Methylomonas paludis sp. nov., the first acidtolerant member of the genus Methylomonas, from an acidic wetland

International Journal of Systematic and Evolutionary Microbiology

Volumn 63, Issue PART6, 2013, Pages 2282-2289

  Danilova, Olga V ^a   Kulichevskaya, Irina S ^a   Rozova, Olga N ^b   Detkova, Ekaterina N ^a   Bodelier, Paul L E ^c   Trotsenko, Yuri A ^b   Dedysh, Svetlana N ^a  

^a WINOGRADSKY INSTITUTE OF MICROBIOLOGY   (Russian Federation)

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

^c NETHERLANDS INSTITUTE OF ECOLOGY NIOO KNAW   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

AMINOTRANSFERASE; FORMATE DEHYDROGENASE; GLUCOSE 6 PHOSPHATE DEHYDROGENASE; HEXULOSE PHOSPHATE SYNTHASE; HYDROXYPYRUVATE REDUCTASE; METHANOL DEHYDROGENASE; RIBULOSEBISPHOSPHATE CARBOXYLASE; RNA 16S; SERINE GLYOXYLATE AMINOTRANSFERASE; UNCLASSIFIED DRUG;

ARTICLE; BACTERIAL STRAIN; BACTERIUM CULTURE; BACTERIUM IDENTIFICATION; ENZYME ACTIVITY; ESCHERICHIA COLI; METHYLOMONAS; METHYLOMONAS PALUDIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PH; PRIORITY JOURNAL; TEMPERATURE; WETLAND;

BACTERIA (MICROORGANISMS); GAMMAPROTEOBACTERIA; METHYLOCOCCACEAE; METHYLOMONAS; NEGIBACTERIA; SPHAGNUM;

EID: 84878851917     PISSN: 14665026     EISSN: None     Source Type: Journal    
DOI: 10.1099/ijs.0.045658-0     Document Type: Article

References (42)

