Sinorhizobium Meliloti Strain Research Articles

Reclassification of type strains of Rhizobium indigoferae and Sinorhizobium kummerowiae into the species Rhizobium leguminosarum and Sinorhizobium meliloti, respectively.

The species Rhizobium indigoferae and Sinorhizobium kummerowiae were isolated from legume nodules and the 16S rRNA sequences of their respective type strains, CCBAU 71042T and CCBAU 71714T, were highly divergent from those of the other species of the genera Rhizobium and Sinorhizobium, respectively. However, the 16S rRNA gene sequences obtained for strains CCBAU 71042T and CCBAU 71714T several years after description, were different from the original ones, showing 100 % similarity to the type strains of Rhizobium leguminosarum and Sinorhizobium meliloti, respectively. Phylogenetic analyses of two housekeeping genes, recA and atpD, confirmed the high phylogenetic closeness of strains CCBAU 71042T and CCBAU 71714T to the respective type strains of R. leguminosarum and S. meliloti. In the present work, we compared the genomes of the type strains of R. indigoferae and S. kummerowiae available in several culture collections with those of the respective type strains of R. leguminosarum and S. meliloti, some of them obtained in this study. The calculated average nucleotide identity-blast and digital DNA-DNA hybridization values in both cases were higher than those recommended for species differentiation, supporting the proposal for the reclassification of the type strains of R. indigoferae and S. kummerowiae into the species R. leguminosarum and S. meliloti, respectively.

Genotype-by-genotype interkingdom cross-talk between symbiotic nitrogen fixing Sinorhizobium meliloti strains and Trichoderma species

In the understanding of the molecular interaction between plants and their microbiome, a key point is to identify simplified models of the microbiome including relevant bacterial and fungal partners which could also be effective in plant growth promotion. Here, as proof-of-concept, we aim to identify the possible molecular interactions between symbiotic nitrogen-fixing rhizobia and soil fungi (Trichoderma spp.), hence shed light on synergistic roles rhizospheric fungi could have in the biology of symbiotic nitrogen fixation bacteria. We selected 4 strains of the model rhizobium Sinorhizobium meliloti and 4 Trichoderma species (T. velutinum, T. tomentosum, T. gamsii and T. harzianum). In an experimental scheme of 4 ×4 strains x species combinations, we investigated the rhizobia physiological and transcriptomic responses elicited by fungal spent media, as well as spent media effects on rhizobia-host legume plant (alfalfa, Medicago sativa L.) symbiosis. Fungal spent media had large effects on rhizobia, specific for each fungal species and rhizobial strains combination, indicating a generalized rhizobia genotype x fungal genotype interaction, including synergistic, neutral and antagonistic effects on alfalfa symbiotic phenotypes. Differential expression of a high number of genes was shown in rhizobia strains with up to 25% of total genes differentially expressed upon treatment of cultures with fungal spent media. Percentages over total genes and type of genes differentially expressed changed according to both fungal species and rhizobial strain. To support the hypothesis of a relevant rhizobia genotype x fungal genotype interaction, a nested Likelihood Ratio Test indicated that the model considering the fungus-rhizobium interaction explained 23.4% of differentially expressed genes. Our results provide insights into molecular interactions involving nitrogen-fixing rhizobia and rhizospheric fungi, highlighting the panoply of genes and genotypic interactions (fungus, rhizobium, host plant) which may concur to plant symbiosis.

Selection of effective and competitive Sinorhizobium meliloti strains that nodulate alfalfa under low temperature

Rhizobia strain selection is mostly based on nodulation efficiency with host-plant. Selected strains also require a high capacity to compete with indigenous soil rhizobia under various abiotic stresses to prevent nodule occupation by competitive but low-efficient native strains. In this experiment, three highly-efficient strains were selected out of six genetically-divergent strains, based on nodulation speed, nitrogenase activity, and alfalfa biomass accumulation under spring conditions. Strain competitiveness was assessed by determining the percent of alfalfa nodules occupancy by selected tagged strains. Two alfalfa populations, A-TF0 and A-TF7, differing in their tolerance to freezing as well as two soils originating from south and north of Quebec containing indigenous rhizobia were tested. More nodules were recorded on roots of freezing-tolerant alfalfa in southern soil. Highly-efficient strain NRG34, isolated from northern Canada, proved to be very competitive as shown by a greater nodule occupancy percentage than any other strain in cold soil.

