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PubMed2025

Partners in root nodule symbiosis respond uniquely to heavy metal stresses in a host genotype-dependent manner.

The mutualistic symbiosis between legume roots and soil rhizobia culminates in the formation of root nodules, where nitrogen is fixed. Root nodule symbiosis is inhibited by heavy metal stress. In this study, we investigated the relative responses of the symbiotic partners to a non-essential heavy metal cadmium (Cd) and an essential heavy metal zinc (Zn) stress and identified patterns in gene expression. We performed dual transcriptomics in nodules, using the Medicago truncatula-Sinorhizobium meliloti symbiotic system. Phenotypes were measured in the wild-type Medicago truncatula and a mutant in an ABC transporter gene (Mtabcg36), which showed compromised nodule formation in control conditions and further after heavy metal treatment. We observed that the rhizobia were particularly sensitive to Zn in mutant nodules. The greatest degree of differential gene expression in the host plant were observed under Cd and Zn treatments in wild-type nodules. Most Cd-regulated host genes were also differentially regulated by Zn, revealing little discernment between an essential and a non-essential ion under increased exposure. Furthermore, the host response to both the stresses affected auxin and iron homeostasis genes in a host genotype-dependent manner. Our results suggested impaired cadmium export from the mutant nodules. These results have potential implications in agricultural management systems and bioremediation strategies.

Symbiosis↗
PubMed2026

Genomic and Molecular Interaction Analysis of NodD1 in a Novel Bradyrhizobium yuanmingense sp. B64 Isolate for Nodulation and Symbiosis of Legume Plants.

Rhizobial bacteria are known for their ability to fix nitrogen for leguminous plants and their essential function for sustainable agriculture. This study characterizes the taxonomic status and functional potential of the Bradyrhizobium B64 isolate using integrated genomic and molecular approaches. The whole genome of the B64 isolate was sequenced via Illumina paired-end technology. Species delimitation was performed using average nucleotide identity (ANI) and digital DNA-DNA Hybridization (dDDH). The NodD1 protein structure was modeled using AlphaFold3 and validated by Ramachandran plot analysis. Molecular docking was then conducted to evaluate interactions between NodD1 and four signaling flavonoids: Apigenin, Daidzein, Genistein, and Naringenin. Genomic analysis revealed a maximum ANI of 94.4% and dDDH values between 51.4 and 62.4%. Since these values fall below the standard prokaryotic thresholds (ANI&#x2009;<&#x2009;95%; dDDH&#x2009;<&#x2009;70%), the B64 isolate is identified as a novel species. Physiological assays confirmed nitrogen fixation (1.97 ppm), IAA production (3.67 ppm), and phosphate solubilization (26.10 ppm). Structural validation showed 100% of NodD1 residues in allowed regions, ensuring high model reliability. Docking simulations demonstrated strong binding affinities across all flavonoids, with binding free energies ranging from -&#x2009;8.8 to -&#x2009;9.0&#xa0;kcal/mol. Daidzein exhibited the highest thermodynamic stability (-&#x2009;9.0&#xa0;kcal/mol), whereas apigenin showed the most extensive residue interaction network. The B64 isolate is a novel Bradyrhizobium species with a high symbiotic capacity. The stable NodD1-flavonoid interactions provide a molecular basis for efficient nodulation, positioning B64 as a promising candidate for developing lipo-chitooligosaccharide (LCO)-based biofertilizers.

Bradyrhizobium↗
PubMedDate not supplied

Study of the inducer effect of molasses and soybean cake on synthesis and excretion of nodulation factors in different strains of Bradyrhizobium japonicum.

It is known that the synthesis of nodulation factors by the bacteria within the genera Rhizobium is induced by different compounds, mainly of flavonoid nature exudated by the legume plants. The capacity of different compounds to act as inducers of nod genes on three Bradyrhizobium japonicum strains was studied in this paper and this effect was compared using two concentrations of the inducer. Induced Nod factors were observed among the strains exposed to the inducers. The profiles and amount of induced Nod factors depend on the type and concentration of the inducer, and the strains.

