1887

Abstract

sp. KL28 is an aerobic, rod-shaped bacterium that was isolated from the soil of Changwon, South Korea, based on its ability to grow in the presence of linear alkylphenols (C1–C5). Despite several studies on strain KL28, it could not be assigned to any known species in the genus . The name ‘ was proposed for KL28, but the strain had not until now been characterized taxonomically and the name currently has no standing in the bacterial nomenclature. A 16S rRNA gene sequence based phylogenetic analysis suggested an affiliation of strain KL28 with the group, with DSM 16006 as the most closely related type strain (99.1 % similarity). A multilocus phylogenetic sequence analysis performed by concatenating 16S rRNA, , and partial gene sequences showed that isolate KL28 could be differentiated from DSM 16006 (sequence similarity 93.7 %). Genomic comparisons of strain KL28 with the type strains of the species in the group using average nucleotide index based on (ANIb) and genome-to genome distances (GGDC) revealed 87.06 % and 32.20 % similarities with DSM 16006, respectively, as the closest type strain. Both values are far from the thresholds established for species differentiation. These results, together with differences in phenotypic features and chemotaxonomic analyses [fatty acids and whole-cell matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS], support the proposal of strain KL28 ( = JCM 16553 = KCTC 22206) as the type strain of a novel species, for which the formerly proposed name, ‘’, is correctly latinized as sp. nov.

Funding
This study was supported by the:
  • Spanish MINECO (Award CGL2011-24318)
  • National Research Foundation of Korea (Award CSD2009-00006)
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.000529
2015-11-01
2024-04-16
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/65/11/4013.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.000529&mimeType=html&fmt=ahah

