Effects of slow-release fertilizers in relay maize remains unclear. Our aim was to reveal the mechanism mediated by slow-release fertilizers that increases maize yield and nitrogen agronomic efficiency (NAE) in different cropping systems. A two-factor split-plot design was conducted, with the main factor being cropping systems: Strip relay intercropping (SI) and monocropping maize (MM). Sub-factor was N type: 0 kg ha⁻1 (N0), normal urea at 300 kg ha⁻1 (U300), and slow-release fertilizer at 300 kg ha⁻1 (S300), N rate (300 kg ha⁻1) was applied consistently both years. Compared to MM under the same N treatment, SI significantly reduced root length (RL, -21.0

Strip intercropping improves productivity through enhanced light interception. In this study, we quantified the effects of strip width on light interception of soybean across six strip widths (2.2 m, 2.5 m, 2.8 m, 3.1 m, 3.4 m, 3.7 m) when intercropped with maize. Results showed that photosynthetically active radiation (PAR) in western rows of intercropped soybeans peaked at 11:30 a.m., whereas in eastern rows, it occurred at 1:00 p.m. Across 2.2 m to 3.7 m, PAR in the western rows of intercropped soybeans was 6.1% higher than that of the eastern rows for the whole growth period. During the R5 stage, compared to eastern rows, radiation use efficiency (RUE), dry matter accumulation, and leaf area of soybean in western rows increased by 4.0%, 7.4%, and 6.7%, respectively. Compared to the 2.2 m strip width, grain yields in eastern rows of 2.5-3.7 m strip widths were 8.5%, 54.7%, 56.5%, 63.4%, and 69.0% higher than those of the 2.2 m strip width, respectively. PAR had the strongest influence on dry matter and leaf area at a 3.7 m strip width, while RUE had the strongest influence at 3.1 m strip widths. These findings advance our understanding of light partitioning in strip intercropping and support future climate-adaptive intercropping systems' modeling.

Plants encounter dynamic light environments in natural field conditions, and species differ in their physiological and biochemical mechanisms for acclimating to fluctuating light (FL). The manner in which soybean (Glycine max (L.) Merr.) coordinates multiple physiological adjustments to FL remains poorly understood. This study assessed the effects of FL on soybean morphology and photosynthetic traits by examining changes in photosynthetic gas exchange parameters and chlorophyll (Chl) a fluorescence under alternating high- and low-light conditions. Results indicated that soybeans exposed to FL exhibited reduced dry matter accumulation, smaller and thinner leaves, and a lower Chl a/Chl b levels - characteristics typically associated with plants grown under continuous low-light. Despite these morphological similarities, their photosynthetic gas exchange rates and photosynthetic capacity were maintained at levels comparable to those under steady high light, unlike plants grown under constant low-light. Thus, acclimation to FL is distinct from adaptation to sustained low-light conditions. Correlation analyses revealed that the decline in carbon assimilation under FL primarily stemmed from two factors: the slow recovery of stomatal conductance upon transition to high light and the delayed relaxation of nonphotochemical quenching when light intensity decreased. Therefore, the reduction in carbon assimilation under FL cannot be attributed to low-light phase adjustments but rather reflects a lag in photosynthetic responsiveness to changing light conditions.

High natural heavy metal levels in Southwest China’s soils often lead to farmland contamination, and developing cost-effective risk mitigation strategies is crucial for safe agricultural production. This study evaluated profile reconstruction of a copper (Cu)- and cadmium (Cd)-contaminated vegetable production base in Kunming via deep soil mixing. Soil profile analysis revealed a clear surface accumulation of Cd and available Cu/Cd in the topsoil. Deep plowing to a depth of 50 cm effectively reduced the available Cu and Cd concentrations in the newly formed topsoil from 5.60±1.81 mg kg⁻¹ to 2.09±1.77 mg kg⁻¹ (a 63% reduction) and from 0.143±0.064 mg kg⁻¹ to 0.032±0.035 mg kg⁻¹ (a 78% reduction), respectively. The intervention reduced the mean total Cd concentration to 0.22±0.11 mg kg⁻¹, alongside a drop in the Cd exceedance rate from 80% to 20%. Soil pH and phosphorus/potassium contents remained stable; however, levels of soil organic matter and available nitrogen declined significantly. Field experiments confirmed that deep plowing effectively reduced the Cu and Cd contents in the edible parts of vegetables. Therefore, deep tillage presents a practical and rapid strategy for mildly contaminated sites with vertical metal accumulation, allowing for simultaneous production and remediation.

