Comparison of nucleotide diversity and symbiotic properties of Rhizobium meliloti populations from annual Medicago species

Characterization and diversity of rhizobia nodulating selected tree legumes in Ghana

The study was conducted to assess the characteristics and diversity of the rhizobia that nodulate some prominent tree legumes in three soils of Ghana. Five introduced and/or indigenous tree legumes were initially assessed for nodulation in three Ghanaian soils. After 12 weeks of growth in nursery pots the 200 rhizobial strains isolated from their nodules were characterized culturally, metabolically and phenotypically. Sixty of these isolates were selected randomly and their genotypic characteristics determined using PCR-RFLP of 16S rRNA and intergenic spacer (ITS) genes. Each tree legume was nodulated by isolates classified as fast or very fast-growers or by isolates classified as slow- or very slow-growers with 54 % of all the 200 isolates belonging to fast- or very fast-growers. Morphologically, eighty five percent of the colonies formed on yeast extract mannitol agar were wet and gummy while 70 % were acid tolerant, i.e. they were able to grow at a pH of 3.5. Combined restriction of the 16S rRNA genes of the 60 rhizobial isolates with five restriction enzymes clearly distinguished seven different clusters at 80 % similarity level. The majority of A. lebbeck isolates were distinct from those of the Acacias and L. leucocephala. The M. thonningii isolates were related to L. leucocephala isolates. Simple PCR of the ITS DNA provided several distinct band sizes indicating great variation among the isolates and restriction of the ITS with three different enzymes did not yield many further differences. Molecular techniques revealed a great diversity among the rhizobia that nodulate tree legumes in the tropics and this may explain why many introduced and/or indigenous trees are able to form nodules with indigenous rhizobia in this region.

Genome sequence of Ensifer meliloti strain WSM1022; a highly effective microsymbiont of the model legume Medicago truncatula A17

Ensifer meliloti WSM1022 is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as a legume microsymbiont of Medicago. WSM1022 was isolated in 1987 from a nodule recovered from the roots of the annual Medicago orbicularis growing on the Cyclades Island of Naxos in Greece. WSM1022 is highly effective at fixing nitrogen with M. truncatula and other annual species such as M. tornata and M. littoralis and is also highly effective with the perennial M. sativa (alfalfa or lucerne). In common with other characterized E. meliloti strains, WSM1022 will nodulate but fixes poorly with M. polymorpha and M. sphaerocarpos and does not nodulate M. murex. Here we describe the features of E. meliloti WSM1022, together with genome sequence information and its annotation. The 6,649,661 bp high-quality-draft genome is arranged into 121 scaffolds of 125 contigs containing 6,323 protein-coding genes and 75 RNA-only encoding genes, and is one of 100 rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project.

Bradyrhizobium daqingense sp. nov., isolated from soybean nodules

Thirteen slow-growing rhizobial strains isolated from root nodules of soybean (Glycine max L.) grown in Daqing city in China were classified in the genus Bradyrhizobium based on 16S rRNA gene sequence analysis. Multilocus sequence analysis of IGS, atpD, glnII and recA genes revealed that the isolates represented a novel clade in this genus. DNA-DNA relatedness lower than 42.5 % between the representative strain CCBAU 15774(T) and the type strains of the closely related species Bradyrhizobium liaoningense USDA 3622(T), Bradyrhizobium yuanmingense CCBAU 10071(T) and Bradyrhizobium betae LMG 21987(T), further confirmed that this group represented a novel species. CCBAU 15774(T) shared seven cellular fatty acids with the three above-mentioned species, but the fatty acids 15 : 0 iso and summed feature 5 (18 : 2ω6,9c and/or 18 : 0 anteiso) were unique for this strain. The respiratory quinone in CCBAU 15774(T) was ubiquinone-10 and the cellular polar lipids were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, cardiolipin and unknown aminolipid, polar lipid and phospholipid. In addition, some phenotypic features could be used to differentiate the novel group from the related species. On basis of these results, we propose the name Bradyrhizobium daqingense sp. nov., with CCBAU 15774(T) ( = LMG 26137(T) = HAMBI 3184(T) = CGMCC 1.10947(T)) as the type strain. The DNA G+C content of the type strain is 61.2 mol% (T(m)).

