Moderately haloalkaliphilic aerobic methylobacteria

Microbiology

Volumn 76, Issue 3, 2007, Pages 253-265

  Trotsenko, Yu A ^a   Doronina, N V ^b   Li, Ts D ^b   Reshetnikov, A S ^b  

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

^b PUSHCHINO STATE UNIVERSITY   (Russian Federation)

Author keywords

Aerobic methylobacteria; Bioremediation; Ecophysiology and osmoadaptation; Halo(alkali)philes; Phylogeny; Taxonomy

Indexed keywords

EID: 34250897933     PISSN: 00262617     EISSN: None     Source Type: Journal    
DOI: 10.1134/S0026261707030010     Document Type: Review

References (100)

1. Kashner, D., Microbial Life in Extreme Environments, Kushner, D.J., Ed., London: Academic, 1978
2. [Russ. Transl. Zhizn' mikrobov v ekstremal'nykh usloviyakh, Moscow: Mir, 1981].
3. Ventosa, A., Nieto, J.J., and Oren, A., Biology of Moderately Halophilic Aerobic Bacteria, Microbiol. Mol. Biol. Rev, 1998, vol. 62, pp. 504-544.
4. Skerman, V.B.D., McGowan, V., and Sneath, P.H.A., (Ed.). Approved Lists of Bacterial Names, Int. J. Syst Bacterial, 1980, vol. 30, pp. 225-420.
5. Roberts, M.F., Organic Compatible Solutes of Halotolerant and Halophilic Microorganisms, Saline Systems, 2005, vol. 5, pp. 1-30.
6. Yamamoto, M., Seriu, Y., Kouno, K., Okamoto, R., and Inui, T., Isolation and Characterization of Marine Methanol-Utilizing Bacteria, J. Ferment. Technol., 1978, vol. 56, pp. 451-458.
7. Yamamoto, M., Iwaki, H., Kouno, K., and Inui, T., Identification of Marine Methanol-Utilizing Bacteria, J. Ferment. Technol., 1980, vol. 58, pp. 99-106.
8. Strand, S.E. and Lidstrom, M.E., Characterization of a New Marine Methylotroph, FEMS Microbiol. Letts., 1984, vol. 21, pp. 247-251.
9. Janvier, M., Frehel, C., Grimont, F., and Gasser, F., Methylophaga marina gen. nov., sp. nov. and Methylophaga thalassica sp. nov., Marine Methylotrophs, Int. J. Syst Bacterial., 1985, vol. 35, pp. 131-139.
10. Padan, E., Bibi, E., Ito, M., and Krulwich, T.A., Alkaline pH Homeostasis in Bacteria: New Insights, Biochim. Biophys. Acta, 2005, vol. 1717, pp. 67-88.
11. de Zwart, J.M.M., Nelisse, P.N., and Kuenen, J.G., Isolation and Characterization of Methylophaga sulfidovorans sp.nov.: An Obligately Methylotrophic, Aerobic, Dimethylsulfide Oxidizing Bacterium from a Microbial Mat, FEMS Microbiol. Ecol., 1996, vol.20, pp. 261-270.
12. Doronina, N.V., Krauzova, V.I., and Trotsenko, Yu.A., Methylophaga limanica sp. nov.: A New Species of Moderately Halophilic, Aerobic, Methylotrophic Bacteria, Mikrobiologiya, 1997, vol. 66, no. 4, pp. 528-533
13. [Microbiology (Engl. Transl.), vol. 66, no. 4, pp. 434-440].
14. Janvier, M., Regnault, B., and Grimont, P., Development and Use of Fluorescent 16S rRNA-Targeted Probes for the Specific Detection of Methylophaga Species by in Situ Hybridization in Marine Sediments, Res. Microbiol., 2003, vol. 154, no. 7, pp. 483-90.
15. 12-Independent Strains of Methylophaga marina Isolated from Red Sea Algae, Mikrobiologiya, 2007, vol. 76, no. 1, pp. 88-94
16. [Microbiology (Engl. Transl.), vol. 76, no. 1, pp. 75-81].
