1887

Abstract

The indigo-reducing, facultatively anaerobic and obligately alkaliphilic strains Bf-1, Bf-2 and Bf-4 were isolated from an indigo fermentation liquor used for dyeing, which uses sukumo [composted Polygonum indigo (Polygonum tinctorium Lour.) leaves] as a basic ingredient and was obtained from a craft centre in Date City, Hokkaido, Japan. The 16S rRNA gene sequence analyses indicated that the closest neighbours of strain Bf-1 are Bacillus maritimus DSM 100413 (98.3 % 16S rRNA gene sequence similarity), Bacillus persicus DSM 25386 (98.2 %) and Bacillus rigiliprofundi LMG 28275 (97.7 %). The 16S rRNA gene sequence of strain Bf-1 was almost identical to the sequences of strains Bf-2 and Bf-4 (99.9 %). Cells of strain Bf-1 stained Gram-positive and formed straight rods that achieved motility through a pair of subpolar flagella. Strain Bf-1 grew at temperatures of between 15 and 45 °C with optimum growth at 33‒40 °C. The strain grew in the pH range of pH 8‒12, with optimum growth at pH 10. The isoprenoid quinone detected was menaquinone-7 (MK-7), and the DNA G+C content was 41.7 %. The whole-cell fatty acid profile mainly (>10 %) consisted of iso-C15 : 0 and iso-C16 : 0. Phylogenetically related neighbours, although demonstrating high 16S rRNA gene sequence similarity (>97.6 %) with strain Bf-1, exhibited less than 9 % relatedness in DNA–DNA hybridization experiments. Based on evidence from this polyphasic study, the isolates represent a novel species, for which the name Bacillus fermenti sp. nov. is proposed. The type strain of this species is Bf-1 (=JCM 31807=NCIMB 15079).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.002636
2018-02-16
2019-10-18
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/68/4/1123.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.002636&mimeType=html&fmt=ahah

References

  1. Song J, Imanaka H, Imamura K, Kajitani K, Nakanishi K. Development of a highly efficient indigo dyeing method using indican with an immobilized β-glucosidase from Aspergillus niger. J Biosci Bioeng 2010; 110: 281– 287 [CrossRef] [PubMed]
    [Google Scholar]
  2. 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]
  3. 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]
  4. 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]
  5. 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]
  6. Yumoto I, Hirota K, Nodasaka Y, Tokiwa Y, Nakajima K. Alkalibacterium indicireducens sp. nov., an obligate alkaliphile that reduces indigo dye. Int J Syst Evol Microbiol 2008; 58: 901– 905 [CrossRef] [PubMed]
    [Google Scholar]
  7. 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]
  8. 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]
  9. 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]
  10. 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]
  11. 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]
  12. Hirota K, Nishita M, Matsuyama H, Yumoto I. Paralkalibacillus indicireducens gen., nov., sp. nov., an indigo-reducing obligate alkaliphile isolated from indigo fermentation liquor used for dyeing. Int J Syst Evol Microbiol 2017; 67: 4050– 4056 [CrossRef] [PubMed]
    [Google Scholar]
  13. 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]
  14. 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]
  15. Barrow GI, Feltham RKA. (editors) Cowan and Steel's Manual for the Identification of Medical Bacteria, 3rd ed. Cambridge: Cambridge University Press; 1993; [Crossref]
    [Google Scholar]
  16. 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]
  17. Marmur J. A procedure for the isolation of deoxyribonucleic acid from micro-organisms. J Mol Biol 1961; 3: 208– IN1 [CrossRef]
    [Google Scholar]
  18. 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]
  19. 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]
  20. Staneck JL, Roberts GD. Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 1974; 28: 226– 231 [PubMed]
    [Google Scholar]
  21. 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]
  22. 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]
  23. 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]
  24. 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]
  25. 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]
  26. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4: 406– 425 [CrossRef] [PubMed]
    [Google Scholar]
  27. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20: 406– 416 [CrossRef]
    [Google Scholar]
  28. 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]
  29. 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]
  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. Pal D, Mathan Kumar R, Kaur N, Kumar N, Kaur G et al. Bacillus maritimus sp. nov., a novel member of the genus Bacillus isolated from marine sediment. Int J Syst Evol Microbiol 2017; 67: 60– 66 [CrossRef] [PubMed]
    [Google Scholar]
  33. Didari M, Amoozegar MA, Bagheri M, Mehrshad M, Schumann P et al. Bacillus persicus sp. nov., a halophilic bacterium from a hypersaline lake. Int J Syst Evol Microbiol 2013; 63: 1229– 1234 [CrossRef] [PubMed]
    [Google Scholar]
  34. Kumar RM, Kaur G, Kumar A, Bala M, Singh NK et al. Taxonomic description and genome sequence of Bacillus campisalis sp. nov., a member of the genus Bacillus isolated from a solar saltern. Int J Syst Evol Microbiol 2015; 65: 3235– 3240 [CrossRef] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.002636
Loading
/content/journal/ijsem/10.1099/ijsem.0.002636
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most Cited This Month

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