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Volume 58, Issue 3

gen. nov., sp. nov., a zeaxanthin-producing bacterium of the family isolated from freshwater Free

Abstract

A yellow-pigmented, Gram-negative, strictly aerobic, rod-shaped bacterium (TDMA-5) was isolated from a freshwater sample collected at Misasa (Tottori, Japan). The DNA G+C content was 38.6 mol%. Major fatty acids were iso-C, iso-C 3-OH and summed feature 4 (iso-C 2-OH and/or C 7). MK-7 was the predominant respiratory quinone. Zeaxanthin was the major carotenoid pigment produced; flexirubin-type pigments were not produced. TDMA-5 was sensitive to gamma-irradiation. The strain degraded gelatin, casein, starch, Tween 80 and DNA. Phylogenetic analysis based on the 16S rRNA gene sequence placed TDMA-5 in a distinct lineage in the family , sharing 89.4–93.4 % sequence similarity with members of the nearest genus . Strain TDMA-5 could be distinguished from the other members of the family by a number of chemotaxonomic and phenotypic characteristics. Based on its unique phenotypic, genotypic and phylogenetic features, strain TDMA-5 represents a novel genus and species, for which the name gen. nov., sp. nov. is proposed. The type strain of is TDMA-5 (=NBRC 102579 =CCUG 54348).

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2008-03-01
2024-04-18
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References

