1887

Abstract

A light-yellow-coloured bacterium, designated strain PTJT-5, was isolated from the stem of A. Gray collected from Taibai Mountain in Shaanxi Province, north-west China, and was subjected to a taxonomic study by using a polyphasic approach. The novel isolate grew optimally at 25–28 °C and pH 6.0–7.0. Flexirubin-type pigments were produced. Cells were Gram-reaction-negative, strictly aerobic, rod-shaped and non-motile. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain PTJT-5 was a member of the phylum , exhibiting the highest sequence similarity to NJ-8 (87.7 %). The major cellular fatty acids were iso-C, iso-C G, iso-C and iso-C 3-OH. The only polyamine was homospermidine and the major polar lipid was phosphatidylethanolamine. The only respiratory quinone was MK-7 and the DNA GC content was 40.3 mol%. Based on the phenotypic, phylogenetic and genotypic data, strain PTJT-5 is considered to represent 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 PTJT-5 ( = CCTCC AB 2013017 = KCTC 32316). An emended description of is also proposed.

Funding
This study was supported by the:
  • National Natural Science Foundation of China (Award 31100001)
  • Natural Science Foundation of Shaanxi Province, China (Award 2012JQ3006)
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.051607-0
2013-10-01
2024-10-03
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/63/10/3769.html?itemId=/content/journal/ijsem/10.1099/ijs.0.051607-0&mimeType=html&fmt=ahah

