Wiley-Online-Library: Physiologia Plantarum: Table of Contents

Integrated Transcriptomic and Metabolomic Profiling Reveals Developmental Reprogramming of Flavonoid Biosynthesis in Styphnolobium japonicum Flowers

Thu, 11 Jun 2026 21:01:26 -0700

ABSTRACT

Styphnolobium japonicum is valued for its flavonoid-rich flowers, yet the developmental regulation of these metabolites remains unclear. Here, we integrated transcriptomic and metabolomic analyzes across four floral stages to reveal dynamic changes in flavonoid biosynthesis. Flavonoids emerged as the predominant metabolites, showing distinct stage-specific accumulation. Early stages showed high expression of CHS and F3H, with naringenin and eriodictyol as dominant metabolites. Mid-development maintained FLS-driven flavonol production, yielding quercetin and kaempferol derivatives. Late stages exhibited coordinated upregulation of CYP93C and HIDH, driving isoflavone (genistein) enrichment, alongside ANS and F3GT upregulation, enhancing anthocyanin glycosylation. Weighted gene co-expression and KEGG enrichment analyzes further supported a temporal reprogramming from primary metabolism to specialized bioactive compound production. Coordinated gene–metabolite patterns highlighted a temporal reprogramming from primary metabolism to targeted bioactive compound production. This study provides molecular insight into flavonoid biosynthesis during floral development and offers a framework for metabolic enhancement in S. japonicum.

Sustainable Mitigation of Tungsten Nanoparticle Contamination via Chitosan‐Driven Regulation of Photosynthesis and Lignin Metabolism in Chickpea

Fahed A. Aloufi, Riyadh F. Halawani — Wed, 10 Jun 2026 16:19:25 -0700

ABSTRACT

Tungsten nanoparticles (WNPs) impose severe phytotoxicity, highlighting the need for sustainable mitigation strategies. Here, we investigated the physiological and metabolic mechanisms by which chitosan nanoparticles (CSNPs) alleviate WNP stress in chickpea. Seeds were primed with 20 μg mL⁻¹ CSNPs and grown in soil contaminated with 500 mg kg⁻¹ WNPs. WNP exposure markedly suppressed growth and triggered oxidative stress, whereas CSNP application restored biomass accumulation, increasing shoot and root dry weight in response to CSNPs (by 76%–129%) and CSNPs + WNPs (by 99%–109%). CSNPs improved photosynthetic performance, as reflected by an increase in net photosynthetic rate, partially compensating for the high reduction induced by WNPs, and thereby enhanced carbon assimilation. Consequently, soluble sugars and starch accumulated in shoots and roots by 39%–70% under combined CSNP and WNP treatment. Increased carbon availability promoted amino acid biosynthesis, including glutamine, glutamate, proline, and phenylalanine, which function in osmotic adjustment and antioxidant defense, and activated the phenylpropanoid pathway via enhanced phenylalanine ammonia-lyase activity, thereby contributing to the mitigation of nanoparticle-induced stress. The enhanced phenylalanine pool was preferentially channeled into lignin biosynthesis via upregulation of COMT and CAD, resulting in a 130%–161% increase in lignin content. Collectively, these findings demonstrate that CSNPs mitigate WNP toxicity by restoring photosynthetic carbon flux and reallocating assimilates toward stress-responsive metabolites and lignin-based structural defense.

Exogenous Syringic Acid Mitigates Arsenic Toxicity in Lettuce Plants: A Physiological, Antioxidant, and Metabolomics Investigation

