Loktanella cinnabarina sp. nov., isolated from a deep subseafloor sediment, and emended description of the genus Loktanella

International Journal of Systematic and Evolutionary Microbiology

Volumn 63, Issue PART4, 2013, Pages 1390-1395

  Tsubouchi, Taishi ^a   Shimane, Yasuhiro ^a   Mori, Kozue ^a   Miyazaki, Masayuki ^a   Tame, Akihiro ^b   Uematsu, Katsuyuki ^b   Maruyama, Tadashi ^a   Hatada, Yuji ^a  

^a JAPAN AGENCY FOR MARINE EARTH SCIENCE AND TECHNOLOGY   (Japan)

^b MARINE WORKS JAPAN LTD   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; RNA 16S;

AEROBIC BACTERIUM; ALPHAPROTEOBACTERIA; ARTICLE; BACTERIAL CELL; BACTERIAL STRAIN; BACTERIUM COLONY; BACTERIUM ISOLATE; DNA BASE COMPOSITION; GENUS; GRAM NEGATIVE BACTERIUM; HETEROTROPHY; JAPAN; LOKTANELLA; LOKTANELLA CINNABARINA; LOKTANELLA HONGKONGENSIS; NEW SPECIES; NONHUMAN; NUCLEOTIDE SEQUENCE; PHENOTYPE; PHYLOGENY; PRIORITY JOURNAL; RHODOBACTERACEAE; RNA SEQUENCE; SALT TOLERANCE; SEDIMENT; SEQUENCE HOMOLOGY;

EID: 84876071385     PISSN: 14665026     EISSN: None     Source Type: Journal    
DOI: 10.1099/ijs.0.043174-0     Document Type: Article

References (33)

