1887

Abstract

A Gram-stain-negative, rod-shaped bacterium, designated as strain GL-C-18, was isolated from soil sample collected at Mu Us Sandy Land, China, and its taxonomic position was investigated using a polyphasic approach. Growth was observed in the presence of 0–1 % (w/v) NaCl (optimum, 0 %), pH 6.0–9.0 (optimum, pH 7.0–8.0) and 20–37 °C. On the basis of 16S rRNA gene sequence similarity, strain GL-C-18 belonged to the family Sphingomonadaceae and was most closely related to Sphingosinicella vermicomposti YC7378 (95.7 %), Sphingomonas oligophenolica S213 (95.0 %) and Sphingobium boeckii 301 (94.8 %). The draft genome of strain GL-C-18 was 6.09 Mb, and the G+C content was 66.0 %. The average nucleotide identity value to Sphingosinicella vermicomposti YC7378 was 83.7 %. The predominant respiratory quinone was Q-10. The major fatty acids were C18 : 1ω7c, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C16:0 and C14 : 0 2OH. The main polar lipids were sphingoglycolipid, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine. On the basis of chemotaxonomic, phylogenetic and phenotypic evidence, strain GL-C-18 represents a novel species of the genus Sphingomonas , for which the name Sphingomonas deserti sp. nov. is proposed. The type strain is GL-C-18 (=ACCC 60076=KCTC 62411).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003168
2018-12-13
2019-10-19
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, 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]
  3. 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]
  4. 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]
  5. 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]
  6. 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]
  7. Siddiqi MZ, Choi GM, Kim SY, Choi KD, Im WT. Sphingomonas agri sp. nov., a bacterium isolated from soil. Int J Syst Evol Microbiol 2017;67:4429–4434 [CrossRef][PubMed]
    [Google Scholar]
  8. Huang Y, Wei Z, Danzeng W, Kim MC, Zhu G et al. Sphingomonas antarctica sp. nov., isolated from Antarctic tundra soil. Int J Syst Evol Microbiol 2017;67:4064–4068 [CrossRef][PubMed]
    [Google Scholar]
  9. Wübbeler JH, Oppermann-Sanio FB, Ockenfels A, Röttig A, Osthaar-Ebker A et al. Sphingomonas jeddahensis sp. nov., isolated from Saudi Arabian desert soil. Int J Syst Evol Microbiol 2017;67:4057–4063 [CrossRef][PubMed]
    [Google Scholar]
  10. Chung EJ, Jo EJ, Yoon HS, Song GC, Jeon CO et al. Sphingomonas oryziterrae sp. nov. and Sphingomonas jinjuensis sp. nov. isolated from rhizosphere soil of rice (Oryza sativa L.). Int J Syst Evol Microbiol 2011;61:2389–2394 [CrossRef][PubMed]
    [Google Scholar]
  11. Lin SY, Hameed A, Hsu YH, Liu YC, Hung MH et al. Sphingomonas colocasiae sp. nov., isolated from taro (Colocasia esculanta). Int J Syst Evol Microbiol 2018;68:133–140 [CrossRef][PubMed]
    [Google Scholar]
  12. Madhaiyan M, Alex THH, Cho H, Kim SJ, Weon HY et al. Sphingomonas jatrophae sp. nov. and Sphingomonas carotinifaciens sp. nov., two yellow-pigmented endophytes isolated from stem tissues of Jatropha curcas L. Int J Syst Evol Microbiol 2017;67:5150–5158 [CrossRef][PubMed]
    [Google Scholar]
  13. Lee JH, Kim DI, Choe HN, Lee SD, Seong CN et al. 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]
  14. Thaller MC, D'Andrea MM, Marmo P, Civitareale C, Casu F et al. Sphingomonas turrisvirgatae sp. nov., an agar-degrading species isolated from freshwater. Int J Syst Evol Microbiol 2018;68:2794–2799 [CrossRef][PubMed]
    [Google Scholar]
  15. Choi GM, Jo JH, Kang MS, Kim MS, Lee SY et al. Sphingomonas aquatica sp. nov., isolated from tap water. Int J Syst Evol Microbiol 2017;67:845–850 [CrossRef][PubMed]
    [Google Scholar]
  16. 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]
