Quantitative Community Fingerprinting Methods for Estimating the Abundance of Operational Taxonomic Units in Natural Microbial Communities

Abstract

Molecular fingerprinting techniques offer great promise for analyzing changes in microbial community structure, especially when dealing with large number of samples. However, a serious limitation has been the lack of quantification offered by such techniques since the relative abundances of the identified operational taxonomic units (OTUs) in the original samples are not measured. A quantitative fingerprinting approach designated "qfingerprinting" is proposed here. This method involves serial dilutions of the sample of interest and further systematic fingerprinting of all dilution series. Using the ultimate dilutions for which OTU are still PCR amplifiable and taking into account peak size inaccuracy and peak reproducibility, the relative abundance of each OTU is then simultaneously determined over a scale spanning several orders of magnitude. The approach was illustrated by using a quantitative version of automated ribosomal intergenic spacer analysis (ARISA), here called qARISA. After validating the concept with a synthetic mixture of known DNA targets, qfingerprinting was applied to well-studied marine sediment samples to examine specific changes in OTU abundance associated with sediment depth. The new strategy represents a major advance for the detailed quantitative description of specific OTUs within complex communities. Further ecological applications of the new strategy are also proposed.

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“…r-project.org/)); we chose 2 bp. To identify the best window frame (out of the 20 possible starting with a shift value of 0.1), we used the 'interactive binning algorithm' (Ramette, 2009). This algorithm binned the peaks for each frame, calculated the relative fluorescence intensity of each binned peak by dividing its height by the total peak height of the sample and omitted peaks with values o0.5% (considered as background).…”