sp. nov., a benzene-degrading marine bacterium isolated from estuary sediment Free

Abstract

A Gram-stain-negative, aerobic, motile, flagellated rod-shaped bacterium, designated ST58-10, was isolated from an estuarine sediment in the Republic of Korea. The strain was able to degrade benzene. Growth of strain ST58-10 was observed at 4–35 °C (optimum, 20–25 °C), pH 5–9 (optimum, pH 7–8) and 1–8 % NaCl (optimum, 3 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain ST58-10 formed a phyletic lineage within the genus of the family Strain ST58-10 was most closely related to PAMC 27536 (99.6 %) and CL-YJ9 (98.3 %), and to other members of the genus (94.5–91.5 %). However, the mean value estimated by using the Genome-to-Genome Distance Calculator was 50.6±7.4 % with PAMC 27536 and 30.9±2.8 with CL-YJ9, respectively. An average nucleotide identity value was 89.0 % with PAMC 27536 and 85.6 % with CL-YJ9, respectively. The major fatty acids of strain ST58-10 were summed feature 3 (comprising C 7/C 6), summed feature 8 (comprising C 7/C 6), C and C 3-OH, and contained ubiquinone (Q-8) as the sole isoprenoid quinone. Phosphatidylethanolamine, phosphatidylglycerol, three unidentified aminolipids, an unidentified glycolipid and an unidentified lipid were detected as polar lipids. The DNA G+C content of strain ST58-10 was 58.78 mol%. On the basis of the phenotypic, chemotaxonomic and molecular properties, strain ST58-10 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is ST58-10 (=KCTC 52193=NBRC 112103).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.002561
2018-02-01
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/68/2/651.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.002561&mimeType=html&fmt=ahah

