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Comparative Genomic Analysis of N2-Fixing and Non-N2-Fixing Paenibacillus spp.: Organization, Evolution and Expression of the Nitrogen Fixation Genes. PLoS Genetics 2014

Comparative Genomic Analysis of N2-Fixing and Non-N2-Fixing Paenibacillus spp.: Organization, Evolution and Expression of the Nitrogen Fixation Genes. PLoS Genetics 2014 | Publications | Scoop.it

We provide here a comparative genome analysis of 31 strains within the genus Paenibacillusincluding 11 new genomic sequences of N2-fixing strains. The heterogeneity of the 31 genomes (15 N2-fixing and 16 non-N2-fixing Paenibacillus strains) was reflected in the large size of the shell genome, which makes up approximately 65.2% of the genes in pan genome. Large numbers of transposable elements might be related to the heterogeneity. We discovered that a minimal and compact nif cluster comprising nine genes nifB, nifH, nifD, nifK, nifE, nifN, nifX,hesA and nifV encoding Mo-nitrogenase is conserved in the 15 N2-fixing strains. The nif cluster is under control of a σ70-depedent promoter and possesses a GlnR/TnrA-binding site in the promoter. Suf system encoding [Fe–S] cluster is highly conserved in N2-fixing and non-N2-fixing strains. Furthermore, we demonstrate that the nif cluster enabled Escherichia coli JM109 to fix nitrogen. Phylogeny of the concatenated NifHDK sequences indicates that Paenibacillus andFrankia are sister groups. Phylogeny of the concatenated 275 single-copy core genes suggests that the ancestral Paenibacillus did not fix nitrogen. The N2-fixing Paenibacillus strains were generated by acquiring the nif cluster via horizontal gene transfer (HGT) from a source related to Frankia. During the history of evolution, the nif cluster was lost, producing some non-N2-fixing strains, and vnf encoding V-nitrogenase or anf encoding Fe-nitrogenase was acquired, causing further diversification of some strains. In addition, some N2-fixing strains have additional nif and nif-like genes which may result from gene duplications. The evolution of nitrogen fixation in Paenibacillus involves a mix of gain, loss, HGT and duplication of nif/anf/vnfgenes. This study not only reveals the organization and distribution of nitrogen fixation genes inPaenibacillus, but also provides insight into the complex evolutionary history of nitrogen fixation.

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Replicon-Dependent Differentiation of Symbiosis-Related Genes in Sinorhizobium Strains Nodulating Glycine max. Appl Environ Microbiol 2014

In order to investigate the genetic differentiation of Sinorhizobium strains nodulating Glycine max and related microevolutionary mechanisms, three housekeeping genes (SMc00019, truA, and thrA) and 16 symbiosis-related genes on the chromosome (7 genes), pSymA (6 genes), and pSymB (3 genes) were analyzed. Five distinct species were identified among the test strains by calculating the average nucleotide identity (ANI) of SMc00019-truA-thrA:Sinorhizobium fredii, Sinorhizobium sojae, Sinorhizobium sp. I, Sinorhizobiumsp. II, and Sinorhizobium sp. III. These species assignments were also supported by population genetics and phylogenetic analyses of housekeeping genes and symbiosis-related genes on the chromosome and pSymB. Different levels of genetic differentiation were observed among these species or different replicons.S. sojae was the most divergent from the other test species and was characterized by its low intraspecies diversity and limited geographic distribution. Intergenic recombination dominated the evolution of 19 genes from different replicons. Intraspecies recombination happened frequently in housekeeping genes and symbiosis-related genes on the chromosome and pSymB, whereas pSymA genes showed a clear pattern of lateral-transfer events between different species. Moreover, pSymA genes were characterized by a lower level of polymorphism and recombination than those on the chromosome and pSymB. Taken together, genes from different replicons of rhizobia might be involved in the establishment of symbiosis with legumes, but these symbiosis-related genes might have evolved differently according to their corresponding replicons.

