1887

Abstract

Obligately alkaliphilic, indigo-reducing strains, designated Bps-1, Bps-2 and Bps-3, were isolated from an indigo fermentation liquor used for dyeing, which was produced from (composted indigo leaves) obtained from a craft centre in Data City, Hokkaido, Japan, by using medium containing cellulase-treated . The 16S rRNA gene sequence phylogeny suggested that Bps-1 has a distinctive position among the alkaliphilic species of the genus , with its closest neighbours being DSM 8715, DSM 26864 and DSM 485 (96.1, 95.8 and 95.5 % 16S rRNA gene sequence similarities, respectively). The 16S rRNA sequence of strain Bps-1 was identical to those of strains Bps-2 and Bps-3. Cells of the novel isolate were Gram-stain-positive and were facultatively anaerobic straight rods that were motile by means of a pair of flagella (subpolar and centre sides). Spherical endospores were formed in the terminal position. Strain Bps-1 grew between 18 and 40 °C with optimum growth at 33 °C. The isolate grew in the pH range 8‒11, with optimum growth at pH 9‒10. The isoprenoid quinone detected was menaquinone-7 (MK-7), and the DNA G+C content was 40.3 %. The whole-cell fatty acid profile (>10 %) mainly consisted of anteiso-C, iso-C and C. On the basis of the phenotypic, chemotaxonomic and phylogenetic data, the isolates represent a novel species of a novel genus, for which the name gen. nov., sp. nov. is proposed. The type strain of this species is Bps-1 (JCM 31808=NCIMB 15080), with strains Bps-2 and Bps-3 representing additional strains of the species.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.002248
2017-10-01
2020-01-22
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/67/10/4050.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.002248&mimeType=html&fmt=ahah

