1887

Abstract

During a study of the bacterial community in forest soil of Kyonggi University, Suwon, South Korea, a glistening yellow-pigmented, Gram-stain-negative, aerobic, motile and rod-shaped bacterium, designated strain C-1-16, was isolated. This strain was non-sporulating, catalase-negative and oxidase-positive. It was able to grow at 20–42 °C, at pH 6.0–9.0 and with 0–0.5 % (w/v) NaCl. This strain was taxonomically characterized by a polyphasic approach. Based on the results of 16S rRNA gene sequence analysis, strain C-1-16 formed a lineage within the family of the phylum and closely related to the genera (93.53 % sequence similarity), (92.52–90.75 %), (91.99–91.19 %) and (91.88–91.78 %). Flexirubin-type pigment was present for strain C-1-16. The only respiratory quinone was menaquinone-7 (MK-7) and the major polar lipid was phosphatidylethanolamine. The predominant fatty acids of strain C-1-16 were iso-C, iso-C 3-OH, iso-C G, summed feature 3 (C 6 and/or C 7c) and C. The genomic DNA G+C content of this novel strain was 45.5 mol%. On the basis of phenotypic, genotypic and phylogenetic analysis, strain C-1-16 represents a novel species of a new genus in the family , for which the name gen. nov., sp. nov. is proposed. The type strain of is C-1-16 (=KEMB 900-374=KACC 18717=JCM 31293).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.001354
2016-11-01
2020-04-02
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/66/11/4347.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.001354&mimeType=html&fmt=ahah

