Analysis of environmental microbial communities by reverse sample genome probing

Journal of Microbiological Methods

Volumn 53, Issue 2, 2003, Pages 211-219

  Greene, E Anne ^a   Voordouw, Gerrit ^a  

^a UNIVERSITY OF CALGARY   (Canada)

Author keywords

16S rRNA; Environmental microbial communities; Reverse sample genome probing

Indexed keywords

BACTERIAL DNA; RNA 16S;

BACTERIAL FLORA; BACTERIUM IDENTIFICATION; CROSS HYBRIDIZATION; DNA HYBRIDIZATION; GENOME; MICROBIAL DIVERSITY; MOLECULAR CLONING; NONHUMAN; PRIORITY JOURNAL; REVIEW; RHIZOSPHERE; RNA PROBE; SOIL POLLUTION; SPECIES DIFFERENCE;

EID: 0037400887     PISSN: 01677012     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0167-7012(03)00024-1     Document Type: Review

References (32)

1. Bagwell C.E., Lovell C.R. Persistence of selected Spartina alterniflora rhizoplane diazotrophs exposed to natural and manipulated environmental variability. Appl. Environ. Microbiol. 66:2000;4625-4633.
2. Beja O., Suzuki M.T., Koonin E.V., Aravind L., Hadd A., Nguyen L.P., Villacorta R., Amjadi M., Garrigues C., Jovanovich S.B., Feldman R.A., DeLong E.F. Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage. Environ. Microbiol. 2:2000;516-529.
3. Beja O., Suzuki M.T., Heidelberg J.F., Nelson W.C., Preston C.M., Hamada T., Eisen J.A., Fraser C.M., DeLong E.F. Unsuspected diversity among marine aerobic anoxygenic phototrophs. Nature. 415:2002;630-633.
4. Chao W.-L., Tien C.-C., Chao C.-C. Investigation of the effect of different kinds of fertilizers on the compositions of a soil microbial community using the molecular biology technique. J. Chin. Agric. Chem. Soc. 35:1997;252-262.
5. Cho J.-C., Tiedje J.M. Bacterial species determination from DNA-DNA hybridization by using genome fragments and DNA microarrays. Appl. Environ. Microbiol. 67:2001;3677-3682.
6. Cho J.-C., Tiedje J.M. Quantitative detection of microbial genes by using DNA microarrays. Appl. Environ. Microbiol. 68:2002;1425-1430.
7. Frostegård Å., Courteois S., Ramisse V., Clerc S., Bernillon D., Le Gall F., Jeannin P., Nesme X., Simonet P. Qantification of bias related to the extraction of DNA directly from soils. Appl. Environ. Microbiol. 65:1999;5409-5420.
8. Greene E.A., Kay J.G., Jaber K., Stehmeier L.G., Voordouw G. Composition of soil microbial communities enriched on a mixture of aromatic hydrocarbons. Appl. Environ. Microbiol. 66:2000;5282-5289.
9. Greene E.A., Kay J.G., Stehmeier L.G., Voordouw G. Microbial community composition at an ethane pyrolysis plant site at different hydrocarbon inputs. FEMS Microbiol. Ecol. 40:2002;233-241.
10. Greer C.W., Whyte L.G., Lawrence J.R., Masson L., Brousseau R. New molecular tools are creating innovative ways to address environmental challenges. Environ. Sci. Technol. 35:2001;364 A-370 A.
11. Holben W.E., Jansson J.K., Chelm B.K., Tiedje J.M. DNA probe method for the detection of specific microorganisms in the soil bacterial community. Appl. Environ. Microbiol. 54:1988;703-711.
12. Hubert C., Shen Y., Voordouw G. Composition of toluene-degrading microbial communities from soil at different concentrations of toluene. Appl. Environ. Microbiol. 65:1999;3064-3070.
13. Jackson C.R., Harper J.P., Willoughby D., Roden E.E., Churchill P.E. A simple, efficient method for the separation of humic substances and DNA from environmental samples. Appl. Environ. Microbiol. 63:1997;4993-4995.
14. Kisand V., Cuadros R., Wikner J. Phylogeny of culturable estuarine bacteria catabolizing riverine organic matter in the Northern Baltic sea. Appl. Environ. Microbiol. 68:2002;379-388.
15. Koizumi Y., Kelly J.J., Nakagawa T., Urakawa H., El-Fantroussi S., Al-Muzaini S., Fukui M., Urushigawa Y., Stahl D.A. Parallel characterization of anaerobic toluene- and ethylbenzene-degrading consortia by PCR-denaturing gradient gel electrophoresis, RNA-DNA membrane hybridization, and DNA microarray technology. Appl. Environ. Microbiol. 68:2002;3215-3225.
