Soybean Nodules Research Articles

Soil P-stimulating bacterial communities: response and effect assessment of long-term fertilizer and rhizobium inoculant application

BackgroundPhosphorus (P) plays a vital role in plant growth. The pqqC and phoD genes serve as molecular markers for inorganic and organic P breakdown, respectively. However, the understanding of how P-mobilizing bacteria in soil respond to long-term fertilization and rhizobium application is limited. Herein, soil that had been treated with fertilizer and rhizobium for 10 years was collected to investigate the characteristics of P-mobilizing bacterial communities. Five treatments were included: no fertilization (CK), phosphorus fertilizer (P), urea + potassium fertilizer (NK), NPK, and PK + Bradyrhizobium japonicum 5821 (PK + R).ResultsThe soybean nodule dry weight was highest in the P treatment (1.93 g), while the soybean yield peaked in the PK + R treatment (3025.33 kg ha− 1). The abundance of the pqqC gene increased in the rhizosphere soil at the flowering-podding stage and in the bulk soil at the maturity stage under the P treatment, while its abundance increased in the bulk soil at the flowering-podding stage and in the rhizosphere soil at the maturity stage under the PK + R treatment. The abundance of the phoD gene was enhanced in the bulk soil at the flowering-podding stage under the PK + R treatment. The Shannon and Ace indexes of pqqC- and phoD-harboring bacteria were higher in the rhizosphere soil at maturity under the PK + R treatment compared to other treatments. Furthermore, a comprehensive analysis of the neutral community model and co-occurrence pattern demonstrated that the application of P fertilizer alone led to an increase in the distribution and dynamic movement of pqqC-harboring bacteria, but resulted in a decrease in complexity of network structure. On the other hand, rhizobium inoculation enhanced the distribution and dynamic movement of phoD-harboring bacteria, as well as the stability and complexity of the network structure. Pseudomonas and Nitrobacter, as well as Steptomyces, Stella, and Nonomuraea, may be crucial genera regulating the composition and function of pqqC- and phoD-harboring communities, respectively.ConclusionsThese findings affirm the crucial role of fertilization and rhizobium inoculation in regulating pqqC- and phoD-harboring bacterial communities, and highlight the significance of long-term phosphate-only fertilization and rhizobium inoculation in enhancing dissolved inorganic phosphorus and mineralized organophosphorus, respectively.

Combined Effect of Arbuscular Mycorrhizal Fungi and Bradyrhizobium japonicum on Growth, Yield and Nodulation in Soybean

Response of soybean for combined application of AM fungi and Bradyrhizobium japonicum were studied in pot culture experiment in completely randomized design (CRD). Dual inoculation of AM fungi and B. japonicum improved growth, yield, AMF colonization and nodulation in soybean plant, in comparison to single inoculation. Increase in the level of AMF inoculation promoted the growth significantly. Dry weight of the plant was 5.54 g/ plant and 6.02 g/ plant in plants treated with B. japonicum and AMF respectively, which significantly increased to 7.36 g/ plant up on combined application. Similar results were obtained in plant height, No. of pods /plant, seed index, nodulation, AMF density and colonization and chlamydospore population in soybean rhizosphere. Thus, the experiment signifies the importance of combined application for the improvement of crop growth and yield.

Effects of Biochar and Bradyrhizobium Inoculation on Nodulation, Growth, and Grain Yield of Soybean in the Guinea Savanna Agroecological Zone of Ghana

