Long-term effects of mineral versus organic fertilizers on activity and structure of the methanotrophic community in agricultural soils

Environmental Microbiology

Volumn 5, Issue 10, 2003, Pages 867-877

  Seghers, Dave ^a   Top, Eva M ^a,b   Reheul, Dirk ^a   Bulcke, Robert ^a   Boeckx, Pascal ^a   Verstraete, Willy ^a   Siciliano, Steven D ^a,c  

^a GHENT UNIVERSITY   (Belgium)

^b UNIVERSITY OF IDAHO   (United States)

^c UNIVERSITY OF SASKATCHEWAN   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ALPHAPROTEOBACTERIA; CROPS, AGRICULTURAL; FATTY ACIDS; FERTILIZERS; GAMMAPROTEOBACTERIA; MANURE; METHANE; METHYLOCOCCACEAE; MINERALS; NITRATES; OXIDATION-REDUCTION; PHYLOGENY; QUATERNARY AMMONIUM COMPOUNDS; RNA, RIBOSOMAL, 16S; SOIL; SOIL MICROBIOLOGY;

BACTERIA (MICROORGANISMS); METHYLOCOCCACEAE; NEGIBACTERIA;

EID: 0141676330     PISSN: 14622912     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1462-2920.2003.00477.x     Document Type: Article

References (37)