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Comparative genomics of rhizobia nodulating soybean suggests extensive recruitment of lineage-specific genes in adaptations. PNAS 2012

The rhizobium–legume symbiosis has been widely studied as the model of mutualistic evolution and the essential component of sustainable agriculture. Extensive genetic and recent genomic studies have led to the hypothesis that many distinct strategies, regardless of rhizobial phylogeny, contributed to the varied rhizobium–legume symbiosis. We sequenced 26 genomes of Sinorhizobium and Bradyrhizobium nodulating soybean to test this hypothesis. The Bradyrhizobium core genome is disproportionally enriched in lipid and secondary metabolism, whereas several gene clusters known to be involved in osmoprotection and adaptation to alkaline pH are specific to the Sinorhizobium core genome. These features are consistent with biogeographic patterns of these bacteria. Surprisingly, no genes are specifically shared by these soybean microsymbionts compared with other legume microsymbionts. On the other hand, phyletic patterns of 561 known symbiosis genes of rhizobia reflected the species phylogeny of these soybean microsymbionts and other rhizobia. Similar analyses with 887 known functional genes or the whole pan genome of rhizobia revealed that only the phyletic distribution of functional genes was consistent with the species tree of rhizobia. Further evolutionary genetics revealed that recombination dominated the evolution of core genome. Taken together, our results suggested that faithfully vertical genes were rare compared with those with history of recombination including lateral gene transfer, although rhizobial adaptations to symbiotic interactions and other environmental conditions extensively recruited lineage-specific shell genes under direct or indirect control through the speciation process.

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Robust Markers Reflecting Phylogeny and Taxonomy of Rhizobia. PLoS ONE 2012

Robust Markers Reflecting Phylogeny and Taxonomy of Rhizobia. PLoS ONE 2012 | Publications | Scoop.it

Genomic ANI (Average Nucleotide Identity) has been found to be able to replace DNA-DNA hybridization in prokaryote taxonomy. The ANI of each of the core genes that has a phylogeny congruent with the reference species tree of rhizobia was compared to the genomic ANI. This allowed us to identify three housekeeping genes (SMc00019-truA-thrA) whose ANI reflected the intraspecies and interspecies genomic ANI among rhizobial strains, revealing an ANI gap (≥2%) between the inter- and intra-species comparisons. The intraspecies (96%) and interspecies (94%) ANI boundaries calculated from three genes (SMc00019-truA-thrA) provided a criterion for bacterial species definition and confirmed 621/629 of known interspecies relationships withinBradyrhizobium, Mesorhizobium, Sinorhizobium and Rhizobium. Some widely studied strains should be renamed. The SMc00019-truA-thrA ANI also correlates well with the genomic ANI of strains in Agrobacterium, Methylobacterium, Ralstonia, Rhodopseudomonas, Cupriavidus andBurkholderia, suggesting their wide applicability in other bacteria.

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Genetic diversity of nodulating and non-nodulating rhizobia associated with wild soybean (Glycine soja Sieb. & Zucc.) in different ecoregions of China. FEMS Microbiol Ecol 2011

Genetic diversity of nodulating and non-nodulating rhizobia associated with wild soybean (Glycine soja Sieb. & Zucc.) in different ecoregions of China. FEMS Microbiol Ecol 2011 | Publications | Scoop.it

A total of 99 bacterial isolates that originated from root nodules of Glycine soja were characterized with restriction analyses of amplified 16S ribosomal DNA and 16S–23S rDNA intergenic spacers (ITS), and sequence analyses of 16S rRNA, rpoB, atpD, recA and nodCgenes. When tested for nodulation of G. soja, 72 of the isolates were effective symbionts, and these belonged to five species:Bradyrhizobium japonicum, Bradyrhizobium elkanii, Bradyrhizobium yuanmingense, Bradyrhizobium liaoningense and Sinorhizobium fredii. All of these, except some B. yuanmingense strains, also formed effective nodules on the domesticated soybean Glycine max. The remaining 27 isolates did not nodulate either host, but were identified as Rhizobium. Phylogeny nodC in the G. soja symbionts suggested that this symbiosis gene was mainly maintained by vertical gene transfer. Different nodC sublineages and rrs-ITS clusters reflected the geographic origins of isolates in this stud

