Sphingobacterium composti sp. nov., a novel DNase-producing bacterium isolated from compost

Journal of Microbiology and Biotechnology

Volumn 16, Issue 11, 2006, Pages 1728-1733

  Ten, Leonid N ^a,b   Liu, Qing Mei ^a   Im, Wan Taek ^a   Aslam, Zubair ^a   Lee, Sung Taik ^a  

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

^b NATIONAL UNIVERSITY OF UZBEKISTAN   (Uzbekistan)

Author keywords

Compost; Polyphasic taxonomy; Sphingobacterium composti sp. nov.

Indexed keywords

BACTERIAL DNA; CASEIN; CATALASE; CELLULOSE; CHITIN; COLLAGEN; CYTOSINE; DEOXYRIBONUCLEASE; FATTY ACID; GUANINE; MENAQUINONE; OXIDOREDUCTASE; RNA 16S; STARCH; XYLAN;

AEROBIC BACTERIUM; ANIMAL CELL; ARTICLE; BACTERIAL STRAIN; BACTERIUM IDENTIFICATION; BACTERIUM ISOLATION; COMPOST; CONTROLLED STUDY; DNA CONTENT; DNA DEGRADATION; ENZYME SYNTHESIS; FATTY ACID ANALYSIS; GENE CLUSTER; GENUS; GRAM NEGATIVE BACTERIUM; MACROMOLECULE; MICROBIAL DEGRADATION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHENOTYPE; PHYLOGENY; RNA SEQUENCE; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SPECIES IDENTIFICATION; SPHINGOBACTERIUM; SPHINGOBACTERIUM COMPOSTI; TAXONOMY;

BACTERIA (MICROORGANISMS); NEGIBACTERIA; SPHINGOBACTERIUM;

EID: 33845590365     PISSN: 10177825     EISSN: 17388872     Source Type: Journal    
DOI: None     Document Type: Article

References (33)

