Terminal restriction fragment length polymorphism for soil microbial community fingerprinting

Soil Science Society of America Journal

Volumn 75, Issue 1, 2011, Pages 102-111

  Aiken, Jane T ^a  

^a UNIVERSITY OF WESTERN SYDNEY   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

16S RRNA GENE; BACTERIAL COMMUNITY; BASE PAIRS; CAPILLARY SYSTEM; CHAIN REACTION; COMMUNITY COMPOSITION; COMMUNITY VARIABILITY; GENESCAN; GENETIC ANALYSIS; HALF-WIDTH; LINEAR RELATIONSHIPS; PEAK DETECTION; POPULATION STRUCTURES; SIZING ACCURACY; SIZING ALGORITHMS; SOIL COMMUNITY; SOIL MICROBIAL COMMUNITY; SOIL SCIENCE; SPECIES RICHNESS; SPLIT PEAK; STANDARD PROTOCOLS; TECHNICAL ASPECTS; TERMINAL RESTRICTION FRAGMENT LENGTH POLYMORPHISMS;

ECOLOGY; FLUORESCENCE; FORESTRY; POLYMORPHISM; RNA; SOILS; STANDARDS;

POPULATION STATISTICS;

ABUNDANCE; ACCURACY ASSESSMENT; ALGORITHM; BACTERIUM; COMMUNITY COMPOSITION; FLUORESCENCE; FRAGMENTATION; GEL; GENETIC ANALYSIS; LINEARITY; POLYMERASE CHAIN REACTION; POLYMORPHISM; POPULATION STRUCTURE; RESOLUTION; SOFTWARE; SOIL MICROORGANISM; SPECIES RICHNESS;

BACTERIA (MICROORGANISMS);

EID: 78751505512     PISSN: 03615995     EISSN: None     Source Type: Journal    
DOI: 10.2136/sssaj2008.0088     Document Type: Article

References (33)

