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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo International Journal of Systematic and Evolutionary Microbiology

Volume 69, Issue 11

sp. nov., isolated from mountain soil Free

Abstract

A Gram-stain-negative, strictly aerobic, motile, yellow, rod-shaped bacterium, designated ZDH117, was isolated from soilsampled atthe Danxialandformin Guangdong Province, PR China. The 16S rRNA gene sequence of strain ZDH117 had highest similarityvalues to DSM 7418 (97.5 %), CP1D (97.3 %) and KACC 14949 (97.2 %). However, phylogenetic analyses based on 16S rRNA gene sequences demonstrated that strain ZDH117 clustered with 541 (96.17 %) and DSM 19645 (95.95 %). The genomic average nucleotide identity values of ZDH117 with DSM 7418, CP1Dand KACC T were 75.1, 75.2 and 75.0 %, respectively. The G+C content of the genomic DNA was 67.6 mol%. Strain ZDH117 was characterized to have ubiquinone-10 as the predominant respiratory quinone, sym-homospermidine as the major polyamine and summed feature 8 (Cω6 and/or Cω7), C-2OH, C and summed feature 3 (Cω6 and/or Cω7) as the major cellular fatty acids (>5 % of total). The predominant polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, sphingoglycolipid, an unidentified phospholipid and three unidentified lipids. On the basis of its phenotypic, chemotaxonomic and phylogenetic characteristics, strain ZDH117 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is ZDH117 (=KCTC 62894=CCTCCAB 2018262).

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Keyword(s): 16S rRNA sequence , Mountain soil , Polyphasic taxonomy and Sphingomonas gilva
© 2019 The Authors
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2019-11-01
2025-12-10