Mesorhizobium silamurunense sp. nov., isolated from root nodules of Astragalus species

Four rhizobial strains representing a previously defined novel group in the genus Mesorhizobium and isolated from Astragalus species in China were further characterized using a polyphasic approach. Phylogenetic analysis of 16S rRNA gene sequences showed that these Gram-negative bacteria belonged to the genus Mesorhizobium , with Mesorhizobium plurifarium LMG 11892T as the closest neighbour sharing a sequence similarity of 99.8 %. Comparative sequence analysis of the atpD, recA, glnII, rpoB, nodC and nifH genes, SDS-PAGE of whole-cell soluble proteins, DNA–DNA hybridization, fatty acid profiles and a series of phenotypic and physiological tests differentitated the novel group from all recognized species of the genus Mesorhizobium . Based on the data obtained in the present and previous studies, this group represents a novel species within the genus Mesorhizobium , for which the name Mesorhizobium silamurunense sp. nov. is proposed. The type strain is CCBAU 01550T ( = HAMBI 3029T = LMG 24822T), and could form effective nodules on Astragalus membranaceus, Astragalus adsurgens and Caragana intermedia, and ineffective nodules on Phaseolus vulgaris in cross-nodulation tests.

Comparison of rhizobia that nodulate Medicago laciniata and Medicago truncatula present in a single Tunisian arid soil

The rhizobia present in a single arid region Tunisian soil that nodulate Medicago laciniata and Medicago truncatula were compared. All isolates, 40 from each host, were Sinorhizobium meliloti based on 16S rRNA polymerase chain reaction restriction fragment length polymorphism (PCR–RFLP) patterns and subsequent confirmation by sequence analysis of the 16S rRNA genes in four representatives from each host species. There was no apparent relationship between Medicago host species of isolation and the nodulating rhizobial genome as determined by repetitive extragenic palandromic PCR. The isolates of M. laciniata were distinguished from those of M. truncatula present in the same soil by variation in PCR–RFLP of nifDK, indicating that this dissimilarity is originally genetic and not geographic. While forming effective symbioses with their own respective isolates, both M. laciniata and M. truncatula formed ineffective true nodules, nodule-like structures, or no nodules at all in cross-inoculation tests, as confirmed by the histological observations.

Development of a lab-made microarray for analyzing the genetic diversity of nitrogen fixing symbionts Sinorhizobium meliloti and Sinorhizobium medicae

Some bacterial species, like nitrogen-fixing Sinorhizobium that interact with Medicago plants, are prone to frequent horizontal gene transfers. Investigation of their genetic structure requires to study polymorphism patterns at many loci. Although DNA microarrays represent a method of choice for high throughput analysis of polymorphisms, this technology yet remains an expensive and heavy approach, thus depriving most of research groups from this powerful tool. In an attempt to overcome this limitation, we have developed a simple genotyping procedure by DNA microarrays, and have evaluated its ability to characterize a Sinorhizobium population. Thirty 18- to 24-mer oligonucleotide probes were designed to target the most frequent mutations in three polymorphic loci of Sinorhizobium meliloti and S. medicae. Probe hybridization efficiency was compared on two spotting surfaces: nylon membranes and epoxy-coated glass slides. Epoxy-coated glass slides revealed more sensitive than nylon membranes and allowed discrimination of single mismatches. Using this procedure, an uncharacterized population consisting of 33 S. meliloti/S. medicae isolates was successfully genotyped.

Phenotypical and genotypical characteristics of root-nodulating bacteria isolated from annual Medicago spp. in Soummam Valley (Algeria)

AIMS

In the framework of agro-pastoral system management using local annual medics coupled with their native root-nodulating bacteria to extend pasture zones, increase forage yields and improve ovine and bovine breeding in Algeria, we investigated diversity of rhizobia from annual Medicago spp. (Medicago arabica, Medicago polymorpha, Medicago minima and Medicago orbicularis).

METHODS AND RESULTS

Ten nodulating-isolates were characterized by morphological, cultural, physiological and biochemical features, SDS-PAGE analysis and PCR-RFLP of 16S rDNA. The results show some degree of genetic diversity among the isolates; three can be affiliated to Sinorhizobium meliloti, one to Rhizobium galegae and six were separate.

CONCLUSIONS

Local annual medics would have a high degree of specificity in their symbiotic interaction. Furthermore, our results support the presence of Rh. galegae in the Mediterranean region.

SIGNIFICANCE AND IMPACT OF THE STUDY

This work is a preliminary step towards selection of efficient symbiotic Medicago-rhizobia to develop inoculants for management of agro-pastoral systems using local annual medics in Algeria.

Nitrogen-fixing sinorhizobia with Medicago laciniata constitute a novel biovar (bv. medicaginis) of S. meliloti

Sixty-eight new rhizobial isolates were obtained from root-nodules of Medicago laciniata and from Mediterranean soils in Tunisia and France. All of them were identified as Sinorhizobium meliloti on the basis of PCR-RFLP analyses of 16S rDNA and the intergenic spacer sequence between 16S and 23S rDNAs. DNA/DNA hybridization, phenotypic characterization and 16S rRNA gene sequencing led to the conclusion that they belong the same taxon. All new isolates shared the ability to nodulate and fix nitrogen with M. laciniata except 11 of them not capable of fixing nitrogen with this plant and originating from French soils containing no efficiently adapted symbionts with M. laciniata. The nitrogen-fixing rhizobia on M. laciniata differed markedly from the other S. meliloti or Sinorhizobium medicae isolates and references in their symbiotic traits such as nifDK RFLP diversity, nodA sequences and nitrogen effectiveness with tree other different annual Medicago species (M. truncatula, M. polymorpha and M. sauvagei). Two infrasubspecific (biovar) divisions are therefore proposed within S. meliloti: bv. medicaginis for Sinorhizobium efficient on M. laciniata and bv. meliloti for the classically known S. meliloti group represented by the strains ATCC9930(T) and RCR 2011 efficient on M. sativa.

