Reclassification of Methylobacterium chloromethanicum and Methylobacterium dichloromethanicum as later subjective synonyms of Methylobacterium extorquens and of Methylobacterium lusitanum as a later subjective synonym of Methylobacterium rhodesianum

Journal of General and Applied Microbiology

Volumn 51, Issue 5, 2005, Pages 287-299

  Kato, Yuko ^a   Asahara, Mika ^a   Arai, Daisuke ^a   Goto, Keiichi ^a   Yokota, Akira ^b  

^a Mitsui Norin Co Ltd ^*  (Japan)

^b UNIVERSITY OF TOKYO   (Japan)

Author keywords

Hypervariable region; Methylobacterium; Methylobacterium chloromethanicum; Methylobacterium dichloromethanicum; Methylobacterium extorquens; Methylobacterium lusitanum; Methylobacterium rhodesianum

Indexed keywords

DNA 16S; GENOMIC DNA;

ARTICLE; BACTERIAL STRAIN; CLASSIFICATION; CONTROLLED STUDY; DNA DNA HYBRIDIZATION; DNA EXTRACTION; FATTY ACID ANALYSIS; GENE CLUSTER; GENE SEQUENCE; METHYLOBACTERIUM; METHYLOBACTERIUM CHLOROMETHANICUM; METHYLOBACTERIUM DICHLOROMETHANICUM; METHYLOBACTERIUM EXTORQUENS; METHYLOBACTERIUM LUSITANUM; METHYLOBACTERIUM RHODESIANUM; MONOPHYLY; NEW SPECIES; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; RIBOTYPING; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SPECIES DIFFERENCE;

BACTERIAL TYPING TECHNIQUES; BASE COMPOSITION; DNA, BACTERIAL; DNA, RIBOSOMAL; FATTY ACIDS; METHYLOBACTERIUM; METHYLOBACTERIUM EXTORQUENS; MOLECULAR SEQUENCE DATA; NUCLEIC ACID HYBRIDIZATION; PHYLOGENY; RIBOTYPING; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA;

BACTERIA (MICROORGANISMS); METHYLOBACTERIUM; METHYLOBACTERIUM CHLOROMETHANICUM; METHYLOBACTERIUM DICHLOROMETHANICUM; METHYLOBACTERIUM EXTORQUENS; METHYLOBACTERIUM LUSITANUM; METHYLOBACTERIUM ORGANOPHILUM; METHYLOBACTERIUM RHODESIANUM;

EID: 29144453498     PISSN: 00221260     EISSN: 13498037     Source Type: Journal    
DOI: 10.2323/jgam.51.287     Document Type: Article

References (35)

