Virgibacillus litoralis sp. nov., a moderately halophilic bacterium isolated from saline soil

Abstract

A Gram-positive, moderately halophilic, endospore-forming, catalase- and oxidase-positive, motile, rod-shaped, aerobic bacterium, designated strain JSM 089168T, was isolated from saline soil collected from Naozhou Island, Leizhou Bay, South China Sea. The organism was able to grow with 2–25% (w/v) total salts (optimum, 5–10%), at pH 6.0–10.0 (optimum, pH 8.0) and 10–45°C (optimum, 30°C). meso-Diaminopimelic acid was present in the cell-wall peptidoglycan. The strain contained MK-7 as the predominant menaquinone, and diphosphatidylglycerol and phosphatidylglycerol as the major polar lipids. The major cellular fatty acids were anteiso-C15:0, iso-C15:0 and anteiso-C17:0, and the DNA G + C content was 40.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain JSM 089168T should be assigned to the genus Virgibacillus, being related most closely to the type strains of Virgibacillus carmonensis (sequence similarity 97.6%), Virgibacillus necropolis (97.3%) and Virgibacillus halodenitrificans (97.1%). Levels of DNA–DNA relatedness between strain JSM 089168T and the type strains of V. carmonensis, V. necropolis and V. halodenitrificans were 20.4, 14.3 and 12.0%, respectively. The combination of phylogenetic analysis, DNA–DNA relatedness, phenotypic characteristics and chemotaxonomic data supported the view that strain JSM 089168T represents a novel species of the genus Virgibacillus, for which the name Virgibacillus litoralis sp. nov. is proposed. The type strain is JSM 089168T (=DSM 21085T =KCTC 13228T).

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References

  1. An SY, Asahara M, Goto K, Kasai H, Yokota A (2007) Virgibacillus halophilus sp. nov., spore-forming bacteria isolated from soil in Japan. Int J Syst Evol Microbiol 57:1607–1611. doi:10.1099/ijs.0.64307-0

    PubMed  Article  Google Scholar 

  2. Atlas RM, Parks LC (1993) Handbook of microbiological media. CRC Press, Boca Raton, pp 542–544

    Google Scholar 

  3. Chen YG, Cui XL, Pukall R, Li HM, Yang YL, Xu LH, Wen ML, Peng Q, Jiang CL (2007) Salinicoccus kunmingensis sp. nov., a moderately halophilic bacterium isolated from a salt mine in Yunnan, south-west China. Int J Syst Evol Microbiol 57:2327–2332. doi:10.1099/ijs.0.64783-0

    PubMed  Article  CAS  Google Scholar 

  4. Chen YG, Cui XL, Fritze D, Chai LH, Schumann P, Wen ML, Wang YX, Xu LH, Jiang CL (2008) Virgibacillus kekensis sp. nov., a moderately halophilic bacterium isolated from a salt lake in China. Int J Syst Evol Microbiol 58:647–653. doi:10.1099/ijs.0.65365-0

    PubMed  Article  CAS  Google Scholar 

  5. Chen YG, Zhang YQ, Huang K, Tang SK, Cao Y, Shi JX, Xiao HD, Cui XL, Li WJ (2009) Pigmentiphaga litoralis sp. nov., a facultatively anaerobic bacterium isolated from tidal flat sediment. Int J Syst Evol Microbiol 59:521–525. doi:10.1099/ijs.0.002949-0

    PubMed  Article  CAS  Google Scholar 

  6. Chun J, Lee JH, Jung Y, Kim M, Kim S, Kim BK, Lim YW (2007) EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. Int J Syst Evol Microbiol 57:2259–2261. doi:10.1099/ijs.0.64915-0

    PubMed  Article  CAS  Google Scholar 

  7. Collins MD, Pirouz T, Goodfellow M, Minnikin DE (1977) Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 100:221–230

    PubMed  CAS  Google Scholar 

  8. Cowan ST, Steel KJ (1965) Manual for the identification of medical bacteria. Cambridge University Press, London

    Google Scholar 

  9. Cui XL, Mao PH, Zeng M, Li WJ, Zhang LP, Xu LH, Jiang CL (2001) Streptomonospora salina gen, nov., sp. nov., a new member of the family Nocardiopsaceae. Int J Syst Evol Microbiol 51:357–363