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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 [View Article][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; 50:1563–1589 [View Article][PubMed]
     [Google Scholar]
  3. Lee KB, Liu CT, Anzai Y, Kim H, Aono T et al. The hierarchical system of the 'Alphaproteobacteria': description of Hyphomonadaceae fam. nov., Xanthobacteraceae fam. nov. and Erythrobacteraceaefam. nov. Int J Syst Evol Microbiol 2005; 55:1907–1919 [View Article][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 adhaesivasp. nov., Sphingomonas capsulata comb. nov., and two genospecies of the genus Sphingomonas. Microbiol Immunol 1990; 34:99–119 [View Article][PubMed]
     [Google Scholar]
  5. 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; 52:1485–1496 [View Article][PubMed]
     [Google Scholar]
  6. Busse HJ, Denner EB, 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 [View Article][PubMed]
     [Google Scholar]
  7. Chen H, Jogler M, Rohde M, Klenk HP, Busse HJ 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 [View Article][PubMed]
     [Google Scholar]
  8. 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 [View Article][PubMed]
     [Google Scholar]
  9. Feng GD, Yang SZ, Xiong X, Li HP, Zhu HH. 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 [View Article][PubMed]
     [Google Scholar]
  10. Gao JL, Sun P, Wang XM, Cheng S, Lv F et al. Sphingomonaszeicaulis sp. nov., an endophytic bacterium isolated from maize root. Int J Syst Evol Microbiol 2016; 66:3755–3760
     [Google Scholar]
  11. Yan ZF, Lin P, Won KH, Li CT, Park G et al. Sphingomonas rhizophila sp. nov., isolated from rhizosphere of Hibiscus syriacus. Int J Syst Evol Microbiol 2018; 68:681–686 [View Article][PubMed]
     [Google Scholar]
  12. Ko Y, Hwang WM, Kim M, Kang K, Ahn TY. Sphingomonas silvisoli sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2017; 67:2704–2710 [View Article][PubMed]
     [Google Scholar]
  13. Xue H, Piao CG, Wang XZ, Lin CL, Guo MW et al. Sphingomonas aeria sp. nov., isolated from air. Int J Syst Evol Microbiol 2018; 68:2866–2871 [View Article][PubMed]
     [Google Scholar]
  14. Zhou XK, Mi QL, Yao JH, Wu H, Liu XM et al. Sphingomonas tabacisoli sp. nov., a member of the genus Sphingomonas, isolated from rhizosphere soil of Nicotiana tabacum L. Int J Syst Evol Microbiol 2018; 68:2574–2579 [View Article][PubMed]
     [Google Scholar]
  15. Li X, Yu Y, Choi L, Song Y, Wu M et al. Phenylobacterium soli sp. nov., isolated from arsenic and cadmium contaminated farmland soil. Int J Syst Evol Microbiol 2019; 69:1398–1403 [View Article][PubMed]
     [Google Scholar]
  16. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991; 173:697–703 [View Article][PubMed]
     [Google Scholar]
  17. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997; 25:4876–4882 [View Article][PubMed]
     [Google Scholar]
  18. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol 2013; 30:2725–2729 [View Article][PubMed]
     [Google Scholar]
  19. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
     [Google Scholar]
  20. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article][PubMed]
     [Google Scholar]
  21. Rzhetsky A, Nei M. Theoretical foundation of the minimum-evolution method of phylogenetic inference. Mol Biol Evol 1993; 10:1073–1095 [View Article][PubMed]
     [Google Scholar]
  22. 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 [View Article][PubMed]
     [Google Scholar]
  23. Xu P, Li WJ, Tang SK, Zhang YQ, Chen GZ et al. Naxibacter alkalitolerans gen. nov., sp. nov., a novel member of the family 'Oxalobacteraceae' isolated from China. Int J Syst Evol Microbiol 2005; 55:1149–1153 [View Article][PubMed]
     [Google Scholar]
  24. Cowan ST, Steel KJ. Manual for the Identification of Medical Bacteria London: Cambridge University Press; 1965
     [Google Scholar]
  25. Dong XZ, Cai MY. Determinative Manual for Routine. Bacteriology Beijing: Scientific Press; 2001
     [Google Scholar]
  26. Moore DD, Dowhan D. Preparation and analysis of DNA. In Ausubel FW, Brent R, Kingston RE, Moore DD, Seidman JG et al. (editors) Current Protocols in Molecular Biology New York: Wiley; 1995 pp. 2–11
     [Google Scholar]
  27. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article][PubMed]
     [Google Scholar]
  28. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article][PubMed]
     [Google Scholar]
  29. 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 [View Article][PubMed]
     [Google Scholar]
  30. Tamaoka J, Komagata K. Determination of DNA base composition by reversed-phase high-performance liquid chromatography. FEMS Microbiol Lett 1984; 25:125–128 [View Article]
     [Google Scholar]
  31. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
     [Google Scholar]
  32. Kroppenstedt RM. Separation of bacterial menaquinones by hplc using reverse phase (rp18) and a silver loaded ion exchanger as stationary phases. J Liq Chromatogr 1982; 5:2359–2367 [View Article]
     [Google Scholar]
  33. Busse J, Auling G. Polyamine pattern as a chemotaxonomic marker within the proteobacteria. Syst Appl Microbiol 1988; 11:1–8 [View Article]
     [Google Scholar]
  34. 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 [View Article]
     [Google Scholar]
  35. Collins MD, Jones D. Lipids in the Classification and Identification of Coryneform Bacteria Containing Peptidoglycans Based on 2, 4-diaminobutyric Acid. J Appl Bacteriol 1980; 48:459–470 [View Article]
     [Google Scholar]
  36. Huang HD, Wang W, Ma T, Li GQ, Liang FL et al. Sphingomonas sanxanigenens sp. nov., isolated from soil. Int J Syst Evol Microbiol 2009; 59:719–723 [View Article][PubMed]
     [Google Scholar]
  37. Pal R, Bala S, Dadhwal M, Kumar M, Dhingra G et al. Hexachlorocyclohexane-degrading bacterial strains Sphingomonas paucimobilis B90A, UT26 and Sp+, having similar lin genes, represent three distinct species, Sphingobium indicum sp. nov., Sphingobium japonicum sp. nov. and Sphingobium francense sp. nov., and reclassification of [Sphingomonas] chungbukensis as Sphingobium chungbukense comb. nov. Int J Syst Evol Microbiol 2005; 55:1965–1972 [View Article][PubMed]
     [Google Scholar]
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Sphingomonas gilva sp. nov., isolated from mountain soil
Int J Syst Evol Microbiol 69, 3472 (2019); https://doi.org/10.1099/ijsem.0.003645
/content/journal/ijsem/10.1099/ijsem.0.003645
/content/journal/ijsem/10.1099/ijsem.0.003645
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