1887

Abstract

A Gram-stain-negative, rod-shaped, non-motile, aerobic, catalase-negative and oxidase-positive bacterium, designated strain Sn-9-2, was isolated from a cave soil sample collected from Tiandong cave, Guizhou Province, south-west PR China. Growth occurred at 15–40 °C (optimum, 30 °C), at pH 5.0–9.0 (optimum, pH 7.0–8.0) and with 0–1 % NaCl (w/v). The predominant respiration quinone was ubiquinone-10 (Q-10). The major cellular fatty acids were summed feature 8 (Cω7 or Cω6; 83.9 %) and C (5.8 %). The major polar lipids were phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylcholine, phosphatidylglycerol, three unidentified phospholipids, two unidentified glycolipids, two unidentified polar lipids and one unidentified aminolipid. The DNA G+C content of strain Sn-9-2 was 67.5 mol%. Based on the results of 16S rRNA gene sequence analysis, the nearest phylogenetic neighbours of strain Sn-9-2 (MF958452) were identified as (FR733686) DSM 9035 (97.5 %), (jgi.1053054) DSM 432 (97.2 %) and ATCC 700314 RCTF01000015 (96.9 %). The average nucleotide identity values were 78.0, 77.4 and 77.6 % and the digital DNA–DNA hybridization values were 21.8, 22.0 and 18.8 % between strain Sn-9-2 and DSM 9035, DSM 432 and DSM 11105, respectively. The DNA–DNA hybridization data indicated that strain Sn-9-2 represented a novel genomic species. On the basis of the results of phylogenetic analysis, chemotaxonomic data, physiological characteristics and DNA–DNA hybridization data, strain Sn-9-2 should represent a novel species of the genus , for which the name sp. nov. is proposed. The type strain is Sn-9-2 (=KCTC 62308=CCTCC AB 2018270).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003585
2019-10-08
2019-10-14
Loading full text...

Full text loading...

References

  1. Irgens RL, Kersters K, Segers P, Gillis M, Staley JT. Aquabacter spiritensis, gen. nov., sp. nov. an aerobic, gas-vacuolate aquatic bacterium. Arch Microbiol 1991;155:137–142 [CrossRef]
    [Google Scholar]
  2. Reasoner DJ, Geldreich EE. A new medium for the enumeration and subculture of bacteria from potable water. Appl Environ Microbiol 1985;49:1–7[PubMed]
    [Google Scholar]
  3. Baumgarten J, Reh M, Schlegel HG. Taxonomic studies on some gram-positive coryneform hydrogen bacteria. Arch Microbiol 1974;100:207–217 [CrossRef]
    [Google Scholar]
  4. Wiegel J, Wilke D, Baumgarten J, Opitz R, Schlegel HG. Transfer of the Nitrogen-Fixing Hydrogen Bacterium Corynebacterium autotrophicum Baumgarten et al. to Xanthobacter gen. nov. Int J Syst Bacteriol 1978;28:573–581 [CrossRef]
    [Google Scholar]
  5. Padden AN, Rainey FA, Kelly DP, Wood AP. Xanthobacter tagetidis sp. nov., an organism associated with Tagetes species and able to grow on substituted thiophenes. Int J Syst Bacteriol 1997;47:394–401 [CrossRef][PubMed]
    [Google Scholar]
  6. Li WJ, Xu P, Schumann P, Zhang YQ, Pukall R et al. Georgenia ruanii sp. nov., a novel actinobacterium isolated from forest soil in Yunnan (China), and emended description of the genus Georgenia. Int J Syst Evol Microbiol 2007;57:1424–1428 [CrossRef][PubMed]
    [Google Scholar]
  7. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012;62:716–721 [CrossRef][PubMed]
    [Google Scholar]
  8. 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]
  9. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987;4:406–425 [CrossRef][PubMed]
    [Google Scholar]
  10. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981;17:368–376 [CrossRef][PubMed]
    [Google Scholar]
  11. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971;20:406–416 [CrossRef]
    [Google Scholar]
  12. Kumar S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Mol Biol Evol 2016;33:1870–1874 [CrossRef][PubMed]
    [Google Scholar]
  13. 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]
  14. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985;39:783–791 [CrossRef][PubMed]
    [Google Scholar]
  15. 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]
  16. Christensen H, Angen O, Mutters R, Olsen JE, Bisgaard M. DNA-DNA hybridization determined in micro-wells using covalent attachment of DNA. Int J Syst Evol Microbiol 2000;50:1095–1102 [CrossRef][PubMed]
    [Google Scholar]
  17. Xi L, Zhang Z, Qiao N, Zhang Y, Li J et al. Complete genome sequence of the novel thermophilic polyhydroxyalkanoates producer Aneurinibacillus sp. XH2 isolated from Gudao oilfield in China. J Biotechnol 2016;227:54–55 [CrossRef][PubMed]
    [Google Scholar]
  18. 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 [CrossRef][PubMed]
    [Google Scholar]
  19. 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 [CrossRef][PubMed]
    [Google Scholar]
  20. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O et al. International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 1987;37:463–464
    [Google Scholar]
  21. 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]
  22. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018;68:461–466 [CrossRef][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 [CrossRef][PubMed]
    [Google Scholar]
  24. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009;106:19126–19131 [CrossRef][PubMed]
    [Google Scholar]
  25. Skerman VBD. A Guide to the Identification of the Genera of Bacteria, 2nd ed. Baltimore: Williams & Wilkins; 1967
    [Google Scholar]
  26. Gregersen T. Rapid method for distinction of gram-negative from gram-positive bacteria. European Journal of Applied Microbiology and Biotechnology 1978;5:123–127 [CrossRef]
    [Google Scholar]
  27. Xu P, Li WJ, Tang SK, Zhang YQ, Chen GZ et al. Naxibacter alkalitolerans gen. nov., sp. nov., a novel member of the family 'Oxalobacteraceae' isolated from China. Int J Syst Evol Microbiol 2005;55:1149–1153 [CrossRef][PubMed]
    [Google Scholar]
  28. 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.607–655
    [Google Scholar]
  29. Minnikin DE, Collins MD, Goodfellow M. Fatty Acid and Polar Lipid Composition in the Classification of Cellulomonas, Oerskovia and Related Taxa. J Appl Bacteriol 1979;47:87–95 [CrossRef]
    [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 [CrossRef]
    [Google Scholar]
  31. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newwark, DE: MIDI Inc 1990
    [Google Scholar]
  32. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977;100:221–230 [CrossRef][PubMed]
    [Google Scholar]
  33. Tamaoka J. Analysis of bacterial menaquinone mixtures by reverse-phase high-performance liquid chromatography. Methods Enzymol 1986;123:31–36 [CrossRef][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003585
Loading
/content/journal/ijsem/10.1099/ijsem.0.003585
Loading

Data & Media loading...

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