Mon, 08 Jun 2026 15:54:47 -0700

ABSTRACT

Arsenic (As) contamination in agricultural water and soil poses a growing threat to leafy vegetable safety, with lettuce being particularly vulnerable due to its high water content and direct consumption without processing. This study investigated the capacity of exogenous syringic acid (SyA) to mitigate As-induced toxicity in lettuce plants, integrating physiological, biochemical, and untargeted metabolomics approaches. Arsenic significantly reduced plant biomass (31% and 53% in fresh and dry weight), impaired stomatal conductance, and suppressed net CO₂ assimilation. However, the SyA application, particularly at 10 μM, significantly restored biomass, photosynthetic performance, and redox homeostasis under As stress. Notably, SyA enhanced antioxidant capacity, as reflected by elevated FRAP and CUPRAC activities and increased accumulation of the phenolic compounds. Untargeted metabolomics revealed that As exposure broadly reprogrammed secondary metabolism, including activation of the phenylpropanoid and shikimate pathways with notable accumulation of flavonoid glycosides and alkaloids, consistent with a shift toward oxidative defense. Conversely, SyA at 500 μM exerted phytotoxic effects even under nonstress conditions, confirming a biphasic, concentration-dependent mode of action with a critical threshold between 250 and 500 μM. The findings suggest that an optimized concentration of SyA can act as a metabolic modulator, fine-tuning the plant responses to As by boosting the antioxidant defense system.

Multiomics Reveal Low Temperatures Play Positive Roles in Flavonoids and Phenolic Accumulation in Meconopsis punicea

Sun, 07 Jun 2026 22:36:07 -0700

ABSTRACT

Meconopsis punicea, a Himalayan alpine medicinal herb, faces low-temperature constraints due to shifting thermal niches at high altitudes. Low temperature constrains plant growth and development but aids the accumulation of active compounds. However, the response mechanisms of plant seedlings to low temperatures remain unclear. In this study, metabolomic and transcriptomic analyses were performed to investigate the dynamic changes and molecular regulatory mechanisms of flavonoids and phenolic compounds. The results revealed that under low-temperature stress, the expression levels of related genes and the content of flavonoid and phenolic compounds increased significantly with treatment duration, indicating that these compounds actively participate in the low-temperature response. Specifically, in the comparison between 0 and 5 days low-temperature treatment (M0 vs. M5), 7905 differentially expressed genes (DEGs) were significantly upregulated and 21,823 DEGs were downregulated. In the comparison between 0 and 10 days low-temperature treatments (M0 vs. M10), 6253 genes were significantly upregulated and 8754 were downregulated. These DEGs were primarily enriched in metabolic processes and phenylpropanoid biosynthesis. Additionally, through correlation analysis and weighted gene co-expression network analysis (WGCNA), we identified the low-temperature-responsive transcription factor GASA11. With prolonged treatment, most metabolites show an increased level. In conclusion, this study elucidates the specific response mechanisms of flavonoids and phenolic compounds in Meconopsis punicea under low temperatures. These findings enrich the current understanding of plant metabolic responses to low temperatures and provide an important reference for subsequent in-depth studies on the roles of GASA11 and other key genes involved in flavonoid biosynthesis in the low-temperature adaptive responses of Meconopsis punicea.

Ice Nucleation and Freezing Consequences in Perennial Plants

Sun, 07 Jun 2026 17:00:39 -0700

ABSTRACT

The precise location where ice forms in plants affects the physical constraint it exerts on the different biological compartments (cells, tissues, organs). It is therefore critical to understand where and how ice nucleates to predict the extent of low temperature damage. On one hand, extracellular ice formation can protect living plant cells by lowering their intracellular freezing point through water efflux and an increase in osmolyte concentration. On the other hand, extended freezing-induced dehydration may cause damage and rupture of the plasma membrane. The location and pattern of ice formation in plants are marked by high spatio-temporal variability in relation to the type of plant tissue, its developmental stage, and the nature of the initial ice nucleus. This review focuses on the mechanisms and dynamics of intrinsic ice nucleation and subsequent propagation in perennial plants. We describe the factors that influence ice nucleation, such as the nature of nucleating agents and other biophysical conditions. We also highlight the shortcomings of studies on plant freezing, especially regarding laboratory studies, and emphasize the need to investigate ice nucleation in plants using interdisciplinary approaches. We finally provide a practical workflow to guide new experimenters in this research field.