  1. Alcantara, S. & Sanchez, S.(1999). Influence of carbon and nitrogen sources on Flavobacterium growth and zeaxanthin biosynthesis. J Ind Microbiol Biotechnol 23, 697–700.[CrossRef] [Google Scholar]
  2. Asker, D., Beppu, T. & Ueda, K.(2007a).Mesoflavibacter zeaxanthinifaciens gen. nov., sp. nov., a novel zeaxanthin-producing marine bacterium of the family Flavobacteriaceae. Syst Appl Microbiol 30, 291–296.[CrossRef] [Google Scholar]
  3. Asker, D., Beppu, T. & Ueda, K.(2007b).Zeaxanthinibacter enoshimensis gen. nov., sp. nov., a novel zeaxanthin-producing marine bacterium of the family Flavobacteriaceae, isolated from seawater off Enoshima Island, Japan. Int J Syst Evol Microbiol 57, 837–843.[CrossRef] [Google Scholar]
  4. Asker, D., Beppu, T. & Ueda, K.(2007c).Sphingomonas astaxanthinifaciens sp. nov., a novel astaxanthin-producing bacterium of the family Sphingomonadaceae isolated from Misasa, Tottori, Japan. FEMS Microbiol Lett 273, 140–148.[CrossRef] [Google Scholar]
  5. Berry, A., Janssens, D., Humbelin, M., Jore, J. P., Hoste, B., Cleenwerck, I., Vancanneyt, M., Bretzel, W., Mayer, A. F. & other authors(2003).Paracoccus zeaxanthinifaciens sp. nov., a zeaxanthin-producing bacterium. Int J Syst Evol Microbiol 53, 231–238.[CrossRef] [Google Scholar]
  6. Collins, M. D.(1994). Isoprenoid quinones. In Chemical Methods in Prokaryotic Systematics, pp. 265–310. Edited by M. Goodfellow & A. G. O'Donnell. Chichester: Wiley.
  7. Felsenstein, J.(1993).phylip (phylogeny inference package), version 3.5. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle, USA.
  8. Gallego, V., Garcia, M. T. & Ventosa, A.(2006).Pedobacter aquatilis sp. nov., isolated from drinking water, and emended description of the genus Pedobacter. Int J Syst Evol Microbiol 56, 1853–1858.[CrossRef] [Google Scholar]
  9. Hundle, B. S., O'Brien, D. A., Beyer, P., Kleinig, H. & Hearst, J. E.(1993). In vitro expression and activity of lycopene cyclase and beta-carotene hydroxylase from Erwinia herbicola. FEBS Lett 315, 329–334.[CrossRef] [Google Scholar]
  10. Hwang, C. Y., Choi, D. H. & Cho, B. C.(2006).Pedobacter roseus sp. nov., isolated from a hypertrophic pond, and emended description of the genus Pedobacter. Int J Syst Evol Microbiol 56, 1831–1836.[CrossRef] [Google Scholar]
  11. Kametani, K. & Matsumura, T.(1983). Determination of 238U, 234U, 226Ra and 228Ra in spring waters of Sanin district. Radioisotopes 32, 18–21 (in Japanese).[CrossRef] [Google Scholar]
  12. Kim, K. H., Ten, L. N., Liu, Q. M., Im, W. T. & Lee, S. T.(2006).Sphingobacterium daejeonense sp. nov., isolated from a compost sample. Int J Syst Evol Microbiol 56, 2031–2036.[CrossRef] [Google Scholar]
  13. Kim, M. K., Na, J. R., Cho, D. H., Soung, N. K. & Yang, D. C.(2007).Parapedobacter koreensis gen. nov., sp. nov. Int J Syst Evol Microbiol 57, 1336–1341.[CrossRef] [Google Scholar]
  14. Kwon, S. W., Kim, B. Y., Lee, K. H., Jang, K. Y., Seok, S. J., Kwon, J. S., Kim, W. G. & Weon, H. Y.(2007).Pedobacter suwonensis sp. nov., isolated from the rhizosphere of Chinese cabbage (Brassica campestris). Int J Syst Evol Microbiol 57, 480–484.[CrossRef] [Google Scholar]
  15. Lagarde, D., Beuf, L. & Vermaas, W.(2000). Increased production of zeaxanthin and other pigments by application of genetic engineering techniques to Synechocystis sp. strain PCC 6803. Appl Environ Microbiol 66, 64–72.[CrossRef] [Google Scholar]
  16. Margesin, R., Spröer, C., Schumann, P. & Schinner, F.(2003).Pedobacter cryoconitis sp. nov., a facultative psychrophile from alpine glacier cryoconite. Int J Syst Evol Microbiol 53, 1291–1296.[CrossRef] [Google Scholar]
  17. McDermott, J. C., Britton, G. & Goodwin, T. W.(1973). Carotenoid biosynthesis in a Flavobacterium sp.: stereochemistry of hydrogen elimination in the desaturation of phytoene to lycopene, rubixanthin and zeaxanthin. Biochem J 134, 1115–1117. [Google Scholar]
  18. Mesbah, M. & Whitman, W. B.(1989). Measurement of deoxyguanosine/thymidine ratios in complex mixtures by high-performance liquid chromatography for determination of the mole percentage guanine + cytosine of DNA. J Chromatogr 479, 297–306.[CrossRef] [Google Scholar]
  19. Nelis, H. J. & De Leenheer, A. P.(1989). Profiling and quantitation of bacterial carotenoids by liquid chromatography and photodiode array detection. Appl Environ Microbiol 55, 3065–3071. [Google Scholar]
  20. Norris, J. R., Ribbons, D. W. & Varma, A. K. (editors)(1985).Methods in Microbiology, vol. 18. London: Academic Press.
