Different atmospheric methane-oxidizing communities in european beech and norway spruce soils

Applied and Environmental Microbiology

Volumn 76, Issue 10, 2010, Pages 3228-3235

  Degelmann, Daniela M ^a   Borken, Werner ^a   Drake, Harold L ^a   Kolb, Steffen ^a  

^a UNIVERSITY OF BAYREUTH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

16S RRNA GENE; ATMOSPHERIC METHANES; DISTANCE-CUTOFF; DRY WEIGHT; ENERGY SOURCE; EUROPEAN BEECH; FOREST SOILS; IN-SITU; MEMBRANE-BOUND; METHANOTROPHS; MONOOXYGENASES; NORWAY SPRUCE; POTENTIAL EFFECTS; PROTEIN LEVEL; SOIL SAMPLE; SPRUCE SOIL; SPRUCE STANDS; TEMPERATE FORESTS; TREE SPECIES; UPLAND SOIL;

ATMOSPHERIC CHEMISTRY; ECOSYSTEMS; FORESTRY; GENES; METHANE; RNA; SOIL SURVEYS;

SOILS;

METHANE; METHANE MONOOXYGENASE; OXYGENASE; RNA 16S;

ABUNDANCE; CONIFEROUS FOREST; DECIDUOUS FOREST; FOREST SOIL; GENE EXPRESSION; GENOTYPE; METHANE; METHANOTROPHY; MICROBIAL COMMUNITY; OXIDATION; SOIL MICROORGANISM; SPECIES DIVERSITY;

ARTICLE; BACTERIUM; BEECH; BIODIVERSITY; CLASSIFICATION; GENETICS; GENOTYPE; ISOLATION AND PURIFICATION; METABOLISM; MICROBIOLOGY; MOLECULAR GENETICS; NORWAY; NUCLEOTIDE SEQUENCE; PHYLOGENY; SPRUCE; TREE;

BACTERIA; BIODIVERSITY; FAGUS; GENOTYPE; METHANE; MOLECULAR SEQUENCE DATA; NORWAY; OXYGENASES; PHYLOGENY; PICEA; RNA, RIBOSOMAL, 16S; SOIL MICROBIOLOGY; TREES;

ECOSYSTEMS; FAGUS SYLVATICA; FORESTS; GENES; METHANE; NUCLEIC ACIDS; OXIDATION; PICEA ABIES;

FAGUS; FAGUS SYLVATICA; PICEA; PICEA ABIES;

EID: 77952276202     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.02730-09     Document Type: Article

References (55)