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Distinctive Mesorhizobium populations associated with Cicer arietinum L. in alkaline soils of Xinjiang, China. Plant Soil 2012

Distinctive Mesorhizobium populations associated with Cicer arietinum L. in alkaline soils of Xinjiang, China. Plant Soil 2012 | Publications | Scoop.it
Background and aims

Rhizobia associated with chickpea in the main chickpea production zone of Xinjiang, China have never been investigated. Here, we present the first systematic investigation of these rhizobia’s genetic diversity and symbiotic interactions with their host plant.

Methods

Ninety-five isolates obtained from chickpea nodules in eight alkaline-saline (pH 8.24–8.45) sites in Xinjiang were characterized by nodulation test, symbiotic gene analysis, PCR-based restriction fragment length polymorphism (RFLP) of the 16S rRNA gene and 16S–23S rRNA intergenic spacer (IGS), BOX-PCR, phylogenies of 16S rRNA and housekeeping genes (atpD, recA and glnII), multilocus sequence analysis (MLSA) and DNA–DNA hybridization.

Results

All 95 isolates were identified within the genus of Mesorhizobium. Similarities less than 96.5% in MLSA and DNA–DNA hybridization values (<50%) between the new isolates and the definedMesorhizobium species, and high similarities (>98%) of symbiotic genes (nodC and nifH) with those of the well studied chickpea microsymbioints Mesorhizobium ciceri and Mesorhizobium mediterraneum were found.

Conclusions

Chickpea rhizobia in alkaline-saline soils of Xinjiang, China, form a population distinct from the defined Mesorhizobium species. All these chickpea rhizobia in Xinjiang harbored symbiotic genes highly similar to the type strains of two well-studied chickpea rhizobia, M. ciceri and M. mediterraneum, evidencing the possible lateral transfer of symbiotic genes among these different rhizobial species. On the other hand, chickpea may strongly select rhizobia with a unique symbiotic gene background.

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Associations Among Rhizobial Chromosomal Background, nod Genes, and Host Plants Based on the Analysis of Symbiosis of Indigenous Rhizobia and Wild Legumes Native to Xinjiang. Microbial Ecol 2010

Associations Among Rhizobial Chromosomal Background, nod Genes, and Host Plants Based on the Analysis of Symbiosis of Indigenous Rhizobia and Wild Legumes Native to Xinjiang. Microbial Ecol 2010 | Publications | Scoop.it

The associations among rhizobia chromosomal background, nodulation genes, legume plants, and geographical regions are very attractive but still unclear. To address this question, we analyzed the interactions among rhizobia rDNA genotypes, nodC genotypes, legume genera, as well as geographical regions in the present study. Complex relationships were observed among them, which may be the genuine nature of their associations. The statistical analyses indicate that legume plant is the key factor shaping both rhizobia genetic and symbiotic diversity. In the most cases of our results, the nodC lineages are clearly associated with rhizobial genomic species, demonstrating that nodulation genes have co-evolved with chromosomal background, though the lateral transfer of nodulation genes occurred in some cases in a minority. Our results also support the hypothesis that the endemic rhizobial populations to a certain geographical area prefer to have a wide spectrum of hosts, which might be an important event for the success of both legumes and rhizobia in an isolated region.

