1887

Abstract

A Gram-stain-positive, strictly aerobic, rod-shaped, non-motile bacterium, designated strain XH274, was isolated from a deep sub-seafloor sediment sample collected from the South Pacific Gyre (41° 58′ S 163° 11′ W) during the Integrated Ocean Drilling Program (IODP) Expedition 329. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain XH274 belonged to the genus and shared the highest 16S rRNA gene sequence similarity with KSL-2 (96.81 %), MDN22 (96.74 %) and RHLT2-1 (96.61 %). The DNA G+C content of strain XH274 was 74.6 mol%. The cell wall of strain XH274 contained -2,6-diaminopimelic acid as the diagnostic diamino acid, and ribose, glucose, galactose and mannose as the major whole-cell sugars. The major fatty acids were iso-C, Cω9 and Cω8. The major respiratory quinone was menaquinone-8(H). The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and two unknown phospholipids. On the basis of data from the polyphasic analysis, strain XH274 is considered to represent a novel species in the genus , for which the name Nocardioides sp. nov. is proposed. The type strain is XH274 ( = DSM 27278 = JCM 19260).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.059873-0
2014-07-01
2020-01-17
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/64/7/2217.html?itemId=/content/journal/ijsem/10.1099/ijs.0.059873-0&mimeType=html&fmt=ahah

