Progress and perspective of systematics of rhizobia

Abstract:

Originally, rhizobia refer to the legume-nodulating symbiotic Gram-negative bacteria, belonging to Class Alpha- and Beta-proteobacteria in Phylum Proteobacteria. Recently, the developments in systematic technology of bacteria and the studies of more novel isolates have greatly changed the taxonomy of rhizobia. In the newest classification, some species in the genus Rhizobium within Class Alphaproteobacteria have been reclassified: several species were maintained in Rhizobium, while two novel genera, Pararhizobium and Neorhizobium, were proposed. In addition, two genera Agrobacterium and Allorhizobium were restored and re-amended. Both symbiotic and nonsymbiotic bacteria were included in these genera. Though the name of Sinorhizobium in Class Alphaproteobacteria has been replaced by Ensifer, the former is still being used widely especially in the studying of symbiotic bacteria. In relation to the systematic methodology, the most important development in the last decade is that whole genomic sequencing and average nucleotide identity (ANI) have been applied to replace the traditional DNA relatedness. Because of the higher conservation of 16S rRNA gene sequence in rhizobial phylogeny, it is usually used in determining the phylogenetic position in the level of genus. Combination of multilocus sequence analysis (MLSA) and whole genome sequencing ANI is now the “Gold Standard” for the definition of bacterial genospecies. Together with the rapid determination of phenotypic features, including biochemical characters, fatty acids and quinones, the systematics of rhizobia developed rapidly in the last decade. In future, the classification system of rhizobia based upon the sequence analysis of whole genome will be more stable, while novel species in some defined genera or corresponding to some new genera will be described when more nodule isolates are studies. Furthermore, the finding of symbiotic promiscuity between Sophora flavescens, a kind of medicinal legume, and various rhizobia harboring distinct nodulation genes, completely broke the knowledge of symbiotic specificity, facilitating the reconsideration of the symbiotic relationship between legumes and rhizobia.