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Rhizobium miluonense sp. nov., a symbiotic bacterium isolated from Lespedeza root nodules. IJSEM 2008

Seventeen strains of lespedeza rhizobia, a previously defined novel group, were further characterized by comparison with phylogenetically related species using a polyphasic approach, including SDS-PAGE of whole-cell proteins, PCR-based restriction fragment length polymorphism analysis of ribosomal intergenic spacer sequences, determination of DNA G+C contents, DNA–DNA hybridization and analysis of phenotypic features. Based on data obtained in the present and previous studies, a novel species, Rhizobium miluonense sp. nov., is proposed for these strains. The type strain of R. miluonense is CCBAU 41251T (=LMG 24208T=HAMBI 2971T). Strain CCBAU 41251T could form ineffective nodules on Phaseolus vulgaris in addition to its original host Lespedeza chinensis.

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Bradyrhizobium elkanii, Bradyrhizobium yuanmingense and Bradyrhizobium japonicum are the main rhizobia associated with Vigna unguiculata and Vigna radiate ... FEMS Microbiol Lett 2008

Bradyrhizobium elkanii, Bradyrhizobium yuanmingense and Bradyrhizobium japonicum are the main rhizobia associated with Vigna unguiculata and Vigna radiate ... FEMS Microbiol Lett 2008 | Publications | Scoop.it

Cowpea (Vigna unguiculata) and mung bean (Vigna radiata) are important legume crops yet their rhizobia have not been well characterized. In the present study, 62 rhizobial strains isolated from the root nodules of these plants grown in the subtropical region of China were analyzed via a polyphasic approach. The results showed that 90% of the analyzed strains belonged to or were related toBradyrhizobium japonicum, Bradyrhizobium liaoningense, Bradyrhizobium yuanmingense and Bradyrhizobium elkanii, while the remaining represented Rhizobium leguminosarum, Rhizobium etli and Sinorhizobium fredii. Diverse nifH and nodC genes were found in these strains and their symbiotic genes were mainly coevolved with the housekeeping genes, indicating that the symbiotic genes were mainly maintained by vertical transfer in the studied rhizobial populations.

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Genetic diversity of rhizobia associated with Vicia faba in three ecological regions of China. Arch Microbiol 2007

Genetic diversity of rhizobia associated with Vicia faba in three ecological regions of China. Arch Microbiol 2007 | Publications | Scoop.it

Abstract

Great genetic diversity was revealed among 75 rhizobal isolates associated with Vicia faba grown in Chinese fields with AFLP, ARDRA, 16S rDNA sequencing, DNA–DNA hybridization, BOX-PCR and RFLP of PCR-amplified nodD and nodC. Most of the isolates were Rhizobium leguminosarum, and six isolates belonged to an unnamed Rhizobium species. In the homogeneity analysis, the isolates were grouped into three clusters corresponding to (1) autumn sowing (subtropical) region where the winter ecotype of V. faba was cultivated, (2) spring sowing (temperate) region where the spring ecotype was grown, and (3) Yunnan province where the intermediate ecotype was sown either in spring or in autumn. Nonrandom associations were found among the nod genotypes, genomic types and ecological regions, indicating an epidemic symbiotic gene transfer pattern among different genomic backgrounds within an ecological region and a relatively limited transfer pattern between different regions. Conclusively, the present results suggested an endemic population structure of V. faba rhizobia in Chinese fields and demonstrated a novel rhizobium associated with faba bean.

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Genetic Divergence of Bradyrhizobium Strains Nodulating Soybeans as Revealed by Multilocus Sequence Analysis of Genes Inside and Outside the Symbiosis Island. Appl Environ Microbiol 2014