This study aimed to identify novel antioxidant peptides derived from stinky tofu. Fifteen peptides were characterized using liquid chromatography-tandem mass spectrometry (LC-MS/MS), and computer-aided screening techniques. P8, P12, and P13 demonstrated the strongest radical scavenging activity. Molecular docking revealed that P12 exhibited more balanced binding to radicals, and its shorter sequence contributed to lower synthesis costs and reduced complexity. P12 interacted with the key active site of Keap1 via hydrogen bonds and van der Waals forces, primarily mediated by Arg415 and Arg380. Cellular experiments demonstrated that P12 effectively reduced intracellular reactive oxygen species (ROS) accumulation and malondialdehyde (MDA) levels, while concurrently enhancing the activities of antioxidant enzyme. P12 competitively binds to Keap1, facilitating the dissociation of Nrf2, thereby promoting the upregulation of cytoprotective proteins. This activation pathway significantly mitigated H₂O₂-induced oxidative damage. These findings highlighted the potential application of novel antioxidant peptides derived from stinky tofu in functional food development.

Napier grass (Pennisetum purpureum), fresh or preserved as silage, is widely used as a component of animal feed in tropical regions. High-temperature and high-humidity in the environment promote the growth of undesirable microorganisms, which prevents lactic acid bacteria (LAB) from becoming dominant during natural fermentation, restrains organic acid accumulation and pH decline, and thereby readily induces ensiling fermentation failure. In this study, we evaluated the fermentation quality, nutritional parameters, and microbial community structure of napier grass silage inoculated with self-screen thermostable Lactobacillus rhamnosus (LR), by fermenting fresh materials at both high (40 °C) and ambient (25 °C) temperatures for 3, 7, 14, and 75 days. The results showed that LR-inoculated silage had higher lactic acid (91.62 ± 0.53 g/kg DM) and acetic acid (32.72 ± 0.97 g/kg DM) contents, while having a lower pH (3.70 ± 0.01) and butyric acid content (5.31 ± 0.23 g/kg DM) than the control (CK) and commercial Lactobacillus plantarum (LP)-inoculated silages at 40 °C on day 75. LR-inoculated silage exhibited higher neutral detergent fiber content at 40 ℃ and higher water-soluble carbohydrates (WSC) content at 25 ℃, while showing lower crude protein and WSC contents than LP at 40 ℃. The results of microbial analyses indicated that on day 14, L. rhamnosus was the dominant species in LR-inoculated silage for both 40 °C (54.37

