sp. nov., isolated from tidal flat sediment Free

Abstract

A Gram-stain-negative, obligately aerobic, cream-coloured, non-gliding, motile with a single polar flagellum and rod-shaped bacterium, designated IMCC34151, was isolated from tidal flat sediment of the Yellow Sea, Republic of Korea. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain IMCC34151 belonged to the genus of the family and shared 94.7–96.8 % sequence similarities to species. Whole-genome sequencing of strain IMCC34151 revealed a genome size of 3.2 Mbp and a DNA G+C content of 62.6 mol%. The strain contained summed feature 8 (C 7 and/or C 6), Ccyclo 8 and C as the major fatty acids and ubiquinone-10 (Q-10) as the major respiratory quinone. The polar lipids detected in the strain were phosphatidylglycerol, diphosphatidylglycerol, two unidentified glycolipids and 12 unidentified lipids. On the basis of its phylogenetic and phenotypic characteristics, strain IMCC34151 is considered to represent a novel species of the genus , for which the name sp. nov. (type strain IMCC34151 =KACC 19595=NBRC 113420) is proposed.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003499
2019-09-01
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/69/9/2651.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.003499&mimeType=html&fmt=ahah

References

  1. Xu XW, Huo YY, Wang CS, Oren A, Cui HL et al. Pelagibacterium halotolerans gen. nov., sp. nov. and Pelagibacterium luteolum sp. nov., novel members of the family Hyphomicrobiaceae . Int J Syst Evol Microbiol 2011; 61:1817–1822 [View Article][PubMed]
    [Google Scholar]
  2. Li Q, Xu Y, Liu K, Cai L, Fu Y et al. Pelagibacterium nitratireducens sp. nov., a marine Alphaproteobacterium isolated from the East China Sea. Curr Microbiol 2013; 66:450–455 [View Article][PubMed]
    [Google Scholar]
  3. Yang N, Sun C. Pelagibacterium lixinzhangensis sp. nov., a novel member of the genus Pelagibacterium . Curr Microbiol 2016; 72:551–556 [View Article][PubMed]
    [Google Scholar]
  4. Wang G, Yu K, Wang Y, Su H, Wu H et al. Pelagibacterium lentulum sp. nov., a marine bacterium from the culture broth of Picochlorum sp. 122. Int J Syst Evol Microbiol 2017; 67:3182–3185 [View Article][PubMed]
    [Google Scholar]
  5. Lu H, Xing P, Phurbu D, Tang Q, Wu Q. Pelagibacterium montanilacus sp. nov., an alkaliphilic bacterium isolated from Lake Cuochuolong on the Tibetan Plateau. Int J Syst Evol Microbiol 2018; 68:2220–2225 [View Article][PubMed]
    [Google Scholar]
  6. Jin HM, Kim JM, Lee HJ, Madsen EL, Jeon CO. Alteromonas as a key agent of polycyclic aromatic hydrocarbon biodegradation in crude oil-contaminated coastal sediment. Environ Sci Technol 2012; 46:7731–7740 [View Article][PubMed]
    [Google Scholar]
  7. Koh CH, Khim JS. The Korean tidal flat of the Yellow Sea: Physical setting, ecosystem and management. Ocean Coast Manag 2014; 102:398–414 [View Article]
    [Google Scholar]
  8. Kim BS, Hm O, Kang H, Park SS, Chun J. Remarkable bacterial diversity in the tidal flat sediment as revealed by 16S rDNA analysis. J Microbiol Biotechn 2004; 14:205–211
    [Google Scholar]
  9. Choi HJ, Jeong TY, Yoon H, Oh BY, Han YS et al. Comparative microbial communities in tidal flats sediment on Incheon, South Korea. J Gen Appl Microbiol 2018; 64:232–239 [View Article][PubMed]
    [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. Ludwig W, Strunk O, Westram R, Richter L, Meier H et al. ARB: a software environment for sequence data. Nucleic Acids Res 2004; 32:1363–1371 [View Article][PubMed]
    [Google Scholar]
  14. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  15. 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]
  16. Rzhetsky A, Nei M. Theoretical foundation of the minimum-evolution method of phylogenetic inference. Mol Biol Evol 1993; 10:1073–1095 [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. 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]
  20. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article][PubMed]
    [Google Scholar]
  21. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article][PubMed]
    [Google Scholar]
  22. Yoon SH, Ha SM, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [View Article][PubMed]
    [Google Scholar]
  23. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article][PubMed]
    [Google Scholar]
  24. Galperin MY, Makarova KS, Wolf YI, Koonin EV. Expanded microbial genome coverage and improved protein family annotation in the COG database. Nucleic Acids Res 2015; 43:D261–D269 [View Article][PubMed]
    [Google Scholar]
  25. Marchler-Bauer A, Zheng C, Chitsaz F, Derbyshire MK, Geer LY et al. CDD: conserved domains and protein three-dimensional structure. Nucleic Acids Res 2013; 41:D348–D352 [View Article][PubMed]
    [Google Scholar]
  26. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article][PubMed]
    [Google Scholar]
  27. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article][PubMed]
    [Google Scholar]
  28. Bernardet JF, Nakagawa Y, Holmes B. Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 2002; 52:1049–1070 [View Article][PubMed]
    [Google Scholar]
  29. Wolfe AJ, Berg HC. Migration of bacteria in semisolid agar. Proc Natl Acad Sci USA 1989; 86:6973–6977 [View Article][PubMed]
    [Google Scholar]
  30. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note. vol. 101 1990 pp. 1–6
    [Google Scholar]
  31. Minnikin DE, O'Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 1984; 2:233–241 [View Article]
    [Google Scholar]
  32. Collins MD, Shah HN, Minnikin DE. A note on the separation of natural mixtures of bacterial menaquinones using reverse phase thin-layer chromatography. J Appl Bacteriol 1980; 48:277–282 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003499
Loading
/content/journal/ijsem/10.1099/ijsem.0.003499
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most cited Most Cited RSS feed