1. Amaral, J. A., and R. Knowles. 1998. Inhibition of methane consumption in forest soils by monoterpenes. J. Chem. Ecol. 24:723-734.
2. Angel, R., and R. Conrad. 2009. In situ measurement of methane fluxes and analysis of transcribed particulate methane monooxygenase in desert soil. Environ. Microbiol. 11:2598-2610.
3. Baani, M., and W. Liesack. 2008. Two isozymes of particulate methane monooxygenase with different methane oxidation kinetics are found in Methylocystis sp. strain SC2. Proc. Natl. Acad. Sci. U. S. A. 105:10203-10208.
4. +, and CO oxidation by methanotrophs and nitrifiers. Microbiol. Rev. 53:68-84.
5. Benson, D. A., I. K. Karsch-Mizrachi, D. J. Lipman, J. Oatell, and D. L. Wheeler. 2008. GenBank. Nucleic Acids Res. 36:D25-D30.
6. Borken, W., Y. J. Xu, and F. Beese. 2003. Conversion of hardwood forests to spruce and pine plantations strongly reduced soil methane sink in Germany. Glob. Chang. Biol. 9:956-966.
7. Chen, Y., M. G. Dumont, N. P. McNamara, P. M. Chamberlain, L. Bodrossy, N. Stralis-Pavese, and J. C. Murrell. 2008. Diversity of the active methanotrophic community in acidic peatlands as assessed by mRNA and SIFPLFA analyses. Environ. Microbiol. 10:446-459.
8. Dalai, R. C., and D. E. Allen. 2008. Greenhouse gas fluxes from natural ecosystems. Aust. J. Bot. 56:369-407.
9. Dedysh, S. N., C. Knief, and P. F. Dunfleld. 2005. Methylocella species are facultatively methanotrophic. J. Bacteriol. 187:4665-4670.
10. 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 bags, representing a novel subtype of serine-pathway methanotrophs. Int. J. Syst. Evol. Microbiol. 50:955-969.
11. Degelmann, D. M., W. Borken, and S. Kolb. 2009. Methane oxidation kinetics differ in European beech and Norway spruce soils. Eur. J. Soil Sci. 60:499-506.
12. Denman, K. L., G. Brasseur, A. Chidthaisong, P. Ciais, P. M. Cox, R. E. Dickinson, D. Hauglustaine, C. Heinze, E. Holland, D. Jacob, U. Lohmann, S. Ramachandran, P. L. da Silva Dias, S. C. Wofsy, and X. Zhang. 2007. Couplings between changes in the climate system and biogeochemistry, p. 499-587. In S. Solomon, D. Qin, M. Manning, Z. Chen, M. Marquis, K. B. Averyt, M. Tignor, and H. L. Miller (ed.), Climate change 2007: the physical science basis. Contribution of working group I to the fourth assessment report of the Intergovernmental Panel on Climate Change. Cambridge University Press, Cambridge, United Kingdom.
13. Dunfleld, P., and R. Knowles. 1995. Kinetics of inhibition of methane oxidation by nitrate, nitrite, and ammonium in a humisol. Appl. Environ. Microbiol. 61:3129-3135.
14. Dunfleld, P. F. 2007. The soil methane sink, p. 152-170. In D. Reay, C. N. Hewitt, K. Smith, and J. Grace (ed.), Greenhouse gas sinks. CABI Publishing, Wallingfort, United Kingdom.
15. Dunfleld, P. F., V. N. Khmelenina, N. E. Suzina, Y. A. Trotsenko, and S. N. Dedysh. 2003. Methylocella sihiestris sp. nov., a novel methanotroph isolated from an acidic forest cambisol. Int. J. Syst. Evol. Microbiol. 53:1231-1239.
16. Dunfleld, 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.
17. Dunfleld, P. F., A. Yuryev, P. Senin, A. V. Smirnova, M. B. Stott, S. Hou, B. Ly, J. H. Saw, Z. Zhou, Y. Ren, J. Wang, B. W. Mountain, M. A. Crowe, T. M. Weatherby, P. L. E. Bodelier, W. Liesack, L. Feng, L. Wang, and M. Alam. 2007. Methane oxidation by an extremely acidophilic bacterium of the phylum Verrucomicrobia. Nature 450:879-882.
18. Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791.
19. Heyer, J., V. F. Galchenko, and P. F. Dunfleld. 2002. Molecular phylogeny of type II methane-oxidizing bacteria isolated from various environments. Microbiology 148:2831-2846.
20. Holmes, A. J., N. J. Owens, and J. C. Murrell. 1995. Detection of novel marine methanotrophs using phylogenetic and functional gene probes after methane enrichment. Microbiology 141:1947-1955.
21. 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.
22. Hutchens, E., S. Radajewski, M. G. Dumont, I. R. McDonald, and J. C. Murrell. 2004. Analysis of methanotrophic bacteria in Movile Cave by stable isotope probing. Environ. Microbiol. 6:111-120.
23. Islam, T., S. Jensen, L. J. Reigstad, O. Larsen, and N. K. Birkeland. 2008. Methane oxidation at 55°C and pH 2 by a thermoacidophilic bacterium belonging to the Verrucomicrobia phylum. Proc. Natl. Acad. Sci. U. S. A. 105:300-304.
24. Jaatinen, K., C. Knief, P. F. Dunfleld, K. Yrjälä, and H. Fritze. 2004. Methanotrophic bacteria in boreal forest soil after fire. FEMS Microbiol. Ecol. 50:195-202.
25. Jones, D. T., W. R. Taylor, and J. M. Thornton. 1992. The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci. 8:275-282.
26. King, G. M., and K. Nanba. 2008. Distribution of atmospheric methane oxidation and methanotrophic communities in Hawaiian volcanic deposits and soils. Microbes Environ. 23:326-330.
27. Klappenbach, J. A., P. R. Saxman, J. R. Cole, and T. M. Schmidt. 2001. rrndb: the ribosomal RNA Operon copy number database. Nucleic Acids Res. 29:181-184.
28. Knief, C., and P. F. Dunfleld. 2005. Response and adaptation of different methanotrophic bacteria to low methane mixing ratios. Environ. Microbiol. 7:1307-1317.