Soybean-maize strip relay intercropping (RI) facilitates an additional harvest of soybean while stabilizing maize yields through optimized resource allocation, representing a crucial approach for expanding soybean cultivation and improving soybean productivity in China. However, the impact of RI on the nutritional quality of soybean seeds and the associated regulatory mechanisms remain unclear. In this study, differences in the metabolomic profiles and nutritional quality of soybean seeds between the RI system and an equivalent-density soybean sole cropping system (SC) were investigated based on three years of field experiments. Results showed that the nutritional quality of soybean seeds from the RI system is significantly enhanced compared to those from the SC system, with increases of 6.97, 21.89, 22.80, 19.18 and 10.94% in the levels of oil, soluble sugars, isoflavones, carotenoids and total carbon, respectively. Conversely, protein content slightly decreased by 2.15%. Metabolomic analysis revealed that RI promotes metabolic pathways associated with carbon fixation and the formation of nutritional quality in soybean seeds. Further artificial shading treatments confirmed that spatiotemporal changes in light conditions within the RI soybean canopy are critical drivers of these improvements. Temporally, shading from maize during the vegetative stage of soybeans decreased light availability in the canopy; however, light recovery following maize harvest increased this availability during the reproductive stage, resulting in a 4.82% increase in carbon fixation in RI seeds compared to SC seeds. Spatially, maintaining a spacing of ≥60 cm between soybean and maize strips effectively mitigated the shading impacts of maize, thereby reducing the marginal disadvantage for soybeans. After maize harvest, the wide-narrow-row configuration improved light conditions in the middle and lower parts of the soybean canopy, alleviating intraspecific shading and enhancing marginal advantages. This effect, akin to light enrichment, led to a 3.51% increase in carbon fixation in RI seeds compared to SC seeds. In conclusion, this study demonstrates that RI alters carbon-nitrogen dynamics and secondary metabolism through the synergistic regulation of temporal light recovery and spatial light enrichment, ultimately enhancing the nutritional quality of soybean seeds. These findings provide a theoretical basis for optimizing strip intercropping systems and promoting the sustainable production of high-quality soybean seeds.

Maize-soybean intercropping enhances resource-use efficiency but exposes soybean to canopy shading, which suppresses photosynthetic carbon assimilation and inhibits nodulation. Although nitrogen (N) management is known to regulate nodulation, whether reduced N application can alleviate shade-induced nodulation inhibition and whether root exudate-mediated rhizosphere microbial responses are involved remain unclear. We examined the effects of three N levels (NN: no N application; RN: reduced N application; CN: conventional N application) and two planting patterns (MS: monocropping; IS: intercropped with maize) on soybean nodulation, root exudate profiles, and rhizosphere cross-kingdom microbial networks. Compared with MS, IS significantly reduced nodule number; however, under RN, nodule weight and average nodule weight were comparable between IS and MS. Nodule starch content under ISRN was 144.00% and 23.04% higher than under ISCN and ISNN, respectively. Metabolomic analysis revealed that differential metabolites under intercropping were predominantly enriched in lipid-related compounds, particularly N-Tetradecanoyl-DL-homoserine lactone (N-C14-HSL) and Panaquinquecol 1, both of which were significantly and positively correlated with nodulation traits and nodule carbon metabolism indicators. Neither bacterial nor fungal α-diversity differed significantly among treatments, whereas community structure was significantly shaped by both planting pattern and N level. Cross-kingdom co-occurrence network analysis revealed that bacterial-fungal linkages increased by 48.6% under IS relative to MS. Module 19 was significantly enriched under RN and positively correlated with nodulation indicators and the relative abundances of N-C14-HSL and Panaquinquecol 1. Five core OTUs, belonging to the orders Phycisphaerales, Spizellomycetales, Sordariales, Rokubacteriales, and Aggregatilineales, showed consistent positive correlations with nodulation traits and both lipid compounds. Collectively, these findings demonstrate that reduced N application alleviates shade-induced nodulation inhibition in intercropped soybean by reshaping root exudate composition and enhancing cross-kingdom bacterial-fungal interactions in the rhizosphere.

Intercropping systems are widely adopted to enhance nutrient use efficiency and overall system productivity. However, shading from tall-stalked crops often lowers phosphorus use efficiency (PUE) and yield in understory crops compared to monocropping. The mechanisms by which soybean maintains PUE and productivity under low light remain poorly understood. We conducted a two-year field screening of 120 soybean genotypes in a maize soybean strip intercropping system, using P use efficiency for seed production (PUES) as the primary evaluation index. Two genotypes with comparable P uptake but contrasting PUES-QH34 (P-efficient) and SK90 (Pinefficient)-were selected for further analysis. QH34 achieved an average PUES of 180.98 g yield g-1 P, compared to 119.44 g yield g-1 P for SK90. The P-efficient genotype exhibited optimized P allocation, with greater partitioning to leaves and seeds during the reproductive stage, while minimizing P investment in stems. It also sustained a higher photosynthetic P use efficiency (PPUE) in the intercropping system by enhancing the allocation of metabolite P to the leaves (163 % higher than the P-inefficient soybean) while reducing the allocation of lipid P (45 % lower than the P-inefficient soybean). Additionally, QH34 showed smaller reductions in leaf mass per area and higher net photosynthetic rates, reflecting structural stability and better adaptability to shade. The enhanced PUE of P-efficient soybean in intercropping is thus driven by strategic P allocation and stable leaf structure, ensuring sustained photosynthetic performance. These findings provide theoretical and practical insights for breeding soybean cultivars with high resource-use efficiency suitable for intercropping systems.