1. Aiken, J. 2006. A soil microbial response to urban wastewater application: Bacterial communities and soil salinity. Ph.D. diss. Univ. of Western Sydney, Penrith South DC, NSW, Australia.
2. Applied Biosystems. 1997. GeneScan reference guide: Chemistry reference for the ABI Prism 377 and ABI 373 DNA sequencers. Applied Biosystems Inc., Foster City, CA.
3. Bent, S.J., J.D. Peirson, and L.J. Forney. 2007. Measuring species richness based on microbial community fingerprints: The emperor has no clothes. Appl. Environ. Microbiol. 73: 2399-2401.
4. Blackwood, C.B., D. Hudleston, D.R. Zak, and J.S. Buyer. 2007. Interpreting ecological diversity indices applied to terminal restriction fragment length polymorphism data: Insights from simulated microbial communities. Appl. Environ. Microbiol. 73: 5276-5283.
5. Clement, B.G., L.E. Kehl, K.L. DeBord, and C.L. Kitts. 1998. Terminal restriction fragment patterns (TRFPs), a rapid, PCR-based method for the comparison of complex bacterial communities J. Microbiol. Methods 31: 135-142.
6. Culman, S.W., H.G. Gauch, C.B. Blackwood, and J.E. Thies. 2008. Analysis of T-RFLP data using analysis of variance and ordination methods: A comparative study. J. Microbiol. Methods 75: 55-63.
7. Dunbar, J., S. Takala, S.M. Barns, J.A. Davis, and C.R. Kuske. 1999. Levels of bacterial community diversity in four arid soils compared by cultivation and 16S rRNA gene cloning. Appl. Environ. Microbiol. 65: 1662-1669.
8. Dunbar, J., L.O. Ticknor, and C.R. Kuske. 2000. Assessment of microbial diversity in four southwestern United States soils by 16S rRNA gene terminal restriction fragment analysis. Appl. Environ. Microbiol. 66: 2943-2950.
9. Dunbar, J., L.O. Ticknor, and C.R. Kuske. 2001. Phylogenetic specificity and reproducibility and new method for analysis of terminal restriction fragment profiles of 16S rRNA genes from bacterial communities. Appl. Environ. Microbiol. 67: 190-197.
10. Fey, A., and R. Conrad. 2000. Effect of temperature on carbon and electron flow and on the archaeal community in methanogenic rice field soil. Appl. Environ. Microbiol. 66: 4790-4797.
11. Gonzalez, J.M., R. Simo, R. Massana, J.S. Covert, E.O. Casamayor, C. PedrosAlio, and M.A. Moran. 2000. Bacterial community structure associated with a dimethylsulfoniopropionate-producing North Atlantic algal bloom. Appl. Environ. Microbiol. 66: 4237-4246.
12. Grant, A., and L.A. Ogilvie. 2003. Terminal restriction fragment length polymorphism data analysis. Appl. Environ. Microbiol. 69: 6342-6343.
13. Heath, L.E., and V.A. Saunders. 2006. Assessing the potential for bacterial DNA profiling for forensic soil comparisons. J. Forensic Sci. 51: 1062-1068.
14. Kaplan, C.W., J.C Astaire, M.E. Sanders, B.S. Reddy, and C.L. Kitts. 2001. 16S ribosomal DNA terminal restriction fragment pattern analysis of bacterial communities in feces of rats fed Lactobacillus acidophilus NCFM. Appl. Environ. Microbiol. 67: 1935-1939.
15. Kitts, C.L. 2001. Terminal restriction fragment patterns: A tool for comparing microbial communities and assessing community dynamics. Curr. Issues Intest. Microbiol. 2: 17-25.
16. Liesack, W., and P.F. Dunfield. 2004. T-RFLP analysis: A rapid fingerprinting method for studying diversity, structure, and dynamics of microbial communities, p. 23-37. In J.F.T. Spencer and A.L. Ragout de Spencer (ed.) Environmental microbiology: Methods and protocols. Methods in Biotechnol. 16. Humana Press, Totowa, NJ.
17. Liu, W., T.L. Marsh, H. Cheng, and L.J. Forney. 1997. Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Appl. Environ. Microbiol. 63: 4516-4522.
18. Liu, W., T.L. Marsh, and L.J. Forney. 1998. Determination of the microbial diversity of anaerobic-aerobic activated sludge by a novel molecular biological technique. Water Sci. Technol. 37: 417-422.
19. Lüdemann, H., I. Arth, and W. Liesack. 2000. Spatial changes in the bacterial community structure along a vertical oxygen gradient in flooded paddy soil cores. Appl. Environ. Microbiol. 66: 754-762.
20. Lukow, T., P.F. Dunfield, and W. Liesack. 2000. 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 Microbiol. Ecol. 32: 241-247.
21. Marsh, T.L. 1999. Terminal restriction fragment length polymorphism (T-RFLP): An emerging method for characterizing diversity among homologous populations of amplification products. Curr. Opin. Microbiol. 2: 323-327.
22. Moeseneder, M.M., J.M. Arrieta, G. Muyzer, C. Winter, and G.J. Herndl. 1999. Optimization of terminal-restriction fragment length polymorphism analysis for complex marine bacterioplankton communities and comparison with denaturing gradient gel electrophoresis. Appl. Environ. Microbiol. 65: 3518-3525.
23. Nagashima, K., T. Hisada, M. Sato, and J. Mochizuki. 2003. Application of new primer-enzyme combinations to terminal restriction fragment length polymorphism profiling of bacterial populations inhuman feces. Appl. Environ. Microbiol. 69: 1251-1262.
24. Osborn, A.M., E.R.B. Moore, and K.N. Timmis. 2000. An evaluation of terminal-restriction fragment length polymorphism (T-RFLP) analysis for the study of microbial community structure and dynamics. Environ. Microbiol. 2: 39-50.
25. Osborne, C.A., G.N. Rees, Y. Bernstein, and P.H. Janssen. 2006. New threshold and confidence estimates for terminal restriction fragment length polymorphism analysis of complex bacterial communities. Appl. Environ. Microbiol. 72: 1270-1278.
26. Sessitsch, A., A. Weilharter, M.H. Gerzabek, H. Kirchmann, and E. Kandeler. 2001. Microbial population structures in soil particle size fractions of a longterm fertilizer field experiment. Appl. Environ. Microbiol. 67: 4215-4224.
27. Singh, B.K., S. Munro, E. Reid, B. Ord, J.M. Potts, E. Patterson, and P. Millard. 2006. Investigating microbial community structure in soils by physiological, biochemical and molecular fingerprinting methods. Eur. J. Soil Sci. 57: 72-82.
28. Southern, E.M. 1979. Measurement of DNA length by gel electrophoresis. Anal. Biochem. 100: 319-323.
29. Speksnijder, A.G.C.L., G.A. Kowalchuk, S. De Jong, E. Kline, J.R. Stephen, and H.J. Laanbroek. 2001. Microvariation artifacts introduced by PCR and cloning of closely related 16S rRNA sequences. Appl. Environ. MicrobioL 67: 469-472.
30. Suzuki, M., M.S. Rappé, and S.J. Giovannoni. 1998. Kinetic bias in estimates of coastal picoplankton community structure obtained by measurements of small-subunit rRNA gene PCR amplicon length heterogeneity. Appl. Environ. Microbiol. 64: 4522-4529.
31. Thies, J. 2007. Soil microbial community analysis using terminal restriction fragment length polymorphisms. Soil Sci. Soc. Am J. 71: 579-591.
32. Trotha, R., U. Reichl, F.L. Thies, D. Sperling, W. König, and B. König. 2002. Adaption of a fragment analysis technique to an automated high-throughput multicapillary electrophoresis device for the precise qualitative and quantitative characterization of microbial communities. Electrophoresis 23: 1070-1079.
33. Ulrich, A., and R. Becker. 2006. Soil parent material is a key determinant of the bacterial community structure in arable soils. FEMS Microbiol. Ecol. 56: 430-433.