Molecular methods for the study of methanotroph ecology

FEMS Microbiology Ecology

Volumn 27, Issue 2, 1998, Pages 103-114

  Murrell, J Colin ^a   McDonald, Ian R ^a   Bourne, David G ^a  

^a UNIVERSITY OF WARWICK   (United Kingdom)

Author keywords

16S rRNA; Fluorescence microscopy; Methane monooxygenase; Methanotroph

Indexed keywords

FRESH WATER; METHANE; METHANE MONOOXYGENASE; OXIDOREDUCTASE; RNA 16S; SEA WATER; TRICHLOROETHYLENE;

BACTERIUM; ECOLOGY; METHANE; METHODOLOGY;

ANTARCTICA; BACTERIAL GROWTH; BACTERIUM ISOLATION; BIODIVERSITY; CHEMICAL INDUSTRY; CULTURE MEDIUM; DEGRADATION; DENATURING GRADIENT GEL ELECTROPHORESIS; DNA PROBE; ECOLOGY; FLUORESCENCE IN SITU HYBRIDIZATION; GENE AMPLIFICATION; METHANOTROPHIC BACTERIUM; MOLECULAR BIOLOGY; NONHUMAN; PHYLOGENY; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; REVIEW; SEDIMENT; SOIL; SOIL TREATMENT; TECHNIQUE; THERMAL SPRING;

EID: 0031716660     PISSN: 01686496     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0168-6496(98)00063-4     Document Type: Article

References (50)