29. Knief, C., S. KoIb, P. L. Bodelier, A. Lipski, and P. F. Dunfleld. 2006. The active methanotrophic community in hydromorphic soils changes in response to changing methane concentration. Environ. Microbiol. 8:321-333.
30. Knief, C., A. Lipski, and P. F. Dunfleld. 2003. Diversity and activity of methanotrophic bacteria in different upland soils. Appl. Environ. Microbiol. 69:6703-6714.
31. Knief, C., S. Vanitchung, N. W. Harvey, R. Conrad, P. F. Dunfleld, and A. Chidthaisong. 2005. Diversity of methanotrophic bacteria in tropical upland soils under different land uses. Appl. Environ. Microbiol. 71:3826-3831.
32. Kolb, S. 2009. The quest for atmospheric methane oxidizers in forest soils. Environ. Microbiol. Rep. 1:336-346.
33. Kolb, S., C. Knief, P. F. Dunfleld, and R. Conrad. 2005. Abundance and activity of uncultured methanotrophic bacteria involved in the consumption of atmospheric methane in two forest soils. Environ. Microbiol. 7:1150-1161.
34. 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.
35. Lane, D. J. 1991. 16S/23S rRNA sequencing, p. 115-175. In E. Stackebrandt and M. Goodfellow (ed.), Nucleic acid techniques in bacterial systematics. John Wiley and Sons Ltd., Chichester, United Kingdom.
36. Ludwig, W., O. Strunk, R. Westram, L. Richter, H. Meier, Yadhukumar, A. Buchner, T. Lai, S. Steppi, G. Jobb, W. Förster, I. Brettske, S. Gerber, A. W. Ginhart, O. Gross, S. Grumann, S. Hermann, R. Jost, A. König, T. Liss, R. Lüßmann, M. May, B. Xonhoff, B. Reichet, R. Strehlow, A. Stamatakis, N. Stuckmann, A. Vilbig, M. Lenke, T. Ludwig, A. Bode, and K.-H. Schleifer. 2004. ARB: a software environment for sequence data. Nucleic Acids Res. 32:1363-1371. (Pubitemid 38854737)
37. Maurer, D., S. KoIb, L. Haumeier, and W. Borken. 2008. Inhibition of atmospheric methane oxidation by monoterpenes in Norway spruce and European beech soils. Soil Biol. Biochem. 40:3014-3020.
38. McDonald, I. R., L. Bodrossy, Y. Chen, and J. C. Murrell. 2008. Molecular ecology techniques for the study of aerobic methanotrophs. Appl. Environ. Microbiol. 74:1305-1315.
39. 4 oxidation without altering community composition of soil methanotrophs. Soil Biol. Biochem. 42:101-107.
40. Menyailo, O. V., and B. A. Hungate. 2003. Interactive effects of tree species and soil moisture on methane consumption. Soil Biol. Biochem. 35:625-628.
41. Messing, J. 1983. New M13 vectors for cloning. Methods Enzymol. 101: 20-78.
42. Muyzer, G., E. C. Dewaal, and A. G. Uitterlinden. 1993. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S ribosomal RNA. Appl. Environ. Microbiol. 59:695-700.
43. Op den Camp, H. J. M., T. Islam, M. B. Stott, H. R. Harhangi, A. Hynes, S. Schouten, M. S. M. Jetten, N. K. Birkeland, A. Pol, and P. F. Dunfleld. 2009. Environmental, genomic and taxonomie perspectives on methanotrophic Verrucomicrobia. Environ. Microbiol. Rep. 1:293-306.
44. Pol, A., K. Heijmans, H. R. Harhangi, D. Tedesco, M. S. M. Jetten, and H. J. M. Op den Camp. 2007. Methanotrophy below pH 1 by a new Verrucomicrobia species. Nature 450:874-878.
45. Saitou, N., and M. Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
46. Schloss, P. D., and J. Handelsman. 2005. Introducing DOTUR, a computer program for defining operational taxonomie units and estimating species richness. Appl. Environ. Microbiol. 71:1501-1506.
47. Schloss, P. D., B. R. Larget, and J. Handelsman. 2004. Integration of microbial ecology and statistics: a test to compare gene libraries. Appl. Environ. Microbiol. 70:5485-5492.
48. Smith, K. A., K. E. Dobbie, B. C. Ball, L. R. Bakken, B. K. Sitaula, S. Hansen, R. Brumme, W. Borken, S. Christensen, A. Prieme, D. Fowler, J. A. Macdonald, U. Skiba, L. Klemedtsson, A. Kasimir-Klemedtsson, A. Degorska, and P. Orlanski. 2000. Oxidation of atmospheric methane in Northern European soils, comparison with other ecosystems, and uncertainties in the global terrestrial sink. Glob. Chang. Biol. 6:791-803.
49. Stackebrandt, E., and B. M. Goebel. 1994. Taxonomie note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int. J. Syst. Bacteriol. 44:846-849.
50. Stolyar, S., A. M. Costello, T. L. Peeples, and M. E. Lidstrom. 1999. Role of multiple gene copies in particulate methane monooxygenase activity in the methane-oxidizing bacterium Methylococcus capsulatus Bath. Microbiology 145: 1235-1244.
51. Stralis-Pavese, N., A. Sessitsch, A. Weilharter, T. Reichenauer, J. Riesing, J. Csontos, J. C. Murrell, and L. Bodrossy. 2004. Optimization of diagnostic microarray for application in analysing landfill methanotroph communities under different plant covers. Environ. Microbiol. 6:347-363.
52. Tamura, K., J. Dudley, M. Nei, and S. Kumar. 2007. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24:1596-1599.
53. Trotsenko, Y. A., and J. C. Murrell. 2008. Metabolic aspects of aerobic obligate methanotrophy. Adv. Appl. Microbiol. 63:183-229.
54. Wintzingerode, F. V., U. B. Goebel, and E. Stackebrandt. 1997. Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol. Rev. 21:213-229.
55. Zaprasis, A., Y. J. Liu, S. J. Liu, H. L. Drake, and M. A. Horn. 2010. Abundance of novel and diverse tfdA-like genes, encoding putative phenoxyalkanoic acid herbicide-degrading dioxygenases, in soil. Appl. Environ. Microbiol. 76:119-128.