1887

Abstract

Strain SJ5A-1, a Gram-stain-negative, coccus-shaped, non-motile, aerobic bacterium, was isolated from the brine–seawater interface of the Erba Deep in the Red Sea, Saudi Arabia. The colonies of strain SJ5A-1 have a beige to pale-brown pigmentation, are approximately 0.5–0.7 µm in diameter, and are catalase and oxidase positive. Growth occurred optimally at 30–33 °C, pH 7.0–7.5, and in the presence of 9.0–12.0 % NaCl (w/v). Phylogenetic analysis of the 16S rRNA gene indicates that strain SJ5A-1 is a member of the genus within the family DSM 18986 is the most closely related described species based on 16S rRNA gene sequence identity (96.7 %). The DNA–DNA hybridization value between strain SJ5A-1 and DSM 18986 was 36.7 %. The major respiratory quinone of strain SJ5A-1 is Q-10; it predominantly uses the fatty acids C (54.2 %), C (11.2 %), C (8.6 %), 11-methyl C 7 (7.7 %), Ccyclo 8 (3.3 %), and C 3-OH (3.5 %), and its major polar lipids are phosphatidylethanolamine, phosphatidylglycerol, phosphocholine, an unknown aminolipid, an unknown phospholipid and two unknown lipids. The genome draft of strain SJ5A-1 as presented here is 4 562 830 bp in size and the DNA G+C content is 68.0 mol%. Based on phenotypic, phylogenetic and genotypic data, strain SJ5A-1 represents a novel species in the genus , for which we propose the name sp. nov. The type strain of is SJ5A-1 (=JCM 19520=ACCC19863).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.002280
2017-11-01
2024-04-19
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/67/11/4358.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.002280&mimeType=html&fmt=ahah

