Classification of halo(alkali)philic and halo(alkali)tolerant methanotrophs provisionally assigned to the genera Methylomicrobium and Methylobacter and emended description of the genus Methylomicrobium

International Journal of Systematic and Evolutionary Microbiology

Volumn 58, Issue 3, 2008, Pages 591-596

  Kalyuzhnaya, Marina G ^a,b   Khmelenina, Valentina ^a   Eshinimaev, Bulat ^a   Sorokin, Dimitry ^c   Fuse, Hiroyuki ^d   Lidstrom, Mary ^b,e   Trotsenko, Yuri ^a,f  

^a SKRYABIN INSTITUTE OF BIOCHEMISTRY AND PHYSIOLOGY OF MICROORGANISMS   (Russian Federation)

^b UNIVERSITY OF WASHINGTON   (United States)

^c WINOGRADSKY INSTITUTE OF MICROBIOLOGY   (Russian Federation)

^d NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^e University of Washington   (United States)

^f PUSHCHINO STATE UNIVERSITY   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

RNA 16S; BACTERIAL DNA; METHANE; RIBOSOME DNA; SODIUM CHLORIDE;

ARTICLE; BACTERIAL STRAIN; DNA DNA HYBRIDIZATION; GENE SEQUENCE; METHANOTROPH; METHANOTROPHIC BACTERIUM; METHYLOBACTER; METHYLOBACTER ALCALIPHILUS; METHYLOMICROBIUM; METHYLOMICROBIUM ALCALIPHILUM; METHYLOMICROBIUM JAPANENSE; METHYLOMICROBIUM KENYENSE; METHYLOMICROBIUM PELAGICUM; NEW SPECIES; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; RNA SEQUENCE; TAXONOMY; CLASSIFICATION; DNA SEQUENCE; GENETICS; GROWTH, DEVELOPMENT AND AGING; METABOLISM; METHYLOCOCCACEAE; MOLECULAR GENETICS; NUCLEIC ACID HYBRIDIZATION; PH; PHYSIOLOGY; RNA GENE; SPECIES DIFFERENCE;

METHYLOBACTER; METHYLOBACTER ALCALIPHILUS; METHYLOMICROBIUM; METHYLOMICROBIUM PELAGICUM;

DNA, BACTERIAL; DNA, RIBOSOMAL; GENES, RRNA; HYDROGEN-ION CONCENTRATION; METHANE; METHYLOCOCCACEAE; MOLECULAR SEQUENCE DATA; NUCLEIC ACID HYBRIDIZATION; PHYLOGENY; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SODIUM CHLORIDE; SPECIES SPECIFICITY;

EID: 44449131579     PISSN: 14665026     EISSN: None     Source Type: Journal    
DOI: 10.1099/ijs.0.65317-0     Document Type: Article

References (32)

