1887

Abstract

A yellow-pigmented strain (JM-1081) isolated from healthy stem tissue of was taxonomically characterized. Cells of the strain were rod-shaped and Gram-stain-negative. Comparative 16S rRNA gene sequence analysis revealed closest relationship to the type strains of (98.1 % similarity), (97.9 %) and (97.8 %). 16S rRNA gene sequence similarities to the type strains of all other species were below 97.8 %. Fatty acid analysis of whole-cell hydrolysates of the strain resulted in a pattern typical of the genus with iso-C 2-OH and/or C 7, iso-C, iso-C 3-OH and C and as major compounds. The polyamine pattern contained predominantly -homospermidine. The major quinone was menaquinone MK-7 and the only identified lipids in the polar lipid profile were phosphatidylethanolamine and phosphatidylserine. In addition, 15 unidentified lipids were detected in moderate to major amounts. Sphingolipid was detected. The diagnostic diamino acid of the peptidoglycan was -diaminopimelic acid. DNA–DNA hybridizations with two of the closely related type strains, those of and , as well as resulted in values below 70 %. In addition to the genotypic differences, differential biochemical and chemotaxonomic properties confirmed that the isolate JM-1081represents a novel species, for which the name sp. nov. is proposed. The type strain is JM-1081 (=LMG 29191=CCM 8652).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.001100
2016-07-01
2021-07-30
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/66/7/2643.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.001100&mimeType=html&fmt=ahah