Formation of grass stands of variegated alfalfa (Medicago varia, M. media) on acidic sod-podzolic soils

The article reports the results of field studies performed at the Field Experimental Station of Russian State Agrarian University – Moscow Timiryazev Agricultural Academy in 2023-2024. The authors studied the effect of the growth regulator Albit, the microbiological fertilizer Sporion and the micronutrient Aquamix on the formation of grass stands of variegated alfalfa (the Agnia and Taisia varieties) and Hungarian sainfoin (the Pavlovsky variety). The study has found that on the acidic sod-podzolic soil with a pHКCl of 4.52, variegated alfalfa (the Agnia and Taisia varieties) inoculated with strains of nodule bacteria Sinorhizobium meliloti, AK 55 and SHM 404B, respectively, formed dense grass stands. On average, over two years, variegated alfalfa of the Agnia variety provided the highest yield when using Sporion in combination with Aquamix – 5.2 t/ha; that of the Taisia variety – in variants of Albit + Aquamix and Sporion + Aquamix– 5.07 and 5.19 t/ha, respectively, which is 20.1%; 18.4, and 21.3% more compared to the control. Hungarian sainfoin has not formed a productive agrophytocenosis on the acidic soil. On average, it was inferior in yield to variegated alfalfa of the Agnia and Taisia varieties by 1.7 and 1.8 times, respectively, in all variants of the experiment.

Effects of Inoculation with Stress-Tolerant Rhizobia on the Response of Alfalfa (Medicago sativa L.) to Combined Salinity and Cadmium Stress

Agricultural soil salinization, which is often combined with heavy-metal contamination, is an ever-growing problem in the current era of global change. Legumes have a high potential for nitrogen fixation and are ideal crops for the reclamation of degraded soils. Alfalfa (Medicago sativa) is a valuable forage crop cultivated worldwide. Alfalfa plants fertilized with nitrogen or inoculated with a salt- and cadmium-tolerant Sinorhizobium meliloti strain were subjected to combined NaCl and CdCl2 stresses. Our results showed that inoculated plants presented higher aerial biomass than nitrogen-fertilized plants when they were exposed to salinity and cadmium together. To assess the mechanisms involved in the plant response to the combined stresses, superoxide dismutase and catalase antioxidant enzymatic activities were determined. Both increased upon stress; however, the increase in catalase activity was significantly less marked for inoculated plants, suggesting that other tolerance mechanisms might be active. Cd accumulation was lower in inoculated plants than in fertilized plants, which appears to imply that inoculation somehow prevented cadmium uptake by the plant roots. Expression analyses of several involved genes suggested that inoculation stimulated the biosynthesis of proline, phytochelatins, and homophytochelatins, together indicating that inoculated plants might be better suited to withstand combined salinity and cadmium stress effects.

Rhizobial nitrogen fixation efficiency shapes endosphere bacterial communities and Medicago truncatula host growth