Increasing soybean production to achieve self-sufficiency has become a pressing challenge for China, Europe, and many other countries and regions in the world. In China, although intercropping and other cropping system adjustments offer pathways to expand soybean planting areas, improving per-unit yield remains a critical constraint. Therefore, improving its productivity is crucial for realizing the sustainable intensification benefits of soybean-based intercropping. Microbial inoculation has been proposed to enhance soybean performance, but quantitative evidence on its effectiveness and key drivers in intercropping systems remains limited. Here, a meta-analysis of 154 observations from 48 publications evaluated the effects of microbial inoculation on intercropped soybean morphology, physiology, and yield in China. Subgroup analyses and random forest modeling were applied to identify environmental and management factors shaping soybean responses. Inoculation improved soybean performance in intercropping systems, increasing yield by 13.36%, whole-plant biomass by 37.83%, nodule number by 91.50%, nodule weight by 72.33%, N uptake by 61.90%, and N content by 43.35%. Remarkably, co-inoculation outperformed single inoculation, with Rhizobium-AMF combinations generating the largest gains in biomass, nitrogen traits, and nodule number. Trait-network analysis showed that co-inoculation produced a highly integrated and synchronized growth network, while that of the single inoculation markedly decoupled with fewer interactions. Seed inoculation was more effective than soil inoculation for enhancing soybean nodulation and plant N content. The benefits of inoculation on shoot biomass and plant N content in intercropped soybeans are particularly evident when nitrogen fertilizer is not applied. Initial soil fertility negatively influenced the response ratio of nodule weight, while climatic factors had minor effects. Overall, this meta-analysis highlights the central role of microbial inoculation, particularly co-inoculation, and seed inoculation in enhancing soybean growth and yield in intercropping, offering a theoretical basis for optimizing intercropping regimes.

Relay strip intercropping of cereals and legumes is a promising approach for enhancing soil organic carbon (SOC). However, crop types may influence plant- and microbial-derived carbon (C) contributing to SOC sequestration. In this study, we quantified the contributions of plant lignin (lignin phenols) and microbial necromass (containing amino sugars) to SOC in maize and soybean strips of an 11-year field experiment. In the relay strip intercropping system, maize and soybean were planted in adjacent strips, enabling comparison with monocropping of maize and soybean. Soil physicochemical properties and C-acquisition enzyme activities at two depths (0-20 cm and 20-40 cm) were considered covariates affecting SOC accumulation. The maize strip in the intercropping system had 14 % more SOC than maize monocropping, and the soybean strip increased SOC content by 11 % in the 0-20 cm depth relative to soybean monocropping, mostly due to an accumulation of microbial-derived C (27-32 % more than that of the monocropping). In contrast, plant-derived C contributed only 6-10 % of the SOC accumulated in the intercropped strips, relative to monocropping SOC. However, the relative inputs to SOC from plant and microbial origin differed in the maize strip and soybean strip. In topsoil (0-20 cm), compared to maize monocropping, the maize strip had 16 % more lignin phenols, 25 % more amino sugars, and 30 % more fungal-derived C, which made a dominant contribution to SOC. In the soil profile (0-40 cm), compared to soybean monocropping, the soybean strip had 74 % more muramic acids, suggesting that bacterial-derived C increased by 56 % of SOC. Overall, our results indicate that in a relay strip intercropping system, microbial necromass plays a more significant role than plant lignin in the long-term buildup of SOC, highlighting the importance of diversified cropping systems in boosting the microbial contribution to de novo SOC formation.

