1887

Abstract

A polyphasic approach was used to characterize an aerobic, Gram-stain-negative, rod-shaped bacterium (designed as strain CC-MHH0539) isolated from the chopped tuber of taro () in Taiwan. Strain CC-MHH0539 was able to grow at 15–30 °C (optimum, 25 °C), at pH 6.0–9.0 (optimum, 7.0) and with 0–1 % (w/v) NaCl. Strain CC-MHH0539 showed highest 16S rRNA gene sequence similarity to LNB2 (96.8 %) 469 (96.5 %), E62-3 (96.4 %) and YC7378 (96.2 %) and <96.1 % similarity to other sphingomonads. Strain CC-MHH0539 was found to cluster mainly with the clade that accommodated members of the genus The dominant cellular fatty acids were C, C 5, C 2-OH, C 7/C 6 and C 7/C 6. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, two sphingoglycolipids and two unidentified phospholipids were detected in strain CC-MHH0539. The DNA G+C content was 69.5 mol%. The respiratory quinone system and predominant polyamine was ubiquinone 10 (Q-10) and -homospermidine, respectively, which is in line with representatives. Based on the distinct phylogenetic, phenotypic and chemotaxonomic traits, strain CC-MHH0539 is considered to represent a novel species of the genus , for which the name sp. nov. is proposed. The type strain is CC-MHH0539 (=BCRC 80933=JCM 31229).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.002471
2018-01-01
2024-11-13
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/68/1/133.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.002471&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 [View Article][PubMed]
    [Google Scholar]
  2. Busse HJ, Kämpfer P, Denner EB. Chemotaxonomic characterisation of Sphingomonas . J Ind Microbiol Biotechnol 1999; 23:242–251 [View Article][PubMed]
    [Google Scholar]
  3. Lin SY, Shen FT, Lai WA, Zhu ZL, Chen WM et al. Sphingomonas formosensis sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium isolated from agricultural soil. Int J Syst Evol Microbiol 2012; 62:1581–1586 [View Article][PubMed]
    [Google Scholar]
  4. 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]
  5. Maruyama T, Park HD, Ozawa K, Tanaka Y, Sumino T et al. Sphingosinicella microcystinivorans gen. nov., sp. nov., a microcystin-degrading bacterium. Int J Syst Evol Microbiol 2006; 56:85–89 [View Article][PubMed]
    [Google Scholar]
  6. 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 [View Article][PubMed]
    [Google Scholar]
  7. 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 [View Article][PubMed]
    [Google Scholar]
  8. Maruyama T, Park HD, Ozawa K, Tanaka Y, Sumino T et al. Sphingosinicella microcystinivorans gen. nov., sp. nov., a microcystin-degrading bacterium. Int J Syst Evol Microbiol 2006; 56:85–89 [View Article][PubMed]
    [Google Scholar]
  9. Geueke B, Busse HJ, Fleischmann T, Kämpfer P, Kohler HP. Description of Sphingosinicella xenopeptidilytica sp. nov., a β-peptide-degrading species, and emended descriptions of the genus Sphingosinicella and the species Sphingosinicella microcystinivorans . Int J Syst Evol Microbiol 2007; 57:107–113 [View Article][PubMed]
    [Google Scholar]
  10. Zhou J, Fries MR, Chee-Sanford JC, Tiedje JM. Phylogenetic analyses of a new group of denitrifiers capable of anaerobic growth of toluene and description of Azoarcus tolulyticus sp. nov. Int J Syst Bacteriol 1995; 45:500–506 [View Article][PubMed]
    [Google Scholar]
  11. Heiner CR, Hunkapiller KL, Chen SM, Glass JI, Chen EY. Sequencing multimegabase-template DNA with BigDye terminator chemistry. Genome Res 1998; 8:557–561 [View Article][PubMed]
    [Google Scholar]
  12. Yim MS, Yau YC, Matlow A, So JS, Zou J et al. A novel selective growth medium-PCR assay to isolate and detect Sphingomonas in environmental samples. J Microbiol Methods 2010; 82:19–27 [View Article][PubMed]
    [Google Scholar]
  13. 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 [View Article][PubMed]
    [Google Scholar]
  14. 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]
  15. 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]
  16. 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]
  17. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  18. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416 [View Article]
    [Google Scholar]
  19. Jukes TH, Cantor CR. Evolution of protein molecules. In Munro HN. (editor) Mammalian Protein Metabolism New York: Academic Press; 1969 pp. 21–32 [Crossref]
    [Google Scholar]
  20. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
    [Google Scholar]
  21. Liu D, Jin X, Sun X, Song Y, Feng L et al. Sphingomonas faucium sp. nov., isolated from canyon soil. Int J Syst Evol Microbiol 2016; 66:2847–2852 [View Article][PubMed]
    [Google Scholar]
  22. Yabuuchi E, Kaneko T, Yano I, Moss CW, Miyoshi N. Sphingobacterium gen. nov., Sphingobacterium spiritivorum comb. nov., Sphingobacterium multivorum comb. nov., Sphingobacterium mizutae sp. nov., and Flavobacterium indologenes sp. nov.: glucose-nonfermenting gram-negative rods in cdc groups IIK-2 and IIb. Int J Syst Bacteriol 1983; 33:580–598 [View Article]
    [Google Scholar]
  23. Bernardet JF, Nakagawa Y, Holmes B. Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 2002; 52:1049–1070 [View Article][PubMed]
    [Google Scholar]
  24. Zhang L, Wang Y, Dai J, Tang Y, Yang Q et al. Bacillus korlensis sp. nov., a moderately halotolerant bacterium isolated from a sand soil sample in China. Int J Syst Evol Microbiol 2009; 59:1787–1792 [View Article][PubMed]
    [Google Scholar]
  25. Murray RGE, Doetsch RN, Robinow CF. Determination and cytological light microscopy. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp. 32–34
    [Google Scholar]
  26. Clarke PH, Cowan ST. Biochemical methods for bacteriology. J Gen Microbiol 1952; 6:187–197 [View Article][PubMed]
    [Google Scholar]
  27. Paisley R. MIS Whole Cell Fatty Acid Analysis by Gas Chromatography Training Manual Newark, DE: MIDI; 1996
    [Google Scholar]
  28. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  29. Miller LT. Single derivatization method for routine analysis of bacterial whole-cell fatty acid methyl esters, including hydroxy acids. J Clin Microbiol 1982; 16:584–586[PubMed]
    [Google Scholar]
  30. 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 [View Article]
    [Google Scholar]
  31. Scherer P, Kneifel H. Distribution of polyamines in methanogenic bacteria. J Bacteriol 1983; 154:1315–1322[PubMed]
    [Google Scholar]
  32. 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 [View Article]
    [Google Scholar]
  33. Collins MD. Isoprenoid quinone analysis in classification and identification. In Goodfellow M, Minnikin DE. (editors) Chemical Methods in Bacterial Systematics London: Academic Press; 1985 pp. 267–287
    [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.002471
Loading
/content/journal/ijsem/10.1099/ijsem.0.002471
Loading

Data & Media loading...

Supplements

Supplementary File 2

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