Oceanobacillus indicireducens sp. nov., a facultative alkaliphile that reduces an indigo dye

International Journal of Systematic and Evolutionary Microbiology

Volumn 63, Issue PART4, 2013, Pages 1437-1442

  Hirota, Kikue ^a   Aino, Kenichi ^a,b   Nodasaka, Yoshinobu ^b   Yumoto, Isao ^a,b  

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

^b HOKKAIDO UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

CASEIN; FATTY ACID; GELATIN; INDIGO CARMINE; RNA 16S;

ARTICLE; BACILLUS; BACTERIAL GROWTH; BACTERIAL STRAIN; CHIRONOMIDAE; CONTROLLED STUDY; DNA DNA HYBRIDIZATION; FLAGELLUM; GENE EXPRESSION PROFILING; GENE SEQUENCE; GRAM POSITIVE BACTERIUM; NONHUMAN; NUCLEOTIDE SEQUENCE; OCEANOBACILLUS INDICIREDUCENS; PH; PHYLOGENY; PRIORITY JOURNAL; WHOLE CELL;

EID: 84874036145     PISSN: 14665026     EISSN: None     Source Type: Journal    
DOI: 10.1099/ijs.0.034579-0     Document Type: Article

References (39)

1. Aino, K., Narihiro, T., Minamida, K., Kamagata, Y., Yoshimune, K. & Yumoto, I. (2010). Bacterial community characterization and dynamics of indigo fermentation. FEMS Microbiol Ecol 74, 174-183.
2. 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.
3. 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 Bacteriol 48, 452-470.
4. 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 Bacteriol 39, 224-229.
5. Felsenstein, J. (1981). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17, 368-376.
6. Fitch, W. M. (1971). Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20, 406-416.
7. Guindon, S. & Gascuel, O. (2003). A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52, 696-704.
8. Heyrman, J., Logan, N. A., Busse, H.-J., Balcaen, A., Lebbe, L., Rodriguez-Diaz, M., Swings, J. & De Vos, P. (2003). Virgibacillus carmonensis sp. nov., Virgibacillus necropolis sp. nov. and Virgibacillus picturae sp. nov., three novel species isolated from deteriorated mural paintings, transfer of the species of the genus Salibacillus to Virgibacillus, as Virgibacillus marismortui comb. nov. and Virgibacillus salexigens com. nov., and emended description of the genus Virgibacillus. Int J Syst Evol Microbiol 53, 501-511.
9. Kim, Y.-G., Choi, D. H., Hyun, S. & Cho, B. C. (2007). Oceanobacillus profundus sp. nov., isolated from a deep-sea sediment core. Int J Syst Evol Microbiol 57, 409-413.
10. 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.
11. Lee, J.-S., Lim, J.-M., Lee, K. C., Lee, J. C., Park, Y.-H. & Kim, C.-J. (2006). Virgibacillus koreensis sp. nov., a novel bacterium from a salt field, and transfer of Virgibacillus picturae to Oceanobacillus as Oceanobacillus picturae comb. nov. with emended descriptions. Int J Syst Evol Microbiol 56, 251-257.
12. Lee, S.-Y., Oh, T.-K., Kim, W. & Yoon, J.-H. (2010). Oceanobacillus locisalsi sp. nov., isolated from a marine solar saltern. Int J Syst Evol Microbiol 60, 2758-2762.
13. Lu, J., Nogi, Y. & Takami, H. (2001). Oceanobacillus iheyensis gen. nov., sp. nov., a deep-sea extremely halotolerant and alkaliphilic species isolated from a depth of 1050 m on the Iheya Ridge. FEMS Microbiol Lett 205, 291-297.
14. Lu, J., Nogi, Y. & Takami, H. (2002). Oceanobacillus iheyensis gen. nov., sp. nov. In Validation List no. 85. Validation of publication of new names and new combinations previously effectively published outside the IJSEM. Int J Syst Evol Microbiol 52, 685-690.
15. Marmur, J. (1961). A procedure for the isolation of deoxyribonucleic acid from micro-organisms. J Mol Biol 3, 208-218.
16. 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 Bacteriol 47, 87-95.
