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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo International Journal of Systematic and Evolutionary Microbiology

Volume 60, Issue 12

sp. nov., isolated from marine sediment Free

Abstract

A Gram-stain-positive, spore-forming, rod-shaped and aerobic bacterium was isolated from a sediment sample from the South Sea in China. The isolate, designated H2, grew at 4–45 °C (optimum 37 °C) and pH 6–10 (optimum pH 7.0). The cell-wall peptidoglycan contained -diaminopimelic acid. The major isoprenoid quinone was MK-7 and the polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unknown aminophospholipid. The major fatty acid was iso-C. The genomic DNA G+C content of strain H2 was 44.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate formed a monophyletic clade with IAM 12464. DNA–DNA relatedness between the isolate and ATCC 14575 was low (27.5 %). Strain H2 also had a phenotypic profile that readily distinguished it from its closest phylogenetic neighbours. It is evident from the combination of genotypic and phenotypic data that the organism should be classified in a novel species of the genus , for which the name sp. nov. is proposed. The type strain is H2 (=CGMCC 1.10115 =JCM 16506).

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2010-12-01
2025-07-20
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References

  1. Albert R. A., Archambault J., Rosselló-Mora R., Tindall B. J., Matheny M. 2005; Bacillus acidicola sp. nov., a novel mesophilic, acidophilic species isolated from acidic Sphagnum peat bogs in Wisconsin. Int J Syst Evol Microbiol 55:2125–2130 [CrossRef]
     [Google Scholar]
  2. Albert R. A., Archambault J., Lempa M., Hurst B., Richardson C., Gruenloh S., Duran M., Worliczek H. L., Huber B. E. other authors 2007; Proposal of Viridibacillus gen. nov. and reclassification of Bacillus arvi , Bacillus arenosi and Bacillus neidei as Viridibacillus arvi gen.nov., comb. nov., Viridibacillus arenosi comb. nov. and Viridibacillus neidei comb. nov. Int J Syst Evol Microbiol 57:2729–2737 [CrossRef]
     [Google Scholar]
  3. Ash C., Farrow J. A. E., Wallbanks S., Collins M. D. 1991; Phylogenetic heterogeneity of the genus Bacillus revealed by comparative analysis of small-subunit-ribosomal RNA sequences. Lett Appl Microbiol 13:202–206
     [Google Scholar]
  4. Ash C., Priest F. G., Collins M. D. 1993; Molecular identification of rRNA group 3 bacilli (Ash, Farrow, Wallbanks and Collins) using a PCR probe test. Proposal for the creation of a new genus Paenibacillus . Antonie van Leeuwenhoek 64:253–260
     [Google Scholar]
  5. Carrasco I. J., Márquez M. C., Xue Y., Ma Y., Cowan D. A., Jones B. E., Grant W. D., Ventosa A. 2007; Bacillus chagannorensis sp. nov., a moderate halophile from a soda lake in Inner Mongolia, China. Int J Syst Evol Microbiol 57:2084–2088 [CrossRef]
     [Google Scholar]
  6. Collins M. D., Howarth O. W., Grund E., Kroppenstedt R. M. 1987; Isolation and structural determination of new members of the vitamin K2 series in Nocardia brasiliensis . FEMS Microbiol Lett 41:35–39 [CrossRef]
     [Google Scholar]
  7. De Ley J., Cattoir H., Reynaerts A. 1970; The quantitative measurements of DNA hybridization from renaturation rates. Eur J Biochem 12:133–142 [CrossRef]
     [Google Scholar]
  8. Felsenstein J. 1985; Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791 [CrossRef]
     [Google Scholar]
  9. Gerhardt P., Murray R. G. E., Costilow R. N., Nester E. W., Wood W. A., Krieg N. R. Phillips G. B. (editors) 1981 Manual of Methods for General Bacteriology Washington, DC: American Society for Microbiology;
     [Google Scholar]
