Diversity of Sinorhizobium meliloti from the Central Asian Alfalfa Gene Center

Variation in genome size and content is common among bacterial strains. Identifying these naturally occurring differences can accelerate our understanding of bacterial attributes, such as ecological specialization and genome evolution. In this study, we used representational difference analysis to identify potentially novel sequences not present in the sequenced laboratory strain Rm1021 of the nitrogen-fixing bacterium Sinorhizobium meliloti. Using strain Rm1021 as the driver and the type strain of S. meliloti ATCC 9930, which has a genome size ϳ370 kilobases bigger than that of strain Rm1021, as the tester, we identified several groups of sequences in the ATCC 9930 genome not present in strain Rm1021. Among the 85 novel DNA fragments examined, 55 showed no obvious homologs anywhere in the public databases. Of the remaining 30 sequences, 24 contained homologs to the Rm1021 genome as well as unique segments not found in Rm1021, 3 contained sequences homologous to those published for another S. meliloti strain but absent in Rm1021, 2 contained sequences homologous to other symbiotic nitrogen-fixing bacteria (Rhizobium etli and Bradyrhizobium japonicum), and 1 contained a sequence homologous to a gene in a non-nitrogen-fixing species, Pseudomonas sp. NK87. Using PCR, we assayed the distribution of 12 of the above 85 novel sequences in a collection of 59 natural S. meliloti strains. The distribution varied widely among the 12 novel DNA fragments, from 1.7% to 72.9%. No apparent correlation was found between the distribution of these novel DNA sequences and their genotypes obtained using multilocus enzyme electrophoresis. Our results suggest potentially high rates of gene gain and loss in S. meliloti genomes.

Section: Discussionmentioning

confidence: 99%

Novel DNA Sequences from Natural Strains of the Nitrogen-Fixing Symbiotic Bacterium Sinorhizobium meliloti

Guo

Sun

Finan

et al. 2005

“…This bacterial diversity, assessed by phenotypic or genotypic analyses, has been reported to be influenced by several factors, including geographical location (32), soil factors (14), and plant species (19,37). Furthermore, at an interspecies level, several studies on S. meliloti and S. medicae natural populations, trapped from various soils (using several Medicago species), reported either the balanced coexistence of the two bacterial species (3,23) or the dominance of one of them (3,31,33,43).At a plant genotype level, host nodulation specificity could also influence the bacterial diversity in soil. Significant variations were detected among rhizobial populations associated with different plant lines of Vicia faba (38), Pisum sativum (10), or Medicago sativa (26).…”

mentioning

confidence: 99%

Effects ofMedicago truncatulaGenetic Diversity, Rhizobial Competition, and Strain Effectiveness on the Diversity of a NaturalSinorhizobiumSpecies Community