BackgroundDespite the knowledge that the soil–plant–microbiome nexus is shaped by interactions amongst its members, very little is known about how individual symbioses regulate this shaping. Even less is known about how the agriculturally important symbiosis of nitrogen-fixing rhizobia with legumes is impacted according to soil type, yet this knowledge is crucial if we are to harness or improve it. We asked how the plant, soil and microbiome are modulated by symbiosis between the model legume Medicago truncatula and different strains of Sinorhizobium meliloti or Sinorhizobium medicae whose nitrogen-fixing efficiency varies, in three distinct soil types that differ in nutrient fertility, to examine the role of the soil environment upon the plant–microbe interaction during nodulation.ResultsThe outcome of symbiosis results in installment of a potentially beneficial microbiome that leads to increased nutrient uptake that is not simply proportional to soil nutrient abundance. A number of soil edaphic factors including Zn and Mo, and not just the classical N/P/K nutrients, group with microbial community changes, and alterations in the microbiome can be seen across different soil fertility types. Root endosphere emerged as the plant microhabitat more affected by this rhizobial efficiency-driven community reshaping, manifested by the accumulation of members of the phylum Actinobacteria. The plant in turn plays an active role in regulating its root community, including sanctioning low nitrogen efficiency rhizobial strains, leading to nodule senescence in particular plant–soil–rhizobia strain combinations.ConclusionsThe microbiome–soil–rhizobial dynamic strongly influences plant nutrient uptake and growth, with the endosphere and rhizosphere shaped differentially according to plant–rhizobial interactions with strains that vary in nitrogen-fixing efficiency levels. These results open up the possibility to select inoculation partners best suited for plant, soil type and microbial community.Dv-bX6Q_Z8DTbrQMTFWdQvVideo

Metabolic and genetic responses to simulated overwintering conditions of alfalfa-rhizobia associations contrasted in their freezing tolerance

AbstractThe study of winter stress tolerance in perennial legumes needs to consider the complete symbiotic system including both plants and bacteria since these two partners are differentially affected by stress conditions. Here, we compared the regrowth after a freezing stress of four different associations of two alfalfa populations differing in freezing tolerance (A-TF0 and A-TF7) inoculated with two Sinorhizobium (Ensifer) meliloti strains (B399 and NRG34) of contrasted adaptation to cold. To understand the contribution of each partner to a better regrowth performance of an association after freezing, we identified molecular traits having major roles in cold acclimation, freezing tolerance, and those involved in the crosstalk between alfalfa and its symbiotic partner. Regrowth after exposure to a freezing stress was 35% larger in the A-TF7 × NRG34 than in the A-TF0 × B399 association. The metabolomic study of roots, crowns and, more specifically, nodules, revealed profound changes in these organs, switching from a sink to support cold acclimation to a source of reserves enabling regrowth after deacclimation. Marked increases in concentrations of stachyose and raffinose, two sugars of the raffinose-family oligosaccharides (RFO), and in the expression level of a gene of the RFO synthetic pathway were observed in response to cold acclimation supporting the importance of a protective role for RFO in alfalfa. Both cold-adapted partners of the symbiotic association contributed to increases in arginine concentration in nodules in response to cold acclimation and deacclimation underscoring the importance of N storage and remobilization for a successful overwintering in alfalfa.

Characterization of an accessory plasmid of Sinorhizobium meliloti and its two replication-modules.

Rhizobia are Gram-negative bacteria known for their ability to fix atmospheric N2 in symbiosis with leguminous plants. Current evidence shows that rhizobia carry in most cases a variable number of plasmids, containing genes necessary for symbiosis or free-living, a common feature being the presence of several plasmid replicons within the same strain. For many years, we have been studying the mobilization properties of pSmeLPU88b from the strain Sinorhizobium meliloti LPU88, an isolate from Argentina. To advance in the characterization of pSmeLPU88b plasmid, the full sequence was obtained. pSmeLPU88b is 35.9 kb in size, had an average GC % of 58.6 and 31 CDS. Two replication modules were identified in silico: one belonging to the repABC type, and the other to the repC. The replication modules presented high DNA identity to the replication modules from plasmid pMBA9a present in an S. meliloti isolate from Canada. In addition, three CDS presenting identity with recombinases and with toxin-antitoxin systems were found downstream of the repABC system. It is noteworthy that these CDS present the same genetic structure in pSmeLPU88b and in other rhizobial plasmids. Moreover, in all cases they are found downstream of the repABC operon. By cloning each replication system in suicide plasmids, we demonstrated that each of them can support plasmid replication in the S. meliloti genetic background, but with different stability behavior. Interestingly, while incompatibility analysis of the cloned rep systems results in the loss of the parental module, both obtained plasmids can coexist together.