ABSTRACT Soybeans are a vital crop globally, significantly contributing to food security, soil fertility, and economic development. However, soil conditions can constrain their productivity, including nutrient deficiencies and acidity. This study explores the combined effects of biochar (BC) and Rhizobium inoculation (RI) on soybean growth, nodulation, and yield. The experiment was conducted over two growing seasons and employed a split-plot design with five BC application rates (0, 2, 4, 6, and 8 t ha− 1) and two RI levels (uninoculated and inoculated) across four replications. The results demonstrated that the integration of BC and RI significantly improved various growth parameters, including nodulation, biomass accumulation, pod number, and grain yield. The highest grain yield was observed at 8 t ha−1 BC with RI, yielding 3394 kg ha−1 in 2021 and 2542 kg ha−1 in 2022. This was identical to the yield attained with the 6 t ha−1 BC rate paired with RI in both years. The inoculated control treatment consistently demonstrated the lowest grain yield. Additionally, it showed a significant (p < .05) impact on the weight of one hundred seeds. The study also revealed significant and consistent relationships among soybeans’ growth and yield features. In conclusion, the findings suggest that the combined application of BC and RI has a positive impact on soybean yield and its key components.

Inorganic nitrogen inhibits symbiotic nitrogen fixation through blocking NRAMP2-mediated iron delivery in soybean nodules

Symbiotic nitrogen fixation (SNF) in legume-rhizobia serves as a sustainable source of nitrogen (N) in agriculture. However, the addition of inorganic N fertilizers significantly inhibits SNF, and the underlying mechanisms remain not-well understood. Here, we report that inorganic N disrupts iron (Fe) homeostasis in soybean nodules, leading to a decrease in SNF efficiency. This disruption is attributed to the inhibition of the Fe transporter genes Natural Resistance-Associated Macrophage Protein 2a and 2b (GmNRAMP2a&2b) by inorganic N. GmNRAMP2a&2b are predominantly localized at the tonoplast of uninfected nodule tissues, affecting Fe transfer to infected cells and consequently, modulating SNF efficiency. In addition, we identified a pair of N-signal regulators, nitrogen-regulated GARP-type transcription factors 1a and 1b (GmNIGT1a&1b), that negatively regulate the expression of GmNRAMP2a&2b, which establishes a link between N signaling and Fe homeostasis in nodules. Our findings reveal a plausible mechanism by which soybean adjusts SNF efficiency through Fe allocation in response to fluctuating inorganic N conditions, offering valuable insights for optimizing N and Fe management in legume-based agricultural systems.

An Efficient and Low-Cost Deep Learning-Based Method for Counting and Sizing Soybean Nodules

Soybeans are an essential source of food, protein, and oil worldwide, and the nodules on their root systems play a critical role in nitrogen fixation and plant growth. In this study, we tackled the challenge of limited high-resolution image quantities and the constraints on model learning by innovatively employing image segmentation technology for an in-depth analysis of soybean nodule phenomics. Through a meticulously designed segmentation algorithm, we broke down large-resolution images into numerous smaller ones, effectively improving the model’s learning efficiency and significantly increasing the available data volume, thus laying a solid foundation for subsequent analysis. In terms of model selection and optimization, after several rounds of comparison and testing, YOLOX was identified as the optimal model, achieving an accuracy of 91.38% on the test set with an R2 of up to 86%, fully demonstrating its efficiency and reliability in nodule counting tasks. Subsequently, we utilized YOLOV5 for instance segmentation, achieving a precision of 93.8% in quickly and accurately extracting key phenotypic indicators such as the area, circumference, length, and width of the nodules, and calculated the statistical properties of these indicators. This provided a wealth of quantitative data for the morphological study of soybean nodules. The research not only enhanced the efficiency and accuracy of obtaining nodule phenotypic data and reduced costs but also provided important scientific evidence for the selection and breeding of soybean materials, highlighting its potential application value in agricultural research and practical production.

