1887

Abstract

Two facultative anaerobic and facultative alkaliphilic indigo-reducing strains, designated F-1 and F-2, were isolated from indigo fermentation liquor produced from couched woad fermentation-based Indian indigo fermentation fluid. The 16S rRNA gene phylogeny showed that WS4937 (99.5%) was the closest neighbour of F-1. The isolated bacterial cells were Gram-stain-positive and facultative anaerobic coccoids. Strain F-1 grew at between 5 and 37 °C with optimum growth between 28‒32 °C. The isolate grew in a pH range of 7.0‒10.5, with optimum growth between pH 9.0‒10.5. The DNA G+C content was 37.6 mol% (HPLC). The whole-cell fatty acid profile mainly consisted (>10 %) of C, C ω9, C and C ω9. The digital DNA–DNA hybridization value between strain F-1 and WS4937 was 52.9 %. Based on their physiological and biochemical characteristics, and phylogenetic and genomic data, the isolates can be discriminated from WS4937. The name sp. nov. is proposed. The type strain of this species is F-1 (JCM 34140=NCIMB 15255).

Funding
This study was supported by the:
  • Institute for Fermentation, Osaka (Award G-2020-3-035)
    • Principle Award Recipient: IsaoYumoto
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/content/journal/ijsem/10.1099/ijsem.0.005239
2022-02-14
2024-05-26
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References

