Population Genomics of the Facultatively Mutualistic Bacteria Sinorhizobium meliloti and S. medicae

Abstract

The symbiosis between rhizobial bacteria and legume plants has served as a model for investigating the genetics of nitrogen fixation and the evolution of facultative mutualism. We used deep sequence coverage (>100×) to characterize genomic diversity at the nucleotide level among 12 Sinorhizobium medicae and 32 S. meliloti strains. Although these species are closely related and share host plants, based on the ratio of shared polymorphisms to fixed differences we found that horizontal gene transfer (HGT) between these species was confined almost exclusively to plasmid genes. Three multi-genic regions that show the strongest evidence of HGT harbor genes directly involved in establishing or maintaining the mutualism with host plants. In both species, nucleotide diversity is 1.5–2.5 times greater on the plasmids than chromosomes. Interestingly, nucleotide diversity in S. meliloti but not S. medicae is highly structured along the chromosome – with mean diversity (θπ) on one half of the chromosome five times greater than mean diversity on the other half. Based on the ratio of plasmid to chromosome diversity, this appears to be due to severely reduced diversity on the chromosome half with less diversity, which is consistent with extensive hitchhiking along with a selective sweep. Frequency-spectrum based tests identified 82 genes with a signature of adaptive evolution in one species or another but none of the genes were identified in both species. Based upon available functional information, several genes identified as targets of selection are likely to alter the symbiosis with the host plant, making them attractive targets for further functional characterization.

The tRNA arg Gene and engA Are Essential Genes on the 1.7-Mb pSymB Megaplasmid of Sinorhizobium meliloti and Were Translocated Together from the Chromosome in an Ancestral Strain

“…The Sinorhizobium genus is expanding as new root nodule isolates are identified from diverse leguminous plants and geographic regions (14,43,56,(77)(78)(79). It will be interesting to see how the chromosome or megaplasmid location of the engA and tRNA arg genes segregates in these newly identified Sinorhizobium species.…”

Biogeography of a Novel Ensifer meliloti Clade Associated with the Australian Legume Trigonella suavissima

“…3). Previous studies have shown that certain loci (e.g., nod genes) that are mapped to the symbiotic megaplasmids in E. meliloti often have complex evolutionary histories, apparently because of frequent horizontal transfer and recombination (19,20,26).…”

“…The entire open reading frame for each locus was examined to aid in the design of primers that would amplify a portion of the gene, ranging in size from 200 to 500 bp. Five loci were chosen to represent the first half of the E. meliloti chromosome (USDA1021 genome annotation positions 1 to 1,735,000), which contains a higher degree of nucleotide diversity and a more positive GC skew (20). These loci, their products, and the respective fragment sizes that were selected for comparison were as follows: edd, phosphogluconate dehydratase, 501 bp; glnD, protein-PII uridylyltransferase, 309 bp; nuoE1, NADH dehydrogenase I chain E protein, 222 bp; ordL2, putative oxidoreductase protein, 432 bp; and zwf, glucose-6-phosphate 1-dehydrogenase, 453 bp.…”

“…Previous wholegenome sequence analyses of diverse E. meliloti and E. medicae strains have shown that chromosomal MLST analyses can provide a robust description of the taxonomic boundaries between Ensifer species (20). In the second part of this study, we used a similar MLST approach to examine the range of megaplasmid genotypes in a subsample of the T. suavissima strains used for chromosomal profiling.…”

The Sinorhizobium meliloti Essential Porin RopA1 Is a Target for Numerous Bacteriophages

“…The idea of bacteriophages linking their own DNA near receptor-encoding genes is an intriguing one. Indeed, in a recent multigenome analysis of S. meliloti and the closely related species Sinorhizobium medicae, the authors concluded that ropA1 was the only chromosomal gene that showed evidence of horizontal transfer between the two species (42). This may be due to this region being a hot spot for prophage insertion.…”