sp. nov., isolated from oil-contaminated soil Free

Abstract

A Gram-stain-positive, non-motile, yellow and rod-shaped actinobacterium, designated strain Brt-A, isolated from oil-contaminated soil, grew at 15–40 °C, at pH 5.5–10.0 and at 0–2 % (w/v) NaCl concentration. This strain was characterized by a polyphasic approach. The 16S rRNA gene sequence analysis showed that strain Brt-A belonged to the genus and is closely related to YIM 101269, SST-39, LNB-140 and RP1 (99.03, 97.00, 96.88, and 96.46 % gene sequence similarity, respectively). The predominant respiratory quinone was MK-9(H); the major polar lipids were phosphatidylglycerol and diphosphatidylglycerol; the predominant polyamines were spermine and spermidine; and the major fatty acids were anteiso-C and iso-C. The cell-wall peptidoglycan contained -diaminopimelic acid; and glucose and ribose were detected as diagnostic sugars from whole-cell hydrolysates. The DNA G+C content was 68.1 mol%. The DNA–DNA relatedness between strain Brt-A and its closely related species of the genus were between 55.0–44.0 %, which fall 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 Brt-A represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is Brt-A (=KEMB 9005-690=KACC 19391=JCM 32157).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.002537
2018-02-01
2024-03-29
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/68/2/529.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.002537&mimeType=html&fmt=ahah

References

  1. Maszenan AM, Seviour RJ, Patel BK, Schumann P, Rees GN. Tessaracoccus bendigoensis gen. nov., sp. nov., a gram-positive coccus occurring in regular packages or tetrads, isolated from activated sludge biomass. Int J Syst Bacteriol 1999; 49:459–468 [View Article][PubMed]
    [Google Scholar]
  2. Li GD, Chen X, Li QY, Xu FJ, Qiu SM et al. Tessaracoccus rhinocerotis sp. nov., isolated from the faeces of Rhinoceros unicornis . Int J Syst Evol Microbiol 2016; 66:922–927 [View Article][PubMed]
    [Google Scholar]
  3. Lee DW, Lee SD. Tessaracoccus flavescens sp. nov., isolated from marine sediment. Int J Syst Evol Microbiol 2008; 58:785–789 [View Article][PubMed]
    [Google Scholar]
  4. Srinivasan S, Sundararaman A, Lee SS. Tessaracoccus defluvii sp. nov., isolated from an aeration tank of a sewage treatment plant. Antonie van Leeuwenhoek 2017; 110:1–9 [View Article][PubMed]
    [Google Scholar]
  5. Chaudhary DK, Kim J. Novosphingobium naphthae sp. nov., from oil-contaminated soil. Int J Syst Evol Microbiol 2016; 66:3170–3176 [View Article][PubMed]
    [Google Scholar]
  6. Marmur J. A procedure for the isolation of deoxyribonucleic acid from micro-organisms. J Mol Biol 1961; 3:208–218 [View Article]
    [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 [View Article][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 and whole-genome assemblies. Int J Syst Evol Microbiol 2017 (in press) [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 [View Article][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 [View Article]
    [Google Scholar]
  13. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][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 [View Article][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 [View Article][PubMed]
    [Google Scholar]
  16. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][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 [View Article][PubMed]
    [Google Scholar]
  18. Doetsch RN. Determinative methods of light microscopy. In Gerhardt P. (editor) Manual of Methods for General Bacteriology Washington, DC, USA: American Society for Microbiology; 1981 pp. 21–33
    [Google Scholar]
  19. Breznak JA, Costilow RN. Physicochemical factors in growth. In Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM, Snyder LR et al. (editors) Methods for General and Molecular Bacteriology, 3rd ed. Washington, DC: American Society for Microbiology; 2007 pp. 309–329
    [Google Scholar]
  20. Chaudhary DK, Kim J. Arvibacter flaviflagrans gen. nov., sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2016; 66:4347–4354 [View Article][PubMed]
    [Google Scholar]
  21. 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]
  22. 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]
  23. Komagata K, Suzuki K. Lipids and cell wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–203 [Crossref]
    [Google Scholar]
  24. 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 [View Article]
    [Google Scholar]
  25. 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]
  26. Busse H-J, Bunka S, Hensel A, Lubitz W. Discrimination of members of the family Pasteurellaceae based on polyamine patterns. Int J Syst Bacteriol 1997; 47:698–708 [View Article]
    [Google Scholar]
  27. Pedrol N, Tiburcio AF. Polyamine determination by TLC and HPLC. In Reigosa Roger MJ. (editor) Handbook of Plant Ecophysiology Techniques Netherlands: Springer; 2001 pp. 335–363
    [Google Scholar]
  28. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  29. Staneck JL, Roberts GD. Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 1974; 28:226–231[PubMed]
    [Google Scholar]
  30. 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 [View Article]
    [Google Scholar]
  31. 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]
  32. Kumari R, Singh P, Schumann P, Lal R. Tessaracoccus flavus sp. nov., isolated from the drainage system of a lindane-producing factory. Int J Syst Evol Microbiol 2016; 66:1862–1868 [View Article][PubMed]
    [Google Scholar]
  33. Wayne LG, Moore WEC, Stackebrandt E, Kandler O, Colwell RR et al. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Microbiol 1987; 37:463–464 [View Article]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.002537
Loading
/content/journal/ijsem/10.1099/ijsem.0.002537
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most cited Most Cited RSS feed