1887

Abstract

The novel bacterial strain C33 was isolated from a freshwater sample collected from the Hapcheon–Changnyeong barrage. The Gram-negative, motile, yellow-pigmented strain C33 was characterized as a rod-shaped and strictly aerobic bacterium. A 16S-rRNA phylogenetic analysis revealed that this strain was most closely related to V2M44, X1-8, and ZLT-5 with 97.1, 97.0, and 95.0 % 16S-rRNA sequence similarities, respectively. The genomic DNA GC content of strain C33 was estimated at 65.0 mol%. The average nucleotide identity of strain C33 relative to V2M44 and ZLT-5 was found to be 77.0 and 75.6%, with average amino-acid identities of 69.9, and 66.7%, and the digital DNA–DNA hybridization values of 21.3 and 17.7 %, respectively. The cells grew at 19–37 °C and pH 6–9 with 0–0.5 % (w/v) NaCl (optimum: 28 °C, pH 6.5, and 0 % NaCl). The major component identified in the polyamine pattern was -homospermidine, and the main ubiquinone was Q-10. The predominant polar lipids characterized were diphophatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, and sphingoglycolipid. Iso-C, C anteiso, and summed feature 3 (C 6 and/or C 7) were found to be the primary cellular fatty acids in strain C33. Based on these genotypic and phenotypic characteristics, strain C33 was classified as a novel species of the genus ; and the name sp. nov. is proposed (=KACC 21511=JCM 33880).