Phosphate Turnover in Various Parts of Nodulated Soybean (Glycine max (L.) Merr.) Plants and the Relation to the Xylem Transport

Phosphorus is a major essential element in plants, and the absorption and transport of P are related to crop growth and productivity. Phosphate (Pi) is absorbed in the roots and transported to the shoot. Plants store surplus Pi in the vacuoles. The characteristics of Pi storage and turnover in various parts of the nodulated soybeans might be related to plant growth and P-use efficiency. This research focused on the changes in the Pi concentrations and Pi contents in each part of young soybean plants grown in Pi-sufficient (50 μM Pi) or Pi-deficient (0 μM Pi) conditions. Also, the Pi flux rate in xylem sap from roots to shoot was determined. The growth of the plants was the same after 7 days of Pi-sufficient and Pi-deficient treatments. During the Pi-deficient period, the Pi concentrations in the roots, leaves, and stems decreased significantly but did not deplete. The decrease in Pi concentration in nodules was much slower than the other parts. After the re-supply of 50 μM Pi in the solution, the Pi concentration increased only a little in each part of the Pi-deficient plants. The Pi concentration and Pi flux in the xylem sap quickly responded to the changes in the Pi concentration in the culture solution.

Rhizosphere flavonoids alleviates the inhibition of soybean nodulation caused by shading under maize-soybean strip intercropping

The flavonoids produced by legume roots are signal molecules that induce nod genes for symbiotic rhizobium. Nevertheless, the promoting effects of flavonoids in root exudates in intercropping system on soybean nodulation are still unknown. A two years of field experiments was carried with maize soybean strip intercropping, i.e., the interspecific row spacing of 30 cm (MS30), 45 cm (MS45), 60 cm (MS60), and sole soybean/maize:SS/MM, and root interaction, i.e., root no barrier (NB) and root polythene-plastic barrier (PB), to evaluate relationships between flavonoids in root exudates and nodulation. We found that root-root interaction between soybean and maize enhances the nodules number and fresh weight in intercropped soybean. This enhancement increase gradually with expansion of interspecific distance. Proportion of nodules with diameter greater than 0.4cm was higher in intercropped soybean with NB than with PB. The expressions of nodules-related genes (GmENOD40, GmNIN2b and GmEXPB2) were up-regulated. Furthermore, compared with monocropping, isoflavones secretion of soybean roots reduced, flavonoids and flavonols secretion of maize and soybean roots increased under intercropping. The secretion of differential metabolites of flavonoids in the rhizosphere of maize and soybean declined with root barrier. The expressions of GmCHS8 and GmIFS1 in soybean roots were up-regulated and GmICHG was down-regulated under root interaction. The most of the flavonoids and flavonol compounds were positively correlated with nodule diameter. The nodules number, the nodules fresh weight and the proportion of nodules with a diameter greater than 0.2 cm increased in different genotypes of soybean treated with maize root exudate, which promoted the improvement of nitrogen fixation capacity. Therefore, maize-soybean strip intercropping combined with reasonable spacing to enhance the positive effect of underground root interaction, and improve the nodulation and nitrogen fixation capacity of intercropping soybean.

SymRK regulates G-protein signaling during nodulation in soybean (Glycine max) by modifying RGS phosphorylation and activity.

Molecular inter-species dialogue between leguminous plants and nitrogen-fixing rhizobia results in the development of symbiotic root nodules. This is initiated by several nodulation-related receptors present on the surface of root hair epidermal cells. We have shown previously that specific subunits of heterotrimeric G proteins and their regulatory RGS (regulator of G-protein signaling) proteins act as molecular links between the receptors and downstream components during nodule formation in soybeans. Nod factor receptor 1 (NFR1) interacts with and phosphorylates RGS proteins to regulate the G-protein cycle. Symbiosis receptor-like kinases (SymRK) phosphorylate Gα to make it inactive and unavailable for Gβγ. We now show that like NFR1, SymRK also interacts with the RGS proteins to phosphorylate them. Phosphorylated RGS has higher GTP accelerating activity, which favors conversion of active Gα to its inactive form. Phosphorylation of RGS proteins is physiologically relevant, as overexpression of a phospho-mimic version of RGS protein enhances nodule formation in soybean. These results reveal an intricate fine-tuning of the G-protein signaling during nodulation, where a negative regulator (Gα) is effectively deactivated by RGS due to the concerted efforts of several receptor proteins to ensure adequate nodulation.