Maize-soybean relay cropping increases land-equivalent ratio, but shading often limits soybean productivity. Optimizing strip relay configurations improves the light environment for soybean, enhancing its photosynthetic capacity and yield. In a four-year trial, we tested maize-soybean relay strip cropping at interspecific distances of 30, 45, 60 and 75 cm, and monocropping soybean. We measured photosynthetic characteristics, photosynthate allocation, root traits, nitrogen (N) uptake and yield to elucidate the canopy-root synergy driving spacing-induced yield gains and identify the optimal interspecific distance. Increasing interspecific distance significantly improved canopy transmittance and photosynthetically active radiation (PAR). The 60 cm treatment (MS60) increased transmittance and upregulated leaf antioxidant enzyme activity, thereby enhancing leaf area index, SPAD and net photosynthetic rate. Compared with other relay cropping treatments, MS60 increased 13C content and sucrose accumulation by 17.8%-69.7% and 7.1%-34.9%, respectively, and increased N uptake by 20.1% on average. The dual boost in carbon and nitrogen accumulation led to an 11.6%-29.3% yield increase under MS60, with a soybean yield of 1.9 t ha-1 that was close to the monocropped soybean yield of 2.1 t ha-1. This yield advantage was attributed to increased canopy radiation and carbon (C) accumulation that increased root development and N uptake. MS60 optimizes the balance between interspecific compensation and intraspecific competition in the relay strip cropping system, increasing maize yield while maintaining soybean yield at monoculture levels. (c) 2025 Crop Science Society of China and Institute of Crop Science, CAAS. Production and hosting by Elsevier B.V. on behalf of KeAi Communications Co., Ltd. This is an open access article under the CC BY-NCND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

Soybean is an important global crop used for oil, food, and feed production. To increase yield and land-use efficiency, growers often plant soybean at a high density or use intercropping systems. Under these systems, soybeans frequently experience shade stress, which directly affects agronomic traits such as plant height. Although researchers have well documented the genetic basis of plant height under normal conditions, the loci responsible for height variation under shade stress remain largely unexplored. Therefore, we performed a restricted two-stage multi-locus multi-allele genome-wide association study (RTM-GWAS) using SNP linkage disequilibrium block (SNPLDB) markers to identify QTLs associated with soybean plant height under shade stress. We evaluated a natural population of 181 soybean accessions for plant height traits under both normal and shaded conditions across four environments for three years. Using the Soybean40K chip, we derived 11,463 SNPLDB markers and identified 42, 33, and 28 significant SNPLDBs associated with plant height, average internode length, and number of main-stem nodes, respectively. For each SNPLDB, we estimated haplotype (allele) effects and assembled QTL-allele matrices to summarize the population's genetic composition. Four SNPLDB loci proved stable across multiple environments, exhibiting high -lg(p) values and explaining substantial phenotypic variation. Finally, we projected that 80 candidate genes resided within 180 kb of these stable loci, and we identified four strong candidate genes linked to plant height traits based on combined positional and functional evidence. These results clarify genetic factors that influence soybean height under shading and could aid development of high-yielding soybean varieties.

The soybean-maize strip intercropping system enhances soybean yield while maintaining maize production, improving nitrogen use efficiency, and fostering intercropping mutualism. However, vigorous weed growth in warm and humid regions competes for nitrogen, while elevated soil temperatures accelerate nitrification, promoting nitrogen loss, especially during the peak nitrogen demand period of maize. Plastic film mulching, which conserves moisture, regulates temperature, and suppresses weeds, can improve the soil environment. A two-year field experiment was conducted with polyethylene (PE) films of various thicknesses (0.01, 0.014, 0.02 millimeters) and colors (black, white, silver-black) with an un-mulched control plot. Soil nitrogen content, microbial diversity, soil properties, and crop productivity were analyzed. The results indicated that plastic film mulching significantly altered soil nutrient availability and rhizosphere microbial community structures, while simultaneously enhancing crop productivity. The 0.014 mm black and white films performed best, showing a positive association with enhanced nitrogen transformation indices, which coincided with increased available nitrogen, biomass, and crop yield. However, long-term soil nutrient depletion remains a risk, suggesting the need for strategies like organic fertilizers or crop rotation to maintain soil fertility and ecological sustainability.