Lipopolysaccharide profiles from nodules as markers of bradyrhizobium strains nodulating wild legumes

To develop the use of electrophoretic lipopolysaccharide profiles for Bradyrhizobium strain identification, we studied the feasibility of using electrophoresis of whole legume nodule homogenates to obtain distinctive lipopolysaccharide profiles. The electrophoretic patterns were the same whether we used nodule extracts, bacteroids, or cultured bacteria as samples, and there was no evidence of changes in the ladder-like pattern during the nodulation process. To assess the reliability of using lipopolysaccharide profiling performed with individual nodules for studying the diversity and microdistribution of the rhizobia nodulating wild shrub legumes, we used a population of Adenocarpus foliolosus seedlings. We obtained 75 different profiles from the 147 nodules studied. There was no dominant profile in the sample, and a plant with different nodules generally produced different profiles. Electrophoresis of legume root nodules proved to be a fast and discriminating technique for determining the diversity of a bradyrhizobial population, although it did not allow the genetic relationships among the nodulating strains to be studied.

Genetic relationship of Sinorhizobium meliloti and Sinorhizobium medicae strains isolated from Caucasian region

Sinorhizobium meliloti and Sinorhizobium medicae are two closely related species of the genus Sinorhizobium showing a similar host range, nodulating leguminous species of the genera Medicago, Melilotus and Trigonella, but their phylogenic relationship has not been elucidated yet. In this paper we report the application of three different molecular markers, (i) RFLP of nodD genes, (ii) 16S-23S rDNA intergenic gene spacer fingerprinting and (iii) amplification fragment length polymorphism to S. meliloti and S. medicae strains isolated from the Caucasian area, which is the region of origin of the host plant Medicago. The analysis of data could suggest the origin of S. medicae strains from an ancestral S. meliloti population.

Microbial biodiversity: approaches to experimental design and hypothesis testing in primary scientific literature from 1975 to 1999

Research interest in microbial biodiversity over the past 25 years has increased markedly as microbiologists have become interested in the significance of biodiversity for ecological processes and as the industrial, medical, and agricultural applications of this diversity have evolved. One major challenge for studies of microbial habitats is how to account for the diversity of extremely large and heterogeneous populations with samples that represent only a very small fraction of these populations. This review presents an analysis of the way in which the field of microbial biodiversity has exploited sampling, experimental design, and the process of hypothesis testing to meet this challenge. This review is based on a systematic analysis of 753 publications randomly sampled from the primary scientific literature from 1975 to 1999 concerning the microbial biodiversity of eight habitats related to water, soil, plants, and food. These publications illustrate a dominant and growing interest in questions concerning the effect of specific environmental factors on microbial biodiversity, the spatial and temporal heterogeneity of this biodiversity, and quantitative measures of population structure for most of the habitats covered here. Nevertheless, our analysis reveals that descriptions of sampling strategies or other information concerning the representativeness of the sample are often missing from publications, that there is very limited use of statistical tests of hypotheses, and that only a very few publications report the results of multiple independent tests of hypotheses. Examples are cited of different approaches and constraints to experimental design and hypothesis testing in studies of microbial biodiversity. To prompt a more rigorous approach to unambiguous evaluation of the impact of microbial biodiversity on ecological processes, we present guidelines for reporting information about experimental design, sampling strategies, and analyses of results in publications concerning microbial biodiversity.

Genetic diversity of Sinorhizobium populations recovered from different medicago varieties cultivated in Tunisian soils

A collection of 468 rhizobial isolates was obtained from different ecological areas of Tunisia by trapping them on Medicago sativa cv. Gabes, Medicago scutelleta cv. Kelson, Medicago truncatula, and Medicago ciliaris. A subsample of 134 rhizobia was chosen to determine their plasmid profile, and 89 isolates were subjected to multilocus enzyme electrophoresis (MLEE) and PCR/RFLP analysis using 16S, IGS (inter genic spacer), and nifKD probes. Twenty-five representatives from these isolates were evaluated for their nodulation and nitrogen fixation capacities. MLEE studies revealed two groups with highly heterogeneous host specificity and geographical origin. The discriminatory power was found to be slightly better with the amplified ribosomal intergenic region, than the nifKD genes. Divisions detected by nifKD amplified DNA analysis matched those established by ribosomal PCR- RFLPs. The comparison between different analyses revealed that MLEE illustrated better phenotypic properties of isolates than PCR-RFLP or plasmid content analysis. Clear distinction between Sinorhizobium meliloti and Sinorhizobium medicae were observed by analysis of the IGS symbiotic regions between nifD and nifK genes. Were able to distinguish three inoculation groups; isolates trapped from M. sativa cv. Gabes and M. scutelleta cv. Kelson formed one inoculation group which was more closely related to isolates trapped from M. truncatula than those trapped from M. ciliaris.

