1887

Abstract

Three Gram-variable, moderately halophilic, motile, endospore-forming rods, designated P2-C2, P3-H5 and P3-B8, were isolated from marine sediment of the Southwest Indian Ocean by using the microfluidic streak plate method. Phylogeny based on 16S rRNA gene sequences showed that strains P2-C2 and P3-H5 formed a robust cluster within the genus and exhibited 16S rRNA gene similarity levels of 95.3–96.8 and 94.9–96.3 % to the type strains of species, respectively. The 16S rRNA gene similarity between P2-C2 and P3-H5 was 97.6 %. Strain P3-B8 has an identical 16S rRNA gene sequence to strain P3-H5. For all the novel strains, the predominant cellular fatty acids were -C and -C, the main menaquinone was MK-7, and the polar lipid profiles contained diphosphatidylglycerol and phosphatidylglycerol. The genomic DNA G+C contents of strains P2-C2, P3-H5 and P3-B8 were 38.3, 37.3 and 37.5 mol%, respectively. Combined data from phenotypic and genotypic studies demonstrated that strains P2-C2 and P3-H5/P3-B8 are representatives of two different novel species of the genus , for which the name sp. nov. and are proposed. The type strains are P2-C2 (=CGMCC 1.16138=NBRC 113014) and P3-H5 (=CGMCC 1.16139=NBRC 113015).

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2018-06-01
2024-11-03
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References