17. 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 Microbiol 55, 1525-1530.
18. Nam, J.-H., Bae, W. & Lee, D.-H. (2008). Oceanobacillus caeni sp. nov., isolated from a Bacillus-dominated wastewater treatment system in Korea. Int J Syst Evol Microbiol 58, 1109-1113.
19. Namwong, S., Tanasupawat, S., Lee, K. C. & Lee, J.-S. (2009). Oceanobacillus kapialis sp. nov., from fermented shrimp paste in Thailand. Int J Syst Evol Microbiol 59, 2254-2259.
20. 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 Bacteriol 49, 1025-1031.
21. Raats, D. & Halpern, M. (2007). Oceanobacillus chironomi sp. nov., a halotolerant and facultatively alkaliphilic species isolated from a chironomid egg mass. Int J Syst Evol Microbiol 57, 255-259.
22. Romano, I., Lama, L., Nicolaus, B., Poli, A., Gambacorta, A. & Giordano, A. (2006). Oceanobacillus oncorhynchi subsp. incaldanensis subsp. nov., an alkalitolerant halophile isolated from an algal mat collected from a sulfurous spring in Campania (Italy), and emended description of Oceanobacillus oncorhynchi. Int J Syst Evol Microbiol 56, 805-810.
23. Saitou, N. & Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406-425.
24. Staneck, J. L. & Roberts, G. D. (1974). Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 28, 226-231.
25. Takahara, Y. & Tanabe, O. (1960). Studies on the reduction of indigo in industrial fermentation vat (VII). J Ferment Technol 38, 329-331.
26. Tamaoka, J. & Komagata, K. (1984). Determination of DNA base composition by reversed-phase high-performance liquid chromatography. FEMS Microbiol Lett 25, 125-128.
27. 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 Evol 28, 2731-2739.
28. Teather, R. M. & Wood, P. J. (1982). Use of Congo red-polysaccharide interactions in enumeration and characterization of cellulolytic bacteria from the bovine rumen. Appl Environ Microbiol 43, 777-780.
29. 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 Res 22, 4673-4680.
30. Tominaga, T., An, S.-Y., Oyaizu, H. & Yokota, A. (2009). Oceanobacillus soja sp. nov. isolated from soy sauce production equipment in Japan. J Gen Appl Microbiol 55, 225-232.
31. Wang, L., Liu, W.-Y., Gu, Z.-J., Chen, S.-F. & Yang, S.-S. (2010). Oceanobacillus manasiensis sp. nov., a moderately halophilic bacterium isolated from the salt lakes of Xinjiang, China. J Microbiol 48, 312-317.
32. Whon, T. W., Jung, M.-J., Roh, S. W., Nam, Y. D., Park, E.-J., Shin, K.-S. & Bae, J.-W. (2010). Oceanobacillus kimchii sp. nov. isolated from a traditional Korean fermented food. J Microbiol 48, 862-866.
33. Yang, J.-Y., Huo, Y.-Y., Xu, X.-W., Meng, F.-X., Wu, M. & Wang, C.-S. (2010). Oceanobacillus neutriphilus sp. nov., isolated from activated sludge in a bioreactor. Int J Syst Evol Microbiol 60, 2409-2414.
34. Yumoto, I., Yamazaki, K., Sawabe, T., Nakano, K., Kawasaki, K., Ezura, Y. & Shinano, H. (1998). Bacillus horti sp. nov., a new gramnegative alkaliphilic bacillus. Int J Syst Bacteriol 48, 565-571.
35. 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 Microbiol 51, 349-355.
36. 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 Microbiol 52, 85-90.
37. 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 Microbiol 54, 2379-2383.
38. Yumoto, I., Hirota, K., Nodasaka, Y. & Nakajima, K. (2005). Oceanobacillus oncorhynchi sp. nov., a halotolerant obligate alkaliphile isolated from the skin of a rainbow trout (Oncorhynchus mykiss), and emended description of the genus Oceanobacillus. Int J Syst Evol Microbiol 55, 1521-1524.
39. 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 Microbiol 58, 901-905.