Oxidative Status of Medicago truncatula Seedlings after Inoculation with Rhizobacteria of the Genus Pseudomonas, Paenibacillus and Sinorhizobium

An increasing number of scientists working to raise agricultural productivity see the potential in the roots and the soil adjacent to them, together with a wealth of micro-organisms. The first mechanisms activated in the plant during any abiotic or biotic stress concern changes in the oxidative status of the plant. With this in mind, for the first time, an attempt was made to check whether the inoculation of seedlings of the model plant Medicago truncatula with rhizobacteria belonging to the genus Pseudomonas (P. brassicacearum KK5, P. corrugata KK7), Paenibacillus borealis KK4 and a symbiotic strain Sinorhizobium meliloti KK13 would change the oxidative status in the days following inoculation. Initially, an increase in H2O2 synthesis was observed, which led to an increase in the activity of antioxidant enzymes responsible for regulating hydrogen peroxide levels. The main enzyme involved in the reduction of H2O2 content in the roots was catalase. The observed changes indicate the possibility of using the applied rhizobacteria to induce processes related to plant resistance and thus to ensure protection against environmental stress factors. In the next stages, it seems reasonable to check whether the initial changes in the oxidative state affect the activation of other pathways related to plant immunity.

Methods of increasing the productivity of various varieties and hybrids of variegated alfalfa in the conditions of arable farming biologization

Two-year studies of variegated alfalfa (Medicago varia Mart.) of the following varieties and hybrids were carried out: Pastbischnaya 88, Taisia, Agnia VIC, 506 and SGP, as well as observations of their reaction to inoculation. Strains of nodule bacteria Sinorhizobium meliloti were used as inoculants: SHM1-105, 415, A-1, A-5, and a control variant without inoculation. As a result of research, it was revealed that the minimum length of stems in 2021 was fixed in the Pastbischnaya 88 + 415 variant, and amounted to 12.5 cm, in 2022 — Taisia with A1 and SHM1-105, 8.8 cm each. The maximum length of stems in 2021 was marked by a hybrid 506 in a combination of A1 and SHM1-105 strains, the indicator was 40.4 and 40.3, respectively, in 2022 — Agnia VIC + A5, 28 cm. In 2021, the Pastbischnaya 88 variety with the strain SHM1-105 turned out to be the most competitive, its share prevailed over the unseeded admixture, and reached 54.8%, in 2022 variant Agnia VIC + 415 was distinguished with this indicator, with a mass fraction of 65.45%. The positive effect of inoculation was revealed, the best symbiotic varietal microbial systems were determined. The strain of nodule bacteria 415 is marked by a complex effect on all varieties of variegated alfalfa. According to the yield of dry weight (3.3 t/ha on average), the Taisia variety and the SGP hybrid were distinguished.

Crossing Bacterial Genomic Features and Methylation Patterns with MeStudio: An Epigenomic Analysis Tool.

DNA methylation is one of the most observed epigenetic modifications. It is present in eukaryotes and prokaryotes and is related to several biological phenomena, including gene flow and adaptation to environmental conditions. The widespread use of third-generation sequencing technologies allows direct and easy detection of genome-wide methylation profiles, offering increasing opportunities to understand and exploit the epigenomic landscape of individuals and populations. Here, we present a pipeline named MeStudio, with the aim of analyzing and combining genome-wide methylation profiles with genomic features. Outputs report the presence of DNA methylation in coding sequences (CDSs) and noncoding sequences, including both intergenic sequences and sequences upstream of the CDS. We apply this novel tool, showing the usage and performance of MeStudio, on a set of single-molecule real-time sequencing outputs from strains of the bacterial species Sinorhizobium meliloti.

