Methylobacterium persicinum sp. nov., Methylobacterium komagatae sp. nov., Methylobacterium brachiatum sp. nov., Methylobacterium tardum sp. nov. and Methylobacterium gregans sp. nov., isolated from freshwater

International Journal of Systematic and Evolutionary Microbiology

Volumn 58, Issue 5, 2008, Pages 1134-1141

  Kato, Yuko ^a   Asahara, Mika ^a   Goto, Keiichi ^a   Kasai, Hiroaki ^b   Yokota, Akira ^c  

^a Mitsui Norin Co Ltd ^*  (Japan)

^b MARINE BIOTECHNOLOGY INSTITUTE   (Japan)

^c UNIVERSITY OF TOKYO   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; CYTOSINE; DNA TOPOISOMERASE (ATP HYDROLYSING) B; FATTY ACID; FRESH WATER; GUANINE; RNA 16S; UBIQUINONE; DNA TOPOISOMERASE (ATP HYDROLYSING); RIBOSOME DNA;

AEROBIC BACTERIUM; ARTICLE; BACTERIUM ISOLATE; CLADISTICS; CONTROLLED STUDY; DNA CONTENT; DNA DNA HYBRIDIZATION; GENE SEQUENCE; GRAM NEGATIVE BACTERIUM; JAPAN; METHYLOBACTERIUM; METHYLOBACTERIUM BRACHIATUM; METHYLOBACTERIUM GREGANS; METHYLOBACTERIUM KOMAGATAE; METHYLOBACTERIUM PERSICINUM; METHYLOBACTERIUM TARDUM; NEW SPECIES; NONHUMAN; NUCLEOTIDE SEQUENCE; PHENOTYPE; PHYLOGENY; PRIORITY JOURNAL; STRAIN DIFFERENCE; STRAIN IDENTIFICATION; TAXONOMY; BACTERIUM IDENTIFICATION; CHEMISTRY; CLASSIFICATION; DNA BASE COMPOSITION; DNA SEQUENCE; FOOD INDUSTRY; GENETICS; ISOLATION AND PURIFICATION; MICROBIOLOGY; MOLECULAR GENETICS; RNA GENE; SPECIES DIFFERENCE;

METHYLOBACTERIUM; NEGIBACTERIA;

BACTERIAL TYPING TECHNIQUES; BASE COMPOSITION; DNA GYRASE; DNA, BACTERIAL; DNA, RIBOSOMAL; FATTY ACIDS; FOOD INDUSTRY; FRESH WATER; GENES, RRNA; JAPAN; METHYLOBACTERIUM; MOLECULAR SEQUENCE DATA; PHENOTYPE; PHYLOGENY; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY;

EID: 47049106678     PISSN: 14665026     EISSN: None     Source Type: Journal    
DOI: 10.1099/ijs.0.65583-0     Document Type: Article

References (29)

