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Characterization Of Microbial Diversity By Determining Terminal Restriction Fragment Length Polymorphisms Of Genes Encoding 16S RRNA.

W. T. Liu, T. Marsh, H. Cheng, L. Forney
Published 1997 · Biology, Medicine
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A quantitative molecular technique was developed for rapid analysis of microbial community diversity in various environments. The technique employed PCR in which one of the two primers used was fluorescently labeled at the 5' end and was used to amplify a selected region of bacterial genes encoding 16S rRNA from total community DNA. The PCR product was digested with restriction enzymes, and the fluorescently labeled terminal restriction fragment was precisely measured by using an automated DNA sequencer. Computer-simulated analysis of terminal restriction fragment length polymorphisms (T-RFLP) for 1,002 eubacterial sequences showed that with proper selection of PCR primers and restriction enzymes, 686 sequences could be PCR amplified and classified into 233 unique terminal restriction fragment lengths or "ribotypes." Using T-RFLP, we were able to distinguish all bacterial strains in a model bacterial community, and the pattern was consistent with the predicted outcome. Analysis of complex bacterial communities with T-RFLP revealed high species diversity in activated sludge, bioreactor sludge, aquifer sand, and termite guts; as many as 72 unique ribotypes were found in these communities, with 36 ribotypes observed in the termite guts. The community T-RFLP patterns were numerically analyzed and hierarchically clustered. The pattern derived from termite guts was found to be distinctly different from the patterns derived from the other three communities. Overall, our results demonstrated that T-RFLP is a powerful tool for assessing the diversity of complex bacterial communities and for rapidly comparing the community structure and diversity of different ecosystems.
This paper references
Phylogenetic relationships ofThiomicrospira species and their identification in deep-sea hydrothermal vent samples by denaturing gradient gel electrophoresis of 16S rDNA fragments
G. Muyzer (1995)
Genetic diversity in Sargasso Sea bacterioplankton
S. Giovannoni (1990)
Development of an rRNA-targeted oligonucleotide probe specific for the genus Acinetobacter and its application for in situ monitoring in activated sludge.
Michael Wagner (1994)
High diversity in DNA of soil bacteria.
V. Torsvik (1990)
Bacterial community fingerprinting of amplified 16S and 16–23S ribosomal DNA gene sequences and restriction endonuclease analysis(ARDRA)
A. Massol-Deya (1995)
Identification of mycobacteria to the species level by automated restriction enzyme fragment length polymorphism analysis
Martin Ti (1995)
Remarkable archaeal diversity detected in a Yellowstone National Park hot spring environment.
S. Barns (1994)
Dependence on the taxon composition of clone libraries for PCR amplified, naturally occurring 16S rDNA, on the primer pair and the cloning system used
F. Rainey (2005)
Detection and analysis of two serotypes of ammonia-oxidizing bacteria in sewage plants by flow cytometry
A. Volsch (1990)
Degradation of toluene and m-xylene and transformation of o-xylene by denitrifying enrichment cultures.
P. J. Evans (1991)
Rapid Identification of Rhizobia by Restriction Fragment Length Polymorphism Analysis of PCR-Amplified 16S rRNA Genes.
G. Laguerre (1994)
Bacterial community structures of phosphate-removing and non-phosphate-removing activated sludges from sequencing batch reactors.
P. Bond (1995)
Phylogenetic identification and in situ detection of individual microbial cells without cultivation.
R. Amann (1995)
Anaerobic oxidation of ammonium is a biologically mediated process.
A. A. van de Graaf (1995)
Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing.
T. M. Schmidt (1991)
Molecular Cloning: A Laboratory
A. Press (1989)
Detection and enumeration of bacteria in soil by direct DNA extraction and polymerase chain reaction.
C. Picard (1992)
Profiling complex microbial populations by denaturing gradient gel electrophoresis analysis of polym
Gerard Muyzer (1993)
Molecular sequence accuracy: analysing imperfect data.
David J. States (1992)
Estimation of diversity and community structure through restriction fragment length polymorphism distribution analysis of bacterial 16S rRNA genes from a microbial mat at an active, hydrothermal vent system, Loihi Seamount, Hawaii.
C. Moyer (1994)
Molecular technique for rapid identification of mycobacteria.
E. Avaniss-Aghajani (1996)
Effect of genome size and rrn gene copy number on PCR amplification of 16S rRNA genes from a mixture of bacterial species.
V. Farrelly (1995)
16S rRNA sequences reveal numerous uncultured microorganisms in a natural community
D. M. Ward (1990)
A computer analysis of primer and probe hybridization potential with bacterial small-subunit rRNA sequences.
C. Brunk (1996)
Genetic Diversity through the Looking Glass: Effect of Enrichment Bias.
J. Dunbar (1997)
The Ribosomal Database Project (RDP)
B. Maidak (1996)
Recognition of chimeric small-subunit ribosomal DNAs composed of genes from uncultivated microorganisms.
E. D. Kopczynski (1994)
Phylogeny of not-yet-cultured spirochetes from termite guts.
B. Paster (1996)
Interference of humic acids and DNA extracted directly from soil in detection and transformation of recombinant DNA from bacteria and a yeast.
C. Tebbe (1993)
Potential risks of gene amplification by PCR as determined by 16S rDNA analysis of a mixed-culture of strict barophilic bacteria
W. Liesack (2006)
Nonradioactive method to study genetic profiles of natural bacterial communities by PCR-single-strand-conformation polymorphism.
D. Lee (1996)
Intraspecific variation in small-subunit rRNA sequences in GenBank: why single sequences may not adequately represent prokaryotic taxa.
R. Clayton (1995)
Evaluation of prokaryotic diversity by restrictase digestion of 16S rDNA directly amplified from hypersaline environments
A. Martínez-Murcia (1995)
Characterization of universal small-subunit rRNA hybridization probes for quantitative molecular microbial ecology studies.
D. Zheng (1996)
Differential amplification of rRNA genes by polymerase chain reaction.
A. L. Reysenbach (1992)

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Tara N. Jennings (2011)
Bacterial Communities on Macroalgae
Michael W Friedrich (2012)
Microbial communities in paddy fields in the Mekong delta of Vietnam
Thi Xuan Do (2012)
Abundance and diversity of mucosa-associated hydrogenotrophic microbes in the healthy human colon
Gerardo M. Nava (2012)
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James M. Waters (2012)
Microbiological and Chemical Aspects of Corrosion of Sheet Steel in the
Jonathan Robert Bostrom (2010)
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