Pedobacter roseus sp. nov., isolated from a hypertrophic pond, and emended description of the genus Pedobacter

International Journal of Systematic and Evolutionary Microbiology

Volumn 56, Issue 8, 2006, Pages 1831-1836

  Hwang, Chung Yeon ^a   Choi, Dong Han ^a   Cho, Byung Cheol ^a  

^a Seoul National University   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL RNA; RNA 16S;

ARTICLE; BACTERIAL GENE; BACTERIAL GROWTH; BACTERIAL STRAIN; BACTERIUM IDENTIFICATION; BACTERIUM ISOLATION; CHEMOTAXONOMY; DNA CONTENT; DNA SEQUENCE; FATTY ACID ANALYSIS; GENE SEQUENCE; GRAM NEGATIVE BACTERIUM; KOREA; MICROBIAL MORPHOLOGY; NONHUMAN; NUCLEOTIDE SEQUENCE; PEDOBACTER HEPARINUS; PEDOBACTER ROSEUS; PHENOTYPE; PHYLOGENY; PRIORITY JOURNAL; SPHINGOBACTERIACEAE; STRAIN DIFFERENCE; TAXONOMY;

BACTEROIDES; DNA, BACTERIAL; FRESH WATER; HYDROGEN-ION CONCENTRATION; KOREA; MOLECULAR SEQUENCE DATA; NUCLEIC ACID HYBRIDIZATION; PHYLOGENY; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S; SEQUENCE HOMOLOGY, NUCLEIC ACID; SPECIES SPECIFICITY; TEMPERATURE; WATER MICROBIOLOGY;

BACTERIA (MICROORGANISMS); NEGIBACTERIA; PEDOBACTER; PEDOBACTER HEPARINUS; PEDOBACTER ROSEUS; SPHINGOBACTERIACEAE;

EID: 33747883185     PISSN: 14665026     EISSN: None     Source Type: Journal    
DOI: 10.1099/ijs.0.64045-0     Document Type: Article

References (28)

1. Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. (1990). Basic local alignment search tool. J Mol Biol 215, 403-410.
2. Bauer, A. W., Kirby, W. M. M., Sherris, J. C. & Turck, M. (1966). Antibiotic susceptibility testing by a standardized single disk method. Am J Clin Pathol 45, 493-496.
3. Cole, J. R., Chai, B., Marsh, T. L. & 8 other authors (2003). The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. Nucleic Acids Res 31, 442-443.
4. Collins, M. D. (1985). Analysis of isoprenoid quinones. Methods Microbiol 18, 329-366.
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. Gosink, J. J., Woese, C. R. & Staley, J. T. (1998). Polaribacter gen. nov., with three new species, P. irgensii sp. nov., P. franzmannii sp. nov. and P. filamentus sp. nov., gas vacuolated polar marine bacteria of the Cytophaga-Flavobacterium-Bacteroides group and reclassification of 'Flectobacillus glomeratus' as Polaribacter glomeratus comb. nov. Int J Syst Bacteriol 48, 223-235.
8. Hansen, G. H. & Sørheim, R. (1991). Improved method for phenotypical characterization of marine bacteria. J Microbiol Methods 13, 231-241.
9. Jeon, Y. S., Chung, H., Park, S., Hur, I., Lee, J. H. & Chun, J. (2005). jPHYDIT: a JAVA-based integrated environment for molecular phylogeny of ribosomal RNA sequences. Bioinformatics 21, 3171-3173.
10. Jukes, T. H. & Cantor, C. R. (1969). Evolution of protein molecules. In Mammalian Protein Metabolism, pp. 21-132. Edited by H. N. Munro. New York: Academic Press.
11. Kato, M., Muto, Y., Tanaka-Bandoh, K., Watanabe, K. & Ueno, K. (1995). Sphingolipid composition in Bacteroides species. Anaerobe 1, 135-139.
12. Keswani, J. & Whitman, W. B. (2001). Relationship of 16S rRNA sequence similarity to DNA hybridization in prokaryotes. Int J Syst Evol Microbiol 51, 667-678.
13. Kumar, S., Tamura, K. & Nei, M. (2004). MEGA 3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5, 150-163.
14. Lane, D. J. (1991). 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics, pp. 115-175. Edited by E. Stackebrandt & M. Goodfellow. Chichester: Wiley.
15. 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.
16. Mesbah, M., Premachandran, U. & Whitman, W. B. (1989). Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 39, 159-167.
17. Minnikin, D. E., O'Donnell, A. G., Goodfellow, M., Alderson, G., Athalye, M., Schaal, K. & Parlett, J. H. (1984). An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2, 233-241.
18. Posada, D. & Crandall, K. A. (1998). MODELTEST: testing the model of DNA substitution. Bioinformatics 14, 817-818.
19. AL emend. In Bergey's Manual for Systematic Bacteriology, vol. 3, pp. 2015-2050. Edited by J. T. Staley, M. P. Bryant, N. Pfennig & J. G. Holt. Baltimore: Williams & Wilkins.
20. Saitou, N. & Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406-425.
21. Shivaji, S., Chaturvedi, P., Reddy, G. S. N. & 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.
22. 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.
23. Stackebrandt, E. & Goebel, B. M. (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. 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.
25. Swofford, D. L. (1998). PAUP* - Phylogenetic Analysis Using Parsimony, version 4. Sunderland, MA: Sinauer Associates.
26. 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.
27. 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.
28. Zimmermann, J., Langer, R. & Cooney, C. L. (1990). Specific plate assay for bacterial heparinase. Appl Environ Microbiol 56, 3593-3594.