  17. 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 [CrossRef][PubMed]
    [Google Scholar]
  18. Lee Y, Jeon CO. Sphingomonas frigidaeris sp. nov., isolated from an air conditioning system. Int J Syst Evol Microbiol 2017;67:3907–3912 [CrossRef][PubMed]
    [Google Scholar]
  19. Janssen PH, Yates PS, Grinton BE, Taylor PM, Sait M. Improved culturability of soil bacteria and isolation in pure culture of novel members of the divisions Acidobacteria, Actinobacteria, Proteobacteria, and Verrucomicrobia. Appl Environ Microbiol 2002;68:2391–2396 [CrossRef][PubMed]
    [Google Scholar]
  20. Liu L, Li L, Song Z, Wang S, Zhang J et al. Parapedobacter deserti sp. nov., an endophytic bacterium isolated from Haloxylon ammodendron stems. Int J Syst Evol Microbiol 2017;67:2148–2152 [CrossRef][PubMed]
    [Google Scholar]
  21. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematics Chichester: Wiley; 1991
    [Google Scholar]
  22. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012;62:716–721 [CrossRef][PubMed]
    [Google Scholar]
  23. 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]
  24. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981;17:368–376 [CrossRef][PubMed]
    [Google Scholar]
  25. 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 [CrossRef][PubMed]
    [Google Scholar]
  26. Li B, Yang X, Tan H, Ke B, He D et al. Vibrio parahaemolyticus O4:K8 forms a potential predominant clone in southern China as detected by whole-genome sequence analysis. Int J Food Microbiol 2017;244:90–95 [CrossRef][PubMed]
    [Google Scholar]
  27. Varghese NJ, Mukherjee S, Ivanova N, Konstantinidis KT, Mavrommatis K et al. Microbial species delineation using whole genome sequences. Nucleic Acids Res 2015;43:6761–6771 [CrossRef][PubMed]
    [Google Scholar]
  28. 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]
  29. 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]
  30. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013;14:60–73 [CrossRef][PubMed]
    [Google Scholar]
  31. Sims GE, Jun SR, Wu GA, Kim SH. Alignment-free genome comparison with feature frequency profiles (FFP) and optimal resolutions. Proc Natl Acad Sci USA 2009;106:2677–2682 [CrossRef][PubMed]
    [Google Scholar]
  32. Dong XZ, Cai MY. Determination of biochemical properties. In Manual for the Systematic Identification of General Bacteria Beijing: Science Press; 2001
    [Google Scholar]
  33. 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]
  34. Komagata K, Suzuki K. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1987;19:161–207
    [Google Scholar]
  35. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  36. Ohta H, Hattori R, Ushiba Y, Mitsui H, Ito M et al. Sphingomonas oligophenolica sp. nov., a halo- and organo-sensitive oligotrophic bacterium from paddy soil that degrades phenolic acids at low concentrations. Int J Syst Evol Microbiol 2004;54:2185–2190 [CrossRef][PubMed]
    [Google Scholar]
  37. Kämpfer P, Meurer U, Esser M, Hirsch T, Busse HJ. Sphingomonas pseudosanguinis sp. nov., isolated from the water reservoir of an air humidifier. Int J Syst Evol Microbiol 2007;57:1342–1345 [CrossRef][PubMed]
    [Google Scholar]
  38. Chen H, Jogler M, Rohde M, Klenk HP, Busse HJ et al. Sphingobium limneticum sp. nov. and Sphingobium boeckii sp. nov., two freshwater planktonic members of the family Sphingomonadaceae, and reclassification of Sphingomonas suberifaciens as Sphingobium suberifaciens comb. nov. Int J Syst Evol Microbiol 2013;63:735–743 [CrossRef][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003168
Loading
/content/journal/ijsem/10.1099/ijsem.0.003168
Loading

Data & Media loading...

Supplements

Supplementary data

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