated from rice roots. Int J Syst Evol Microbiol 2016;66:302–307 [CrossRef][PubMed]
    [Google Scholar]
  8. Chen Q, Zhang J, Wang CH, Jiang J, Kwon SW et al. Novosphingobium chloroacetimidivorans sp. nov., a chloroacetamide herbicide-degrading bacterium isolated from activated sludge. Int J Syst Evol Microbiol 2014;64:2573–2578 [CrossRef][PubMed]
    [Google Scholar]
  9. Glaeser SP, Bolte K, Busse HJ, Kämpfer P, Grossart HP et al. Novosphingobium aquaticum sp. nov., isolated from the humic-matter-rich bog lake Grosse Fuchskuhle. Int J Syst Evol Microbiol 2013;63:2630–2636 [CrossRef][PubMed]
    [Google Scholar]
  10. Sohn JH, Kwon KK, Kang JH, Jung HB, Kim SJ. Novosphingobium pentaromativorans sp. nov., a high-molecular-mass polycyclic aromatic hydrocarbon-degrading bacterium isolated from estuarine sediment. Int J Syst Evol Microbiol 2004;54:1483–1487 [CrossRef][PubMed]
    [Google Scholar]
  11. Yuan J, Lai Q, Zheng T, Shao Z. Novosphingobium indicum sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium isolated from a deep-sea environment. Int J Syst Evol Microbiol 2009;59:2084–2088 [CrossRef][PubMed]
    [Google Scholar]
  12. Lu S, Park M, Ro HS, Lee DS, Park W et al. Analysis of microbial communities using culture-dependent and culture-independent approaches in an anaerobic/aerobic SBR reactor. J Microbiol 2006;44:155–161[PubMed]
    [Google Scholar]
  13. Yoon SH, Ha SM, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017;67:1613–1617 [CrossRef][PubMed]
    [Google Scholar]
  14. Nawrocki EP, Eddy SR. Query-dependent banding (QDB) for faster RNA similarity searches. PLoS Comput Biol 2007;3:e56 [CrossRef][PubMed]
    [Google Scholar]
  15. Felsenstein J. Phylip (Phylogeny Inference Package), Version 3.6a Seattle, WA: Department of Genetics, University of Washington; 2002
    [Google Scholar]
  16. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014;30:1312–1313 [CrossRef][PubMed]
    [Google Scholar]
  17. Wang Q, Garrity GM, Tiedje JM, Cole JR. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 2007;73:5261–5267 [CrossRef][PubMed]
    [Google Scholar]
  18. Chang HW, Sung Y, Kim KH, Nam YD, Roh SW et al. Development of microbial genome-probing microarrays using digital multiple displacement amplification of uncultivated microbial single cells. Environ Sci Technol 2008;42:6058–6064 [CrossRef][PubMed]
    [Google Scholar]
  19. Stackebrandt E, Frederiksen W, Garrity GM, Grimont PA, Kämpfer P et al. Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 2002;52:1043–1047 [CrossRef][PubMed]
    [Google Scholar]
  20. Stackebrandt E, Ebers J. Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 2006;33:152–155
    [Google Scholar]
  21. Kim M, Oh HS, Park SC, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014;64:346–351 [CrossRef][PubMed]
    [Google Scholar]
  22. Rosselló-Móra R, Amann R. Past and future species definitions for Bacteria and Archaea. Syst Appl Microbiol 2015;38:209–216 [CrossRef][PubMed]
    [Google Scholar]
  23. Gomori G. Preparation of buffers for use in enzyme studies. In Colowick SP, Kaplan NO. (editors) Methods in Enzymology New York: Academic Press; 1955; pp.138–146
    [Google Scholar]
  24. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P. (editor) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994; pp.607–654
    [Google Scholar]
  25. Lányí B. Classical and rapid identification methods for medically important bacteria. Methods Microbiol 1987;19:1–67
    [Google Scholar]
  26. Gonzalez JM, Saiz-Jimenez C. A fluorimetric method for the estimation of G+C mol% content in microorganisms by thermal denaturation temperature. Environ Microbiol 2002;4:770–773 [CrossRef][PubMed]
    [Google Scholar]
  27. Minnikin DE, O'Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 1984;2:233–241 [CrossRef]
    [Google Scholar]
  28. Komagata K, Suzuki K. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1987;19:161–208[CrossRef]
    [Google Scholar]
  29. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101 Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  30. Minnikin DE, Patel PV, Alshamaony L, Goodfellow M. Polar lipid composition in the classification of Nocardia and related bacteria. Int J Syst Bacteriol 1977;27:104–117 [CrossRef]
    [Google Scholar]
  31. Busse H-J, Bunka S, Hensel A, Lubitz W. Discrimination of members of the family Pasteurellaceae based on polyamine patterns. Int J Syst Bacteriol 1997;47:698–708 [CrossRef]
    [Google Scholar]
  32. Busse HJ, Kämpfer P, Denner EB. Chemotaxonomic characterisation of Sphingomonas. J Ind Microbiol Biotechnol 1999;23:242–251 [CrossRef][PubMed]
    [Google Scholar]
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