References

  1. Breznak J. A., Costilow R. N.. 2007; Physicochemical factors in growth. In Methods for General and Molecular Bacteriology, 3rd edn. pp.309–329 Edited by Beveridge T. J., Breznak J. A., Marzluf G. A., Schmidt T. M., Snyder L. R.. Washington, D. C: American Society for Microbiology;
    [Google Scholar]
  2. Collins M. D., Jones D.. 1981; Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiol Rev45:316–354[PubMed]
    [Google Scholar]
  3. Cowan S. T., Steel K. J.. 1965; Manual for the Identification of Medical Bacteria London: Cambridge University Press;
    [Google Scholar]
  4. Dahal R. H., Kim J.. 2016; Rhabdobacter roseus gen. nov., sp. nov., isolated from soil. Int J Syst Evol Microbiol66:308–314[CrossRef]
    [Google Scholar]
  5. Doetsch R. N.. 1981; Determinative methods of light microscopy. In Manual of Methods for General Bacteriology pp21–33 Edited by Gerhardt P.. Washington, DC: American Society for Microbiology;
    [Google Scholar]
  6. Felsenstein J.. 1981; Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol17:368–376 [CrossRef][PubMed]
    [Google Scholar]
  7. Felsenstein J.. 1985; Confidence limits on phylogenies: an approach using the bootstrap. Evolution39:783–791 [CrossRef]
    [Google Scholar]
  8. Fitch W. M.. 1971; Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool20:406–416 [CrossRef]
    [Google Scholar]
  9. Frank J. A., Reich C. I., Sharma S., Weisbaum J. S., Wilson B. A., Olsen G. J.. 2008; Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes. Appl Environ Microbiol74:2461–2470 [CrossRef][PubMed]
    [Google Scholar]
  10. Hall T. A.. 1999; BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser41:95–98
    [Google Scholar]
  11. Hemraj V., Diksha S., Avneet G.. 2013; A review on commonly used biochemical test for bacteria. Innovare J Life Sci1:1–7
    [Google Scholar]
  12. Jin L., Shin S. Y., Lee H. G., Ahn C. Y., Oh H. M.. 2013; Lacibacter daechungensis sp. nov., isolated from deep freshwater of a reservoir. Int J Syst Evol Microbiol63:4519–4523[CrossRef]
    [Google Scholar]
  13. Kämpfer P., Lodders N., Falsen E.. 2011; Hydrotalea flava gen. nov., sp. nov., a new member of the phylum Bacteroidetes and allocation of the genera Chitinophaga, sediminibacterium, lacibacter, flavihumibacter, flavisolibacter, niabella, niastella, segetibacter, parasegetibacter, terrimonas, fam. Int J Syst Evol Microbiol61:518–523[CrossRef]
    [Google Scholar]
  14. Kang H., Kim H., Lee B. I., Joung Y., Joh K.. 2014; Sediminibacterium goheungense sp. nov., isolated from a freshwater reservoir. Int J Syst Evol Microbiol64:1328–1333[CrossRef]
    [Google Scholar]
  15. Kim O. S., Cho Y. J., Lee K., Yoon S. H., Kim M., Na H., Park S. C., Jeon Y. S., Lee J. H. et al. 2012; Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol62:716–721 [CrossRef][PubMed]
    [Google Scholar]
  16. Kim Y. J., Nguyen N. L., Weon H. Y., Yang D. C.. 2013a; Sediminibacterium ginsengisoli sp. nov., isolated from soil of a ginseng field, and emended descriptions of the genus Sediminibacterium and of Sediminibacterium salmoneum. Int J Syst Evol Microbiol63:905–912 [CrossRef][PubMed]
    [Google Scholar]
  17. Kim J. K., He D., Liu Q. M., Park H. Y., Jung M. S., Yoon M. H., Kim S. C., Im W. T.. 2013b; Novosphingobium ginsensosidimutans sp. nov., with the ability to convert ginsenoside. Int J Syst Evol Microbiol23:444–450
    [Google Scholar]
  18. Kim S. J., Ahn J. H., Weon H. Y., Hong S. B., Seok S. J., Kwon S. W.. 2015; Parasegetibacter terrae sp. nov., isolated from paddy soil and emended description of the genus Parasegetibacter. Int J Syst Evol Microbiol65:113–116 [CrossRef][PubMed]
    [Google Scholar]
  19. Kimura M.. 1980; A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol16:111–120 [CrossRef][PubMed]
    [Google Scholar]
  20. Komagata K., Suzuki K.. 1987; Lipids and cell wall analysis in bacterial systematics. Methods Microbiol19:161–203[CrossRef]
    [Google Scholar]
  21. Lee J. C., Kim S. G., Whang K. S.. 2014; Novosphingobium aquiterrae sp. nov., isolated from ground water. Int J Syst Evol Microbiol64:3282–3287 [CrossRef][PubMed]
    [Google Scholar]
  22. Lin S. Y., Hameed A., Liu Y. C., Hsu Y. H., Lai W. A., Huang H. I., Young C. C.. 2014; Novosphingobium arabidopsis sp. nov., a DDT-resistant bacterium isolated from the rhizosphere of Arabidopsis thaliana. Int J Syst Evol Microbiol64:594–598 [CrossRef][PubMed]
    [Google Scholar]
  23. Ludwig W., Strunk O., Klugbauer S., Klugbauer N., Weizenegger M., Neumaier J., Bachleitner M., Schleifer K. H.. 1998; Bacterial phylogeny based on comparative sequence analysis. Electrophoresis19:554–568 [CrossRef][PubMed]
    [Google Scholar]
  24. Marmur J.. 1961; A procedure for the isolation of deoxyribonucleic acid from micro-organisms. J Mol Biol3:208–218 [CrossRef]
    [Google Scholar]
  25. Mesbah M., Premachandran U., Whitman W. B.. 1989; Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol39:159–167 [CrossRef]
    [Google Scholar]
  26. Minnikin D. E., O'Donnell A. G., Goodfellow M., Alderson G., Athalye M., Schaal A., Parlett J. H.. 1984; An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods2:233–241 [CrossRef]
    [Google Scholar]
  27. Pham V. H., Kim J.. 2012; Cultivation of unculturable soil bacteria. Trends Biotechnol30:475–484 [CrossRef][PubMed]
    [Google Scholar]
  28. Pham V. H., Kim J., Jeong S. W.. 2014; Enhanced isolation and culture of highly efficient psychrophilic oil-degrading bacteria from oil-contaminated soils in South Korea. J Environ Biol35:1145–1149[PubMed]
    [Google Scholar]
  29. Powers E. M.. 1995; Efficacy of the Ryu nonstaining KOH technique for rapidly determining gram reactions of food-borne and waterborne bacteria and yeasts. Appl Environ Microbiol61:3756–3758[PubMed]
    [Google Scholar]
  30. Qu J. H., Yuan H. L.. 2008; Sediminibacterium salmoneum gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from sediment of a eutrophic reservoir. Int J Syst Evol Microbiol58:2191–2194 [CrossRef][PubMed]
    [Google Scholar]
  31. Qu J. H., Yuan H. L., Yang J. S., Li H. F., Chen N.. 2009; Lacibacter cauensis gen. nov., sp. nov., a novel member of the phylum Bacteroidetes isolated from sediment of a eutrophic lake. Int J Syst Evol Microbiol59:1153–1157 [CrossRef][PubMed]
    [Google Scholar]
  32. Reichenbach H.. 1992; The order Cytophagales. In The Prokaryotes, 2nd edn.vol. 4 pp3631–3675 Edited by Balows A., Trüper H. G., Dworkin M., Harder W., Schleifer K. H.. New York, NY: Springer;[CrossRef]
    [Google Scholar]
  33. Saitou N., Nei M.. 1987; The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol4:406–425[PubMed]
    [Google Scholar]
  34. Sasser M.. 1990; Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc;
  35. Shiratori H., Tagami Y., Morishita T., Kamihara Y., Beppu T., Ueda K.. 2009; Filimonas lacunae gen. nov., sp. nov., isolated from fresh water. Int J Syst Evol Microbiol59:1137–1142[CrossRef]
    [Google Scholar]
  36. Smibert R. M., Krieg N. R.. 1994; Phenotypic characterization. In Methods for General and Molecular Bacteriology , pp.607–654 Edited by Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R.. Washington, DC: American Society for Microbiology;
    [Google Scholar]
  37. Tamura K., Stecher G., Peterson D., Filipski A., Kumar S.. 2013; mega6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol30:2725–2729 [CrossRef][PubMed]
    [Google Scholar]
  38. Thompson J. D., Gibson T. J., Plewniak F., Jeanmougin F., Higgins D. G.. 1997; The clustal_x windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res25:4876–4882 [CrossRef][PubMed]
    [Google Scholar]
  39. Tindall B. J., Sikorski J., Smibert R. A., Krieg N. R.. 2007; Phenotypic characterization and the principles of comparative systematics. In Methods for General and Molecular Bacteriology, 3rd edn. pp330–393 Edited by Reddy C. A., Beveridge T. J., Breznak J. A., Marzluf G. A., Schmidt T. M., Snyder L. R.. Washington, D. C: ASM Press;
    [Google Scholar]
  40. Zhang K., Tang Y., Zhang L., Dai J., Wang Y., Luo X., Liu M., Luo G., Fang C.. 2009; Parasegetibacter luojiensis gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from a forest soil. Int J Syst Evol Microbiol59:3058–3062 [CrossRef][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.001354
Loading
/content/journal/ijsem/10.1099/ijsem.0.001354
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