Paired Medicago receptors mediate broad-spectrum resistance to nodulation by Sinorhizobium meliloti carrying a species-specific gene

Plants have evolved the ability to distinguish between symbiotic and pathogenic microbial signals. However, potentially cooperative plant-microbe interactions often abort due to incompatible signaling. The Nodulation Specificity 1 (NS1) locus in the legume Medicago truncatula blocks tissue invasion and root nodule induction by many strains of the nitrogen-fixing symbiont Sinorhizobium meliloti. Controlling this strain-specific nodulation blockade are two genes at the NS1 locus, designated NS1a and NS1b, which encode malectin-like leucine-rich repeat receptor kinases. Expression of NS1a and NS1b is induced upon inoculation by both compatible and incompatible Sinorhizobium strains and is dependent on host perception of bacterial nodulation (Nod) factors. Both presence/absence and sequence polymorphisms of the paired receptors contribute to the evolution and functional diversification of the NS1 locus. A bacterial gene, designated rns1, is required for activation of NS1-mediated nodulation restriction. rns1 encodes a type I-secreted protein and is present in approximately 50% of the nearly 250 sequenced S. meliloti strains but not found in over 60 sequenced strains from the closely related species Sinorhizobium medicae. S. meliloti strains lacking functional rns1 are able to evade NS1-mediated nodulation blockade.

Эффективность симбиоза люцерны хмелевидной с новыми штаммами ризобий

New strains of Sinorhizobium meliloti were isolated from nodules of wild hop alfalfa growing in different districts of the Moscow region. Strain LX1 was isolated from the nodules of wild hop alfalfa, on the basis of which the Mira variety was created. Strain LX6 was isolated from alfalfa living in conditions of very low fertility and moisture deficiency at the Ivankovo reservoir dam. Strains LX2 and LX5 — on the railway embankment, LX3 and LX4 — on a relatively fertile area of the meadow. In the field experiment, LX1 strains provided the highest efficiency of symbiosis with the hop-shaped alfalfa variety. The increase in productivity for dry matter reached 81%, for seeds 87%. The LX6 strain increased seed yield by 86%. The best results for the selection number VIK 32-28 were obtained by inoculation with strains LX4 and LX6. Productivity for dry matter increased by 26 and 21%, for seeds — by 112 and 150%. In the vegetation experiment, an accelerated method of selecting highly effective macro- and micro symbionts in non-sterile conditions was optimized. On the 35th day after the emergence of seedlings, the herbage capacity was visually determined. The most powerful were the plant-microbial systems "variety of the Mira + strains LX3, LX6, LX2 and LX1". The height of elongated shoots was 11.8 ± 1.5 … 15.3 ± 1.6 cm, bushiness of 3.7 ± 0.5 … 4.0 ± 0.6 stems, symbiosis efficiency of 18–102%. Positive correlations were revealed between productivity and plant height (r = 0.42 ± 0.40), bushiness (r = 0.57 ± 0.36), number of nodules (r = 0.62 ± 0.35).

Genome-Wide Association Studies across Environmental and Genetic Contexts Reveal Complex Genetic Architecture of Symbiotic Extended Phenotypes.