1. Bowman, J. P., Sly, L. I., Nichols, P. D. & Hayward, A. C. (1993). Revised taxonomy of the methanotrophs: description of Methylobacter gen. nov., emendation of Methylococcus, validation of Methylosinus and Methylocystis species, and a proposal that the family Methylococcaceae includes only the group I methanotrophs. Int J Syst Bacteriol 43, 735-753.
2. Bowman, J. P., Sly, L. I. & Stackebrandt, E. (1995). The phylogenetic position of the family Methylococcaceae. Int J Syst Bacteriol 45, 182-185.
3. Bowman, J. P., McCammon, S. A. & Skerratt, J. H. (1997). Methylosphaera hansonii gen. nov., sp. nov., a psychrophilic, group I methanotroph from Antarctic marine-salinity, meromictic lakes. Microbiology 143, 1451-1459.
4. Cho, J.-C. & Giovannoni, S. J. (2003). Fulvimarina pelagi gen. nov., sp. nov., a marine bacterium that forms a deep evolutionary lineage of descent in the order 'Rhizobiales'. Int J Syst Evol Microbiol 53, 1853-1859.
5. Dedysh, S. N., Belova, S. E., Bodelier, P. L. E., Smirnova, K. V., Khmelenina, V. N., Chidthaisong, A., Trotsenko, Y. A., Liesack, W. & Dunfield, P. F. (2007). Methylocystis heyeri sp. nov., a novel type II methanotrophic bacterium possessing 'signature' fatty acids of type I methanotrophs. Int J Syst Evol Microbiol 57, 472-479.
6. Edwards, U., Rogall, T., Blöcker, H., Emde, M. & Böttger, E. C. (1989). Isolation and direct complete nucleotide determination of entire genes. Characterization of a gene coding for 16S ribosomal RNA. Nucleic Acids Res 17, 7843-7853.
7. Felsenstein, J. (2004). PHYLIP: phylogeny inference package, version 3.6. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle, USA.
8. Fuse, H., Ohta, M., Takimura, O., Murakami, K., Inoue, H., Yamaoka, Y., Oclarit, J. M. & Omori, T. (1998). Oxidation of trichloroethylene and dimethyl sulfide by a marine Methylomicrobium strain containing soluble methane monooxygenase. Biosci Biotechnol Biochem 62, 1925-1931.
9. Hanson, R. S. & Hanson, T. E. (1996). Methanotrophic bacteria. Microbiol Rev 60, 439-471.
10. Heyer, J., Berger, U., Hardt, M. & Dunfield, P. F. (2005). Methylohalobius crimeensis gen. nov., sp. nov., a moderately halophilic, methanotrophic bacterium isolated from hypersaline lakes of Crimea. Int J Syst Evol Microbiol 55, 1817-1826.
11. Higgins, I. J., Best, D. J. & Hammond, R. C. (1980). New findings in methane-utilizing bacteria highlight their importance in the biosphere and their commercial potential. Nature 286, 561-564.
12. Higgins, D. G., Thompson, J. D. & Gibson, T. J. (1996). Using CLUSTAL for multiple sequence alignments. Methods Enzymol 266, 383-402.
13. Johnson, J. L. (1994). Similarity analysis of DNAs. In Methods for General and Molecular Bacteriology, pp. 655-682. Edited by P. Gerhardt, R. G. E. Murray, W. A. Wood & N. R. Krieg. Washington, DC: American Society for Microbiology.
14. Kaluzhnaya, M. G., Khmelenina, V. N., Eshinimaev, B. Ts, Suzina, N. E, Nikitin, D., Solonin, A., Lin, J.-L, McDonald, I. R., Murrell, J. C. & Trotsenko, Y. A. (2001). Taxonomic characterization of new alkaliphilic and alkalitolerant methanotrophs from soda lakes of the Southeastern Transbaikal region and description of Methylomicrobium buryatense sp. nov. Syst Appl Microbiol 24, 166-176.
15. Kalyuzhnaya, M. G., Khmelenina, V. N., Starostina, N. G., Baranova, S. B., Suzina, N. E. & Trotsenko, Y. A. (1998). A new moderately halophilic methanotroph of the genus Methylobacter. Microbiology (English translation of Mikrobiologiia) 67, 438-444.