1. Hanson, R.S. and Hanson, T.E. (1996) Methanotrophic bacteria. Microbiol. Rev. 60, 439-471.
2. 1 Compounds (Murrell, J.C. and Kelly, D.P., Eds.), pp. 121-133. Intercept Press, Andover, UK.
3. Conrad, R. (1995) Soil microbial processes involved in production and consumption of atmospheric trace gases. Adv. Microb. Ecol. 14, 207-250.
4. King, G.M. (1992) Ecological aspects of methane oxidation, a key determinant of global methane dynamics. Adv. Microb. Ecol. 12, 431-468.
5. Bodrossy, L., Murrell, J.C., Dalton, H., Kalman, M., Puskas, L.G. and Kovacs, K. (1995) Heat-tolerant methanotrophic bacteria from the hot water effluent of a natural gas field. Appl. Environ. Microbiol. 61, 3549-3555.
6. Bowman, J.P., McCammon, S.A. and 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.
7. McDonald, I.R., Hall, G.H., Pickup, R.W. and Murrell, J.C. (1996) Methane oxidation potentials and preliminary analysis of methanotrophs in a blanket peat bog using molecular ecology techniques. FEMS Microbiol. Ecol. 21, 197-211.
8. Dedysh, S.N., Panikov, N.S. and Tiedje, J.M. (1998) Acidophilic methanotrophic communities from Sphagnum peat bogs. Appl. Environ. Microbiol. 64, 922-929.
9. Khmelenina, V.N., Kalyuzhnaya, M.G., Starostina, N.G., Suzina, N.E. and Trotsenko, Y.A. (1997) Isolation and characterisation of halotolerant alkaliphilic methanotrophic bacteria from Tuva soda lakes. Curr. Microbiol. 35, 257-261.
10. Whittenbury, R., Davies, S.L. and Davey, J.F. (1970) Exospores and cysts formed by methane utilizing bacteria. J. Gen. Microbiol. 61, 219-226.
11. Bowman, J.P., Sly, L.I., Nicholas, P.D. and Hayward, A.C. (1993) Revised taxonomy of the methanotrophs: description of Methylobacter gen. nov., emendation of Methylococcus, validation of Methylosinus species and a proposal that the family Methylococcaceae includes only group I methanotrophs. Int. J. Syst. Bacteriol. 43, 735-753.
12. Bowman, J.P., Sly, L.I. and Stackebrandt, E. (1995) The phylogenetic position of the family Methylococceae. Int. J. Syst. Bacteriol. 45, 182-185.
13. Bodrossy, L., Holmes, E.M., Holmes, A.J., Kovacs, K.L. and Murrell, J.C. (1997) Analysis of 16S rRNA and methane monooxygenase gene sequences reveals a novel group of thermotolerant and thermophilic methanotrophs, Methylocaldum gen. nov. Arch. Microbiol. 168, 493-503.
14. Anthony, C. (1986) Bacterial oxidation of methane and methanol. Adv. Microb. Physiol. 27, 113-210.
15. 1 Compounds (Murrell, J.C. and Kelly, D.P., Eds.) pp. 65-80. Intercept Press, Andover, UK.
16. Lipscomb, J.D. (1994) Biochemistry of the soluble methane monooxygenase. Annu. Rev. Microbiol. 48, 371-399.
17. Murrell, J.C. (1992) Genetics and molecular biology of methanotrophs. FEMS Microbiol. Rev. 88, 233-248.
18. McDonald, I.R., Uchiyama, H., Kambe, S., Yagi, O. and Murrell, J.C. (1997) The soluble methane monooxygenase gene cluster of the trichloroethylene degrading methanotroph Methylocystis sp. strain M. Appl. Environ. Microbiol. 64, 1898-1904.
19. Nguyen, H.T., Shiemke, A.K., Jacobs, S.J., Hales, B.J., Lidstrom, M.E. and Chan, S.I. (1994) The nature of the copper ions in the membranes containing the particulate methane monooxygenase from Methylococcus capsulatus (Bath). J. Biol. Chem. 269, 14995-15005.
20. Nguyen, H.T., Elliott, S.J., Yip, J.H. and Chan, S.I. (1998) The particulate methane monooxygenase from Methylococcus capsulatus (Bath) is a novel copper-containing three-subunit enzyme. J. Biol. Chem. 273, 7957-7966.
21. Zahn, J.A. and Dispirito, A.A. (1996) Membrane-associated methane monooxygenase from Methylococcus capsulatus (Bath). J. Bacteriol. 178, 1018-1029.
22. Semrau, J.D., Chistoserdov, A., Lebron, J., Costello, A., Davignino, J., Kenna, E., Holmes, A.J., Finch, R., Murrell, J.C. and Lidstrom, M.E. (1995) Particulate methane monooxygenase genes in methanotrophs. J. Bacteriol. 177, 3071-3079.
23. McTavish, H., Fuchs, J.A. and Hopper, A.B. (1993) Sequence of the gene encoding for ammonia monooxygenase in Nitrosomonas europaea. J. Bacteriol. 175, 2436-2444.
24. Norton, J.M., Low, J.M. and Klotz, M.G. (1996) The gene encoding ammonia monooxygenase subunit A exists in three nearly identical copies in Nitrosospira sp. NpAV. FEMS Microbiol. Lett. 139, 181-188.
25. Koh, S.-C., Bowman, J.P. and Sayler, G.S. (1993) Soluble methane monooxygenase production and trichloroethylene degradation by a type I methanotroph Methylomonas methanica 68-1. Appl. Environ. Microbiol. 59, 960-967.
26. Nielsen, A.K., Gerdes, K. and Murrell, J.C. (1997) Copper-dependent reciprocal transcriptional regulation of methane monooxygenase genes in Methylococcus capsulatus and Methylosinus trichosporium. Mol. Microbiol. 25, 399-409.