1. Adamsen, A.P.S., and King, G.M. (1993) Methane consumption in temperate and sub-arctic forest soils - rates, vertical zonation, and responses to water and nitrogen. Appl Environ Microbiol 59: 485-490.
2. Bedard, C., and Knowles, R. (1997) Some properties of methane oxidation in a thermally stratified lake. Can J Fish Aquat Sci 54: 1639-1645.
3. Bender, M., and Conrad, R. (1993) Kinetics of methane oxidation in oxic soils. Chemosphere 26: 687-696.
4. Blake, D.R., and Rowland, F.S. (1988) Continuing worldwide increase in tropospheric methane, 1978-87. Science 239: 1129-1131.
5. Boeckx, P., Van Cleemput, O., and Meyer, T. (1998) The influence of land use and pesticides on methane oxidation in some Belgian soils. Biol Fertil Soils 27: 293-298.
6. Boon, N., De Windt, W., Verstraete, W., and Top, E.M. (2002) Evaluation of nested PCR-DGGE (denaturing gradient gel electrophoresis) with group-specific 16s rRNA primers for the analysis of bacterial communities from different waste-water treatment plants. FEMS Microbiol Ecol 39: 101-112.
7. Bronson, K.F., and Mosier, A.R. (1994) Suppression of methane oxidation in aerobic soil by nitrogen fertilizers, nitrification inhibitors and urease inhibitors. Biol Fertil Soils 17: 263-268.
8. Cavigelli, M.A., Robertson, G.P., and Klug, M.J. (1995) Fatty-acid methyl-ester (fame) profiles as measures of soil microbial community structure. Plant Soil 170: 99-113.
9. Crill, P.M., Martikainen, P.J., Nykanen, H., and Silvola, J. (1994) Temperature and N-fertilization effects on methane oxidation in a drained peatland soil. Soil Biol Biochem 26: 1331-1339.
10. Dunfield, P., and Knowles, R. (1995) Kinetics of inhibition of methane oxidation by nitrate, nitrite, and ammonium in a humisol. Appl Environ Microbiol 61: 3129-3135.
11. El Fantroussi, S., Mahillon, J., Naveau, H., and Agathos, S.N. (1997) Introduction and PCR detection of Desulfomonile tiedjei in soil slurry microcosms. Biodegradation 8: 125-133.
12. Eller, G., and Frenzel, P. (2001) Changes in activity and community structure of methane-oxidizing bacteria over the growth period of rice. Appl Environ Microbiol 67: 2395-2403.
13. Garbeva, P., van Overbeek, L.S., van Vuurde, J.W.L., and van Elsas, J.D. (2001) Analysis of endophytic bacterial communities of potato by plating and denaturing gradient gel electrophoresis (DGGE) of 16S rDNA based PCR fragments. Microb Ecol 41: 369-383.
14. Graham, D.W., Chaudhary, J.A., Hanson, R.S., and Arnold, R.G. (1993) Factors affecting competition between type-I and type-II methanotrophs in 2-organism, continuous-flow reactors. Microb Ecol 25: 1-17.
15. Hanson, R.S., and Hanson, T.E. (1996) Methanotrophic bacteria. Microbiol Rev 60: 439-455.
16. Henckel, T., Friedrich, M., and Conrad, R. (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.
17. Hermansson, A., and Lindgren, P.E. (2001) Quantification of ammonia-oxidizing bacteria in arable soil by real-time PCR. Appl Environ Microbiol 67: 972-976.
18. Holmes, A.J., Roslev, P., McDonald, I.R., Iversen, N., Henriksen, K., and Murrell, J.C. (1999) Characterization of methanotrophic bacterial populations in soils showing atmospheric methane uptake. Appl Environ Microbiol 65: 3312-3318.
19. Horz, H.P., Raghubanshi, A.S., Heyer, E., Kammann, C., Conrad, R., and Dunfield, P.F. (2002) Activity and community structure of methane-oxidising bacteria in a wet meadow soil. Fems Microbiol Ecol 41: 247-257.
20. Hutsch, B.W. (1996) Methane oxidation in soils of two long-term fertilization experiments in germany. Soil Biol Biochem 6: 773-782.
21. Hutsch, B.W. (1998) Methane oxidation in arable soil as inhibited by ammonium, nitrite, and organic manure with respect to soil pH. Biol Fertil Soils 28: 27-35.
22. Hutsch, B.W. (2001) Methane oxidation in non-flooded soils as affected by crop production - invited paper. Eur J Agron 14: 237-260.
23. Hutsch, B.W., Webster, C.P., and Powlson, D.S. (1993) Long-term effects of nitrogen-fertilization on methane oxidation in soil of the broadbalk wheat experiment. Soil Biol Biochem 25: 1307-1315.
24. IPPC (International Panel on Climate Change) (2001) Climate Change 2001. The Scientific Basis. Cambridge: Cambrigde University Press.
25. 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.
26. Kowalchuk, G.A., Naoumenko, Z.S., Derikx, P.J.L., Felske, A., Stephen, J.R., and Arkhipchenko, I.A. (1999) Molecular analysis of ammonia-oxidizing bacteria of the beta subdivision of the class proteobacteria in compost and composted materials. Appl Environ Microbiol 65: 396-403.
27. Mosier, A., Schimel, D., Valentine, D., Bronson, K., and Parton, W. (1991) Methane and nitrous-oxide fluxes in native, fertilized and cultivated grasslands. Nature 350: 330-332.
28. Muyzer, G., de Waal, E.C., and Uitterlinden, A. (1993) Profiling of complex microbial populations using denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16s rRNA. Appl Environ Microbiol 59: 695-700.
29. Ovreas, L., Jensen, S., Daae, F.L., and Torsvik, V. (1998) Microbial community changes in a perturbed agricultural soil investigated by molecular and physiological approaches. Appl Environ Microbiol 64: 2739-2742.
30. Reay, D.S., Radajewski, S., Murrell, J.C., McNamara, N., and Nedwell, D.B. (2001) Effects of land-use on the activity and diversity of methane oxidizing bacteria in forest soils. Soil Biol Biochem 33: 1613-1623.
31. Roslev, P., and Iversen, N. (1999) Radioactive fingerprinting of microorganisms that oxidize atmospheric methane in different soils. Appl Environ Microbiol 65: 4064-4070.
32. Steudler, P.A., Bowden, R.D., Melillo, J.M., and Aber, J.D. (1989) Influence of nitrogen-fertilization on methane uptake in temperate forest soils. Nature 341: 314-316.
33. Tlustos, P., Willison, T.W., Baker, J.C., Murphy, D.V., Pavlikova, D., Goulding, K.W.T., and Powlson, D.S. (1998) short-term effects of nitrogen on methane oxidation in soils. Biol Fertil Soils 28: 64-70.
34. Top, E.M., Mphekgo, P.M., Clerinx, M., Goris, J., De Vos, P., and Verstraete, W. (1999) Methane oxidation as a method to evaluate the removal of 2,4-dichlorophenoxyactic acid (2,4-D) from soil by plasmid-mediated bioaugmentation. FEMS Microbiol Ecol 28: 203-213.
35. Ward, J.H. (1963) Hierarchial grouping to optimize an objective function. J Am Stat AJ Am Stat Assoc 58: 236-244.
36. 4 oxidation in soils fertilized with organic and inorganic-N; differential effects. Soil Biol Biochem 28: 135-136.
37. Wise, M.G., McArthur, J.V., and Shimkets, L.J. (1999) Methanotroph diversity in landfill soil: isolation of novel type I and type II methanotrophs whose presence was suggested by culture-independent 16s ribosomal DNA analysis. Appl Environ Microbiol 65: 4887-4897.