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Legume-rhizobia symbioses of species in the sub-family Papilionoideae with indeterminate nodules excluding the IRLC.
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Rhizobial symbiosis genes are often carried on symbiotic islands or plasmids that can be transferred (horizontal transfer) between different bacterial species. Symbiosis genes involved in horizontal transfer have different phylogenies with respect to the core genome of their 'host'. Here, the literature on legume-rhizobium symbioses in field soils...
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Context 1
... Xinjiang, China, isolates of Rhizobium multihospitium were obtained from a number of plant species from different tribes: Lathyrus odorata, Vicia hirsuta (Fabeae), Astragalus aksuensis, Astragalus sp., Oxytropis glabra, Oxytropis meinshausenii (Galegeae), Alhagi sp., Caragana jubata, Halimodendron halodendron (Hedysareae) ( Table 2); Robinia pseudoacacia (Robineae), Sophora alopecurioides (Sophoreae) ( Table 3); Lotus frondosus and Lotus tenuis (Loteae) ( Table 4). The nifH and nodD sequences of these isolates were 100% similar to those of Rhizobium lusitanum P1-7 T and D. neptuniae J1 T [55], and it was suggested that nifH and nodD genes of the three rhizobial species may have the same origin. ...Context 2
... incongruence occurs between core and symbiosis genes for Azorhizobium, Bradyrhizobium, Burkholderia, Ensifer, Mesorhizobium, Methylobacterium, Microvirga, Neorhizobium, Ochrobactrum, Rhizobium, and Phyllobacterium associated with Papilionoideae legumes with indeterminate nodules excluding the IRLC (Table 3). ...Context 3
... was concluded that Mesorhizobium strains isolated from Aspalathus spp., Argyrolobium spp. (Genisteae, Table 3), Otholobium spp., and Psoralea spp. (Psoraleeae , Table 4), and Burkholderia isolated from Podalyria calyptrata (Table 3) show high degrees of horizontal transfer of nodulation genes among closely related species. ...Context 4
... Table 3), Otholobium spp., and Psoralea spp. (Psoraleeae , Table 4), and Burkholderia isolated from Podalyria calyptrata (Table 3) show high degrees of horizontal transfer of nodulation genes among closely related species. In associated studies, a Mesorhizobium isolate from Psoralea sp., characterized on 16S rRNA and housekeeping gene sequences, aligned closely to Ensifer on nifH sequence, and a Mesorhizobium isolate from Psoralea oligophylla aligned closely to Burkholderia on nodA sequence (Table 4) [68]. ...Similar publications
One of the greatest inputs of available nitrogen into the biosphere occurs through the biological N2-fixation to ammonium as result of the symbiosis between rhizobia and leguminous plants. These interactions allow increased crop yields on nitrogen-poor soils. Exopolysaccharides (EPS) are key components for the establishment of an effective symbiosi...
Citations
... It has been estimated that the nod gene phylogeny might correlate with the host plant, but not with rhizobial species (Liu et al. 2023). Considering that almost all the faba bean rhizobia are species in the genus Rhizobium, and they harbored similar nod genes, it could be estimated that the lateral gene transfer has happened rather frequently among these species with similar genomic background, although it may also happen between less related species (Andrews et al. 2018). ...
As a legume crop widely cultured in the world, faba bean (Vicia faba L.) forms root nodules with diverse Rhizobium species in different regions. However, the symbionts associated with this plant in Mexico have not been studied. To investigate the diversity and species/symbiovar affiliations of rhizobia associated with faba bean in Mexico, rhizobia were isolated from this plant grown in two Mexican sites in the present study. Based upon the analysis of recA gene phylogeny, two genotypes were distinguished among a total of 35 isolates, and they were identified as Rhizobium hidalgonense and Rhizobium redzepovicii, respectively, by the whole genomic sequence analysis. Both the species harbored identical nod gene cluster and the same phylogenetic positions of nodC and nifH. So, all of them were identified into the symbiovar viciae. As a minor group, R. hidalgonense was only isolated from slightly acid soil and R. redzepovicii was the dominant group in both the acid and neutral soils. In addition, several genes related to resistance to metals (zinc, copper etc.) and metalloids (arsenic) were detected in genomes of the reference isolates, which might offer them some adaptation benefits. As conclusion, the community composition of faba bean rhizobia in Mexico was different from those reported in other regions. Furthermore, our study identified sv. viciae as the second symbiovar in the species R. redzepovicii. These results added novel evidence about the co-evolution, diversification and biogeographic patterns of rhizobia in association with their host legumes in distinct geographic regions.
