The identification of bacteria based on phenotypic characteristics is generally
not accurate because several species are difficult to be distinguished phenotypically. In
case of rhizobia, the current classification is mainly based on DNA sequences
[especially a DNA sequence encoding small subunit ribosomal RNA (16S rDNA)],
DNA homologies, phylogenetic relationships and the locations of symbiotic genes. The
16S rDNA is very useful for estimating the evolutionary relationships and identifying
bacteria. The most dramatic progress in the construction of microbial phylogeny is
based on sequence analysis of 16S rDNA. The 16S rDNA sequences mainly support the
proposal of novel genera and species of rhizobia. In some cases, several genera are
identical in 16S rDNA sequence analysis. The other regions, such as large subunit
ribosomal RNA gene (23S rDNA) as well as intergenic spacer between 16S and 23S
rRNA sequences (16S-23S IGS), are suitable alternatives for classification and
identification purposes. Multilocus sequence analysis (MLSA), which employs a set of
nucleotide sequences including 16S rDNA, house keeping genes and symbiotic genes,
has the greater potential for rhizobial classification. Sequence analysis is currently the
most promising method for identification of rhizobial genera.
Keywords: Dendrogram, Genotypic diversity, Housekeeping gene, Intergenic
spacer between 16S and 23S rRNA sequences (16S-23S IGS), Multilocus
sequence analysis (MLSA), Multilocus sequence typing (MLST), Phylogenetic
tree, Rhizobia, Small subunit ribosomal RNA (16S rDNA), Symbiotic gene.