1. Anthony, C. & Zatman, L. J. (1964). The microbial oxidation of methanol. 2. The methanol-oxidizing enzyme of Pseudomonas sp. M 27. Biochem J 92, 614-621.
2. Auman, A. J. & Lidstrom, M. E. (2002). Analysis of sMMO-containing type I methanotrophs in Lake Washington sediment. Environ Microbiol 4, 517-524.
3. Auman, A. J., Stolyar, S., Costello, A. M. & Lidstrom, M. E. (2000). Molecular characterization of methanotrophic isolates from freshwater lake sediment. Appl Environ Microbiol 66, 5259-5266.
4. Beschastny, A. P., Sokolov, A. P., Khmelenina, V. N. & Trotsenko, Y. A. (1992). Purification and properties of pyrophosphate-dependent phosphofructokinase of obligate methanotroph Methylomonas methanica. Biochemistry (Moscow) 57, 1215-1221.
5. Blackmore, M. A. & Quayle, J. R. (1970). Microbial growth on oxalate by a route not involving glyoxylate carboligase. Biochem J 118, 53-59.
6. Bowman, J. P., Sly, L. I., Cox, J. M. & Hayward, A. C. (1990). Methylomonas fodinarum sp. nov. and Methylomonas aurantiaca sp. nov.: two closely related type I obligate methanotrophs. Syst Appl Microbiol 13, 279-287.
7. Bowman, J. P., Skerratt, J. H., Nichols, P. D. & Sly, L. I. (1991). Phospholipid fatty acid and lipopolysaccharide fatty acid signature lipids in methane-utilizing bacteria. FEMS Microbiol Ecol 85, 15-22.
8. 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.
9. Chen, Y., Dumont, M. G., McNamara, N. P., Chamberlain, P. M., Bodrossy, L., Stralis-Pavese, N. & Murrell, J. C. (2008). Diversity of the active methanotrophic community in acidic peatlands as assessed by mRNA and SIP-PLFA analyses. Environ Microbiol 10, 446-459.
10. Dedysh, S. N., Liesack, W., Khmelenina, V. N., Suzina, N. E., Trotsenko, Y. A., Semrau, J. D., Bares, A. M., Panikov, N. S. & Tiedje, J. M. (2000). Methylocella palustris gen. nov., sp. nov., a new methaneoxidizing acidophilic bacterium from peat bogs, representing a novel subtype of serine-pathway methanotrophs. Int J Syst Evol Microbiol 50, 955-969.
11. Dedysh, S. N., Khmelenina, V. N., Suzina, N. E., Trotsenko, Y. A., Semrau, J. D., Liesack, W. & Tiedje, J. M. (2002). Methylocapsa acidiphila gen. nov., sp. nov., a novel methane-oxidizing and dinitrogen-fixing acidophilic bacterium from Sphagnum bog. Int J Syst Evol Microbiol 52, 251-261.
12. Dedysh, S. N., Ricke, P. & Liesack, W. (2004). NifH and NifD phylogenies: an evolutionary basis for understanding nitrogen fixation capabilities of methanotrophic bacteria. Microbiology 150, 1301-1313.
13. Dedysh, S. N., Belova, S. E., Bodelier, P. L., 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.
14. Dianou, D., Ueno, C., Ogiso, T., Kimura, M. & Asakawa, S. (2012). Diversity of cultivable methane-oxidizing bacteria in microsites of a rice paddy field: investigation by cultivation method and fluorescence in situ hybridization (FISH). Microbes Environ 27, 278-287.
15. Eller, G., Stubner, S. & Frenzel, P. (2001). Group-specific 16S rRNA targeted probes for the detection of type I and type II methanotrophs by fluorescence in situ hybridisation. FEMS Microbiol Lett 198, 91-97.
16. Felsenstein, J. (1989). PHYLIP - phylogeny inference package (version 3.2). Cladistics 5, 164-166.
17. Ferenci, T., Strom, T. & Quayle, J. R. (1974). Purification and properties of 3-hexulose phosphate synthase and phospho-3-hexuloisomerase from Methylococcus capsulatus. Biochem J 144, 477-486.
18. Graham, D. W., Korich, D. G., LeBlanc, R. P., Sinclair, N. A. & Arnold, R. G. (1992). Applications of a colorimetric plate assay for soluble methane monooxygenase activity. Appl Environ Microbiol 58, 2231-2236.
19. Holmes, A. J., Costello, A., Lidstrom, M. E. & Murrell, J. C. (1995). Evidence that particulate methane monooxygenase and ammonia monooxygenase may be evolutionarily related. FEMS Microbiol Lett 132, 203-208.
20. Hutchens, E., Radajewski, S., Dumont, M. G., McDonald, I. R. & Murrell, J. C. (2004). Analysis of methanotrophic bacteria in Movile Cave by stable isotope probing. Environ Microbiol 6, 111-120.