References

  1. Ahmed I., Ehsan M., Sin Y., Paek J., Khalid N., Hayat R., Chang Y. H. 2014; Sphingobacterium pakistanensis sp. nov., a novel plant growth promoting rhizobacteria isolated from rhizosphere of Vigna mungo. Antonie Van Leeuwenhoek 105:325–333 [View Article][PubMed]
    [Google Scholar]
  2. Albert R. A., Waas N. E., Pavlons S. C., Pearson J. L., Ketelboeter L., Rosselló-Móra R., Busse H. J. 2013; Sphingobacterium psychroaquaticum sp. nov., a psychrophilic bacterium isolated from Lake Michigan water. Int J Syst Evol Microbiol 63:952–958 [View Article][PubMed]
    [Google Scholar]
  3. Altenburger P., Kämpfer P., Makristathisc A., Lubitza W., Busse H. J. 1996; Classification of bacteria isolated from a medieval wall painting. J Biotechnol 47:39–52 [View Article]
    [Google Scholar]
  4. Brosius J., Palmer M. L., Kennedy P. J., Noller H. F. 1978; Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli . PNAS 75:4801–4805 [View Article][PubMed]
    [Google Scholar]
  5. Busse H.-J., Bunka S., Hensel A., Lubitz W. 1997; Discrimination of members of the family Pasteurellaceae based on polyamine patterns. Int J Syst Evol Microbiol 47:698–708 [View Article]
    [Google Scholar]
  6. Busse J., Auling G. 1988; Polyamine pattern as a chemotaxonomic marker within the Proteobacteria . Syst Appl Microbiol 11:1–8 [CrossRef]
    [Google Scholar]
  7. Du J., Singh H., Won K., Yang J. E., Jin F. X., Yi T. H. 2015; Sphingobacterium mucilaginosum sp. nov., isolated from rhizosphere soil of a rose. Int J Syst Evol Microbiol 65:2949–2954 [View Article][PubMed]
    [Google Scholar]
  8. Felsenstein J. 1985; Confidence limits on Phylogenies: an approach using the bootstrap. Evolution 39:783–791 [View Article]
    [Google Scholar]
  9. Felsenstein J. 2005 PHYLIP (Phylogeny Inference Package) Version 3.6. Distributed by the Author Seattle: University of Washington, Department of Genome Sciences;
    [Google Scholar]
  10. Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R. 1994 Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology;
    [Google Scholar]
  11. Hamana K., Matsuzaki S. 1991; Polyamine distributions in the Flavobacterium-Cytophaga-Sphingobacterium complex. Can J Microbiol 37:885–888 [View Article][PubMed]
    [Google Scholar]
  12. Jukes T. H., Cantor C. R. 1969; Evolution of the protein molecules. In Mammalian Protein Metabolism pp 21–132 Edited by Munro H. N. USA: Academic Press; [CrossRef]
    [Google Scholar]
  13. Kato M., Muto Y., Tanaka-Bandoh K., Watanabe K., Ueno K. 1995; Sphingolipid composition in Bacteroides species. Anaerobe 1:135–139 [View Article][PubMed]
    [Google Scholar]
  14. Kim K. H., Ten L. N., Liu Q. M., Im W. T., Lee S. T. 2006; Sphingobacterium daejeonense sp. nov., isolated from a compost sample. Int J Syst Evol Microbiol 56:2031–2036 [View Article][PubMed]
    [Google Scholar]
  15. Kim M., Oh H. S., Park S. C., Chun J. 2014; Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 64:346–351 [View Article][PubMed]
    [Google Scholar]
  16. 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 Microbiol 62:716–721 [View Article]
    [Google Scholar]
  17. Kämpfer P. 1990; Evaluation of the Titertek-Enterobac-Automated System (TTE-AS) for identification of members of the family Enterobacteriaceae . Zentralbl Bakteriol 273:164–172 [View Article][PubMed]
    [Google Scholar]
  18. Kämpfer P., Steiof M., Dott W. 1991; Microbiological characterization of a fuel-oil contaminated site including numerical identification of heterotrophic water and soil bacteria. Microb Ecol 21:227–251 [View Article][PubMed]
    [Google Scholar]
  19. Kämpfer P., Kroppenstedt R. M. 1996; Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. Can J Microbiol 42:989–1005 [View Article]
    [Google Scholar]
  20. Lane D. J. 1991; 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics pp 115–175 Edited by Stackebrandt E., Goodfellow. M. Wiley Chichester, United Kingdom;
    [Google Scholar]
  21. Liu J., Yang L. L., Xu C. K., Xi J. Q., Yang F. X., Zhou F., Zhou Y., Mo M. H., Li W. J. 2012; Sphingobacterium nematocida sp. nov., a nematicidal endophytic bacterium isolated from tobacco. Int J Syst Evol Microbiol 62:1809–1813 [View Article][PubMed]
    [Google Scholar]
  22. Liu R., Liu H., Zhang C. X., Yang S. Y., Liu X. H., Zhang K. Y., Lai R. 2008; Sphingobacterium siyangense sp. nov., isolated from farm soil. Int J Syst Evol Microbiol 58:1458–1462 [View Article][PubMed]
    [Google Scholar]
  23. Ludwig W., Strunk O., Westram R., Richter L., Meier H., Yadhukumar, Buchner A., Lai T., Steppi S. et al. 2004; ARB: a software environment for sequence data. Nucleic Acids Res 32:1363–1371 [View Article][PubMed]
    [Google Scholar]
  24. Mehnaz S., Weselowski B., Lazarovits G. 2007; Sphingobacterium canadense sp. nov., an isolate from corn roots. Syst Appl Microbiol 30:519–524 [View Article][PubMed]
    [Google Scholar]
  25. Montero-Calasanz M. C., Göker M., Rohde M., Spröer C., Schumann P., Busse H. J., Schmid M., Tindall B. J., Klenk H. P. et al. 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 [View Article][PubMed]
    [Google Scholar]
  26. Peng S., Hong D. D., Xin Y. B., Jun L. M., Hong W. G. 2014; Sphingobacterium yanglingense sp. nov., isolated from the nodule surface of soybean. Int J Syst Evol Microbiol 64:3862–2866 [CrossRef]
    [Google Scholar]
  27. Pitcher D. G., Saunders N. A., Owen R. J. 1989; Rapid extraction of bacterial genomic DNA with guanidium thiocyanate. Lett Appl Microbiol 8:151–156 [View Article]
    [Google Scholar]
  28. Pruesse E., Peplies J., Glöckner F. O. 2012; SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 28:1823–1829 [View Article][PubMed]
    [Google Scholar]
  29. Reichenbach H. 1989; The order Cytophagales Leadbetter 1974, 99AL. In Bergey's Manual of Systematic Bacteriology vol. 3 pp 2011–2073 Edited by Staley J. T., Bryant M. P., Pfennig N., Holt J. C. Baltimore: Williams & Wilkins;
    [Google Scholar]
  30. Schumann P. 2011; Peptidoglykan structure. In Methods in Microbiology (Taxonomy of Prokaryotes) vol. 38 pp 101–129 Edited by Rainey F. A., Oren A. London: Academic Press;
    [Google Scholar]
  31. 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]
  32. Stamatakis A. 2006; RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688–2690 [View Article][PubMed]
    [Google Scholar]
  33. Steyn P. L., Segers P., Vancanneyt M., Sandra P., Kersters K., Joubert J. J. 1998; Classification of heparinolytic bacteria into a new genus, Pedobacter, comprising four species: Pedobacter heparinus comb. nov., Pedobacter piscium comb. nov., Pedobacter africanus sp. nov. and Pedobacter saltans sp. nov. proposal of the family Sphingobacteriaceae fam. nov. Int J Syst Bacteriol 48:165–177 [View Article][PubMed]
    [Google Scholar]
  34. Stolz A., Busse H.-J., Kämpfer P. 2007; Pseudomonas knackmussii sp. nov. Int J Syst Evol Microbiol 57:572–576 [View Article][PubMed]
    [Google Scholar]
  35. Tindall B. J. 1990b; Lipid composition of Halobacterium lacusprofundi . FEMS Microbiol Lett 66:199–202 [View Article]
    [Google Scholar]
  36. Tindall B. J. 1990a; A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 13:128–130 [CrossRef]
    [Google Scholar]
  37. Yabuuchi E., Kaneko T., Yano I., Moss C. W., Miyoshi N. 1983; 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 33:580–598 [CrossRef]
    [Google Scholar]
  38. Yarza P., Richter M., Peplies J., Euzeby J., Amann R., Schleifer K. H., Ludwig W., Glöckner F. O., Rosselló-Móra R. et al. 2008; The All-Species Living Tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst Appl Microbiol 31:241–250 [View Article][PubMed]
    [Google Scholar]
  39. Yoo S. H., Weon H. Y., Jang H. B., Kim B. Y., Kwon S. W., Go S. J., Stackebrandt E. 2007; Sphingobacterium composti sp. nov., isolated from cotton-waste composts. Int J Syst Evol Microbiol 57:1590–1593 [View Article][PubMed]
    [Google Scholar]
  40. Ziemke F., Höfle M. G., Lalucat J., Rosselló-Mora R. 1998; Reclassification of Shewanella putrefaciens Owen's genomic group II as Shewanella baltica sp. nov. Int J Syst Bacteriol 48:179–186 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.001100
Loading
/content/journal/ijsem/10.1099/ijsem.0.001100
Loading

Data & Media loading...

Most cited this month Most Cited RSS feed

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