Diversity in methane enrichments from agricultural soil revealed by DGGE separation of PCR amplified 16S rDNA fragments

FEMS Microbiology Ecology

Volumn 26, Issue 1, 1998, Pages 17-26

  Jensen, Sigmund ^a   Øvreås, Lise ^b   Daae, Frida Lise ^b   Torsvik, Vigdis ^b  

^a NORWEGIAN UNIVERSITY OF LIFE SCIENCES   (Norway)

^b UNIVERSITY OF BERGEN   (Norway)

Author keywords

Denaturing gradient gel electrophoresis; Enrichment; Methanotroph; Phylogeny; Soil

Indexed keywords

METHANE; RIBOSOME DNA;

AGRICULTURE; ARTICLE; BACTERIUM DETECTION; DENATURING GRADIENT GEL ELECTROPHORESIS; ENERGY RESOURCE; METHANOTROPHIC BACTERIUM; NONHUMAN; PHYLOGENY; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; SOIL;

EID: 0032080387     PISSN: 01686496     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0168-6496(98)00017-8     Document Type: Article

References (43)

1. 1 Compounds (Murrell, J.C. and Kelly, D.P., Eds.) pp. 1-14. Intercept Ltd., Andover.
2. [2] Khalil, M.A.K. and Rasmussen, R.A. (1985) Causes of increasing atmospheric methane: depletion of hydroxyl radicals and the rise of emissions. Atmos. Environ. 19, 397-407.
3. [3] Oremland, R.S. and Culbertson, C.W. (1992) Evaluation of methyl fluoride and dimethyl ether as inhibitors of aerobic methane oxidation. Appl. Environ. Microbiol. 58. 2983-2992.
4. [4] King, G.M. (1992) Ecological aspects of methane oxidation. a key determinant of global methane dynamics. Adv. Microb. Ecol. 12, 431-468.
5. [5] Hanson, R.S. and Hanson, T.E. (1996) Methanotrophic bacteria. Microbiol. Rev. 60, 439-471.
6. [6] Anthony, C. (1991) Assimilation of carbon by methylotrophs. In: Biology of Methylotrophs (Goldberg, I. and Rokem. J.S., Eds.), pp. 79-109. Butterworth-Heinemann, Stoneham. MA.
7. 1 mixing ratios. FEMS Microbiol. Ecol. 101, 261-270.
8. [8] Roslev, P., Iversen, N. and Henriksen, K. (1997) Oxidation and assimilation of atmospheric methane by soil methane oxidizers. Appl. Environ. Microbiol. 63, 874-880.
9. [9] Tsien, H.C., Bratina, B.J., Tsuji. K. and Hanson, R.S. (1990) Use of oligodeoxynucleotidc signature probes for identification of physiological groups of methylotrophic bacteria. Appl. Environ. Microbiol. 56. 2858-2865.
10. [10] Miguez, C.B., Bourque, D., Sealy. J.A., Greer, C.W. and Groleau, D. (1997) Detection and isolation of methanotrophic bacteria possessing soluble methane monooxygenase (sMMO) genes using the polymerase chain reaction (PCR). Microb. Ecol. 33, 21-31.
11. [11] Murrell, J.C., Mcgowan, V. and Cardy, D.L.N. (1993) Detection of methylotrophic bacteria in natural samples by molecular probing techniques. Chemosphere 26, 1-4.
12. [12] Schink, B. (1992) Syntrophism among prokaryotes. In: The Prokaryotes: Vol. I, (Balows, A., Trüper, H.G., Dworkin. M.. Harder, W. and Schleifer, K.H., Eds.), pp. 276-299. Springer-Verlag, New York.
13. [13] Whittenbury, R., Phillips, K.C. and Wilkinson, J.F. (1970) Enrichment, isolation and some properties of methane-utilizing bacteria. J. Gen. Microbiol. 61, 205-218.
14. [14] Bowman, J.P., Sly, L.I. and Stackebrandt, E. (1995) The phylogenetic position of the family Methylococcaceae. Int. J. Syst. Bacteriol. 45, 182-185.
15. [15] Tsuji, K., Tsien, H.C., Hanson. R.S.. DePalma, S.R. and LaRoche, S. (1990) 16S ribosomal RNA sequence analysis for determination of phylogenelic relationship among methylotrophs. J. Gen. Microbiol. 136, 1-10.
16. [16] Muyzer. G.. Hottenträger, S., Teske, A. and Wawer. C. (1996) Denaturing gradient gel electrophoresis of PCR-amplified 16S rDNA A new molecular approach to analyse the genetic diversity of mixed microbial communities. Mol. Microb. Ecol. Manual 3.4.4. 1-23.
17. [17] Muyzer, G., De Waal, E.G. 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.
18. [18] Rölleke, S., Muyzer, G., Wawer, C., Wanner, G. and Lubitz, W. (1996) Identification of bacteria in a biodegraded wall painting by denaturing gradient gel electrophoresis of PCR-amplified gene fragments coding for 16S rRNA. Appl. Environ. Microbiol. 62, 2059-2065.
19. [19] Wawer, C. and Muyzer, G. (1995) Genetic diversity of Desulfovibrio spp. in environmental samples analyzed by denaturing gradient gel electrophoresis. Appl. Environ. Microbiol. 61, 2203-2210.
20. [20] 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.
21. [21] Øvreas, L., Forney, L.. Daae, F.L. and Torsvik, V. (1997) Distribution of bacterioplankton in meromictic lake Sælenvannet, as determined by denaturing gradient gel electrophoresis of PCR-amplified gene fragments coding for 16S rRNA. Appl. Environ. Microbiol. 63, 3367-3373.
