Rhizobia Isolated from the Relict Legume Vavilovia formosa Represent a Genetically Specific Group within Rhizobium leguminosarum biovar viciae

Abstract

Twenty-two rhizobia strains isolated from three distinct populations (North Ossetia, Dagestan, and Armenia) of a relict legume Vavilovia formosa were analysed to determine their position within Rhizobium leguminosarum biovar viciae (Rlv). These bacteria are described as symbionts of four plant genera Pisum, Vicia, Lathyrus, and Lens from the Fabeae tribe, of which Vavilovia is considered to be closest to its last common ancestor (LCA). In contrast to biovar viciae, bacteria from Rhizobium leguminosarum biovar trifolii (Rlt) inoculate plants from the Trifolieae tribe. Comparison of house-keeping (hkg: 16S rRNA, glnII, gltA, and dnaK) and symbiotic (sym: nodA, nodC, nodD, and nif H) genes of the symbionts of V. formosa with those of other Rlv and Rlt strains reveals a significant group separation, which was most pronounced for sym genes. A remarkable feature of the strains isolated from V. formosa was the presence of the nodX gene, which was commonly found in Rlv strains isolated from Afghanistan pea genotypes. Tube testing of different strains on nine plant species, including all genera from the Fabeae tribe, demonstrated that the strains from V. formosa nodulated the same cross inoculation group as the other Rlv strains. Comparison of nucleotide similarity in sym genes suggested that their diversification within sym-biotypes of Rlv was elicited by host plants. Contrariwise, that of hkg genes could be caused by either local adaptation to soil niches or by genetic drift. Long-term ecological isolation, genetic separation, and the ancestral position of V. formosa suggested that symbionts of V. formosa could be responsible for preserving ancestral genotypes of the Rlv biovar. may be traced using specialised symbiotic (sym) genes representing the accessory parts of bacterial genomes, which differ in their natural histories from housekeeping genes (hkg) representing the core parts of genomes [4]. As a result of co-evolutionary processes, symbiosis is formed between tightly co-adapted cross-inoculation groups of rhizobia and legumes, and their coevolution is directed by a set of symbiosis-specific genes from each partner [5][6][7]. In some rhizobia, sym genes are more susceptible to autonomous horizontal gene transfer than hkg genes, because they are located on plasmids-mobile elements of the genome [3]. This results in an intensive recombination of host specific and chromosomal markers [8]. For example, Rhizobium leguminosarum is composed of two biovars, which have diverged based on their plasmid-encoded host ranges [9]. Biovar viciae (Rlv) nodulates legumes from the Fabeae tribe, while biovar trifolii (Rlt) nodulates clovers from the Trifolieae tribe; however, they show a conservative chromosomal arrangement of hkg markers (Figure 1).Even so, divergent evolution of rhizobia is not restricted to sym genes. Application of the average nucleotide identity (ANI) method has demonstrated that a local R. leguminosarum population could be separated into five genomic species, differing in their hkg genes, representing their cor...

Search for Ancestral Features in Genomes of Rhizobium leguminosarum bv. viciae Strains Isolated from the Relict Legume Vavilovia formosa

“…Specifically, primitive "Afghan" pea lines represent the evolutionary precursors for cultural (European) lines [18], which underwent the prolonged domestication and breeding histories and probably represent a "derived" P. sativum germplasm. The remarkable feature of vavilovia's symbionts is the uniform presence of the gene nodX [19,20], which is essential for nodulation of "Afghan" pea lines, but it is not required for European pea nodulation [21]. The tube test showed that vavilovia belongs to the same cross-inoculation group as the pea, vetch, lentil, and vetchling [19].…”

“…The remarkable feature of vavilovia's symbionts is the uniform presence of the gene nodX [19,20], which is essential for nodulation of "Afghan" pea lines, but it is not required for European pea nodulation [21]. The tube test showed that vavilovia belongs to the same cross-inoculation group as the pea, vetch, lentil, and vetchling [19]. their extra-chromosomal (on large plasmids or on chromids) location typical for the Rhizobiaceae species [14].…”

“…The remarkable feature of vavilovia's symbionts is the uniform presence of the gene nodX [19,20], which is essential for nodulation of "Afghan" pea lines, but it is not required for European pea nodulation [21]. The tube test showed that vavilovia belongs to the same cross-inoculation group as the pea, vetch, lentil, and vetchling [19]. Previously, Kimeklis et al [19,22] showed that at the gene level (especially in sym genes) rhizobia isolated from Vavilovia nodules represent a well-defined group within R. leguminosarum bv.…”

“…viciae, which is genetically different from the strains isolated from Pisum and Vicia species. Considering the presumed ancestral status of vavilovia, its proximity to the LCA of the Fabeae tribe, and its long-term ecological isolation of vavilovia's symbionts [19], we can expect that vavilovia could also support the ancestral symbionts closely related to the LCA of R. leguminosarum bv. viciae.…”

“…viciae required to probe this hypothesis represented the priorities of our research. Previously, Kimeklis et al [19,22] showed that at the gene level (especially in sym genes) rhizobia isolated from Vavilovia nodules represent a well-defined group within R. leguminosarum bv. viciae, which is genetically different from the strains isolated from Pisum and Vicia species.…”