    PubMed  CAS  Google Scholar 

  10. Doetsch RN (1981) Determinative methods of light microscopy. In: Gerhardt P, Murray RGE, Costilow RN, Nester EW, Wood WA, Krieg NR, Phillips GH (eds) Manual of methods for general bacteriology. American Society for Microbiology, Washington, DC, pp 21–33

    Google Scholar 

  11. Ezaki T, Hashimoto Y, Yabuuchi E (1989) 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 39:224–229

    Google Scholar 

  12. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evol Int J Org Evol 39:783–791. doi:10.2307/2408678

    Google Scholar 

  13. Felsenstein J (1997) An alternative least-squares approach to inferring phylogenies from pairwise distances. Syst Biol 46:101–111. doi:10.2307/2413638

    PubMed  CAS  Google Scholar 

  14. Gregersen T (1978) Rapid method for distinction of Gram-negative from Gram-positive bacteria. Eur J Appl Microbiol Biotechnol 5:123–127. doi:10.1007/BF00498806

    Article  Google Scholar 

  15. Hasegawa T, Takizawa M, Tanida S (1983) A rapid analysis for chemical grouping of aerobic actinomycetes. J Gen Appl Microbiol 29:319–322. doi:10.2323/jgam.29.319

    Article  CAS  Google Scholar 

  16. Heyndrickx M, Lebbe L, Kersters K, De Vos P, Forsyth G, Logan NA (1998) Virgibacillus: a new genus to accommodate Bacillus pantothenticus (Proom, Knight 1950) Emended description of Virgibacillus pantothenticus. Int J Syst Bacteriol 48:99–106

    Google Scholar 

  17. Heyndrickx M, Lebbe L, Kersters K, Hoste B, De Wachter R, De Vos P, Forsyth G, Logan NA (1999) Proposal of Virgibacillus proomii sp. nov. and emended description of Virgibacillus pantothenticus (Proom and Knight 1950) Heyndrickx et al. 1998. Int J Syst Bacteriol 49:1083–1090

    PubMed  CAS  Article  Google Scholar 

  18. Heyrman J, Logan NA, Busse HJ, Balcaen A, Lebbe L, Rodriguez-Diaz M, Swings J, De Vos P (2003) 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 53:501–511. doi:10.1099/ijs.0.02371-0

    PubMed  Article  CAS  Google Scholar 

  19. Hopwood DA, Bibb MJ, Chater KF, Kieser T, Bruton CJ, Kieser HM, Lydiate DJ, Smith CP, Ward JM (1985) Preparation of chromosomal, plasmid and phage DNA. In: Hopwood DA, Bibb MJ, Chater KF, Kieser T, Bruton CJ, Kieser HM, Lydiate DJ, Smith CP, Ward JM, Schrempf H (eds) Genetic manipulation of Streptomyces: a laboratory manual. F. Crowe and Sons, Norwich, pp 79–80

    Google Scholar 

  20. Hua NP, Hamza-Chaffai A, Vreeland RH, Isoda H, Naganuma T (2008) Virgibacillus salarius sp. nov., a halophilic bacterium isolated from a Saharan salt lake. Int J Syst Evol Microbiol 58:2409–2414. doi:10.1099/ijs.0.65693-0

    PubMed  Article  CAS  Google Scholar 

  21. Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120. doi:10.1007/BF01731581

    PubMed  Article  CAS  Google Scholar 

  22. Kluge AG, Farris FS (1969) Quantitative phyletics and the evolution of anurans. Syst Zool 18:1–32. doi:10.2307/2412407

    Article  Google Scholar 

  23. Komagata K, Suzuki K (1987) Lipid and cell wall analysis in bacterial systematics. Methods Microbiol 19:161–203

    Article  CAS  Google Scholar 

  24. Lee JS, Lim JM, Lee KC, Lee JC, Park YH, Kim CJ (2006) Virgibacillus koreensis sp. nov., a novel bacterium from salt field, and transfer of Virgibacillus picturae to the genus Oceanobacillus as Oceanobacillus picturae comb. nov. with emended descriptions. Int J Syst Evol Microbiol 56:251–257. doi:10.1099/ijs.0.63734-0