Bacterial Proteins↗
PubMed2001

Lectin-like glycoprotein PsNLEC-1 is not correctly glycosylated and targeted in boron-deficient pea nodules.

Symbiosome development was studied in pea root nodules from plants growing in the absence of boron (B). Rhizobia released into the host cells of nodules from B-deficient plants developed to abnormal endophytic forms with an altered electrophoretic lipopolysaccharide pattern. Immunostaining after sodium dodecyl sulfate-polyacrylamide gel electrophoresis and electroblotting of nodule homogenates with antibodies that recognize glycoprotein components showed that two previously described lectin-like glycoproteins (PsNLEC-1A and PsNLEC-1B) did not harbor the carbohydrate epitope normally recognized by specific monoclonal antibodies. Material derived from B-deficient nodules, however, still contained three antigenic isoforms with similar electrophoretic mobilities to PsNLEC-1 isoforms A, B, and C. These could be detected following immunoblotting and immunostaining with a specific antiserum originating from the purified PsNLEC protein that had been heterologously expressed in Escherichia coli. Immunogold localization of PsNLEC-1 sugar epitopes in B-deficient nodules showed that they were associated mostly with cytoplasmic vesicles rather than normal localization in the symbiosome compartment of mature infected cells. These results suggest that a modification of the glycosyl-moieties of PsNLEC-1 and an alteration of vesicle targeting occur during the development of pea nodules in the absence of B, and that these changes are associated with the development of aberrant nonfunctional symbiosomes.

Animals↗
PubMed2007

Inactivation of the nodH gene in Sinorhizobium sp. BR816 enhances symbiosis with Phaseolus vulgaris L.

Sulfate modification on Rhizobium Nod factor signaling molecules is not a prerequisite for successful symbiosis with the common bean (Phaseolus vulgaris L.). However, many bean-nodulating rhizobia, including the broad host strain Sinorhizobium sp. BR816, produce sulfated Nod factors. Here, we show that the nodH gene, encoding a sulfotransferase, is responsible for the transfer of sulfate to the Nod factor backbone in Sinorhizobium sp. BR816, as was shown for other rhizobia. Interestingly, inactivation of nodH enables inoculated bean plants to fix significantly more nitrogen under different experimental setups. Our studies show that nodH in the wild-type strain is still expressed during the later stages of symbiosis. This is the first report on enhanced nitrogen fixation by blocking Nod factor sulfation.

Bacterial Proteins↗
PubMed2007

Negotiation of mutualism: rhizobia and legumes.

The evolution and persistence of biological cooperation have been an important puzzle in evolutionary theory. Here, we suggest a new approach based on bargaining theory to tackle the question. We present a mechanistic model for negotiation of benefits between a nitrogen-fixing nodule and a legume plant. To that end, we first derive growth rates for the nodule and plant from metabolic models of each as a function of material fluxes between them. We use these growth rates as pay-off functions in the negotiation process, which is analogous to collective bargaining between a firm and a workers' union. Our model predicts that negotiations lead to the Nash bargaining solution, maximizing the product of players' pay-offs. This work introduces elements of cooperative game theory into the field of mutualistic interactions. In the discussion of the paper, we argue for the benefits of such an approach in studying the question of biological cooperation.

Biological Evolution↗
PubMed2004

Nonlegumes, legumes, and root nodules harbor different arbuscular mycorrhizal fungal communities.

Legumes are an important plant functional group since they can form a tripartite symbiosis with nitrogen-fixing Rhizobium bacteria and phosphorus-acquiring arbuscular mycorrhizal fungi (AMF). However, not much is known about AMF community composition in legumes and their root nodules. In this study, we analyzed the AMF community composition in the roots of three nonlegumes and in the roots and root nodules of three legumes growing in a natural dune grassland. We amplified a portion of the small-subunit ribosomal DNA and analyzed it by using restriction fragment length polymorphism and direct sequencing. We found differences in AMF communities between legumes and nonlegumes and between legume roots and root nodules. Different plant species also contained different AMF communities, with different AMF diversity. One AMF sequence type was much more abundant in legumes than in nonlegumes (39 and 13%, respectively). Root nodules contained characteristic AMF communities that were different from those in legume roots, even though the communities were similar in nodules from different legume species. One AMF sequence type was found almost exclusively in root nodules. Legumes and root nodules have relatively high nitrogen concentrations and high phosphorus demands. Accordingly, the presence of legume- and nodule-related AMF can be explained by the specific nutritional requirements of legumes or by host-specific interactions among legumes, root nodules, and AMF. In summary, we found that AMF communities vary between plant functional groups (legumes and nonlegumes), between plant species, and between parts of a root system (roots and root nodules).

