The Variability of the 16S rRNA Gene in Bacterial Genomes and Its Consequences for Bacterial Community Analyses

By Tomás Vetrovský, Petr Baldrian. PLoS ONE, 2013

1,127 citations recorded by the source corpus.

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.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/be420b316493c8d0fe72e641103057754ec2cf8b

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Citations in the corpus

Current overview on the study of bacteria in the rhizosphere by modern molecular techniques: a mini‒review (2015, background): “The numbers of rRNA gene copies are related to the life strategy of bacteria; taxa with low copy numbers and inhabit low nutrient environment (oligotrophic) (Větrovský and Baldrian, 2013; Kang et al., 2010).”
Characterization of the Gut Microbiome Using 16S or Shotgun Metagenomics (2016, background): “Moreover, reduced diversity and/or imbalances in the gut microbiome have been associated with a variety of phenotypes, including obesity (Turnbaugh et al., 2009; Turnbaugh and Gordon, 2009), inflammatory bowel diseases (IBD) (Knights et al., 2013; Huttenhower et al., 2014b; Kostic et al., 2014;…”
Effects of rising CO₂ on the harmful cyanobacterium Microcystis (2016, background): “However, this is complicated by the fact that bacterial genomes often have multiple copies of this gene, and the different copies are not always 100% identical in their DNA sequence (Větrovský and Baldrian, 2013).”
Forest Soil Bacteria: Diversity, Involvement in Ecosystem Processes, and Response to Global Change (2017, background): “where both the content of organic matter and the allocation of C by tree roots are high (43, 103).”
A comparative and functional genomics analysis of the genus Romboutsia provides insight into adaptation to an intestinal lifestyle (2019, background): “Sequence divergence in the 16S 263 rRNA gene is not uncommon within individual prokaryotic genomes (51, 52).”
rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development (2014, background): “Divergence of 16S sequences within Thermoanaerobacterium strains has been described before (18).”