1887

Abstract

A Gram-stain-negative bacterium, designated strain YJ09, was isolated from spinach farming field soil at Shinan in the Republic of Korea. Cells of strain YJ09 were found to be strictly aerobic, non-motile, non-spore-forming creamy-yellow rods which can grow at 20–37 °C (optimum, 30 °C), at pH 6.0–9.0 (optimum, pH 7.0–8.0) and at salinities of 0–0.5 % (w/v) NaCl (optimum, 0 % NaCl). The 16S rRNA gene sequence analysis showed that strain YJ09 belongs to the genus with high sequence similarities to GP20-2 (98.0 %), HKS-06 (97.7 %) and JS5 (97.4 %). The results of phylogenetic analysis indicated that strain YJ09 formed a distinct phyletic line in the genus and the results of DNA–DNA relatedness studies demonstrated that strain YJ09 could be separated from its closest relatives in the genus . The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, unidentified glycolipids, an unidentified phospholipid and sphingoglycolipid. The predominant ubiquinone and polyamine components were Q-10 and spermidine, respectively. The major fatty acids were C ω7 C and C ω7 and/or iso-C 2-OH. The DNA G+C content of this novel isolate was 65.9 mol%. On the basis of phenotypic, chemotaxonomic properties and phylogenetic analyses in this study, strain YJ09 is considered to represent a novel species in the genus , for which the name sp. nov. is proposed. The type strain is YJ09 (=KACC 19551=NBRC 113247).

Funding
This study was supported by the:
  • Kyung-Sook Whang , Ministry of Agriculture, Food and Rural Affairs, Republic of Korea (as part of the Genome Technology to Business Translation Program) , (Award 918016-4)
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2020-06-05
2020-07-02
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References

