Intragenomic diversity of Rhizobium leguminosarum bv. trifolii clover nodule isolates

Abstract

BackgroundSoil bacteria from the genus Rhizobium are characterized by a complex genomic architecture comprising chromosome and large plasmids. Genes responsible for symbiotic interactions with legumes are usually located on one of the plasmids, named the symbiotic plasmid (pSym). The plasmids have a great impact not only on the metabolic potential of rhizobia but also underlie genome rearrangements and plasticity.ResultsHere, we analyzed the distribution and sequence variability of markers located on chromosomes and extrachromosomal replicons of Rhizobium leguminosarum bv. trifolii strains originating from nodules of clover grown in the same site in cultivated soil. First, on the basis of sequence similarity of repA and repC replication genes to the respective counterparts of chromids reported in R. leguminosarum bv. viciae 3841 and R. etli CFN42, chromid-like replicons were distinguished from the pool of plasmids of the nodule isolates studied. Next, variability of the gene content was analyzed in the different genome compartments, i.e., the chromosome, chromid-like and 'other plasmids'. The stable and unstable chromosomal and plasmid genes were detected on the basis of hybridization data. Displacement of a few unstable genes between the chromosome, chromid-like and 'other plasmids', as well as loss of some markers was observed in the sampled strains. Analyses of chosen gene sequences allowed estimation of the degree of their adaptation to the three genome compartments as well as to the host.ConclusionsOur results showed that differences in distribution and sequence divergence of plasmid and chromosomal genes can be detected even within a small group of clover nodule isolates recovered from clovers grown at the same site. Substantial divergence of genome organization could be detected especially taking into account the content of extrachromosomal DNA. Despite the high variability concerning the number and size of plasmids among the studied strains, conservation of the location as well as dynamic distribution of the individual genes (especially replication genes) of a particular genome compartment were demonstrated. The sequence divergence of particular genes may be affected by their location in the given genome compartment. The 'other plasmid' genes are less adapted to the host genome than the chromosome and chromid-like genes.

Rhizobial communities in symbiosis with legumes: genetic diversity, competition and interactions with host plants

“…They were maintained in syntenic blocks and revealed high level of nucleotide identity of homologous segments, also in the case of symbiosis-related genes located on pSyms [30]. Thus, the architecture of rhizobial genomes and the classification of replicons as plasmids/chromids or symbiotic/nonsymbiotic plasmids seem to be of minor importance [30,32].…”

Rhizobial plasmids — replication, structure and biological role

“…Most of Rlt strains had a large (>1 Mb), extrachromosomal replicon. The genes located on individual plasmids differed in their adaptation to the host genome, indicating that the putative evolutionary acquisition of these plasmids occurred at different times [94]. Furthermore, it was found that the Rlt nodule strains belonging to defined genetic groups and varying in the plasmid profile differ also in metabolic capabilities and symbiotic effectiveness with clover [95].…”

“…Conservation of gene location especially those of chromid-like replicons, was reported. The 'other plasmids' genes were less adapted to the host genome than the chromosome and chromid-like genes [94]. The properties of chromids, which may be sometimes inconclusive, raise the question about the robustness of this concept at all.…”

“…Among Rlt isolates from root nodules of clover plants growing at the same site, substantial divergence of their genome organization, especially as regards the plasmid DNA content, was demonstrated [94]. The strains harbored from 3 to 6 plasmids (mostly equipped with repABC type replication system), whose size ranged approximately from 150 kb to 1380 kb.…”

“…The accessory component is significant to the cell, however, very variable, and has an apparently mosaic structure. In some species, such as R. leguminosarum, the accessory component may comprise up to 35-45% of the total genome [6,94]. However, accessory genes could also be found in the chromosome as chromosomal islands.…”