DNA, Fungal↗
PubMed1976

Synthesis and turnover of leghaemoglobin in lupin root nodules.

1. The problem of whether leghaemoglobin is synthesized on plant of bacterial ribosomes in root nodules of yellow lupin has been examined. 2. Leghaemoglobin, soluble plant protein and soluble bacteroid protein were labelled with 14C administered by uptake of 14CO2. 3. Exposure of roots to 1 mM D-threo-chloramphenicol resulted in inhibition of soluble bacteroid protein synthesis, but leghaemoglobin synthesis and soluble plant protein synthesis were unaffected. This result is consistent with leghaemoglobin being synthesized on plant ribosomes. 4. After nitrogen-fixing plants had been supplied with a pulse of 14CO2, the decay of specific radioactivity of nodule protein fractions was observed. Leghaemoglobin had an apparent half-life of 18 days and is a stable protein in nitrogen-fixing yellow lupin nodules.

Chloramphenicol↗
PubMed2005

Symbiotic leghemoglobins are crucial for nitrogen fixation in legume root nodules but not for general plant growth and development.

Hemoglobins are ubiquitous in nature and among the best-characterized proteins. Genetics has revealed crucial roles for human hemoglobins, but similar data are lacking for plants. Plants contain symbiotic and nonsymbiotic hemoglobins; the former are thought to be important for symbiotic nitrogen fixation (SNF). In legumes, SNF occurs in specialized organs, called nodules, which contain millions of nitrogen-fixing rhizobia, called bacteroids. The induction of nodule-specific plant genes, including those encoding symbiotic leghemoglobins (Lb), accompanies nodule development. Leghemoglobins accumulate to millimolar concentrations in the cytoplasm of infected plant cells prior to nitrogen fixation and are thought to buffer free oxygen in the nanomolar range, avoiding inactivation of oxygen-labile nitrogenase while maintaining high oxygen flux for respiration. Although widely accepted, this hypothesis has never been tested in planta. Using RNAi, we abolished symbiotic leghemoglobin synthesis in nodules of the model legume Lotus japonicus. This caused an increase in nodule free oxygen, a decrease in the ATP/ADP ratio, loss of bacterial nitrogenase protein, and absence of SNF. However, LbRNAi plants grew normally when fertilized with mineral nitrogen. These data indicate roles for leghemoglobins in oxygen transport and buffering and prove for the first time that plant hemoglobins are crucial for symbiotic nitrogen fixation.

Adenosine Triphosphate↗
PubMedDate not supplied

[Lipopolysaccharides of rhizobiaceae: structure and biosynthesis].

The lipopolysaccharides (LPS) are major components of the outer membrane of Gram negative bacteria and, because of their location, are important mediators in the interaction between these bacteria and their environment and other organisms. The alpha-Proteobacterial family Rhizobiaceae includes the rhizobia and agrobacteria, microorganisms which establish symbiotic or parasitic relationships with plants. Mutants deficient in LPS biosynthesis show anomalous interactions with their hosts. The agronomical relevance of the relationship between rhizobia and agrobacteria with plants has promoted a large number of studies on the LPS from these bacteria. The complete structures of one or several domains of LPS from Rhizobiaceae have been determined in the last years. Additionally, several metabolic steps in the biosynthesis of these molecules have been elucidated. This review aims at the description of the more recent findings on the structure and biosynthesis of LPS in Rhizobium, Sinorhizobium and Agrobacterium.