  1. Kosako Y, Yabuuchi E, Naka T, Fujiwara N, Kobayashi K. 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 Immunol 2000; 44:563–575 [CrossRef][PubMed]
    [Google Scholar]
  2. Anzai Y, Kim H, Park JY, Wakabayashi H, Oyaizu H et al. Phylogenetic affiliation of the pseudomonads based on 16S rRNA sequence. Int J Syst Evol Microbiol 2000; 50 Pt 4:1563–1589 [CrossRef][PubMed]
    [Google Scholar]
  3. Lee K-B, Liu C-T, Anzai Y, Kim H, Aono T et al. The hierarchical system of the 'Alphaproteobacteria': description of Hyphomonadaceae fam. nov., Xanthobacteraceae fam. nov. and Erythrobacteraceae fam. nov. Int J Syst Evol Microbiol 2005; 55:1907–1919 [CrossRef][PubMed]
    [Google Scholar]
  4. Yabuuchi E, Yano I, Oyaizu H, Hashimoto Y, Ezaki T et al. 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 Immunol 1990; 34:99–119 [CrossRef]
    [Google Scholar]
  5. Takeuchi M, Kawai F, Shimada Y, Yokota A. 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 Microbiol 1993; 16:227–238 [CrossRef]
    [Google Scholar]
  6. 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]
  7. Yabuuchi E, Kosako Y, Naka T, Suzuki S, Yano I. Proposal of Sphingomonas suberifaciens (van Bruggen, Jochimsen and Brown 1990) comb. nov., Sphingomonas natatoria (Sly 1985) comb. nov., Sphingomonas ursincola (Yurkov et al. 1997) comb. nov., and emendation of the genus Sphingomonas . Microbiol Immunol 1999; 43:339–349 [CrossRef]
    [Google Scholar]
  8. Yabuuchi E, Kosako Y, Fujiwara N, Naka T, Matsunaga I et al. 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 2002:1485–1496
    [Google Scholar]
  9. Busse H-J, Denner EBM, Buczolits S, Salkinoja-Salonen M, Bennasar A et al. 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 2003; 53:1253–1260 [CrossRef][PubMed]
    [Google Scholar]
  10. Chen H, Jogler M, Rohde M, Klenk H-P, Busse H-J et al. Reclassification and emended description of Caulobacter leidyi as Sphingomonas leidyi comb. nov., and emendation of the genus Sphingomonas . Int J Syst Evol Microbiol 2012; 62:2835–2843 [CrossRef][PubMed]
    [Google Scholar]
  11. Feng G-D, Yang S-Z, Xiong X, Li H-P, Zhu H-H. Sphingomonas spermidinifaciens sp. nov., a novel bacterium containing spermidine as the major polyamine, isolated from an abandoned lead-zinc mine and emended descriptions of the genus Sphingomonas and the species Sphingomonas yantingensis and Sphingomonas japonica . Int J Syst Evol Microbiol 2017; 67:2160–2165 [CrossRef][PubMed]
    [Google Scholar]
  12. DeLong EF. Archaea in coastal marine environments. Proc Natl Acad Sci U S A 1992; 89:5685–5689 [CrossRef][PubMed]
    [Google Scholar]
  13. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007; 23:2947–2948 [CrossRef][PubMed]
    [Google Scholar]
  14. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [CrossRef][PubMed]
    [Google Scholar]
  15. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [CrossRef][PubMed]
    [Google Scholar]
  16. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416 [CrossRef]
    [Google Scholar]
  17. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [CrossRef][PubMed]
    [Google Scholar]
  18. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16:111–120 [CrossRef][PubMed]
    [Google Scholar]
  19. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [CrossRef][PubMed]
    [Google Scholar]
  20. Ezaki T, Hashimoto Y, Yabuuchi E. 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 1989; 39:224–229 [CrossRef]
    [Google Scholar]
  21. Yoon S-H, Ha S-M, 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]
  22. Ahn J-H, Kim B-C, Kim S-J, Lee G-H, Song J et al. Sphingomonas parvus sp. nov. isolated from a ginseng-cultivated soil. J Microbiol 2015; 53:673–677 [CrossRef][PubMed]
    [Google Scholar]
  23. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O et al. International Committee on systematic bacteriology. Report of the AD hoc Committee on reconciliation of approches to bacterial Systematics. Int J Syst Bacteriol 1987; 37:463–464
    [Google Scholar]
  24. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [CrossRef][PubMed]
    [Google Scholar]
  25. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:75 [CrossRef][PubMed]
    [Google Scholar]
  26. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ et al. The seed and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res 2014; 42:D206–D214 [CrossRef][PubMed]
    [Google Scholar]
  27. Yoon S-H, Ha S-M, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [CrossRef][PubMed]
    [Google Scholar]
  28. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [CrossRef][PubMed]
    [Google Scholar]
  29. Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 2019; 10:2182 [CrossRef][PubMed]
    [Google Scholar]
  30. Lefort V, Desper R, Gascuel O. FastME 2.0: a comprehensive, accurate, and fast distance-based phylogeny inference program. Mol Biol Evol 2015; 32:2798–2800 [CrossRef][PubMed]
    [Google Scholar]
  31. Farris JS. Estimating phylogenetic trees from distance matrices. Am Nat 1972; 106:645–668 [CrossRef]
    [Google Scholar]
  32. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. Dna-Dna hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [CrossRef][PubMed]
    [Google Scholar]
  33. Murray RGE, Doetsch RN, Robinow F. Determinative and cytological light microscopy. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp 21–41
    [Google Scholar]
  34. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp 607–654
    [Google Scholar]
  35. Leifson E. Determination of carbohydrate metabolism of marine bacteria. J Bacteriol 1963; 85:1183–1184 [CrossRef][PubMed]
    [Google Scholar]
  36. Bauer AW, Kirby WM, Sherris JC, Turck M. Antibiotic susceptibility testing by a standardized single disk method. Am J Clin Pathol 1966; 45:493–496 [CrossRef][PubMed]
    [Google Scholar]
  37. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  38. Collins MD, Jones D. Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiol Rev 1981; 45:316–354 [CrossRef][PubMed]
    [Google Scholar]
  39. Yabuuchi E, Kosako Y, Naka T, Suzuki S, Yano I. Proposal of Sphingomonas suberifaciens (van Bruggen, Jochimsen and brown 1990) comb. nov., Sphingomonas natatoria (Sly 1985) comb. nov., Sphingomonas ursincola (Yurkov et al. 1997) comb. nov., and emendation of the genus Sphingomonas . Microbiol Immunol 1999; 43:339–349 [CrossRef][PubMed]
    [Google Scholar]
  40. Yabuuchi E, Yano I, Oyaizu H, Hashimoto Y, Ezaki T et al. 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 Immunol 1990; 34:99–119 [CrossRef][PubMed]
    [Google Scholar]
  41. Busse J, Auling G. Polyamine pattern as a chemotaxonomic marker within the Proteobacteria . Syst Appl Microbiol 1988; 11:1–8 [CrossRef]
    [Google Scholar]
  42. Busse H-J, Bunka S, Hensel A, Lubitz W. Discrimination of members of the family Pasteurellaceae based on polyamine patterns. Int J Syst Evol Microbiol 1997; 47:698–708 [CrossRef]
    [Google Scholar]
  43. Stolz A, Busse H-J, Kämpfer P. Pseudomonas knackmussii sp. nov. Int J Syst Evol Microbiol 2007; 57:572–576 [CrossRef][PubMed]
    [Google Scholar]
  44. Siddiqi MZ, Choi G-M, Kim SY, Choi KD, Im W-T. Sphingomonas agri sp. nov., a bacterium isolated from soil. Int J Syst Evol Microbiol 2017; 67:4429–4434 [CrossRef][PubMed]
    [Google Scholar]
  45. Lee JH, Kim DI, Kang JW, Seong CN. Sphingomonas lutea sp. nov., isolated from freshwater of an artificial reservoir. Int J Syst Evol Microbiol 2016; 66:5493–5499 [CrossRef][PubMed]
    [Google Scholar]
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