Analysing microbial community structure by means of terminal restriction fragment length polymorphism (T-RFLP)

Molecular Approaches to Soil, Rhizosphere and Plant Microorganism Analysis

Volumn , Issue , 2006, Pages 84-98

  Blackwood, Christopher B ^a  

^a KENT STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 70449128236     PISSN: None     EISSN: None     Source Type: Book    
DOI: None     Document Type: Chapter

References (56)

1. Blackwood, C.B. and Buyer, J.S. (2006) Evaluating the physical-capture method of terminal restriction fragment length polymorphism. Soil Biology and Biochemistry, submitted.
2. Blackwood, C.B. and Paul, E.A. (2003) Eubacterial community structure and population size within the soil light fraction, rhizosphere, and heavy fraction of several agricultural systems. Soil Biology and Biochemistry 35, 1245-1255.
3. Blackwood, C.B., Marsh, T., Kim, S.H. and Paul, E.A. (2003) Terminal restriction fragment length polymorphism data analysis for quantitative comparison of microbial communities. Applied and Environmental Microbiology 69, 926-932.
4. Blackwood, C.B., Oaks, A., and Buyer, J.S. (2005) Phylum- and class-specific PCR primers for general microbial community analysis. Applied and Environmental Microbiology 71, 6193-6198.
5. Blackwood, C.B., Dell, C., Smucker, A.J.M. and Paul, E.A. (2006) Eubacterial communities in different soil macroaggregate environments and cropping systems. Soil Biology and Biochemistry 38, 720-728.
6. Brodie, E., Edwards, S. and Clipson, N. (2003) Soil fungal community structure in a temperate upland grassland soil. FEMS Microbiology Ecology 45, 105-114.
7. Bruce, K.D. (1997) Analysis of mer gene subclasses within bacterial communities in soils and sediments resolved by fluorescent-PCR-restriction fragment length polymorphism profiling. Applied and Environmental Microbiology 63, 4914-4919.
8. Clement, B.G., Kehl, L.E., DeBord, K.L. and Kitts, C.L. (1998) Terminal restriction fragment patterns (TRFPs), a rapid, PCR-based method for the comparison of complex bacterial communities. Journal of Microbiological Methods 31, 135-142.
9. Cole, J.R., Chai, B., Marsh, T.L., Farris, R.J., Wang, Q., Kulam, S.A., Chandra, S., McGarrell, D.M., Schmidt, T.M., Garrity, G.M. and Tiedje, J.M. (2003) The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. Nucleic Acids Research 31, 442-443.
10. Curtis, T.P. and Sloan, W.T. (2005) Exploring microbial diversity - a vast below. Science 309, 1331-1333.
11. Donovan, S.E., Purdy, K.J., Kane, M.D. and Eggleton, P. (2004) Comparison of Euryarchaea strains in the guts and food-soil of the soil-feeding termite Cubitermes fungifaber across different soil types. Applied and Environmental Microbiology 70, 3884-3892.
12. Dunbar, J., Ticknor, L.O. and Kuske, C.R. (2001) Phylogenetic specificity and reproducibility and new method for analysis of terminal restriction fragment profiles of 16S rRNA genes from bacterial communities. Applied and Environmental Microbiology 67, 190-197.
13. Dunbar, J., Barns, S.M., Ticknor, L.O. and Kuske, C.R. (2002) Empirical and theoretical bacterial diversity in four Arizona soils. Applied and Environmental Microbiology 68, 3035-3045.
14. Dunfield, K.E. and Germida, J.J. (2003) Seasonal changes in the rhizosphere microbial communities associated with field-grown genetically modified canola (Brassica napus). Applied and Environmental Microbiology 69, 7310-7318.
15. Dykhuizen, D.E. (1998) Santa Rosalia revisited: why are there so many species of bacteria? Antonie van Leeuwenhoek 73, 25-33.
16. Edel-Hermann, W., Dreumont, C., Perez-Piqueres, A. and Steinberg, C. (2004) Terminal restriction fragment length polymorphism analysis of ribosomal RNA genes to assess changes in fungal community structure in soils. FEMS Microbiology Ecology 47, 397-404.
17. Egert, M. and Friedrich, M.W. (2003) Formation of pseudo-terminal restriction fragments, a PCR-related bias affecting terminal restriction fragment length polymorphism analysis of microbial community structure. Applied and Environmental Microbiology 69, 2555-2562.
18. Egert, M., Marhan, S., Wagner, B., Scheu, S. and Friedrich, M.W. (2004) Molecular profiling of 16S rRNA genes reveals diet-related differences of microbial communities in soil, gut, and casts of Lumbricus terrestris L. (Oligochaeta: Lumbricidae). FEMS Microbiology Ecology 48, 187-197.