1. Barrow, G. I. & Feltham, R. K. A. (1993). Cowan and Steel's Manual for the Identification of Medical Bacteria, 3rd edn. Cambridge: Cambridge University Press.
2. Ezaki, T., Hashimoto, Y. & Yabuuchi, E. (1989). Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in micro-dilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 39, 224-229.
3. Felsenstein, J. (1981). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17, 368-376.
4. Felsenstein, J. (1985). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783-791.
5. Fitch, W. M. (1971). Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20, 406-416.
6. Hosoya, S. & Yokota, A. (2007). Loktanella atrilutea sp. nov., isolated from seawater in Japan. Int J Syst Evol Microbiol 57, 1966-1969.
7. Ivanova, E. P., Zhukova, N. V., Lysenko, A. M., Gorshkova, N. M., Sergeev, A. F., Mikhailov, V. V. & Bowman, J. P. (2005). Loktanella agnita sp. nov. and Loktanella rosea sp. nov., from the north-west Pacific Ocean. Int J Syst Evol Microbiol 55, 2203-2207.
8. 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.
9. Kroppenstedt, R. M. (1985). Fatty acid and menaquinone analysis of actinomycetes and related organisms. In Chemical Methods in Bacterial Systematics (Society for Applied Bacteriology Technical Series vol. 20), pp. 173-199. Edited by M. Goodfellow & D. E. Minnikin. New York: Academic Press.
10. Kumar, Y., Westram, R., Behrens, S., Fuchs, B., Glöckner, F. O., Amann, R., Meier, H. & Ludwig, W. (2005). Graphical representation of ribosomal RNA probe accessibility data using ARB software package. BMC Bioinformatics 6, 61.
11. Kumar, Y., Westram, R., Kipfer, P., Meier, H. & Ludwig, W. (2006). Evaluation of sequence alignments and oligonucleotide probes with respect to three-dimensional structure of ribosomal RNA using ARB software package. BMC Bioinformatics 7, 240.
12. 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, UK: Wiley.
13. Lau, S. C., Tsoi, M. M., Li, X., Plakhotnikova, I., Wu, M., Wong, P.-K. & Qian, P.-Y. (2004). Loktanella hongkongensis sp. nov., a novel member of the a-Proteobacteria originating from marine biofilms in Hong Kong waters. Int J Syst Evol Microbiol 54, 2281-2284.
14. Lee, S. D. (2012). Loktanella tamlensis sp. nov., isolated from seawater. Int J Syst Evol Microbiol 62, 586-590.
15. Ludwig, W., Strunk, O., Westram, R., Richter, L., Meier, H., Yadhukumar, Buchner, A., Lai, T., Steppi, S. & other authors (2004). ARB: a software environment for sequence data. Nucleic Acids Res 32, 1363-1371.
16. Mesbah, M., Premachandran, U. & Whitman, W. B. (1989). Precise measurement of the G+C content of deoxyribonucleic acid by highperformance liquid chromatography. Int J Syst Bacteriol 39, 159-167.
17. 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.
18. Minnikin, D. E., O'Donnell, A. G., Goodfellow, M., Alderson, G., Athalye, M., Schaal, A. & Parlett, J. H. (1984). An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2, 233-241.
19. Moon, Y. G., Seo, S. H., Lee, S. D. & Heo, M. S. (2010). Loktanella pyoseonensis sp. nov., isolated from beach sand, and emended description of the genus Loktanella. Int J Syst Evol Microbiol 60, 785-789.
20. Nishijima, M., Araki-Sakai, M. & Sano, H. (1997). Identification of isoprenoid quinones by frit-FAB liquid chromatography-mass spectrometry for the chemotaxonomy of microorganisms. J Microbiol Methods 28, 113-122.
21. Rautela, G. S. & Cowling, E. B. (1966). Simple cultural test for relative cellulolytic activity of fungi. Appl Microbiol 14, 892-898.
22. Saitou, N. & Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406-425.
23. Smibert, R. M. & Krieg, N. R. (1994). Phenotypic characteristics. In Manual of 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. Swan, A. (1954). The use of a bile-aesculin medium and of Maxted's technique of Lancefield grouping in the identification of enterococci (group D streptococci). J ClinPathol 7, 160-163.
25. Tang, J. C., Taniguchi, H., Chu, H., Zhou, Q. & Nagata, S. (2009). Isolation and characterization of alginate-degrading bacteria for disposal of seaweed wastes. Lett Appl Microbiol 48, 38-43.
26. Tavaré, S. (1986). Some probabilistic and statistical problems in the analysis of DNA sequences. Lect Math Life Sci 17, 57-86 (American Mathematical Society).
27. Van Trappen, S., Mergaert, J. & Swings, J. (2004). Loktanella salsilacus gen. nov., sp. nov., Loktanella fryxellensis sp. nov. and Loktanella vestfoldensis sp. nov., new members of the Rhodobacter group, isolated from microbial mats in Antarctic lakes. Int J Syst Evol Microbiol 54, 1263-1269.
28. Wayne, L. G., Brenner, D. J., Colwell, R. R., Grimont, P. A. D., Kandler, O., Krichevsky, M. I., Moore, L. H., Moore, W. E. C., Murray, R. G. E. & other authors (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.
29. Weon, H.-Y., Kim, B.-Y., Yoo, S.-H., Kim, J.-S., Kwon, S.-W., Go, S.-J. & Stackebrandt, E. (2006). Loktanella koreensis sp. nov., isolated from sea sand in Korea. Int J Syst Evol Microbiol 56, 2199-2202.
30. Wilson, K. (1987). Preparation of genomic DNA from bacteria. In Current Protocols in Molecular Biology, pp. 2.4.1-2.4.5. Edited by F. M. Ausubel, R. Brent, R. E. Kingston, D. D. Moore, J. G. Seidman, J. A. Smith & K. Struhl. New York: Green Publishing & Wiley-Interscience.
31. Yoon, J.-H., Kang, S.-J., Lee, S.-Y. & Oh, T.-K. (2007). Loktanella maricola sp. nov., isolated from seawater of the East Sea in Korea. Int J Syst Evol Microbiol 57, 1799-1802.
32. Yoon, J.-H., Jung, Y.-T. & Lee, J.-S. (2013). Loktanella litorea sp. nov., isolated from seawater. Int J Syst Evol Microbiol 63, 175-180.
33. Zwickl, D. & Holder, M. (2004). Model parameterization, prior distributions, and the general time-reversible model in Bayesian phylogenetics. Syst Biol 53, 877-888.