Elevated Nitrogen and Phosphorus Levels Suggest High Metabolic Demands in Himalayan High‐Elevation Plants

Fri, 05 Jun 2026 06:51:35 -0700

ABSTRACT

Nutrient contents in plant tissues reflect adaptations and environmental constraints, varying across and within species along ecological gradients. Interspecific differences reflect long-term adaptations, while intraspecific variations may indicate acclimation to present conditions. Examining these responses across elevational ranges is therefore crucial for understanding how nutrients influence species performance. We investigated whether organ nutrients play a significant role at the upper limits of the world's highest occurring herbaceous angiosperms by analysing intraspecific and interspecific variations in leaf carbon (C), nitrogen (N), and phosphorus (P) contents in 22 species, and root N and P contents in 15 species along a gradient from 4560 to 6150 m a.s.l. in the Western Himalaya. Our findings reveal contrasting patterns in nutrient contents. Interspecifically, leaf N and P decreased and C:N increased with elevation, indicating selective pressure for adaptations to reduced nutrient availability. In contrast, intraspecific leaf N content generally increased with increasing elevation. Root N trend did not change interspecifically with elevation, while overall intraspecific trends increased. Surprisingly, subnival species at the highest localities around 6000 m had relatively high tissue N and P contents. This suggests that high-elevation Himalayan herbs require high nutrient levels, likely for photosynthesis, to achieve a positive annual carbon gain during the short growing season and to accumulate sufficient root reserves. Elevated N and P content, especially at the highest localities, imply that the upper limits of the world's highest-growing plants may not be limited by nutrient acquisition constraints.

Auxin Transport Gene, ClPILS6, Promotes Branching in Transgenic Poplar by Altering Auxin Homeostasis

Ye Yang, Xinyi Liu, Tianhao Guo, Weiyang Hu, Jin Xu — Thu, 04 Jun 2026 17:43:44 -0700

ABSTRACT

Cunninghamia lanceolata (Chinese fir) is an important fast-growing timber species in southern China, and its branching characteristics directly affect timber yield and quality. Within the regulatory network of plant branching, the auxin signaling pathway plays a central regulatory role; however, the specific functions of related genes during lateral bud development in Chinese fir remain poorly characterized. Therefore, a hub gene, ClPILS6 (PIN-LIKE6), was identified in the lateral buds of Chinese fir. As a member of the auxin transporter family, ClPILS6 is specifically expressed in buds, lacks transcriptional activation activity, and its expression is significantly induced by exogenous IAA. Overexpression (OE) of ClPILS6 significantly promoted lateral branch development and soluble sugar accumulation while altering auxin homeostasis. Furthermore, ClSPL8 (SQUAMOSA promoter binding protein-like) binds to the promoter of ClPILS6 and represses its transcription. In summary, these findings reveal the important role of ClPILS6 in branching development and provide a significant theoretical basis for molecular breeding improvement in gymnosperms.

Microalgal Cell Wall Dynamics at Different Growth Stages Under Cold Stress Conditions: A Study of Ultrastructure and Chemical Composition

María González‐Hourcade, Francesco G. Gentili, Dinesh Fernando — Thu, 04 Jun 2026 17:21:08 -0700

ABSTRACT

Microalgae have been gaining attention for biotechnological purposes in different fields, such as food, energy, cosmetics, and bioremediation. However, due to habitat variation across the planet, there is still a scarcity of information on microalgae development in extreme environments, such as those with low temperatures. The aim of this study was to investigate the effects of growth stage and cold stress (5°C) on cell wall features, including ultrastructure, and main polysaccharides in three microalgal species from Northern Sweden: Coelastrella sp. 3–4, Chlorella vulgaris sp. 13–1, and Scenedesmus sp. B2-2. All microalgal strains grown at 25°C showed increased cell wall thickness between the exponential and stationary phases by around 45%, with Scenedesmus showing an increase of up to 230%. Under cold stress, the cell wall thickness between the exponential and stationary phases had the greatest increase of 68% in Scenedesmus. However, both Chlorella vulgaris sp. 13–1 and Scenedesmus sp. B2-2 showed that cold stress stimulated the formation of a thicker cell wall during exponential growth compared to control growth conditions. The layer configuration showed a differentiation, with Chlorella presenting a bilayer cell wall and the cell walls of Coelastrella and Scenedesmus being mainly composed of several layers distinguishable by transmission electron microscopy. Cold stress altered the microalgal cell wall ultrastructure and morphology. Glycosyl-linkage analysis did not show a change in the composition of the main cell wall polysaccharides under cold stress.