1. Atlas, R. M. 1993. In L. C. Parks (ed.). Handbook of Microbiological Media. CRC Press, Boca Raton, Florida.
2. Buck, J. D. 1982. Nonstaining (KOH) method for determination of Gram reactions of marine bacteria. Appl. Environ. Microbiol. 44: 992-993.
3. Cappuccino, J. G. and N. Sherman. 2002. Microbiology: A Laboratory Manual, 6th Ed. Benjamin Cummings, San Francisco.
4. Felsenstein, J. 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39: 783-791.
5. Fitch, W. M. 1972. Toward defining the course of evolution: Minimum change for a specific tree topology. Syst. Zool. 20: 406-416.
6. Hall, M. G. 1999. BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl. Acids Symp. Ser. 41: 95-98.
7. Holmes, B., R. J. Owen, and R. E. Weaver. 1981. Flavobacterium multivorum, a new species isolated from human clinical specimens and previously known as group IIk, biotype 2. Int. J. Syst. Bacteriol. 31: 21-34.
8. Holmes, B., R. J. Owen, and D. G. Hollis. 1982. Flavobacterium spiritivorum, a new species isolated from human clinical specimens. Int. J. Syst. Bacteriol. 32: 157-165.
9. Holmes, B., R. E. Weaver, A. G. Steigerwalt, and D. J. Brenner. 1988. A taxonomic study of Flavobacterium spiritivorum and Sphingobacterium mizutae: Proposal of Flavobacterium yabuuchiae sp. nov. and Flavobacterium mizutaii comb. nov. Int. J. Syst. Bacteriol. 38: 348-353.
10. Keswani, J. and W. B. Whitman. 2001. Relationship of 16S rRNA sequence similarity to DNA hybridization in prokaryotes. Int. J. Syst. Evol. Microbiol. 51: 667-678.
11. Kim, M. K., W.-T. Im, H. Ohta, M. Lee, and S.-T. Lee. 2005. Sphingopyxis granuli sp. nov., a β-glucosidase producing bacterium in the family Sphingomonadaceae in α-4 subclass of the Proteobacteria. J. Microbiol. 43: 152-157.
12. Kim, K.-H., L. N. Ten, Q.-M. Liu, W.-T. Im, and S.-T. Lee. 2006. Sphingobacterium daejeonense sp. nov., isolated from a compost sample. Int. J. Syst. Bacteriol. (in press).
13. Kimura, M. 1983. The Neutral Theory of Molecular Evolution. Cambridge University Press, Cambridge.
14. Kouker, G. and K.-E Jaeger. 1987. Specific and sensitive plate assay for bacterial lipases. Appl. Environ. Microbiol. 53: 211-213.
15. Kumar, S., K. Tamura, and M. Nei. 2004. MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment briefings. Bioinformatics 5: 150-163.
16. Mesbah, M., U. Premachandran, and W. Whitman. 1989. Precise measurement of the G+C content of deoxyribonucleic acid by high performance liquid chromatography. Int. J. Syst. Bacteriol. 39: 159-167.
17. Moore, D. D. 1995. Preparation and analysis of DNA, pp. 2-11. In F. W. Ausubel, R. Brent, R. E. Kingston, D. D. Moore, J. G. Seidman, J. A. Smith, and K. Struhl (eds.), Current Protocols in Molecular Biology. Wiley, New York, U.S.A.
18. Saitou, N. and M. Nei. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Molec. Biol. Evol. 4: 406-425.
19. Sasser, M. 1990. Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Technical Note 101. Newark, DE: MIDI. U.S.A.
20. T. J. Microbiol. Biotechnol. 6: 68-69.
21. Shivaji, S., M. K. Ray, S. N. Rao, L. Saisree, M. V. Jagannadham, G. S. Kumar, G. S. N. Reddy, and P. M. Bhargava. 1992. Sphingobacterium antarcticus sp. nov., a psychotrophic bacterium from soils of Schirmacher Oasis, Antarctica. Int. J. Syst. Bacteriol. 42: 102-106.
22. Steyn, P. L., P. Segers, M. Vancanneyt, P. Sandra, K. Kersters, and J. J. Joubert. 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.
23. Stackebrandt, E. and B. M. Goebel. 1994. Taxonomic note: A place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int. J. Syst. Bacteriol. 44: 846-849.
24. Takeuchi, M. and A. Yokota. 1992. Proposals of Sphingobacterium faecium sp. nov., Sphingo bacterium 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.
25. Ten, L. N., W.-T. Im, M.-K. Kim, M.-S. Kang, and S.-T. Lee. 2004. Development of a plate technique for screening of polysaccharide-degrading microorganisms by using a mixture of insoluble chromogenic substrates. J. Microbiol. Meth. 56: 375-382.
26. Ten, L. N., W.-T. Im, M.-K. Kim, and S.-T. Lee. 2005. A plate assay for simultaneous screening of polysaccharide-and protein-degrading microorganisms. Lett. Appl. Microbiol. 40: 92-98.
27. Thompson, J. D., T. J. Gibson, F. Plewniak, F. Jeanmougin, and D. Higgins. 1997. The Clustal_X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 24: 4876-4882.
28. Tschech, A. and N. Pfennig. 1984. Growth yield increase linked to caffeate reduction in Acetobacterium woodii. Arch. Microbiol. 137: 163-167.
29. Wayne, L. G., D. J. Brenner, R. R. Colwell, et al. 1987. International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int. J. Syst. Bacteriol. 37: 463-464.
30. Widdel, F., G. W. Kohring, and F. Mayer. 1983. Studies on dissimilatory sulfate-reducing bacteria that decompose fatty acids. 3. Characterization of filamentous gliding Desulfonema limicola gen. nov. sp. nov., and Desulfonema magnum sp. nov. Arch. Microbiol. 134: 286-294.
31. Widdel, F. and F. Bak. 1992. Gram-negative mesophilic sulfate reducing bacteria, pp. 3352-3378. In A. Balows, H. G. Trüper, M. Dworkin, W. Harder, and K. H. Schleifer (eds.), The Prokaryotes, 2nd Ed. Springer, New York.
32. Yabuuchi, E., T. Kaneko, I. Yano, C. W. Moss, and N. Miyoshi. 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.
33. Yeo, H. S., O. S. Lee, I. S. Lee, H. S. Kim, T. S. Yu, and Y. J. Jeong. 2004. Gluconacetobacter persimmonis sp. nov., isolated from Korean traditional persimmon vinegar. J. Microbiol. Biotechnol. 14: 276-283.