17. Doronina, N.V., Tourova, T.P., and Trotsenko, Y.A., Methylarcula marina gen. nov., sp. nov. and Methylarcula terricola sp. nov.: Novel Aerobic, Moderately Halophilic, Facultatively Methylotrophic Bacteria from Coastal Saline Environments, Int. J. Syst. Evol. Microbiol., 2000, vol. 50, pp. 1849-1859.
18. Baker, S.C., Kelly, D.P., and Murrell, J.C., Microbial Degradation of Methanesulfonic Acid: a Missing Link in the Biogeochemical Sulphur Cycle, Nature, 1991, vol. 350, pp. 627-628.
19. Holmes, A.J., Kelly, D.P., Baker, S.C., Thompson, A.S., DeMarco, P., Kenna, E.M., and Murrell, J.C., Methylo-sulfonomonas methylovora gen nov., sp. nov. and Marinosulfonomonas methylotropha gen. nov. sp. nov.: Novel Methylotrophs Able To Grow on Methanesulfonic Acid, Arch. Microbiol., 1997, vol. 167, pp. 46-53.
20. Lee, J.H., Kim, Y.S., Choi, T.-J., Lee, W.J., and Kim, Y.T., Paracoccus haeundaensis sp. nov., a Gram-Negative, Halophilic, Astaxanthin-Producing Bacterium, Int. J. Syst. Evol. Microbiol., 2004, vol.54, pp. 1699-1702.
21. Schaefer, J.K. and Goodwin, K.D., MacDonald I.R., Murrell J.C., Oremland R.S. Leisingera methylohalidivorans gen. nov., sp. nov., a Marine Methylotroph That Grows on Methyl Bromide, Int. J. Syst. Evol. Microbiol., 2002, vol. 52, pp. 851-859.
22. Zavarzin, G.A., Epicontinental Soda Lakes as the Probable Relic Biotopes of Formation of Terrestrial Biota, Mikrobiologiya, 1993, vol. 62, no. 5, pp. 789-800.
23. Grant, W.D and Jones, B.E, Alkaline Environments, Encyclopedia of microbiology, Lederberg, J., Ed., Academic Press, 2000, V. 1, pp. 126-133.
24. Zavarzin, G.A., Zhilina, T.N., and Kevbrin, V.V., The Alkaliphilic Microbial Community and Its Functional Diversity, Mikrobiologiya, 1999, vol. 68, no. 5, pp. 579-599
25. [Microbiology (Engl. Transl.), vol.68, no.5, pp. 503-521].
26. Zhilina, T.N. and Zavarzin, G.A., Alkaliphilic Anaerobic Community at pH 10, Curr. Microbiol., 1994, vol. 29, pp. 109-112.
27. Gerasimenko, L.M., Dubinin, A.V., and Zavarzin, G.A., Alkaliphilic Cyanobacteria from Soda Lakes of Tuva and Their Ecophysiology, Mikrobiologiya, 1996, vol. 65, no. 6, pp. 844-849
28. [Microbiology (Engl. Transl.), vol. 65, no. 6, pp. 736-740].
29. Sorokin, D.Yu., On the Possibility of Nitrification in Extremely Alkaline Soda Biotopes, Mikrobiologiya, 1998, vol. 67, no. 3, pp. 404-408
30. [Microbiology (Engl. Transl.), vol. 67, no. 3, pp. 335-339].
31. Yumoto, I., Yamasaki, K., Sawabe, T., Nakano, K., Kawasaki, K., Ezura, Y., and Shinano, H., Bacillus horti sp.nov., a New Gram-Negative Alkaliphilic Bacillus, Int. J. Syst. Bacterial., 1998, vol. 48, pp. 565-571.
32. Joye, S.B., Connell, T.L., Miller, L.G., Oremland, R.S., and Jellison, R.S., Oxidation of Ammonia and Methane in An Alkaline, Saline Lake, Limnol. Oceanogr., 1999, vol. 44, no. 1, pp. 178-188.
33. Tourova, T.P., Garnova, E.S., and Zhilina, T.N., Phylogenetic Diversity of Alkaliphilic Anaerobic Saccharolytic Bacteria Isolated from Soda Lakes, Mikrobiologiya, 1999, vol. 68, no. 5, pp. 701-709
34. [Microbiology (Engl. Transl.), vol. 68, no. 5, pp. 615-622].