19. Engebretson, J.J. and Moyer, C.L. (2003) Fidelity of select restriction endonucleases in determining microbial diversity by terminal-restriction fragment length polymorphism. Applied and Environmental Microbiology 69, 4823- 4829.
20. Gans, J., Wolinsky, M. and Dunbar, J. (2005) Computational improvements reveal great bacterial diversity and high metal toxicity in soil. Science 309, 1387-1390.
21. Girvan, M.S., Bullimore, J., Pretty, J.N., Osborn, A.M. and Ball, A.S. (2003) Soil type is the primary determinant of the composition of the total and active bacterial communities in arable soils. Applied and Environmental Microbiology 69, 1800-1809.
22. Grant, A. and Ogilvie, L.A. (2004) Name that microbe: rapid identification of taxa responsible for individual fragments in fingerprints of microbial community structure. Molecular Ecology Notes 4, 133-136.
23. Hackl, E., Zechmeister-Boltenstern, S., Bodrossy, L. and Sessitsch, A. (2004) Comparison of diversities and compositions of bacterial populations inhabiting natural forest soils. Applied and Environmental Microbiology 70, 5057-5065.
24. Hartmann, M., Frey, B., Kolliker, R. and Widmer, F. (2005) Semi-automated genetic analyses of soil microbial communities: comparison of T-RFLP and RISA based on descriptive and discriminative statistical approaches. Journal of Microbiological Methods 61, 349-360.
25. Ikeda, S., Roberts, D.M., Watanabe, K.N. and Ytow, N. (2004) Microbial community analyses using a simple, rapid detection method for DNA fingerprints with a fluorescence scanner. Journal of Bioscience and Bioengineering 98, 500-503.
26. Kaplan, C.W. and Kitts, C.L. (2003) Variation between observed and true terminal restriction fragment length is dependent on true TRF length and purine content. Journal of Microbiological Methods 54, 121-125.
27. Kennedy, N., Brodie, E., Connolly, J. and Clipson, N. (2004) Impact of lime, nitrogen and plant species on bacterial community structure in grassland microcosms. Environmental Microbiology 6, 1070-1080.
28. Kent, A.D., Smith, D.J., Benson, B.J. and Triplett, E.W. (2003) Web-based phylogenetic assignment tool for analysis of terminal restriction fragment length polymorphism profiles of microbial communities. Applied and Environmental Microbiology 69, 6768-6776.
29. Kuske, C.R., Ticknor, L.O., Miller, M.E., Dunbar, J.M., Davis, J.A., Barns, S.M. and Belnap, J. (2002) Comparison of soil bacterial communities in rhizospheres of three plant species and the interspaces in an arid grassland. Applied and Environmental Microbiology 68, 1854-1863.
30. LaMontagne, M.G., Schimel, J.P. and Holden, P.A. (2003) Comparison of subsurface and surface soil bacterial communities in California grassland as assessed by terminal restriction fragment length polymorphisms of PCR-amplified 16S rRNA genes. Microbial Ecology 46, 216-227.
31. Legendre, P. and Gallagher, E.D. (2001) Ecologically meaningful transformations for ordination of species data. Oecologia 129, 271-280.
32. Legendre, P. and Legendre, L. (1998) Numerical Ecology. Elsevier, Amsterdam, The Netherlands.
33. Liu, W.-T., Marsh, T.L., Cheng, H. and Forney, L.J. (1997) Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Applied and Environmental Microbiology 63, 4516-4522.
34. Ludwig, W., Strunk, O., Westram, R., Richter, L., Meier, H., Yadhukumar, Buchner, A., Lai, T., Steppi, S., Jobb, G., Forster, W., Brettske, I., Gerber, S., Ginhart, A.W., Gross, O., Grumann, S., Hermann, S., Jost, R., Konig, A., Liss, T., Lussmann, R., May, M., Nonhoff, B., Reichel, B., Strehlow, R., Stamatakis, A., Stuckmann, N., Vilbig, A., Lenke, M., Ludwig, T., Bode, A. and Schleifer, K.-H. (2004) ARB: a software environment for sequence data. Nucleic Acids Research 32, 1363-1371.
35. Marsh, T.L., Saxman, P., Cole, J. and Tiedje, J. (2000) Terminal restriction fragment length polymorphism analysis program, a web-based research tool for microbial community analysis. Applied and Environmental Microbiology 66, 3616-3620.
36. Mengoni, A., Grassi, E. and Bazzicalupo, M. (2002) Cloning method for taxonomic interpretation of T-RFLP patterns. Biotechniques 33, 990-992.