References

  1. Albuquerque L., Rainey F. A., Nobre M. F., da Costa M. S. ( 2012 ). Hydrotalea sandarakina sp. nov., isolated from a hot spring runoff, and emended descriptions of the genus Hydrotalea and the species Hydrotalea flava . . Int J Syst Evol Microbiol 62, 16031608. [View Article] [PubMed]
    [Google Scholar]
  2. An D. S., Lee H. G., Im W. T., Liu Q. M., Lee S. T. ( 2007 ). Segetibacter koreensis gen. nov., sp. nov., a novel member of the phylum Bacteroidetes, isolated from the soil of a ginseng field in South Korea. . Int J Syst Evol Microbiol 57, 18281833. [View Article] [PubMed]
    [Google Scholar]
  3. Bernardet J.-F., Nakagawa Y., Holmes B. Subcommittee on the taxonomy of Flavobacterium and Cytophaga-like bacteria of the International Committee on Systematics of Prokaryotes ( 2002 ). Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. . Int J Syst Evol Microbiol 52, 10491070. [View Article] [PubMed]
    [Google Scholar]
  4. Bowman J. P. ( 2000 ). Description of Cellulophaga algicola sp. nov., isolated from the surfaces of Antarctic algae, and reclassification of Cytophaga uliginosa (ZoBell and Upham 1944) Reichenbach 1989 as Cellulophaga uliginosa comb. nov.. Int J Syst Evol Microbiol 50, 18611868.[PubMed]
    [Google Scholar]
  5. Busse H.-J., Auling G. ( 1988 ). Polyamine pattern as a chemotaxonomic marker within the Proteobacteria . . Syst Appl Microbiol 11, 18. [View Article]
    [Google Scholar]
  6. Cleenwerck I., Vandemeulebroecke K., Janssens D., Swings J. ( 2002 ). Re-examination of the genus Acetobacter, with descriptions of Acetobacter cerevisiae sp. nov. and Acetobacter malorum sp. nov.. Int J Syst Evol Microbiol 52, 15511558. [View Article] [PubMed]
    [Google Scholar]
  7. Doetsch R. N. ( 1981 ). Determinative methods of light microscopy. . In Manual of Methods for General Bacteriology, pp. 2133. Edited by Gerhardt P., Murray R. G. E., Costilow R. N., Nester E. W., Wood W. A., Krieg N. R., Phillips G. B. . Washington, DC:: American Society for Microbiology;.
    [Google Scholar]
  8. Felsenstein J. ( 1985 ). Confidence limits on phylogenies: an approach using the bootstrap. . Evolution 39, 783791. [View Article]
    [Google Scholar]
  9. Felsenstein J. ( 2006 ). phylip (phylogeny inference package), version 3.66. . Distributed by the author. Department of Genome Sciences, University of Washington;, Seattle, USA:.
    [Google Scholar]
  10. Fitch W. M. ( 1971 ). Towards defining the course of evolution: minimum change for a specific tree topology. . Syst Zool 20, 406416. [View Article]
    [Google Scholar]
  11. Kämpfer P., Young C. C., Sridhar K. R., Arun A. B., Lai W. A., Shen F. T., Rekha P. D. ( 2006 ). Transfer of [Flexibacter] sancti, [Flexibacter] filiformis, [Flexibacter] japonensis and [Cytophaga] arvensicola to the genus Chitinophaga and description of Chitinophaga skermanii sp. nov.. Int J Syst Evol Microbiol 56, 22232228. [View Article] [PubMed]
    [Google Scholar]
  12. 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, Ferruginibacter, Filimonas and Hydrotalea to the family Chitinophagaceae fam. nov.. Int J Syst Evol Microbiol 61, 518523. [View Article] [PubMed]
    [Google Scholar]
  13. Kim B. Y., Weon H. Y., Yoo S. H., Hong S. B., Kwon S. W., Stackebrandt E., Go S. J. ( 2007 ). Niabella aurantiaca gen. nov., sp. nov., isolated from a greenhouse soil in Korea. . Int J Syst Evol Microbiol 57, 538541. [View Article] [PubMed]
    [Google Scholar]
  14. Kim B.-C., Poo H., Lee K. H., Kim M. N., Kwon O.-Y., Shin K.-S. ( 2012a ). Mucilaginibacter angelicae sp. nov., isolated from the rhizosphere of Angelica polymorpha Maxim. . Int J Syst Evol Microbiol 62, 5560. [View Article] [PubMed]
    [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. & other authors ( 2012b ). Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. . Int J Syst Evol Microbiol 62, 716721. [View Article] [PubMed]
    [Google Scholar]
  16. Kim Y. J., Nguyen N. L., Weon H. Y., Yang D. C. ( 2013 ). 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 Microbiol 63, 905912. [View Article] [PubMed]
    [Google Scholar]
  17. Kimura M. ( 1980 ). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. . J Mol Evol 16, 111120. [View Article] [PubMed]
    [Google Scholar]
  18. Lane D. J. ( 1991 ). 16S–23S rRNA sequencing. . In Nucleic Acid Techniques in Bacterial Systematics, pp. 125175. Edited by Stackebrandt E., Goodfellow M. . Chichester:: Wiley;.
    [Google Scholar]
  19. Lim J. H., Baek S.-H., Lee S.-T. ( 2009 ). Ferruginibacter alkalilentus gen. nov., sp. nov. and Ferruginibacter lapsinanis sp. nov., novel members of the family ‘Chitinophagaceae’ in the phylum Bacteroidetes, isolated from freshwater sediment. . Int J Syst Evol Microbiol 59, 23942399. [View Article] [PubMed]
    [Google Scholar]
  20. Lin Y.-C., Uemori K., de Briel D. A., Arunpairojana V., Yokota A. ( 2004 ). Zimmermannella helvola gen. nov., sp. nov., Zimmermannella alba sp. nov., Zimmermannella bifida sp. nov., Zimmermannella faecalis sp. nov. and Leucobacter albus sp. nov., novel members of the family Microbacteriaceae . . Int J Syst Evol Microbiol 54, 16691676. [View Article] [PubMed]
    [Google Scholar]
  21. 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
    [Google Scholar]