DNA Methylation of MYB Sites of Chickpea CabHLH92 During Salt Stress and Fusarium Wilt Under Influence of Trichoderma asperellum T42

Nidhi Rai, Shashi Pandey Rai, Birinchi Kumar Sarma — Wed, 03 Jun 2026 16:30:27 -0700

ABSTRACT

DNA methylation has proved vital in the regulation of genes under stress. CpG islands in promoter regions act as regulatory hubs for initiating transcription. The abiotic stress-responsive chickpea transcription factor CabHLH92 has a CpG island in the promoter and has been of interest in the study. Through bisulfite conversion and PCR sequencing, the methylation status was tracked in the CpG island of CabHLH92 under stress. Salt stress induced hypermethylation at a MYB binding site 3 in the CpG island, but Fusarium wilt [Fusarium oxysporum f. sp. ciceris (Foc)] did not and the chickpea plants remained vulnerable to the disease. Application of Trichoderma asperellum T42 induced demethylation in two different MYB binding sites (1, 2) in the CpG island under Foc stress and positively associated with wilt tolerance by chickpea plants. Expression of CabHLH92 in salt-stressed conditions was enhanced, whereas the associated MYB gene CaMYB78 was reduced, confirming that hypermethylation at MYB binding site 3 is negatively associated with CabHLH92 and CaMYB78 interactions in salt-stressed conditions. Interestingly, expression of these genes was reversed in Fusarium wilt-stressed conditions in the presence of T42. T42-induced demethylation in the MYB binding sites 1 and 2 facilitated binding of CaMYB78 to CabHLH92 and positively impacted expression of CaMYB78. The study's outcomes provided deep insights into the epigenetic interplay of the three MYB binding sites (1, 2, 3) in the CabHLH92 promoter in relation to CaMYB78 and stress tolerance (salt and Fusarium wilt) in the presence and absence of T. asperellum T42.

Phytochrome‐Dependent Regulation of CO2 Gas Exchange and Switching Between Respiratory and Photosynthetic Carbon Metabolism in Wheat Leaves

Valery Lyubimov, Anatoly Kosobryukhov — Tue, 02 Jun 2026 16:13:31 -0700

ABSTRACT

The spectral composition of light in the red and far-red bands is an essential environmental factor regulating plant growth. The rate of PAR-saturated CO₂ assimilation of the dark-adapted plants increased 2.7-fold after short-term red-light irradiation. Dark respiration decreased and the ratio photosynthesis/respiration increased from 2.7 to 12.4. The activity of the NAD-glyceraldehyde phosphate dehydrogenase decreased by 40%–50%, while the activity of the NADP-enzyme increased by 1.8–2.0-fold, and the carboxylase activity of Rubisco increased by 2.5–3.0-fold. The activities of both dehydrogenases were returned to control levels by plants being exposed to far red light. Rubisco activity was also returned to near control levels. The dose dependence of NADP-glyceraldehyde phosphate dehydrogenase activity increased linearly up to 17–20 kJ m⁻² red light, and the NAD-dependent one decreased linearly up to 8–10 kJ m⁻² red light. The fresh and dry weight of whole plants increased by 40%–45% when they were exposed to short-duration red light for 15 days. The results suggest that phytochrome is involved in switching from dark respiratory metabolism to photosynthetic metabolism and leads to the accumulation of additional plant biomass during ontogeny.

Intelligent Bioelectrical Sensing and Deep Learning Framework for Non‐Invasive Monitoring of Plant Alkaline Stress

Tue, 02 Jun 2026 16:08:18 -0700

ABSTRACT

Alkaline stress disrupts ion balance and physiological homeostasis in plants, yet its timely assessment remains challenging because conventional phenotyping methods are often destructive, discontinuous, or delayed relative to the onset of stress symptoms. In this study, we developed a non-invasive plant electrophysiological sensing framework for the identification of alkaline stress in Clivia. Thin-film patch electrodes were used to record bioelectrical signals under five alkaline gradients (pH 7.0, 7.5, 8.0, 8.5, and 9.0) in a controlled environment. The acquired signals were subjected to wavelet denoising and normalization, and were then analyzed using a dedicated deep learning model, the Spatial Channel Alkaline Stress Network (SCANet). To provide a more rigorous evaluation of generalization, model performance was assessed using plant-wise five-fold cross-validation. Under this protocol, SCANet achieved 97.51% ± 0.77% accuracy, 97.55% ± 0.75% precision, 97.51% ± 0.77% recall, and 97.52% ± 0.77% F₁-score, outperforming representative convolutional and transformer-based baselines. Ablation experiments further showed that both the spatial reconstruction module and the channel reconstruction module contributed to performance improvement, and that a 30 s input window provided the best balance between signal completeness and discrimination. These results indicate that plant electrophysiological signals can support accurate, non-destructive identification of alkaline stress levels under controlled conditions, and that the proposed sensing-analysis framework may be useful for stress phenotyping and intelligent monitoring of plant status.

