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

et al. (2012) Population Genomics of the Facultatively Mutualistic Bacteria Sinorhizobium meliloti and S. medicae. PLoS Genet 8(8): e1002868. doi:10.1371/journal.pgen.1002868 Population Genomics of the Facultatively Mutualistic Bacteria Sinorhizobium meliloti and S. medicae Brendan Epstein 0 1 Antoine Branca 0 1 Joann Mudge 0 1 Arvind K. Bharti 0 1 Roman Briskine 0 1 Andrew D. Farmer 0 1 Masayuki Sugawara 0 1 Nevin D. Young 0 1 Michael J. Sadowsky 0 1 Peter Tiffin 0 1 Nancy A. Moran, Yale University, United States of America 0 a Current address: Institute for Evolution and Biodiversity, University of Mu nster, Mu nster, Germany b Current address: Graduate School of Environmental Science. Hokkaido University , Sapporo , Japan 1 1 Department of Plant Biology, University of Minnesota , St. Paul , Minnesota, United States of America, 2 National Center for Genome Resources , Santa Fe , New Mexico, United States of America, 3 Department of Computer Science and Engineering, University of Minnesota , Minneapolis , Minnesota, United States of America, 4 Department of Soil , Water, and Climate , University of Minnesota , St. Paul , Minnesota, United States of America, 5 Department of Plant Pathology, University of Minnesota , Saint Paul , Minnesota, United States of America, 6 BioTechnology Institute , St. Paul, Minnesota , United States of America 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 (.1006) 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 (hp) 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. - Funding: This work was supported by National Science Foundation (http://www.nsf.gov/), grant 0820005. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. Analyses of genome sequences can provide a nearly complete description of the nature and extent of nucleotide diversity segregating within and among species. There have been multiple investigations into genomic diversity in microbial communities using librarybased and megtagenomic approaches [1] and phylogenomic studies of relatedness among microbial species [2]. By contrast, there have been few genome-wide surveys of nucleotide diversity within a prokaryotic species, and those studies have often focused on variation in genome content [35] rather than nucleotide diversity. Yet it is clear that population-genomic analyses provide an opportunity to greatly expand our understanding of the evolutionary forces shaping diversity within prokaryotic lineages [69] and identify targets of strong positive selection without bias that may be introduced when focusing on a limited number of genes or phenotypes of prior interest [10]. Prokaryotic species are often studied because they are either pathogens, of environmental or industrial importance, or because they form mutualistic associations with eukaryotes. The latter group includes members of the genera Rhizobium, Sinorhizobium (now Ensifer), Bradyrhizobium, Azorhizobium, and Mesorhizobium, collectively referred to as the rhizobia, a group of gram-negative bacteria that form symbiotic associations with legume plants. When growing in symbiosis with legumes, rhizobia convert atmospheric nitrogen (N2), which is unavailable to plants, into ammonia, which plants can use for the synthesis of amino acids. This symbiosis is estimated to contribute nearly half of all current biological nitrogen fixation [11] and is a key component of agricultural systems that are not dependent on synthetic fertilizers [12]. One of the best characterized rhizobial species is Sinorhizobium meliloti (now Ensifer meliloti). The interaction between S. meliloti and the closely related species S. medicae with the model legume M. truncatula, the genome of which was recently sequenced [13], has been the subject of extensive biochemical, molecular genetic [14 16], and evolutionary investigation [1720]. The genomes of both S. meliloti and S. medicae consist of a single circular chromosome (,3.65 Mb) plus two large symbiotic (sym) plasmids (,1.3 and ,1.6 Mb) [21,22]. Sinorhizobium spp. also contain auxiliary Facultative mutualisms are relationships between two species that can live independently, but derive benefits when living together with their mutualistic partners. The facultative mutualism between rhizobial bacteria and legume plants contributes approximately half of all biologically fixed nitrogen, an essential plant nutrient, and is an important source of nitrogen to both natural and agricultural ecosystems. We resequenced the genomes of 44 strains of two closely related species of the genus Sinorhizobium that form facultative mutualisms with the model legme Medicago truncatula. These data provide one of the most complete examinations of genomic diversity segregating within microbial species that are not causative agents of human illness. Our analyses reveal that horizontal gene transfer, a common source of new genes in microbial species, disproportionately affects genes with direct roles in the rhizobia-plant symbiosis. Analyses of nucleotide diversity segregating within each species suggests that strong selection, along with genetic hitchhiking has sharply reduced diversity along an entire chromosome half in S. meliloti. Despite the two species ecological similarity, we did not find evidence for selection acting on the same genetic targets. In additio (...truncated)