Rangin

Brunel

Cleyet-Marel

et al. 2008

We investigated the genetic diversity and symbiotic efficiency of 223 Sinorhizobium sp. isolates sampled from a single Mediterranean soil and trapped with four Medicago truncatula lines. DNA molecular polymorphism was estimated by capillary electrophoresis-single-stranded conformation polymorphism and restriction fragment length polymorphism on five loci (IGS NOD , typA, virB11, avhB11, and the 16S rRNA gene). More than 90% of the rhizobia isolated belonged to the Sinorhizobium medicae species (others belonged to Sinorhizobium meliloti), with different proportions of the two species among the four M. truncatula lines. The S. meliloti population was more diverse than that of S. medicae, and significant genetic differentiation among bacterial populations was detected. Single inoculations performed in tubes with each bacterial genotype and each plant line showed significant bacterium-plant line interactions for nodulation and N 2 fixation levels. Competition experiments within each species highlighted either strong or weak competition among genotypes within S. medicae and S. meliloti, respectively. Interspecies competition experiments showed S. meliloti to be more competitive than S. medicae for nodulation. Although not highly divergent at a nucleotide level, isolates collected from this single soil sample displayed wide polymorphism for both nodulation and N 2 fixation. Each M. truncatula line might influence Sinorhizobium soil population diversity differently via its symbiotic preferences. Our data suggested that the two species did not evolve similarly, with S. meliloti showing polymorphism and variable selective pressures and S. medicae showing traces of a recent demographic expansion. Strain effectiveness might have played a role in the species and genotype proportions, but in conjunction with strain adaptation to environmental factors.The rhizobium-legume nitrogen-fixing association is a good model for studying symbiosis and coevolution between organisms. In this mutualistic association, bacteria form nodules on plant roots (more rarely on the stem), where atmospheric nitrogen is reduced to ammonium available for the plant. Among the various plant-bacterium couples studied so far, the Medicago truncatula association with Sinorhizobium meliloti is particularly interesting (8) and has often been studied as a model system for genetic description of the molecular pathways involved in the establishment of the symbiosis (16). M. truncatula has the ability to form an efficient symbiosis with two bacterial species, S. meliloti (9) and its sister species, Sinorhizobium medicae (29).The genetic diversity of these two bacterial species, especially S. meliloti, has usually been described as quite important (2,7,11,40). This bacterial diversity, assessed by phenotypic or genotypic analyses, has been reported to be influenced by several factors, including geographical location (32), soil factors (14), and plant species (19,37). Furthermore, at an interspecies level, several studies on S. meliloti and S. medicae natural pop...

“…Prior to the S. meliloti Rm1021 sequencing project, there was already interest in genes located on accessory plasmids. Population analysis revealed that some plasmids are widespread in indigenous rhizobial populations and occur at frequencies of at least 50% (1,4,56). It is assumed that rhizobial accessory plasmids are interchangeable among indigenous rhizobial populations.…”

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confidence: 99%

Sequence Analysis of the 144-Kilobase Accessory Plasmid pSmeSM11a, Isolated from a DominantSinorhizobium melilotiStrain Identified during a Long-Term Field Release Experiment

Stiens

Schneiker

Keller

et al. 2006

The genome of Sinorhizobium meliloti type strain Rm1021 consists of three replicons: the chromosome and two megaplasmids, pSymA and pSymB. Additionally, many indigenous S. meliloti strains possess one or more smaller plasmids, which represent the accessory genome of this species. Here we describe the complete nucleotide sequence of an accessory plasmid, designated pSmeSM11a, that was isolated from a dominant indigenous S. meliloti subpopulation in the context of a long-term field release experiment with genetically modified S. meliloti strains. Sequence analysis of plasmid pSmeSM11a revealed that it is 144,170 bp long and has a mean G؉C content of 59.5 mol%. Annotation of the sequence resulted in a total of 160 coding sequences. Functional predictions could be made for 43% of the genes, whereas 57% of the genes encode hypothetical or unknown gene products. Two plasmid replication modules, one belonging to the repABC replicon family and the other belonging to the plasmid type A replicator region family, were identified. Plasmid pSmeSM11a contains a mobilization (mob) module composed of the type IV secretion system-related genes traG and traA and a putative mobC gene. A large continuous region that is about 42 kb long is very similar to a corresponding region located on S. meliloti Rm1021 megaplasmid pSymA. Single-base-pair deletions in the homologous regions are responsible for frameshifts that result in nonparalogous coding sequences. Plasmid pSmeSM11a carries additional copies of the nodulation genes nodP and nodQ that are responsible for Nod factor sulfation. Furthermore, a tauD gene encoding a putative taurine dioxygenase was identified on pSmeSM11a. An acdS gene located on pSmeSM11a is the first example of such a gene in S. meliloti. The deduced acdS gene product is able to deaminate 1-aminocyclopropane-1-carboxylate and is proposed to be involved in reducing the phytohormone ethylene, thus influencing nodulation events. The presence of numerous insertion sequences suggests that these elements mediated acquisition of accessory plasmid modules.