35. Gorlenko, V.M., Namsaraev, B.B., Kulyrova, A.V., Zavarzina, D.G., and Zhilina, T.N., The Activity of Sulfate-reducing Bacteria in Bottom Sediments of Soda Lakes of the Southeastern Transbaikal Region, Mikrobiologiya, 1999, vol. 68, no. 5, pp. 664-670
36. [Microbiology (Engl. Transl.), vol. 68, no. 5, pp. 580-585].
37. Kalyuzhnaya, M.G., Khmelenina, V.N., Suzina, N.B., Lysenko, A.M., and Trotsenko, Yu.A., New Methanotrophic Isolates from Soda Lakes of the Southern Transbaikal Region, Mikrobiologiya (UK), 1999, vol.68, no. 5, pp. 677-685
38. [Microbiology (Engl. Transl.), vol. 68, no. 5, pp. 592-600].
39. Trotsenko, Yu.A. and Khmelenina, V.N., The Biology and Osmoadaptation of Haloalkaliphilic Methanotrophs, Mikrobiologiya, 2002, vol. 71, no. 2, pp. 149-159
40. [Microbiology (Engl. Transl.), vol.71, no. 2, pp. 123-132].
41. Kelly, D.P., Baker, S.C., Tricket, J., Davey, M., and Murrell, J.C., Methane Sulfonate Utilization by a Novel Methylotrophic Bacterium Involves An Unusual Monooxygenase, Microbiology (UK), 1994, vol. 140, pp. 1419-1426.
42. Doronina, N.V. and Trotsenko, Yu.A., Aerobic Methylotrophic Bacterial Communities of Hypersaline Ecosystems, Mikrobiologiya, 1997, vol. 66, no. 1, pp. 175-181
43. [Microbiology (Engl. Transl.), vol. 66, no. 1, pp. 111-117].
44. Doronina, N.V., Darmaeva, Ts.D., and Trotsenko, Y.A., Methylophaga alcalica sp. nov., a New Alkaliphilic and Moderately Halophilic, Obligately Methylotrophic Bacterium from the East Mongolian Saline Soda Lake, Int. J. Syst. Evol. Microbiol., 2003, vol. 53, pp. 223-229.
45. Doronina, N.V., Darmaeva, Ts.D., and Trotsenko, Y.A., Methylophaga natronica sp.nov., a New Alkaliphilic and Moderately Halophilic, Restricted-Facultatively Methylotrophic Bacterium from Soda Lake of the Southern Transbaikal Region, Syst. Appl. Microbiol., 2003, vol. 26, pp. 382-389.
46. Doronina, N.V, Darmaeva, Ts.D., and Trotsenko, Yu.A., Novel Aerobic Methylotrophic Isolates from the Soda Lakes of the Southern Transbaikal Region, Mikrobiologiya, 2001, vol. 70, no. 3, pp. 398-404
47. [Microbiology (Engl. Transl.), vol. 70, no. 3, pp. 342-348].
48. Raj, H.D., Oligotrophic Methylotrophs: Ancylobacter (Basonym "Microcyclus" Orskov) Raj gen. nov, Crit. Rev. Microbiol., 1989, vol. 17, pp. 89-106.
49. Namsaraev, B.B. and Zavarzin, G.A., Trophic Relations in Methane-Oxidizing Cultures, Mikrobiologiya, 1972, vol. 41, no. 6, pp. 999-1006.
50. Bock, E. and Sand, W., The Microbiology of Masonry Biodeterioration, J. Appl. Bacteriol., 1993, vol. 74, no. 3, pp. 503-514.
51. Gorbushina, A.A., Lyalikova, N.N., Vlasov, D.Yu., and Khizhnyak, T.V., Microbial Communities on the Monuments of Moscow and St. Petersburg: Biodiversity and Trophic Relations, Mikrobiologiya, 2002, vol. 71, no. 3, pp. 409-417
52. [Microbiology (Engl. Transl.), vol.71, no. 3, pp. 350-356].
53. Kussmaul, M., Wilimzig, M., and Bock, E., Methanotrophs and Methanogens in Masonry, Appl. Environ. Microbiol., 1998, vol. 64, pp. 4530-4532.
54. Knief , C. and Dunfield, P.F., Response and Adaptation of Different Methanotrophic Bacteria to Low Methane Mixing Ratios, Environ. Microbiol., 2005, vol. 7, pp. 1307-1317.