  22. McCammon S. A., Bowman J. P. ( 2000 ). Taxonomy of Antarctic Flavobacterium species: description of Flavobacterium gillisiae sp. nov., Flavobacterium tegetincola sp. nov., and Flavobacterium xanthum sp. nov., nom. rev. and reclassification of [Flavobacterium] salegens as Salegentibacter salegens gen. nov., comb. nov.. Int J Syst Evol Microbiol 50, 10551063. [View Article] [PubMed]
    [Google Scholar]
  23. 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 Bacteriol 39, 159167. [View Article]
    [Google Scholar]
  24. 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 Microbiol 58, 21912194. [View Article] [PubMed]
    [Google Scholar]
  25. 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 Microbiol 59, 11531157. [View Article] [PubMed]
    [Google Scholar]
  26. Saitou N., Nei M. ( 1987 ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. . Mol Biol Evol 4, 406425.[PubMed]
    [Google Scholar]
  27. Sasser M. ( 1990 ). Identification of bacteria by gas chromatography of cellular fatty acids. , MIDI Technical Note 101. Newark, DE:: MIDI Inc.; http://www.microbialid.com/PDF/TechNote_101.pdf
    [Google Scholar]
  28. Schenkel E., Berlaimont V., Dubois J., Helson-Cambier M., Hanocq M. ( 1995 ). Improved high-performance liquid chromatographic method for the determination of polyamines as their benzoylated derivatives: application to P388 cancer cells. . J Chromatogr B Biomed Appl 668, 189197. [View Article] [PubMed]
    [Google Scholar]
  29. Shiratori H., Tagami Y., Morishita T., Kamihara Y., Beppu T., Ueda K. ( 2009 ). Filimonas lacunae gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from fresh water. . Int J Syst Evol Microbiol 59, 11371142. [View Article] [PubMed]
    [Google Scholar]
  30. Smibert R. M., Krieg N. R. ( 1994 ). Phenotypic characterization. . In Methods for General and Molecular Bacteriology, pp. 607654. Edited by Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R. . Washington, DC:: American Society for Microbiology;.
    [Google Scholar]
  31. Strobel G. A., Daisy B. ( 2003 ). Bioprospecting for microbial endophytes and their natural products. . Microbiol Mol Biol Rev 67, 491502. [View Article] [PubMed]
    [Google Scholar]
  32. Tamura K., Dudley J., Nei M., Kumar S. ( 2007 ). mega4: molecular evolutionary genetics analysis (mega) software version 4.0. . Mol Biol Evol 24, 15961599. [View Article] [PubMed]
    [Google Scholar]
  33. 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, 48764882. [View Article] [PubMed]
    [Google Scholar]
  34. Tindall B. J. ( 1990 ). A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. . Syst Appl Microbiol 13, 128130. [View Article]
    [Google Scholar]
  35. Wang Y., Cai F., Tang Y., Dai J., Qi H., Rahman E., Peng F., Fang C. ( 2011 ). Flavitalea populi gen. nov., sp. nov., isolated from soil of a Euphrates poplar (Populus euphratica) forest. . Int J Syst Evol Microbiol 61, 15541560. [View Article] [PubMed]
    [Google Scholar]
  36. 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, 17771782. [View Article] [PubMed]
    [Google Scholar]
  37. Weon H. Y., Yoo S. H., Kim Y. J., Son J. A., Kim B. Y., Kwon S. W., Koo B. S. ( 2009 ). Chitinophaga niabensis sp. nov. and Chitinophaga niastensis sp. nov., isolated from soil. . Int J Syst Evol Microbiol 59, 12671271. [View Article] [PubMed]
    [Google Scholar]
  38. Wilson K. ( 1987 ). Preparation of genomic DNA from bacteria. . In Current Protocols in Molecular Biology, pp. 241245. Edited by Ausubel F. M., Brent R., Kingston R. E., Moore D. D., Seidman J. G., Smith J. A., Struhl K. . New York:: Greene Publishing and Wiley Interscience;.
    [Google Scholar]
  39. Xie C. H., Yokota A. ( 2003 ). Phylogenetic analyses of Lampropedia hyalina based on the 16S rRNA gene sequence. . J Gen Appl Microbiol 49, 345349. [View Article] [PubMed]
    [Google Scholar]
  40. Xie C. H., Yokota A. ( 2006 ). Reclassification of [Flavobacterium] ferrugineum as Terrimonas ferruginea gen. nov., comb. nov., and description of Terrimonas lutea sp. nov., isolated from soil. . Int J Syst Evol Microbiol 56, 11171121. [View Article] [PubMed]
    [Google Scholar]
  41. Xu P., Li W.-J., Tang S.-K., Zhang Y.-Q., Chen G.-Z., Chen H.-H., Xu L.-H., Jiang C.-L. ( 2005 ). Naxibacter alkalitolerans gen. nov., sp. nov., a novel member of the family ‘Oxalobacteraceae’ isolated from China. . Int J Syst Evol Microbiol 55, 11491153. [View Article] [PubMed]
    [Google Scholar]
  42. Yoon M. H., Im W. T. ( 2007 ). Flavisolibacter ginsengiterrae gen. nov., sp. nov. and Flavisolibacter ginsengisoli sp. nov., isolated from ginseng cultivating soil. . Int J Syst Evol Microbiol 57, 18341839. [View Article] [PubMed]
    [Google Scholar]
  43. Zhang K. D., Tang Y. L., Zhang L., Dai J., Wang Y., Luo X. S., Liu M., Luo G. C., Fang C. X. ( 2009 ). Parasegetibacter luojiensis gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from a forest soil. . Int J Syst Evol Microbiol 59, 30583062. [View Article] [PubMed]
    [Google Scholar]
  44. Zhang N. N., Qu J.-H., Yuan H.-L., Sun Y. M., Yang J.-S. ( 2010 ). Flavihumibacter petaseus gen. nov., sp. nov., isolated from soil of a subtropical rainforest. . Int J Syst Evol Microbiol 60, 16091612. [View Article] [PubMed]
    [Google Scholar]
/content/journal/ijsem/10.1099/ijs.0.051607-0
Loading
/content/journal/ijsem/10.1099/ijs.0.051607-0
Loading

Data & Media loading...

Supplements

Supplementary material 1

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