  10. Goodfellow M., Orchard V. A. 1974; Antibiotic sensitivity of some nocardioform bacteria and its value as a criterion for taxonomy. J Gen Microbiol 83:375–387 [CrossRef]
     [Google Scholar]
  11. Goodfellow M., Stainsby F. M., Davenport R., Chun J., Curtis T. 1998; Activated sludge foaming: the true extent of actinomycete diversity. Water Sci Technol 37:511–519 [CrossRef]
     [Google Scholar]
  12. Gordon R. E., Mihm J. M. 1957; A comparative study of some strains received as nocardiae. J Bacteriol 73:15–27
     [Google Scholar]
  13. Gordon R. E., Haynes W. C., Pang C. H.-N. 1973; The Genus Bacillus US Department of Agriculture Handbook. no. 427 . Washington, DC: Agricultural Research Service;
     [Google Scholar]
  14. Gordon R. E., Barnett D. A., Handerhan J. E., Pang C. H.-N. 1974; Nocardia coeliaca , Nocardia autotrophica , and the nocardin strain. Int J Syst Bacteriol 24:54–63 [CrossRef]
     [Google Scholar]
  15. Gordon R. E., Hyde J. L., Moore J. A. Jr 1977; Bacillus firmus-Bacillus lentus : a series or one species?. Int J Syst Bacteriol 27:256–262 [CrossRef]
     [Google Scholar]
  16. Heyrman J., Vanparys B., Logan N. A., Balcaen A., Rodriguez-Diaz M., Felske A., De Vos P. 2004; Bacillus novalis sp. nov., Bacillus vireti sp. nov., Bacillus soli sp. nov., Bacillus botaviensis sp. nov.and Bacillus drentensis sp. nov., from the Drentse A grasslands. Int J Syst Evol Microbiol 54:47–57 [CrossRef]
     [Google Scholar]
  17. Huß V. A. R., Festl H., Schleifer K. H. 1983; Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. Syst Appl Microbiol 4:184–192 [CrossRef]
     [Google Scholar]
  18. Jahnke K. D. 1992; basic computer program for evaluation of spectroscopic DNA renaturation data from Gilford System 2600 spectrophotometer on a PC/XT/AT type personal computer. J Microbiol Methods 15:61–73 [CrossRef]
     [Google Scholar]
  19. Kämpfer P. 1994; Limits and possibilities of total fatty acid analysis for classification and identification of Bacillus species. Syst Appl Microbiol 17:86–98 [CrossRef]
     [Google Scholar]
  20. Kämpfer P., Kroppenstedt R. M. 1996; Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. Can J Microbiol 42:989–1005 [CrossRef]
     [Google Scholar]
  21. Kämpfer P., Rosselló-Mora R, Falsen E., Busse H.-J., Tindall B. J. 2006; Cohnella thermotolerans gen. nov., sp. nov. and classification of ‘ Paenibacillus hongkongensis ’ as Cohnella hongkongensis sp. nov.. Int J Syst Evol Microbiol 56:781–786 [CrossRef]
     [Google Scholar]
  22. 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 [CrossRef]
     [Google Scholar]
  23. Ko K. S., Oh W. S., Lee M. Y., Lee J. H., Lee H., Peck K. R., Lee N. Y., Song J.-H. 2006; Bacillus infantis sp. nov. and Bacillus idriensis sp. nov., isolated from a patient with neonatal sepsis. Int J Syst Evol Microbiol 56:2541–2544 [CrossRef]
     [Google Scholar]
  24. Kumar S., Tamura K., Nei M. 2004; mega3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5:150–163 [CrossRef]
     [Google Scholar]
  25. Lim J.-M., Jeon C. O., Kim C.-J. 2006a; Bacillus taeanensis sp. nov., a halophilic Gram-positive bacterium from a solar saltern in Korea. Int J Syst Evol Microbiol 56:2903–2908 [CrossRef]
     [Google Scholar]
  26. Lim J.-M., Jeon C. O., Lee S.-M., Lee J.-C., Xu L.-H., Jiang C.-L., Kim C.-J. 2006b; Bacillus salarius sp. nov., a halophilic spore-forming bacterium isolated from a salt lake in China. Int J Syst Evol Microbiol 56:373–377 [CrossRef]
     [Google Scholar]
  27. Lu Z., Liu Z., Wang L., Zhang Y., Qi W., Goodfellow M. 2001; Saccharopolyspora flava sp. nov. and Saccharopolyspora thermophila sp. nov., novel actinomycetes from soil. Int J Syst Evol Microbiol 51:319–325
