Hymenobacter daecheongensis sp. nov., isolated from stream sediment

International Journal of Systematic and Evolutionary Microbiology

Volumn 59, Issue 5, 2009, Pages 1183-1187

  Xu, Jin Li ^a,b   Liu, Qing Mei ^a   Yu, Hong Shan ^b   Jin, Feng Xie ^b   Lee, Sung Taik ^a   Im, Wan Taek ^a  

^a Korea Advanced Institute of Science and Technology (KAIST)   (South Korea)

^b DALIAN POLYTECHNIC UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOSINE; GUANINE; RNA 16S; BACTERIAL DNA; FATTY ACID; RIBOSOME DNA;

ARTICLE; BACTERIAL STRAIN; BACTERIUM IDENTIFICATION; BACTERIUM ISOLATION; CHEMOTAXONOMY; CONTROLLED STUDY; DNA BASE COMPOSITION; DNA CONTENT; GRAM NEGATIVE AEROBIC RODS AND COCCI; HYMENOBACTER DAECHEONGENSIS; LIPID COMPOSITION; NEW SPECIES; NONHUMAN; NUCLEOTIDE SEQUENCE; PHENOTYPE; PHYLOGENETIC TREE; PRIORITY JOURNAL; SEDIMENT; SEQUENCE ANALYSIS; SOUTH KOREA; STREAM (RIVER); TYPE STRAIN; CLASSIFICATION; DNA SEQUENCE; FLEXIBACTERACEAE; GENETICS; ISOLATION AND PURIFICATION; KOREA; MICROBIOLOGY; MOLECULAR GENETICS; PHYLOGENY; PHYSIOLOGY; RIVER; RNA GENE; SPECIES DIFFERENCE;

BACTERIA (MICROORGANISMS); HYMENOBACTER; NEGIBACTERIA;

BACTERIAL TYPING TECHNIQUES; DNA, BACTERIAL; DNA, RIBOSOMAL; FATTY ACIDS; FLEXIBACTERACEAE; GENES, RRNA; GEOLOGIC SEDIMENTS; KOREA; MOLECULAR SEQUENCE DATA; PHENOTYPE; PHYLOGENY; RIVERS; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY;

EID: 67649824082     PISSN: 14665026     EISSN: None     Source Type: Journal    
DOI: 10.1099/ijs.0.002444-0     Document Type: Article

References (30)

