1887

Abstract

During a study of bacterial diversity in forest soil, strain G-3-2, a Gram-stain-negative, light brown-coloured, non-motile, rod- or coccoid-shaped bacterium, was isolated. It was able to grow at 15–37 °C, at pH 5.5–10.0 and at 0–0.5 % (w/v) NaCl concentration. The strain was taxonomically characterized by a polyphasic approach. Based on the 16S rRNA gene sequence analysis, strain G-3-2 belongs to the genus Ramlibacter and is closely related to Ramlibacter ginsenosidimutans BXN5-27 (98.69 % sequence similarity), Ramlibacter henchirensis TMB834 (96.98 %), Ramlibacter tataouinensis TTB310 (96.49 %) and Ramlibacter solisilvae 5-10 (96.42 %). The only respiratory quinone was ubiquinone-8. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The predominant fatty acids of strain G-3–2 were C16 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1 ω6c), C17 : 0 cyclo, summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C10 : 0 3-OH. The genomic DNA G+C content of this novel strain was 68.9 mol%. The DNA–DNA relatedness between strain G-3-2 and R. ginsenosidimutans BXN5-27 was 44.7 %, which falls below the threshold value of 70 % for the strain to be considered as novel. The morphological, physiological, chemotaxonomic and phylogenetic analyses clearly distinguished this strain from its closest phylogenetic neighbours. Thus, strain G-3-2 represents a novel species of the genus Ramlibacter , for which the name Ramlibacter monticola sp. nov. is proposed. The type strain is G-3-2 (=KEMB 9005-573=KACC 19175=JCM 31918).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.002314
2017-09-27
2019-10-17
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/67/11/4468.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.002314&mimeType=html&fmt=ahah

References

  1. Heulin T, Barakat M, Christen R, Lesourd M, Sutra L et al. Ramlibacter tataouinensis gen. nov., sp. nov., and Ramlibacter henchirensis sp. nov., cyst-producing bacteria isolated from subdesert soil in Tunisia. Int J Syst Evol Microbiol 2003; 53: 589– 594 [CrossRef] [PubMed]
    [Google Scholar]
  2. Lee HJ, Lee SH, Lee SS, Lee JS, Kim Y et al. Ramlibacter solisilvae sp. nov., isolated from forest soil, and emended description of the genus Ramlibacter. Int J Syst Evol Microbiol 2014; 64: 1317– 1322 [CrossRef] [PubMed]
    [Google Scholar]
  3. Wang L, An DS, Kim SG, Jin FX, Kim SC et al. Ramlibacter ginsenosidimutans sp. nov., with ginsenoside-converting activity. J Microbiol Biotechnol 2012; 22: 311– 315 [CrossRef] [PubMed]
    [Google Scholar]
  4. Chaudhary DK, Kim J. Novosphingobium naphthae sp. nov., from oil-contaminated soil. Int J Syst Evol Microbiol 2016; 66: 3170– 3176 [CrossRef] [PubMed]
    [Google Scholar]
  5. Chaudhary DK, Kim J. Chryseobacterium nepalense sp. nov., isolated from oil-contaminated soil. Int J Syst Evol Microbiol 2017; 67: 646– 652 [CrossRef] [PubMed]
    [Google Scholar]
  6. Marmur J. A procedure for the isolation of deoxyribonucleic acid from micro-organisms. J Mol Biol 1961; 3: 208– 218 [CrossRef]
    [Google Scholar]
  7. Frank JA, Reich CI, Sharma S, Weisbaum JS, Wilson BA et al. Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes. Appl Environ Microbiol 2008; 74: 2461– 2470 [CrossRef] [PubMed]
    [Google Scholar]
  8. 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 [CrossRef] [PubMed]
    [Google Scholar]
  9. 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 [CrossRef] [PubMed]
    [Google Scholar]
  10. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 1999; 41: 95– 98
    [Google Scholar]
  11. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4: 406– 425 [PubMed]
    [Google Scholar]
  12. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20: 406– 416 [CrossRef]
    [Google Scholar]
  13. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17: 368– 376 [CrossRef] [PubMed]
    [Google Scholar]
  14. 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 [CrossRef] [PubMed]
    [Google Scholar]
  15. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16: 111– 120 [CrossRef] [PubMed]
    [Google Scholar]
  16. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39: 783– 791 [CrossRef] [PubMed]
    [Google Scholar]
  17. Yarza P, Richter M, Peplies J, Euzeby J, Amann R et al. The all-species living tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst Appl Microbiol 2008; 31: 241– 250 [CrossRef] [PubMed]
    [Google Scholar]
  18. 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 [CrossRef]
    [Google Scholar]
  19. Doetsch RN. Determinative methods of light microscopy. In Gerhardt P. (editor) Manual of Methods for General Bacteriology Washington, DC: American Society for Microbiology; 1981; pp. 21– 33
    [Google Scholar]
  20. Powers EM. Efficacy of the Ryu nonstaining KOH technique for rapidly determining gram reactions of food-borne and waterborne bacteria and yeasts. Appl Environ Microbiol 1995; 61: 3756– 3758 [PubMed]
    [Google Scholar]
  21. Chaudhary DK, Kim J. Arvibacter flaviflagrans gen. nov., sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2016; 66: 4347– 4354 [CrossRef] [PubMed]
    [Google Scholar]
  22. Breznak JA, Costilow RN. Physicochemical factors in growth. In Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM, Snyder LR. (editors) Methods for General and Molecular Bacteriology, 3rd ed. Washington, DC: American Society for Microbiology; 2007; pp. 309– 329
    [Google Scholar]
  23. Hemraj V, Diksha S, Avneet G. A review on commonly used biochemical test for bacteria. Innovare J Life Sci 2013; 1: 1– 7
    [Google Scholar]
  24. Chaudhary DK, Kim J. Sphingomonas naphthae sp. nov., isolated from oil-contaminated soil. Int J Syst Evol Microbiol 2016; 66: 4621– 4627 [CrossRef] [PubMed]
    [Google Scholar]
  25. Tindall BJ, Sikorski J, Smibert RA, Krieg NR. Phenotypic characterization and the principles of comparative systematics. In Reddy CA, Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM. et al. (editors) Methods for General and Molecular Bacteriology, 3rd ed. Washington, DC: ASM Press; 2007; pp. 330– 393
    [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, USA: American Society for Microbiology; 1994; pp. 607– 654
    [Google Scholar]
  27. Cowan ST, Steel KJ. Manual for the Identification of Medical Bacteria London: Cambridge University Press; 1965
    [Google Scholar]
  28. 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 [CrossRef]
    [Google Scholar]
  29. Komagata K, Suzuki K. Lipids and cell wall analysis in bacterial systematics. Methods Microbiol 1987; 19: 161– 203 [Crossref]
    [Google Scholar]
  30. Hiraishi A, Ueda Y, Ishihara J, Mori T. Comparative lipoquinone analysis of influent sewage and activated sludge by high-performance liquid chromatography and photodiode array detection. J Gen Appl Microbiol 1996; 42: 457– 469 [CrossRef]
    [Google Scholar]
  31. 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]
  32. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  33. Mesbah M, Premachandran U, Whitman WB. Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 1989; 39: 159– 167 [CrossRef]
    [Google Scholar]
  34. 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 [CrossRef]
    [Google Scholar]
  35. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O et al. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Microbiol 1987; 37: 463– 464 [CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.002314
Loading
/content/journal/ijsem/10.1099/ijsem.0.002314
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most Cited This Month

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