References

  1. Ausubel F. M., Brent R., Kingston R. E., Moore D. D., Seidman J. G., Smith J. A., Struhl K.. (editors) ( 1995;). Short Protocols in Molecular Biology: a Compendium of Methods from Current Protocols in Molecular Biology, , 3rd edn.. New York:: Wiley;.
    [Google Scholar]
  2. Becker B., Lechevalier M. P., Lechevalier H. A.. ( 1965;). Chemical composition of cell-wall preparations from strains of various form-genera of aerobic actinomycetes. . Appl Microbiol 13:, 236–243.[PubMed]
    [Google Scholar]
  3. Beveridge T. J., Lawrence J. R., Murray R. G. E.. ( 2007;). Sampling and staining for light microscopy. . In Methods for General and Molecular Bacteriology, , 3rd edn., pp. 19–33. Edited by Reddy C. A., Beveridge T. J., Breznak J. A., Marzluf G. A., Schmidt T. M., Snyder L. R... Washington, DC:: American Society for Microbiology;.
    [Google Scholar]
  4. Collins M. D., Shah H. N.. ( 1984;). Fatty acid, menaquinone and polar lipid composition of Rothia dentosacariosa. . Arch Microbiol 137:, 247–249. [CrossRef]
    [Google Scholar]
  5. Dastager S. G., Lee J. C., Ju Y. J., Park D. J., Kim C. J.. ( 2009;). Nocardioides sediminis sp. nov., isolated from a sediment sample. . Int J Syst Evol Microbiol 59:, 280–284. [CrossRef][PubMed]
    [Google Scholar]
  6. Kim O. S., Cho Y. J., Lee K., Yoon S. H., Kim M., Na H., Park S. C., Jeon Y. S., Lee J. H.. & other authors ( 2012;). Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. . Int J Syst Evol Microbiol 62:, 716–721. [CrossRef][PubMed]
    [Google Scholar]
  7. Kimura M.. ( 1980;). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. . J Mol Evol 16:, 111–120. [CrossRef][PubMed]
    [Google Scholar]
  8. Komagata K., Suzuki K.. ( 1987;). Lipid and cell-wall analysis in bacterial systematics. . Methods Microbiol 19:, 161–207. [CrossRef]
    [Google Scholar]
  9. Mackie T., McCartney J. E.. ( 1989;). Microscopy. . In Mackie and McCartney’s Practical Medical Microbiology, , 13th edn., pp. 11–37. Edited by Collee J. G., Duguid J. P., Fraser A. G., Marmion B. P... Edinburgh:: Churchill Livingstone;.
    [Google Scholar]
  10. Mesbah M., Whitman W. B.. ( 1989;). Measurement of deoxyguanosine/thymidine ratios in complex mixtures by high-performance liquid chromatography for determination of the mole percentage guanine + cytosine of DNA. . J Chromatogr A 479:, 297–306. [CrossRef][PubMed]
    [Google Scholar]
  11. 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 Methods 2:, 233–241. [CrossRef]
    [Google Scholar]
  12. Montero-Calasanz M. del C., Göker M., Rohde M., Spröer C., Schumann P., Busse H.-J., Schmid M., Tindall B. J., Klenk H.-P., Camacho M.. ( 2013;). Chryseobacterium hispalense sp. nov., a plant-growth-promoting bacterium isolated from a rainwater pond in an olive plant nursery, and emended descriptions of Chryseobacterium defluvii, Chryseobacterium indologenes, Chryseobacterium wanjuense and Chryseobacterium gregarium. . Int J Syst Evol Microbiol 63:, 4386–4395. [CrossRef][PubMed]
    [Google Scholar]
  13. Moore E. R. B., Arnscheidt A., Krüger A., Strömpl C., Mau M.. ( 1999;). Simplified protocols for the preparation of genomic DNA from bacterial cultures. . In Molecular Microbial Ecology Manual 1.6.1, pp. 1–15. Edited by Akkermans A. D. L., van Elsas J. D., de Bruijn F. J... Dordrecht:: Kluwer;.
    [Google Scholar]
  14. Prauser H.. ( 1976;). Nocardioides, a new genus of the order Actinomycetales. . Int J Syst Bacteriol 26:, 58–65. [CrossRef]
    [Google Scholar]
  15. Sasser, M. (1990). Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. Newark, DE: MIDI Inc.
  16. Schleifer K. H., Kandler O.. ( 1972;). Peptidoglycan types of bacterial cell walls and their taxonomic implications. . Bacteriol Rev 36:, 407–477.[PubMed]
    [Google Scholar]
  17. Stackebrandt E., Goebel B. M.. ( 1994;). Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. . 44:, 846–849.
    [Google Scholar]
  18. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S.. ( 2011;). mega5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. . Mol Biol Evol 28:, 2731–2739. [CrossRef][PubMed]
    [Google Scholar]
  19. 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 Res 25:, 4876–4882. [CrossRef][PubMed]
    [Google Scholar]
  20. Tindall B. J., Sikorski J., Smibert R. M., Krieg N. R.. ( 2007;). Phenotypic characterization and the principles of comparative systematics. . In Methods for General and Molecular Microbiology, pp. 330–393. Edited by Reddy C. A., Beveridge T. J., Breznak J. A., Marzluf G. A., Schmidt T. M., Snyder L. R... Washington, DC:: American Society for Microbiology;.
    [Google Scholar]
  21. Yi H., Chun J.. ( 2004a;). Nocardioides aestuarii sp. nov., isolated from tidal flat sediment. . Int J Syst Evol Microbiol 54:, 2151–2154. [CrossRef][PubMed]
    [Google Scholar]
  22. Yi H., Chun J.. ( 2004b;). Nocardioides ganghwensis sp. nov., isolated from tidal flat sediment. . Int J Syst Evol Microbiol 54:, 1295–1299. [CrossRef][PubMed]
    [Google Scholar]
  23. Yoon J. H., Kim I. G., Lee M. H., Oh T. K.. ( 2005;). Nocardioides kribbensis sp. nov., isolated from an alkaline soil. . Int J Syst Evol Microbiol 55:, 1611–1614. [CrossRef][PubMed]
    [Google Scholar]
  24. Yoon J. H., Park S., Kang S. J., Lee J. S., Lee K. C., Oh T. K.. ( 2010;). Nocardioides daedukensis sp. nov., a halotolerant bacterium isolated from soil. . Int J Syst Evol Microbiol 60:, 1334–1338. [CrossRef][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.059873-0
Loading
/content/journal/ijsem/10.1099/ijs.0.059873-0
Loading

Data & Media loading...

Most cited articles

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