The genus Bradyrhizobium has been considered to be a taxonomically difficult group. In this study, phylogenetics and evolutionary genetics analyses were used to investigate divergence levels among Bradyrhizobium strains nodulating soybeans in China. Eleven genospecies were identified by sequence analysis of three phylogenetic and taxonomic markers (SMc00019, thrA, and truA). This was also supported by analyses of eight genes outside the symbiosis island (“off-island” genes; SMc00019, thrA, truA, fabB, glyA, phyR, exoN, and hsfA). However, seven genes inside the symbiosis island (“island” genes; nifA, nifH, nodC, nodV,fixA, trpD, and rhcC2) showed contrasting lower levels of nucleotide diversity and recombination rates than did off-island genes. Island genes had significantly incongruent gene phylogenies compared to the species tree. Four phylogenetic clusters were observed in island genes, and the epidemic cluster IV (harbored byBradyrhizobium japonicum, Bradyrhizobium diazoefficiens, Bradyrhizobium huanghuaihaiense, Bradyrhizobium liaoningense, Bradyrhizobium daqingense,Bradyrhizobium sp. I, Bradyrhizobium sp. III, and Bradyrhizobium sp. IV) was not found in Bradyrhizobium yuanmingense, Bradyrhizobium sp. II, orBradyrhizobium elkanii. The gene flow level of island genes among genospecies is discussed in the context of the divergence level of off-island genes.

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High-Resolution Transcriptomic Analyses of Sinorhizobium sp. NGR234 Bacteroids in Determinate Nodules of Vigna unguiculata and Indeterminate Nodules of Leucaena leucocephala. PLoS ONE 2013

High-Resolution Transcriptomic Analyses of Sinorhizobium sp. NGR234 Bacteroids in Determinate Nodules of Vigna unguiculata and Indeterminate Nodules of Leucaena leucocephala. PLoS ONE 2013 | Publications | Scoop.it

The rhizobium-legume symbiosis is a model system for studying mutualistic interactions between bacteria and eukaryotes. Sinorhizobium sp. NGR234 is distinguished by its ability to form either indeterminate nodules or determinate nodules with diverse legumes. Here, we presented a high-resolution RNA-seq transcriptomic analysis of NGR234 bacteroids in indeterminate nodules of Leucaena leucocephala and determinate nodules of Vigna unguiculata. In contrast to exponentially growing free-living bacteria, non-growing bacteroids from both legumes recruited several common cellular functions such as cbb3 oxidase, thiamine biosynthesis, nitrate reduction pathway (NO-producing), succinate metabolism, PHB (poly-3-hydroxybutyrate) biosynthesis and phosphate/phosphonate transporters. However, different transcription profiles between bacteroids from two legumes were also uncovered for genes involved in the biosynthesis of exopolysaccharides, lipopolysaccharides, T3SS (type three secretion system) and effector proteins, cytochrome bd ubiquinol oxidase, PQQ (pyrroloquinoline quinone), cytochrome c550, pseudoazurin, biotin, phasins and glycolate oxidase, and in the metabolism of glutamate and phenylalanine. Noteworthy were the distinct expression patterns of genes encoding phasins, which are thought to be involved in regulating the surface/volume ratio of PHB granules. These patterns are in good agreement with the observed granule size difference between bacteroids from L. leucocephala and V. unguiculata.

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Plant-activated bacterial receptor adenylate cyclases modulate epidermal infection in the Sinorhizobium meliloti–Medicago symbiosis. PNAS 2012

Legumes and soil bacteria called rhizobia have coevolved a facultative nitrogen-fixing symbiosis. Establishment of the symbiosis requires bacterial entry via root hair infection threads and, in parallel, organogenesis of nodules that subsequently are invaded by bacteria. Tight control of nodulation and infection is required to maintain the mutualistic character of the interaction. Available evidence supports a passive bacterial role in nodulation and infection after the microsymbiont has triggered the symbiotic plant developmental program. Here we identify in Sinorhizobium meliloti, the Medicago symbiont, a cAMP-signaling regulatory cascade consisting of three receptor-like adenylate cyclases, a Crp-like regulator, and a target gene of unknown function. The cascade is activated specifically by a plant signal during nodule organogenesis. Cascade inactivation results in a hyperinfection phenotype consisting of abortive epidermal infection events uncoupled from nodulation. These findings show that, in response to a plant signal, rhizobia play an active role in the control of infection. We suggest that rhizobia may modulate the plant’s susceptibility to infection. This regulatory loop likely aims at optimizing legume infection.