27. Lidstrom, M.E., Anthony, C., Biville, F., Gasser, F., Goodwin, P., Hanson, R.S. and Harms, N. (1994) New unified nomenclature for genes involved in the oxidation of methanol in Gram-negative bacteria. FEMS Microbiol. Lett. 177, 103-106.
28. McDonald, I.R. and 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.
29. Sundh, I., Borga, P., Nilsson, M. and Svensson, B.H. (1995) Estimation of cell numbers of methanotrophic bacteria in boreal peatlands based on analysis of specific phospholipid fatty acids. FEMS Microbiol. Ecol. 18, 103-112.
30. Iversen, N. (1996) Methane oxidation in coastal marine sediments. In: Microbiology of Atmospheric Trace Gases: Sources, Sinks and Global Change Processes (Murrell, J.C. and Kelly, D.P., Eds.) pp. 51-68. Springer, Berlin.
31. Holmes, A.J., Owens, N.J.P. and Murrell, J.C. (1995) Detection of novel marine methanotrophs using phylogenetic and functional gene probes after methane enrichment. Microbiology 141, 1947-1955.
32. Amann, R.I., Krumholz, L. and Stahl, D.A. (1990) Fluorescent-oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental studies in microbiology. J. Bacteriol. 172, 762-770.
33. Amann, R.I., Ludwig, W. and Schleifer, K.H. (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59, 143-169.
34. Tsien, H.C., Bratina, B.J., Tsuji, K. and Hanson, R.S. (1990) Use of oligodeoxynucleotide signature probes for identification of physiological groups of methylotrophic bacteria. Appl. Environ. Microbiol. 56, 2858-2865.
35. 1 Compounds (Murrell, J.C. and Kelly, D.P., Eds.), pp. 285-302. Intercept Press, Andover, UK.
36. Holmes, A.J., Owens, N.J.P. and Murrell, J.C. (1996) Molecular analysis of enrichment cultures of marine methane oxidising bacteria. J. Exp. Mar. Biol. Ecol. 203, 27-38.
37. Kemp, P.F., Lee, S. and LaRoche, J. (1993) Estimating the growth rate of slowly growing marine bacteria from RNA content. Appl. Environ. Microbiol. 59, 2594-2601.
38. McDonald, I.R., Kenna, E.M. and Murrell, J.C. (1995) Detection of methanotrophic bacteria in environmental samples with the PCR. Appl. Environ. Microbiol. 61, 116-121.
39. Holmes, A.J., Costello, A., Lidstrom, M.E. and Murrell, J.C. (1995) Evidence that particulate methane monooxygenase and ammonia monooxygenase may be evolutionarily related. FEMS Microbiol. Lett. 132, 203-208.
40. McDonald, I.R. and Murrell, J.C. (1997) The particulate methane monooxygenase gene pmoA and its use as a functional gene probe for methanotrophs. FEMS Microbiol. Lett. 156, 205-210.
41. Rotthauwe, J.H., Witzel, K.P. and Liesack, W. (1997) The ammonia monooxygenase structural gene amoA as a functional marker: molecular fine-scale analysis of natural ammonia-oxidising populations. Appl. Environ. Microbiol. 63, 4704-4712.
42. Muyzer, G., De Waal, E.C. and Uitterlinden, A.G. (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl. Environ. Microbiol. 59, 695-700.
43. Ferris, M.J., Muyzer, G. and Ward, D.M. (1996) Denaturing gradient gel electrophoresis profiles of 16S rRNA-defined populations inhabiting a hot spring microbial mat community. Appl. Environ. Microbiol. 62, 340-346.
44. Wawer, C. and Muyzer, G. (1995) Genetic diversity of Desulfovibrio spp. in environmental samples analysed by denaturing gradient gel electrophoresis of [NiFe] hydrogenase gene fragments. Appl. Environ. Microbiol. 61, 2203-2210.
45. Fesefeldt, A. and Gliesche, C.G. (1997) Identification of Hyphomicrobium spp. using PCR-amplified fragments of the mxaF gene as a molecular marker. Syst. Appl. Microbiol. 20, 387-396.
46. Kowalchuk, G.A., Stephen, J.R., De Boer, W., Prosser, J.I., Embley, T.M. and Woldendorp, J.A. (1997) Analysis of ammonia-oxidising bacteria of the β subdivision of the class Proteobacteria in coastal sand dunes by denaturing gradient gel electrophoresis and sequencing of PCR-amplified 16S ribosomal DNA fragments. Appl. Environ. Microbiol. 63, 1489-1497.
47. Vallaeys, T., Topp, E., Muyzer, G., Macheret, V., Laguerre, G., Rigaud, A. and Soulas, G. (1997) Evaluation of denaturing gradient gel electrophoresis in the detection of 16S rDNA sequence variation in rhizobia and methanotrophs. FEMS Microbiol. Ecol. 24, 279-285.
48. Jensen, S., Ovreas, L., Daae, F.L. and Torsvik, V. (1998) Diversity in methane enrichments from agricultural soil revealed by DGGE separation of PCR amplified 16S rDNA fragments. FEMS Microbiol. Ecol. 26, 17-26.
49. Lidstrom, M.E. (1996) Environmental molecular biology approaches: promises and pitfalls. In: Microbiology of Atmospheric Trace Gases: Sources, Sinks and Global Change Processes (Murrell, J.C. and Kelly, D.P., Eds.) pp. 121-134. Springer, Berlin.
50. Suzuki, M.T. and Giovannoni, S.J. (1996) Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl. Environ. Microbiol. 62, 625-630.