1. Bousfield, I. J. & 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. Doronina, N. V., Trostenko, Y. A., Tourova, T. P., Kuznetzov, B. B. & 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.
3. Doronina, N. V., Trotsenko, Y. A., Kuznetsov, B. B., Tourova, T. P. & 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.
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. Gallego, V., García, M. T. & Ventosa, A. (2005a). Methylobacterium hispanicum sp. nov. and Methylobacterium aquaticum sp. nov., isolated from drinking water. Int J Syst Evol Microbiol 55, 281-287.
7. Gallego, V., García, M. T. & Ventosa, A. (2005b). Methylobacterium variabile sp. nov., a methylotrophic bacterium isolated from an aquatic environment. Int J Syst Evol Microbiol 55, 1429-1433.
8. Gallego, V., García, M. T. & Ventosa, A. (2005c). Methylobacterium isbiliense sp. nov., isolated from the drinking water system of Sevilla, Spain. Int J Syst Evol Microbiol 55, 2333-2337.
9. Gallego, V., García, M. T. & Ventosa, A. (2006). Methylobacterium adhaesivum sp. nov., a methylotrophic bacterium isolated from drinking water. Int J Syst Evol Microbiol 56, 339-342.
10. Goto, K., Omura, T., Hara, Y. & 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.
11. Gräf, W. & Bauer, L. (1973). Roter Bakterienaufwuchs ( Corynebacterium rubrum n. spec.) in Leitungswassersystemen. Zentralbl Bakteriol [Orig B] 157, 291-303 (in German).
12. Green, P. (1992). The genus Methylobacterium. In The Prokaryotes, 2nd edn, pp. 2342-2349. Edited by A. Balows, H. G. Trüper, M. Dworkin, W. Harder & K. H. Schleifer. New York: Springer-Verlag.
13. Green, P. N., Bousfield, I. J. & 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.
14. Hall, T. A. (1999). BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41, 95-98.
15. Ito, H. & Iizuka, H. (1971). Taxonomic studies on a radio-resistant Pseudomonas. Part XII. Studies on the microorganisms of cereal grain. Agric Biol Chem 35, 1566-1571.
16. Kasai, H., Tamura, T. & Harayama, S. (2000). Intrageneric relationship among Micromonospora species deduced from gyrB-based phylogeny and DNA relatedness. Int J Syst Evol Microbiol 50, 127-134.
17. Kato, Y., Asahara, M., Arai, D., Goto, K. & Yokota, A. (2005). 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. J Gen Appl Microbiol 51, 287-299.
18. Kato, Y., Asahara, M., Arai, D., Goto, K. & Yokota, A. (2006). Methylobacterium chloromethanicum pro synon. Methylobacterium extorquens; Methylobacterium dichloromethanicum pro synon. Methylobacterium extorquens; Methylobacterium lusitanum pro synon. Methylobacterium rhodesianum. In Notification of Changes in Taxonomic Opinion Previously Published Outside the IJSEM, List of Changes in Taxonomic Opinion no. 4. Int J Syst Evol Microbiol 56, 1463.
19. 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.
20. Kumar, S., Tamura, K. & Nei, M. (2004). MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5, 150-163.
21. Patt, T. E., Cole, G. C. & Hanson, R. S. (1976). Methylobacterium, a new genus of facultatively methylotrophic bacteria. Int J Syst Bacteriol 26, 226-229.
22. Saitou, N. & Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406-425.
23. Sano, H., Sakai, M. & Nichijima, M. (1996). Application of MS to the search for products from marine bacteria. J Mass Spectrom Soc Jpn 44, 377-391 (in Japanese).
24. Satomi, M., Kimura, B., Hamada, T., Harayama, S. & Fujii, T. (2002). Phylogenetic study of the genus Oceanospirillum based on 16S rRNA and gyrB genes: emended description of the genus Oceanospirillum, description of Pseudospirillum gen. nov., Oceanobacter gen. nov. and Terasakiella gen. nov. and transfer of Oceanospirillum jannaschii and Pseudomonas stanieri to Marinobacterium as Marinobacterium jannaschii comb. nov. and Marinobacterium stanieri comb. nov. Int J Syst Evol Microbiol 52, 739-747.
25. Stackebrandt, E. & 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.
26. Thompson, J. D., Higgins, D. G. & 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.
27. Urakami, T. & Komagata, K. (1984). Protomonas, a new genus of facultatively methylotrophic bacteria. Int J Syst Bacteriol 34, 188-201.
28. Venkateswaran, K., Moser, D. P., Dollhopf, M. E., Lies, D. P., Saffarini, D. A., MacGregor, B. J., Ringelberg, D. B., White, D. C., Nishijima, M. & other authors (1999). Polyphasic taxonomy of the genus Shewanella and description of Shewanella oneidensis sp. nov. Int J Syst Bacteriol 49, 705-724.
29. Yamamoto, S. & Harayama, S. (1995). PCR amplification and direct sequencing of gyrB genes with universal primers and their application to the detection and taxonomic analysis of Pseudomonas putida strains. Appl Environ Microbiol 61, 1104-1109.