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Biodiversity and Biogeography of Rhizobia Associated with Soybean Plants Grown in the North China Plain. Appl Environ Microbiol 2011

As the putative center of origin for soybean and the second largest region of soybean production in China, the North China Plain covers temperate and subtropical regions with diverse soil characteristics. However, the soybean rhizobia in this plain have not been sufficiently studied. To investigate the biodiversity and biogeography of soybean rhizobia in this plain, a total of 309 isolates of symbiotic bacteria from the soybean nodules collected from 16 sampling sites were studied by molecular characterization. These isolates were classified into 10 genospecies belonging to the genera Sinorhizobium andBradyrhizobium, including four novel groups, with S. fredii (68.28%) as the dominant group. The phylogeny of symbiotic genes nodC and nifH defined four lineages among the isolates associated with Sinorhizobium fredii, Bradyrhizobiumelkanii, B. japonicum, and B. yuanmingense, demonstrating the different origins of symbiotic genes and their coevolution with the chromosome. The possible lateral transfer of symbiotic genes was detected in several cases. The association between soil factors (available N, P, and K and pH) and the distribution of genospecies suggest clear biogeographic patterns: Sinorhizobium spp. were superdominant in sampling sites with alkaline-saline soils, while Bradyrhizobiumspp. were more abundant in neutral soils. This study clarified the biodiversity and biogeography of soybean rhizobia in the North China Plain.

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Diversity and Biogeography of Rhizobia Isolated from Root Nodules of Glycine max Grown in Hebei Province, China. Microbial Ecol 2011

Diversity and Biogeography of Rhizobia Isolated from Root Nodules of Glycine max Grown in Hebei Province, China. Microbial Ecol 2011 | Publications | Scoop.it

A total of 215 rhizobial strains were isolated and analyzed with 16S rRNA gene, 16S–23S intergenic spacer, housekeeping genes atpD, recA, and glnII, and symbiotic genes nifH and nodC to understand the genetic diversity of soybean rhizobia in Hebei province, China. All the strains except one were symbiotic bacteria classified into nine genospecies in the genera of Bradyrhizobium andSinorhizobium. Surveys on the distribution of these rhizobia in different regions showed thatBradyrhizobium japonicum and Bradyrhizobium elkanii strains were found only in neutral to slightly alkaline soils whereas Bradyrhizobium yuanmingense, Bradyrhizobium liaoningense-related strains and strains of five Sinorhizobium genospecies were found in alkaline–saline soils. Correspondence and canonical correspondence analyses on the relationship of rhizobial distribution and their soil characteristics reveal that high soil pH, electrical conductivity, and potassium content favor distribution of the B. yuanmingense and the five Sinorhizobium species but inhibit B. japonicum andB. elkanii. High contents of available phosphorus and organic matters benefit Sinorhizobium frediiand B. liaoningense-related strains and inhibit the others groups mentioned above. The symbiotic gene (nifH and nodC) lineages among B. elkanii, B. japonicum, B. yuanmingense, andSinorhizobium spp. were observed in the strains, signifying that vertical gene transfer was the main mechanism to maintain these genes in the soybean rhizobia. However, lateral transfer of symbiotic genes commonly in Sinorhizobium spp. and rarely in Bradyrhizobium spp. was also detected. These results showed the genetic diversity, the biogeography, and the soil determinant factors of soybean rhizobia in Hebei province of China.