Rhizobia cystathionine γ-lyase-derived H2S delays nodule senescence in soybean.

Hydrogen sulphide (H2S) is required for optimal establishment of soybean (Glycine max)-Sinorhizobium fredii symbiotic interaction, yet its role in regulating the nitrogen fixation-senescence transition remains poorly understood. A S. fredii cystathionine γ-lyase (CSE) mutant deficient in H2S synthesis showed early nodule senescence characterized by reduced nitrogenase activity, structural changes in nodule cells, and accelerated bacteroid death. In parallel, the CSE mutant facilitated the generation of reactive oxygen species (ROS) and elicited antioxidant responses. We observed that H2S-mediated persulfidation of cysteine C31/C80 in ascorbate peroxidase (APX) and C32 in APX2 modulated enzyme activity, thereby participating in hydrogen peroxide (H2O2) detoxification and delaying nodule senescence. Comparative transcriptomic analysis revealed a significant up-regulation of GmMYB128, an MYB transcription factor (TF), in the CSE mutant nodules. Functional analysis through overexpression and RNAi lines of GmMYB128 demonstrated its role as a positive regulator in nodule senescence. MYB128-OE inoculated with the CSE mutant strain exhibited a reduction in nitrogenase activity and a significant increase in DD15 expression, both of which were mitigated by NaHS addition. Changes at the protein level encompassed the activation of plant defenses alongside turnover in carbohydrates and amino acids. Our results suggest that H2S plays an important role in maintaining efficient symbiosis and preventing premature senescence of soybean nodules.

Soybean symbiotic-nodule zonation and cell differentiation are defined by NIN2 signaling and GH3-dependent auxin homeostasis

Symbiotic nodules comprise two classes, indeterminate and determinate, defined by the presence/absence of apical meristem and developmental zonation. Why meristem and zonation are absent from determinate nodules remains unclear. Here, we define cell types in developing soybean nodules, highlighting the undifferentiated infection zones and differentiated nitrogen-fixation zones. Auxin governs infection zone maintenance. GRETCHEN HAGEN 3 (GH3) enzymes deactivate auxin by conjugation and promote cell differentiation. gh3 mutants increased undifferentiated cells and enlarged infection zones. The central symbiosis-transcription factor NIN2a activates GH3.1 to reduce auxin levels and facilitates cell differentiation. High auxin promotes NIN2a protein accumulation and enhances signaling, further deactivating auxin and depleting infection zones. Our findings shed light on the NIN2a-GH3-auxin module that drives soybean nodule cell differentiation. This study challenges our understanding of determinate nodule development and proposes that the regulation of nodule zonation offers valuable insights into broader mechanisms of cell differentiation across plant species.

Application of Protein Hydrolysate Improved the Productivity of Soybean under Greenhouse Cultivation

Protein hydrolysates are plant biostimulants containing amino acids, oligopeptides, and peptides in their composition. When supplied to plants, protein hydrolysates (HPs) have been identified to improve nitrogen metabolism, enhance the activity of antioxidant enzymes, boost plant defense response to stresses, and positively impact the quantity and quality of products. Soybean is a crucial global commodity, with nitrogen being the primary nutrient for crop development as it directly affects productivity. This study aimed to evaluate the effect of an HP-based biostimulant on the N metabolism in nodulated soybean plants and their productivity. A greenhouse experiment was conducted to test two modes of application of the 0.20% HP-based biostimulant. Soybean plants, growing in pots, were treated with 0.20% HP either via seed treatment or foliar application (at growth stages V3 and V5). Activities of enzymes and compounds related to N metabolism, gene expression, and productivity components were analyzed. It was observed that the mode of application did not significantly influence the results. The application of HPs increased the concentration of nitrate, amino acids, and ureides in soybean leaves. It also positively altered the expression of genes such as nitrate reductase, urease, and asparagine. Additionally, it enhanced productivity, resulting in plants with a greater number and weight of pods and grains. Therefore, it is possible to consider HPs as a stimulator for increasing soybean productivity, even under non-stressing conditions.

