Gordonia alkaliphila sp. nov., an actinomycete isolated from tidal flat sediment

International Journal of Systematic and Evolutionary Microbiology

Volumn 63, Issue 1, 2013, Pages 327-331

  Cha, Ju Hee ^a   Cha, Chang Jun ^a  

^a Chung Ang University   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

CARDIOLIPIN; MANNOSIDE; PHOSPHATIDYLETHANOLAMINE; PHOSPHATIDYLGLYCEROL; PHOSPHATIDYLINOSITOL; RNA 16S;

ACTINOBACTERIA; ARTICLE; BACTERIUM ISOLATION; GORDONIA; GORDONIA ALKALIPHILA; GORDONIA HIRSUTA; GORDONIA HYDROPHOBICA; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RNA SEQUENCE; SEDIMENT; TIDAL FLAT SEDIMENT;

BACTERIAL TYPING TECHNIQUES; BASE COMPOSITION; DNA, BACTERIAL; FATTY ACIDS; GEOLOGIC SEDIMENTS; GORDONIA BACTERIUM; MOLECULAR SEQUENCE DATA; PHOSPHOLIPIDS; PHYLOGENY; REPUBLIC OF KOREA; RNA, RIBOSOMAL, 16S; SEAWATER; SEQUENCE ANALYSIS, DNA; VITAMIN K 2;

GORDONIA (ACTINOMYCETE); GORDONIA HIRSUTA; GORDONIA HYDROPHOBICA;

EID: 84872481034     PISSN: 14665026     EISSN: None     Source Type: Journal    
DOI: 10.1099/ijs.0.039289-0     Document Type: Article

References (36)

1. Atlas, R. M. (1993). Handbook of Microbiology Media. Edited by L. C. Parks. Boca Raton, FL: CRC Press.
2. Bendinger, B., Rainey, F. A., Kroppenstedt, R. M., Moormann, M. & Klatte, S. (1995). Gordona hydrophobica sp. nov., isolated from biofilters for waste gas treatment. Int J Syst Bacteriol 45, 544-548.
3. Collins, M. D. (1985). Analysis of isoprenoid quinones. Methods Microbiol 18, 329-366.
4. Drzyzga, O., Navarro Llorens, J. M., Fernández de Las Heras, L., García Fernández, E. & Perera, J. (2009). Gordonia cholesterolivorans sp. nov., a cholesterol-degrading actinomycete isolated from sewage sludge. Int J Syst Evol Microbiol 59, 1011-1015.
5. 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.
6. Felsenstein, J. (1981). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17, 368-376.
7. Felsenstein, J. (1985). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783-791.
8. Felsenstein, J. (2005). PHYLIP (phylogeny inference package) version 3.6. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle, USA.
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, vol. 3, pp. 21-132. Edited by H. N. Munro. New York: Academic Press.
11. Kampfer, P., Young, C. C., Chu, J. N., Frischmann, A., Busse, H. J., Arun, A. B., Shen, F. T. & Rekha, P. D. (2011). Gordonia humi sp. nov., isolated from soil. Int J Syst Evol Microbiol 61, 65-70.
12. Kim, S. B., Brown, R., Oldfield, C., Gilbert, S. C. & Goodfellow, M. (1999). Gordonia desulfuricans sp. nov., a benzothiophene-desulphurizing actinomycete. Int J Syst Bacteriol 49, 1845-1851.
13. Kim, S. B., Brown, R., Oldfield, C., Gilbert, S. C., Iliarionov, S. & Goodfellow, M. (2000). Gordonia amicalis sp. nov., a novel dibenzothiophene-desulphurizing actinomycete. Int J Syst Evol Microbiol 50, 2031-2036.
14. Kim, K. K., Lee, K. C., Klenk, H. P., Oh, H. M. & Lee, J. S. (2009). Gordonia kroppenstedtii sp. nov., a phenol-degrading actinomycete isolated from a polluted stream. Int J Syst Evol Microbiol 59, 1992-1996.
15. 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.
16. Klatte, S., Kroppenstedt, R. M., Schumann, P., Altendorf, K. & Rainey, F. A. (1996). Gordona hirsuta sp. nov. Int J Syst Bacteriol 46, 876-880.
17. Kutchma, A. J., Roberts, M. A., Knaebel, D. B. & Crawford, D. L. (1998). Small-scale isolation of genomic DNA from Streptomyces mycelia or spores. Biotechniques 24, 452-456.
18. 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.
19. le Roes, M., Goodwin, C. M. & Meyers, P. R. (2008). Gordonia lacunae sp. nov., isolated from an estuary. Syst Appl Microbiol 31, 17-23.
20. Linos, A., Berekaa, M. M., Steinbuchel, A., Kim, K. K., Sproer, C. & Kroppenstedt, R. M. (2002). Gordonia westfalica sp. nov., a novel rubber-degrading actinomycete. Int J Syst Evol Microbiol 52, 1133-1139.
21. 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.
22. Minnikin, D. E., Alshamaony, L. & Goodfellow, M. (1975). Differentiation of Mycobacterium, Nocardia, and related taxa by thin-layer chromatographic analysis of whole-organism methanolysates. J Gen Microbiol 88, 200-204.
23. 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.
24. Park, S., Kang, S. J., Kim, W. & Yoon, J. H. (2009). Gordonia hankookensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 59, 3172-3175.
25. Saitou, N. & Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406-425.
26. 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.
27. Soddell, J. A., Stainsby, F. M., Eales, K. L., Seviour, R. J. & Goodfellow, M. (2006). Gordonia defluvii sp. nov., an actinomycete isolated from activated sludge foam. Int J Syst Evol Microbiol 56, 2265-2269.
28. Stackebrandt, E. (1988). Phylogenetic relationships vs. phenotypic diversity: how to achieve a phylogenetic classification system of the eubacteria. Can J Microbiol 34, 552-556.
29. Tamura, K., Dudley, J., Nei, M. & Kumar, S. (2007). MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24, 1596-1599.
30. Teather, R. M. & Wood, P. J. (1982). Use of Congo red-polysaccharide interactions in enumeration and characterization of cellulolytic bacteria from the bovine rumen. Appl Environ Microbiol 43, 777-780.
31. Tindall, B. J. (1990a). A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 13, 128-130.
32. Tindall, B. J. (1990b). Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 66, 199-202.
33. Tsukamura, M. (1971). Proposal of a new genus, Gordona, for slightly acid-fast organisms occurring in sputa of patients with pulmonary disease and in soil. J Gen Microbiol 68, 15-26.
34. 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.
35. Yoon, J. H., Lee, J. J., Kang, S. S., Takeuchi, M., Shin, Y. K., Lee, S. T., Kang, K. H. & Park, Y. H. (2000). Gordonia nitida sp. nov., a bacterium that degrades 3-ethylpyridine and 3-methylpyridine. Int J Syst Evol Microbiol 50, 1203-1210.
36. Zhi, X.-Y., Li, W.-J. & Stackebrandt, E. (2009). An update of the structure and 16S rRNA gene sequence-based definition of higher ranks of the class Actinobacteria, with the proposal of two new suborders and four new families and emended descriptions of the existing higher taxa. Int J Syst Evol Microbiol 59, 589-608.