  21. Ntougias, S., Fasseas, C. & Zervakis, G. I.(2007).Olivibacter sitiensis gen. nov., sp. nov., isolated from alkaline olive-oil mill wastes in the region of Sitia, Crete. Int J Syst Evol Microbiol 57, 398–404.[CrossRef] [Google Scholar]
  22. Perrière, G. & Gouy, M.(1996). WWW-query: an on-line retrieval system for biological sequence banks. Biochimie 78, 364–369.[CrossRef] [Google Scholar]
  23. Rosa-Putra, S., Hemmerlin, A., Epperson, J., Bach, T. J., Guerra, L. H. & Rohmer, M.(2001). Zeaxanthin and menaquinone-7 biosynthesis in Sphingobacterium multivorum via the methylerythritol phosphate pathway. FEMS Microbiol Lett 204, 347–353.[CrossRef] [Google Scholar]
  24. Saitou, N. & Nei, M.(1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425. [Google Scholar]
  25. Shivaji, S., Ray, M. K., Rao, N. S., Saisree, L., Jagannadham, M. V., Kumar, G. S., Reddy, G. S. N. & Bhargava, P. M.(1992).Sphingobacterium antarcticus sp. nov., a psychrotrophic bacterium from the soils of Schirmacher Oasis, Antarctica. Int J Syst Bacteriol 42, 102–106.[CrossRef] [Google Scholar]
  26. Shivaji, S., Chaturvedi, P., Reddy, G. S. & Suresh, K.(2005).Pedobacter himalayensis sp. nov., from the Hamta glacier located in the Himalayan mountain ranges of India. Int J Syst Evol Microbiol 55, 1083–1088.[CrossRef] [Google Scholar]
  27. Smibert, R. M. & Krieg, N. R.(1994). Phenotypic characterization, In Methods for General and Molecular Bacteriology, pp. 607–654. Edited by P. Gerhardt, R. G. E. Murray, W. A. Wood & N. R. Krieg. Washington, DC: American Society for Microbiology.
  28. Steyn, P. L., Segers, P., Vancanneyt, M., Sandra, P., Kersters, K. & Joubert, J. J.(1998). Classification of heparinolytic bacteria into a new genus, Pedobacter, comprising four species: Pedobacter heparinus comb. nov., Pedobacter piscium comb. nov., Pedobacter africanus sp. nov. and Pedobacter saltans sp. nov. Proposal of the family Sphingobacteriaceae fam. nov. Int J Syst Bacteriol 48, 165–177.[CrossRef] [Google Scholar]
  29. Takeuchi, M. & Yokota, A.(1992). Proposals of Sphingobacterium faecium sp. nov., Sphingobacterium piscium sp. nov., Sphingobacterium heparinum comb. nov., Sphingobacterium thalpophilum comb. nov. and two genospecies of the genus Sphingobacterium, and synonymy of Flavobacterium yabuuchiae and Sphingobacterium spiritivorum. J Gen Appl Microbiol 38, 465–482.[CrossRef] [Google Scholar]
  30. Ten, L. N., Liu, Q.-M., Im, W.-T., Lee, M., Yang, D.-C. & Lee, S.-T.(2006).Pedobacter ginsengisoli sp. nov., a DNase-producing bacterium isolated from soil of a ginseng field in South Korea. Int J Syst Evol Microbiol 56, 2565–2570.[CrossRef] [Google Scholar]
  31. Thompson, J. D., Higgins, D. G. & Gibson, T. J.(1994).clustalw: 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.[CrossRef] [Google Scholar]
  32. Vanparys, B., Heylen, K., Lebbe, L. & De Vos, P.(2005).Pedobacter caeni sp. nov., a novel species isolated from a nitrifying inoculum. Int J Syst Evol Microbiol 55, 1315–1318.[CrossRef] [Google Scholar]
  33. Yabuuchi, E., Kaneko, T., Yano, I., Moss, C. W. & Miyoshi, N.(1983).Sphingobacterium gen. nov., Sphingobacterium spiritivorum comb. nov., Sphingobacterium multivorum comb. nov., Sphingobacterium mizutae sp. nov., and Flavobacterium indologenes sp. nov.: glucose-nonfermenting gram-negative rods in CDC groups IIK-2 and IIb. Int J Syst Bacteriol 33, 580–598.[CrossRef] [Google Scholar]
  34. Yoon, J.-H., Lee, M.-H., Kang, S.-J., Park, S.-Y. & Oh, T.-K.(2006).Pedobacter sandarakinus sp. nov., isolated from soil. Int J Syst Evol Microbiol 56, 1273–1277.[CrossRef] [Google Scholar]
  35. Yoon, M.-H., Ten, L. N., Im, W.-T. & Lee, S.-T.(2007).Pedobacter panaciterrae sp. nov., isolated from soil in South Korea. Int J Syst Evol Microbiol 57, 381–386.[CrossRef] [Google Scholar]
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Nubsella zeaxanthinifaciens gen. nov., sp. nov., a zeaxanthin-producing bacterium of the family Sphingobacteriaceae isolated from freshwater
Int J Syst Evol Microbiol 58, 601 (2008); https://doi.org/10.1099/ijs.0.65493-0
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Phylogenetic trees based on the 16S rRNA gene sequences of strain TDMA-5 and representative members of related genera in the family . [PDF](21 KB)

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Scanning electron micrograph of strain TDMA-5 grown on LB agar at 30 °C. Cells were long rods after 3 days cultivation. Bar, 1 µm.

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Whole-cell fatty acid profile of strain TDMA-5 . [PDF](21 KB)

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