Comparative proteomics analysis of root and nodule mitochondria of soybean.

Legumes perform symbiotic nitrogen fixation through rhizobial bacteroids housed in specialised root nodules. The biochemical process is energy-intensive and consumes a huge carbon source to generate sufficient reducing power. To maintain the symbiosis, malate is supplied by legume nodules to bacteroids as their major carbon and energy source in return for ammonium ions and nitrogenous compounds. To sustain the carbon supply to bacteroids, nodule cells undergo drastic reorganisation of carbon metabolism. Here, a comprehensive quantitative comparison of the mitochondrial proteomes between root nodules and uninoculated roots was performed using data-independent acquisition proteomics, revealing the modulations in nodule mitochondrial proteins and pathways in response to carbon reallocation. Corroborated our findings with that from the literature, we believe nodules preferably allocate cytosolic phosphoenolpyruvates towards malate synthesis in lieu of pyruvate synthesis, and nodule mitochondria prefer malate over pyruvate as the primary source of NADH for ATP production. Moreover, the differential regulation of respiratory chain-associated proteins suggests that nodule mitochondria could enhance the efficiencies of complexes I and IV for ATP synthesis. This study highlighted a quantitative proteomic view of the mitochondrial adaptation in soybean nodules.

Rhizobium Inoculant and Seed-Applied Fungicide Effects Improve the Drought Tolerance of Soybean Plants as an Effective Agroecological Solution under Climate Change Conditions.

Rhizobial inoculation in combination with fungicidal seed treatment is an effective solution for improving soybean resistance to modern climate changes due to the maximum implementation of the plant's stress-protective antioxidant properties and their nitrogen-fixing potential, which will contribute to the preservation of the environment. Model ecosystems at different stages of legume-rhizobial symbiosis formation, created by treatment before sowing soybean seeds with a fungicide (fludioxonil, 25 g/L) and inoculation with an active strain of Bradyrhizobium japonicum (titer 109 cells per mL), were subjected to microbiological, biochemical, and physiological testing methods in controlled and field conditions. Seed treatment with fungicide and rhizobia showed different patterns in the dynamics of key antioxidant enzymes in soybean nodules under drought conditions. Superoxide dismutase activity increased by 32.7% under moderate stress, while catalase increased by 90.6% under long-term stress. An increase in the antioxidant enzyme activity induced the regulation of lipoperoxidation processes during drought and after the restoration of irrigation. Regeneration after stress was evident in soybean plants with a combination of fungicide seed treatment and rhizobial inoculant, where enzyme levels and lipoperoxidation processes returned to control plant levels. Applying seed treatment with fungicide and Rhizobium led to the preservation of the symbiotic apparatus functioning in drought conditions. As proof of this, molecular nitrogen fixation by nodules has a higher efficiency of 25.6% compared to soybeans without fungicide treatment. In the field, fungicidal treatment of seeds in a complex with rhizobia inoculant induced prolongation of the symbiotic apparatus functioning in the reproductive period of soybean ontogenesis. This positively affected the nitrogen-fixing activity of soybeans during the pod formation stage by more than 71.7%, as well as increasing soybean yield by 12.7% in the field. The application of Rhizobium inoculant and fungicide to seeds contributed to the development of antioxidant protection of soybean plants during droughts due to the activation of key enzymatic complexes and regulation of lipoperoxidation processes, which have a positive effect on nitrogen fixation and productivity of soybeans. This is a necessary element in soybean agrotechnologies to improve plant adaptation and resilience in the context of modern climate change.