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Population mixing of Rhizobium leguminosarum bv. viciae nodulating Vicia faba: the role of recombination and lateral gene transfer. FEMS Microbiol Ecol 2010

Population mixing of Rhizobium leguminosarum bv. viciae nodulating Vicia faba: the role of recombination and lateral gene transfer. FEMS Microbiol Ecol 2010 | Publications | Scoop.it

The level and mechanisms of population mixing among faba bean (Vicia faba) rhizobia of different geographic origins (three ecoregions of China and several Western countries) were analysed by sequencing three chromosomal housekeeping loci (atpD, recA and glnII) and one nodulation gene (nodD). Eight distinct sublineages of Rhizobium leguminosarum bv. viciae (Rlv) were identified by concatenated sequences of chromosomal loci. structure analysis revealed admixture patterns of Rlv populations of different geographic origins. Recombination, particularly among these chromosomal loci, was revealed to be an important microevolutionary force in shaping the observed genetic diversity and the phylogeny of Rlv. The phylogeny of nodD is largely independent of that of the chromosomal loci, reflecting multiple gene transfers between sublineages and possibly selection imposed by different faba bean gene pools. The dominant nodulation genotype of faba bean rhizobia in the spring growing region of China is identical to the prevalent type of Europe, while the winter growing region of China has another related, but distinct, dominant nodulation genotype. Although several geographically specific sublineages of Rlv were observed, recombination and lateral gene transfer have driven the process of population mixing among different ecoregions of China or between China and countries to the west.

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Screening of high effective alfalfa rhizobial strains with a comprehensive protocol - Annals Microbiol 2008

Screening of high effective alfalfa rhizobial strains with a comprehensive protocol - Annals Microbiol 2008 | Publications | Scoop.it

Ninety-six alfalfa rhizobial strains were screened with a two-step strategy to select high effective and competitive microsymbionts for this plant grown in Inner Mongolia. Firstly, all the strains were inoculated to surface-sterilised seeds sown in vermiculite and grown in greenhouse. After grown 45 days, the shoot dry weight, number and nitrogenase activity of nodules were recorded and statistically analysed to select the more effective strains. Secondly, the competitiveness of 4 more effective strains designated in first step were evaluated by inoculation of each strain to alfalfa seeds grown in natural so il collected from Inner Mongolia. The nodule occupancy of each inoculated strain was assayed with BOX-PCR fingerprinting. With this strategy, 4 strains, all isolated from the same eco-region, were claimed as the best symbionts with alfalfa in that soil. The statistically designated best strains were exactly the most competitive and most effective ones in the second step, and the results were further confirmed by a field experiment. This study offered an efficient strategy to select rhizobial inoculants and demonstrated the possibility that the local rhizobial population might be highly effective and competitive for the epidemic legumes there.

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Rhizobium fabae sp. nov., a bacterium that nodulates Vicia faba. IJSEM 2008

Six strains were isolated from root nodules of Vicia faba grown in Nanchang, Yifeng, Taihu, Huaibei, Bengbu and Lujiang, in the middle and lower reaches of the Yangtze River. According to phylogenetic analyses of 16S rRNA gene,atpD and recA sequences, these strains belong to the genus Rhizobium, withRhizobium etli and Rhizobium leguminosarum as the closest related species. CCBAU 33202T, a representative of these novel isolates, showed sequence similarity to its closest relatives R. etli CFN 42T and R. leguminosarum USDA 2370T of 99.5 and 99.1 % for the 16S rRNA gene, 91.9 and 91.9 % for atpD and 90.3 and 93.2 % for recA. The strains from this study could also be differentiated from R. etli CFN 42T and R. leguminosarum USDA 2370T by 16S–IGS RFLP and SDS-PAGE of whole-cell proteins, fatty acid profiles and several phenotypic characteristics. DNA–DNA hybridization yielded relatedness of 19 and 14–43 %, respectively, with R. etli CFN 42T and strains representing different biovars of R. leguminosarum. All data obtained in this study showed that these V. faba isolates belong to a novel species, for which the nameRhizobium fabae sp. nov. is proposed. The type strain, CCBAU 33202T (=LMG 23997T =JCM 14381T), was isolated from Nanchang.