Carbohydrate Sequence↗
PubMed1984

A transmissible plant shoot factor promotes uptake hydrogenase activity in Rhizobium symbionts.

Shoot/root grafting studies showed organ and host cultivar effects on net H(2) evolution from Pisum sativum L. root nodules. Net H(2) evolution from those nodules represents the sum of H(2) formed by Rhizobium nitrogenase and H(2) oxidized by any uptake hydrogenase present in the bacteria. Grafts between pea cultivars ;JI1205' or ;Alaska' and ;Feltham First' in symbioses with R. leguminosarum 128C53 showed that shoots of both JI1205 and Alaska increased H(2) uptake significantly (P </= 0.05) in Feltham First root nodules. The same plants also had less net H(2) evolution at similar rates of C(2)H(2) reduction than plants formed by grafting Feltham First shoots on Feltham First roots. Although JI1205 and Alaska shoots increased H(2)-uptake activity of Feltham First root nodules 28 days after the graft was made, intermediate to high levels of H(2) uptake activity were still present in nodules on roots of both JI1205 and Alaska grafted to Feltham First shoots. These results indicate the presence of a transmissible shoot factor(s) which can increase uptake hydrogenase activity in a Rhizobium symbiont and show that root genotype also can influence that parameter.Parallel grafting experiments using the same pea cultivars in symbioses with R. leguminosarum strain 300, which lacks uptake hydrogenase activity, suggested that a transmissible shoot factor(s) altered H(2) formation from nitrogenase by changing the electron allocation coefficient of that enzyme complex.The root and shoot factor(s) detected in this study had no permanent effect on strain 128C53. Bacterial cells isolated from Feltham First nodules with low H(2) uptake activity formed root nodules on JI1205 and Alaska with high H(2) uptake activity. Bacteroids isolated from nodules on intact JI1205, Alaska, or Feltham First plants with high, medium, or low H(2) uptake activity, respectively, maintained those phenotypes during in vitro assays.

Journal Article↗
PubMed2006

Interplay of Darwinian and frequency-dependent selection in the host-associated microbial populations.

In order to analyze the microevolutionary processes in host-associated microorganisms, we simulated the dynamics of rhizobia populations composed of a parental strain and its mutants possessing the altered fitness within "plant-soil" system. The population dynamics was presented as a series of cycles (each one involves "soil-->rhizosphere-->nodules-->soil" succession) described using recurrent equations. For representing the selection and mutation pressures, we used a universal approach based on calculating the shifts in the genetic ratios of competing bacterial genotypes within the particular habitats and across several habitats. Analysis of the model demonstrated that a balanced polymorphism may be established in rhizobia population: mutants with an improved fitness do not supplant completely the parental strain while mutants with a decreased fitness may be maintained stably. This polymorphism is caused by a rescue of low-fitted genotypes via negative frequency-dependent selection (FDS) that is implemented during inoculation of nodules and balances the Darwinian selection that occurs during multiplication or extinction of bacteria at different habitats. The most diverse populations are formed if the rhizobia are equally successful in soil and nodules, while a marked preference for any of these habitats results in the decrease of diversity. Our simulation suggests that FDS can maintain the mutualistic rhizobia-legume interactions under the stress conditions deleterious for surviving the bacterial strains capable for intensive N2 fixation. Genetic consequences of releasing the modified rhizobia strains may be addressed using the presented model.

Colony Count, Microbial↗
PubMed2006

Plant water status, ethylene evolution, N(2)-fixing efficiency, antioxidant activity and lipid peroxidation in Cicer arietinum L. nodules as affected by short-term salinization and desalinization.