21. Jaatinen, K., Tuittila, E.-S., Laine, J., Yrjälä, K. & Fritze, H. (2005). Methane-oxidizing bacteria in a Finnish raised mire complex: effects of site fertility and drainage. Microb Ecol 50, 429-439.
22. Johnson, P. A. & Quayle, J. R. (1964). Microbial growth on C-1 compounds. 6. Oxidation of methanol, formaldehyde and formate by methanol-grown Pseudomonas AM-1. Biochem J 93, 281-290.
23. Kalyuzhnaya, M. G., Khmelenina, V. N., Kotelnikova, S., Holmquist, L., Pedersen, K. & Trotsenko, Y. A. (1999). Methylomonas scandinavica sp. nov., a new methanotrophic psychrotrophic bacterium isolated from deep igneous rock ground water of Sweden. Syst Appl Microbiol 22, 565-572.
24. Kip, N., Dutilh, B. E., Pan, Y., Bodrossy, L., Neveling, K., Kwint, M. P., Jetten, M. S. & Op den Camp, H. J. (2011a). Ultra-deep pyrosequencing of pmoA amplicons confirms the prevalence of Methylomonas and Methylocystis in Sphagnum mosses from a Dutch peat bog. Env Microb Rep 3, 667-673.
25. Kip, N., Ouyang, W., van Winden, J., Raghoebarsing, A., van Niftrik, L., Pol, A., Pan, Y., Bodrossy, L., van Donselaar, E. G. & other authors (2011b). Detection, isolation, and characterization of acidophilic methanotrophs from Sphagnum mosses. Appl Environ Microbiol 77, 5643-5654.
26. Kornberg, A. & Horecker, B. L. (1955). Glucose-6-phosphate dehydrogenase. Methods Enzymol 1, 323-327.
27. 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.
28. 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.
29. Lüke, C., Krause, S., Cavigiolo, S., Greppi, D., Lupotto, E. & Frenzel, P. (2010). Biogeography of wetland rice methanotrophs. Environ Microbiol 12, 862-872.
30. McDonald, I. R. & Murrell, J. C. (1997). The methanol dehydrogenase structural gene mxaF and its use as a functional gene probe for methanotrophs and methylotrophs. Appl Environ Microbiol 63, 3218-3224.
31. Miguez, C. B., Bourque, D., Sealy, J. A., Greer, C. W. & Groleau, D. (1997). Detection and isolation of methanotrophic bacteria possessing soluble methane monooxygenase (sMMO) genes using the polymerase chain reaction (PCR). Microb Ecol 33, 21-31.
32. Morris, S. A., Radajewski, S., Willison, T. W. & Murrell, J. C. (2002). Identification of the functionally active methanotroph population in a peat soil microcosm by stable-isotope probing. Appl Environ Microbiol 68, 1446-1453.
33. Ogiso, T., Ueno, C., Dianou, D., Huy, T. V., Katayama, A., Kimura, M. & Asakawa, S. (2012). Methylomonas koyamae sp. nov., a type I methane-oxidizing bacterium from floodwater of a rice paddy field. Int J Syst Evol Microbiol 62, 1832-1837.
34. Owen, R. J., Hill, L. R. & Lapage, S. P. (1969). Determination of DNA base compositions from melting profiles in dilute buffers. Biopolymers 7, 503-516.
35. Reynolds, E. S. (1963). The use of lead citrate at high pH as an electron-opaque stain in electron microscopy. J Cell Biol 17, 208-212.
36. Schacterle, G. R. & Pollack, R. L. (1973). A simplified method for the quantitative assay of small amounts of protein in biologic material. Anal Biochem 51, 654-655.
37. Söhngen, N. L. (1906). Uber bakterien, welche methan ab kohlenstoffnahrung and energiequelle gebrauchen. Parasitenkd Infectionskr 15, 513-517.
38. van Dijken, J. P. & Quayle, J. R. (1977). Fructose metabolism in four Pseudomonas species. Arch Microbiol 114, 281-286.
39. Vorobev, A. V., Baani, M., Doronina, N. V., Brady, A. L., Liesack, W., Dunfield, P. F. & Dedysh, S. N. (2011). Methyloferula stellata gen. nov., sp. nov., an acidophilic, obligately methanotrophic bacterium possessing only a soluble methane monooxygenase. Int J Syst Evol Microbiol 61, 2456-2463.
40. Weisburg, W. G., Barns, S. M., Pelletier, D. A. & Lane, D. J. (1991). 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173, 697-703.
41. Whittenbury, R. & Krieg, N. R. (1984). Genus II. Methylomonas. In Bergey's Manual of Systematic Bacteriology, vol. 1, pp. 260-261. Edited by N. R. Krieg & J. G. Holt. Baltimore: Williams & Wilkins Co.
42. Whittenbury, R., Phillips, K. C. & Wilkinson, J. F. (1970). Enrichment, isolation and some properties of methane-utilizing bacteria. J Gen Microbiol 61, 205-218.