1. Bousfield, I. J. and Green, P. N. (1985) Reclassification of bacteria of genus Protomonas Urakami and Komagata 1984 in the genus Methylobacterium (Patt, Cole, and Hanson) Emend. Green and Bousfield 1983. Int. J. Syst. Bacteriol., 35, 209.
2. Bratina, B. J., Brusseau, G. A., and Hanson, R. S. (1992) Use of 16S rRNA analysis to investigate phylogeny of mothylotrophic bacteria. Int. J. Syst. Bacteriol., 42, 645-648.
3. Doronina, N. V., Sokolov, A. P., and Trotsenko, Y. A. (1996) Isolation and initial characterization of aerobic chloromethane-utilizing bacteria. FEMS Microbiol. Lett., 142, 179-183.
4. Doronina, N. V., Trotsenko, Y. A., Kuznetsov, B. B., Tourova, T. P., and Salkinoja-Salonen, M. S. (2002) Methylobacterium suomiense sp. nov. and Methylobacterium lusitanum sp. nov., aerobic, pink-pigmented, facultatively methylotrophic bacteria. Int. J. Syst. Evol. Microbiol., 52, 773-777.
5. Doronina, N. V., Trotsenko, Y. A., Tourova, T. P., Kuznetsov, B. B., and Leisinger, T. (2000) Methylophlia helvetica sp. nov. and Methylobacterium dichloromethanicum sp. nov. - Novel aerobic facultatively methylotrophic bacteria utilizing dichloromethane. Syst. Appl. Microbiol., 23, 210-218.
6. Ezaki, T., Hashimoto, Y., and Yabuuchi, E. (1989) Fluorometric deoxyribonucleic acid-deoxyribonucleic acid and hybridization in microdilution 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.
7. Felsenstein, J. (1985) Confidence limits on phylogenies: An approach using the bootstrap. Evolution, 39, 783-791.
8. Furuhata, K. and Koike, A. K. (1993) Isolation of Methylobacterium spp. from drinking tank-water and resistance of isolates to chlorine. Jpn. J. Publ. Health, 40. 1047-1053.
9. Furuhata, K., Koike, A. K., and Matsumoto, A. (1989) Growth and survival of a chlorine resistive gram-negative rod bacterium, Protomonas extorquens isolated dominantly from drinking tank-water. Bull. Jpn. Soc. Microb. Ecol., 4, 35-47.
10. Galli, R. and Leisinger, T. (1988) Plasmid analysis and cloning of the dichloromethane-utilization genes of Methylobacterium sp. DM4. J. Gen. Microbiol., 134, 943-952.
11. Goto, K., Fujita, R., Kato, Y., Asahara, M., and Yokota, A. (2004) Reclassification of Brevibacillus brevis strains NCIMB 13288 and DSM 6472 (=NRRL NRS-887) as Aneurinibacillus danicus sp. nov. and Brevibacillus limnophilus sp. nov. Int. J. Syst. Evol. Microbiol., 54, 419-427.
12. Goto, K., Kato, Y., Asahara, M., and Yokota, A. (2002a) Evolution of the hypervariable region in the 16S rDNA sequence as index for rapid species identification in the genus Paenibacillus. J. Gen. Appl. Microbiol., 48, 281-285.
13. Goto, K., Mochida, K., Asahara, M., Suzuki, M., and Yokota, A. (2002b) Application of the hypervariable region of the 16S rDNA sequence as an index for the rapid identification of species in the genus Alicyclobacillus. J. Gen. Appl. Microbiol., 48, 243-250.
14. Goto, K., Omura, T., Hara, Y., and Sadaie, Y. (2000) Application of the partial 16S rDNA sequence as an index for rapid identification of species in the genus Bacillus. J. Gen. Appl. Microbiol., 46, 1-8.
15. Green, P. N. and Bousfield, I. J. (1982) A taxonomic study of some gram-negative facultatively methylotrophic bacteria. J. Gen. Microbiol., 128, 623-638.
16. Green, P. N. and Bousfield, I. J. (1983) Emendation of Methylobacterium Patt, Cole, and Hanson 1976; Methylobacterium rhodinum (Heumann 1962) comb. nov. corring.; Methylobacterium radiotolerans (Ito and Iizuka 1971) comb. nov. corring.; and Methylobacterium mesophilicum (Austin and Goodfellow 1979) comb. nov. Int. J. Syst. Bacteriol., 33, 875-877.
17. Green, P. N., Bousfield, I. J., and Hood, D. (1988) Three new Methylobacterium species: M. rhodesianum sp. nov., M. zatmanii sp. nov., and M. fujisawaense sp. nov. Int. J. Syst. Bacteriol., 38, 124-127.
18. Hiraishi, A., Furuhata, K., Matsumoto, A., Koike, K. A., Fukuyama, M., and Tabuchi, K. (1995) Phenotypic and genetic diversity of chlorine-resistant Methylobacterium strains isolated from various environments. Appl. Environ. Microbiol., 61, 2099-2107.
19. Hiraishi, A. and Shimada, K. (2001) Aerobic anoxygenic photosynthetic bacteria with zinc-bacteriochlorophyll. J. Gen. Appl. Microbiol., 47, 161-180.
20. Hood, D., Dow, C. S., and Green, P. N. (1987) DNA:DNA hybridization studies on the pink pigmented facultative methylotrophs. J. Gen. Microbiol., 133, 709-720.
21. Kimura, M. (1980) A simple method for estimating evolutionary rates of base substitution through comparative studies of nucleotide sequences. J. Mol. Evol., 16, 111-120.
22. Lapage, S. P., Sneath, P. H. A., Lessel, E. F., Skerman, V. B. D., Seeliger, H. P. R., and Clark, W. A. (ed.) (1992) International Code of Nomenclature of Bacteria (1990 Revision). Bacteriological Code, American Society for Microbiology, Washington, DC.
23. McDonald, I. R., Doronina, N. V., Trotsenko, Y. A., McAnulla, C., and Murrell, J. C. (2001) Hyphomicrobium chloromethanicum sp. nov. and Methylobacterium chloromethanicum sp. nov., chloromethane-utilizing bacteria isolated from a polluted environment. Int. J. Syst. Evol. Microbiol., 51, 119-122.
24. Patt, T. E., Cole, G. C., and Hanson, R. S. (1976) Methylobacterium, a new genus of facultatively methylotrophic bacteria. Int. J. Syst. Bacteriol., 26, 226-229.
25. Sadaie, Y., Yata, K., Fujita, M., Sagai, H., Itaya, M., Kasahara, Y., and Ogasawara, N. (1997) Nucleotide sequence and analysis of the phoB-rrnE-groESL region of the Bacillus subtilis chromosome. Microbiology, 143, 1861-1866.
26. Saitou, N. and Nei, M. (1987) The neighbour-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol., 4, 406-425.
27. Sokal, R. R. and Michener, C. D. (1958) A statistical method for evaluating systematic relationship. Univ. Kansas Sci. Bull., 28, 1409-1438.
28. Stackebrandt, E. and 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.
29. Tamaoka, J. and Komagata, K. (1984) Determination of DNA base composition by reverse-phase high-performance liquid chromatography. FEMS Microbiol. Lett., 25, 125-128.
30. Thompson, J. D., Higgins, D. G., and Gibson, T. J. (1994) CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
31. Treisman, R. (1989) Purification of plasmid DNA. In Molecular Cloning, 2nd ed., ed. by Smabrook, J., Fritsch, E. F., and Maniatis, T., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N. Y., Chapter 1, pp. 40-41.
32. Tuji, K., Tsien, H. C., Hanson, R. S., Depalma, S. R., Scholtz, R., and Larhoche, S. (1990) 16S ribosomal RNA sequence analysis for determination of phylogenetic relationship among methylotrophs. J. Gen. Microbiol., 136, 1-10.
33. Urakami, T., Akira, H., Suzuki, K., and Komagata, K. (1993) Further studies of the genus Methylobacterium and description of Methylobacterium aminovorans sp. nov. Int. J. Syst. Bacteriol., 43, 504-513.
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., Stackebrandt, E., Starr, M. P., and Trüper, H. G. (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. Wood, A. P., Kelly, D. P., McDonald, I. R., Jordan, S. L., Morgan, T. D., Khan, S., Murrell, J. C., and Borodina, E. (1998) A novel pink-pigmented facultative methylotroph, Methylobacterium thiocyanatum sp. nov., capable of growth on thiocyanate or cyanate as sole nitrogen sources. Arch. Microbiol., 169, 148-158.