Salinity induced changes in ethylene evolution, antioxidant defense system, N(2)-fixing efficiency and membrane integrity in relation to water and mineral status in chickpea (Cicer arietinum L.) nodules were studied under screen house conditions. At vegetative stage (55-65 DAS) plants were exposed to single saline irrigation (Cl(-) dominated) of levels 0, 2.5, 5.0 and 10.0dSm(-1) and sampled after 3d. The other set of treated plants was desalinized by flooding and the plants were sampled after further 3d. Water potential (Psiw) of leaf and osmotic potential (Psis) of leaf and nodules significantly decreased from -0.44 to -0.56MPa and from -0.65 to -1.15MPa and from -0.75 to -1.77MPa, respectively upon salinization. RWC of leaf and nodules also reduced from 86.05% to 73.30% and 94.70% to 89.98%, respectively. The decline in Psis of nodules was due to accumulation of proline and total soluble sugar. In comparison to control, the increase in ethylene (C(2)H(4)) production was 35-108% higher and correspondingly increase in 1-aminocycloprane-1-carboxylic acid (ACC) content (37-126%) and ACC oxidase activity (31-118%) was also noticed. Similarly, marked increase in H(2)O(2) (25-139%) and thiobarbituric acid substances (TBRAS, 11-133%) contents was seen. N(2)-fixing efficiency i.e. N(2)-ase activity, leghemoglobin and N contents of nodules declined significantly after saline irrigation. The induction in specific activity of antioxidant enzymes was confirmed by the increase in activity of superoxide dismutase, peroxidase, ascorbate peroxidase, glutathione reductase and glutathione transferase, whereas reverse was true for catalase. These activated enzymes could not overcome the accumulation of H(2)O(2) in nodules. Ascorbic acid content also declined from 20 to 38%, whereas Na(+)/K(+) ratio and Cl(-) content were significantly enhanced. Upon desalinization, a partial recovery in all above metabolic processes and water relations parameters was noticed. It is suggested that ethylene in relation to water status and lipid peroxidation and along with other metabolic processes has an important role in induced nodules senescence under salinity.

Antioxidants↗
PubMed1998

Direct detection of radicals in intact soybean nodules: presence of nitric oxide-leghemoglobin complexes.

Electron paramagnetic resonance spectroscopy has been employed to examine the nature of the metal ions and radicals present in intact root nodules of soybean plants grown in the absence of nitrate. The spectra obtained from nodules of different ages using this non-invasive technique show dramatic differences, suggesting that there are both qualitative and quantitative changes in the metal ion and radical species present. A major component of the spectra obtained from young nodules is assigned to a complex (Lb-NO) of nitric oxide (NO.) with the heme protein leghemoglobin (Lb). This Lb-NO species, which has not been previously detected in intact root nodules of plants grown in the absence of nitrate, is thought to be formed by reaction of nitric oxide with iron(II) leghemoglobin. The nitric oxide may be generated from arginine via a nitric oxide synthase-like activity present in the nodules of the soybean plants, in a manner analogous to that recently described for Lupinus albus. This Lb-NO complex is present at lower concentrations in older nodules, and is almost completely absent from senescent nodules. Exposure of young and mature nodules to oxidant stress, in the form of hydrogen peroxide, results in changes in the EPR spectra, with the loss of the signals from the Lb-NO complex and appearance of absorptions similar to those from untreated senescent nodules. These results suggest that there are characteristic changes in both the metal ion complexes and radicals present in intact root nodules of different ages, and support the theory that nitric oxide and other radicals play a significant role in determining the nitrogen fixing activity of root nodules; the modulatory activity of NO. may involve regulation of gene activity.

Electron Spin Resonance Spectroscopy↗
PubMed1985

Deletion analysis of Rhizobium meliloti symbiotic promoters.

Previous examination of DNA sequences located 5' to Rhizobium meliloti nif transcription units has shown that extensive sequence homology exists among them. Here we have examined these reiterated sequences for their role in symbiotic gene regulation. Promoter deletion analysis has shown that although an extensive upstream DNA sequence 9160 bp) is required for full heterologous activation of the R. meliloti nifHDK promoter by the Klebsiella pneumoniae nifA protein in Escherichia coli, this region is not required for expression of R. Meliloti nif promoters in root nodules from plants grown under greenhouse conditions. In addition, a minimum functional symbiotic promoter sequence is defined, and a DNA sequence difference affecting regulation of two symbiotic promoters is discussed.

Bacterial Proteins↗