A moderately halophilic, obligate alkaliphile (growth range pH 8–12), designated strain YN-1, was isolated from indigo balls obtained from Ibaraki, Japan. The cells of the isolate stained Gram-positive, and were aerobic, non-motile, sporulating rods which grew optimally at pH 9. The strain grew in 3–14 % NaCl with optimum growth in 5 % NaCl. It hydrolysed casein and Tweens 20, 40 and 60, but not gelatin, starch, DNA or pullulan. Its major isoprenoid quinone was MK-7 and its cellular fatty acid profile mainly consisted of anteiso-C, anteiso-C and anteiso-C. 16S rRNA phylogeny suggested that strain YN-1 was a member of group 7 (alkaliphiles) of the genus , with the closest relative being DSM 8720 (similarity 99.5 %). However, DNA–DNA hybridization showed a low DNA–DNA relatedness (7 %) of strain YN-1 with . DSM 8720. Owing to the significant differences in phenotypic and chemotaxonomic characteristics, and phylogenetic and DNA–DNA relatedness data, the isolate merits classification as a new species, for which the name is proposed. The type strain of this species is YN-1 (=JCM 14604=NCIMB 14282).


Article metrics loading...

Loading full text...

Full text loading...



  1. Aono, R. & Horikoshi, K.(1983). Chemical composition of cell walls of alkalophilic strains of Bacillus. J Gen Microbiol 129, 1083–1087. [Google Scholar]
  2. Aono, R., Ito, M. & Machida, T.(1999). Contribution of the cell wall component teichuronopeptide to pH homeostasis and alkaliphily in the alkaliphile Bacillus lentus C-125. J Bacteriol 181, 6600–6606. [Google Scholar]
  3. Barrow, G. I. & Feltham, R. K. A.(1993).Cowan and Steel's Manual for the Identification of Medical Bacteria, 3rd edn. Cambridge: Cambridge University Press.
  4. Clejan, S., Krulwich, T. A., Mondrus, K. R. & Seto-Yung, D.(1986). Membrane lipid composition of obligately and facultatively alkalophilic strains of Bacillus spp. J Bacteriol 168, 334–340. [Google Scholar]
  5. Duckworth, A. W., Grant, W. D., Jones, B. E. & van Steenbergen, R.(1996). Phylogenetic diversity of soda lake alkaliphiles. FEMS Microbiol Ecol 19, 181–191.[CrossRef] [Google Scholar]
  6. 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.[CrossRef] [Google Scholar]
  7. Felsenstein, J.(1985). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783–791.[CrossRef] [Google Scholar]
  8. Goto, T., Matsuno, T., Hishinuma-Narisawa, M., Yamazaki, K., Matsuyama, H., Inoue, N. & Yumoto, I.(2005). Cytochrome c and bioenergetic hypothetical model for alkaliphilic Bacillus spp. J Biosci Bioeng 100, 365–379.[CrossRef] [Google Scholar]
  9. Hamasaki, N., Shirai, S., Niitsu, M., Kakinuma, K. & Oshima, T.(1993). An alkalophilic Bacillus sp. produces 2-phenylethylamine. Appl Environ Microbiol 59, 2720–2722. [Google Scholar]
  10. Higashibata, A., Fujiwara, T. & Fukumori, Y.(1998). Studies on the respiratory system in alkaliphilic Bacillus; a proposed new respiratory mechanism. Extremophiles 2, 83–92.[CrossRef] [Google Scholar]
  11. Hirota, N. & Imae, Y.(1983). Na+-driven flagella motors of an alkalophilic Bacillus strain YN-1. J Biol Chem 258, 10577–10581. [Google Scholar]
  12. Horikoshi, K.(1991).Microorganisms in Alkaline Environments. Weinheim: VCH.
  13. Hugh, R. & Leifson, E.(1953). The taxonomic significance of fermentative versus oxidative metabolism of carbohydrates by various Gram-negative bacteria. J Bacteriol 66, 24–26. [Google Scholar]
  14. 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]
  15. Kitazume, Y., Mutoh, M., Shiraki, M. & Koyama, N.(2006). Involvement of Lys-308 in the FAD-dependent oxidase activity of NADH dehydrogenase from an alkaliphilic Bacillus. Res Microbiol 157, 956–959.[CrossRef] [Google Scholar]
