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f Polygonibacillus indicireducens gen. nov., sp. nov., an indigo-reducing and obligate alkaliphile isolated from indigo fermentation liquor for dyeing

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  • Authors: Kikue Hirota1​ ,  Takahiro Okamoto1​,2​ ,  Hidetoshi Matsuyama2​ , Isao Yumoto1​,3​
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    • 1​ 1​Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan 2​ 2​School of Biological Science and Engineering, Tokai University, Minamisawa, Minami-ku, Sapporo 005-8601, Japan 3​ 3​Laboratory of Molecular Environmental Microbiology, Graduate School of Agriculture, Hokkaido University, Kita-ku, Sapporo 060-8589, Japan
  • Correspondence Isao Yumoto [email protected]
  • First Published Online: 01 November 2016, International Journal of Systematic and Evolutionary Microbiology 66: 4650-4656, doi: 10.1099/ijsem.0.001405
  • Subject: New taxa - Firmicutes and related organisms
  • Received:
  • Accepted:
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Polygonibacillus indicireducens gen. nov., sp. nov., an indigo-reducing and obligate alkaliphile isolated from indigo fermentation liquor for dyeing, Page 1 of 1

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  • Obligately alkaliphilic and halophilic strains, designated In2-9 and D2-7, were isolated from a fermented Polygonum indigo (Polygonum tinctorium Lour.) liquor sample obtained from a craft centre in Date City, Hokkaido, Japan. The 16S rRNA gene sequence phylogeny suggested that strain In2-9 is a member of the genus Bacillus with the closest relatives being the alkaliphilic species of the genus Bacillus , Bacillus hemicellulosilyticusJCM 9152 (96.4 % 16S rRNA gene sequence similarity) and Bacillus alcalophilus DSM 485 (96.5 %). Cells of the isolate stained Gram-positive and were facultatively anaerobic straight rods that were motile by peritrichous flagella. Strain In2-9 grew between 13 and 45 °C with optimum growth at approximately 35–37 °C. The isolates grew in the pH range of 8–12 with optimum growth at pH 10. The isoprenoid quinone detected was menaquinone-6 (MK-6) and the DNA G+C content was 39.4 mol%. The whole-cell fatty acid profile mainly (>10 %) consisted of iso-C15 : 0, anteiso-C15 : 0 and C16 : 0. Spore shape and location and chemotaxonomic characteristics revealed that the isolates were distinctly different from phylogenetic neighbouring alkaliphilic species of the genus Bacillus . On the basis of phenotypic and chemotaxonomic characteristics and phylogenetic data, the isolates represent a novel species of a new genus, for which the name Polygonibacillus indicireducens gen. nov., sp. nov. is proposed. The type strain of the type species is In2-9 (=JCM 30831=NCIMB 14982), and strain D2-7 is an additional strain of the species.

  • The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene sequence of strains In2-9 and D2-7 are LC054224 and LC054225, respectively, and those for the rpoB gene sequences of strains In2-9 and D2-7 are LC160335 and LC160336, respectively. Other sequences determined in this study have been deposited as LC160337.

  • A supplementary table and four supplementary figures are available with the online Supplementary Material.

  • Abbreviations:
    meso-DAP meso-diaminopimelic acid
    TEM transmission electron microscopy