Genotypic characterization of Bradyrhizobium strains nodulating small Senegalese legumes by 16S-23S rRNA intergenic gene spacers and amplified fragment length polymorphism fingerprint analyses

We examined the genotypic diversity of 64 Bradyrhizobium strains isolated from nodules from 27 native leguminous plant species in Senegal (West Africa) belonging to the genera Abrus, Alysicarpus, Bryaspis, Chamaecrista, Cassia, Crotalaria, Desmodium, Eriosema, Indigofera, Moghania, Rhynchosia, Sesbania, Tephrosia, and Zornia, which play an ecological role and have agronomic potential in arid regions. The strains were characterized by intergenic spacer (between 16S and 23S rRNA genes) PCR and restriction fragment length polymorphism (IGS PCR-RFLP) and amplified fragment length polymorphism (AFLP) fingerprinting analyses. Fifty-three reference strains of the different Bradyrhizobium species and described groups were included for comparison. The strains were diverse and formed 27 groups by AFLP and 16 groups by IGS PCR-RFLP. The sizes of the IGS PCR products from the Bradyrhizobium strains that were studied varied from 780 to 1,038 bp and were correlated with the IGS PCR-RFLP results. The grouping of strains was consistent by the three methods AFLP, IGS PCR-RFLP, and previously reported 16S amplified ribosomal DNA restriction analysis. For investigating the whole genome, AFLP was the most discriminative technique, thus being of particular interest for future taxonomic studies in Bradyrhizobium, for which DNA is difficult to obtain in quantity and quality to perform extensive DNA:DNA hybridizations.

Genetic diversity and phylogeny of rhizobia that nodulate acacia spp. in morocco assessed by analysis of rRNA genes

Forty rhizobia nodulating four Acacia species (A. gummifera, A. raddiana, A. cyanophylla, and A. horrida) were isolated from different sites in Morocco. These rhizobia were compared by analyzing both the 16S rRNA gene (rDNA) and the 16S-23S rRNA spacer by PCR with restriction fragment length polymorphism (RFLP) analysis. Analysis of the length of 16S-23S spacer showed a considerable diversity within these microsymbionts, but RFLP analysis of the amplified spacer revealed no additional heterogeneity. Three clusters were identified when 16S rDNA analysis was carried out. Two of these clusters include some isolates which nodulate, nonspecifically, the four Acacia species. These clusters, A and B, fit within the Sinorhizobium lineage and are closely related to S. meliloti and S. fredii, respectively. The third cluster appeared to belong to the Agrobacterium-Rhizobium galegae phylum and is more closely related to the Agrobacterium tumefaciens species. These relations were confirmed by sequencing a representative strain from each cluster.

Rapid identification of Medicago nodulating strains by using two oligonucleotide probes complementary to 16S rDNA sequences

Symbiotic bacteria associated with the Medicago genus are separated into two closely related species named Sinorhizobium meliloti and Sinorhizobium medicae. To discriminate rapidly between these two bacterial species, two 15-base DNA probes, 16Smfs and 16Smed, were designed from the alignment of 16S rDNA sequences to differentiate S. meliloti from S. medicae. Their specificities were evaluated by dot-blot hybridization experiments on 25 reference strains representing 13 species of Rhizobium and Sinorhizobium, and by comparison with all 16S rDNA sequences available in the GenBank data base. No cross-reaction was found with 16Smed, which was thus considered species specific for S. medicae. By contrast, as expected according to the 16S rDNA sequence alignment, the labeled 16Smfs probe cross-hybridized with the DNAs of S. meliloti, Sinorhizobium fredii, and Sinorhizobium saheli but not with the DNA of S. medicae. Since S. saheli and S. fredii do not nodulate Medicago, 16Smed and 16Smfs can be routinely used to characterize the two Sinorhizobium species nodulating Medicago from pure cultures or from Medicago root nodules. Fifty strains isolated from eight annual Medicago species were then characterized by using colony hybridizations. Sinorhizobium meliloti was more frequently obtained (> 80% isolates) than was S. medicae. Both Sinorhizobium species seemed to be trapped by annual Medicago and no plant-host specificity was detected.