16. Kalyuzhnaya, M. G., Khmelenina, V. N., Suzina, N. E., Lysenko, A. M. & Trotsenko, Y. A. (1999). New methanotrophic isolates from soda lakes of the southern Transbaikal region. Microbiology (English translation of Mikrobiologiia) 68, 592-600.
17. Katayama-Fujimura, Y., Komatsu, Y., Kuralshi, H. & Kaneko, T. (1984). Estimation of DNA base composition by high performance liquid chromatography of its nuclease P1 hydrolysate. Agric Biol Chem 48, 3169-3172.
18. Khmelenina, V. N., Kelyuzhnaya, M. G., Starostina, N. G., Suzina, N. E. & Trotsenko, Y. A. (1997). Isolation and characterization of halotolerant alkaliphilic methanotrophic bacteria from Tuva soda lakes. Curr Microbiol 35, 257-261.
19. Khmelenina, V. N., Kalyuzhnaya, M. G., Sakharovsky, V. G., Suzina, N. E., Trotsenko, Y. A. & Gottschalk G. (1999). Osmoadaptation in halophilic and alkaliphilic methanotrophs. Arch Microbiol 172, 321-329.
20. Lin, J.-L., Radajewski, S., Eshinimaev, B. T., Trotsenko, Y. A., McDonald, I. R. & Murrell, J. C. (2004). Molecular diversity of methanotrophs in Transbaikal soda lake sediments and identification of potentially active populations by stable isotope probing. Environ Microbiol 6, 1049-1060.
21. Miller, J. A., Kalyuzhnaya, M. G., Noyes, E, Lara, J. C., Lidstrom, M. E. & Chistoserdova, L. (2005). Labrys methylaminiphilus sp. nov., a novel facultatively methylotrophic bacterium from a freshwater lake sediment. Int J Syst Evol Microbiol 55, 1247-1253.
22. Nercessian, O., Kalyuzhnaya, M. G., Joye, S., Lidstrom, M. E. & Chistoserdova, L. (2005). Analysis of fae and fhcD genes in Mono Lake, California. Appl Environ Microbiol 71, 8949-8953.
23. Reshetnikov, A. S., Khmelenina, V. N. & Trotsenko, Y. A. (2006). Characterization of the ectoine biosynthesis genes of haloalkalotolerant obligate methanotroph "Methylomicrobium alcaliphilum 207". Arch Microbiol 184, 286-297.
24. Sieburth, J. M., Johnson, P. W., Eberhardt M. A., Sieracki, M. E., Lidstrom, M. & Laux, D. (1987). The first methane-oxidizing bacterium from the upper mixed layer of the deep ocean. Methylomonas pelagica sp. nov. Curr Microbiol 14, 285-293.
25. Sorokin, D. Y., Jones, B. E. & Kuenen, J. G. (2000). A novel obligately methylotrophic, methane-oxidizing Methylomicrobium species from a highly alkaline environment. Extremophiles 4, 145-155.
26. Trotsenko, Y. A. & Khmelenina, V. N. (2002a). Biology of extremophilic and extremotolerant methanotrophs. Arch Microbiol 177, 123-131.
27. Trotsenko, Y. A. & Khmelenina, V. N. (2002b). Biology and osmoadaptation of haloalkaliphilic methanotrophs. Microbiology (English translation of Mikrobiologiia) 71, 123-132.
28. Trotsenko, Yu. A., Doronina, N. V. & Khmelenina, V. N. (2005). Biotechnological potential of methylotrophic bacteria: a review of current status and future prospects. Appl Biochem Microbiol (English translation of Prikl Biokhim Mikrobiol) 41, 437-441.
29. Wartiainen, I., Hestnes, A. G., McDonald, I. R. & Svenning, M. M. (2006). Methylobacter tundripaludum sp. nov., a methane-oxidizing bacterium from Arctic wetland soil on the Svalbard islands, Norway (78° N). Int J Syst Evol Microbiol 56, 109-113.
30. Whalen, S. C. & Reeburgh, W. S. (1990). Consumption of atmospheric methane by tundra soils. Nature 346, 160-162.
31. Whittenbury, R., Phillips, K. C. & Wilkinson, J. F. (1970). Enrichment, isolation and some properties of methane-utilizing bacteria. J Gen Microbiol 61, 205-218.
32. Wise, M. G., McArthur, J. V. & Shimkets, L. J. (2001). Methylosarcina fibrata gen. nov., sp. nov. and Methylosarcina quisquiliarum sp. nov., novel type I methanotrophs. Int J Syst Evol Microbiol 51, 611-621.