1887

Abstract

Two Gram-stain-negative, non-motile, non-spore-forming, rod-shaped bacterial strains, designated 3B-2 and 10AO, were isolated from a sand sample collected from the west coast of the Korean peninsula by using low-nutrient media, and their taxonomic positions were investigated in a polyphasic study. The strains did not grow on marine agar. They grew optimally at 30 °C and pH 6.5–7.5. Strains 3B-2 and 10AO shared 97.5 % 16S rRNA gene sequence similarity and mean level of DNA–DNA relatedness of 12 %. In phylogenetic trees based on 16S rRNA gene sequences, strains 3B-2 and 10AO, together with several uncultured bacterial clones, formed independent lineages within the evolutionary radiation encompassed by the phylum . Strains 3B-2 and 10AO contained MK-7 as the predominant menaquinone and iso-C and Cω5 as the major fatty acids. The DNA G+C contents of strains 3B-2 and 10AO were 42.8 and 44.6 mol%, respectively. Strains 3B-2 and 10AO exhibited very low levels of 16S rRNA gene sequence similarity (<85.0 %) to the type strains of recognized bacterial species. These data were sufficient to support the proposal that the novel strains should be differentiated from previously known genera of the phylum . On the basis of the data presented, we suggest that strains 3B-2 and 10AO represent two distinct novel species of a new genus, for which the names gen. nov., sp. nov. (the type species; type strain 3B-2  = KCTC 23018  = CCUG 58939) and sp. nov. (type strain 10AO  = KCTC 23019  = CCUG 58938) are proposed.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.025874-0
2011-05-01
2020-01-24
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/61/5/1066.html?itemId=/content/journal/ijsem/10.1099/ijs.0.025874-0&mimeType=html&fmt=ahah

References

  1. Amann R. I. , Ludwig W. , Schleifer K.-H. . ( 1995; ). Phylogenetic identification and in situ detection of individual microbial cells without cultivation. . Microbiol Rev 59:, 143–169.[PubMed]
    [Google Scholar]
  2. Arun A. B. , Young C.-C. , Chen W.-M. , Hung M.-H. , Lai W.-A. , Chou J.-H. , Rekha P. D. , Shen F.-T. , Su S. P. . ( 2009; ). Belliella pelovolcani sp. nov., isolated from a mud-volcano in Taiwan. . Int J Syst Evol Microbiol 59:, 2534–2537. [CrossRef] [PubMed]
    [Google Scholar]
  3. Bae J.-W. , Rhee S.-K. , Park J. R. , Kim B.-C. , Park Y.-H. . ( 2005; ). Isolation of uncultivated anaerobic thermophiles from compost by supplementing cell extract of Geobacillus toebii in enrichment culture medium. . Extremophiles 9:, 477–485. [CrossRef] [PubMed]
    [Google Scholar]
  4. Bollmann A. , Lewis K. , Epstein S. S. . ( 2007; ). Incubation of environmental samples in a diffusion chamber increases the diversity of recovered isolates. . Appl Environ Microbiol 73:, 6386–6390. [CrossRef] [PubMed]
    [Google Scholar]
  5. Bowman J. P. , Nichols C. M. , Gibson J. A. E. . ( 2003; ). Algoriphagus ratkowskyi gen. nov., sp. nov., Brumimicrobium glaciale gen. nov., sp. nov., Cryomorpha ignava gen. nov., sp. nov. and Crocinitomix catalasitica gen. nov., sp. nov., novel flavobacteria isolated from various polar habitats. . Int J Syst Evol Microbiol 53:, 1343–1355. [CrossRef] [PubMed]
    [Google Scholar]
  6. Brettar I. , Christen R. , Höfle M. G. . ( 2004; ). Aquiflexum balticum gen. nov., sp. nov., a novel marine bacterium of the CytophagaFlavobacteriumBacteroides group isolated from surface water of the central Baltic Sea. . Int J Syst Evol Microbiol 54:, 2335–2341. [CrossRef] [PubMed]
    [Google Scholar]
  7. Bruns A. , Cypionka H. , Overmann J. . ( 2002; ). Cyclic AMP and acyl homoserine lactones increase the cultivation efficiency of heterotrophic bacteria from the central Baltic Sea. . Appl Environ Microbiol 68:, 3978–3987. [CrossRef] [PubMed]
    [Google Scholar]
  8. Connon S. A. , Giovannoni S. J. . ( 2002; ). High-throughput methods for culturing microorganisms in very-low-nutrient media yield diverse new marine isolates. . Appl Environ Microbiol 68:, 3878–3885. [CrossRef] [PubMed]
    [Google Scholar]
  9. Cowan S. T. , Steel K. J. . ( 1965; ). Manual for the Identification of Medical Bacteria. London:: Cambridge University Press;.
