1887

Abstract

A Gram-staining-negative, strictly aerobic, non-motile strain, SYSUP0001, was isolated from tubers of Gastrodia elata Blume. The 16S rRNA gene sequence result indicated that SYSUP0001 represents a member of the genus Sphingomonas , with the highest sequence similarity (97.7 %) to the type strain of Sphingomonas ginsengisoli . SYSUP0001 grew at 14–37 °C and pH 6–8, with optimum growth at 28 °C and pH 7. Tolerance to NaCl was up to 3 % (w/v) with optimum growth in the absence of NaCl. The respiratory quinone was Q-10. The major fatty acids were C18 : 1ω7c, Summed feature 3 (C16 : 1ω7c/C16 : 1ω6c), and C16 : 0. The polar lipids were diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), sphingoglycolipid (SGL), phosphatidylcholine (PC) and four unidentified polar lipids (L). The DNA G+C content was 67.5 %. The average nucleotide identity (ANI) values between SYSUP0001 and closely related members of the genus Sphingomonas were below the cut-off level (95–96 %) for species delineation. On the basis of the phenotypic, phylogenetic and chemotaxonomic characterizations, SYSUP0001 represents a novel species of the genus Sphingomonas , for which the name Sphingomonasmesophila sp. nov. is proposed. The type strain is SYSUP0001 (=KCTC 62179 =CGMCC 1.16462).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003263
2019-02-08
2019-10-18
Loading full text...

Full text loading...

References

  1. 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]
  2. 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]
  3. 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]
  4. 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]
  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 [CrossRef][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 [CrossRef][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 [CrossRef][PubMed]
    [Google Scholar]
  8. 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 [CrossRef][PubMed]
    [Google Scholar]
  9. Kim SJ, Moon JY, Lim JM, Ahn JH, Weon HY et al. Sphingomonas aerophila sp. nov. and Sphingomonas naasensis sp. nov., isolated from air and soil, respectively. Int J Syst Evol Microbiol 2014;64:926–932 [CrossRef][PubMed]
    [Google Scholar]
  10. Yun SS, Siddiqi MZ, Lee SY, Kim MS, Choi K et al. Sphingomonas hankyongensis sp. nov. isolated from tap water. Arch Microbiol 2016;198:767–771 [CrossRef][PubMed]
    [Google Scholar]
  11. Asker D, Beppu T, Ueda K. Sphingomonas jaspsi sp. nov., a novel carotenoid-producing bacterium isolated from Misasa, Tottori, Japan. Int J Syst Evol Microbiol 2007;57:1435–1441 [CrossRef][PubMed]
    [Google Scholar]
  12. Lee JH, Kim DI, Choe HN, Lee SD, Seong CN. Sphingomonas limnosediminicola sp. nov. and Sphingomonas palustris sp. nov., isolated from freshwater environments. Int J Syst Evol Microbiol 2017;67:2834–2841 [CrossRef][PubMed]
    [Google Scholar]
  13. Huang HY, Li J, Zhao GZ, Zhu WY, Yang LL et al. Sphingomonas endophytica sp. nov., isolated from Artemisia annua L. Int J Syst Evol Microbiol 2012;62:1576–1580 [CrossRef][PubMed]
    [Google Scholar]
  14. Qin S, Li J, Chen HH, Zhao GZ, Zhu WY et al. Isolation, diversity, and antimicrobial activity of rare actinobacteria from medicinal plants of tropical rain forests in Xishuangbanna, China. Appl Environ Microbiol 2009;75:6176–6186 [CrossRef][PubMed]
    [Google Scholar]
  15. Khieu TN, Liu MJ, Nimaichand S, Quach NT, Chu-Ky S et al. Characterization and evaluation of antimicrobial and cytotoxic effects of Streptomyces sp. HUST012 isolated from medicinal plant Dracaena cochinchinensis Lour. Front Microbiol 2015;6:574 [CrossRef][PubMed]
    [Google Scholar]
  16. 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 [CrossRef][PubMed]
    [Google Scholar]
  17. Kovacs N. Identification of Pseudomonas pyocyanea by the oxidase reaction. Nature 1956;178:703–704 [CrossRef][PubMed]
    [Google Scholar]
  18. Gonzalez C, Gutierrez C, Ramirez C. Halobacterium vallismortis sp. nov. An amylolytic and carbohydrate-metabolizing, extremely halophilic bacterium. Can J Microbiol 1978;24:710–715 [CrossRef][PubMed]
    [Google Scholar]
  19. Li WJ, Xu P, Schumann P, Zhang YQ, Pukall R et al. Georgenia ruanii sp. nov., a novel actinobacterium isolated from forest soil in Yunnan (China), and emended description of the genus Georgenia. Int J Syst Evol Microbiol 2007;57:1424–1428 [CrossRef][PubMed]
    [Google Scholar]
  20. 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]
  21. 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]
  22. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981;17:368–376 [CrossRef][PubMed]
    [Google Scholar]
  23. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971;20:406–416 [CrossRef]
    [Google Scholar]
  24. 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]
  25. 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 [CrossRef][PubMed]
    [Google Scholar]
  26. 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]
  27. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985;39:783–791 [CrossRef][PubMed]
    [Google Scholar]
  28. An DS, Liu QM, Lee HG, Jung MS, Kim SC et al. Sphingomonas ginsengisoli sp. nov. and Sphingomonas sediminicola sp. nov. Int J Syst Evol Microbiol 2013;63:496–501 [CrossRef][PubMed]
    [Google Scholar]
  29. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977;100:221–230 [CrossRef][PubMed]
    [Google Scholar]
  30. 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 [CrossRef]
    [Google Scholar]
  31. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark: Microbial ID, Inc; 1990
    [Google Scholar]
  32. Minnikin DE, Collins MD, Goodfellow M. Fatty acid and polar lipid composition in the classification of Cellulomonas, Oerskovia and related taxa. J Appl Bacteriol 1979;47:87–95 [CrossRef]
    [Google Scholar]
  33. 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 [CrossRef]
    [Google Scholar]
  34. 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]
  35. 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]
  36. Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M et al. Versatile and open software for comparing large genomes. Genome Biol 2004;5:R12–2483 [CrossRef][PubMed]
    [Google Scholar]
  37. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016;32:929–931 [CrossRef][PubMed]
    [Google Scholar]
  38. Lagesen K, Hallin P, Rødland EA, Staerfeldt HH, Rognes T et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007;35:3100–3108 [CrossRef][PubMed]
    [Google Scholar]
  39. Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997;25:955–964 [CrossRef][PubMed]
    [Google Scholar]
  40. Delcher AL, Harmon D, Kasif S, White O, Salzberg SL. Improved microbial gene identification with GLIMMER. Nucleic Acids Res 1999;27:4636–4641 [CrossRef][PubMed]
    [Google Scholar]
  41. Tatusov RL, Koonin EV, Lipman DJ. A genomic perspective on protein families. Science 1997;278:631–637 [CrossRef][PubMed]
    [Google Scholar]
  42. Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B et al. The COG database: an updated version includes eukaryotes. BMC Bioinformatics 2003;4:41 [CrossRef][PubMed]
    [Google Scholar]
  43. Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M. KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res 2007;35:W182–W185 [CrossRef][PubMed]
    [Google Scholar]
  44. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009;106:19126–19131 [CrossRef][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003263
Loading
/content/journal/ijsem/10.1099/ijsem.0.003263
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most Cited This Month

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error