A goal of modern biology is to develop the genotype-phenotype (G→P) map, a predictive understanding of how genomic information generates trait variation that forms the basis of both natural and managed communities. As microbiome research advances, however, it has become clear that many of these traits are symbiotic extended phenotypes, being governed by genetic variation encoded not only by the host's own genome, but also by the genomes of myriad cryptic symbionts. Building a reliable G→P map therefore requires accounting for the multitude of interacting genes and even genomes involved in symbiosis. Here, we use naturally occurring genetic variation in 191 strains of the model microbial symbiont Sinorhizobium meliloti paired with two genotypes of the host Medicago truncatula in four genome-wide association studies (GWAS) to determine the genomic architecture of a key symbiotic extended phenotype-partner quality, or the fitness benefit conferred to a host by a particular symbiont genotype, within and across environmental contexts and host genotypes. We define three novel categories of loci in rhizobium genomes that must be accounted for if we want to build a reliable G→P map of partner quality; namely, (i) loci whose identities depend on the environment, (ii) those that depend on the host genotype with which rhizobia interact, and (iii) universal loci that are likely important in all or most environments. IMPORTANCE Given the rapid rise of research on how microbiomes can be harnessed to improve host health, understanding the contribution of microbial genetic variation to host phenotypic variation is pressing, and will better enable us to predict the evolution of (and select more precisely for) symbiotic extended phenotypes that impact host health. We uncover extensive context-dependency in both the identity and functions of symbiont loci that control host growth, which makes predicting the genes and pathways important for determining symbiotic outcomes under different conditions more challenging. Despite this context-dependency, we also resolve a core set of universal loci that are likely important in all or most environments, and thus, serve as excellent targets both for genetic engineering and future coevolutionary studies of symbiosis.

Discordant population structure among rhizobium divided genomes and their legume hosts.

Symbiosis often occurs between partners with distinct life history characteristics and dispersal mechanisms. Many bacterial symbionts have genomes comprising multiple replicons with distinct rates of evolution and horizontal transmission. Such differences might drive differences in population structure between hosts and symbionts and among the elements of the divided genomes of bacterial symbionts. These differences might, in turn, shape the evolution of symbiotic interactions and bacterial evolution. Here we use whole genome resequencing of a hierarchically structured sample of 191 strains of Sinorhizobium meliloti collected from 21 locations in southern Europe to characterize population structures of this bacterial symbiont, which forms a root nodule symbiosis with the host plant Medicago truncatula. S. meliloti genomes showed high local (within-site) variation and little isolation by distance. This was particularly true for the two symbiosis elements, pSymA and pSymB, which have population structures that are similar to each other, but distinct from both the bacterial chromosome and the host plant. Given limited recombination on the chromosome, compared to the symbiosis elements, distinct population structures may result from differences in effective gene flow. Alternatively, positive or purifying selection, with little recombination, may explain distinct geographical patterns at the chromosome. Discordant population structure between hosts and symbionts indicates that geographically and genetically distinct host populations in different parts of the range might interact with genetically similar symbionts, potentially minimizing local specialization.

Impact of Sinorhizobium meliloti strains and plant population on regrowth and nodule regeneration of alfalfa after a freezing event

PurposeThe increase in frequency of freeze–thaw episodes with the diminution of snow cover protection due to climate change compromises the winter survival of alfalfa (Medicago sativa L.). Symbiosis with cold-tolerant rhizobial strains can improve the ability of alfalfa to survive and grow under stressful conditions.MethodsSix strains of Sinorhizobium (Ensifer) meliloti were tested in combination with two alfalfa populations bred to differ in their levels of freezing tolerance. Plants of each different combination were grown for eight weeks in a growth chamber before being exposed to temperatures promoting their acclimation to cold. Plants were then exposed to a freezing stress (-11ºC) and regrown for three weeks. Shoot, root and nodule biomass were measured before cold acclimation and three weeks after the freezing stress.ResultsAfter freezing stress, the alfalfa population A-TF7 had shoot and root biomasses that were respectively 19% and 15% larger than cultivar A-TF0. Alfalfa plants inoculated with strain NRG34 showed both a larger shoot biomass and a higher nodule dry weight than plants inoculated with any other strains. Assessment of freezing damages on nodules showed that plants inoculated with NRG34 had the largest proportion of undamaged nodules or of nodules with a regeneration zone.ConclusionThis study shows for the first time a relationship between nodule and shoot regrowth after a freezing stress, the latter being linked with the proportion of nodules showing less freezing damage. Our results demonstrated that both the choice of alfalfa populations and S. meliloti strains adapted to stress are complementary to increasing alfalfa persistence.

