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Abstract

A Gram-stain-positive, moderately halophilic, strictly aerobic, endospore-forming, rod-shaped bacterium, strain JSM 102062, was isolated from a non-saline farm soil sample collected from Dehang Canyon in Hunan, PR China. Growth occurred with 0.5–20 % (w/v) NaCl (optimum 4–7 %) at pH 5.5–11.0 (optimum pH 8.0) and at 20–50 °C (optimum 30–35 °C). Contained cell-wall peptidoglycan based on -diaminopimelic acid and possessed menaquinone-7 (MK-7) as the major respiratory isoprenoid quinone. The major cellular fatty acids were anteiso-C, anteiso-C and iso-C. The polar lipid pattern consisted of diphosphatidylglycerol, phosphatidylglycerol, five unidentified phospholipids and an unidentified glycolipid. The DNA G+C content was 44.1 mol%. Phylogeny based on 16S rRNA gene sequences indicated that strain JSM 102062 belonged to the genus , sharing high 16S rRNA gene sequence similarities to EN8d (99.4 %) and NHBX5 (98.3 %). The whole genomic analysis showed that strain JSM 102062 constituted a different taxon separated from the recognized species. Combined data from phenotypic and genotypic studies demonstrated that strain JSM 102062 represents a noval species of the genus , for which the name sp. nov. is proposed; the type strain is JSM 102062 (=CCTCC AB 2014166 = CGMCC 1.12957=DSM 28949=KCTC 33541).

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2019-11-21
2024-04-19
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References