Metabolic Dynamics and Modular Regulatory Mechanisms of Leaf Abscission in Cyclocarya paliurus Stem Segments In Vitro

Tue, 02 Jun 2026 15:45:23 -0700

ABSTRACT

Leaf abscission is extremely severe during the Cyclocarya paliurus stem segment formation in vitro culture, and stem segment development is hindered after leaf abscission. To explore the dynamic regulatory mechanisms of metabolites in the leaf abscission process of C. paliurus, the emerged leaves of C. paliurus stem segments were cultured for 22 days (T0) in vitro; leaves at 27 days (T1) and leaves that had fallen after ≥ 32 days (T2) were used as materials for analysis of the types and contents of metabolites by liquid chromatography–tandem mass spectrometry (LC–MS/MS). A total of 2160 differentially accumulated metabolites (DAMs) were obtained across the three collected time points. KEGG enrichment analysis showed significant enrichments in both flavonoid biosynthesis and C5-branched dibasic acid metabolism. Based on co-expression network analysis, four modules significantly associated with abscission were identified. The turquoise module genes (CAT1-like, RAX2-like MYB, E2 4-like, and RBOH) promote flavonoid metabolite biosynthesis and synergistically drive abscission through oxidative stress and cell wall degradation. In contrast, the yellow module genes (14-3-3, MAPKK, ERF4, and ERF2) tend to maintain C5-branched dibasic acid metabolism and auxin transport homeostasis, while suppressing the ABA/ethylene-driven senescence pathway. The green module genes (Aux/IAA13-like, OPCL1) and blue module genes (HCT, CALDH) weaken auxin signaling and cell wall structural stability. These four modules work synergistically to collectively promote the leaf abscission process in C. paliurus. This study provides novel insights into the molecular regulatory mechanisms underlying leaf abscission in stem segments of C. paliurus cultured in vitro.

CaCRF6, A Cytokinin Response Factor, Confers Cold Tolerance in Capsicum

Sun, 31 May 2026 19:18:59 -0700

ABSTRACT

Cytokinin response factors (CRFs), a subfamily attached to the transcription factor AP2/ERF family, are extensively involved in the responses to abiotic stresses in plants. However, the role of CRFs in cold tolerance remains poorly characterized in Capsicum. In this study, the cold tolerance of 14 accessions was screened in Capsicum, and it was found that accession C3 displayed strong cold tolerance, while accession C88 exhibited opposite characteristics. Transcriptome profiling revealed that 2223 genes, including 897 up-regulated and 1326 down-regulated genes, were commonly differentially expressed (DEGs) in response to cold treatment in both C3 and C88. It was interesting that the plant-pathogen interaction was among the most significant pathways. Notably, the expression of CaCRF6 was obviously up-regulated in C3 (92.80-fold) than that in C88 (4.04-fold) at cold treatment, which suggested that CaCRF6 was closely related to cold tolerance in Capsicum. Subsequently, CaCRF6 was silenced by Virus-induced gene silencing to study its function at cold stress, and the results showed that silencing CaCRF6 reduced cold tolerance of C3, accompanied by the increases in content of malondialdehyde, electrolyte leakage, and reactive oxygen species, as well as a decrease in the maximal photochemical efficiency of PSII. These results indicate that CaCRF6 plays a critical role in coping with cold stress in Capsicum, which provides new insights into understanding cold tolerance in Capsicum.