References

  1. Giovannoni SJ, Rappé M. Evolution, diversity and molecular ecology of marine prokaryotes. In Kirchman DL. (editor) Microbial Ecology of the Oceans New York: Wiley; 2000 pp. 47–84
    [Google Scholar]
  2. Woese CR, Stackebrandt E, Weisburg WG, Paster BJ, Madigan MT et al. The phylogeny of purple bacteria: the alpha subdivision. Syst Appl Microbiol 1984; 5:315–326 [View Article][PubMed]
    [Google Scholar]
  3. Buchan A, González JM, Moran MA. Overview of the marine Roseobacter lineage. Appl Environ Microbiol 2005; 71:5665–5677 [View Article][PubMed]
    [Google Scholar]
  4. Choi DH, Cho BC. Shimia marina gen. nov., sp. nov., a novel bacterium of the Roseobacter clade isolated from biofilm in a coastal fish farm. Int J Syst Evol Microbiol 2006; 56:1869–1873 [View Article][PubMed]
    [Google Scholar]
  5. Dai X, Wang BJ, Yang QX, Jiao NZ, Liu SJ. Yangia pacifica gen. nov., sp. nov., a novel member of the Roseobacter clade from coastal sediment of the East China Sea. Int J Syst Evol Microbiol 2006; 56:529–533 [View Article][PubMed]
    [Google Scholar]
  6. Tang K, Huang H, Jiao N, Wu CH, Ch W. Phylogenomic analysis of marine Roseobacters. PLoS One 2010; 5:e11604 [View Article][PubMed]
    [Google Scholar]
  7. Yang Y, Sun J, Tang K, Lin D, Li C et al. Ponticoccus lacteus sp. nov. of the family Rhodobacteraceae, isolated from surface seawater. Int J Syst Evol Microbiol 2015; 65:1247–1250 [View Article][PubMed]
    [Google Scholar]
  8. Martens T, Heidorn T, Pukall R, Simon M, Tindall BJ et al. Reclassification of Roseobacter gallaeciensis Ruiz-Ponte et al. 1998 as Phaeobacter gallaeciensis gen. nov., comb. nov., description of Phaeobacter inhibens sp. nov., reclassification of Ruegeria algicola (Lafay et al. 1995) Uchino et al. 1999 as Marinovum algicola gen. nov., comb. nov., and emended descriptions of the genera Roseobacter, Ruegeria and Leisingera. Int J Syst Evol Microbiol 2016; 56:1293–1304 [View Article][PubMed]
    [Google Scholar]
  9. Wagner-Döbler I, Biebl H. Environmental biology of the marine Roseobacter lineage. Annu Rev Microbiol 2006; 60:255–280 [View Article][PubMed]
    [Google Scholar]
  10. Hwang CY, Cho BC. Ponticoccus litoralis gen. nov., sp. nov., a marine bacterium in the family Rhodobacteraceae. Int J Syst Evol Microbiol 2008; 58:1332–1338 [View Article][PubMed]
    [Google Scholar]
  11. Wang Y, Cao H, Zhang G, Bougouffa S, Lee OO et al. Autotrophic microbe metagenomes and metabolic pathways differentiate adjacent Red Sea brine pools. Sci Rep 2013; 3:1748 [View Article][PubMed]
    [Google Scholar]
  12. Antunes A, Ngugi DK, Stingl U. Microbiology of the Red Sea (and other) deep-sea anoxic brine lakes. Environ Microbiol Rep 2011; 3:416–433 [View Article][PubMed]
    [Google Scholar]
  13. Labrenz M, Collins MD, Lawson PA, Tindall BJ, Braker G et al. Antarctobacter heliothermus gen. nov., sp. nov., a budding bacterium from hypersaline and heliothermal Ekho Lake. Int J Syst Bacteriol 1998; 48:1363–1372 [View Article][PubMed]
    [Google Scholar]
  14. Ostle AG, Holt JG. Nile blue A as a fluorescent stain for poly-β-hydroxybutyrate. Appl Environ Microbiol 1982; 44:238–241[PubMed]
    [Google Scholar]
  15. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General, Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp. 607–654
    [Google Scholar]
  16. Dong XZ, Cai MY. (editors) Chapter 14. Determination of biochemical characteristics. Manual for the Systematic Identification of General Bacteria Beijing: Science Press (in Chinese); 2001 pp. 370–398
    [Google Scholar]
  17. Fraser SL, Jorgensen JH. Reappraisal of the antimicrobial susceptibilities of Chryseobacterium and Flavobacterium species and methods for reliable susceptibility testing. Antimicrob Agents Chemother 1997; 41:2738–2741[PubMed]
    [Google Scholar]
  18. Schmieder R, Edwards R. Quality control and preprocessing of metagenomic datasets. Bioinformatics 2011; 27:863–864 [View Article][PubMed]
    [Google Scholar]
  19. Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics 2008; 24:713–714 [View Article][PubMed]
    [Google Scholar]
  20. Li R, Zhu H, Ruan J, Qian W, Fang X et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 2010; 20:265–272 [View Article][PubMed]
    [Google Scholar]
  21. Liu B, Shi Y, Yuan J, Hu X, Zhang H et al. Estimation of genomic characteristics by analyzing k–mer frequency in de novo genome projects. arXiv 2012; 2013:1308
    [Google Scholar]
  22. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015; 25:1043–1055 [View Article][PubMed]
    [Google Scholar]
  23. Delcher AL, Harmon D, Kasif S, White O, Salzberg SL. Improved microbial gene identification with GLIMMER. Nucleic Acids Res 1999; 27:4636–4641 [View Article][PubMed]
    [Google Scholar]
  24. Delcher AL, Bratke KA, Powers EC, Salzberg SL. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 2007; 23:673–679 [View Article][PubMed]
    [Google Scholar]
  25. Lagesen K, Hallin P, Rødland EA, Staerfeldt HH, Rognes T et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007; 35:3100–3108 [View Article][PubMed]
    [Google Scholar]
  26. Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997; 25:955–964 [View Article][PubMed]
    [Google Scholar]
  27. De Ley J. Reexamination of the association between melting point, buoyant density, and chemical base composition of deoxyribonucleic acid. J Bacteriol 1970; 101:738–754[PubMed]
    [Google Scholar]
  28. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997; 25:4876–4882 [View Article][PubMed]
    [Google Scholar]
  29. 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]
  30. 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]
  31. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI technical note 101. Newark: MIDI Inc; 1990
    [Google Scholar]
  32. Bligh EG, Dyer WJ. A rapid method of total lipid extraction and purification. Can J Biochem Physiol 1959; 37:911–917 [View Article][PubMed]
    [Google Scholar]
  33. Tindall BJ, Sikorski J, Smibert RM, Kreig NR. Phenotypic characterization and the principles of comparative systematics. In Reddy CA, Beveridge TJ, Breznak JA, Marzluf G, Schmidt TM. et al. (editors) Methods for General and Molecular Microbiology, 3rd ed. Washington, DC: ASM Press; 2007 pp. 330–393
    [Google Scholar]
  34. Stackebrandt E, Goebel BM. Taxonomic note: a place for DNA–DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Evol Microbiol 1994; 44:846–849 [View Article]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.002280
Loading
/content/journal/ijsem/10.1099/ijsem.0.002280
Loading

Data & Media loading...

Supplements

Supplementary File 1

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