    [Google Scholar]
  10. Ezaki T. , Hashimoto Y. , Yabuuchi E. . ( 1989; ). 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 39:, 224–229. [CrossRef]
    [Google Scholar]
  11. Finster K. W. , Herbert R. A. , Lomstein B. A. . ( 2009; ). Spirosoma spitsbergense sp. nov. and Spirosoma luteum sp. nov., isolated from a high Arctic permafrost soil, and emended description of the genus Spirosoma . . Int J Syst Evol Microbiol 59:, 839–844. [CrossRef] [PubMed]
    [Google Scholar]
  12. Handelsman J. . ( 2004; ). Metagenomics: application of genomics to uncultured microorganisms. . Microbiol Mol Biol Rev 68:, 669–685. [CrossRef] [PubMed]
    [Google Scholar]
  13. Janssen P. H. , Yates P. S. , Grinton B. E. , Taylor P. M. , Sait M. . ( 2002; ). Improved culturability of soil bacteria and isolation in pure culture of novel members of the divisions Acidobacteria, Actinobacteria, Proteobacteria, and Verrucomicrobia . . Appl Environ Microbiol 68:, 2391–2396. [CrossRef] [PubMed]
    [Google Scholar]
  14. Joseph S. J. , Hugenholtz P. , Sangwan P. , Osborne C. A. , Janssen P. H. . ( 2003; ). Laboratory cultivation of widespread and previously uncultured soil bacteria. . Appl Environ Microbiol 69:, 7210–7215. [CrossRef] [PubMed]
    [Google Scholar]
  15. Kaeberlein T. , Lewis K. , Epstein S. S. . ( 2002; ). Isolating “uncultivable” microorganisms in pure culture in a simulated natural environment. . Science 296:, 1127–1129. [CrossRef] [PubMed]
    [Google Scholar]
  16. Keller M. , Zengler K. . ( 2004; ). Tapping into microbial diversity. . Nat Rev Microbiol 2:, 141–150. [CrossRef] [PubMed]
    [Google Scholar]
  17. Komagata K. , Suzuki K. . ( 1987; ). Lipid and cell wall analysis in bacterial systematics. . Methods Microbiol 19:, 161–207. [CrossRef]
    [Google Scholar]
  18. Lányí B. . ( 1987; ). Classical and rapid identification methods for medically important bacteria. . Methods Microbiol 19:, 1–67. [CrossRef]
    [Google Scholar]
  19. Liu Y. , Li H. , Jiang J.-T. , Liu Y.-H. , Song X.-F. , Xu C.-J. , Liu Z.-P. . ( 2009; ). Algoriphagus aquatilis sp. nov., isolated from a freshwater lake. . Int J Syst Evol Microbiol 59:, 1759–1763. [CrossRef] [PubMed]
    [Google Scholar]
  20. Ludwig, W., Euzéby, J. & Whitman, W. B. (2008). Draft taxonomic outline of the Bacteroidetes, Planctomycetes, Chlamydiae, Spirochaetes, Fibrobacteres, Fusobacteria, Acidobacteria, Verrucomicrobia, Dictyoglomi, and Gemmatimonadetes. http://www.bergeys.org/outlines/Bergeys_Vol_4_Outline.pdf
  21. 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]
  22. Morris R. M. , Rappé M. S. , Connon S. A. , Vergin K. L. , Siebold W. A. , Carlson C. A. , Giovannoni S. J. . ( 2002; ). SAR11 clade dominates ocean surface bacterioplankton communities. . Nature 420:, 806–810. [CrossRef] [PubMed]
    [Google Scholar]
  23. Nakagawa Y. , Hamana K. , Sakane T. , Yamasato K. . ( 1997; ). Reclassification of Cytophaga aprica (Lewin 1969) Reichenbach 1989 in Flammeovirga gen. nov. as Flammeovirga aprica comb. nov. and of Cytophaga difluens (ex Stanier 1940; emend. Lewin 1969) Reichenbach 1989 in Persicobacter gen. nov. as Persicobacter difluens comb. nov. . Int J Syst Bacteriol 47:, 220–223. [CrossRef]
    [Google Scholar]
