1887

Abstract

A Gram-stain-positive, rod-shaped bacterium, designated strain NH3, was isolated from a sediment sample from the South China Sea and was subjected to a polyphasic taxonomic study. The isolate grew optimally at 37 °C and pH 9. Strain NH3 had cell-wall peptidoglycan based on -diaminopimelic acid and MK-7 as the predominant menaquinone. The cellular fatty acid profile included significant amounts of iso-C and iso-C. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The DNA G+C content of strain NH3 was 40.3 mol%. Phylogenetic analysis of the 16S rRNA gene sequence revealed that strain NH3 was a member of rRNA group 6 of the genus , which includes alkalitolerant, alkaliphilic and halotolerant species. The closest phylogenetic relatives were 1139 (96.82 % 16S rRNA gene sequence similarity), DSM 8715 (96.76 %), Kh10-101 (96.76 %) and MS 6 (96.47 %). Strain NH3 could be distinguished from these phylogenetically close neighbours based on a number of phenotypic properties. On the basis of phenotypic and chemotaxonomic characteristics and phylogenetic data, we conclude that strain NH3 ( = CGMCC 1.10116  = JCM 16507) merits classification as the type strain of a novel species, for which the name sp. nov. is proposed.

Funding
This study was supported by the:
  • National Natural Science Foundation of China (NSFC) (Award 30970009)
  • Special Fund for Public Welfare Industrial (Agriculture) Research of China (Award 200903001)
  • Basic Research Foundation of Beijing Institute of Technology (Award 20091642006 and 20081642008)
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.023671-0
2011-05-01
2024-04-25
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/61/5/1078.html?itemId=/content/journal/ijsem/10.1099/ijs.0.023671-0&mimeType=html&fmt=ahah