     [Google Scholar]
  28. Marmur J., Doty P. 1962; Determination of base composition of deoxyribonucleic acid from its denaturation temperature. J Mol Biol 5:109–118 [CrossRef]
     [Google Scholar]
  29. Minnikin D. E., O'Donnell A. G., Goodfellow M., Alderson G., Athalye M., Schaal A., Parlett J. H. 1984; An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2:233–241 [CrossRef]
     [Google Scholar]
  30. Nazina T. N., Tourova T. P., Poltaraus A. B., Novikova E. V., Grigoryan A. A., Ivanova A. E., Lysenko A. M., Petrunyaka V. V., Osipov G. A. other authors 2001; Taxonomic study of aerobic thermophilic bacilli: descriptions of Geobacillus subterraneus gen. nov., sp. nov. and Geobacillus uzenensis sp. nov. from petroleum reservoirs and transfer of Bacillus stearothermophilus , Bacillus thermocatenulatus , Bacillus thermoleovorans , Bacillus kaustophilus , Bacillus thermoglucosidasius and Bacillus thermodenitrificans to Geobacillus as the new combinations G. stearothermophilus , G. thermocatenulatus , G. thermoleovorans , G.kaustophilus , G. thermoglucosidasius and G. thermodenitrificans . Int J Syst Evol Microbiol 51:433–446
     [Google Scholar]
  31. Nielsen P., Rainey F. A., Outtrup H., Priest F. G., Fritze D. 1994; Comparative 16S rDNA sequence analysis of some alkaliphilic bacilli and the establishment of a sixth rRNA group within the genus Bacillus . FEMS Microbiol Lett 117:61–66 [CrossRef]
     [Google Scholar]
  32. Nielsen P., Fritze D., Priest F. G. 1995; Phenetic diversity of alkaliphilic Bacillus strains: proposal for nine new species. Microbiology 141:1745–1761 [CrossRef]
     [Google Scholar]
  33. Priest F. G., Goodfellow M., Todd C. 1988; A numerical classification of the genus Bacillus . J Gen Microbiol 134:1847–1882
     [Google Scholar]
  34. Rainey F. A., Ward-Rainey N., Kroppenstedt R. M., Stackebrandt E. 1996; The genus Nocardiopsis represents a phylogenetically coherent taxon and a distinct actinomycete lineage: proposal of Nocardiopsiaceae fam. nov. Int J Syst Bacteriol 46:1088–1092 [CrossRef]
     [Google Scholar]
  35. Saitou N., Nei M. 1987; The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425
     [Google Scholar]
  36. Sasser M. 1990 Identification of bacteria by gas chromatography of cellular fatty acids , MIDI Technical Note 101 Newark, DE: MIDI Inc;
     [Google Scholar]
  37. Schleifer K. H. 1985; Analysis of the chemical composition and primary structure of murein. Methods Microbiol 18:123–156
     [Google Scholar]
  38. Schlesner H., Lawson P. A., Collins M. D., Weiss N., Wehmeyer U., Völker H., Thomm M. 2001; Filobacillus milensis gen. nov., sp. nov., a new halophilic spore-forming bacterium with Orn-d-Glu-type peptidoglycan. Int J Syst Evol Microbiol 51:425–431
     [Google Scholar]
  39. Shida O., Takagi H., Kadowaki K., Komagata K. 1996; Proposal for two new genera, Brevibacillus gen. nov. and Aneurinibacillus gen. nov. Int J Syst Bacteriol 46:939–946 [CrossRef]
     [Google Scholar]
  40. Smibert R. M., Krieg N. R. 1994; Phenotypic characterization.. In Methods for General and Molecular Bacteriology pp 607–654 Edited by Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R. Washington, DC: American Society for Microbiology;
     [Google Scholar]
  41. Stackebrandt E., Goebel B. M. 1994; Taxonomic note: a place for DNA–DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44:846–849 [CrossRef]
     [Google Scholar]
  42. Stackebrandt E., Liesack W. 1993; Nucleic acids and classification. In Handbook of New Bacterial Systematics pp 152–189 Edited by Goodfellow M., O'Donnell A. G. London: Academic Press;
     [Google Scholar]
