Diversity and Activity of Methanotrophic Bacteria in Different Upland Soils

Applied and Environmental Microbiology

Volumn 69, Issue 11, 2003, Pages 6703-6714

  Knief, Claudia ^a   Lipski, André ^b   Dunfield, Peter F ^a  

^a MAX PLANCK INSTITUTE FOR TERRESTRIAL MICROBIOLOGY   (Germany)

^b UNIVERSITY OF OSNABRÜCK   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ACIDITY; COMBUSTION; GAS CHROMATOGRAPHY; METHANE; OXIDATION; SOILS;

METHANOTROPHIC BACTERIA (MB);

BACTERIA;

FATTY ACID; METHANE; METHANE MONOOXYGENASE;

ARTICLE; GAS CHROMATOGRAPHY; GENE SEQUENCE; GRAM NEGATIVE BACTERIUM; MASS SPECTROMETRY; METHANOTROPHIC BACTERIUM; METHYLOCALDUM; METHYLOCYSTIS; METHYLOSINUS; NONHUMAN; NUCLEOTIDE SEQUENCE; OXIDATION; PH; SAMPLING; SEQUENCE ANALYSIS; SOIL;

ALPHAPROTEOBACTERIA; CARBON ISOTOPES; ECOSYSTEM; FATTY ACIDS; GAMMAPROTEOBACTERIA; HYDROGEN-ION CONCENTRATION; METHANE; MOLECULAR SEQUENCE DATA; OXYGENASES; PHYLOGENY; SEQUENCE ANALYSIS, DNA; SOIL; SOIL MICROBIOLOGY;

ALPHAPROTEOBACTERIA; BACTERIA (MICROORGANISMS); GAMMAPROTEOBACTERIA; METHYLOCALDUM; METHYLOCYSTIS; METHYLOSINUS; NEGIBACTERIA;

EID: 0242405670     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.69.11.6703-6714.2003     Document Type: Article

References (48)