Funding
This study was supported by the:
  • Woojun Park , Korea University , (Award K2006821)
  • Woojun Park , the National Institute of Biological Resources , (Award NIBR202002108)
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004503
2020-10-13
2020-10-20
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. Shin SC, Kim SJ, Ahn DH, Lee JK, Park H. Draft genome sequence of Sphingomonas echinoides ATCC 14820. J Bacteriol 2012; 194:194 [CrossRef][PubMed]
    [Google Scholar]
  4. 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]
  5. 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]
  6. Eguchi M, Ostrowski M, Fegatella F, Bowman J, Nichols D et al. Sphingomonas alaskensis strain AFO1, an abundant oligotrophic ultramicrobacterium from the North Pacific. Appl Environ Microbiol 2001; 67:4945–4954 [CrossRef][PubMed]
    [Google Scholar]
  7. Shi T, Fredrickson JK, Balkwill DL. Biodegradation of polycyclic aromatic hydrocarbons by Sphingomonas strains isolated from the terrestrial subsurface. J Ind Microbiol Biotechnol 2001; 26:283–289 [CrossRef][PubMed]
    [Google Scholar]
  8. Zhu L, Si M, Li C, Xin K, Chen C et al. Sphingomonas gei sp. nov., isolated from roots of Geum aleppicum. Int J Syst Evol Microbiol 2015; 65:1160–1166 [CrossRef][PubMed]
    [Google Scholar]
  9. Hsueh PR, Teng LJ, Yang PC, Chen YC, Pan HJ et al. Nosocomial infections caused by Sphingomonas paucimobilis: clinical features and microbiological characteristics. Clin Infect Dis 1998; 26:676–681 [CrossRef][PubMed]
    [Google Scholar]
  10. Leys NMEJ, Ryngaert A, Bastiaens L, Verstraete W, Top EM et al. Occurrence and phylogenetic diversity of Sphingomonas strains in soils contaminated with polycyclic aromatic hydrocarbons. Appl Environ Microbiol 2004; 70:1944–1955 [CrossRef][PubMed]
    [Google Scholar]
  11. Kaur J, Kaur J, Niharika N, Lal R. Sphingomonas laterariae sp. nov., isolated from a hexachlorocyclohexane-contaminated dump site. Int J Syst Evol Microbiol 2012; 62:2891–2896 [CrossRef][PubMed]
    [Google Scholar]
  12. Moreno-Forero SK, van der Meer JR. Genome-wide analysis of Sphingomonas wittichii RW1 behaviour during inoculation and growth in contaminated sand. ISME J 2015; 9:150–165 [CrossRef][PubMed]
    [Google Scholar]
  13. Zhang D-C, Schumann P, Redzic M, Zhou Y-G, Liu H-C et al. Nocardioides alpinus sp. nov., a psychrophilic actinomycete isolated from alpine glacier cryoconite. Int J Syst Evol Microbiol 2012; 62:445–450 [CrossRef][PubMed]
    [Google Scholar]
  14. Kim M, Shin B, Lee J, Park HY, Park W. Culture-independent and culture-dependent analyses of the bacterial community in the phycosphere of cyanobloom-forming Microcystis aeruginosa. Sci Rep 2019; 9:20416 [CrossRef][PubMed]
    [Google Scholar]
  15. Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 2013; 41:D590–596 [CrossRef][PubMed]
    [Google Scholar]
  16. Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ et al. Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res 2003; 31:3497–3500 [CrossRef][PubMed]
    [Google Scholar]
  17. Kumar S, Nei M, Dudley J, Tamura K. MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief Bioinform 2008; 9:299–306 [CrossRef][PubMed]
    [Google Scholar]
  18. Wagner J, Coupland P, Browne HP, Lawley TD, Francis SC et al. Evaluation of PacBio sequencing for full-length bacterial 16S rRNA gene classification. BMC Microbiol 2016; 16:274 [CrossRef][PubMed]
    [Google Scholar]
  19. Chin C-S, Alexander DH, Marks P, Klammer AA, Drake J et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 2013; 10:563–569 [CrossRef][PubMed]
    [Google Scholar]
  20. Paul BJ, Ross W, Gaal T, Gourse RL. rRNA transcription in Escherichia coli. Annu Rev Genet 2004; 38:749–770 [CrossRef][PubMed]
    [Google Scholar]
  21. Yona AH, Bloom-Ackermann Z, Frumkin I, Hanson-Smith V, Charpak-Amikam Y et al. tRNA genes rapidly change in evolution to meet novel translational demands. Elife 2013; 2:e01339 [CrossRef][PubMed]
    [Google Scholar]
  22. 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]
  23. Meier-Kolthoff JP, Klenk HP, Göker M. Taxonomic use of DNA G+C content and DNA-DNA hybridization in the genomic age. Int J Syst Evol Microbiol 2014; 64:352–356 [CrossRef][PubMed]
    [Google Scholar]
  24. Konstantinidis KT, Tiedje JM. Towards a genome-based taxonomy for prokaryotes. J Bacteriol 2005; 187:6258–6264 [CrossRef][PubMed]
    [Google Scholar]
  25. Luo C, Rodriguez-R LM, Konstantinidis KT. MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences. Nucleic Acids Res 2014; 42:e73 [CrossRef][PubMed]
    [Google Scholar]
  26. Park C, Lee YS, Park S-Y, Park W. Methylobacterium currus sp. nov., isolated from a car air conditioning system. Int J Syst Evol Microbiol 2018; 68:3621–3626 [CrossRef][PubMed]
    [Google Scholar]
  27. Hiraishi A, Ueda Y, Ishihara J, Mori T. Comparative lipoquinone analysis of influent sewage and activated sludge by high-performance liquid chromatography and photodiode array detection. J Gen Appl Microbiol 1996; 42:457–469 [CrossRef]
    [Google Scholar]
  28. Hamana K, Matsuzaki S. Polyamine distribution patterns serve as a phenotypic marker in the chemotaxonomy of the Proteobacteria. Can J Microbiol 1993; 39:304–310 [CrossRef]
    [Google Scholar]
  29. 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]
  30. Hamana K, Matsuzaki S. Polyamines as a chemotaxonomic marker in bacterial systematics. Crit Rev Microbiol 1992; 18:261–283 [CrossRef][PubMed]
    [Google Scholar]
  31. Sasser M. Bacterial identification by gas chromatographic analysis of fatty acids methyl esters (GC-FAME). MIDI Technical Note 1990; 1502:10
    [Google Scholar]
  32. 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]
  33. Zhang JY, Liu XY, Liu SJ. Sphingomonas changbaiensis sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2010; 60:790–795 [CrossRef][PubMed]
    [Google Scholar]
  34. 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 [CrossRef][PubMed]
    [Google Scholar]
  35. Zhou XY, Zhang L, Su XJ, Hang P, Hu B et al. Sphingomonas flavalba sp. nov., isolated from a procymidone-contaminated soil. Int J Syst Evol Microbiol 2019; 69:2936–2941 [CrossRef][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004503
Loading
/content/journal/ijsem/10.1099/ijsem.0.004503
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
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