References

  1. Cho J. H., Jung D. K., Lee K., Rhee S. ( 2009;). Crystal structure and functional analysis of the extradiol dioxygenase LapB from a long-chain alkylphenol degradation pathway in Pseudomonas . J Biol Chem 284 3432134330 [View Article] [PubMed].
    [Google Scholar]
  2. Cowan S. T., Steel K. J. ( 1974;). Characters of Gram-negative bacteria. . In Manual for the Identification of Medical Bacteria, pp. 77122. Edited by Cowan S. T. , 2nd edn.., London: Cambridge University Press;.
    [Google Scholar]
  3. Felsenstein J. ( 1981;). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17 368376 [View Article] [PubMed].
    [Google Scholar]
  4. Gomila M., Peña A., Mulet M., Lalucat J., García-Valdés E. ( 2015;). Phylogenomics and systematics in Pseudomonas . Front Microbiol 6 214 [View Article] [PubMed].
    [Google Scholar]
  5. Goris J., Konstantinidis K. T., Klappenbach J. A., Coenye T., Vandamme P., Tiedje J. M. ( 2007;). DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 57 8191 [View Article] [PubMed].
    [Google Scholar]
  6. Jeong J. J., Kim J. H., Kim C. K., Hwang I., Lee K. ( 2003;). 3- and 4-alkylphenol degradation pathway in Pseudomonas sp. strain KL28: genetic organization of the lap gene cluster and substrate specificities of phenol hydroxylase and catechol 2,3-dioxygenase. Microbiology 149 32653277 [View Article] [PubMed].
    [Google Scholar]
  7. Jukes T., Cantor C. ( 1969;). Evolution of protein molecules. . In Mammalian Protein Metabolism, pp. 21132. Edited by Munro H. N. vol. 3 New York: Academic Press; [View Article].
    [Google Scholar]
  8. King E. O., Ward M. K., Raney D. E. ( 1954;). Two simple media for the demonstration of pyocyanin and fluorescin. J Lab Clin Med 44 301307 [PubMed].
    [Google Scholar]
  9. Lalucat J. ( 1988;). Analysis of refractile (R) bodies. Methods Microbiol 20 7990. [CrossRef]
    [Google Scholar]
  10. Lee K., Veeranagouda Y. ( 2009;). Ultramicrocells form by reductive division in macroscopic Pseudomonas aerial structures. Environ Microbiol 11 11171125 [View Article] [PubMed].
    [Google Scholar]
  11. Lee K., Lim E. J., Kim K. S., Huang S. L., Veeranagouda Y., Rehm B. H. ( 2014;). An alginate-like exopolysaccharide biosynthesis gene cluster involved in biofilm aerial structure formation by Pseudomonas alkylphenolia . Appl Microbiol Biotechnol 98 41374148 [View Article] [PubMed].
    [Google Scholar]
  12. Lim J. Y., Lee K., Hwang I. ( 2014;). Complete genome sequence of the mushroom-like aerial structure-forming Pseudomonas alkylphenolia, a platform bacterium for mass production of poly-β-d-mannuronates. J Biotechnol 192 2021 [View Article] [PubMed].
    [Google Scholar]
  13. Markowitz V. M., Chen I. M., Palaniappan K., Chu K., Szeto E., Pillay M., Ratner A., Huang J., Woyke T., other authors. ( 2014;). IMG 4 version of the integrated microbial genomes comparative analysis system. Nucleic Acids Res 42 (D1), D560D567 [View Article] [PubMed].
    [Google Scholar]
  14. Meier-Kolthoff J. P., Auch A. F., Klenk H. P., Göker M. ( 2013;). Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 14 60 [View Article] [PubMed].
    [Google Scholar]
  15. Mulet M., Lalucat J., García-Valdés E. ( 2010;). DNA sequence-based analysis of the Pseudomonas species. Environ Microbiol 12 15131530 [PubMed].
    [Google Scholar]
  16. Mulet M., Gomila M., Lemaitre B., Lalucat J., García-Valdés E. ( 2012a;). Taxonomic characterisation of Pseudomonas strain L48 and formal proposal of Pseudomonas entomophila sp. nov. Syst Appl Microbiol 35 145149 [View Article] [PubMed].
    [Google Scholar]
  17. Mulet M., Gomila M., Scotta C., Sánchez D., Lalucat J., García-Valdés E. ( 2012b;). Concordance between whole-cell matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry and multilocus sequence analysis approaches in species discrimination within the genus Pseudomonas . Syst Appl Microbiol 35 455464 [View Article] [PubMed].
    [Google Scholar]
  18. Nei M., Kumar S. ( 2000). Molecular Evolution and Phylogenetics New York: Oxford University Press;.
    [Google Scholar]
  19. Otterlei M., Ostgaard K., Skjåk-Braek G., Smidsrød O., Soon-Shiong P., Espevik T. ( 1991;). Induction of cytokine production from human monocytes stimulated with alginate. J Immunother (1991) 10 286291 [View Article] [PubMed].
    [Google Scholar]
  20. Parte A. C. ( 2014;). LPSN—list of prokaryotic names with standing in nomenclature. Nucleic Acids Res 42 (D1), D613D616 [View Article] [PubMed].
    [Google Scholar]
  21. Richter M., Rosselló-Móra R. ( 2009;). Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 106 1912619131 [View Article] [PubMed].
    [Google Scholar]
  22. Sasser M. ( 1990). Identification of bacteria by gas chromatography of cellular fatty acids MIDI Technical Note 101 Newark, DE: MIDI Inc;.
    [Google Scholar]
  23. Veeranagouda Y., Basavaraja C., Bae H. S., Liu K. H., Lee K. ( 2011;). Augmented production of poly-β-d-mannuronate and its acetylated forms by Pseudomonas . Process Biochem 46 328334 [View Article].
    [Google Scholar]
  24. Zhao H., Liu H., Chen Y., Xin X., Li J., Hou Y., Zhang Z., Zhang X., Xie C., other authors. ( 2006;). Oligomannurarate sulfate, a novel heparanase inhibitor simultaneously targeting basic fibroblast growth factor, combats tumor angiogenesis and metastasis. Cancer Res 66 87798787 [View Article] [PubMed].
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.000529
Loading
/content/journal/ijsem/10.1099/ijsem.0.000529
Loading

Data & Media loading...

Supplements

Supplementary Data

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