Context: Light intensity and photosynthetic products (such as sugars) co-regulate leaf development, and the resulting structural plasticity significantly determines the photosynthetic efficiency. In intercropped maize, leaf structural development under asymmetric light may critically influence photosynthetic efficiency and yield potential, yet the underlying mechanisms remain poorly understood. Objective: We investigated how asymmetric light affects bilateral leaf development and photosynthesis, and elucidated physiological mechanisms ensuring yield stability. Methods: Two years of field experiments were conducted under gradient asymmetric light conditions with different bandwidths (1.6-2.8 m), and were verified by unilateral shading simulations experiments. Results: Our investigation revealed that reduced unilateral light transmittance increased the photosynthetic rate (Pn) in unshaded leaves while decreasing Pn in shaded leaves. Compared to the unilateral 70% light treatment, unilateral 10% light transmittance significantly increased the Pn of unshaded leaves by 10.4% but reduced that of shaded leaves by 34.8%. Leaf sucrose content decreased by 35.3% (unshaded) and 45.1% (shaded), respectively. Additionally, both leaf width and bundle sheath cell relative area significantly decreased, whereas third-order vein density increased significantly. Correlation analysis and random forest analysis revealed unshaded leaf Pn enhancement correlated positively with increased third-order vein density and decreased leaf width and unilateral transmittance, whereas shaded leaf Pn improvement depended on bundle sheath cell relative area. The differential contributions of light and sugar on bilateral leaves to vein characteristics suggest independent regulatory mechanisms governing leaf vein development. Hexose levels positively correlated with vein relative cross-sectional area and bundle sheath cells relative area, suggesting its role in mediating the vein density and cross-sectional area trade-off. Moreover, C-labeling experiments revealed that asymmetric light significantly enhanced C export from unshaded leaves compared to bilateral shading. The sugar export rate increased progressively with decreasing unilateral light transmittance. Under optimal asymmetric light conditions (bandwidth 1.6-2.0 m, unilateral transmittance 35.6%), maize yield showed no significant difference from the control. However, yield decreased by 18.5% and 26.9% when bandwidth increased to 2.4 m and 2.8 m, respectively, with corresponding reductions in light transmittance. These results were corroborated by unilateral shading simulation trials. Conclusions: Optimal bandwidths of 1.6-2.0 m (unilateral light transmittance >= 35.6%) maximize intercropped maize performance, where improved sugar export from unshaded leaves compensates for photosynthetic decline in shaded leaves, ensuring yield stability. Implications: The research advances the crop marginal advantage theory and provides novel insights for maximizing crop photosynthetic potential.