  24. Nedashkovskaya O. I. , Vancanneyt M. , Van Trappen S. , Vandemeulebroecke K. , Lysenko A. M. , Rohde M. , Falsen E. , Frolova G. M. , Mikhailov V. V. , Swings J. . ( 2004; ). Description of Algoriphagus aquimarinus sp. nov., Algoriphagus chordae sp. nov. and Algoriphagus winogradskyi sp. nov., from sea water and algae, transfer of Hongiella halophila Yi and Chun 2004 to the genus Algoriphagus as Algoriphagus halophilus comb. nov. and emended descriptions of the genera Algoriphagus Bowman et al. 2003 and Hongiella Yi and Chun 2004. . Int J Syst Evol Microbiol 54:, 1757–1764. [CrossRef] [PubMed]
    [Google Scholar]
  25. Nedashkovskaya O. I. , Kim S. B. , Lysenko A. M. , Park M. S. , Mikhailov V. V. , Bae K. S. , Park H. Y. . ( 2005; ). Roseivirga echinicomitans sp. nov., a novel marine bacterium isolated from the sea urchin Strongylocentrotus intermedius, and emended description of the genus Roseivirga . . Int J Syst Evol Microbiol 55:, 1797–1800. [CrossRef] [PubMed]
    [Google Scholar]
  26. Nedashkovskaya O. I. , Kim S. B. , Vancanneyt M. , Lysenko A. M. , Shin D. S. , Park M. S. , Lee K. H. , Jung W. J. , Kalinovskaya N. I. et al. ( 2006; ). Echinicola pacifica gen. nov., sp. nov., a novel flexibacterium isolated from the sea urchin Strongylocentrotus intermedius . . Int J Syst Evol Microbiol 56:, 953–958. [CrossRef] [PubMed]
    [Google Scholar]
  27. Nedashkovskaya O. I. , Kim S. B. , Shin D. S. , Beleneva I. A. , Mikhailov V. V. . ( 2007; ). Fulvivirga kasyanovii gen. nov., sp. nov., a novel member of the phylum Bacteroidetes isolated from seawater in a mussel farm. . Int J Syst Evol Microbiol 57:, 1046–1049. [CrossRef] [PubMed]
    [Google Scholar]
  28. Rappé M. S. , Giovannoni S. J. . ( 2003; ). The uncultured microbial majority. . Annu Rev Microbiol 57:, 369–394. [CrossRef] [PubMed]
    [Google Scholar]
  29. Reichenbach H. . ( 1992; ). The order Cytophagales . . In The Prokaryotes, , 2nd edn., vol. 4, pp. 3631–3675. Edited by Balows A. , Trüper H. G. , Dworkin M. , Harder W. , Schleifer K. H. . . New York:: Springer;.[CrossRef]
    [Google Scholar]
  30. Sasser, M. (1990). Identification of bacteria by gas chromatography of cellular fatty acids. Technical Note 101. Newark, DE: MIDI, Inc.
  31. Schmidt M. , Priemé A. , Stougaard P. . ( 2006; ). Rhodonellum psychrophilum gen. nov., sp. nov., a novel psychrophilic and alkaliphilic bacterium of the phylum Bacteroidetes isolated from Greenland. . Int J Syst Evol Microbiol 56:, 2887–2892. [CrossRef] [PubMed]
    [Google Scholar]
  32. Srisukchayakul P. , Suwanachart C. , Sangnoi Y. , Kanjana-Opas A. , Hosoya S. , Yokota A. , Arunpairojana V. . ( 2007; ). Rapidithrix thailandica gen. nov., sp. nov., a marine gliding bacterium isolated from samples collected from the Andaman sea, along the southern coastline of Thailand. . Int J Syst Evol Microbiol 57:, 2275–2279. [CrossRef] [PubMed]
    [Google Scholar]
  33. Staley J. T. , Konopka A. . ( 1985; ). Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats. . Annu Rev Microbiol 39:, 321–346. [CrossRef] [PubMed]
    [Google Scholar]
  34. Stevenson B. S. , Eichorst S. A. , Wertz J. T. , Schmidt T. M. , Breznak J. A. . ( 2004; ). New strategies for cultivation and detection of previously uncultured microbes. . Appl Environ Microbiol 70:, 4748–4755. [CrossRef] [PubMed]
    [Google Scholar]
