Shimia marina gen. nov., sp. nov., a novel bacterium of the Roseobacter clade isolated from biofilm in a coastal fish farm

International Journal of Systematic and Evolutionary Microbiology

Volumn 56, Issue 8, 2006, Pages 1869-1873

  Choi, Dong H ^a,b   Cho, Byung C ^a  

^a Seoul National University   (South Korea)

^b Korea Research Institute of Ships and Ocean Engineering   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; FATTY ACID; RNA 16S;

ARTICLE; BACTERIAL GENE; BACTERIAL GROWTH; BACTERIAL METABOLISM; BACTERIAL STRAIN; BACTERIUM EXAMINATION; BACTERIUM IDENTIFICATION; BACTERIUM ISOLATION; BIOCHEMISTRY; BIOFILM; CLADISTICS; COASTAL WATERS; CULTURE MEDIUM; DNA CONTENT; FATTY ACID ANALYSIS; GENE SEQUENCE; GRAM NEGATIVE BACTERIUM; MARINE ENVIRONMENT; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PISCICULTURE; PRIORITY JOURNAL; RHODOBACTERACEAE; ROSEOBACTER; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SHIMIA MARINA; SOUTH KOREA; STRAIN DIFFERENCE; THALASSOBIUS GELATINOVORUS; THALASSOBIUS MEDITERRANEUS; TRANSPORT MEDIUM;

AGAR; AQUACULTURE; BASE COMPOSITION; BIOFILMS; CULTURE MEDIA; FATTY ACIDS; HYDROGEN-ION CONCENTRATION; KOREA; LOCOMOTION; MARINE BIOLOGY; MOLECULAR SEQUENCE DATA; PHYLOGENY; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S; ROSEOBACTER; SALTS; SEQUENCE HOMOLOGY, NUCLEIC ACID; SPECIES SPECIFICITY; TEMPERATURE;

BACTERIA (MICROORGANISMS); RHODOBACTERACEAE; ROSEOBACTER; RUEGERIA GELATINOVORANS; THALASSOBIUS MEDITERRANEUS;

EID: 33747879303     PISSN: 14665026     EISSN: None     Source Type: Journal    
DOI: 10.1099/ijs.0.64235-0     Document Type: Article

References (24)

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. Arahal, D. R., Macián, M. C., Garay, E. & Pujalte, M. J. (2005). Thalassobius mediterraneus gen. nov., sp. nov., and reclassification of Ruegeria gelatinovorans as Thalassobius gelatinovorus comb. nov. Int J Syst Evol Microbiol 55, 2371-2376.
3. Buchan, A., González, J. M. & Moran, M. A. (2005). Overview of the marine Roseobacter lineage. Appl Environ Microbiol 71, 5665-5677.
4. Choi, D. H., Kim, Y.-G., Hwang, C. Y., Yi, H., Chun, J. & Cho, B. C. (2006). Tenacibaculum litoreum sp. nov., isolated from tidal flat sediment. Int J Syst Evol Microbiol 56, 635-640.
5. 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.
6. Collins, M. D. (1985). Analysis of isoprenoid quinones. Methods Microbiol 18, 329-366.
7. Dang, H. & Lovell, C. R. (2000). Bacterial primary colonization and early succession on surfaces in marine waters as determined by amplified rRNA gene restriction analysis and sequence analysis of 16S rRNA genes. Appl Environ Microbiol 66, 467-475.
8. Fitch, W. M. (1971). Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20, 406-416.
9. Giovannoni, S. J. & Rappé, M. S. (2000). Evolution, diversity and molecular ecology of marine prokaryotes. In Microbial Ecology of the Oceans, pp. 47-84. Edited by D. L. Kirchman. New York: Wiley.
10. Hansen, G. H. & Sørheim, R. (1991). Improved method for phenotypical characterization of marine bacteria. J Microbiol Methods 13, 231-241.
11. 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.
12. 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.
13. Kumar, S., Tamura, K. & Nei, M. (2004). MEGA3: 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. Lyman, J. & Fleming, R. H. (1940). Composition of sea water. J Mar Res 3, 134-146.
16. Marmur, J. (1961). A procedure for the isolation of deoxyribonucleic acid from microorganisms. J Mol Biol 3, 208-218.
17. 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.
18. 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.
19. Ostle, A. G. & Holt, J. G. (1982). Nile blue A as a fluorescent stain for poly-β-hydroxybutyrate. Appl Environ Microbiol 44, 238-241.
20. Rüger, H.-J. & Höfle, M. G. (1992). Marine star-shaped-aggregate-forming bacteria: Agrobacterium atlanticum sp. nov.; Agrobacterium meteori sp. nov.; Agrobacterium ferrugineum sp. nov., nom. rev.; Agrobacterium gelatinovorum sp. nov., nom. rev.; and Agrobacterium stellulatum sp. nov., nom. rev. Int J Syst Bacteriol 42, 133-143.
21. Saitou, N. & Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406-425.
22. Selje, N., Simon, M. & Brinkhoff, T. (2004). A newly discovered Roseobacter cluster in temperate and polar oceans. Nature 427, 445-448.
23. 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.
24. Uchino, Y., Hirata, A., Yokota, A. & Sugiyama, J. (1998). Reclassification of marine Agrobacterium species: proposals of Stappia stellulata gen. nov., comb. nov., Stappia aggregata sp. nov., nom. rev., Ruegeria atlantica gen. nov., comb. nov., Ruegeria gelatinovora comb. nov., Ruegeria algicola comb. nov., and Ahrensia kieliense gen. nov., sp. nov., nom. rev. J Gen Appl Microbiol 44, 201-210.