1887

Abstract

A novel Gram-stain-positive, facultatively aerobic, slightly halophilic, endospore-forming bacterium, designated G6-18, was isolated from saline soil collected in Yingkou, Liaoning, PR China. Cells of strain G6-18 grew at 10–37 °C (optimum, 30 °C), at pH 6.0–9.0 (optimum, pH 8.0) and in the presence of 2–15 % (w/v) NaCl (optimum, 5 %). The strain could be clearly distinguished from the related species of the genus by its phylogenetic position and biochemical characteristics. It presented MK-7 as the major quinone and the dominant cellular fatty acids were iso-C, anteiso-C, C and iso-C. The polar lipids consisted of diphosphatidylglycerol and phosphatidylglycerol as the major components. The G+C content of strain G6-18 genome was 35.3 mol%. 16S rRNA analysis showed that strain G6-18 had the highest similarity to DSM 15140, reaching 97.0 %, followed by CGMCC 1.6333 with a value of 96.3 %. The average nucleotide identity values between strain G6-18 and DSM 15140, KCTC 33762, CGMCC 1.6333 and DSM 107811 were 74.3, 72.0, 73.2 and 72.8 %, respectively, and the digital DNA–DNA hybridization values between strain G6-18 and the neighbouring strains were 15.6, 13.8, 14.2 and 14.2 %, respectively. Based on phenotypic, chemotaxonomic and phylogenetic inferences, strain G6-18 represents a novel species of the genus , for which the name sp. nov. (=CGMCC 1.12058=DSM 25428) is proposed.

Funding
This study was supported by the:
  • State Key Laboratory of Oil and Gas Reservoir Geology and Exploitation (Award 2016E-1205)
    • Principle Award Recipient: LeiWang
  • National Major Science and Technology Projects of China (Award 2016ZX05040-002)
    • Principle Award Recipient: LeiWang
  • National Natural Science Foundation of China (Award Grant No. 41977198)
    • Principle Award Recipient: LeiWang
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2021-07-07
2024-05-14
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References