Molecular Phylogenetic Analysis of Salt-Tolerance-Related Genes in Root-Nodule Bacteria Species Sinorhizobium meliloti

A molecular phylogenetic analysis of salt-tolerance-related genes was carried out using complete genome sequencing data available for 26 Sinorhizobium meliloti strains and for 25 bacterial strains belonging to 17 genera. It was revealed that the genes of the first and the second stages of the response to salt stress (aqpZ, trkH, and trkA, and betICBA) have copies of many of the above- indicated genes on pSymA. Data obtained can provide evidence that this replicon, known to be essential for nitrogen fixation rhizobia activity, also has a significant role in the formation of a stress-related gene pool. The closest putative phylogenetic relatives were identified for all 14 tested genes and these are the first insights into the evolutionary pathways for the formation of a stress-related gene pool in root nodule nitrogen-fixing bacteria.

Phenotypic and genomic signatures of interspecies cooperation and conflict in naturally occurring isolates of a model plant symbiont.

Given the need to predict the outcomes of (co)evolution in host-associated microbiomes, whether microbial and host fitnesses tend to trade-off, generating conflict, remains a pressing question. Examining the relationships between host and microbe fitness proxies at both the phenotypic and genomic levels can illuminate the mechanisms underlying interspecies cooperation and conflict. We examined naturally occurring genetic variation in 191 strains of the model microbial symbiont Sinorhizobium meliloti, paired with each of two host Medicago truncatula genotypes in single- or multi-strain experiments to determine how multiple proxies of microbial and host fitness were related to one another and test key predictions about mutualism evolution at the genomic scale, while also addressing the challenge of measuring microbial fitness. We found little evidence for interspecies fitness conflict; loci tended to have concordant effects on both microbe and host fitnesses, even in environments with multiple co-occurring strains. Our results emphasize the importance of quantifying microbial relative fitness for understanding microbiome evolution and thus harnessing microbiomes to improve host fitness. Additionally, we find that mutualistic coevolution between hosts and microbes acts to maintain, rather than erode, genetic diversity, potentially explaining why variation in mutualism traits persists in nature.

Antagonistic activity of Sinorhizobium meliloti strains against pathogenic fungi isolated from alfalfa in Algerian Sahara

Antagonistic activity of Sinorhizobium meliloti strains against pathogenic fungi isolated from alfalfa in Algerian Sahara

Comparative Genomics across Three Ensifer Species Using a New Complete Genome Sequence of the Medicago Symbiont Sinorhizobium (Ensifer) meliloti WSM1022.

Here, we report an improved and complete genome sequence of Sinorhizobium (Ensifer) meliloti strain WSM1022, a microsymbiont of Medicago species, revealing its tripartite structure. This improved genome sequence was generated combining Illumina and Oxford nanopore sequencing technologies to better understand the symbiotic properties of the bacterium. The 6.75 Mb WSM1022 genome consists of three scaffolds, corresponding to a chromosome (3.70 Mb) and the pSymA (1.38 Mb) and pSymB (1.66 Mb) megaplasmids. The assembly has an average GC content of 62.2% and a mean coverage of 77X. Genome annotation of WSM1022 predicted 6058 protein coding sequences (CDSs), 202 pseudogenes, 9 rRNAs (3 each of 5S, 16S, and 23S), 55 tRNAs, and 4 ncRNAs. We compared the genome of WSM1022 to two other rhizobial strains, closely related Sinorhizobium (Ensifer) meliloti Sm1021 and Sinorhizobium (Ensifer) medicae WSM419. Both WSM1022 and WSM419 species are high-efficiency rhizobial strains when in symbiosis with Medicago truncatula, whereas Sm1021 is ineffective. Our findings report significant genomic differences across the three strains with some similarities between the meliloti strains and some others between the high efficiency strains WSM1022 and WSM419. The addition of this high-quality rhizobial genome sequence in conjunction with comparative analyses will help to unravel the features that make a rhizobial symbiont highly efficient for nitrogen fixation.