55. Kravchenko, I.K. and Bykova, S.A., Oxidation of Atmospheric Methane by Microorganisms of Aerated Soils, Proc. Winogradsky Institute of Microbiology, vol. XII. Collected Articles on the Institute 70th Anniversary, Gal'chenko, V.F., Ed., Moscow: Nauka, 2004.
56. Kussmaul, M., Groengroeft, A., and Koethe, H., Emissions of Porewater Compounds and Gases from the Subaquatic Sediment Disposal Site "Rodewischhafen", Hamburg harbour, Wat. Sci. Tech., 1998, vol. 37, pp. 87-93.
57. Keppler, F. and Hamilton, J.T.G., Braß M., and Röckmann T., Methane Emissions from Terrestrial Plants Under Aerobic Conditions, Nature, 2006, vol.439, pp. 187-191.
58. McDonald, R.C. and Fall, R., Detection of Substantial Emissions of Methanol from Plants To the Atmosphere, Atmos. Environ., 1993, vol. 27 A, pp. 1709-1713.
59. 1 Compounds, Lidstrom, M.E.and Tabita, F.R., Eds., Kluwer Acad. Publ., 1996, pp. 343-350.
60. Galbally, I.E. and Kirstine, W., The Production of Methanol by Flowering Plants and the Global Cycle of Methanol, J. Atmosph. Chemi., 2002, vol. 43, pp. 195-229.
61. Doronina, N.V, Li, Ts.D., Ivanova, E.G., and Trotsenko, Yu.A., Methylophaga murata sp. nov.: a Haloalkaliphilic Aerobic Methylotroph from Deteriorating Marble, Mikrobiologiya, 2005, vol. 74, no. 4, pp. 511-519
62. [Microbiology (Engl. Transl.), vol. 74, no. 4, pp. 440-447].
63. Urakami, T. and Komagata, K., Characterization of Species of Marine Methylotrophs of the Genus Methylophaga, Int. J. Syst. Bacteriol., 1987, vol. 37, pp. 402-406.
64. Janvier, M. and Grimont, F., The Genus Methylophaga, a New Line of Descent within Phylogenetic Branch of Proteobacteria, Res. Microbiol, 1985, vol. 146, pp. 543-550.
65. Nunn, D.N., Day, D., and Anthony, C., The Second Sub-unit of Methanol Dehydrogenase of Methylobacterium extorquens AM1, Biochem. J., 1989, vol. 260, pp. 857-862.
66. Chang, A.K., Lim, C.Y., Kim, S.W., You, H.L., Hahm, K.S., Yoon, S.M., Park, J.K., and Lee, J.S., Purification and Characterization of Two Forms of Methanol Dehydrogenases from a Marine Methylotroph, J. Basic Microbiol., 2002, vol. 42, pp. 238-245.
67. Anderson, D.L. and Lidstrom, M.E., The MoxFG Region Encodes Four Polypeptides in the Methanol-Oxidizing Bacterium Methylobacterium Sp. Strain AM1, J. Bacterial., 1988, vol. 170, pp. 2254-2262.
68. Anderson, D.L., Morris, C.J., Nunn, D.N., Anthony, C., and Lidstrom, M.E., Nucleotide Sequence of the Methylobacterium extorquens AMI moxF and moxJ Genes Involved in Methanol Oxidation, Gene, 1990, vol. 90, pp. 173-176.
69. Chistoserdova, L., Chen, S.-W., Lapidus, A., and Lidstrom, M.E., Methylotrophy in Methylobacterium extorquens AMI from a Genomic Point of View, J. Bacterial., 2003, vol. 185, pp. 2980-2987.
70. Kimura, T., Sugahara, I., Hanai, K., and Asahi, T., Purification and Characterization of a New γ-Glutamylmeth-ylamide-Dissimilating Enzyme System from Methylophaga sp. AA-30, Biosci. Biotechnol. Biochem., 1995, vol. 59, pp. 648-655.
71. Doronina, N.V. and Trotsenko, Y.A., The N-Methylglutamate Pathway Is Involved in Haloadaptation of Some Aerobic Methylobacteria, Microbial response to stress: What's new and how can it be applied? Sa-Correia, I., Fialho, A.M., and Viegas, C.A., Eds., Grafica Povoense, Lda. Portugal, 1997, p. 156.
