Abstract
16S ribosomal RNA currently represents the most important target of study in bacterial ecology. Its use for the description of bacterial diversity is, however, limited by the presence of variable copy numbers in bacterial genomes and sequence variation within closely related taxa or within a genome. Here we use the information from sequenced bacterial genomes to explore the variability of 16S rRNA sequences and copy numbers at various taxonomic levels and apply it to estimate bacterial genome and DNA abundances. In total, 7,081 16S rRNA sequences were in silico extracted from 1,690 available bacterial genomes (1–15 per genome). While there are several phyla containing low 16S rRNA copy numbers, in certain taxa, e.g., the Firmicutes and Gammaproteobacteria, the variation is large. Genome sizes are more conserved at all tested taxonomic levels than 16S rRNA copy numbers. Only a minority of bacterial genomes harbors identical 16S rRNA gene copies, and sequence diversity increases with increasing copy numbers. While certain taxa harbor dissimilar 16S rRNA genes, others contain sequences common to multiple species. Sequence identity clusters (often termed operational taxonomic units) thus provide an imperfect representation of bacterial taxa of a certain phylogenetic rank. We have demonstrated that the information on 16S rRNA copy numbers and genome sizes of genome-sequenced bacteria may be used as an estimate for the closest related taxon in an environmental dataset to calculate alternative estimates of the relative abundance of individual bacterial taxa in environmental samples. Using an example from forest soil, this procedure would increase the abundance estimates of Acidobacteria and decrease these of Firmicutes. Using the currently available information, alternative estimates of bacterial community composition may be obtained in this way if the variation of 16S rRNA copy numbers among bacteria is considered.
Highlights
RRNA sequences and especially the 16S rRNA represent the most important current targets of study in bacterial evolution and ecology, including the determination of phylogenetic relationships among taxa, the exploration of bacterial diversity in the environment and the quantification of the relative abundance of taxa of various ranks [1]
In silico analysis of sequenced bacterial genomes Of a total of 1,690 available bacterial genomes that belonged to 909 identified bacterial species and 454 genera, most available genomes belonged to the Proteobacteria
Some 15% of bacterial genomes contain only a single 16S rRNA copy, it seems that most bacterial phyla may contain bacteria with more than one copy and one half of the currently analyzed genomes harbor five or more copies. 16S rRNA copy numbers have been found to show both narrow and wide variation within the tested bacterial genera [22,23]
Summary
RRNA sequences and especially the 16S rRNA represent the most important current targets of study in bacterial evolution and ecology, including the determination of phylogenetic relationships among taxa, the exploration of bacterial diversity in the environment and the quantification of the relative abundance of taxa of various ranks [1]. The gene is universally distributed, allowing the analysis of phylogenetic relationships among distant taxa. 16S rRNA is still subject to variation, especially in certain variable regions. While the presence of variable regions allows sufficient diversification to provide a tool for classification, the presence of conserved regions enabled the design of suitable PCR primers or hybridization probes for various taxa at different taxonomic levels ranging from individual strains to whole phyla [3]
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