Strip intercropping systems (SIs) improves grain yield through enhanced canopy light interception (LI) and radiation-use efficiency, but structural and physiological heterogeneity caused by configurations that complicates light-use mechanisms. Precise quantification of LI and canopy photosynthesis (Ac) is essential for configuration design and yield improvement. We developed a three-dimensional canopy photosynthesis model (3DCPM) integrating ray-tracing algorithms, leaf-level light-response functions, and leaf-azimuth angle parameter to simulates LI and Ac of soybean-maize SIs with different strip width configurations. The model was verified its high accuracy in 3D structure reconstruction by measured leaf area and plant height of two crops. Based on that, the LI and Ac of soybean-maize SIs in spatial-temporal heterogeneity were been quantified. Our results showed that Ac was enhanced in SIs relative to the corresponding sole-cropping combination, with the Ac equivalence index reaching up to 4.35 in M2S2 and 4.03 in M2S4, indicating that the intercropping advantage was mainly driven by enhanced maize Ac associated with border-row advantages. Maize Ac depended more on the withincanopy distribution of photosynthetically active radiation rather than on total LI, whereas soybean Ac was more closely depended to total LI. Maize predominantly intercepted direct radiation in the upper canopy, and Ac peaked in the morning and afternoon due mainly to enhanced photosynthesis in wide rows. By contrast, soybean, mainly captured diffuse light in the lower canopy, with LI and Ac peaking at midday. These complementary patterns formed a spatiotemporal light-use synergy that enhanced system-level Ac. Strip-width impacts on diurnal LI and Ac patterns are minimized under conditions dominated by diffuse radiation. Integrating distinct photosynthetic parameters for wide- and narrow-row maize and for each soybean row allows the model to capture canopy heterogeneity in LI and Ac; this row-specific integration underpins its spatially explicit simulations. This study provides a novel modeling tool for accurate assess of photosynthetic processes and a theoretical foundation for understanding the high efficiency utilization mechanism of SIs, which laying a technical foundation for climate-smart, resource-efficient cropping strategies.

Infection by Fusarium verticillioides causes field mold in soybean and reduces seed quality, yet the defensive role of pods as the first protective barrier remains poorly understood. Here, we compared a resistant cultivar (D49) and a susceptible cultivar (ND12). Phenotypic analysis showed that D49 exhibits stronger resistance to pathogen infection. Integrated transcriptomic and metabolomic analyses revealed that isoflavonoid and lipid biosynthetic pathways are specifically activated in the resistant genotype upon infection. Metabolite quantification demonstrated that isoflavonoids accumulate earlier and to higher levels in D49, whereas ND12 shows delayed and weaker induction. In addition, D49 undergoes dynamic remodeling of the cuticle wax barrier, characterized by reduced cutin monomers and increased wax accumulation, while ND12 displays a weaker structural response and a decline in wax content after infection. These results suggest that resistance is achieved through the coordinated action of early isoflavonoid accumulation and adaptive restructuring of the cuticle-wax barrier. Using WGCNA we found three candidate transcription factor genes (GmEGL3, BHLH149, and GmERF9) as potential regulators linking isoflavonoid metabolism and lipid barrier formation, providing molecular insights for soybean resistance breeding.

Rhizosphere-associated plant growth-promoting rhizobacteria (PGPR) critically enhance plant defense and growth. Our previous study identified Pseudomonas chlororaphis IRHB3 from the soybean rhizosphere and demonstrated its efficacy in suppressing soil-borne disease and promoting plant growth. However, the molecular mechanisms underlying IRHB3 colonization of soybean roots remain poorly characterized. In this study, spatiotemporal colonization dynamics revealed that IRHB3 rapidly adhered to the root surfaces and colonized the endosphere through the root tip, with cortical proliferation coinciding with lateral root formation. Transcriptional profiling indicated that early colonization activated pattern-triggered immunity (PTI) and differentially regulated genes associated with transmembrane signaling receptor kinase signaling, mitogen-activated protein kinase cascade, reactive oxygen species (ROS) burst, and phytohormone signaling. Following endosphere colonization, IRHB3 reprogrammed host transcriptional priorities toward developmental processes, upregulating photosynthesis-related genes and phytohormone pathways that facilitate root morphogenesis. Notably, multiple transcription factor families were dynamically induced during colonization. Crucially, transient overexpression of early adhesion-responsive GmWRKY22 or GmWRKY29 in soybean hairy roots suppressed IRHB3 colonization and dynamically modulated ROS biosynthesis-related RBOHs expression, whereas RNAi-mediated silencing of either gene enhanced bacterial colonization and attenuated ROS responses. Collectively, our findings demonstrate that soybean co-opts PTI machinery for the early detection of beneficial rhizobacteria while dynamically balancing defense-growth trade-offs. This work provides a mechanistic framework for optimizing PGPR applications in legume cultivation systems.