72. 1-Compounds, Murrell, J.C. and Kelly, D.P., Eds., Andover: Intercept, UK, 1993, pp. 15-33.
73. Bacic, M.K., Newell, S.Y., and Yoch, D.C., Release of Dimethylsulfide from Dimethylsulfoniopropionate by Plant-Associated Salt Marsh Fungi, Appl. Environ. Microbiol., 1998, vol. 64, pp. 1484-1489.
74. Hoeft, S.E., Rogers, D.R., and Visscher, P.T., Metabolism of Methyl Bromide and Dimethyl Sulfide by Marine Bacteria Isolated from Coastal and Open Waters, Aquat. Microb. Ecol, 2000, vol. 21, pp. 221-230.
75. Saigne, C. and Legrand, M., Measurements of Methanesulfonic Acid in Antarctic Ice, Nature, 1987, vol. 330, pp. 240-242.
76. Higgins, T.P., Davey, M., Tricket, J., Kelly, D.P., and Murrell, J.C., Metabolism of Methanesulfonic Acid Involves a Multicomponent Monooxygenase System, Microbiology (UK), 1996, vol. 124, pp. 251-260.
77. De Marco, P., Moradas-Ferreira, P., Higgins, T.P., McDonald, I., Kenna, E.M., and Murrell, J.C., Molecular Analysis of a Novel Methanesulfonic Acid Monooxygenase from the Methylotroph Methylosulfonomonas methylovora, J. Bacterial., 1999, vol.181, pp. 2244-2251.
78. Reichenbecher, W. and Murrell, J.C., Purification and Partial Charactirization of the Hydroxylase Component of the Methanesulfonic Acid Monooxygenase from Methylosulfonomonas methylovora Strain M2, Eur. J. Biochem., 2000, vol. 267, pp. 4763-4769.
79. Jamashad, M., De Marco, P., Pacheco, C.C., Hanczar, T., and Murrell, J.C., Identification, Mutagenesis and Transcriptional Analysis of the Methanesulfonate Transport Operon of Methylosulfonomonas methylovora, Appl. Environ. Microbiol., 2006, vol. 72, pp. 276-283.
80. Baxter, N.J., De Marco, P., Wood, A.P., and Murrell, J.C., Duplicate Copies of Genes Encoding Methane Sulfonate Monooxygenase in Marinosulfonomonas methylotropha Strain Tr3 and Detection of Methane-Sulfonate Utilizers in the Environment, Appl. Environ. Microbiol., 2002, vol. 68, pp. 289-296.
81. Thiemann, B. and Imhoff, I.F., The Effect of Salt on the Lipid Composition of Ectothiorhodospira, Arch. Microbiol., 1991, vol. 156, pp. 376-384.
82. Khmelenina, V.N., Kalyuzhnaya, M.G., and Trotsenko, Yu.A., Physiological and Biochemical Properties of a Haloalkalitolerant Methanotroph, Mikrobiologiya, 1997, vol. 66, no. 4, pp. 447-453
83. [Microbiology (Engl. Transl.), vol. 66, no. 4, pp. 365-370].
84. Hochachka, P.W. and Somero G.N., Biochemical Adaptation, Princeton: Princeton Univ. Press, 1984 [Russ. Transl. M.: Mir, 1998].
85. Galinski, E.A. and Truper, H.G., Microbial Behaviour in Salt-Stressed Ecosystems, FEMS Microbiol. Rev., 1994, vol. 15, pp. 95-108.
86. Galinski, E.A., Pfeiffer, H.P., and Truper, H.G., 1,4,5,6Tetrahydro-2- Methyl-4-Pyrimidine Carboxylic Acid, a Novel Cyclic Amino Acid from Halophilic Phototrophic Bacteria of the Genus Ectothiorhodospira, Eur. J. Biochem., 1985, vol. 149, pp. 135-139.
87. Galinski, E.A, Osmoadaptation in Bacteria, Adv. Microbial. Physiol., 1995, vol. 37, pp. 273-328.