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Rhizobium multihospitium sp. nov., isolated from multiple legume species native of Xinjiang, China. IJSEM 2008

Thirty-one rhizobial strains isolated from nodules of legumes native of Xinjiang, China, were characterized. These strains were classified as belonging to the genus Rhizobium based on amplified 16S rDNA restriction analysis (ARDRA). The strains were distinguished from recognized Rhizobium species using analysis of 16S–23S rDNA intergenic spacers (IGS-RFLP), SDS-PAGE analysis of whole proteins and BOX-PCR; the test strains always formed a distinct cluster with patterns that were quite different from those of the reference rhizobial strains used. According to the phylogenetic analysis based on the 16S rRNA gene, the test strains belonged to the genus Rhizobium, withRhizobium tropici, Rhizobium rhizogenes and Rhizobium lusitanum as the closest related species, with 99.6, 99.2 and 99.4 % sequence similarities, respectively, between the type strains of the three Rhizobium species and strain CCBAU 83401T. Phylogenetic analyses of the representative strains using IGS and atpD, recA and glnII genes all confirmed the phylogenetic arrangements obtained using the 16S rRNA gene. The DNA–DNA relatedness values between strain CCBAU 83401T and strains CCBAU 83364, CCBAU 83345 and CCBAU 83523 ranged from 80.8 to 100 %, showing that they belong to the same species. The DNA–DNA relatedness between strain CCBAU 83401T and R. tropici IIB CIAT 899T, R. tropici IIA CFN 299, R. rhizogenes LMG 150T and R. lusitanum P1-7T were 26.9, 27.7, 38.2 and 22.6 %, respectively, clearly indicating that strain CCBAU 83401T represents a novel species. Phenotypic characterization of four representative strains, CCBAU 83401T, CCBAU 83364, CCBAU 83345 and CCBAU 83523, showed several distinctive features that differentiated them from closely related species. The 31 strains had identical nodD and nifH genes, which were very similar to those of the bean-nodulating R. lusitanum, Devosia neptuniae and R. tropici IIB. Based upon these results, the strains from this study are considered to represent a novel species, for which the name Rhizobium multihospitium sp. nov. is proposed. The DNA G+C content ranged from 65.3 to 66.0 mol% (Tm). The type strain is CCBAU 83401T (=LMG 23946T=HAMBI 2975T), which nodulatesRobinia pseudoacacia, but not Leucaena leucocephala, Phaseolus vulgaris, Pisum sativum or Medicago sativa.

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Characterization of symbiotic and endophytic bacteria isolated from root nodules of herbaceous legumes grown in Qinghai-Tibet plateau and... Arch Microbiol 2007

Characterization of symbiotic and endophytic bacteria isolated from root nodules of herbaceous legumes grown in Qinghai-Tibet plateau and... Arch Microbiol 2007 | Publications | Scoop.it

Abstract

Qinghai–Tibet plateau is the highest place in the world and the environment in that plateau is hard for animals and plants, with low temperature, low concentration of oxygen and high solar radiation. In this study, 61 root nodule isolates from Vicia, Oxytropis, Medicago, Melilotus and Onobrychisspecies grown in Qinghai–Tibet plateau and in loess plateau were comparatively characterized. Based upon the results of numerical taxonomy, ARDRA, AFLP, DNA–DNA hybridization and 16S rDNA sequencing, the isolates were classified as Rhizobium leguminosarum, Sinorhizobium meliloti,Sinorhizobium fredii, Mesorhizobium sp., Phyllobacterium sp., Stenotrophomonas sp. and two non-symbiotic groups related to Agrobacterium and Enterobacteriaceae. The strains isolated from Qinghai–Tibet plateau and from the loess plateau were mixed in these species or groups. Oxytropisspp. and Medicago archiducis-nicolai grown in Qinghai–Tibet plateau were recorded as new hosts for R. leguminosarum, as well as Oxytropis glabra and Medicago lupulina for S. fredii. In addition, strains resistant to high alkaline (pH 11) and high concentration of NaCl (3–5%, w/v) were found in each of the rhizobial species. This was the first systematic study of rhizobia isolated from Qinghai–Tibet plateau

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