... Thus, Chouhan et al. (2022) reported that LGT and recombination would facilitate genetic recombination, allow the emergence of new rhizobia strains, and help some legumes to adapt and invade new geographical areas. This is also evidenced by the occurrence of phylogenetically similar symbiotic genes in different rhizobial species (Andrews et al. 2018;Wang et al. 2019;Wardell et al. 2022). ...
In this work, we analyzed the effect of water stress and acid pH on the growth of the endemic fodder legume Chamaecytisus albidus, inoculated with four strains of Bradyrhizobium, from three different symbiovars previously isolated from the plant grown in different eco-geographical areas of Morocco. We also assessed the competitiveness of the three symbiovars for plant nodulation under water stress and acidity. We analyzed the strain’s nodulation ability, rates of nodules occupancy, shoot, and root dry weights of plants grown at -100, -80, and − 60 MPa water potential, and 6.0 and 7.0 pH values. The strains CM64 and CJ2 belong to the symbiovar genistearum and strains CA20 and CB10 to the symbiovars retamae and lupini, respectively. The strains CB10 and CJ2 were the most infective regardless of the pH and water potential at which the plants were grown. The strain CB10 was also the most abundant in nodules from plants grown at any conditions examined. Reductions in the water potential altered the nodulation ability, the strains CB10 and CJ2 still being the more infective. These strains were also the most infective at pH 6.0 and 7.0. The highest values of shoot and root dry weights were recorded in plants inoculated with strain CA20 under all the irrigation regimes used. The reduction from 100% to 80 and 60% field capacity decreased the shoot dry weight of the plants by 31.23 and 67.06%, respectively. Moreover, there was a 37.95 and 61.74% decrease in plant root dry weight when grown at 80 and 60% of field capacity, respectively. Despite variations in the efficiency of each strain, overall, the pH did not affect either the SDW or the RDW of the plants. The inoculation of C. albidus with a mix of the four strains did not result in further improvement of nodulation or symbiotic efficiency. These results show that water deficiency drastically affects the growth of C. albidus and that the retamae symbiovar was the most effective under the conditions examined. This is the first report on the competitiveness of symbiovars for the nodulation of a legume under stress.
... present study on D. cinerea-Ensifer reinforces the notion that Ensifer is the dominant root nodule microsymbiont of native and invasive legumes in alkaline soils of India, and that the enormous genetic diversity of Ensifer has been created through horizontal gene transfer (HGT) resulting in several mosaic combinations of core and sym genes Sankhla et al. 2017;Andrews et al. 2018;Chouhan et al. 2022). ...
Dichrostachys cinerea (L.) Wight & Arn, which belongs to the Mimosoid clade of the legume subfamily Caesalpinioideae, was introduced into India and has since become invasive across wide areas of the country. It is nodulated, and like all other mimosoids it has indeterminate nodules with its microsymbionts housed in membrane-bound symbiosomes rather than within cell wall-enclosed fixation threads. Fifty-eight bacterial strains were isolated from root nodules on plants growing in soils from 13 sampling sites in India with various agroclimatic conditions. Genetic analysis of 36 strains resulted in diverse RAPD genotypes, with equal composition of Ensifer and Bradyrhizobium as its root nodule microsymbionts. Multi locus sequence analysis (MLSA) of 12 strains using the recA, glnII, atpD and 16S rRNA genes revealed significant genetic diversity forming novel clades and lineages and are potential new species. The D. cinerea strains were variants of local symbionts previously described as rhizobia associated with native and exotic mimosoid trees, as well as rhizobia associated with the non-mimosoid Caesalpinioid shrub Chamaecrista pumila and wild Papilionoid legumes from India. The symbiosis essential genes (nodA and nifH) of the D. cinerea strains were diverse and clustered according to geographical origin. Mosaic combinations of core and sym genes were harbored by both Ensifer and Bradyrhizobium suggesting gradual diversification and microevolution of rhizobia under pressure from the host in combination with edaphic and environmental factors. The dominant microsymbionts of native and invasive legumes, including D. cinerea, in alkaline soils of India are essentially of the ‘E. aridi’ and B. yuanmingense types. Dichrostachys cinerea rhizobia were symbiotically efficient on their homologous host, but also have ability to nodulate the crop Vigna radiata, and hence may be good candidates to be used for inoculants on legume crops as well as on Mimosoid trees (P. cineraria, V. nilotica, V. raddiana, S. senegal) used in sustainable agroforestry practices to enhance soil nitrogen content.
... Among these plasmids, one plasmid, called the symbiotic plasmid (pSym), carries the majority of the genes involved in nodulation (nod) and N fixation (nif and fix) 7,18,21 . However, other plasmids can also carry other copies of these genes (e.g., fixGHIS and NOQP), as well as, in some strains, the only copy of fixL 8,9,34 . ...