  1. Rappé MS, Giovannoni SJ. The uncultured microbial majority. Annu Rev Microbiol 2003; 57:369–394 [View Article][PubMed]
    [Google Scholar]
  2. Lok C. Mining the microbial dark matter. Nature 2015; 522:270–273 [View Article][PubMed]
    [Google Scholar]
  3. Dong L, Chen DW, Liu SJ, Du W. Automated chemotactic sorting and single-cell cultivation of microbes using droplet microfluidics. Sci Rep 2016; 6:24192 [View Article][PubMed]
    [Google Scholar]
  4. Jiang CY, Dong L, Zhao JK, Hu X, Shen C et al. High-throughput single-cell cultivation on microfluidic streak plates. Appl Environ Microbiol 2016; 82:2210–2218 [View Article][PubMed]
    [Google Scholar]
  5. Proom H, Knight BC. Bacillus pantothenticus (n.sp.). J Gen Microbiol 1950; 4:539–541 [View Article][PubMed]
    [Google Scholar]
  6. Heyndrickx M, Lebbe L, Kersters K, De Vos P, Forsyth G et al. Virgibacillus: a new genus to accommodate Bacillus pantothenticus (Proom and Knight 1950). Emended description of Virgibacillus pantothenticus . Int J Syst Bacteriol 1998; 48:99–106 [View Article]
    [Google Scholar]
  7. Wainø M, Tindall BJ, Schumann P, Ingvorsen K. Gracilibacillus gen. nov., with description of Gracilibacillus halotolerans gen. nov., sp. nov.; transfer of Bacillus dipsosauri to Gracilibacillus dipsosauri comb. nov., and Bacillus salexigens to the genus Salibacillus gen. nov., as Salibacillus salexigens comb. nov. Int J Syst Bacteriol 1999; 49:821–831 [View Article][PubMed]
    [Google Scholar]
  8. Heyrman J, Logan NA, Busse HJ, Balcaen A, Lebbe L et al. Virgibacillus carmonensis sp. nov., Virgibacillus necropolis sp. nov. and Virgibacillus picturae sp. nov., three novel species isolated from deteriorated mural paintings, transfer of the species of the genus Salibacillus to Virgibacillus, as Virgibacillus marismortui comb. nov. and Virgibacillus salexigens comb. nov., and emended description of the genus Virgibacillus . Int J Syst Evol Microbiol 2003; 53:501–511 [View Article][PubMed]
    [Google Scholar]
  9. Zhang DC, Schumann P, Wu J, Franca L, Neuner K et al. Virgibacillus flavescens sp. nov. isolated from sediment of the Yellow Sea in China. Int J Syst Evol Microbiol 2016; 66:1138–1143 [Crossref]
    [Google Scholar]
  10. Daroonpunt R, Tanasupawat S, Kudo T, Ohkuma M, Itoh T. Virgibacillus kapii sp. nov., isolated from Thai shrimp paste (Ka-pi). Int J Syst Evol Microbiol 2016; 66:1832–1837 [View Article][PubMed]
    [Google Scholar]
  11. Amziane M, Metiaz F, Darenfed-Bouanane A, Djenane Z, Selama O et al. Virgibacillus natechei sp. nov., a moderately halophilic bacterium isolated from sediment of a saline lake in southwest of Algeria. Curr Microbiol 2013; 66:462–466 [View Article][PubMed]
    [Google Scholar]
  12. Yin X, Yang Y, Wang S, Zhang G. Virgibacillus oceani sp. nov. isolated from ocean sediment. Int J Syst Evol Microbiol 2015; 65:159–164 [View Article][PubMed]
    [Google Scholar]
  13. Sundararaman A, Srinivasan S, Lee JH, Lee SS. Virgibacillus jeotgali sp. nov., isolated from Myeolchi-jeotgal, a traditional Korean high-salt-fermented anchovy. Int J Syst Evol Microbiol 2016; 67:158–163 [View Article][PubMed]
    [Google Scholar]
  14. Amziane M, Darenfed-Bouanane A, Abderrahmani A, Selama O, Jouadi L et al. Virgibacillus ainsalahensis sp. nov., a moderately halophilic bacterium isolated from sediment of a saline lake in South of Algeria. Curr Microbiol 2017; 74:219–223 [View Article][PubMed]
    [Google Scholar]
  15. Niederberger TD, Steven B, Charvet S, Barbier B, Whyte LG. Virgibacillus arcticus sp. nov., a moderately halophilic, endospore-forming bacterium from permafrost in the Canadian high Arctic. Int J Syst Evol Microbiol 2009; 59:2219–2225 [View Article][PubMed]
    [Google Scholar]
  16. Carrasco IJ, Márquez MC, Ventosa A. Virgibacillus salinus sp. nov., a moderately halophilic bacterium from sediment of a saline lake. Int J Syst Evol Microbiol 2009; 59:3068–3073 [View Article][PubMed]
    [Google Scholar]
  17. Kämpfer P, Arun AB, Busse HJ, Langer S, Young CC et al. Virgibacillus soli sp. nov., isolated from mountain soil. Int J Syst Evol Microbiol 2011; 61:275–280 [View Article][PubMed]
    [Google Scholar]
  18. Lee SY, Kang CH, Oh TK, Yoon JH. Virgibacillus campisalis sp. nov., from a marine solar saltern. Int J Syst Evol Microbiol 2012; 62:347–351 [View Article][PubMed]
    [Google Scholar]
  19. Hopkins DW, Macnaughton SJ, O'Donnell AG. A dispersion and differential centrifugation technique for representatively sampling microorganisms from soil. Soil Biol Biochem 1991; 23:217–225 [View Article]
    [Google Scholar]
  20. Denariaz G, Payne WJ, Le Gall J. A halophilic denitrifier, Bacillus halodenitrificans sp. nov. Int J Syst Bacteriol 1989; 39:145–151 [View Article]
    [Google Scholar]
  21. Yoon JH, Oh TK, Park YH. Transfer of Bacillus halodenitrificans Denariaz et al. 1989 to the genus Virgibacillus as Virgibacillus halodenitrificans comb. nov. Int J Syst Evol Microbiol 2004; 54:2163–2167 [View Article][PubMed]
    [Google Scholar]
  22. Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics 2008; 24:713–714 [View Article][PubMed]
    [Google Scholar]
  23. Angiuoli SV, Gussman A, Klimke W, Cochrane G, Field D et al. Toward an online repository of Standard Operating Procedures (SOPs) for (meta)genomic annotation. OMICS 2008; 12:137–141 [View Article][PubMed]
    [Google Scholar]
  24. 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][PubMed]
    [Google Scholar]
  25. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article][PubMed]
    [Google Scholar]
  26. 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][PubMed]
    [Google Scholar]
  27. Talavera G, Castresana J. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol 2007; 56:564–577 [View Article][PubMed]
    [Google Scholar]
  28. 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]
  29. Kluge AG, Farris JS. Quantitative phyletics and the evolution of anurans. Syst Zool 1969; 18:1–32 [View Article]
    [Google Scholar]
  30. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  31. Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W et al. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 2010; 59:307–321 [View Article][PubMed]
    [Google Scholar]
  32. 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 [View Article][PubMed]
    [Google Scholar]
  33. 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][PubMed]
    [Google Scholar]
  34. Kim M, Oh HS, Park SC, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [View Article][PubMed]
    [Google Scholar]
  35. Gordon RE, Barnett DA, Handerhan JE, Pang CHN. Nocardia coeliaca, Nocardia autotrophica, and the nocardin strain. Int J Syst Bacteriol 1974; 24:54–63 [View Article]
    [Google Scholar]
  36. Williams ST, Goodfellow M, Alderson G, Wellington EM, Sneath PH et al. Numerical classification of Streptomyces and related genera. J Gen Microbiol 1983; 129:1743–1813 [View Article][PubMed]
    [Google Scholar]
  37. Lányi B. Classical and rapid identification methods for medically important bacteria. Methods Microbiol 1988; 19:1–67 [Crossref]
    [Google Scholar]
  38. Lechevalier MP, Lechevalier H. Chemical composition as a criterion in the classification of aerobic actinomycetes. Int J Syst Bacteriol 1970; 20:435–443 [View Article]
    [Google Scholar]
  39. 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]
  40. Tang SK, Wang Y, Chen Y, Lou K, Cao LL et al. Zhihengliuella alba sp. nov., and emended description of the genus Zhihengliuella . Int J Syst Evol Microbiol 2009; 59:2025–2031 [View Article][PubMed]
    [Google Scholar]
  41. Collins MD, Goodfellow M, Minnikin DE. Isoprenoid quinones in the classification of coryneform and related bacteria. J Gen Microbiol 1979; 110:127–136 [View Article][PubMed]
    [Google Scholar]
  42. Kroppenstedt RM. Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded ion exchanger as stationary phases. J Liq Chromatogr 1982; 5:2359–2367 [View Article]
    [Google Scholar]
  43. 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]
  44. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, Technical Note 101. Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  45. Hua NP, Hamza-Chaffai A, Vreeland RH, Isoda H, Naganuma T. Virgibacillus salarius sp. nov., a halophilic bacterium isolated from a Saharan salt lake. Int J Syst Evol Microbiol 2008; 58:2409–2414 [View Article][PubMed]
    [Google Scholar]
  46. Yoon JH, Kang SJ, Lee SY, Lee MH, Oh TK. Virgibacillus dokdonensis sp. nov., isolated from a Korean island, Dokdo, located at the edge of the East Sea in Korea. Int J Syst Evol Microbiol 2005; 55:1833–1837 [View Article][PubMed]
    [Google Scholar]
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