16. Leveille S.A., Leduc L.G., Ferroni G.D., Telang A.J., Voordouw G. Monitoring of bacteria in acid mine environments by reverse sample genome probing. Can. J. Microbiol. 47:2001;431-442.
17. Marmur J. A procedure for the isolation of deoxyribonucleic acid from micro-organisms. J. Mol. Biol. 3:1961;208-218.
18. Nemati M., Voordouw G. Identification and characterization of sulfate-reducing bacteria involved in microbially influenced corrosion in oil fields. Corrosion 2000. 2000;00126-1-00126-9 NACE International, Houston, TX.
19. Rondon M.R., August P.R., Bettermann A.D., Brady S.F., Grossman T.H., Liles M.R., Loiacono K.A., Lynch B.A., MacNeil I.A., Minor C., Tiong C.L., Gilman M., Osburne M.S., Clardy J., Handelsman J., Goodman R.M. Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl. Environ. Microbiol. 66:2000;2541-2547.
20. Sambrook J., Fritsch E.F., Maniatis T. Molecular Cloning: A Laboratory Manual. 2nd ed. 1989;Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
21. Shen Y., Stehmeier L.G., Voordouw G. Identification of hydrocarbon-degrading bacteria in soil by reverse sample genome probing. Appl. Environ. Microbiol. 64:1998;637-645.
22. Telang A.J., Ebert S., Foght J.M., Westlake D.W.S., Jenneman G.E., Gevertz D., Voordouw G. The effect of nitrate injection on the microbial community in an oil field as monitored by reverse sample genome probing. Appl. Environ. Microbiol. 63:1997;1785-1793.
23. Telang A.J., Ebert S., Foght J.M., Westlake D.W.S., Voordouw G. Effects of two diamine biocides on the microbial community from an oil field. Can. J. Microbiol. 44:1998;1060-1065.
24. Telang A.J., Jenneman G.E., Voordouw G. Sulfur cycling in mixed cultures of sulfide-oxidizing and sulfate- or sulfur-reducing bacteria. Can. J. Microbiol. 45:1999;905-913.
25. Torsvik V., Sørheim R., Goksøyr J. Total bacterial diversity in soil and sediment communities - a review. J. Ind. Microbiol. 17:1996;170-178.
26. Voordouw G., Strang J.D., Wilson F.R. Organization of genes encoding [Fe] hydrogenase in Desulfovibrio vulgaris subsp. oxamicus Monticello. J. Bacteriol. 171:1989;3881-3889.
27. Voordouw G., Niviere V., Ferris F.G., Fedorak P.M., Westlake D.W.S. The distribution of hydrogenase genes in Desulfovibrio and their use in identification of species from the oil field environment. Appl. Environ. Microbiol. 56:1990;3748-3754.
28. Voordouw G., Voordouw J.K., Karkhoff-Schweizer R.R., Fedorak P.M., Westlake D.W.S. Reverse sample genome probing, a new technique for identification of bacteria in environmental samples by DNA hybridization, and its application to the identification of sulfate-reducing bacteria in oil field samples. Appl. Environ. Microbiol. 57:1991;3070-3078.
29. Voordouw G., Voordouw J.K., Jack T.R., Foght J., Fedorak P.M., Westlake D.W.S. Identification of distinct communities of sulfate-reducing bacteria in oil fields by reverse sample genome probing. Appl. Environ. Microbiol. 58:1992;3542-3552.
30. Voordouw G., Shen Y., Harrington C.S., Telang A.J., Jack T.R., Westlake D.W.S. Quantitative reverse sample genome probing of microbial communities and its application to oil field production waters. Appl. Environ. Microbiol. 59:1993;4101-4114.
31. Wayne L.G., Brenner D.J., Colwell R.R., Grimont P.A.D., Kandler O., Krichevsky M.I., Moore L.H., Moore W.E.C., Murray R.G.E., Stackebrandt E., Starr M.P., Trüper H.G. Report of the ad-hoc-committee on reconciliation of approaches to bacterial systematics. Int. J. Syst. Bacteriol. 37:1987;463-464.
32. Wu L., Thompson D.K., Bagwell C.E., Tiedje J.M., Zhou J. Community genome arrays: an approach for detection and quantification of selected bacterial taxa in environmental samples. Proceedings 102nd General Meeting of the American Society of Microbiology, Salt Lake City, UT, Abstract Q-50:2002.