... can be maintained in various diverging bacteria lineages. The results of several studies have shown that horizontal transfer of symbiosis-related genes is far more frequent between closely related strains within a single species or genus than between species of different genera [7][8][9]37,67 . In these cases, the phylogenetic analysis of more than two symbiosis genes can be required. ...
Red clover (Trifolium pratense L.) is a forage legume cultivated worldwide. This plant is capable of establishing a nitrogen-fixing symbiosis with Rhizobium leguminosarum symbiovar trifolii strains. To date, no comparative analysis of the symbiotic properties and heterogeneity of T. pratense microsymbionts derived from two distinct geographic regions has been performed. In this study, the symbiotic properties of strains originating from the subpolar and temperate climate zones in a wide range of temperatures (10–25 °C) have been characterized. Our results indicate that all the studied T. pratense microsymbionts from two geographic regions were highly efficient in host plant nodulation and nitrogen fixation in a wide range of temperatures. However, some differences between the populations and between the strains within the individual population examined were observed. Based on the nodC and nifH sequences, the symbiotic diversity of the strains was estimated. In general, 13 alleles for nodC and for nifH were identified. Moreover, 21 and 61 polymorphic sites in the nodC and nifH sequences were found, respectively, indicating that the latter gene shows higher heterogeneity than the former one. Among the nodC and nifH alleles, three genotypes (I–III) were the most frequent, whereas the other alleles (IV–XIII) proved to be unique for the individual strains. Based on the nodC and nifH allele types, 20 nodC-nifH genotypes were identified. Among them, the most frequent were three genotypes marked as A (6 strains), B (5 strains), and C (3 strains). Type A was exclusively found in the temperate strains, whereas types B and C were identified in the subpolar strains. The remaining 17 genotypes were found in single strains. In conclusion, our data indicate that R. leguminosarum sv. trifolii strains derived from two climatic zones show a high diversity with respect to the symbiotic efficiency and heterogeneity. However, some of the R. leguminosarum sv. trifolii strains exhibit very good symbiotic potential in the wide range of the temperatures tested; hence, they may be used in the future for improvement of legume crop production.
... Through the ability of bacteroids to reduce atmospheric N 2 to NH 3 in root nodules, legume plants are an option for use in sustainable agriculture in place of chemical N fertilizers [12]. About 70% of legume species are able to enter into a symbiotic relationship with compatible strains of N 2 -fixing rhizobia in soils [13,14]. The legume/rhizobia symbiosis can contribute about 80% of N to agricultural systems [15], as well as to soil health. ...
Improving the efficiency of the legume–rhizobia symbiosis in African soils for increased grain yield would require the use of highly effective strains capable of nodulating a wide range of legume plants. This study assessed the photosynthetic functioning, N2 fixation, relative symbiotic effectiveness (%RSE) and C assimilation of 22 jack bean (Canavalia ensiformis L.) microsymbionts in Eswatini soils as a first step to identifying superior isolates for inoculant production. The results showed variable nodule number, nodule dry matter, shoot biomass and photosynthetic rates among the strains tested under glasshouse conditions. Both symbiotic parameters and C accumulation differed among the test isolates at the shoot, root and whole-plant levels. Although 7 of the 22 jack bean isolates showed much greater relative symbiotic efficiency than the commercial Bradyrhizobium strain XS21, only one isolate (TUTCEeS2) was statistically superior to the inoculant strain, which indicates its potential for use in inoculant formulation after field testing. Furthermore, the isolates that recorded high %RSE elicited greater amounts of fixed N.
... Also, the nodC sequences of strains WYCCWR 13022, WYCCWR 12699 and WYCCWR 12677, three B. zhengyangense strains including WYCCWR 13023 T , WYCCWR 12678 and WYCCWR 12774, B. guangxiense CCBAU 53363 T , B. guangzhouense CCBAU 51670 T and B. guangdongense CCBAU 51649 T were identical and clearly separated from other Bradyrhizobium species (Figure 5 and Figure S4). This indicates that horizontal transfer of nodA, nodC and nifH genes involved in nodulating peanut is common between Bradyrhizobium species in soils used to grow the crop in China [5,6]. ...