  35. Tamaoka J. , Komagata K. . ( 1984; ). Determination of DNA base composition by reverse-phase high-performance liquid chromatography. . FEMS Microbiol Lett 25:, 125–128. [CrossRef]
    [Google Scholar]
  36. Tang Y. , Dai J. , Zhang L. , Mo Z. , Wang Y. , Li Y. , Ji S. , Fang C. , Zheng C. . ( 2009; ). Dyadobacter alkalitolerans sp. nov., isolated from desert sand. . Int J Syst Evol Microbiol 59:, 60–64. [CrossRef] [PubMed]
    [Google Scholar]
  37. Torsvik V. , Øvreås L. , Thingstad T. F. . ( 2002; ). Prokaryotic diversity–magnitude, dynamics, and controlling factors. . Science 296:, 1064–1066. [CrossRef] [PubMed]
    [Google Scholar]
  38. Vancanneyt M. , Nedashkovskaya O. I. , Snauwaert C. , Mortier S. , Vandemeulebroecke K. , Hoste B. , Dawyndt P. , Frolova G. M. , Janssens D. , Swings J. . ( 2006; ). Larkinella insperata gen. nov., sp. nov., a bacterium of the phylum ‘Bacteroidetes’ isolated from water of a steam generator. . Int J Syst Evol Microbiol 56:, 237–241. [CrossRef] [PubMed]
    [Google Scholar]
  39. Vaz-Moreira I. , Nobre M. F. , Nunes O. C. , Manaia C. M. . ( 2007; ). Pseudosphingobacterium domesticum gen. nov., sp. nov., isolated from home-made compost. . Int J Syst Evol Microbiol 57:, 1535–1538. [CrossRef] [PubMed]
    [Google Scholar]
  40. Wayne L. G. , Brenner D. J. , Colwell R. R. , Grimont P. A. D. , Kandler O. , Krichevsky M. I. , Moore L. H. , Moore W. E. C. , Murray R. G. E. et al. ( 1987; ). International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. . Int J Syst Bacteriol 37:, 463–464. [CrossRef]
    [Google Scholar]
  41. Weon H.-Y. , Kim B.-Y. , Yoo S.-H. , Lee S.-Y. , Kwon S.-W. , Go S.-J. , Stackebrandt E. . ( 2006; ). Niastella koreensis gen. nov., sp. nov. and Niastella yeongjuensis sp. nov., novel members of the phylum Bacteroidetes, isolated from soil cultivated with Korean ginseng. . Int J Syst Evol Microbiol 56:, 1777–1782. [CrossRef] [PubMed]
    [Google Scholar]
  42. Ying J.-Y. , Wang B.-J. , Yang S.-S. , Liu S.-J. . ( 2006; ). Cyclobacterium lianum sp. nov., a marine bacterium isolated from sediment of an oilfield in the South China Sea, and emended description of the genus Cyclobacterium . . Int J Syst Evol Microbiol 56:, 2927–2930. [CrossRef] [PubMed]
    [Google Scholar]
  43. Yoon J.-H. , Kim H. , Kim S.-B. , Kim H.-J. , Kim W. Y. , Lee S. T. , Goodfellow M. , Park Y.-H. . ( 1996; ). Identification of Saccharomonospora strains by the use of genomic DNA fragments and rRNA gene probes. . Int J Syst Bacteriol 46:, 502–505. [CrossRef]
    [Google Scholar]
  44. Yoon J.-H. , Lee S. T. , Park Y.-H. . ( 1998; ). Inter- and intraspecific phylogenetic analysis of the genus Nocardioides and related taxa based on 16S rDNA sequences. . Int J Syst Bacteriol 48:, 187–194. [CrossRef] [PubMed]
    [Google Scholar]
  45. Yoon J.-H. , Kim I.-G. , Shin D.-Y. , Kang K. H. , Park Y.-H. . ( 2003; ). Microbulbifer salipaludis sp. nov., a moderate halophile isolated from a Korean salt marsh. . Int J Syst Evol Microbiol 53:, 53–57. [CrossRef] [PubMed]
    [Google Scholar]
  46. Zengler K. , Toledo G. , Rappé M. , Elkins J. , Mathur E. J. , Short J. M. , Keller M. . ( 2002; ). Cultivating the uncultured. . Proc Natl Acad Sci U S A 99:, 15681–15686. [CrossRef] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.025874-0
Loading
/content/journal/ijsem/10.1099/ijs.0.025874-0
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