1. Auman, A. J., S. Stolyar, A. M. Costello, and M. E. Lidstrom. 2000. Molecular characterization of methanotrophic isolates from freshwater lake sediment. Appl. Environ. Microbiol. 66:5259-5266.
2. 4 mixing ratios. FEMS Microbiol. Ecol. 101:261-270.
3. Benstead, J., and G. M. King. 1997. Response of methanotrophic activity in forest soil to methane availability. FEMS Microbiol. Ecol. 23:333-340.
4. Bourne, D. G., I. R. McDonald, and J. C. Murrell. 2001. Comparison of pmoA PCR primer sets as tools for investigating methanotroph diversity in three Danish soils. Appl. Environ. Microbiol. 67:3802-3809.
5. Bowman, J. P., S. A. McCammon, and J. H. Skerratt. 1997. Methylosphaera hansonii gen. nov., sp. nov., a psychrophilic, group I methanotroph from Antarctic marine-salinity, meromictic lakes. Microbiology 143:1451-1459.
6. Bowman, J. P., J. H. Skerratt, P. D. Nichols, and L. I. Sly. 1991. Phospholipid fatty acid and liposaccharide fatty acid signature lipids in methane utilizing bacteria. FEMS Microbiol. Ecol. 85:15-22.
7. Bowman, J. P., L. I. Sly, P. D. Nichols, and A. C. Hayward. 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.
8. Bull, I. D., N. R. Parekh, G. H. Hall, P. Ineson, and R. P. Evershed. 2000. Detection and classification of atmospheric methane oxidizing bacteria in soil. Nature 405:175-178.
9. 2O, and NO). Microbiol. Rev. 60:609-640.
10. Costello, A. M., and M. E. Lidstrom. 1999. Molecular characterization of functional and phylogenetic genes from natural populations of methanotrophs in lake sediments. Appl. Environ. Microbiol. 65:5066-5074.
11. Dedysh, S. N., V. N. Khmelenina, N. E. Suzina, Y. A. Trotsenko, J. D. Semrau, W. Liesack, and J. M. Tiedje. 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., W. Liesack, V. N. Khmelenina, N. E. Suzina, Y. A. Trotsenko, J. D. Semrau, A. M. Bares, N. S. Panikov, and J. M. Tiedje. 2000. Methylocella palustris gen. nov., sp. nov., a new methane-oxidizing acidophilic bacterium from peat bogs, representing a novel subtype of serine-pathway methanotrophs. Int. J. Syst. Evol. Microbiol. 50:955-969.
13. Dunfield, P. F., and R. Conrad. 2000. Starvation alters the apparent half-saturation constant for methane in the type II methanotroph Methylocystis strain LRI. Appl. Environ. Microbiol. 66:4136-4138.
14. Dunfield, P. F., V. N. Khmelenina, N. E. Suzina, Y. A. Trotsenko, and S. N. Dedysh. 2003. Methylocella silvestris sp. nov., a novel methanotrophic bacterium isolated from an acidic forest cambisol. Int. J. Syst. Evol. Microbiol. 53:1231-1239.
15. Dunfield, P. F., W. Liesack, T. Henckel, R. Knowles, and R. Conrad. 1999. High-affinity methane oxidation by a soil enrichment culture containing a type II methanotroph. Appl. Environ. Microbiol. 65:1009-1014.
16. Dunfield, P. F., M. T. Yimga, S. N. Dedysh, U. Berger, W. Liesack, and J. Heyer. 2002. Isolation of a Methylocystis strain containing a novel pmoA-like gene. FEMS Microbiol. Ecol. 41:17-26.
17. Felsenstein, J. 1993. PHYLIP: phylogeny inference package. University of Washington, Seattle.
18. Fjellbirkeland, A., V. Torsvik, and L. Øvreås. 2001. Methanotrophic diversity in an agricultural soil as evaluated by denaturing gradient gel electrophoresis profiles of pmoA, mxaF and 16S rDNA sequences. Antonie Leeuwenhoek 79:209-217.
19. Guckert, J. B., D. B. Ringelberg, D. C. White, R. S. Hanson, and B. J. Bratina. 1991. Membrane fatty acids as phenotypic markers in the polyphasic taxonomy of methylotrophs within the Proteobacteria. J. Gen. Microbiol. 137:2631-2641.
20. + inhibition. Appl. Environ. Microbiol. 64:4291-4298.
21. Hanson, R. S., and T. E. Hanson. 1996. Methanotrophic bacteria. Microbiol. Rev. 60:439-471.
22. Henckel, T., M. Friedrich, and R. Conrad. 1999. Molecular analyses of the methane-oxidizing microbial community in rice field soil by targeting the genes of the 16S rRNA, particulate methane monooxygenase, and methanol dehydrogenase. Appl. Environ. Microbiol. 65:1980-1990.
23. Henckel, T., U. Jäckel, S. Schnell, and R. Conrad. 2000. Molecular analyses of novel methanotrophic communities in forest soil that oxidize atmospheric methane. Appl. Environ. Microbiol. 66:1801-1808.
24. Heyer, J., V. F. Galchenko, and P. F. Dunfield. 2002. Molecular phylogeny of type II methane-oxidizing bacteria isolated from various environments. Microbiology 148:2831-2846.
25. Heyer, J., Y. Malashenko, U. Berger, and E. Budkova. 1984. Verbreitung methanotropher Bakterien. Z. Allg. Mikrobiol. 24:725-744.
26. Hoffmann, T., H. P. Horz, D. Kemnitz, and R. Conrad. 2002. Diversity of the particulate methane monooxygenase gene in methanotrophic samples from different rice field soils in China and The Philippines. Syst. Appl. Microbiol. 25:267-274.