References

  1. Agnew M. D., Koval S. F., Jarrell K. F. 1995; Isolation and characterization of novel alkaliphiles from bauxite-processing waste and description of Bacillus vedderi sp. nov., a new obligate alkaliphile. Syst Appl Microbiol 18:221–230 [CrossRef]
    [Google Scholar]
  2. 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 [View Article][PubMed]
    [Google Scholar]
  3. Albert R. A., Archambault J., Lempa M., Hurst B., Richardson C., Gruenloh S., Duran M., Worliczek H. L., Huber B. E. et al. 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 [View Article][PubMed]
    [Google Scholar]
  4. Borchert M. S., Nielsen P., Graeber I., Kaesler I., Szewzyk U., Pape T., Antranikian G., Schäfer T. 2007; Bacillus plakortidis sp. nov. and Bacillus murimartini sp. nov., novel alkalitolerant members of rRNA group 6. Int J Syst Evol Microbiol 57:2888–2893 [View Article][PubMed]
    [Google Scholar]
  5. Chun J., Lee J.-H., Jung Y., Kim M., Kim S., Kim B. K., Lim Y. W. 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 [View Article][PubMed]
    [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 [View Article]
    [Google Scholar]
  7. Das S. K., Mishra A. K., Tindall B. J., Rainey F. A., Stackebrandt E. 1996; Oxidation of thiosulfate by a new bacterium, Bosea thiooxidans (strain BI-42) gen. nov., sp. nov.: analysis of phylogeny based on chemotaxonomy and 16S ribosomal DNA sequencing. Int J Syst Bacteriol 46:981–987 [View Article][PubMed]
    [Google Scholar]
  8. Felsenstein J. 1981; Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376 [View Article][PubMed]
    [Google Scholar]
  9. Felsenstein J. 1985; Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791 [View Article]
    [Google Scholar]
  10. Felsenstein, J. (2004). phylip (phylogeny inference package) version 3.6. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle, USA.
  11. Fritze D. 1996; Bacillus haloalkaliphilus sp. nov.. Int J Syst Bacteriol 46:98–101 [View Article]
    [Google Scholar]
  12. 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]
  13. 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[PubMed] [CrossRef]
    [Google Scholar]
  14. Gordon R. E., Haynes W. C., Pang C. H.-N. 1973 The genus Bacillus Agriculture Handbook no. 427 Washington, DC: US Department of Agriculture;
    [Google Scholar]
  15. 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 [View Article]
    [Google Scholar]
  16. Gordon R. E., Hyde J. L., Moore J. A. Jr 1977; Bacillus firmusBacillus lentus: a series or one species?. Int J Syst Bacteriol 27:256–262 [View Article]
    [Google Scholar]
  17. Hayashi T., Akiba T., Horikoshi K. 1988; Production and purification of new maltohexaose-forming amylases from alkalophilic Bacillus sp. H-167. Agric Biol Chem 52:443–448 [CrossRef]
    [Google Scholar]
  18. Heyrman J., Vanparys B., Logan N. A., Balcaen A., Rodríguez-Díaz M., Felske A., De Vos P. 2004; Bacillus novalis sp. nov., Bacillus vireti sp. nov., Bacillus soli sp. nov., Bacillus bataviensis sp. nov. and Bacillus drentensis sp. nov., from the Drentse A grasslands. Int J Syst Evol Microbiol 54:47–57 [View Article][PubMed]
    [Google Scholar]
  19. Horikoshi K. 1971; Production of alkaline enzymes by alkalophilic microorganisms. Part I. Alkaline protease produced by Bacillus no. 221. Agric Biol Chem 36:1407–1414 [CrossRef]
    [Google Scholar]
  20. Horikoshi K. 1999 Alkaliphiles Tokyo: Kodansha;
    [Google Scholar]
  21. 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]
  22. Kämpfer P., Kroppenstedt R. M. 1996; Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. Can J Microbiol 42:989–1005 [View Article]
    [Google Scholar]
  23. Kanso S., Patel B. K. C. 2003; Microvirga subterranea gen. nov., sp. nov., a moderate thermophile from a deep subsurface Australian thermal aquifer. Int J Syst Evol Microbiol 53:401–406 [View Article][PubMed]
    [Google Scholar]
  24. 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 [View Article][PubMed]
    [Google Scholar]
  25. Kluge A. G., Farris F. S. 1969; Quantitative phyletics and the evolution of anurans. Syst Zool 18:1–32 [View Article]
    [Google Scholar]
  26. Komagata K., Suzuki K. 1987; Lipid and cell wall analysis in bacterial systematics. Methods Microbiol 19:161–207 [View Article]
    [Google Scholar]
  27. La Scola B., Mallet M. N., Grimont P. A. D., Raoult D. 2003; Bosea eneae sp. nov., Bosea massiliensis sp. nov. and Bosea vestrisii sp. nov., isolated from hospital water supplies, and emendation of the genus Bosea (Das et al. 1996). Int J Syst Evol Microbiol 53:15–20 [View Article][PubMed]
    [Google Scholar]
  28. Li Z., Kawamura Y., Shida O., Yamagata S., Deguchi T., Ezaki T. 2002; Bacillus okuhidensis sp. nov., isolated from the Okuhida spa area of Japan. Int J Syst Evol Microbiol 52:1205–1209 [View Article][PubMed]
    [Google Scholar]
  29. Lim J.-M., Jeon C. O., Lee S.-M., Lee J.-C., Xu L.-H., Jiang C.-L., Kim C.-J. 2006a; Bacillus salarius sp. nov., a halophilic, spore-forming bacterium isolated from a salt lake in China. Int J Syst Evol Microbiol 56:373–377 [View Article][PubMed]
    [Google Scholar]
  30. Lim J.-M., Jeon C. O., Kim C.-J. 2006b; Bacillus taeanensis sp. nov., a halophilic Gram-positive bacterium from a solar saltern in Korea. Int J Syst Evol Microbiol 56:2903–2908 [View Article][PubMed]
    [Google Scholar]
  31. 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[PubMed]
    [Google Scholar]
  32. Marmur J., Doty P. 1962; Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature. J Mol Biol 5:109–118 [View Article][PubMed]