  1. Carrasco IJ, Márquez MC, Xue Y, Ma Y, Cowan DA et al. Sediminibacillus halophilus gen. nov., sp. nov., a moderately halophilic, Gram-positive bacterium from a hypersaline lake. Int J Syst Evol Microbiol 2008; 58:1961–1967 [View Article]
    [Google Scholar]
  2. Wang X, Xue Y, Ma Y. Sediminibacillus albus sp. nov., a moderately halophilic, Gram-positive bacterium isolated from a hypersaline lake, and emended description of the genus Sediminibacillus Carrasco et al. 2008. Int J Syst Evol Microbiol 2009; 59:1640–1644 [View Article]
    [Google Scholar]
  3. García MT, Gallego V, Ventosa A, Mellado E. Thalassobacillus devorans gen. nov., sp. nov., a moderately halophilic, phenol-degrading, Gram-positive bacterium. Int J Syst Evol Microbiol 2005; 55:1789–1795 [View Article]
    [Google Scholar]
  4. Spring S, Ludwig W, Marquez MC, Ventosa A, Schleifer KH. Halobacillus gen. nov., with descriptions of Halobacillus litoralis sp. nov. and Halobacillus trueperi sp. nov., and transfer of Sporosarcina halophila to Halobacillus halophilus comb. nov. Int J Syst Bacteriol 1996; 46:492–496 [View Article]
    [Google Scholar]
  5. Chen YG, Chen J, Chen QH, Tang SK, Zhang YQ et al. Yaniella soli sp. nov., a new actinobacterium isolated from non-saline forest soil in China. Antonie van Leeuwenhoek 2010; 98:395–401 [View Article]
    [Google Scholar]
  6. Chen YG, Peng DJ, Chen QH, Zhang YQ, Tang SK et al. Jeotgalibacillus soli sp. nov., isolated from non-saline forest soil, and emended description of the genus Jeotgalibacillus . Antonie van Leeuwenhoek 2010; 98:415–421 [View Article]
    [Google Scholar]
  7. Chen YG, Hao DF, Chen QH, Zhang YQ, Liu JB et al. Bacillus hunanensis sp. nov., a slightly halophilic bacterium isolated from non-saline forest soil. Antonie van Leeuwenhoek 2011; 99:481–488 [View Article]
    [Google Scholar]
  8. Chen YG, Zhang YQ, Chen QH, Klenk HP, He JW et al. Bacillus xiaoxiensis sp. nov., a slightly halophilic bacterium isolated from non-saline forest soil. Int J Syst Evol Microbiol 2011; 61:2095–2100 [View Article]
    [Google Scholar]
  9. Chen QH, Chen JH, Ruan Y, Zhang YQ, Tang SK et al. Sphingomonas hunanensis sp. nov., isolated from forest soil. Antonie van Leeuwenhoek 2011; 99:753–760 [View Article]
    [Google Scholar]
  10. Logan NA, Berge O, Bishop AH, Busse HJ, De Vos P et al. Proposed minimal standards for describing new taxa of aerobic, endospore-forming bacteria. Int J Syst Evol Microbiol 2009; 59:2114–2121 [View Article]
    [Google Scholar]
  11. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhard 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]
  12. Buck JD. Nonstaining (KOH) method for determination of gram reactions of marine bacteria. Appl Environ Microbiol 1982; 44:992–993
    [Google Scholar]
  13. Atlas RM. Parks LC. editor Handbook of Microbiological Media Boca Raton, FL: CRC Press; 1993
    [Google Scholar]
  14. Chen YG, Cui XL, Pukall R, Li HM, Yang YL et al. Salinicoccus kunmingensis sp. nov., a moderately halophilic bacterium isolated from a salt mine in Yunnan, south-west China. Int J Syst Evol Microbiol 2007; 57:2327–2332 [View Article]
    [Google Scholar]
  15. Ventosa A, Quesada E, Rodriguez-Valera F, Ruiz-Berraquero F, Ramos-Cormenzana A. Numerical taxonomy of moderately halophilic gram-negative rods. Microbiology 1982; 128:1959–1968 [View Article]
    [Google Scholar]
  16. Hopwood DA, Bibb MJ, Chater KF, Kieser T, Bruton CJ et al. Preparation of chromosomal, plasmid and phage DNA. In: Genetic Manipulation of Streptomyces: a Laboratory Manual Norwich: John Innes Foundation; 1985 pp 79–80
    [Google Scholar]
  17. Cui XL, Xu LH, Zeng M, Li WJ, Mao PH et al. Streptimonospora salina gen. nov., sp. nov., a new member of the family Nocardiopsaceae . Int J Syst Evol Microbiol 2001; 51:357–363 [View Article]
    [Google Scholar]
  18. 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]
    [Google Scholar]
  19. 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]
    [Google Scholar]
  20. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article]
    [Google Scholar]
  21. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article]
    [Google Scholar]
  22. Kluge AG, Farris JS. Quantitative Phyletics and the evolution of anurans. Syst Zool 1969; 18:1–32 [View Article]
    [Google Scholar]
  23. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article]
    [Google Scholar]
  24. 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]
    [Google Scholar]
  25. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article]
    [Google Scholar]
  26. Luo R, Liu B, Xie Y, Li Z, Huang W et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 2012; 1:18 [View Article]
    [Google Scholar]
  27. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016; 32:929–931 [View Article]
    [Google Scholar]
  28. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60–73 [View Article]
    [Google Scholar]
  29. 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]
    [Google Scholar]
  30. 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]
  31. Hasegawa T, Takizawa M, Tanida S. A rapid analysis for chemical grouping of aerobic actinomycetes. J Gen Appl Microbiol 1983; 29:319–322 [View Article]
    [Google Scholar]
  32. Groth I, Schumann P, Weiss N, Martin K, Rainey FA. Agrococcus jenensis gen. nov., sp. nov., a new genus of actinomycetes with diaminobutyric acid in the cell wall. Int J Syst Bacteriol 1996; 46:234–239 [View Article]
    [Google Scholar]
  33. 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 [View Article]
    [Google Scholar]
  34. Collins MD, Jones D. Lipids in the classification and identification of coryneform bacteria containing peptidoglycans based on 2, 4-diaminobutyric acid. J Appl Bacteriol 1980; 48:459–470 [View Article]
    [Google Scholar]
  35. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. USFCC Newsl 1990; 20:16
    [Google Scholar]
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