27. Holmes, A. J., A. Costello, M. E. Lidstrom, and J. C. Murrell. 1995. Evidence that particulate methane monooxygenase and ammonia monooxygenase may be evolutionarily related. FEMS Microbiol. Lett. 132:203-208.
28. Holmes, A. J., P. Roslev, I. R. McDonald, N. Iversen, K. Henriksen, and J. C. Murrell. 1999. Characterization of methanotrophic bacterial populations in soils showing atmospheric methane uptake. Appl. Environ. Microbiol. 65:3312-3318.
29. Horz, H.-P., A. S. Raghubanshi, J. Heyer, C. Kammann, R. Conrad, and P. F. Dunfield. 2002. Activity and community structure of methane-oxidising bacteria in a wet meadow soil. FEMS Microbiol. Ecol. 41:247-257.
30. Horz, H.-P., M. T. Yimga, and W. Liesack. 2001. Detection of methanotroph diversity on roots of submerged rice plants by molecular retrieval of pmoA, mmoX, mxaF, and 16S rRNA and ribosomal DNA, including pmoA-based terminal restriction fragment length polymorphism profiling. Appl. Environ. Microbiol. 67:4177-4185.
31. Intergovernmental Panel on Climate Change. 2001. The scientific basis - contribution of working group I to the third assessment report of the Intergovernmental Panel on Climate Change (IPCC). In J. T. Houghton, Y. Ding, D. J. Griggs, M. Noguer, P. J. van der Linden, and D. Xiaosu (ed.), Climate change 2001. Cambridge University Press, Cambridge, United Kingdom.
32. Jensen, S., A. J. Holmes, R. A. Olsen, and J. C. Murrell. 2000. Detection of methane oxidizing bacteria in forest soil by monooxygenase PCR amplification. Microb. Ecol. 39:282-289.
33. Kandeler, E., and H. Gerber. 1988. Short-term assay of soil urease activity using colorimetric determination of ammonium. Biol. Fertil. Soils 6:68-72.
34. 13C-labeled fatty acids. Environ. Microbiol., in press.
35. Kolb, S., C. Knief, S. Stubner, and R. Conrad. 2003. Quantitative detection of methanotrophs in soil by novel pmoA-targeted real-time PCR assays. Appl. Environ. Microbiol. 69:2423-2429.
36. Le Mer, J., and P. Roger. 2001. Production, oxidation, emission and consumption of methane by soils: a review. Eur. J. Soil Biol. 37:25-50.
37. Lipski, A., and K. Altendorf. 1997. Identification of heterotrophic bacteria isolated from ammonia-supplied experimental biofilters. Syst. Appl. Microbiol. 20:448-457.
38. McDonald, I. R., and J. C. Murrell. 1997. The particulate methane monooxygenase gene pmoA and its use as a functional gene probe for methanotrophs. FEMS Microbiol. Lett. 156:205-210.
39. Nichols, P. D., J. B. Guckert, and D. C. White. 1986. Determination of monounsaturated fatty acid double-bond position and geometry for microbial monocultures and complex consortia by capillary GC-MS of their dimethyl disulfide adducts. J. Microbiol. Methods 5:49-55.
40. Nichols, P. D., G. A. Smith, C. P. Antworth, R. S. Hanson, and D. C. White. 1985. Phospholipid and lipopolysaccharide normal and hydroxy fatty acids as potential signatures for methane-oxidizing bacteria. FEMS Microbiol. Ecol. 31:327-335.
41. Pacheco-Oliver, M., I. R. McDonald, D. Groleau, J. C. Murrell, and C. B. Miguez. 2002. Detection of methanotrophs with highly divergent pmoA genes from Arctic soils. FEMS Microbiol. Lett. 209:313-319.
42. Reay, D. S., S. Radajewski, J. C. Murrell, N. McNamara, and D. B. Nedwell. 2001. Effects of land use on the activity and diversity of methane oxidizing bacteria in forest soils. Soil Biol. Biochem. 33:1613-1623.
43. Rieley, G. 1994. Derivatization of organic compounds prior to gas chromatographic-combustion-isotope ratio mass spectrometric analysis: identification of isotope fractionation processes. Analyst 119:915-919.
44. Roslev, P., and N. Iversen. 1999. Radioactive fingerprinting of microorganisms that oxidize atmospheric methane in different soils. Appl. Environ. Microbiol. 65:4064-4070.
45. Steinkamp, R., W. Zimmer, and H. Papen. 2001. Improved method for detection of methanotrophic bacteria in forest soils by PCR. Curr. Microbiol. 42:316-322.
46. Strunk, O., O. Gross, B. Reichel, M. May, S. Hermann, N. Stuckman, B. Nonhoff, M. Lenke, A. Ginhart, A. Vilbig, T. Ludwig, A. Bode, and K. H. Schleifer. 1998. ARB: a software environment for sequence data. Technische Universität München, Munich, Germany.
47. Weisburg, W. G., S. M. Barns, D. A. Pelletier, and D. J. Lane. 1991. 16S ribosomal DNA amplification for phylogenetic study. J. Bacteriol. 173:697-703.
48. Willison, T. W., C. P. Webster, K. W. T. Goulding, and D. S. Powlson. 1995. Methane oxidation in temperate soils: effects of land use and the chemical form of nitrogen fertilizer. Chemosphere 30:539-546.