Gramella aestuarii sp. nov., isolated from a tidal flat, and emended description of Gramella echinicola

International Journal of Systematic and Evolutionary Microbiology

Volumn 63, Issue PART8, 2013, Pages 2872-2878

  Jeong, Sang Hyeon ^a   Jin, Hyun Mi ^a   Jeon, Che Ok ^a  

^a Chung Ang University   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; BACTERIAL RNA; CATALASE; FATTY ACID; GENOMIC DNA; MENAQUINONE; OXIDOREDUCTASE; PHOSPHATIDYLETHANOLAMINE; RNA 16S; SODIUM CHLORIDE;

ARTICLE; BACTERIAL CELL; BACTERIAL GENE; BACTERIAL GROWTH; BACTERIAL STRAIN; BACTERIUM; BACTERIUM ISOLATION; GENE SEQUENCE; GRAM NEGATIVE BACTERIUM; GRAMELLA AESTUARII; GRAMELLA ECHINICOLA; NONHUMAN; NUCLEOTIDE SEQUENCE; PH; PHENOTYPE; PHYLOGENY; PRIORITY JOURNAL; SEQUENCE HOMOLOGY;

BACTERIAL TYPING TECHNIQUES; BASE COMPOSITION; DNA, BACTERIAL; FATTY ACIDS; FLAVOBACTERIACEAE; GEOLOGIC SEDIMENTS; MOLECULAR SEQUENCE DATA; NUCLEIC ACID HYBRIDIZATION; PHOSPHATIDYLETHANOLAMINES; PHYLOGENY; REPUBLIC OF KOREA; RNA, RIBOSOMAL, 16S; SEAWATER; SEQUENCE ANALYSIS, DNA; VITAMIN K 2;

EID: 84880995663     PISSN: 14665026     EISSN: None     Source Type: Journal    
DOI: 10.1099/ijs.0.048694-0     Document Type: Article

References (42)