  1. Cardon D. Natural Dyes: Sources, Tradition, Technology and Science Archetype Publications Ltd; 2007
    [Google Scholar]
  2. Chavan RB. eds Indigo Dye and Reduction Techniques Cambridge: Woodhead Publishing Ltd; 2015 pp 37–67
    [Google Scholar]
  3. 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 [View Article] [PubMed]
    [Google Scholar]
  4. Aino K, Hirota K, Okamoto T, Tu Z, Matsuyama H et al. Microbial communities associated with indigo fermentation that thrive in anaerobic alkaline environments. Front Microbiol 2018; 9:1–16 [View Article] [PubMed]
    [Google Scholar]
  5. Lopes H de FS, Tu Z, Sumi H, Yumoto I. Analysis of bacterial flora of indigo fermentation fluids utilizing composted indigo leaves (sukumo) and indigo extracted from plants (Ryukyu-ai and Indian indigo). J Biosci Bioeng 2021; 132:279–286 [View Article] [PubMed]
    [Google Scholar]
  6. Padden AN, Dillon VM, John P, Edmonds J, Collins MD et al. Clostridium used in mediaeval dyeing. Nature 1998; 396:225 [View Article]
    [Google Scholar]
  7. Padden AN, Dillon VM, Edmonds J, Collins MD, Alvarez N et al. An indigo-reducing moderate thermophile from a woad vat, Clostridium isatidis sp. nov. Int J Syst Bacteriol 1999; 49:1025–1031 [View Article] [PubMed]
    [Google Scholar]
  8. 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 [View Article] [PubMed]
    [Google Scholar]
  9. Hirota K, Nishita M, Tu Z, Matsuyama H, Yumoto I. Bacillus fermenti sp. nov., an indigo-reducing obligate alkaliphile isolated from indigo fermentation liquor for dyeing. Int J Syst Evol Microbiol 2018; 68:1123–1129 [View Article] [PubMed]
    [Google Scholar]
  10. 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 [View Article] [PubMed]
    [Google Scholar]
  11. 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 [View Article] [PubMed]
    [Google Scholar]
  12. 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 [View Article] [PubMed]
    [Google Scholar]
  13. 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 [View Article] [PubMed]
    [Google Scholar]
  14. 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 [View Article]
    [Google Scholar]
  15. 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 [View Article] [PubMed]
    [Google Scholar]
  16. 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 [View Article] [PubMed]
    [Google Scholar]
  17. 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 [View Article] [PubMed]
    [Google Scholar]
  18. 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 [View Article] [PubMed]
    [Google Scholar]
  19. Siebert A, Huptas C, Wenning M, Scherer S, Doll EV. Fundicoccus ignavus gen. nov., sp. nov., a novel genus of the family Aerococcaceae isolated from bulk tank milk. Int J Syst Evol Microbiol 2020; 70:4774–4781 [View Article] [PubMed]
    [Google Scholar]
  20. Collins MD, Hutson RA, Falsen E, Sjödén B. Facklamia tabacinasalis sp. nov., from powdered tobacco. Int J Syst Bacteriol 1999; 49 Pt 3:1247–1250 [View Article] [PubMed]
    [Google Scholar]
  21. 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 [View Article] [PubMed]
    [Google Scholar]
  22. Barrow GI, Feltham RKA. eds Cowan and Steel’s Manual for the Identification of Medical Bacteria, 3rd edn. Cambridge: Cambridge University Press; 1993 [View Article]
    [Google Scholar]
  23. Nakamura K, Hiraishi A, Yoshimi Y, Kawaharasaki M, Masuda K et al. Microlunatus phosphovorus gen. nov., sp. nov., a new gram-positive polyphosphate-accumulating bacterium isolated from activated sludge. Int J Syst Bacteriol 1995; 45:17–22 [View Article]
    [Google Scholar]
  24. Marmur J. A procedure for the isolation of deoxyribonucleic acid from micro-organisms. J Molecul Biol 1961; 3:208 [View Article]
    [Google Scholar]
  25. Tamaoka J, Komagata K. Determination of DNA base composition by reversed-phase high-performance liquid chromatography. FEMS Microbiol Lett 1984; 25:125–128 [View Article]
    [Google Scholar]
  26. 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 [View Article] [PubMed]
    [Google Scholar]
  27. Staneck JL, Roberts GD. Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 1974; 28:226–231 [View Article] [PubMed]
    [Google Scholar]
  28. 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
    [Google Scholar]
  29. 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 [View Article]
    [Google Scholar]
  30. Komagata K, Suzuki K-I. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–207
    [Google Scholar]
  31. 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 [View Article] [PubMed]
    [Google Scholar]
  32. 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 [View Article] [PubMed]
    [Google Scholar]
  33. Guindon S, Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 2003; 52:696–704 [View Article] [PubMed]
    [Google Scholar]
  34. Tamura K, Stecher G, Kumar S. MEGA11: Molecular Evolutionary Genetics Analysis version 11. Mol Biol Evol 2021; 38:3022–3027 [View Article]
    [Google Scholar]
  35. Tavaré S. Some probabilistic and statistical problems in the analysis of DNA sequencies. In Miura RM. eds Lectures on Mathematics in the Life Sciences. Vol. 17. Providence American Mathematical Society; 1986 pp 57–58
    [Google Scholar]
  36. Brewer MJ, Butler A, Cooksley SL, Freckleton R. The relative performance of AIC, AICC and BIC in the presence of unobserved heterogeneity. Methods Ecol Evol 2016; 7:679–692 [View Article]
    [Google Scholar]
  37. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:75 [View Article] [PubMed]
    [Google Scholar]
  38. Rodriguez-R LM, Konstantinidis KT. Bypassing cultivation to identify bacterial species. Microbe Magazine 2014; 9:111–118 [View Article]
    [Google Scholar]
  39. Yoon S-H, Ha S-M, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617 [View Article] [PubMed]
    [Google Scholar]
  40. Yoon S-H, Ha S-M, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [View Article] [PubMed]
    [Google Scholar]
  41. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article] [PubMed]
    [Google Scholar]
  42. Konstantinidis KT, Tiedje JM. Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci USA 2005; 102:2567–2572 [View Article] [PubMed]
    [Google Scholar]
  43. Varghese NJ, Mukherjee S, Ivanova N, Konstantinidis KT, Mavrommatis K et al. Microbial species delineation using whole genome sequences. Nucleic Acids Res 2015; 43:6761–6771 [View Article] [PubMed]
    [Google Scholar]
  44. Na S-I, Kim YO, Yoon S-H, Ha S-M, Baek I et al. UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018; 56:280–285 [View Article] [PubMed]
    [Google Scholar]
  45. 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 [View Article] [PubMed]
    [Google Scholar]
  46. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article] [PubMed]
    [Google Scholar]
  47. Thompson CC, Chimetto L, Edwards RA, Swings J, Stackebrandt E et al. Microbial genomic taxonomy. BMC Genomics 2013; 14:913 [View Article] [PubMed]
    [Google Scholar]
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