Decoding Hormone Signaling Dynamics in Arabidopsis Under Combined Stress: How Different Abiotic Stress Responses Are Fine‐Tuned by High Temperatures

Sun, 31 May 2026 17:45:01 -0700

ABSTRACT

Climate models predict that episodes of extreme heat will intensify in both frequency and severity in the upcoming decades, significantly impacting plant growth, productivity, and survival. In addition, plants in natural environments are often exposed to many other stress factors simultaneously, triggering responses even more complex and difficult to predict. Understanding how plants integrate multiple abiotic stress signals is essential for improving resilience to increasingly complex environmental conditions. In this study, we investigated how heat stress (HS) modulates hormonal signaling networks when occurring in combination with other abiotic stressors. We focused on three specific combinations: salinity and heat (S + HS), water deficit and heat (WD + HS), and high light and heat (HL + HS). Through a comprehensive meta-analysis of publicly available RNA-seq datasets from Arabidopsis thaliana, we assessed the proportion of differentially expressed transcripts associated with major hormone signaling pathways, with particular attention to abscisic acid (ABA) and jasmonic acid (JA). Because transcription factors represent a central layer of stress integration, we also examined the expression pattern of different heat shock factors (HSFs) and analyzed how their activity is potentially associated with hormone responses under each stress combination. Our results reveal that HS substantially alters both ABA and JA responses in a stress-specific manner, amplifying or attenuating hormone dynamics depending on the co-occurring stress. This work highlights the importance of hormonal crosstalk and signal integration in shaping plant responses to stress combinations that include HS and provides a foundation for developing crop improvement strategies aimed at enhancing tolerance to climate change-associated stress combinations.

Pit Membrane Thickness Determines Differences in Embolism Resistance Among Brassica oleracea Genotypes

Sun, 31 May 2026 17:30:40 -0700

ABSTRACT

As drought events become more severe, understanding drought-tolerance traits in crops is vital for food security. Brassica oleracea L., a widely consumed vegetable (including cabbage, cauliflower, and broccoli), has seen a rise in cultivation, but the response of different genotypes to drought remains poorly studied. Here, we investigated the mechanisms underlying drought resistance in seven genotypes of B. oleracea (two grandparental lines and five F2 genotypes) by examining stem anatomical and hydraulic traits, as well as stomatal characteristics, leaf dimensions, and stomatal regulation under drought conditions. Detailed measurements of stem anatomical traits were obtained using light and electron microscopy, while stem hydraulic vulnerability was assessed using the Optical Vulnerability method. The seven genotypes displayed contrasting water-use and hydraulic strategies. Under well-watered conditions, initial stomatal conductance (g _sΨ0) showed considerable variation independent of their leaf and stomata size and density, while the leaf water potential at 90% stomatal closure (Ψg _s90) was similar among genotypes. Stomatal safety margins (SSM) were positive across genotypes, confirming coordination between stomatal regulation and xylem hydraulics, and mainly driven by stem P ₅₀, which was approximately 1 MPa lower in the most tolerant genotype. Embolism resistance was best explained by the thickness of the intervessel pit membrane, highlighting the importance of including anatomical traits in plant drought tolerance studies. To conclude, the intraspecific variation observed in anatomical, hydraulic and stomatal traits among our B. oleracea genotypes indicates potential adaptability to drought and suggests that more drought-tolerant genotypes could be identified within this crop species through targeted, human-mediated crosses.

Exogenous Quercetin Enhances Salt Tolerance in Apocynum venetum Seedlings: Insights From Physiology and Transcriptomic Regulation

Xueqing Zhao, Zeeshan Ali Buttar, Bing Zhao, Li Jiang — Thu, 28 May 2026 06:24:49 -0700