1. Atlas, R. M. (1993). Handbook of Microbiological Media. Edited by L. C. Parks. Boca Raton, FL: CRC Press.
2. Baik, K. S., Seong, C. N., Moon, E. Y., Park, Y.-D., Yi, H. & Chun, J. (2006). Hymenobacter rigui sp. nov., isolated from wetland freshwater. Int J Syst Evol Microbiol 56, 2189-2192.
3. Benson, D. A., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J. & Wheeler, D. L. (2005). GenBank. Nucleic Acids Res 33, D34-D38.
4. Buck, J. D. (1982). Nonstaining (KOH) method for determination of gram reactions of marine bacteria. Appl Environ Microbiol 44, 992-993.
5. Buczolits, S., Denner, E. B. M., Vybiral, D., Wieser, M., Kämpfer, P. & Busse, H. J. (2002). Classification of three airborne bacteria and proposal of Hymenobacter aerophilus sp. nov. Int J Syst Evol Microbiol 52, 445-456.
6. Buczolits, S., Denner, E. B. M., Kämpfer, P. & Busse, H. J. (2006). Proposal of Hymenobacter norwichensis sp. nov., classification of 'Taxeobacter ocellatus', 'Taxeobacter gelupurpurascens' and 'Taxeobacter chitinovorans' as Hymenobacter ocellatus sp. nov., Hymenobacter gelipurpurascens sp. nov. and Hymenobacter chitinivorans sp. nov., respectively, and emended description of the genus Hymenobacter Hirsch et al. 1999. Int J Syst Evol Microbiol 56, 2071-2078.
7. Cole, J. R., Chai, B., Farris, R. J., Wang, Q., Kulam, S. A., McGarrell, D. M., Garrity, G. M. & Tiedje, J. M. (2005). The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis. Nucleic Acids Res 33, D294-D296.
8. Collins, M. D., Hutson, R. A., Grant, I. R. & Patterson, M. F. (2000). Phylogenetic characterization of a novel radiation-resistant bacterium from irradiated pork: description of Hymenobacter actinosclerus sp. nov. Int J Syst Evol Microbiol 50, 731-734.
9. Fautz, E. & Reichenbach, H. (1980). A simple test for flexirubin-type pigments. FEMS Microbiol Lett 8, 87-91.
10. Felsenstein, J. (1985). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783-791.
11. Garrity, G. M. & Holt, J. G. (2001). The road map to the Manual. In Bergey's Manual of Systematic Bacteriology, 2nd edn, pp. 119-166. Edited by D. R. Boone, R. W. Castenholz & G.M. Garrity. New York: Springer.
12. Hall, T. A. (1999). BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41, 95-98.
13. Hiraishi, A., Ueda, Y., Ishihara, J. & Mori, T. (1996). Comparative lipoquinone analysis of influent sewage and activated sludge by highperformance liquid chromatography and photodiode array detection. J Gen Appl Microbiol 42, 457-469.
14. Hirsch, P., Ludwig, W., Hethke, C., Sittig, M., Hoffmann, B. & Gallikowski, C. A. (1998). Hymenobacter roseosalivarius gen. nov., sp. nov. from continental Antarctica soils and sandstone: bacteria of the Cytophaga/Flavobacterium/Bacteroides line of phylogenetic descent. Syst Appl Microbiol 21, 374-383.
15. Im, W.-T., Kang, M. S., Park, H. Y., Kim, M.-K. & Lee, S.-T. (2003). Culturable bacterial strain's diversity of environmental samples. In Proceedings of the International Meeting of the Federation of Korean Microbiological Societies, abstract B4023, p. 165. Seoul: Federation of Korean Microbiological Societies.
16. Kim, M.-K., Im, W.-T. & Lee, S.-T. (2008). Hymenobacter soli sp. nov., isolated from grass soil. Int J Syst Evol Microbiol 58, 211-213.
17. Kimura, M. (1983). The Neutral Theory of Molecular Evolution. Cambridge: Cambridge University Press.
18. Kouker, G. & Jaeger, K.-E. (1987). Specific and sensitive plate assay for bacterial lipases. Appl Environ Microbiol 53, 211-213.
19. Kumar, S., Tamura, K. & Nei, M. (2004). MEGA3: integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Brief Bioinform 5, 150-163.
20. 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.
21. Moore, D. D. & Dowhan, D. (1995). Preparation and analysis of DNA. In Current Protocols in Molecular Biology, pp. 2-11. Edited by F. W. Ausubel, R. Brent, R. E. Kingston, D. D. Moore, J. G. Seidman, J. A. Smith & K. Struhl. New York: Wiley.
22. Saitou, N. & Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406-425.
23. Sasser, M. (1990). Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. Newark, DE: MIDI Inc.
24. Ten, L. N., Im, W.-T., Kim, M.-K., Kang, M.-S. & Lee, S.-T. (2004). Development of a plate technique for screening of polysaccharidedegrading microorganisms by using a mixture of insoluble chromogenic substrates. J Microbiol Methods 56, 375-382.
25. Ten, L. N., Jung, H.-M., Yoo, S.-A., Im, W.-T. & Lee, S.-T. (2008). Lysobacter daecheongensis sp. nov., isolated from sediment of stream near the Daechung dam in South Korea. J Microbiol 46, 519-524.
26. Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F. & Higgins, D. G. (1997). The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25, 4876-4882.
27. Tschech, A. & Pfennig, N. (1984). Growth yield increase linked to caffeate reduction in Acetobacterium woodii. Arch Microbiol 137, 163-167.
28. Widdel, F. & Bak, F. (1992). Gram-negative mesophilic sulfate reducing bacteria. In The Prokaryotes, 2nd edn, pp. 3352-3378. Edited by A. Balows, H. G. Trüper, M. Dworkin, W. Harder & K. H. Schleifer. New York: Springer-Verlag.
29. Widdel, F., Kohring, G.-W. & Mayer, F. (1983). Studies on dissimilatory sulfate-reducing bacteria that decompose fatty acids. III. Characterization of the filamentous gliding Desulfonema limicola gen. nov. sp. nov., and Desulfonema magnum sp. nov. Arch Microbiol 134, 286-294.
30. Zhang, Q., Liu, C., Tang, Y., Zhou, G., Shen, P., Fang, C. & Yokota, A. (2007). Hymenobacter xinjiangensis sp. nov., a radiation-resistant bacterium isolated from the desert of Xinjiang, China. Int J Syst Evol Microbiol 57, 1752-1756.