  16. Krulwich, T. A., Hicks, D. B., Swartz, T. H. & Ito, M.(2007). Bioenergetic adaptations that support alkaliphily. In Physiology and Biochemistry of Extremophiles, pp. 311–329. Edited by C. Gerday & N. Glansdorff. Washington, DC: American Society for Microbiology.
  17. Marmur, J.(1961). A procedure for the isolation of deoxyribonucleic acid from microorganisms. J Mol Biol 3, 208–218.[CrossRef] [Google Scholar]
  18. Nielsen, P., Rainey, F. A., Ottrup, 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]
  19. 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]
  20. 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, 2307–2315. [Google Scholar]
  21. Ota, K., Kiyomiya, A., Koyama, N. & Nosoh, Y.(1975). The basis of the alkalophilic property of a species of Bacillus. J Gen Microbiol 86, 259–266.[CrossRef] [Google Scholar]
  22. Saitou, N. & Nei, M.(1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425. [Google Scholar]
  23. Tamaoka, J. & Komagata, K.(1984). Determination of DNA base composition by reversed-phase high-performance liquid chromatography. FEMS Microbiol Lett 25, 125–128.[CrossRef] [Google Scholar]
  24. 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.[CrossRef] [Google Scholar]
  25. Teather, R. M. & Wood, P. J.(1982). Use of Congo red polysaccharide interaction in enumeration of cellulolytic bacteria from bovine rumen. Appl Environ Microbiol 43, 777–780. [Google Scholar]
  26. Thompson, J. D., Higgins, D. G. & Gibson, T. J.(1994).clustalw: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22, 4673–4680.[CrossRef] [Google Scholar]
  27. Thongaram, T., Kosono, S., Ohkuma, M., Hongoh, Y., Kitada, M., Yoshinoka, T., Trakulnaleamsai, S., Noparatnaraporn, N. & Kudo, T.(2003). Gut of higher termites as a niche for alkaliphiles as shown by culture-based and culture-independent studies. Microbes Environ 18, 152–159.[CrossRef] [Google Scholar]
  28. Xu, X., Koyama, N., Cui, M., Yamagishi, A., Nosoh, Y. & Oshima, T.(1991). Nucleotide sequence of the gene encoding NADH dehydrogenase from an alkalophile, Bacillus sp. strain YN-1. J Biochem (Tokyo) 109, 678–683. [Google Scholar]
  29. Yumoto, I.(2007). Environmental and taxonomic biodiversities of Gram-positive alkaliphiles. In Physiology and Biochemistry of Extremophiles, pp. 295–310. Edited by C. Gerday & N. Glansdorff. Washington, DC: American Society for Microbiology.
  30. Yumoto, I., Nakajima, K. & Ikeda, K.(1997). Comparative study on cytochrome content of alkaliphilic Bacillus strains. J Ferment Bioeng 83, 466–469.[CrossRef] [Google Scholar]
  31. 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.[CrossRef] [Google Scholar]
  32. Yumoto, I., Yamazaki, K., Hishinuma, M., Nodasaka, Y., Suemori, A., Nakajima, K., Inoue, N. & Kawasaki, K.(2001).Pseudomonas alcaliphila sp. nov., a novel facultatively psychrophilic alkaliphile isolated from seawater. Int J Syst Evol Microbiol 51, 349–355. [Google Scholar]
  33. Yumoto, I., Hirota, K., Goto, T., Nodasaka, Y. & Nakajima, K.(2005).Bacillus oshimensis sp. nov., a moderately halophilic, non-motile alkaliphile. Int J Syst Evol Microbiol 55, 907–911.[CrossRef] [Google Scholar]

Data & Media loading...


Maximum-parsimony phylogenetic tree constructed on the basis of 16S rRNA gene sequence data of strain YN-1 and other related organisms. Bootstrap percentages (based on 1000 replicates) are shown at branch points. Bar, 10 changes per nucleotide position.


Minimum-evolution phylogenetic tree constructed on the basis of 16S rRNA gene sequence data of strain YN-1 and other related organisms. Bootstrap percentages (based on 1000 replicates) are shown at branch points. Bar, 0.01 changes per nucleotide position.


Most cited this month Most Cited RSS feed

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