Bacterial community characterization and dynamics of indigo fermentation

FEMS Microbiology Ecology

Volumn 74, Issue 1, 2010, Pages 174-183

  Aino, Kenichi ^a   Narihiro, Takashi ^a   Minamida, Kimiko ^a   Kamagata, Yoichi ^a   Yoshimune, Kazuaki ^a   Yumoto, Isao ^a  

^a NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

Author keywords

Alkalibacterium; Amphibacillus; denaturing gradient gel electrophoresis; indigo reduction

Indexed keywords

BACTERIAL DNA; INDIGO; INDOLE DERIVATIVE; RNA 16S;

BACTERIUM; COMMUNITY DYNAMICS; DYE; ELECTROKINESIS; FERMENTATION; MICROBIAL COMMUNITY; MICROBIAL ECOLOGY; POLYMERASE CHAIN REACTION; TEXTILE INDUSTRY;

ARTICLE; BACTERIUM; CLASSIFICATION; DENATURING GRADIENT GEL ELECTROPHORESIS; DNA SEQUENCE; FERMENTATION; GENETICS; ISOLATION AND PURIFICATION; METABOLISM; METAGENOME; MICROBIOLOGY; OXIDATION REDUCTION REACTION; PHYLOGENY; TEXTILE;

BACTERIA; DENATURING GRADIENT GEL ELECTROPHORESIS; DNA, BACTERIAL; FERMENTATION; INDOLES; METAGENOME; OXIDATION-REDUCTION; PHYLOGENY; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; TEXTILES;

JAPAN;

ALKALIBACTERIUM; AMPHIBACILLUS; BACTERIA (MICROORGANISMS); HALOMONAS; OCEANOBACILLUS;

EID: 77956535882     PISSN: 01686496     EISSN: 15746941     Source Type: Journal    
DOI: 10.1111/j.1574-6941.2010.00946.x     Document Type: Article

References (28)

1. Bechtold T, Burtscher E, Amann A Bobleter O (1993) Alkali-stable iron complexes as mediators for the electrochemical reduction of dispersed organic dyestaffs. J Chem Soc Faraday T 89 : 2451 2456.
2. Božič M Kokol V (2008) Ecological alternative to the reduction and oxidation processes in dyeing with vat and sulphur dyes. Dyes Pigments 76 : 299 309.
3. Clark RJH, Cooksey CJ, Daniels MAM Withnall R (1993) Indigo, woad, and Tyrian purple: important vat dyes from antiquity to the present. Endeavour 17 : 191 199.
4. Compton RG, Perkin SJ, Gamblin DP, Davis J, Marken F, Padden AN John P (2000) Clostridium isatidis colonised carbon electrodes: voltammetric evidence for direct solid state redox process. New J Chem 24 : 179 181.
5. Dubé E, Shareck F, Hurtubise Y, Daneault C Beauregard M (2008) Homologous cloning, expression, and characterization of a laccase from Streptomyces coelicolor and enzymatic decolourisation of an indigo dye. Appl Microbiol Biot 79 : 597 603.
6. Ehrenreich A Widdel F (1994) Anaerobic oxidation of ferrous iron by purple bacteria, a new type of phototrophic metabolism. Appl Environ Microb 60 : 4517 4526.
7. Eric LR, Sarah B Isiah MW (1998) Spectroscopic studies of indigo carmine dye in organized media. Appl Spectrosc 52 : 1305 1313.
8. Felsenstein J (1985) Confidence limits on phylogenies: an approach using phylogenies: an approach using the bootstrap. Evolution 39 : 783 791.
9. Imai M, Hirano S Aiba M (1983) Aging of 'nukadoko': changes in flavor constituents. Nippon Nogeik Kaishi 57 : 1113 1120 (in Japanese).
10. Iwasaki M Hiraishi A (1998) A new approach to numerical analyses of microbial quinone profiles in the environment. Microb Environ 13 : 67 76.
11. 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.
12. 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 Micr 55 : 1525 1530.
13. Nakayama J, Hoshiko H, Fukuda M, Tanaka H, Sakamoto N, Tanaka S, Ohue K, Sakai K Sonomoto K (2007) Molecular monitoring of bacterial community structure in long-aged nukadoko: pickling bed of fermented rice bran dominated by slow-growing lactobacilli. J Biosci Bioeng 104 : 481 489.
14. Nicholson SK John P (2005) The mechanisms of bacterial indigo reduction. Appl Microbiol Biot 68 : 117 123.
15. Niimura Y, Koh E, Yanagida F, Suzuki K, Komagata K Kozaki M (1990) Amphibacillus xylanus gen. nov., a facultatively anaerobic spore-forming xylan-digesting bacterium which lacks cytochrome, quinone, and catalase. Int J Syst Bacteriol 40 : 297 301.
16. Padden AN, Dillon VM, Edmonds J, Collins MD, Alvarez N John P (1999) An indigo-reducing moderate thermophile from a woad vat, Clostridium isatidis sp. nov. Int J Syst Bacteriol 49 : 1025 1031.
17. Saitou N Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4 : 406 425.
18. Schmidt H (1997) Indigo - 100 Jahre industrielle Synthese. Chem Uns Zeit 31 : 121 128.
19. Tachimoto M (1993) Sodium requirement in indigo fermentation. Bull Res Inst Agric Res Ishikawa Agric Coll 3 : 42 51.
20. Takahara Y Tanabe O (1960) Studies on the reduction of indigo in industrial fermentation vat (V). J Ferment Technol 38 : 293 297 (in Japanese).
21. Takahara Y Tanabe O (1962) Studies on the reduction of indigo in industrial fermentation vat (XIX). J Ferment Technol 40 : 77 80 (in Japanese).
22. Takahara Y, Takasaki Y Tanabe O (1961) Studies on the reduction of indigo in industrial fermentation vat (XVIII). J Ferment Technol 39 : 183 187 (in Japanese).
23. Takahara Y, Takasaki Y Tanabe O (1962) Studies on the reduction of indigo in industrial fermentation vat (XXI). J Ferment Technol 40 : 103 107 (in Japanese).
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.
25. Thompson JD, Higgins DG Gibson TJ (1994) CLUSTAL W: 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.
26. Toyama S, Kawaguchi Y Yonaha K (1978) Studies on the vat fermentation with Ryukyuai: (3) On the indigo-reducing bacteria. Sci Bull Coll Agric Univ Ryukyus 25 : 225 233 (in Japanese).
27. 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 Micr 54 : 2379 2383.
28. Yumoto I, Hirota K, Nodasaka Y, Tokiwa Y Nakajima K (2008) Alkalibacterium indicireducens sp. nov., an obligate alkaliphile that reduces an indigo dye. Int J Syst Evol Micr 58 : 901 905.