References

  1. González JM, Mayer F, Moran MA, Hodson RE, Whitman WB. Microbulbifer hydrolyticus gen. nov., sp. nov., and Marinobacterium georgiense gen. nov., sp. nov., two marine bacteria from a lignin-rich pulp mill waste enrichment community. Int J Syst Bacteriol 1997; 47:369–376 [View Article][PubMed]
    [Google Scholar]
  2. Baumann P, Bowditch RD, Baumann L, Beaman B. Taxonomy of marine Pseudomonas species: P. stanieri sp. nov.; P. perfectomarina sp. nov., nom. rev.; P. nautica: and P. doudoroffii . Int J Syst Bacteriol 1983; 33:857–865 [View Article]
    [Google Scholar]
  3. Bowditch RD, Baumann L, Baumann P. Description of Oceanospirillum kriegii sp. nov. and O. jannaschii sp. nov. and assignment of two species of Alteromonas to this genus as O. commune comb. nov. and O. vagum comb. nov. Curr Microbiol 1984; 10:221–229 [View Article]
    [Google Scholar]
  4. Satomi M, Kimura B, Hamada T, Harayama S, Fujii T. Phylogenetic study of the genus Oceanospirillum based on 16S rRNA and gyrB genes: emended description of the genus Oceanospirillum, description of Pseudospirillum gen. nov., Oceanobacter gen. nov. and Terasakiella gen. nov. and transfer of Oceanospirillum jannaschii and Pseudomonas stanieri to Marinobacterium as Marinobacterium jannaschii comb. nov. and Marinobacterium stanieri comb. no. Int J Syst Evol Microbiol 2002; 52:739–747 [View Article][PubMed]
    [Google Scholar]
  5. Parte AC. LPSN–list of prokaryotic names with standing in nomenclature. Nucleic Acids Res 2014; 42:D613–D616 [View Article][PubMed]
    [Google Scholar]
  6. Chang HW, Nam YD, Kwon HY, Park JR, Lee JS et al. Marinobacterium halophilum sp. nov., a marine bacterium isolated from the Yellow Sea. Int J Syst Evol Microbiol 2007; 57:77–80 [View Article][PubMed]
    [Google Scholar]
  7. Kim JM, Lee SH, Jung JY, Jeon CO. Marinobacterium lutimaris sp. nov., isolated from a tidal flat. Int J Syst Evol Microbiol 2010; 60:1828–1831 [View Article][PubMed]
    [Google Scholar]
  8. Kim SJ, Park SJ, Yoon DN, Park BJ, Choi BR et al. Marinobacterium maritimum sp. nov., a marine bacterium isolated from Arctic sediment. Int J Syst Evol Microbiol 2009; 59:3030–3034 [View Article][PubMed]
    [Google Scholar]
  9. Huo YY, Xu XW, Cao Y, Wang CS, Zhu XF et al. Marinobacterium nitratireducens sp. nov. and Marinobacterium sediminicola sp. nov., isolated from marine sediment. Int J Syst Evol Microbiol 2009; 59:1173–1178 [View Article][PubMed]
    [Google Scholar]
  10. Kim H, Choo YJ, Song J, Lee JS, Lee KC et al. Marinobacterium litorale sp. nov. in the order Oceanospirillales . Int J Syst Evol Microbiol 2007; 57:1659–1662 [View Article][PubMed]
    [Google Scholar]
  11. Kim H, Oh HM, Yang SJ, Lee JS, Hong JS et al. Marinobacterium marisflavi sp. nov., isolated from a costal seawater. Curr Microbiol 2009; 58:511–515 [View Article][PubMed]
    [Google Scholar]
  12. Kim YG, Jin YA, Hwang CY, Cho BC. Marinobacterium rhizophilum sp. nov., isolated from the rhizosphere of the coastal tidal-flat plant Suaeda japonica . Int J Syst Evol Microbiol 2008; 58:164–167 [View Article][PubMed]
    [Google Scholar]
  13. Alfaro-Espinoza G, Ullrich MS. Marinobacterium mangrovicola sp. nov., a marine nitrogen-fixing bacterium isolated from mangrove roots of Rhizophora mangle . Int J Syst Evol Microbiol 2014; 64:3988–3993 [View Article][PubMed]
    [Google Scholar]
  14. Chimetto LA, Cleenwerck I, Brocchi M, Willems A, de Vos P et al. Marinobacterium coralli sp. nov., isolated from mucus of coral (Mussismilia hispida). Int J Syst Evol Microbiol 2011; 61:60–64 [View Article][PubMed]
    [Google Scholar]
  15. Han SB, Wang RJ, Yu XY, Su Y, Sun C et al. Marinobacterium zhoushanense sp. nov., isolated from surface seawater. Int J Syst Evol Microbiol 2016; 66:3437–3442 [View Article][PubMed]
    [Google Scholar]
  16. Yeon Hwang C, Jung Yoon S, Lee I, Baek K, Mi Lee Y et al. Marinobacterium profundum sp. nov., a marine bacterium from deep-sea sediment. Int J Syst Evol Microbiol 2016; 66:1561–1566 [View Article][PubMed]
    [Google Scholar]
  17. Park S, Jung YT, Kim S, Yoon JH. Marinobacterium aestuariivivens sp. nov., isolated from a tidal flat. Int J Syst Evol Microbiol 2016; 66:1718–1723 [View Article][PubMed]
    [Google Scholar]
  18. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematics New York, NY, USA: John Wiley & Sons; 1991 pp. 115–147
    [Google Scholar]
  19. 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]
  20. Nawrocki EP, Eddy SR. Query-dependent banding (QDB) for faster RNA similarity searches. PLoS Comput Biol 2007; 3:e56 [View Article][PubMed]
    [Google Scholar]
  21. Cole JR, Wang Q, Fish JA, Chai B, Mcgarrell DM et al. Ribosomal Database Project: data and tools for high throughput rRNA analysis. Nucleic Acids Res 2014; 42:D633–D642 [View Article][PubMed]
    [Google Scholar]
  22. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 2013; 30:2725–2729 [View Article][PubMed]
    [Google Scholar]
  23. 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]
  24. Auch AF, von Jan M, Klenk HP, Göker M. Digital DNA–DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2010; 2:117–134 [View Article][PubMed]
    [Google Scholar]
  25. 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]
  26. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp. 607–654
    [Google Scholar]
  27. Lányí B. Classical and rapid identification methods for medically important bacteria. Methods Microbiol 1987; 19:1–67
    [Google Scholar]
  28. Dyksterhouse SE, Gray JP, Herwig RP, Lara JC, Staley JT. Cycloclasticus pugetii gen. nov., sp. nov., an aromatic hydrocarbon-degrading bacterium from marine sediments. Int J Syst Bacteriol 1995; 45:116–123 [View Article][PubMed]
    [Google Scholar]
  29. 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]
  30. Komagata K, Suzuki K. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–208 [Crossref]
    [Google Scholar]
  31. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.002561
Loading
/content/journal/ijsem/10.1099/ijsem.0.002561
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most cited Most Cited RSS feed