Analysis of 16S rRNA gene variability in soil nitrifying bacteria of the genus Nitrosomonas

Abstract

The main goal of the work was to assess variability of 16S rRNA gene sequence within the nitrifying bacterial genus Nitrosomonas to find specific sequences for its detection. To achieve it, we had to find and to assess sequences that are highly conservative on the level of the genus and to find and to assess sequences variable on the level of genus but conserved on the level of species. In the SILVA database of ribosomal RNA sequences, 231 sequences of 16S rRNAs of bacteria of the genus Nitrosomonas were collected, of which were sorted 132 sequences by length from 1400 to 1541 (full-sized gene) nucleotides. We conducted an analysis of the taxon-specificity of sequences conserved at the genus level. More than a hundred full matches were found by the BLAST program in the nr database with other genera of the same and other families. So, in Nitrosomonas 16S rRNA gene are present some highly conservative regions, but they are not genus-specific due to high coincidence with other genera. Wherein, a variable region 994-1041 is highly species-specific for the species N. eutropha. Generally, the sequence of 994-1041 region of Nitrosomonas 16S rRNA genes tends to be clustered, being very close between some species.