References

  1. Aino K, Narihiro T, Minamida K, Kamagata Y, Yoshimune K et al. Bacterial community characterization and dynamics of indigo fermentation. FEMS Microbiol Ecol 2010;74:174–183 [CrossRef][PubMed]
    [Google Scholar]
  2. Yumoto I, Hirota K, Nodasaka Y, Yokota Y, Hoshino T et al. Alkalibacterium psychrotolerans sp. nov., a psychrotolerant obligate alkaliphile that reduces an indigo dye. Int J Syst Evol Microbiol 2004;54:2379–2383 [CrossRef][PubMed]
    [Google Scholar]
  3. Nakajima K, Hirota K, Nodasaka Y, Yumoto I. Alkalibacterium iburiense sp. nov., an obligate alkaliphile that reduces an indigo dye. Int J Syst Evol Microbiol 2005;55:1525–1530 [CrossRef][PubMed]
    [Google Scholar]
  4. Yumoto I, Hirota K, Nodasaka Y, Tokiwa Y, Nakajima K et al. Alkalibacterium indicireducens sp. nov., an obligate alkaliphile that reduces indigo dye. Int J Syst Evol Microbiol 2008;58:901–905 [CrossRef][PubMed]
    [Google Scholar]
  5. Hirota K, Aino K, Nodasaka Y, Morita N, Yumoto I. Amphibacillus indicireducens sp. nov., an alkaliphile that reduces an indigo dye. Int J Syst Evol Microbiol 2013;63:464–469 [CrossRef][PubMed]
    [Google Scholar]
  6. Hirota K, Aino K, Yumoto I. Amphibacillus iburiensis sp. nov., an alkaliphile that reduces an indigo dye. Int J Syst Evol Microbiol 2013;63:4303–4308 [CrossRef][PubMed]
    [Google Scholar]
  7. Hirota K, Aino K, Nodasaka Y, Yumoto I. Oceanobacillus indicireducens sp. nov., a facultative alkaliphile that reduces an indigo dye. Int J Syst Evol Microbiol 2013;63:1437–1442 [CrossRef][PubMed]
    [Google Scholar]
  8. Hirota K, Aino K, Yumoto I. Fermentibacillus polygoni gen. nov., sp. nov., an alkaliphile that reduces indigo dye. Int J Syst Evol Microbiol 2016;66:2247–2253 [CrossRef][PubMed]
    [Google Scholar]
  9. Hirota K, Okamoto T, Matsuyama H, Yumoto I. Polygonibacillus indicireducens gen. nov., sp. nov., an indigo-reducing and obligate alkaliphile isolated from indigo fermentation liquor for dyeing. Int J Syst Evol Microbiol 2016;66:4650–4656 [CrossRef][PubMed]
    [Google Scholar]
  10. Okamoto T, Aino K, Narihiro T, Matsuyama H, Yumoto I. Analysis of microbiota involved in the aged natural fermentation of indigo. World J Microbiol Biotechnol 2017;33:70 [CrossRef][PubMed]
    [Google Scholar]
  11. Nishita M, Hirota K, Matsuyama H, Yumoto I. Development of media to accelerate the isolation of indigo-reducing bacteria, which are difficult to isolate using conventional media. World J Microbiol Biotechnol 2017;33:133 [CrossRef][PubMed]
    [Google Scholar]
  12. Yumoto I, Yamazaki K, Sawabe T, Nakano K, Kawasaki K et al. Bacillus horti sp. nov., a new gram-negative alkaliphilic bacillus. Int J Syst Bacteriol 1998;48:565–571 [CrossRef][PubMed]
    [Google Scholar]
  13. Barrow GI, Feltham RKA. Cowan and Steel's Manual for the Identification of Medical Bacteria, 3rd ed. Cambridge: Cambridge University Press; 1993;[Crossref]
    [Google Scholar]
  14. Yumoto I, Yamazaki K, Hishinuma M, Nodasaka Y, Suemori A et al. Pseudomonas alcaliphila sp. nov., a novel facultatively psychrophilic alkaliphile isolated from seawater. Int J Syst Evol Microbiol 2001;51:349–355 [CrossRef][PubMed]
    [Google Scholar]
  15. Marmur J. A procedure for the isolation of deoxyribonucleic acid from micro-organisms. J Mol Biol 1961;3:208–218 [CrossRef]
    [Google Scholar]
  16. Tamaoka J, Komagata K. Determination of DNA base composition by reversed-phase high-performance liquid chromatography. FEMS Microbiol Lett 1984;25:125–128 [CrossRef]
    [Google Scholar]
  17. Yumoto I, Nakamura A, Iwata H, Kojima K, Kusumoto K et al. Dietzia psychralcaliphila sp. nov., a novel, facultatively psychrophilic alkaliphile that grows on hydrocarbons. Int J Syst Evol Microbiol 2002;52:85–90 [CrossRef][PubMed]
    [Google Scholar]
  18. Staneck JL, Roberts GD. Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 1974;28:226–231[PubMed]
    [Google Scholar]
  19. Minnikin DE, Collins MD, Goodfellow M. Fatty acid and polar lipid composition in the classification of Cellulomonas, Oerskovia and related taxa. J Appl Bacteriol 1979;47:87–95 [CrossRef]
    [Google Scholar]
  20. Collins MD, Jones D. Lipids in the classification and identification of coryneform bacteria containing peptidoglycans based on 2, 4-diaminobutyric acid. J Appl Bacteriol 1980;48:459–470 [CrossRef]
    [Google Scholar]
  21. Paster BJ, Russell MK, Alpagot T, Lee AM, Boches SK et al. Bacterial diversity in necrotizing ulcerative periodontitis in HIV-positive subjects. Ann Periodontol 2002;7:8–16 [CrossRef][PubMed]
    [Google Scholar]
  22. Johnson M, Zaretskaya I, Raytselis Y, Merezhuk Y, McGinnis S et al. NCBI BLAST: a better web interface. Nucleic Acids Res 2008;36:W5–W9 [CrossRef][PubMed]
    [Google Scholar]
  23. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994;22:4673–4680 [CrossRef][PubMed]
    [Google Scholar]
  24. Guindon S, Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 2003;52:696–704 [CrossRef][PubMed]
    [Google Scholar]
  25. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987;4:406–425[PubMed]
    [Google Scholar]
  26. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971;20:406–416 [CrossRef]
    [Google Scholar]
  27. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 2013;30:2725–2729 [CrossRef][PubMed]
    [Google Scholar]
  28. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980;16:111–120 [CrossRef][PubMed]
    [Google Scholar]
  29. Stackebrandt E, Goebel BM. Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Evol Microbiol 1994;44:846–849 [CrossRef]
    [Google Scholar]
  30. 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 [CrossRef][PubMed]
    [Google Scholar]
  31. Ezaki T, Hashimoto Y, Yabuuchi E. 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 1989;39:224–229 [CrossRef]
    [Google Scholar]
  32. Nakamura LK, Roberts MS, Cohan FM. Relationship of Bacillus subtilis clades associated with strains 168 and W23: a proposal for Bacillus subtilis subsp. subtilis subsp. nov. and Bacillus subtilis subsp. spizizenii subsp. nov. Int J Syst Bacteriol 1999;49:1211–1215 [CrossRef][PubMed]
    [Google Scholar]
  33. Switzer Blum J, Burns Bindi A, Buzzelli J, Stolz JF, Oremland RS. Bacillus arsenicoselenatis, sp. nov., and Bacillus selenitireducens, sp. nov.: two haloalkaliphiles from Mono Lake, California that respire oxyanions of selenium and arsenic. Arch Microbiol 1998;171:19–30 [CrossRef][PubMed]
    [Google Scholar]
  34. Nielsen P, Fritze D, Priest FG. Phenetic diversity of alkaliphilic Bacillus strains: proposal for nine new species. Microbiology 1995;141:1745–1761 [CrossRef]
    [Google Scholar]
  35. Nogi Y, Takami H, Horikoshi K. Characterization of alkaliphilic Bacillus strains used in industry: proposal of five novel species. Int J Syst Evol Microbiol 2005;55:2309–2315 [CrossRef][PubMed]
    [Google Scholar]
  36. Dou G, Liu H, He W, Ma Y. Bacillus lindianensis sp. nov., a novel alkaliphilic and moderately halotolerant bacterium isolated from saline and alkaline soils. Antonie van Leeuwenhoek 2016;109:149–158 [CrossRef][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.002248
Loading
/content/journal/ijsem/10.1099/ijsem.0.002248
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most cited articles

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