1. Asker, D., Beppu, T. & Ueda, K. (2007a). Unique diversity of carotenoid-producing bacteria isolated from Misasa, a radioactive site in Japan. Appl Microbiol Biotechnol 77, 383-392.
2. 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.
3. Bauer, M., Kube, M., Teeling, H., Richter, M., Lombardot, T., Allers, E., Würdemann, C. A., Quast, C., Kuhl, H. & other authors (2006). Whole genome analysis of the marine Bacteroidetes 'Gramella forsetii' reveals adaptations to degradation of polymeric organic matter. Environ Microbiol 8, 2201-2213.
4. Bernardet, J.-F. (2011). Family I. Flavobacteriaceae. In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 4, pp. 106-111. Edited by N. R. Krieg, W. Ludwig, W. B. Whitman, B. P. Hedlund, B. J. Paster, J. T. Staley, N. Ward, D. Brown & A. Parte. New York: Springer.
5. Bernardet, J.-F., Nakagawa, Y., Holmes, B. & Subcommittee on the taxonomy of Flavobacterium and Cytophaga-like bacteria of the International Committee on Systematics of Prokaryotes (2002). Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 52, 1049-1070.
6. Biebl, H., Allgaier, M., Tindall, B. J., Koblizek, M., Lünsdorf, H., Pukall, R. & Wagner-Döbler, I. (2005). Dinoroseobacter shibae gen. nov., sp. nov., a new aerobic phototrophic bacterium isolated from dinoflagellates. Int J Syst Evol Microbiol 55, 1089-1096.
7. Bowman, J. P. (2000). Description of Cellulophaga algicola sp. nov., isolated from the surfaces of Antarctic algae, and reclassification of Cytophaga uliginosa (ZoBell and Upham 1944) Reichenbach 1989 as Cellulophaga uliginosa comb. nov. Int J Syst Evol Microbiol 50, 1861-1868.
8. Bruns, A., Rohde, M. & Berthe-Corti, L. (2001). Muricauda ruestringensis gen. nov., sp. nov., a facultatively anaerobic, appendaged bacterium from German North Sea intertidal sediment. Int J Syst Evol Microbiol 51, 1997-2006.
9. Cho, S. H., Chae, S. H., Cho, M., Kim, T. U., Choi, S., Han, J. H., Kim, Y. T., Joung, Y., Joh, K. & other authors (2011). Gramella gaetbulicola sp. nov., a member of the family Flavobacteriaceae isolated from foreshore soil. Int J Syst Evol Microbiol 61, 2654-2658.
10. Cowan, S. T. & Steel, K. J. (1965). Manual for the Identification of Medical Bacteria. London: Cambridge University Press.
11. DeSantis, T. Z., Jr, Hugenholtz, P., Keller, K., Brodie, E. L., Larsen, N., Piceno, Y. M., Phan, R. & Andersen, G. L. (2006). NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Res 34 (Web Server issue), W394-W399.
12. Felsenstein, J. (2002). PHYLIP (phylogeny inference package) version 3.68. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle, USA.
13. Gomori, G. (1955). Preparation of buffers for use in enzyme studies. In Methods in Enzymology, vol. 1, pp. 138-146. Edited by S. P. Colowick & N. O. Kaplan. New York: Academic Press.
14. Gonzalez, J. M. & Saiz-Jimenez, C. (2002). A fluorimetric method for the estimation of G+C mol% content in microorganisms by thermal denaturation temperature. Environ Microbiol 4, 770-773.
15. Jin, H. M., Lee, H. J., Kim, J. M., Park, M. S., Lee, K. & Jeon, C. O. (2011). Litorimicrobium taeanense gen. nov., sp. nov., isolated from a sandy beach. Int J Syst Evol Microbiol 61, 1392-1396.
16. Jin, H. M., Kim, J. M., Lee, H. J., Madsen, E. L. & Jeon, C. O. (2012). Alteromonas as a key agent of polycyclic aromatic hydrocarbon biodegradation in crude oil-contaminated coastal sediment. Environ Sci Technol 46, 7731-7740.
17. Joung, Y., Kim, H., Jang, T., Ahn, T. S. & Joh, K. (2011). Gramella jeungdoensis sp. nov., isolated from a solar saltern in Korea. J Microbiol 49, 1022-1026.
18. Kim, J. M., Lee, S. H., Jung, J. Y. & Jeon, C. O. (2010a). Marinobacterium lutimaris sp. nov., isolated from a tidal flat. Int J Syst Evol Microbiol 60, 1828-1831.
19. Kim, J. M., Jung, J. Y., Chae, H. B., Park, W. & Jeon, C. O. (2010b). Hwanghaeicola aestuarii gen. nov., sp. nov., a moderately halophilic bacterium isolated from a tidal flat of the Yellow Sea. Int J Syst Evol Microbiol 60, 2877-2881.
20. Kim, J. M., Lee, H. J., Kim, S. Y., Song, J. J., Park, W. & Jeon, C. O. (2010c). Analysis of fine-scale population structure of "Candidatus Accumulibacter phosphatis" in enhanced biological phosphorus removal sludge using fluorescence in situ hybridization and flow cytometric sorting. Appl Environ Microbiol 76, 3825-3835.
21. Kim, O. S., Cho, Y. J., Lee, K., Yoon, S. H., Kim, M., Na, H., Park, S. C., Jeon, Y. S., Lee, J. H. & other authors (2012). Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62, 716-721.
22. Komagata, K. & Suzuki, K. (1987). Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 19, 161-207.
