Fluorescent oligonucleotide rDNA probes for specific detection of methane oxidising bacteria

FEMS Microbiology Ecology

Volumn 31, Issue 1, 2000, Pages 29-38

  Bourne, David G ^a   Holmes, Andrew J ^a,b   Iversen, Niels ^c   Murrell, J Colin ^a  

^a UNIVERSITY OF WARWICK   (United Kingdom)

^b MACQUARIE UNIVERSITY   (Australia)

^c AALBORG UNIVERSITY   (Denmark)

Author keywords

16S rDNA probe; Fluorescent in situ hybridisation; Methane oxidising bacteria

Indexed keywords

METHANE; RIBOSOME DNA;

BACTERIUM; DETECTION METHOD; METHANE; METHANOTROPHY;

ARTICLE; BACTERIUM DETECTION; DNA SEQUENCE; FLUORESCENCE IN SITU HYBRIDIZATION; GENE LIBRARY; METHYLOBACTERIUM; NONHUMAN; OLIGONUCLEOTIDE PROBE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL;

METHYLOBACTER; METHYLOCOCCUS;

EID: 0033988335     PISSN: 01686496     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0168-6496(99)00078-1     Document Type: Article

References (38)

1. Hanson R.S., Hanson T.E. Methanotrophic bacteria. Microbiol. Rev. 60:1996;439-471.
2. Murrell J.C. Molecular genetics of methane oxidation. Biodegradation. 5:1994;145-149.
3. Whittenbury R., Phillips K.C., Wilkinson J.G. Enrichment, isolation and some properties of methane utilising bacteria. J. Gen. Microbiol. 61:1970;205-218.
4. Smith K.S., Costello A.M., Lidstrom M.E. Methane and trichloroethylene oxidation by an estuarine methanotroph, Methylobacter sp. Strain BB5.1. Appl. Environ. Microbiol. 63:1997;4617-4620.
5. Holmes A.J., Owens N., Murrell J.C. Detection of novel marine methanotrophs using phylogenetic and functional gene probes after methane enrichment. Microbiology. 141:1995;1947-1955.
6. Murrell, J.C. and Holmes. A.J. (1995) Molecular ecology of marine methanotrophs. In: Molecular Ecology of Aquatic Microbes. NATO ASI Series, Vol. G 38. (Joint, I. Ed.), pp. 366-390. Springer-Verlag, Berlin.
7. Seiburth J.M., Johnson P.W., Eberhardt M.A., Sieracki M.E., Lidstrom M.E., Laux D. The first methane-oxidizing bacterium from the upper mixed layer of the deep ocean. Methylomonas pelagica sp. nov. Curr. Microbiol. 14:1987;285-293.
8. Dedysh S.N., Panikov N.S., Tiedje J.M. Acidophilic methanotrophic communities from Sphagnum peat bogs. Appl. Environ. Microbiol. 64:1998;922-929.
9. McDonald I.R., Hall G.H., Pickup R.W., Murrell J.C. Methane oxidation potentials and preliminary analysis of methanotrophs in a blanket bog peat using molecular ecology techniques. FEMS Microbiol. Ecol. 21:1996;197-211.
10. Ritchie D.A., Edwards C., McDonald I.R., Murrell J.C. Detection of methanogens and methanotrophs in natural environments. Glob. Change Biol. 3:1997;339-350.
11. Bodrossy L., Murrell J.C., Dalton H., Kalman M., Puskas L.G., Kovacs K. Heat-tolerant methanotrophic bacteria from the hot water effluent of a natural gas field. Appl. Environ. Microbiol. 61:1995;3549-3555.
12. Bodrossy L., Holmes E.M., Holmes A.J., Kovacs K.L., Murrell J.C. Analysis of 16S rRNA and methane monooxygenase gene sequences reveals a novel group of thermolerant methanotrophs, Methylocaldum gen. nov. Arch. Microbiol. 168:1997;493-503.
13. Gilbert B., Aßmus B., Hartmann A., Frenzel P. In situ localization of two methanotrophic strains in the rhizosphere of rice plants. FEMS Microbiol. Ecol. 25:1998;117-128.
14. Bowman J.P., McCammon S.A., Skerratt J.H. Methylosphaera hansonii gen. nov., a psychrophilic, group I methanotroph from Antarctic marine-salinity, meromictic lakes. Microbiology. 143:1997;1451-1459.
15. Brusseau G.A., Bulygina E.S., Hanson R.S. Phylogenetic analysis and development of probes for differentiating methylotrophic bacteria. Appl. Environ. Microbiol. 60:1994;626-636.
16. Hanson, R.S., Bratina, B.J. and Brusseau, G.A. (1993) Phylogeny and ecology of methylotrophic bacteria. In: Microbial growth on C1 compounds (Murrell, J.C. and Kelly, D.P., Eds.), pp. 285-302. Intercept Ltd., Andover.
17. Tsien H.C., Brattina B.J., Tsuji K., Hanson R.S. Use of oligonucleotide signature probes for identification of physiological groups of methylotrophic bacteria. Appl. Environ. Microbiol. 56:1990;2858-2865.
