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The goat's rue rhizobia (Neorhizobium galegae) represent a convenient model to study the evolution and speciation of symbiotic bacteria. This rhizobial species is composed of two biovars (bv. orientalis and bv. officinalis), which form N2-fixing nodules with certain species of goat's rue (Galega orientalis and G. officinalis). The cross-inoculation between them results in the formation of nodules unable to fix nitrogen. On the basis of the data on the whole-genome sequencing, we studied the nucleotide polymorphism of 11 N. galegae strains isolated from the North Caucasus ecosystems, where G. orientalis has higher diversity than G. officinalis. The low level of differences in the polymorphism within the group of the sym genes in comparison with the nonsymbiotic genes can be associated with the active participation of host plants in the evolution of rhizobia. The intragenic polymorphism of bv. orientalis proved to be significantly higher than that of bv. officinalis. The level of polymorphism of nonsymbiotic genes was lower than that of the symbiotic genes, which are functionally more homogeneous. The divergence of the nitrogen fixation genes (nif/fix) is more pronounced than that of the nodule formation genes (nod) in the N. galegae biovars. These facts indicate the leading role of the host-specific nitrogen fixation in the evolution of the studied rizhobial species. [ABSTRACT FROM AUTHOR]

For the first time, a comparative study of the influence of two species of earthworms (Aporrectodea caliginosa and Lumbricus terrestris) on the composition of the prokaryotic complex of Umbric Albeluvisols was carried out using the methods of metagenomics. Prokaryotes in the soil and casts were represented mostly by Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Gemmatimonadetes, Planctomycetes, Proteobacteria, and Verrucomicrobia phyla. The passage of soil through the earthworm intestines changed significantly the abundance of some taxa in the soil prokaryotic block, but not general indicators of biodiversity. In the casts of earthworms of both species, a decrease in the abundance of Acidobacteria and Gemmatimonadetes phyla, including predominantly oligotrophic bacteria, was observed. Casts of L. terrestris were characterized by an increase in the proportion of Actinobacteria and Firmicutes phyla, which were mainly represented by copiotrophs and hydrolytic bacteria. In addition, the abundance of Clostridiaceae anaerobic bacteria and Flavobacterium capable of nitrate respiration increased in the casts of L. terrestris, which could be due to the appearance of anaerobic conditions in the biogenically transformed soil. Generally, the changes in the taxonomic structure of prokaryotes in the soil treated by L. terrestris were greater than those in the soil treated by A. caliginosa. These differences among casts of different earthworm species could be due to the specificity of functioning of their digestive systems adapted to transformation of different food sources. [ABSTRACT FROM AUTHOR]

Compared to free-living relatives, bacterial symbionts of plants exhibit higher rates of population diversification (microevolution), as well as of speciation and formation of super-species taxa (macroevolution). Analysis of rhizobia, the N2-fixing symbionts of leguminous plants, suggests that both evolutionary modes are determined by the hosts, which have mutagenic and recombinogenic effects on their microsymbionts, apart from activating the selective processes that determine the fate of newly emerged genotypes in their populations. Migration induced by leguminous plants plays a key role in the evolution of rhizobia, including: (1) joint movement of the symbionts and their hosts into new ecological zones and (2) local circulation of the symbionts in plant‒soil systems. In the first case, allopatric speciation occurs in rhizobia due to transfer of the symbiotically specialized (sym) genes from the introduced strains into local bacteria, which are transformed into novel symbionts. In the second case, a sympatric divergence of Rhizobium populations occurs, resulting in formation of intraspecies taxa (biovars and symbiovars) contrasting in their host ranges. In the evolutionarily advanced rhizobia, Rhizobium leguminosarum and Neorhizobium galegae interacting with galegoid legumes (tribes Fabeae, Galegae, and Trifolieae), these processes are associated with diversification of the sym genes representing the accessory genome parts due to the interaction between bacteria and the hosts differing in their symbiotic affinities. In parallel, formation of new cryptic (genomic) species was revealed in local rhizobia populations, which is associated with divergence of the core genome parts. It may be caused either by genetic drift or by selection for resistance against local edaphic stresses, which in combination with disruptive selection can sufficiently enhance the rhizobia diversity and change the structures of their pangenomes. [ABSTRACT FROM AUTHOR]

Comparative sequence analysis of symbiotic genes (nodA, nodC, nodD, nifH), which are elements of accessory component of the rhizobial genome, demonstrated that the strains of Rhizobium leguminosarum bv. viciae, isolated from the nodules of a relic legume, Vavilovia formosa, the closest relative of hypothetical common ancestor of the tribe Fabeae, represented a group separated from the strains of R. leguminosarum bv. viciae, isolated from other representatives of this tribe (Vicia, Lathyrus, Pisum, Lens). No isolation was observed relative to the genes representing the core component of the rhizobial genome (16S rDNA, ITS, glnII) or relative to host specificity of the rhizobia. The data obtained suggest that sequence divergence of symbiotic genes marks the initial stage of sympatric speciation, which can be classified as the isolation of the relic “vaviloviae” symbiotype, a possible evolutionary precursor of the “viciae” biotype. [ABSTRACT FROM AUTHOR]