Interpreting diversity of proteobacteria based on 16S rrna gene copy number
The application of the 16S rRNA gene diversity analysis has revealed the immense microbial diversity of our planet. At the same time, and after of more than two decades of using this methodology along with several important improvements and new techniques, there is still no universal golden rule on how to estimate prokaryotic diversity in a natural sample, as there is in macroecology. A general assumption during studies of prokaryotic diversity is that each found 16S rRNA gene found corresponds to one cell. However, in this paper it is shown that recent genomic data reveal that this is not the case for several bacterial phyla. Since the Proteobacteria, along with the Firmicutes, are the most abundant and diverse bacterial phyla, in this paper the average 16S rRNA gene copy number is presented at the sub-phylum (α-, β-, γ-, δ- and ε-Proteobacteria), order and family level of the Proteobacteria phylum. At the sub-phylum level the average 16S rRNA gene copy number varied between 2.1±1.3 and 5.8±2.8. Since the 16S rRNA gene copy number affects the relative abundance of each proteobacterial species/phylotype found in a clone library, and subsequently the estimation of diversity, the corrected relative abundances of the found proteobacterial phylotypes were estimated in 37 clone libraries from six different natural habitats. It is suggested, that at least in the cases where Proteobacteria consist 50-75% of the clone library, the corrected abundances should be used for diversity estimations. © 2011 Nova Science Publishers, Inc. All rights reserved.