Absorption and Xylem Transport of 33P-Labeled Phosphorus in Nodulated Soybean Plants

Phosphorus (P) is an essential macro-element for plants, and understanding the characteristics of the absorption and transport of P in crops is essential. The low availability of P restricts the growth, nitrogen fixation, and yield of soybean plants. In this research, the radioisotope 33P was supplied to the culture solution to trace the absorption and transport of P in nodulated soybean plants monitored using an imaging plate. The absorption rate of 33P was almost the same under the light and dark conditions. The absorption rate of 33P in the decapitated roots was near to that of the intact plants under light. These results indicate that the P absorption is not affected by evapotranspiration over a short time period. Conversely, the 33P transport from the roots to the shoot was significantly lower under dark conditions than it was under light conditions, although some 33P reached the top of the shoots under both the light and dark conditions. The transport of P to the shoots depends on the transpiration supplemented by the root pressure. The multiplication value of the 33P concentration in the xylem sap and transpiration rate was almost equivalent to the transport rate of 33P in the intact shoots. This value may be adaptable and used to estimate the transport rate of P for the diagnosis.

Soybean ethylene response factors GmENS1 and GmENS2 promote nodule senescence.

The final phase in root nodule development is nodule senescence. The mechanism underlying the initiation of nodule senescence requires further elucidation. Here, we investigated the intrinsic signals governing soybean (Glycine max L. Merr.) nodule senescence, uncovering ethylene as a key signal in this intricate mechanism. Two AP2/ERF transcription factor genes, GmENS1 and GmENS2 (Ethylene-responsive transcription factors required for Nodule Senescence), exhibit heightened expression levels in both aged nodules and nodules treated with ethylene. Overexpression of either GmENS1 or GmENS2 accelerated senescence in soybean nodules, whereas the knockout or knockdown of both genes delayed senescence and enhanced nitrogenase activity. Furthermore, our findings indicated that GmENS1 and GmENS2 directly bind to the promoters of GmNAC039, GmNAC018, and GmNAC030, encoding three NAC transcription factors essential for activating soybean nodule senescence. Notably, the nodule senescence process mediated by GmENS1 or GmENS2 overexpression was suppressed in the soybean nac039/018/030 triple mutant compared with the wild-type control. These data indicate GmENS1 and GmENS2 as pivotal transcription factors mediating ethylene-induced nodule senescence through the direct activation of GmNAC039/GmNAC018/GmNAC030 expression in soybean.

The role of GmHSP23.9 in regulating soybean nodulation under elevated CO2 condition

Legume-rhizobia symbiosis offers a unique approach to increase leguminous crop yields. Previous studies have indicated that the number of soybean nodules are increased under elevated CO2 concentration. However, the underlying mechanism behind this phenomenon remains elusive. In this study, transcriptome analysis was applied to identify candidate genes involved in regulating soybean nodulation mediated by elevated CO2 concentration. Among the different expression genes (DEGs), we identified a gene encoding small heat shock protein (sHSP) called GmHSP23.9, which mainly expressed in soybean roots and nodules, and its expression was significantly induced by rhizobium USDA110 infection at 14 days after inoculation (DAI) under elevated CO2 conditions. We further investigated the role of GmHSP23.9 by generating transgenic composite plants carrying GmHSP23.9 overexpression (GmHSP23.9-OE), RNA interference (GmHSP23.9-RNAi), and CRISPR-Cas9 (GmHSP23.9-KO), and these modifications resulted in notable changes in nodule number and the root hairs deformation and suggesting that GmHSP23.9 function as an important positive regulator in soybean. Moreover, we found that altering the expression of GmHSP23.9 influenced the expression of genes involved in the Nod factor signaling pathway and AON signaling pathway to modulate soybean nodulation. Interestingly, we found that knocking down of GmHSP23.9 prevented the increase in the nodule number of soybean in response to elevated CO2 concentration. This research has successfully identified a crucial regulator that influences soybean nodulation under elevated CO2 level and shedding new light on the role of sHSPs in legume nodulation.