  1. Ishikawa M, Ishizaki S, Yamamoto Y, Yamasato K. Paraliobacillus ryukyuensis gen. nov., sp. nov., a new Gram-positive, slightly halophilic, extremely halotolerant, facultative anaerobe isolated from a decomposing marine alga. J Gen Appl Microbiol 2002; 48:269–279 [View Article] [PubMed]
    [Google Scholar]
  2. Wang X, Yang J, Lu S, Lai XH, Jin D et al. Paraliobacillus zengyii sp. nov., a slightly halophilic and extremely halotolerant bacterium isolated from Tibetan antelope faeces. Int J Syst Evol Microbiol 2019; 69:1426–1432 [View Article] [PubMed]
    [Google Scholar]
  3. Chen Y-G, Cui X-L, Zhang Y-Q, Li W-J, Wang Y-X et al. Paraliobacillus quinghaiensis sp. nov., isolated from salt-lake sediment in China. Int J Syst Evol Microbiol 2009; 59:28–33 [View Article]
    [Google Scholar]
  4. Cao W-R, Guo L-Y, Du Z-J, Das A, Saren G et al. Paraliobacillus sediminis sp. nov., isolated from East China sea sediment. Int J Syst Evol Microbiol 2017; 67:1577–1581 [View Article]
    [Google Scholar]
  5. Euzeby J. Validation of publication of new names and new combinations previously effectively published outside the IJSEM. Int J Syst Evol Microbiol 2005; 55:1743–1745 [View Article] [PubMed]
    [Google Scholar]
  6. Xu D, Huang J, Zhang J, Fan Q, Liu D. A new species of Halomonas-Halomonas huanghaiensis sp. nov. Wei Sheng Wu Xue Bao 1995; 35:315–321
    [Google Scholar]
  7. Cui XL, Mao PH, Zeng M, Li WJ, Zhang LP 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]
  8. Yoon S-H, Ha S-M, 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]
  9. Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics 2008; 24:713–714 [View Article] [PubMed]
    [Google Scholar]
  10. 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]
  11. Besemer J, Lomsadze A, Borodovsky M. GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res 2001; 29:2607–2618 [View Article] [PubMed]
    [Google Scholar]
  12. Lee I, Ouk Kim Y, Park SC, Chun J. OrthoANI: An improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [View Article] [PubMed]
    [Google Scholar]
  13. Auch AF, Klenk HP, Goker M. Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs. Stand Genomic Sci 2010; 2:142–148 [View Article] [PubMed]
    [Google Scholar]
  14. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007; 23:2947–2948 [View Article] [PubMed]
    [Google Scholar]
  15. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [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. 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]
  18. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article] [PubMed]
    [Google Scholar]
  19. Na S-I, Kim YO, Yoon S-H, Ha S-M, Baek I et al. UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018; 56:280–285
    [Google Scholar]
  20. Saier MH, Reddy VS, Moreno-Hagelsieb G, Hendargo KJ, Zhang Y et al. The transporter classification database (TCDB): 2021 update. Nucleic Acids Res 2021; 49:D461–D467 [View Article] [PubMed]
    [Google Scholar]
  21. Buchfink B, Xie C, Huson DH. Fast and sensitive protein alignment using DIAMOND. Nat Methods 2015; 12:59–60 [View Article] [PubMed]
    [Google Scholar]
  22. Goldberg EB, Arbel T, Chen J, Karpel R, Mackie GA et al. Characterization of a Na+/H+ antiporter gene of Escherichia coli. Proc Natl Acad Sci U S A 1987; 84:2615–2619 [View Article] [PubMed]
    [Google Scholar]
  23. Pinner E, Kotler Y, Padan E, Schuldiner S. Physiological role of NhaB, a specific Na+/H+ antiporter in Escherichia coli. J Biol Chem 1993; 268:1729–1734 [View Article] [PubMed]
    [Google Scholar]
  24. Ivey M, Guffanti A, Zemsky J, Pinner E, Karpel R et al. Cloning and characterization of a putative Ca2+/H+ antiporter gene from Escherichia coli upon functional complementation of Na+/H+ antiporter-deficient strains by the overexpressed gene. J Biol Chem 1993; 268:11296–11303 [View Article] [PubMed]
    [Google Scholar]
  25. Ivey M, Guffanti A, Bossewitch J, Padan E, Krulwich T. Molecular cloning and sequencing of a gene from alkaliphilic Bacillus firmus OF4 that functionally complements an Escherichia coli strain carrying a deletion in the nhaA Na+/H+ antiporter gene. J Biol Chem 1992; 266:23483–23489 [View Article]
    [Google Scholar]
  26. Waser M, Hess-Bienz D, Davies K, Solioz M. Cloning and disruption of a putative Na+/H+ antiporter gene of Enterococcus hirae. J Biol Chem 1992; 267:5396–5400 [View Article] [PubMed]
    [Google Scholar]
  27. Cheng J, Hicks DB, Krulwich TA. The purified Bacillus subtilis tetracycline efflux protein TetA(L) reconstitutes both tetracycline-cobalt/H+ and Na+(K+)/H+ exchange. Proc Natl Acad Sci U S A 1996; 93:14446–14451 [View Article] [PubMed]
    [Google Scholar]
  28. Hamamoto T, Hashimoto M, Hino M, Kitada M, Seto Y et al. Characterization of a gene responsible for the Na+/H+ antiporter system of alkalophilic Bacillus species strain C-125. Mol Microbiol 1994; 14:939–946 [View Article] [PubMed]
    [Google Scholar]
  29. Krulwich TA. Alkaliphiles: “basic” molecular problems of pH tolerance and bioenergetics. Mol Microbiol 1995; 15:403–410 [View Article] [PubMed]
    [Google Scholar]
  30. Padan E, Schuldiner S. Na+/H+ antiporters, molecular devices that couple the Na+ and H+ circulation in cells. J Bioenerg Biomembr 1993; 25:647–669 [View Article] [PubMed]
    [Google Scholar]
  31. Ito M, Guffanti AA, Zemsky J, Ivey DM, Krulwich TA. Role of the nhaC-encoded Na+/H+ antiporter of alkaliphilic Bacillus firmus OF4. J Bacteriol 1997; 179:3851–3857 [View Article] [PubMed]
    [Google Scholar]
  32. Ming H, Nie GX, Jiang HC, TT Y, Zhou EM et al. Paenibacillus frigoriresistens sp. nov., a novel psychrotroph isolated from a peat bog in Heilongjiang, Northern China. Antonie van Leeuwenhoek 2012; 102:297–305 [View Article]
    [Google Scholar]
  33. Smibert RM, Krieg NR. Phenotypic characterization. In Methods for General and Molecular Bacteriology American Society For Microbiology; 1994 pp 611–651
    [Google Scholar]
  34. Leifson E. An atlas of bacterial flagellation. Am J Med Sci 1961; 242:267 [View Article]
    [Google Scholar]
  35. Xu P, Li W-J, Tang S-K, Zhang Y-Q, Chen G-Z 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 [View Article]
    [Google Scholar]
  36. Kovacs N. Identification of Pseudomonas pyocyanea by the oxidase reaction. Nature 1956; 178:703 [View Article] [PubMed]
    [Google Scholar]
  37. Chen L, Chen WF, Xu Z-L, Li W, Zhang XY et al. Sphingomonas oleivorans sp. nov., isolated from oil-contaminated soil. Int J Syst Evol Microbiol 2018; 68:3720–3725 [View Article]
    [Google Scholar]
  38. Sasser M, Kunitsky C, Jackoway G, Ezzell JW, Teska JD et al. Identification of Bacillus anthracis from culture using gas chromatographic analysis of fatty acid methyl esters. J AOAC Int 2005; 88:178–181 [View Article] [PubMed]
    [Google Scholar]
  39. Collins MD, Jones D, Goodfellow M, Minnikin DE. Isoprenoid quinone composition as a guide to the classification of Listeria, Brochothrix, Erysipelothrix and Caryophanon. J Gen Microbiol 1979; 111:453–457 [View Article] [PubMed]
    [Google Scholar]
  40. Minnikin D, O’Donnell A, 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]
  41. Komagata K, Susuki K. Lipid and cell-wall systematics in bacterial systematics. Methods Microbiol 1987; 19:161–207
    [Google Scholar]
  42. Kumar S. A stepwise algorithm for finding minimum evolution trees. Mol Biol Evol 1996; 13:584–593 [View Article] [PubMed]
    [Google Scholar]
  43. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
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