18. Murrell J.C., McDonald I.R., Bourne D.G. Molecular methods for the study of methanotroph ecology. FEMS Microbiol. Ecol. 27:1998;103-114.
19. McDonald I.R., Kenna E.M., Murrell J.C. Detection of methanotrophic bacteria in environmental samples with the PCR. Appl. Environ. Microbiol. 61:1995;116-121.
20. Amann, R.I. (1995) In situ identification of microorganisms by whole cell hybridisation with rRNA-targeted nucleic acid probes. In: Molecular Microbial Ecology (Akkerman, A.D.L., van Elsas, J.D. and de Bruijn, F.J., Eds.), pp. 1-15. Kluwer Academic Publishers, Dordrecht.
21. Amann R., Ludwig W., Schleifer K.H. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59:1995;143-169.
22. Amann R.I., Binder B.J., Olson R.J., Chisholm S.W., Devereux R., Stahl D.A. Combination of 16S rRNA-targeted oligonucleotide probes with flow-cytometry for analysing mixed microbial populations. Appl. Environ. Microbiol. 56:1990;1919-1925.
23. Delong E.F., Wickam G.S., Pace N.R. Phylogenetic stains: ribosomal RNA-based probes for the identification of single cells. Science. 243:1989;1360-1363.
24. Kemp P.F., Lee S., LaRoche J. Estimating the growth rate of slowly growing marine bacteria from RNA content. Appl. Environ. Microbiol. 59:1993;2594-2601.
25. Maidak B.L., Larsen N., McCaughey M.J., Overbeek R., Olsen G.J., Fogel K., Blandy J., Woese C.R. The ribosomal database project. Nucleic Acids Res. 22:1994;3485-3487.
26. Strunk, O., Gross, O., Reichel, B., May, M., Hermann, S., Stuckmann, N., Nonhoff, B., Lenke, M., Vilbig, A., Ludwig, T., Bode, A., Schleifer, K.H. and Ludwig, W. ARB: a software environment for sequence data. Unpublished data.
27. Amann R.I., Krumholz L., Stahl D.A. Fluorescent-oligonucleotide probing of whole cells for determinative, phylogenetic and environmental studies in microbiology. J. Bacteriol. 172:1990;762-770.
28. Stahl, D.A. and Amann, R. (1991) Development and application of nucleic acid probes. In: Nucleic Acid Techniques in Bacterial Systematics (Stackebrandt, E. and Goodfellow, M., Eds.), pp. 205-244. John Wiley and Sons, Chichester.
29. Amann R.I., Lugwig W., Schleifer K.-H. Identification and in situ detection of individual bacterial cells. FEMS Microbiol. Lett. 100:1992;45-50.
30. Marmur J. A procedure for the isolation of deoxyribonucleic acid from microorganisms. J. Mol. Biol. 3:1961;208-218.
31. Giovannoni, S.J. (1991) The polymerase chain reaction. In: Nucleic Acid Techniques in Bacterial Systematics (Stackebrandt, E. and Goodfellow, M., Eds.), pp. 177-203. John Wiley and Sons, Chichester.
32. Lane, D.J. (1991) 16S/23S rRNA sequencing. In: Nucleic Acid Techniques in Bacterial Systematics (Stackebrandt, E. and Goodfellow, M., Eds.), pp. 115-175. John Wiley and Sons, Chichester.
33. Saunders S.E., Burke J.F. Rapid isolation of miniprep DNA for double strand sequencing. Nucleic Acids Res. 18:1990;4948.
34. Sorensen A.H., Torsvik V.L., Torsvik T., Poulsen L.K., Ahring B.K. Whole-cell hybridization of Methanosarcina cells with two new oligonucleotide probes. Appl. Environ. Microbiol. 63:1997;3043-3050.
35. Poulsen L.K., Lan F., Kristensen C.S., Hobolth P., Molin S., Krogfelt K. Spatial distribution of Escherichia coli in the mouse large intestine inferred from rRNA in situ hybridisation. Infect. Immun. 62:1994;5191-5194.
36. Imhoff J.F., Suling J. The phylogenetic relationship among Ectothiorhodospiraceae: a revaluation of their taxonomy on the basis of 16S rDNA analyses. Arch. Microbiol. 165:1996;106-113.
37. Khmelenina V.N., Kalyuzhnaya M.G., Starostina N.G., Suzina N.E., Trotsenko Y.A. Isolation and characterisation of haloltolerant alkaliphilic methanotrophic bacteria from Tuva soda lakes. Curr. Microbiol. 35:1997;257-261.
38. Fuchs B.M., Wallner G., Beisker W., Schwippl I., Ludwig W., Amann R. Flow cytometric analysis of the in situ accessibility of Escherichia coli 16S rRNA for fluorescently labeled oligonucleotide probes. Appl. Environ. Microbiol. 64:1998;4973-4982.