A total of 219 rhizobial strains isolated from peanut grown in soils from six peanut croplands in Zhengyang county, Henan Province, were typed by PCR-RFLP of IGS sequences. Their phylogenetic relationships were refined on representative strains using sequence analyses of 16S rRNA genes, housekeeping genes (atpD, recA, glnII) and symbiosis genes (nodA, nodC and nifH). The 219 rhizobial isolates were classified into 13 IGS types, and twenty representatives were defined within eight Bradyrhizobium genospecies: B. guangdongense covering 5 IGS types (75.2% of total isolates), B. guangzhouense (2 IGS types, 2.7% total isolates), B. zhengyangense (1 IGS type, 11.3% total isolates) and five novel genospecies (5 IGS types, 0.9 to 3.2% total isolates). All representative strains had identical nodA, nodC and nifH sequences except for one nifH sequence. With this one exception, these sequences were identical to those of the type strains of Bradyrhizobium species and several Bradyrhizobium genospecies isolated from peanut in different regions of China. The nodC sequences of all strains showed < 67% similarity to the closest strains on the Genbank database indicating that they are representative of a novel Bradyrhiobium symbiovar. This study has shown that (1) diverse Bradyrhizobium spp. with similar symbiosis genes nodulate peanut in different regions of China. (2) Horizontal transfer of genes involved in nodulating peanut is common between Bradyrhizobium species in soils used to grow the crop in China. (3) The strains studied here are representative of a novel Bradyrhizobium symbiovar that nodulates peanut in China. We propose the name sv. arachis for this novel symbiovar indicating that the strains were isolated from Arachis hypogaea. Results here have practical implications in relation to the selection of rhizobial inoculants for peanut in China.
... Most likely, the symbiotic genes have been transferred horizontally between the B. canariense and B. lupini strains. Horizontal transfer of symbiotic genes between rhizobia including Bradyrhizobium spp. is a widespread process and enables some native strains to emerge as microsymbionts of previously incompatible legumes (Andrews et al. 2018). ...
Background and aimsIn Morocco's semi-arid and sub-humid climates, the fodder legume Lupinus luteus is cultivated for its high economic and ecological value. In this work, we characterized some microsymbionts of L. luteus isolated by trapping from plants grown in soils of the agricultural area of Zaer, Morocco.Methods
The phenotypic and genotypic diversity, the plant growth-promoting abilities, and the symbiotic efficiency of rhizobia isolated from root nodules of L. luteus were analyzed.ResultsBased on their REP-PCR fingerprinting results, eighteen strains were selected for Multilocus sequence analysis (MLSA) using rrs, glnII, gyrB, recA, and rpoB housekeeping genes, which revealed that all the strains belong to the genus Bradyrhizobium. Some strains were close to B. lupini and B. canariense. However, the remaining strains grouped apart from all described Bradyrhizobium species. Phylogenetic analysis of the nodA and nodC symbiotic genes showed that all the strains are members of the symbiovar genistearum. Quantitative evaluation of selected plant growth-promoting activities showed that the strains solubilize phosphate, and produce auxins and siderophores. All the strains used as inoculum in greenhouse experiments significantly improved the growth of L. luteus under nitrogen-free conditions.Conclusions
Bradyrhizobium lupini and B. canariense are the main rhizobia nodulating L. luteus in the Zaer region. In addition to their high nitrogen fixation efficiency, these isolates also exhibit plant growth-promoting activities. These results highlighted one of the major reasons for the success of yellow lupine in this area without nitrogen fertilizers and pointed to the possibility of formulating these rhizobia into an effective inoculum for L. luteus.
... While the genomic and the nod phylogenies were congruent for the two isolates from Salta, a similar relationship was not observed for the isolates from Jujuy. The horizontal gene transfer of symbiotic and nonsymbiotic genes among rhizobia has been well documented in the literature [62][63][64]. The results presented here are consistent with the existence of a common genomic ancestor for the two isolates from Jujuy and for S. psoraleae, which should then have also acquired the corresponding nod information and the ability to nodulate Desmanthus and/or Sesbania and/or Psoralea. ...
Desmanthus spp. are legumes with the ability to associate with diverse α-proteobacteria—a microsymbiont—in order to establish nitrogen-fixing root nodules. A previous investigation from our laboratory revealed that the main bacteria associated with Desmanthus paspalaceus in symbiosis in central Argentina (Province of Santa Fe) were quite diverse and belonged to the genera Rhizobium and Mesorhizobium. To achieve a more extensive view of the local microsymbionts associated with Desmanthus spp., we sampled three different sites in Jujuy and Salta, in northwest Argentina. Matrix-assisted Laser-Desorption-Ionization Time-of-Flight mass spectrometry (MALDI-TOF) typing, 16S-rDNA analysis, and genome sequencing demonstrated that the dominant root-nodule microsymbionts belonged to the genus Sinorhizobium, with some sequenced genomes related to Sinorhizobium mexicanum, Sinorhizobium chiapanecum, and Sinorhizobium psoraleae. An analysis of nodA and nodC markers indicated that, in some of the isolates, horizontal gene transfer appeared to be responsible for the lack of congruence between the phylogenies of the chromosome and of the symbiotic region. These results revealed diverse evolutionary strategies for reaching the current Desmanthus-microsymbiont diversity. What is remarkable beside their observed genetic diversity is that the tolerance profiles of these isolates to abiotic stresses (temperature, salt concentration, pH) were quite coincident with the separation of the sinorhizobia according to place of origin, suggesting possible ecoedaphic adaptations. This observation, together with the higher aerial dry-weight matter that some isolates generated in Desmanthus virgatus cv. Marc when compared to the biomass generated by the commercial strain Sinorhizobium terangae CB3126, distinguish the collected sinorhizobia as constituting valuable germplasm for evaluation in local fields to select for more efficient symbiotic pairs.