88. Da Costa, M.S., Santos, H., and Galinski, E.A., An Overview of the Role and Diversity of Compatible Solutes in Bacteria and Archaea, Advances in Biochemical Engineering/Biotechnology, T. Scheper, Ed., Berlin: Springer, 1998, vol. 61, pp. 117-153.
89. Lous, P. and Galinski, E.S., Characterization of Genes for the Biosynthesis of the Compatible Solute Ectoine from Marinococcus halophilus and Osmoregulated Expression in Escherichia coli, Microbiology (UK), 1997, vol. 143, pp. 1141-1149.
90. Kuhlmann, A.U. and Bremer, E., Osmotically Regulated Synthesis of the Compatible Solute Ectoine in Bacillus pasteurii and Related Bacillus spp., Appl. Environ. Microbiol., 2002, vol. 68, pp. 772-783.
91. Takami, H., Nakasone, K., Takaki, Y., Maeno, G., Sasaki, R., Masui, N., Fuji, F., Hirama, C., Nakamura, Y., Ogasawara, N., Kuhara, S., and Horikoshi, K., Complete Genome Sequence of the Alkaliphilic Bacterium Bacillus halodurans and Genomic Sequence Comparison with Bacillus subtilis, Nucleic Acid Res., 2000, vol. 28, pp. 4317-4331.
92. Heidelberg, J.F., Eisen, J.A., Nelson, W.C., Clayton, R.A., Gwinn, M.L., Dodson, R.J., Haft, D.H., Hikey, E.K., Peterson, J.D., Umayam, L., Gill, S.R., Nelson, K.E., Read, T.D., Tettelin, H., Richardson, D., Ermolaeva, M.D., Vamathevan, J., Bass, S., Qin, H., Dragoi, I., Sellers, P., McDonald, L., Utterback, T., Feishmann, T.B., Nierman, W.C., and White, O., DNA Sequences of Both Chromosomes of the Cholera Pathogen Vibrio cholerae, Nature, 2000, vol. 406, pp. 477-483.
93. Khmelenina, V.N., Kalyuzhnaya, M., Suzina, N.E., Trotsenko, Y.A., and Gottschalk, G., Osmoadaptation in Halophilic and Alkaliphilic Methanotrophs, Arch. Microbiol., 1999, vol. 172, pp. N. 321-329.
94. Ono, H., Sawada, K., Khunajakr, N., Tao, T., Yamamoto, M., Hiramoto, M., Shinmio, A., Takano, M., and Murooka, Y., Characterization of Biosynthetic Enzymes for Ectoine As a Compatible Solute in a Moderately Halophilic Bacterium, Halomonas elongata, J. Bacterial., 1999, vol. 181, pp. 91-99.
95. T, Microbiology (UK), 2004, vol. 150, pp. 3051-3063.
96. Reshetnikov, A.S, Khmelenina, V.N, Mustakhimov, I.I, Ryzhmanova, Y.V, and Trotsenko, Y, Genes and Enzymes of Ectoine Biosynthesis in Haloalkaliphilic Obligate Methanotroph Methylomicrobium alcaliphilum 20Z, Cellular Origins, Life in Extreme Habitats and Astrobiology (COLE). Meeting Proceedings of the Halo -philes, Ljubljana, Seckbach, J., Gunde-Cimerman, N., Plemenitas, A., and Oren, A., Eds., 2004, vol.9, pp. 328-336.
97. Reshetnikov, A.S., Khmelenina, V.N., and Trotsenko, Y.A., Characterization of the Ectoine Biosynthesis Genes of Haloalkalotolerant Obligate Methanotroph "Methylomicrobium Alcaliphilum 20Z", Arch, Microbiol., 2006, vol. 184, pp. 286-296.
98. Reshetnikov, A.S., Khmelenina, V.N., and Trotsenko, Yu.A., Detection of Ectoin Biosynthesis Genes in Halotolerant Aerobic Methylotrophic Bacteria, Dok. AN, 2004, vol. 396, no. 6, pp. 831-834
99. [Doklady Biochemistry and Biophysics (Engl. Transl.), vol. 396, no. 6, pp. 200-202].
100. Margesin, R. and Schinner, F., Potential of Halotolerant and Halophilic Microorganisms for Biotechnology, Extremophiles, 2001, vol. 5, pp. 73-83.