1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 68, Issue 10

Pontibacter terrae sp. nov., isolated from soil Free

Abstract

A bacterial strain, designated 17SD1-15, was isolated from soil. Cells of this strain were Gram-stain-negative and aerobic rods. The major fatty acids of strain 17SD1-15 were iso-C15 : 0 and summed feature 4 (anteiso-C17 : 1 B and/or iso-C17 : 1 I). The polar lipids were phosphatidylethanolamine, one phospholipid and five unidentified lipids. The G+C content of the genomic DNA of strain 17SD1-15 was 49.0 mol%. The 16S rRNA gene sequence analysis showed that strain 17SD1-15 was phylogenetically related to Pontibacter saemangeumensis GCM0142, Pontibacter korlensis X14-1, Pontibacter yuliensis H9X, Pontibacter diazotrophicus H4X and Pontibacter humi SWU8 (98.3, 96.4, 96.4, 96.4 and 96.0 % sequence similarity, respectively). DNA–DNA relatedness between 17SD1-15 and the most closely related type strain of Pontibacter species was 42.9±0.8 %. The low level of DNA–DNA relatedness identified strain 17SD1-15 as a member of a novel species in the genus Pontibacter . The results of genotypic and phenotypic data, including chemotaxonomic traits, showed that strain 17SD1-15 could be distinguished from its phylogenetically related species. Therefore, strain 17SD1-15 represents a novel species within the genus Pontibacter , for which the name Pontibacter terrae sp. nov. is proposed, with the type strain 17SD1-15 (=KCTC 52915=NBRC 113057).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): novel species , polyphasic study and Pontibacter
© 2018 IUMS
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.002964
2018-08-21
2023-03-26
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/68/10/3184.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.002964&mimeType=html&fmt=ahah

References

  1. Nedashkovskaya OI, Kim SB, Suzuki M, Shevchenko LS, Lee MS et al. Pontibacter actiniarum gen. nov., sp. nov., a novel member of the phylum 'Bacteroidetes', and proposal of Reichenbachiella gen. nov. as a replacement for the illegitimate prokaryotic generic name Reichenbachia Nedashkovskaya et al. 2003. Int J Syst Evol Microbiol 2005; 55:2583–2588 [View Article][PubMed]
     [Google Scholar]
  2. Wang Y, Zhang K, Cai F, Zhang L, Tang Y et al. Pontibacter xinjiangensis sp. nov., in the phylum 'Bacteroidetes', and reclassification of [Effluviibacter] roseus as Pontibacter roseus comb. nov. Int J Syst Evol Microbiol 2010; 60:99–103 [View Article][PubMed]
     [Google Scholar]
  3. Osman G, Gao Y, Wang N, Mahmud O, Sun J et al. Pontibacter brevis sp. nov., isolated from rhizosphere soil of Tamarix ramosissima. Int J Syst Evol Microbiol 2018; 68:81–86 [View Article][PubMed]
     [Google Scholar]
  4. Zhang L, Zhang Q, Luo X, Tang Y, Dai J et al. Pontibacter korlensis sp. nov., isolated from the desert of Xinjiang, China. Int J Syst Evol Microbiol 2008; 58:1210–1214 [View Article][PubMed]
     [Google Scholar]
  5. Kang JY, Joung Y, Chun J, Kim H, Joh K et al. Pontibacter saemangeumensis sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2013; 63:565–569 [View Article][PubMed]
     [Google Scholar]
  6. Cao H, Nie Y, Zeng XC, Xu L, He Z et al. Pontibacter yuliensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 2014; 64:968–972 [View Article][PubMed]
     [Google Scholar]
  7. Singh P, Kumari R, Nayyar N, Lal R. Pontibacter aurantiacus sp. nov. isolated from hexachlorocyclohexane (HCH) contaminated soil. Int J Syst Evol Microbiol 2017; 67:1400–1407 [View Article][PubMed]
     [Google Scholar]
  8. Xu L, Zeng XC, Nie Y, Luo X, Zhou E et al. Pontibacter diazotrophicus sp. nov., a novel nitrogen-fixing bacterium of the family Cytophagaceae. PLoS One 2014; 9:e92294 [View Article][PubMed]
     [Google Scholar]
  9. Kim MK, Kang M-S, Srinivasan S, Lee DH, Lee S-Y et al. Complete genome sequence of Hymenobacter sedentarius DG5BT, a bacterium resistant to gamma radiation. Mol Cell Toxicol 2017; 13:199–205 [View Article]
     [Google Scholar]
  10. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991; 173:697–703 [View Article][PubMed]
     [Google Scholar]
  11. Yoon SH, Ha SM, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617 [View Article][PubMed]
     [Google Scholar]
  12. Pruesse E, Peplies J, Glöckner FO. SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 2012; 28:1823–1829 [View Article][PubMed]
     [Google Scholar]
  13. Kimura M. The Neutral Theory of Molecular Evolution Cambridge: Cambridge University Press; 1983
     [Google Scholar]
  14. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article][PubMed]
     [Google Scholar]
  15. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416 [View Article]
     [Google Scholar]
  16. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
     [Google Scholar]
  17. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article][PubMed]
     [Google Scholar]
  18. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
     [Google Scholar]
  19. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
     [Google Scholar]
  20. Collins MD, Jones D. Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiol Rev 1981; 45:316–354[PubMed]
     [Google Scholar]
  21. Shin YK, Lee JS, Chun CO, Kim HJ, Park YH. Isoprenoid quinone profiles of the Leclercia adecarboxylata KCTC 1036T. J Microbiol Biotechnol 1996; 6:68–69
     [Google Scholar]
  22. Gonzalez JM, Saiz-Jimenez C. A fluorimetric method for the estimation of G+C mol% content in microorganisms by thermal denaturation temperature. Environ Microbiol 2002; 4:770–773[PubMed]
     [Google Scholar]
  23. Mahato NK, Tripathi C, Nayyar N, Singh AK, Lal R. Pontibacter ummariensis sp. nov., isolated from a hexachlorocyclohexane-contaminated soil. Int J Syst Evol Microbiol 2016; 66:1080–1087 [View Article][PubMed]
     [Google Scholar]
  24. Ezaki T, Hashimoto Y, Yabuuchi E. 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 1989; 39:224–229 [View Article]
     [Google Scholar]
  25. Stackebrandt E, Frederiksen W, Garrity GM, Grimont PA, Kämpfer P et al. Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 2002; 52:1043–1047 [View Article][PubMed]
     [Google Scholar]
  26. Srinivasan S, Lee JJ, Lee SS, Kim MK. Pontibacter humi sp. nov., isolated from mountain soil. Curr Microbiol 2014; 69:263–269 [View Article][PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.002964
Loading
Pontibacter terrae sp. nov., isolated from soil
Int J Syst Evol Microbiol 68, 3184 (2018); https://doi.org/10.1099/ijsem.0.002964
/content/journal/ijsem/10.1099/ijsem.0.002964
/content/journal/ijsem/10.1099/ijsem.0.002964
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