© 2016 IUMS | Published by the Microbiology Society

  • Aino K., Narihiro T., Minamida K., Kamagata Y., Yoshimune K., Yumoto I..( 2010;). Bacterial community characterization and dynamics of indigo fermentation. . FEMS Microbiol Ecol74:174––183. [CrossRef][PubMed]
     [Google Scholar]
  • Barrow G. I., Feltham R. K. A..( (editors)) ( 1993;). Cowan and Steel's Manual for the Identification of Medical Bacteria, , 3rd edn.. Cambridge:: Cambridge University Press;.[CrossRef]
     [Google Scholar]
  • Blum J. S., Bindi A. B., 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 Microbiology171:19––30.[CrossRef]
     [Google Scholar]
  • Collins M. D., Jones D..( 1980;). Lipids in the classification and identification of coryneform bacteria containing peptidoglycans based on 2, 4-diaminobutyric acid. . J Appl Microbiol48:459––470. [CrossRef]
     [Google Scholar]
  • 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 Bacteriol39:224––229. [CrossRef]
     [Google Scholar]
  • Fitch W. M..( 1971;). Toward defining the course of evolution: minimum change for a specific tree topology. . Syst Zool20:406––416. [CrossRef]
     [Google Scholar]
  • Guindon S., Gascuel O..( 2003;). A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. . Syst Biol52:696––704. [CrossRef][PubMed]
     [Google Scholar]
  • Hirota K., Aino K., Nodasaka Y., Morita N., Yumoto I..( 2013a;). Amphibacillus indicireducens sp. nov., an alkaliphile that reduces an indigo dye. . Int J Syst Evol Microbiol63:464––469. [CrossRef][PubMed]
     [Google Scholar]
  • Hirota K., Aino K., Nodasaka Y., Yumoto I..( 2013b;). Oceanobacillus indicireducens sp. nov., a facultative alkaliphile that reduces an indigo dye. . Int J Syst Evol Microbiol63:1437––1442. [CrossRef][PubMed]
     [Google Scholar]
  • Hirota K., Aino K., Yumoto I..( 2013c;). Amphibacillus iburiensis sp. nov., an alkaliphile that reduces an indigo dye. . Int J Syst Evol Microbiol63:4303––4308. [CrossRef][PubMed]
     [Google Scholar]
  • Hirota K., Aino K., Yumoto I..( 2016;). Fermentibacillus polygoni gen. nov., sp. nov., an alkaliphile that reduces indigo dye. . Int J Syst Evol Microbiol66:2247––2253. [CrossRef][PubMed]
     [Google Scholar]
  • Ki J.-S., Zhang W., Qian P.-Y..( 2009;). Discovery of marine Bacillus species by 16S rRNA and rpoB comparisons and their usefulness for species identification. . J Microbiol Methods77:48––57. [CrossRef][PubMed]
     [Google Scholar]
  • Kimura M..( 1980;). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. . J Mol Evol16:111––120. [CrossRef][PubMed]
     [Google Scholar]
  • Marmur J..( 1961;). A procedure for the isolation of deoxyribonucleic acid from micro-organisms. . J Mol Biol3:208––218. [CrossRef]
     [Google Scholar]
  • Minnikin D. E., Collins M. D., Goodfellow M..( 1979;). Fatty acid and polar lipid composition in the classification of Cellulomonas, Oerskovia and related taxa. . J Appl Microbiol47:87––95. [CrossRef]
     [Google Scholar]
  • Nakajima K., Hirota K., Nodasaka Y., Yumoto I..( 2005;). Alkalibacterium iburiense sp. nov., an obligate alkaliphile that reduces an indigo dye. . Int J Syst Evol Microbiol55:1525––1530. [CrossRef][PubMed]
     [Google Scholar]
  • Nielsen P., Fritze D., Priest F. G..( 1995;). Phenetic diversity of alkaliphilic strains: proposal for nine new species. . Microbiology141:1745––1761. [CrossRef]
     [Google Scholar]
  • Nogi Y., Takami H., Horikoshi K..( 2005;). Characterization of alkaliphilic Bacillus strains used in industry: proposal of five novel species. . Int J Syst Evol Microbiol55:2309––2315. [CrossRef][PubMed]
     [Google Scholar]
  • Padden A. N., Dillon V. M., Edmonds J., Collins M. D., Alvarez N., John P..( 1999;). An indigo-reducing moderate thermophile from a woad vat, Clostridium isatidis sp. nov. . Int J Syst Bacteriol49:1025––1031. [CrossRef][PubMed]
     [Google Scholar]
  • Paster B. J., Russell M. K., Alpagot T., Lee A. M., Boches S. K., Galvin J. L., Dewhirst F. E..( 2002;). Bacterial diversity in necrotizing ulcerative periodontitis in HIV-positive subjects. . Ann Periodontol7:8––16. [CrossRef][PubMed]
     [Google Scholar]
  • Saitou N., Nei M..( 1987;). The neighbor-joining method: a new method for reconstructing phylogenetic trees. . Mol Biol Evol4:406––425.
     [Google Scholar]
  • 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 Microbiol58:2459––2464. [CrossRef][PubMed]
     [Google Scholar]
  • Staneck J. L., Roberts G. D..( 1974;). Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. . Appl Microbiol28:226––231.[PubMed]
     [Google Scholar]
  • Takahara Y., Tanabe O..( 1960;). Studies on the reduction of indigo in industrial fermentation Vat (VI): on the taxonomic characteristics of strain No. S-8. . J Ferment Technol38:297––299.
     [Google Scholar]
  • Tamaoka J., Komagata K..( 1984;). Determination of DNA base composition by reversed-phase high-performance liquid chromatography. . FEMS Microbiol Lett25:125––128. [CrossRef]
     [Google Scholar]
  • Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S..( 2011;). mega5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. . Mol Biol Evol28:2731––2739. [CrossRef][PubMed]
     [Google Scholar]
  • Teather R. M., Wood P. J..( 1982;). Use of Congo red polysaccharide interaction in enumeration of cellulolytic bacteria from bovine rumen. . Appl Environ Microbiol43:777––780.
     [Google Scholar]
  • Thompson J. D., Higgins D. G., Gibson T. J..( 1994;). clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. . Nucleic Acids Res22:4673––4680. [CrossRef][PubMed]
     [Google Scholar]
  • 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 Bacteriol48:565––571. [CrossRef][PubMed]
     [Google Scholar]
  • 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 Microbiol51:349––355. [CrossRef][PubMed]
     [Google Scholar]
  • Yumoto I., Nakamura A., Iwata H., Kojima K., Kusumoto K., Nodasaka Y., Matsuyama H..( 2002;). Dietzia psychralcaliphila sp. nov., a novel, facultatively psychrophilic alkaliphile that grows on hydrocarbons. . Int J Syst Evol Microbiol52:85––90. [CrossRef][PubMed]
     [Google Scholar]
  • Yumoto I., Hirota K., Nodasaka Y., Yokota Y., Hoshino T., Nakajima K..( 2004;). Alkalibacterium psychrotolerans sp. nov., a psychrotolerant obligate alkaliphile that reduces an indigo dye. . Int J Syst Evol Microbiol54:2379––2383. [CrossRef][PubMed]
     [Google Scholar]
  • Yumoto I., Hirota K., Nodasaka Y., Tokiwa Y., Nakajima K..( 2008;). Alkalibacterium indicireducens sp. nov., an obligate alkaliphile that reduces indigo dye. . Int J Syst Evol Microbiol58:901––905. [CrossRef][PubMed]
     [Google Scholar]
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