    [Google Scholar]
  33. 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 117:61–65 [View Article]
    [Google Scholar]
  34. Nielsen P., Fritze D., Priest F. G. 1995; Phenetic diversity of alkaliphilic Bacillus strains: proposal for nine new species. Microbiology 141:1745–1761 [View Article]
    [Google Scholar]
  35. Nogi Y., Takami H., Horikoshi K. 2005; Characterization of alkaliphilic Bacillus strains used in industry: proposal of five novel species. Int J Syst Evol Microbiol 55:2309–2315 [View Article][PubMed]
    [Google Scholar]
  36. Nowlan B., Dodia M. S., Singh S. P., Patel B. K. C. 2006; Bacillus okhensis sp. nov., a halotolerant and alkalitolerant bacterium from an Indian saltpan. Int J Syst Evol Microbiol 56:1073–1077 [View Article][PubMed]
    [Google Scholar]
  37. Olivera N., Siñeriz F., Breccia J. D. 2005; Bacillus patagoniensis sp. nov., a novel alkalitolerant bacterium from the rhizosphere of Atriplex lampa in Patagonia, Argentina. Int J Syst Evol Microbiol 55:443–447 [View Article][PubMed]
    [Google Scholar]
  38. Priest F. G., Goodfellow M., Todd C. 1988; A numerical classification of the genus Bacillus . J Gen Microbiol 134:1847–1882[PubMed]
    [Google Scholar]
  39. 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 Nocardiopsaceae fam. nov.. Int J Syst Bacteriol 46:1088–1092 [View Article][PubMed]
    [Google Scholar]
  40. Saitou N., Nei M. 1987; The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425[PubMed]
    [Google Scholar]
  41. Sasser, M. (1990). Identification of bacteria by gas chromatography of cellular fatty acids, Technical Note 101. Newark, DE: MIDI, Inc.
  42. 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[PubMed]
    [Google Scholar]
  43. 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]
  44. Sorokin I. D., Kravchenko I. K., Tourova T. P., Kolganova T. V., Boulygina E. S., Sorokin D. Y. 2008; Bacillus alkalidiazotrophicus sp. nov., a diazotrophic, low salt-tolerant alkaliphile isolated from Mongolian soda soil. Int J Syst Evol Microbiol 58:2459–2464 [View Article][PubMed]
    [Google Scholar]
  45. Spanka R., Fritze D. 1993; Bacillus cohnii sp. nov., a new, obligately alkaliphilic, oval-spore-forming Bacillus species with ornithine and aspartic acid instead of diaminopimelic acid in the cell wall. Int J Syst Bacteriol 43:150–156 [View Article][PubMed]
    [Google Scholar]
  46. Stackebrandt E., Ebers J. 2006; Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 33:152–155
    [Google Scholar]
  47. 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 [View Article]
    [Google Scholar]
  48. Stackebrandt E., Frederiksen W., Garrity G. M., Grimont P. A. D., Kämpfer P., Maiden M. C. J., Nesme X., Rosselló-Mora R., Swings J. et al. 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 [View Article][PubMed]
    [Google Scholar]
  49. Switzer Blum J., Burns Bindi A., Buzzelli J., Stolz J. F., Oremland R. S. 1998; Bacillus arsenicoselenatis, sp. nov., and Bacillus selenitireducens, sp. nov.: two haloalkaliphiles from Mono Lake, California that respire oxyanions of selenium and arsenic. Arch Microbiol 171:19–30 [View Article][PubMed]
    [Google Scholar]
  50. Tamura K., Dudley J., Nei M., Kumar S. 2007; mega4: molecular evolutionary genetics analysis (mega) software version 4.0. Mol Biol Evol 24:1596–1599 [View Article][PubMed]
    [Google Scholar]
  51. 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 [View Article][PubMed]
    [Google Scholar]
  52. Tindall B. J. 1990; A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 13:128–130 [CrossRef]
    [Google Scholar]
  53. Vedder A. 1934; Bacillus alcalophilus n. sp.; benevens enkele ervaringen met sterk alcalische voedingbodems. Antonie van Leeuwenhoek 1:141–147 (in Dutch) [View Article]
    [Google Scholar]
  54. Wieser M., Worliczek H., Kämpfer P., Busse H.-J. 2005; Bacillus herbersteinensis sp. nov.. Int J Syst Evol Microbiol 55:2119–2123 [View Article][PubMed]
    [Google Scholar]
  55. 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]
  56. Wynter C., Patel B. K., Bain P., de Jersey J., Hamilton S., Inkerman P. A. 1996; A novel thermostable dextranase from a Thermoanaerobacter species cultured from the geothermal waters of the Great Artesian Basin of Australia. FEMS Microbiol Lett 140:271–276 [View Article][PubMed]
    [Google Scholar]
  57. 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 [View Article][PubMed]
    [Google Scholar]
  58. Yamamoto M., Tanaka Y., Horikoshi K. 1972; Alkaline amylases of alkalophilic bacteria. Agric Biol Chem 36:1819–1823 [CrossRef]
    [Google Scholar]
  59. Yumoto I., Yamazaki K., Sawabe T., Nakano K., Kawasaki K., Ezura Y., Shinano H. 1998; Bacillus horti sp. nov., a new gram-negative alkaliphilic bacillus. Int J Syst Bacteriol 48:565–571[PubMed] [CrossRef]
    [Google Scholar]
  60. Yumoto I., Yamaga S., Sogabe Y., Nodasaka Y., Matsuyama H., Nakajima K., Suemori A. 2003; Bacillus krulwichiae sp. nov., a halotolerant obligate alkaliphile that utilizes benzoate and m-hydroxybenzoate. Int J Syst Evol Microbiol 53:1531–1536 [View Article][PubMed]
    [Google Scholar]
  61. 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 [View Article][PubMed]
    [Google Scholar]
  62. 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 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.023671-0
Loading
/content/journal/ijsem/10.1099/ijs.0.023671-0
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Supplementary material 2

PDF

Supplementary material 3

PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error