16S rRNA Gene Sequence Analysis of Drinking Water Using RNA and DNA Extracts as Targets for Clone Library Development |
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Authors: | Randy P Revetta Robin S Matlib Jorge W Santo Domingo |
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Institution: | (1) Office of Research and Development, U.S. Environmental Protection Agency, 26 West Martin Luther King Drive, Cincinnati, OH 45268, USA;(2) Dynamac Corp, 26 West Martin Luther King Drive, Cincinnati, OH 45268, USA; |
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Abstract: | The bacterial composition of chlorinated drinking water was analyzed using 16S rRNA gene clone libraries derived from DNA
extracts of 12 samples and compared to clone libraries previously generated using RNA extracts from the same samples. Phylogenetic
analysis of 761 DNA-based clone sequences showed that unclassified bacteria were the most abundant group, representing nearly
62% of all DNA sequences analyzed. Other phylogenetic groups identified included Proteobacteria (20%), Actinobacteria (9%),
Cyanobacteria (4%), and Bacteroidetes (2%). The composition of RNA-based libraries (1122 sequences) was similar to the DNA-based
libraries with a few notable exceptions: Proteobacteria were more dominant in the RNA clone libraries (i.e., 35% RNA; 20%
DNA). Differences in the Proteobacteria composition were also observed; alpha-Proteobacteria was 22 times more abundant in
the RNA-based clones while beta-Proteobacteria was eight times more abundant in the DNA libraries. Nearly twice as many DNA
operational taxonomic units (OTUs) than RNA OTUs were observed at distance 0.03 (101 DNA; 53 RNA). Twenty-four OTUs were shared
between all RNA- and DNA-based libraries (OTU0.03) representing only 18% of the total OTUs, but 81% (1527/1883) of all sequences. Such differences between clone libraries
demonstrate the necessity of generating both RNA- and DNA-derived clone libraries to compare these two different molecular
approaches for community analyses. |
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