... A substantial number of benefits other than N fixation point to close coordination between the host and the symbiont while acquiring this capacity. The horizontal transfer of genes appears to have played an important role in improving the symbiotic functionality of the bacterium [144,145]. Gaining insight into these evolutionary events could provide a broader base for strain improvement. The genetic engineering tools have demonstrated how specific bacterial functions can be transferred across even unrelated species. ...
Rhizobial symbiotic interactions are known for nitrogen fixation, providing commercial crops and other plants with self-sufficiency in nitrogen requirements. An enormous contribution from nitrogen fixation is vital to the global nitrogen cycle. The symbiotic nitrogen reduces the carbon footprint of crop cultivation, which underlines its importance in agricultural sustainability. Extensive research efforts have been made to understand the symbiotic relationship at molecular, physiological, and ecological levels. This led to the isolation and modification of symbiotic strains for enhanced nitrogen efficiency. During the evaluation of strains for nitrogen fixation in exchange for supporting the bacterium in terms of space and resources, it has been observed that the accrued benefits to the host plants extend well beyond the nitrogen fixation. The symbiotic interaction has been advantageous to the host for better growth and development, tolerating a stressful environment, and even keeping the pathogenic microbial enemies at bay. Additionally, it enabled the availability of the mineral nutrients, which otherwise were inaccessible to the host. In this chapter, we bring together the information with a focus on the role of rhizobial symbiotic interactions that promote plant growth and productivity through phytohormone synthesis, by facilitating the availability of mineral nutrients, and by improving the plant tolerance to sub-optimal growth conditions.
... Alternatively, gene gain via horizontal transfer and duplication can lead to rapid adaptation across symbiotic species. For example, several mutualistic soil bacteria with nitrogen-fixing capabilities have benefited from receiving "symbiont islands" and plasmids enriched with nitrogen-fixing genes (Sullivan and Ronson, 1998;Andrews et al., 2018). Vertically transmitted symbionts are no exception to this phenomenon and can acquire novel phenotypes that benefit Frontiers in Microbiology 02 frontiersin.org ...
Vertically transmitted (VT) microbial symbionts play a vital role in the evolution of their insect hosts. A longstanding question in symbiont research is what genes help promote long-term stability of vertically transmitted lifestyles. Symbiont success in insect hosts is due in part to expression of beneficial or manipulative phenotypes that favor symbiont persistence in host populations. In Spiroplasma , these phenotypes have been linked to toxin and virulence domains among a few related strains. However, these domains also appear frequently in phylogenetically distant Spiroplasma, and little is known about their distribution across the Spiroplasma genus. In this study, we present the complete genome sequence of the Spiroplasma symbiont of Drosophila atripex , a non-manipulating member of the Ixodetis clade of Spiroplasma , for which genomic data are still limited. We perform a genus-wide comparative analysis of toxin domains implicated in defensive and reproductive phenotypes. From 12 VT and 31 non-VT Spiroplasma genomes, ribosome-inactivating proteins (RIPs), OTU-like cysteine proteases (OTUs), ankyrins, and ETX/MTX2 domains show high propensity for VT Spiroplasma compared to non-VT Spiroplasma . Specifically, OTU and ankyrin domains can be found only in VT- Spiroplasma , and RIP domains are found in all VT Spiroplasma and three non-VT Spiroplasma . These domains are frequently associated with Spiroplasma plasmids, suggesting a possible mechanism for dispersal and maintenance among heritable strains. Searching insect genome assemblies available on public databases uncovered uncharacterized Spiroplasma genomes from which we identified several spaid -like genes encoding RIP, OTU, and ankyrin domains, suggesting functional interactions among those domain types. Our results suggest a conserved core of symbiont domains play an important role in the evolution and persistence of VT Spiroplasma in insects.