  43. Stackebrandt E., Fredericksen W., Garrity G. M., Grimont P. A. D, Kämpfer P., Maiden M. C. J, Nesme X., Rosselló-Mora R, Swings J. other authors 2002; Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 52:1043–1047 [CrossRef]
     [Google Scholar]
  44. Thompson J. D., Gibson T. J., Plewniak F., Jeanmougin F., Higgins D. G. 1997; The clustal_x windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882 [CrossRef]
     [Google Scholar]
  45. Venkateswaran K., Kempf M., Chen F., Satomi M., Nicholson W., Kern R. 2003; Bacillus nealsonii sp. nov., isolated from a spacecraft-assembly facility, whose spores are γ -radiation resistant. Int J Syst Evol Microbiol 53:165–172 [CrossRef]
     [Google Scholar]
  46. Wainø M., Tindall B. J., Schumann P., Ingvorsen K. 1999; 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 49:821–831 [CrossRef]
     [Google Scholar]
  47. Wayne L. G., Brenner D. J., Colwell R. R., Grimont P. A. D., Kandler O., Krichevsky M. I., Moore L. H., Moore W. E. C., Murray R. G. E. other authors 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 [CrossRef]
     [Google Scholar]
  48. Wieser M., Worliczek H., Kämpfer P., Busse H.-J. 2005; Bacillus herbersteinensis sp. nov. Int J Syst Evol Microbiol 55:2119–2123 [CrossRef]
     [Google Scholar]
  49. Wu C., Lu X., Qin M., Wang Y., Ruan J. 1989; ). Analysis of menaquinone compound in microbial cells by HPLC. Microbiology [English translation of Microbiology (Beijing) ] 16:176–178
     [Google Scholar]
  50. Xue Y., Ventosa A., Wang X., Ren P., Zhou P., Ma Y. 2008; Bacillus aidingensis sp. nov., a moderately halophilic bacterium isolated from Ai-Ding salt lake in China. Int J Syst Evol Microbiol 58:2828–2832 [CrossRef]
     [Google Scholar]
  51. Yoon J.-H., Weiss N., Lee K.-C., Lee I.-S., Kang K.-H., Park Y.-H. 2001; Jeotgalibacillus alimentarius gen. nov., sp. nov., a novel bacterium isolated from jeotgal with l-lysine in the cell wall, and reclassification of Bacillus marinus Rüger 1983 as Marinibacillus marinus gen. nov., comb. nov. Int J Syst Evol Microbiol 51:2087–2093 [CrossRef]
     [Google Scholar]
  52. Yoon J.-H., Kim I.-G., Kang K.-H., Oh T.-K., Park Y.-H. 2004; Bacillus hwajinpoensis sp. nov. and an unnamed Bacillus genomospecies, novel members of Bacillus rRNA group 6 isolated from sea water of the East Sea and the Yellow Sea in Korea. Int J Syst Evol Microbiol 54:803–808 [CrossRef]
     [Google Scholar]
  53. Zhang J., Zhang Y., Xiao C., Liu Z., Goodfellow M. 2002; Rhodococcus maanshanensis sp. nov., a novel actinomycete from soil. Int J Syst Evol Microbiol 52:2121–2126 [CrossRef]
     [Google Scholar]
  54. Zhang J., Wu D., Zhang J., Liu Z., Song F. 2008; Saccharopolyspora shandongensis sp. nov., isolated from wheat-field soil. Int J Syst Evol Microbiol 58:1094–1099 [CrossRef]
     [Google Scholar]
  55. Zhang J., Song F., Xin Y.-H., Zhang J., Fang C. 2009; Microvirga guangxiensis sp. nov., a novel alphaproteobacterium from soil, and emended description of the genus Microvirga . Int J Syst Evol Microbiol 59:1997–2001 [CrossRef]
     [Google Scholar]
  56. Zhou Y., Wei W., Chen Q., Xu Y., Wang X., Huang X., Lai R. 2008; Bacillus pallidus sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 58:2850–2854 [CrossRef]
     [Google Scholar]
  57. Zhou Y., Xu J., Xu L., Tindall B. J. 2009; Falsibacillus pallidus to replace the homonym Bacillus pallidus Zhou et al. 2008. Int J Syst Evol Microbiol 59:3176–3180 [CrossRef]
     [Google Scholar]
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Bacillus oceanisediminis sp. nov., isolated from marine sediment
Int J Syst Evol Microbiol 60, 2924 (2010); https://doi.org/10.1099/ijs.0.019851-0
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