Effects of the Concentrations of Nitrogen Supplied From Both or One-Half of the Dual-Root System on the Nitrogen Fixation of Soybean Nodules and the Distribution of Absorbed Nitrogen From Roots

Effects of the Concentrations of Nitrogen Supplied From Both or One-Half of the Dual-Root System on the Nitrogen Fixation of Soybean Nodules and the Distribution of Absorbed Nitrogen From Roots

Rapid Identification of Rhizobia Nodulating Soybean by a High-Resolution Melting Analysis

Soybean [Glycine max (L.) Merr.] is one of the most important and oldest crops. Due to its ability to form symbiotic interactions with nitrogen-fixing bacteria, it is a valuable source of nitrogen for agriculture and proteins for humans and livestock. In Europe, for instance, in Poland, the soybean cultivation area is still not large but is gradually increasing due to climate change. The lack of indigenous soybean microsymbionts in Polish soils forces the application of commercial strains to establish effective symbioses. Fast and reliable identification methods are needed to study the persistence, competitiveness, and dispersal of bradyrhizobia introduced as inocula. Our study aimed to apply real-time PCR coupled with high-resolution melting curve (HRM) analysis to detect and differentiate bacterial strains occupying soybean nodules. HRM-PCR was performed on crude extracts from nodules using primers specific for recA, a highly conserved nonsymbiotic gene. By comparing them with the reference strains, we were able to identify and assign Bradyrhiobium strains that had been introduced into field locations in Poland. In conclusion, HRM analysis was proven to be a fast and accurate method for identifying soybean microsymbionts and might be successfully used for identifying other legume-nodulating bacteria.

Molecular Mechanism of GmSNE3 Ubiquitin Ligase-Mediated Inhibition of Soybean Nodulation by Halosulfuron Methyl.

In this study, the role of E3 ubiquitin ligase GmSNE3 in halosulfuron methyl (HSM) inhibiting soybean nodulation was investigated. GmSNE3 was strongly induced by HSM stress, and the overexpression of GmSNE3 significantly reduced the number of soybean nodules. Further investigation found that GmSNE3 could interact with a nodulation signaling pathway 1 protein (GmNSP1a) and GmSNE3 could mediate the degradation of GmNSP1a. Importantly, GmSNE3-mediated degradation of GmNSP1a could be promoted by HSM stress. Moreover, HSM stress and the overexpression of GmSNE3 resulted in a substantial decrease in the expression of the downstream target genes of GmNSP1a. These results revealed that HSM promotes the ubiquitin-mediated degradation of GmNSP1a by inducing GmSNE3, thereby inhibiting the regulatory effect of GmNSP1a on its downstream target genes and ultimately leading to a reduction in nodulation. Our findings will promote a better understanding of the toxic mechanism of herbicides on the symbiotic nodulation between legumes and rhizobia.

Single-cell transcriptome atlases of soybean root and mature nodule reveal new regulatory programs that control the nodulation process

The soybean root system is complex. In addition to being composed of various cell types, the soybean root system includes the primary root, the lateral roots, and the nodule, an organ in which mutualistic symbiosis with N-fixing rhizobia occurs. A mature soybean root nodule is characterized by a central infection zone where atmospheric nitrogen is fixed and assimilated by the symbiont, resulting from the close cooperation between the plant cell and the bacteria. To date, the transcriptome of individual cells isolated from developing soybean nodules has been established, but the transcriptomic signatures of cells from the mature soybean nodule have not yet been characterized. Using single-nucleus RNA-seq and Molecular Cartography technologies, we precisely characterized the transcriptomic signature of soybean root and mature nodule cell types and revealed the co-existence of different sub-populations of B. diazoefficiens–infected cells in the mature soybean nodule, including those actively involved in nitrogen fixation and those engaged in senescence. Mining of the single-cell-resolution nodule transcriptome atlas and the associated gene co-expression network confirmed the role of known nodulation-related genes and identified new genes that control the nodulation process. For instance, we functionally characterized the role of GmFWL3, a plasma membrane microdomain-associated protein that controls rhizobial infection. Our study reveals the unique cellular complexity of the mature soybean nodule and helps redefine the concept of cell types when considering the infection zone of the soybean nodule.