37. Mills, D.K., Fitzgerald, K., Litchfield, C.D. and Gillevet, P.M. (2003) A comparison of DNA profiling techniques for monitoring nutrient impact on microbial community composition during bioremediation of petroleum-contaminated soils. Journal of Microbiological Methods 54, 57-74.
38. Mintie, A.T., Heichen, R.S., Cromack, K., Myrold, D.D. and Bottomley, P.J. (2003) Ammonia-oxidizing bacteria along meadow-to-forest transects in the Oregon cascade mountains. Applied and Environmental Microbiology 69, 3129-3136.
39. Moeseneder, M.M., Arrieta, J.M., Muyzer, G., Winter, C. and Herndl, G.J. (1999) Optimization of terminalrestriction fragment length polymorphism analysis for complex marine bacterioplankton communities and comparison with denaturing gradient gel electrophoresis. Applied and Environmental Microbiology 65, 3518-3525.
40. Moeseneder, M.M., Winter, C., Arrieta, J.M. and Herndl, G.J. (2001) Terminal-restriction fragment length polymorphism (T-RFLP) screening of a marine archaeal clone library to determine the different phylotypes. Journal of Microbiological Methods 44, 159-172.
41. Mummey, D.L. and Stahl, P.D. (2003) Spatial and temporal variability of bacterial 16S rDNA-based T-RFLP patterns derived from soil of two Wyoming grassland ecosystems. FEMS Microbiology Ecology 46, 113-120.
42. Muyzer, G., Dewaal, E.C. 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 ribosomal RNA. Applied and Environmental Microbiology 59, 695-700.
43. Nikolcheva, L.G., Cockshutt, A.M. and Barlocher, F. (2003) Determining diversity of freshwater fungi on decaying leaves: comparison of traditional and molecular approaches. Applied and Environmental Microbiology 69, 2548-2554.
44. Osborn, A.M., Moore, E.R.B. and Timmis, K.N. (2000) An evaluation of terminal-restriction fragment length polymorphism (T-RFLP) analysis for the study of microbial structure and dynamics. Environmental Microbiology 2, 39-50.
45. Osborne, C.A., Galic, M., Sangwan, P. and Janssen, P.H. (2005) PCR-generated artefact from 16S rRNA gene-specific primers. FEMS Microbiology Letters 248, 183-187.
46. Pace, N.R., Stahl, D.A., Lane, D.J. and Olsen, G.J. (1986) The analysis of microbial populations by ribosomal RNA sequences. Advances in Microbial Ecology 9, 1-55.
47. Scheid, D., Stubner, S. and Conrad, R. (2004) Identification of rice root associated nitrate, sulfate and ferric iron reducing bacteria during root decomposition. FEMS Microbiology Ecology 50, 101-110.
48. Schmitt-Wagner, D., Friedrich, M.W., Wagner, B. and Brune, A. (2003) Axial dynamics, stability, and interspecies similarity of bacterial community structure in the highly compartmentalized gut of soil-feeding termites (Cubitermes spp.). Applied and Environmental Microbiology 69, 6018-6024.
49. Sessitsch, A., Gyamfi, S., Stralis-Pavese, N., Weilharter, A. and Pfeifer, U. (2002) RNA isolation from soil for bacterial community and functional analysis: evaluation of different extraction and soil conservation protocols. Journal of Microbiological Methods 51, 171-179.
50. Tan, X.Y., Hurek, T. and Reinhold-Hurek, B. (2003) Effect of N-fertilization, plant genotype and environmental conditions on nifH gene pools in roots of rice. Environmental Microbiology 5, 1009-1015.
51. Torsvik, V., Goksoyr, J. and Daae, F.L. (1990) High diversity of DNA of soil bacteria. Applied and Environmental Microbiology 56, 782-787.
52. Wellington, E.M.H., Berry, A. and Krsek, M. (2003) Resolving functional diversity in relation to microbial community structure in soil: exploiting genomics and stable isotope probing. Current Opinion in Microbiology 6, 295-301.
53. Wintzingerode, F.V., Göbel, U.B. and Stackebrandt, E. (1997) Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiology Reviews 21, 213-229.
54. Wolsing, M. and Prieme, A. (2004) Observation of high seasonal variation in community structure of denitrifying bacteria in arable soil receiving artificial fertilizer and cattle manure by determining T-RFLP of nir gene fragments. FEMS Microbiology Ecology 48, 261-271.
55. Yeager, C.M., Kornosky, J.L., Housman, D.C., Grote, E.E., Belnap, J. and Kuske, C.R. (2004) Diazotrophic community structure and function in two successional stages of biological soil crusts from the Colorado plateau and Chihuahuan desert. Applied and Environmental Microbiology 70, 973-983.
56. Zak, D.R., Blackwood, C.B., and Waldrop, M.P. (2006) A molecular dawn for biogeochemistry. Trends in Ecology and Evolution 21, 288-295.