23. Lányi{dotless}́, B. (1987). Classical and rapid identification methods for medically important bacteria. Methods Microbiol 19, 1-67.
24. Lau, S. C. K., Tsoi, M. M. Y., Li, X., Plakhotnikova, I., Dobretsov, S., Wong, P. K. & Qian, P. Y. (2005). Gramella portivictoriae sp. nov., a novel member of the family Flavobacteriaceae isolated from marine sediment. Int J Syst Evol Microbiol 55, 2497-2500.
25. Lee, S. H., Shim, J. K., Kim, J. M., Choi, H. K. & Jeon, C. O. (2011). Henriciella litoralis sp. nov., isolated from a tidal flat, transfer of Maribaculum marinum Lai et al. 2009 to the genus Henriciella as Henriciella aquimarina nom. nov. and emended description of the genus Henriciella. Int J Syst Evol Microbiol 61, 722-727.
26. Leifson, E. (1963). Determination of carbohydrate metabolism of marine bacteria. J Bacteriol 85, 1183-1184.
27. Math, R. K., Jin, H. M., Kim, J. M., Hahn, Y., Park, W., Madsen, E. L. & Jeon, C. O. (2012a). Comparative genomics reveals adaptation by Alteromonas sp. SN2 to marine tidal-flat conditions: cold tolerance and aromatic hydrocarbon metabolism. PLoS ONE 7, e35784.
28. Math, R. K., Jeong, S. H., Jin, H. M., Park, M. S., Kim, J. M. & Jeon, C. O. (2012b). Kordiimonas aestuarii sp. nov., a marine bacterium isolated from a tidal flat. Int J Syst Evol Microbiol 62, 3049-3054.
29. McCammon, S. A. & Bowman, J. P. (2000). Taxonomy of Antarctic Flavobacterium species: description of Flavobacterium gillisiae sp. nov., Flavobacterium tegetincola sp. nov., and Flavobacterium xanthum sp. nov., nom. rev. and reclassification of [Flavobacterium] salegens as Salegentibacter salegens gen. nov., comb. nov. Int J Syst Evol Microbiol 50, 1055-1063.
30. Minnikin, D. E., Patel, P. V., Alshamaony, L. & Goodfellow, M. (1977). Polar lipid composition in the classification of Nocardia and related bacteria. Int J Syst Bacteriol 27, 104-117.
31. Nedashkovskaya, O. I., Kim, S. B., Lysenko, A. M., Frolova, G. M., Mikhailov, V. V., Bae, K. S., Lee, D. H. & Kim, I. S. (2005). Gramella echinicola gen. nov., sp. nov., a novel halophilic bacterium of the family Flavobacteriaceae isolated from the sea urchin Strongylocentrotus intermedius. Int J Syst Evol Microbiol 55, 391-394.
32. Nedashkovskaya, O. I., Kim, S. B. & Bae, K. S. (2010). Gramella marina sp. nov., isolated from the sea urchin Strongylocentrotus intermedius. Int J Syst Evol Microbiol 60, 2799-2802.
33. Nishijima, M., Takadera, T., Imamura, N., Kasai, H., An, K. D., Adachi, K., Nagao, T., Sano, H. & Yamasato, K. (2009). Microbulbifer variabilis sp. nov. and Microbulbifer epialgicus sp. nov., isolated from Pacific marine algae, possess a rod-coccus cell cycle in association with the growth phase. Int J Syst Evol Microbiol 59, 1696-1707.
34. Park, Y. J., Park, M. S., Lee, S. H., Park, W., Lee, K. & Jeon, C. O. (2011). Luteimonas lutimaris sp. nov., isolated from a tidal flat. Int J Syst Evol Microbiol 61, 2729-2733.
35. Rosselló-Mora, R. & Amann, R. (2001). The species concept for prokaryotes. FEMS Microbiol Rev 25, 39-67.
36. Sambrook, J. & Russell, D. W. (2001). Molecular Cloning: a Laboratory Manual, 3rd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.
37. Sasser, M. (1990). Identification of bacteria by gas chromatography of cellular fatty acids. USFCC Newsl 20, 16.
38. Smibert, R. M. & Krieg, N. R. (1994). Phenotypic characterization. In Methods for General and Molecular Bacteriology, pp. 607-654. Edited by P. Gerhardt. Washington, DC: American Society for Microbiology.
39. Stamatakis, A., Ott, M. & Ludwig, T. (2005). RAxML-OMP: An efficient program for phylogenetic inference on SMPs. In Proceedings of 8th International Conference on Parallel Computing Technologies (PaCT2005), Lecture Notes in Computer Science, 3506, 288-302, Springer.
40. Wang, Q., Garrity, G. M., Tiedje, J. M. & Cole, J. R. (2007). Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73, 5261-5267.
41. Winberg, P. C., Lynch, T. P., Murray, A., Jones, A. R. & Davis, A. R. (2007). The importance of spatial scale for the conservation of tidal flat macrobenthos: An example from New South Wales, Australia. Biol Conserv 134, 310-320.
42. Yurkov, V., Stackebrandt, E., Holmes, A., Fuerst, J. A., Hugenholtz, P., Golecki, J., Gad'on, N., Gorlenko, V. M., Kompantseva, E. I. & Drews, G. (1994). Phylogenetic positions of novel aerobic, bacteriochlorophyll a-containing bacteria and description of Roseococcus thiosulfatophilus gen. nov., sp. nov., Erythromicrobium ramosum gen. nov., sp. nov., and Erythrobacter litoralis sp. nov. Int J Syst Bacteriol 44, 427-434.