ABSTRACT

Soil salinization severely constrains crop yields and quality. Apocynum venetum L. is an important halophytic plant; however, its young seedlings exhibit limited salt tolerance. To elucidate the mechanism by which exogenous quercetin alleviates salt stress in A. venetum seedlings. The present work integrates phenotypic observation, physiological measurement, and transcriptome analysis. There were four treatment groups: HCK (control), HCKN (salt stress), Q3 (quercetin), and Q3 + N (quercetin + salt stress). These findings demonstrated that under salt stress, exogenous quercetin significantly improved phenotypic traits, including plant height, stem, root, and leaves. Quercetin application reduced malondialdehyde (MDA) content to maintain cell membrane stability and restore the photosynthetic system. It also enhanced the activities of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT), thereby promoting the accumulation of proline and soluble proteins and alleviating salt stress damage. Transcriptomic analysis identified 21 differentially expressed genes (DEGs) modulated by quercetin to alleviate salt stress. These DEGs were enriched in pathways associated with glycerophospholipid metabolism, plant hormone signal transduction, and secondary metabolite biosynthesis. Notably, genes such as PIOX (flavonoid synthase) and TPPD (terpenoid phenol synthase) were specifically up-regulated. This upregulation facilitates the synthesis of salt-stress-mitigating secondary metabolites, including flavonoids and terpenoids, which contribute to reducing reactive oxygen species (ROS) and, subsequently, alleviate oxidative damage. The reliability of the RNA-seq data was confirmed by quantitative real-time polymerase chain reaction (qRT-PCR). Collectively, these findings demonstrated that quercetin alleviates salt stress through a dual mechanism: enhancing antioxidant defenses and modulating key molecular pathways.

Fairy Ring Fungus Rewires Rice Lipid Metabolism: A Symbiotic Strategy for Enhanced Growth and Photosynthetic Efficiency

Thu, 28 May 2026 01:03:32 -0700

ABSTRACT

The fairy ring fungus Leucocalocybe mongolica (strain LY9) has shown significant potential as a sustainable biofertilizer, yet its mechanisms for enhancing crop growth remain poorly understood. This study suggests that LY9 significantly improves rice growth and photosynthetic efficiency by reprogramming lipid metabolism in a tissue-specific manner. Using soil transformation experiments with varying LY9 concentrations (10%–50%), we observed dose-dependent increases in tillering (up to 122%), root length (26%), and chlorophyll content (214%). Lipidomic profiling and transcriptomic analyses revealed that LY9 upregulates lysophosphatidylethanolamines (LysoPEs) in rice roots (promoting membrane flexibility and nutrient uptake), while enhancing chloroplast lipids like monogalactosyldiacylglycerol (MGDG) and stress-protective oxylipins in leaves, thereby supporting photosynthetic performance and resilience. LY9 treatment reduced post-harvest soil nutrient concentrations, suggesting enhanced plant nutrient uptake and utilization by the rice plants. These findings provide novel insights into how fungal symbionts optimize plant lipid networks to boost growth, offering a sustainable strategy to reduce dependence on chemical fertilizers in rice cultivation.

Water Potential Isotherms Reveal Different but Coordinated Responses at Leaf and Root Levels Under Controlled Drought

Thu, 28 May 2026 00:56:44 -0700

ABSTRACT

Understanding how leaves and roots modulate their water relations under drought is critical for predicting plant stress resistance/resilience. We compared water relations traits derived on water potential isotherms in 10 young woody and herbaceous species grown under the same soil and irrigation conditions (well-watered vs. mild drought). Measured traits included turgor loss point (Ψ_tlp), osmotic potential at full turgor (π_o), cell wall stiffness (ε), hydraulic capacitance, and structural traits such as dry matter content and saturated water content. Roots consistently showed higher Ψ_tlp and π_o, lower ε, and greater capacitance than leaves, highlighting organ-specific differences in water relation traits. Under drought, both organs primarily adjusted water relation traits via osmotic modification, with larger ε changes in leaves, indicating greater plasticity in this organ. Roots also showed increased dry matter content and reduced water storage capacity. Across species, leaf and root Ψ_tlp were positively coordinated, contrasting with previous studies reporting no clear relationship. Ψ_tlp correlated with π_o in roots, underscoring the dominant role of osmotic adjustment also in this organ. Moreover, species with lower leaf Ψ_tlp displayed greater divergence between leaf and root turgor thresholds, possibly revealing a pattern of hydraulic risk partitioning between organs. Overall, leaves and roots displayed complementary water relations trait strategies across species. Our study provides insights into organ-specific drought responses and emphasizes the role of roots in whole-plant water use strategies.