    PubMed  Article  CAS  Google Scholar 

  25. Mesbah M, Premachandran U, Whitman WB (1989) Precise measurement of the G + C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 39:159–167

    CAS  Google Scholar 

  26. Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M, Schaal A, Parlett JH (1984) An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2:233–241. doi:10.1016/0167-7012(84)90018-6

    Article  CAS  Google Scholar 

  27. Quesada T, Aguilera M, Morillo JA, Ramos-Cormenzana A, Monteoliva-Sánchez M (2007) Virgibacillus olivae sp. nov., isolated from waste wash-water from processing of Spanish-style green olives. Int J Syst Evol Microbiol 57:906–910. doi:10.1099/ijs.0.64550-0

    PubMed  Article  CAS  Google Scholar 

  28. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

    PubMed  CAS  Google Scholar 

  29. Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Technical Note 101. MIDI Inc., Newark

    Google Scholar 

  30. Smibert RM, Krieg NR (1994) Phenotypic characterization. In: Gerhardt P, Murray RGE, Wood WA, Krieg NR (eds) Methods for general and molecular bacteriology. American Society for Microbiology, Washington, DC, pp 607–654

    Google Scholar 

  31. Tamaoka J, Katayama-Fujimura Y, Kuraishi H (1983) Analysis of bacterial menaquinone mixtures by high performance liquid chromatography. J Appl Bacteriol 54:31–36

    CAS  Google Scholar 

  32. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetic analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599. doi:10.1093/molbev/msm092

    Google Scholar 

  33. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882. doi:10.1093/nar/25.24.4876

    PubMed  Article  CAS  Google Scholar 

  34. Ventosa A, Quesada E, Rodriguez-Valera F, Ruiz-Berraquero F, Ramos-Cormenzana A (1982) Numerical taxonomy of moderately halophilic Gram-negative rods. J Gen Microbiol 128:1959–1968

    Google Scholar 

  35. Wang CY, Chang CC, Ng CC, Chen TW, Shyu YT (2008) Virgibacillus chiguensis sp. nov., a novel halophilic bacterium isolated from Chigu, a previously commercial saltern located in southern Taiwan. Int J Syst Evol Microbiol 58:341–345. doi:10.1099/ijs.0.64996-0

    PubMed  Article  CAS  Google Scholar 

  36. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, Moore LH, Moore WEC, Murray RGE (1987) International committee on systematic bacteriology, Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464 other authors

    Google Scholar 

  37. Xiao HD, Chen YG, Liu ZX, Huang K, Li WJ, Cui XL, Zhang L, Yi LB (2009) Phylogenetic diversity of cultivable bacteria associated with a sea anemone from coast of the Naozhou Island in Zhanjiang, China. Acta Microbiol Sin 49:246–250

    CAS  Google Scholar 

  38. Yoon JH, Oh TK, Park YH (2004) Transfer of Bacillus halodenitrificans Denariaz et al. 1989 to the genus Virgibacillus as Virgibacillus halodenitrificans comb. nov. Int J Syst Evol Microbiol 54:2163–2167. doi:10.1099/ijs.0.63196-0

    PubMed  Article  CAS  Google Scholar 

  39. Yoon JH, Kang SJ, Lee SY, Lee MH, Oh TK (2005) 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 55:1833–1837. doi:10.1099/ijs.0.63613-0

    PubMed  Article  CAS  Google Scholar 

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Acknowledgements

This study was supported by grants from the National Natural Science Foundation of China (NSFC; 30860002, 30860013), Jishou University (jsdxkyzz200811), the Ministry of Science and Technology, PR China (2006BAE01A01-9, 863 Program 2007AA021306), The Key Projects of International Cooperation (2007DFB31620) and Yunnan University (2008YB005). We are grateful to Mr Huai-Dong Xiao and Mr Ke Huang for their excellent technical assistance.

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Correspondence to Yan-Qi Liu.

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The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain JSM 089168T is FJ425909.

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Chen, YG., Liu, ZX., Peng, DJ. et al. Virgibacillus litoralis sp. nov., a moderately halophilic bacterium isolated from saline soil. Antonie van Leeuwenhoek 96, 323–329 (2009). https://doi.org/10.1007/s10482-009-9349-0

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Keywords

  • Virgibacillus litoralis sp. nov
  • Halophile
  • South China Sea
  • Naozhou Island