Use of the T-RFLP technique to assess spatial and temporal changes in the bacterial community structure within an agricultural soil planted with transgenic and non-transgenic potato plants

FEMS Microbiology Ecology

Volumn 32, Issue 3, 2000, Pages 241-247

  Lukow, Thomas ^a   Dunfield, Peter F ^a   Liesack, Werner ^a  

^a MAX PLANCK INSTITUTE FOR TERRESTRIAL MICROBIOLOGY   (Germany)

Author keywords

Biomonitoring; Genetic fingerprint; Microbial community; Multivariate analysis of variance; Terminal restriction fragment length polymorphism analysis; Transgenic plant

Indexed keywords

BACTERIUM; COMMUNITY STRUCTURE; SOIL MICROORGANISM; SPATIAL VARIATION; TEMPORAL VARIATION;

ARTICLE; BACTERIAL FLORA; BACTERIUM DETECTION; DNA FINGERPRINTING; MULTIVARIATE ANALYSIS; NONHUMAN; POTATO; PRIORITY JOURNAL; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; SOIL; TRANSGENIC PLANT;

EID: 0034119122     PISSN: 01686496     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0168-6496(00)00033-7     Document Type: Article

References (33)

1. Øvreås L., Jensen S., Daae F.L., Torsvik V. Microbial community changes in a perturbed agricultural soil investigated by molecular and physiological approaches. Appl. Environ. Microbiol. 64:1998;2739-2742.
2. Ferris M.J., Ward D.M. Seasonal distributions of dominant 16S rRNA-defined populations in a hot spring microbial mat examined by denaturing gradient gel electrophoresis. Appl. Environ. Microbiol. 63:1997;1375-1381.
3. Chin K.-J., Lukow T., Conrad R. Effect of temperature on structure and function of the methanogenic archaeal community in an anoxic rice field soil. Appl. Environ. Microbiol. 65:1999;2341-2349.
4. Garland J.L., Mills A.L. Classification and characterization of heterotrophic microbial communities on the basis of patterns of community-level sole-carbon-source utilization. Appl. Environ. Microbiol. 57:1991;2351-2359.
5. Heuer H., Smalla K. Evaluation of community-level catabolic profiling using BIOLOG GN microplates to study microbial community changes in potato phyllosphere. J. Microbiol. Methods. 30:1997;49-61.
6. Smalla K., Wachtendorf U., Heuer H., Liu W.-T., Forney L. Analysis of BIOLOG GN substrate utilization patterns by microbial communities. Appl. Environ. Microbiol. 64:1998;1220-1225.
7. Staley J.T., Konopka A. Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats. Ann. Rev. Microbiol. 39:1985;321-346.
8. Liesack, W., Janssen, P.H., Rainey, F.A., Ward-Rainey, N.L. and Stackebrandt, E. (1997) Microbial diversity in soil: the need for a combined approach using molecular and cultivation techniques. In: Modern Soil Microbiology, (van Elsas, J.D., Trevors, J.T. and Wellington, E.M.H., Eds.), pp. 375-439. Marcel Dekker, New York.
9. Massol-Deyá A., Weller R., Ríos-Hernández L., Zhou J.-Z., Hickey R.F., Tiedje J.M. Succession and convergence of biofilm communities in fixed-film reactors treating aromatic hydrocarbons in groundwater. Appl. Environ. Microbiol. 63:1997;270-276.
10. Schweiger F., Tebbe C.C. A new approach to utilize PCR-single-strand-conformation polymorphism for 16S rRNA gene-based microbial community analysis. Appl. Environ. Microbiol. 64:1998;4870-4876.
11. Engelen B., Meinken K., von Wintzingerode F., Heuer H., Malkomes H.-P., Backhaus H. Monitoring impact of a pesticide treatment on bacterial soil communities by metabolic and genetic fingerprinting in addition to conventional testing procedures. Appl. Environ. Microbiol. 64:1998;2814-2821.
12. Muyzer G., de Waal E.C., Uitterlinden A.G. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl. Environ. Microbiol. 59:1993;695-700.
13. Henckel T., Friedrich M., Conrad R. 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. 65:1999;1980-1990.
14. Ferris M.J., Muyzer G., Ward D.M. Denaturing gradient gel electrophoresis profiles of 16S rRNA-defined populations inhabiting a hot spring microbial mat community. Appl. Environ. Microbiol. 62:1996;340-346.
