1887

Abstract

A Gram-reaction-negative, aerobic, non-motile, white (translucent) and rod-shaped bacterium (designated HKS-06) isolated from soil was characterized by a polyphasic approach to clarify its taxonomic position. Strain HKS-06 was observed to grow optimally at 30 °C and at pH 6.5–7.0 on R2A agar medium. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain HKS-06 belongs to the genus Sphingomonas and is most closely related to Sphingomonas lutea JS5 (97.4 % similarity). The G+C content of the genomic DNA was 64.1 mol%. Chemotaxonomic data [major quinone (Q-10), major polar lipids (phosphatidylethanolamine, phosphatidylglycerol, sphingoglycolipid, phosphatidylcholine, unknown polar lipid) and major fatty acids (summed feature 8, comprising C18 : 1ω7c/ω6c and/or C18 : 1ω6c, C18 : 0 3-OH and C16 : 0)] supported the affiliation of strain HKS-06 to the genus Sphingomonas . Moreover, the physiological and biochemical results and low level of DNA–DNA relatedness [between strain HKS06 and S . lutea JS5 (20.24±1.2 %)] allowed the phenotypic and genotypic differentiation of strain HKS-06 from recognized species of the genus Sphingomonas . The new isolate therefore represents a novel species, for which the name Sphingomonas agri sp. nov. is proposed. The type strain is HKS-06 (=KACC 18880=LMG 29563).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.002306
2017-09-25
2019-12-07
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/67/11/4429.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.002306&mimeType=html&fmt=ahah

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. 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]
  3. 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]
  4. 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]
  5. Huy H, Jin L, Lee KC, Kim SG, Lee JS et al. Sphingomonas daechungensis sp. nov., isolated from sediment of a eutrophic reservoir. Int J Syst Evol Microbiol 2014; 64: 1412– 1418 [CrossRef] [PubMed]
    [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. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991; 173: 697– 703 [CrossRef] [PubMed]
    [Google Scholar]
  8. 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]
  9. 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]
  10. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 1999; 41: 95– 98
    [Google Scholar]
  11. Kimura M. The Neutral Theory of Molecular Evolution Cambridge: Cambridge University Press; 1983; [Crossref]
    [Google Scholar]
  12. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4: 406– 425 [PubMed]
    [Google Scholar]
  13. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20: 406– 416 [CrossRef]
    [Google Scholar]
  14. 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]
  15. Felsenstein J. Confidence limit on phylogenies: an approach using the bootstrap. Evolution 1985; 39: 783– 791 [CrossRef] [PubMed]
    [Google Scholar]
  16. Buck JD, Nonstaining BJD. Nonstaining (KOH) method for determination of gram reactions of marine bacteria. Appl Environ Microbiol 1982; 44: 992– 993 [PubMed]
    [Google Scholar]
  17. Ten LN, Im WT, Kim MK, Kang MS, Lee ST. Development of a plate technique for screening of polysaccharide-degrading microorganisms by using a mixture of insoluble chromogenic substrates. J Microbiol Methods 2004; 56: 375– 382 [CrossRef] [PubMed]
    [Google Scholar]
  18. Mesbah M, Premachandran U, Whitman WB. Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 1989; 39: 159– 167 [CrossRef]
    [Google Scholar]
  19. 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]
  20. 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]
  21. Sasser M. Identification of bacteria through fatty acid analysis. In Klement Z, Rudolph K, Sands DC. (editors) Methods in Phytobacteriology Budapest: Akademiai Kaido; 1990; pp. 199– 204
    [Google Scholar]
  22. 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]
  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 approaches to bacterial systematics. Int J Syst Bacteriol 1987; 37: 463– 464 [Crossref]
    [Google Scholar]
  24. 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]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.002306
Loading
/content/journal/ijsem/10.1099/ijsem.0.002306
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