Quantitative comparisons of 16S rRNA gene sequence libraries from environmental samples - PubMed (original) (raw)

Comparative Study

Quantitative comparisons of 16S rRNA gene sequence libraries from environmental samples

D R Singleton et al. Appl Environ Microbiol. 2001 Sep.

Abstract

To determine the significance of differences between clonal libraries of environmental rRNA gene sequences, differences between homologous coverage curves, CX(D), and heterologous coverage curves, CXY(D), were calculated by a Cramér-von Mises-type statistic and compared by a Monte Carlo test procedure. This method successfully distinguished rRNA gene sequence libraries from soil and bioreactors and correctly failed to find differences between libraries of the same composition.

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Figures

FIG. 1

FIG. 1

Results of selected LIBSHUFF comparisons. Homologous (○) and heterologous (●) coverage curves for 16S rRNA gene sequence libraries from environmental samples are shown. Solid lines indicate the value of (CX − CXY)2 for the original samples at each value of D. D is equal the Jukes-Cantor evolutionary distance determined by the DNADIST program of PHYLIP (3). Broken lines indicate the 950th value (or P = 0.05) of (CX − CXY)2 for the randomized samples. (A) Comparison of clones from grassland soils with odd (X) and even (Y) accession numbers. (B) Comparison of bioreactor clones SBR1 (X) and grassland soil SL clones (Y). (C) Comparison of C0 (X) and S0 (Y) clones from arid soils.

FIG. 2

FIG. 2

Effect of sample size on the discrimination of libraries. A comparison of the SL library from grassland soil (Y; n = variable) to the bioreactor library SBR1 (X; n = 97) (●) and a comparison of the SBR1 (Y; n = variable) library to the SL (X; n = 137) library (○) shown. Each point represents an average of 10 replicates, and the error bars are 1 standard deviation. The broken line indicates P = 0.05.

References

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