22. [22] Pace, N.R., Stahl, D.A., Lane, D.J. and Olsen, G.J. (1986) The analysis of natural microbial populations by ribosomal RNA sequences. Adv. Microb. Ecol. 9, 1-5.
23. [23] Jensen, S. and Olsen, R.A. (1998) Atmospheric methane consumption in adjacent arable and forest soil systems. Soil Biol. Biochem. (in press).
24. [24] Porter, K.C. and Feig, Y.S. (1980) The use of DAP1 for identifying and counting aquatic microflora. Limnol. Occanogr. 25, 943-948.
25. [25] Hobbie, J.E.. Daley, R.J. and Jasper. S. (1977) Use of nucleopore filters for counting bacteria by fluorescence microscopy. Appl. Environ. Microbiol. 33, 1225-1228.
26. [26] Neefs, J.M., Peer, Y.V., Rijk, P.. Chapelle, S. and Wachter, R. (1993) Compilation of small ribosomal subunit RNA structures. Nucleic Acids Res. 21, 3025-3049.
27. [27] Islam, M.S., Hasan, M.K., Miah, M.A.. Sur, G.C., Felsenstein, A., Venkatesan, M., Sack, R.B. and Albert, M.J. (1993) Use of the polymerase chain reaction and fluorescent-antibody methods for detecting viable but nonculturable Shigella dysenteriae type-1 in laboratory microcosms. Appl. Environ. Microbiol. 59, 536-540.
28. [28] Jukes, T.H. and Cantor, C.R. (1969) Evolution of protein molecules. In: Mammalian Protein Metabolism (Munro, H.N., Ed.), pp. 21-132. Academic Press, New York.
29. [29] Fitch, W.M. and Margoliash, E. (1967) Construction of phylogenetic trees based on mutation distance as estimated from cytochrome c sequences is of general applicability. Science 155, 279-284.
30. [30] Holmes, A.J., Owens. N.J.P. and Murrell, J.C. (1996) Molecular analysis of enrichment cultures of marine methane oxidizing bacteria. J. Exp. Mar. Biol. Ecol. 203. 27-38.
31. [31] McDonald, I.R., Hall, G.H., Pickup. R.W. and Murrell. J.C. (1996) Methane oxidation potential and preliminary analysis of methanotrophs in blanket bog peat using molecular ecology techniques. FEMS Microbiol. Ecol. 21, 197-211.
32. [32] McDonald, I.R., Kenna, E.M. and Murreli. J.C. (1995) Detection of methanotrophic bacteria in environmental samples with the PCR. Appl. Environ. Microbiol. 61, 116-121.
33. [33] Bratina, B.J., Brusseau, G.A. and Hanson, R.S. (1992) Use of 16S rRNA analysis to investigate phylogeny of methylotrophic bacteria. Int. J. Syst. Bacteriol. 42, 645-648.
34. [34] Brusseau, G.A., Bulygina, E.S. and Hanson, R.S. (1994) Phylogenetic analysis and development of probes for differentiating methylotrophic bacteria. Appl. Environ. Microbiol. 60. 626-636.
35. [35] Bowman, J.P., Jiénez, L., Rosario, I.. Hazen, T.C. and Sayler, G.S. (1993) Characterization of the methanotrophic bacterial community present in a trichloroethylene-contaminated subsurface groundwater site. Appl. Environ. Microbiol. 59, 2380-2387.
36. [36] Gottschalk, G. (1988) Bacterial Metabolism, 2nd edn. Springer-Verlag, New York.
37. [37] Brønstad, K., Drænen. K., Øvreas, L. and Torsvik, V. (1996) Phenotypic diversity and antibiotic resistance in soil bacterial communities. J. Ind. Microbiol. 17, 253-259.
38. [38] Teske, A., Sigalevich, P., Cohen, Y. and Muyzer, G. (1996) Molecular identification of bacteria from a coculture by denaturing gradient gel electrophoresis of 16S ribosomal DNA fragments as a tool for isolation in pure cultures, Appl. Environ, Microbiol. 62, 4210-4215.
39. [39] 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.
40. [40] Reysenbach, A.L., Giver, L.J., Wickham, G.S. and Pace, N.R. (1992) Differential amplification of rRNA genes by polymerase chain reaction. Appl. Environ. Microbiol. 58, 3417-3418.
41. [41] Kowalchuk, G.A., Stephen, J.R., De Boer, W., Prosser, J.I., Embley, T.M. and Woldendorp, J.W. (1997) Analysis of ammonia-oxidizing bacteria of the β subdivision of the class proteobacleria in coastal sand dunes by denaturing gradient gel electrophoresis and sequencing of PCR-amplified 16S ribosomal DNA fragments. Appl. Environ. Microbiol. 63, 1489-1497.
42. [42] Wang, C.Y. and Wang, Y. (1996) The frequency of chimeric molecules as a consequence of PCR co-amplification of 16S rRNA genes from different bacterial species. Microbiology 142, 1107-1114.
43. [43] Murrell, J.C., Holmes, A.J., McDonald, I.R. and Kenna, E.M. (1996) Molecular ecology of methanotrophs. In: Microbiology of Atmospheric Trace Gases, Sources, Sinks and Global Change Processes. Vol. 39, (Murrell, J.C. and Kelly, D.P., Eds.), pp. 135-151. Springer-Verlag. Berlin.