15. Heuer H., Hartung K., Wieland G., Kramer I., Smalla K. Polynucleotide probes that target a hypervariable region of 16S rRNA genes to identify bacterial isolates corresponding to bands of community fingerprints. Appl. Environ. Microbiol. 65:1999;1045-1049.
16. Stephen J.R., Kowalchuk G.A., Bruns M.-A.V., McCaig A.E., Phillips C.J., Embley M., Prosser J.I. Analysis of beta-subgroup proteobacterial ammonia oxidizer populations in soil by denaturing gradient gel electrophoresis analysis and hierarchical phylogenetic probing. Appl. Environ. Microbiol. 64:1998;2958-2965.
17. Heuer, H. and Smalla, K. (1997) Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) for studying soil microbial communities. In: Modern Soil Microbiology (van Elsas, J.D., Trevors, J.T. and Wellington, E.M.H., Eds.), pp. 353-373. Marcel Dekker, New York.
18. Felske A., Akkermans A.D.L. Spatial homogeneity of abundant bacterial 16S rRNA molecules in grassland soils. Microb. Ecol. 36:1998;31-36.
19. Liu W.-T., Marsh T.L., Cheng H., Forney L.J. Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Appl. Environ. Microbiol. 63:1997;4516-4522.
20. Strittmatter G., Janssens J., Opsomer C., Botterman J. Inhibition of fungal disease development in plants by engineering controlled cell death. Bio/Technology. 13:1995;1085-1089.
21. Strittmatter G., Gheysen G., Gianinazzi-Pearson V., Hahn K., Niebel A., Rohde W., Tacke E. Infections with various types of organisms stimulate transcription from a short promoter fragment of the potato gst1 gene. Mol. Plant-Microbe Interact. 9:1996;68-73.
22. Ogram A., Sayler G.S., Barkay T. The extraction and purification of microbial DNA from sediments. J. Microbiol. Methods. 7:1987;57-66.
23. Smalla K., Cresswell N., Mendonca-Hagler L.C., Wolters A., van Elsas J.D. Rapid DNA extraction protocol from soil for polymerase chain reaction-mediated amplification. J. Appl. Bacteriol. 74:1993;78-85.
24. Miller D.N., Bryant J.E., Madsen E.L., Ghiorse W.C. Evaluation and optimization of DNA extraction and purification procedures for soil and sediment samples. Appl. Environ. Microbiol. 65:1999;4715-4724.
25. 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.
26. Heuer H., Krsek M., Baker P., Smalla K., Wellington E.M.H. Analysis of actinomycete communities by specific amplification of genes encoding 16S rRNA and gel-electrophoretic separation in denaturing gradients. Appl. Environ. Microbiol. 63:1997;3233-3241.
27. Mayrand P.E., Corcoran K.P., Ziegle J.S., Robertson J.M., Hoff L.B., Kronick M.N. The use of fluorescence detection and internal lane standards to size PCR products automatically. Appl. Theor. Electrophor. 3:1992;1-11.
28. Ziegle J.S., Su Y., Corcoran K.P., Nie L., Mayrand P.E., Hoff L.B., McBride L.J., Kronick M.N., Diehl S.R. Application of automated DNA sizing technology for genotyping microsatellite loci. Genomics. 14:1992;1026-1031.
29. Dunbar J., Takala S., Barns S.M., Davis J.A., Kuske C.R. Levels of bacterial community diversity in four arid soils compared by cultivation and 16S rRNA gene cloning. Appl. Environ. Microbiol. 65:1999;1662-1669.
30. Moeseneder M.M., Arrieta J.M., Muyzer G., Winter C., Herndl G.J. Optimization of terminal-restriction fragment length polymorphism analysis for complex marine bacterioplankton communities and comparison with denaturing gradient gel electrophoresis. Appl. Environ. Microbiol. 65:1999;3518-3525.
31. Yang C.-H., Crowley D.E. Rhizosphere microbial community structure in relation to root location and plant iron nutritional status. Appl. Environ. Microbiol. 66:2000;345-351.
32. Lüdemann H., Arth I., Liesack W. Spatial changes in the bacterial community structure along a vertical oxygen gradient in flooded paddy soil cores. Appl. Environ. Microbiol. 66:2000;754-762.
33. Guschin D.Y., Mobarry B.K., Proudnikov D., Stahl D.A., Rittmann B.E., Mirzabekov A.D. Oligonucleotide microchips as genosensors for determinative and environmental studies in microbiology. Appl. Environ. Microbiol. 63:1997;2397-2402.