Blue Light Induces Cultivar‐Specific Metabolic Reprogramming of Bioactive Compounds in Chinese Cabbage Revealed by Widely Targeted Metabolomics

Tue, 26 May 2026 23:04:03 -0700

ABSTRACT

Chinese cabbage is a widely cultivated leafy vegetable with high nutritional value. Contains high levels of vitamin C, dietary fiber, and phytochemical antioxidants, and plays an important role in human nutrition. In this study, the common cultivar 14S23 was used as a control, and two orange-red heart cultivars (15S1094 and 20S530) were exposed to blue light (300 μmol m⁻² s⁻¹) for 3 or 6 h to elucidate the effects of blue light on nutritional quality and underlying regulatory mechanisms. Results demonstrated clear cultivar-specific differences in antioxidant capacity and metabolic responses under blue light. Compared with 14S23, 15S1094 and 20S530 showed significantly higher activities of ascorbate peroxidase (APX), glutathione peroxidase (GPX), and glutathione reductase (GR), as well as greater total antioxidant capacity. Prolonged exposure further enhanced these effects, with the 6 h treatment showing stronger responses than the 3 h. Widely targeted metabolomics analysis showed that blue light induced extensive metabolic reprogramming across cultivars. In particular, amino acids and their derivatives, alkaloids, lignans, coumarins, and specific lipids accumulated to higher levels in 15S1094 and 20S530 than in 14S23. These metabolic changes were associated with enhanced antioxidant capacity and improved nutritional quality. Overall, this study provides new insights into the physiological and metabolic mechanisms underlying blue light-enhanced vegetable quality and offers a basis for developing sustainable strategies to improve postharvest quality in leafy vegetables.

Dormancy Patterns of Apple Trees Grown in a Mild Winter Region: A Breakpoint Model Analysis

Tue, 26 May 2026 22:49:45 -0700

ABSTRACT

Climate change poses a significant challenge to the production of temperate climate fruit trees, since the dormancy of these species is regulated by the chill and heat accumulation during winter and early spring. This study aimed to identify the dormancy evolution patterns of three apple cultivars (“Galaxy,” “Fuji Suprema,” and “Eva”) in a mild winter region over five contrasting years (2018–2022) across two commercial orchards with different microclimates in southern Brazil. Dormancy status of lateral buds of branches was evaluated using the single-node cutting test (Mean Time to Budburst—MTB) and quantified using a linear breakpoint model to determine the rates of dormancy entry, maximum depth of dormancy, and rates of dormancy release. The colder orchard accumulated 51% more Chill Portions (Dynamic Model) than the warmer site, inducing a deeper endodormancy (alpha) but maintaining faster dormancy release rates (Cs). Inter-annual climatic variability strongly influenced the timing (theta) and the rate of entry (Ce). The low-chill cultivar “Eva” did not enter deep endodormancy. Early season chilling significantly accelerated dormancy induction (Ce) but also increased the chilling requirement for dormancy release. The results indicate that cultivars display distinct and highly plastic dormancy dynamics based on microclimate and yearly chilling, emphasizing the need to select cultivars with phenological patterns adapted to specific local conditions for crop resilience and sustainability under climate change.

Responses of Wild and Cultivated Tetraploid Wheat to CO2 Enrichment: Stomatal Optimization of Photosynthesis and Water Use Efficiency

Tue, 26 May 2026 01:00:57 -0700

ABSTRACT

The rising atmospheric concentration of carbon dioxide will influence the anatomical and physiological traits that regulate photosynthesis and water use efficiency (WUE) in crops. To assess how domestication will shape responses to long-term [CO₂] enrichment, we compared wild tetraploid wheat Triticum turgidum ssp. dicoccoides and its cultivated derivative Triticum turgidum ssp. durum. Plants were grown under ambient (a[CO₂]: ~420 μmol mol⁻¹) and naturally elevated (e[CO₂]: ~1000 μmol mol⁻¹) [CO₂] at the Bossoleto CO₂-degassing vent in central Italy. Stomatal density (SD), stomatal size (SS), stomatal kinetics, and photosynthetic parameters, the maximum Rubisco carboxylation rate (Vc_max), the maximum electron transport rate (J _max), and the quantum yield of photosystem II (Φ_PSII), were analyzed. Growth in e[CO₂] reduced SD in both subspecies, indicating an adaptive adjustment to limit transpirational water loss. However, the two taxa differed markedly in SS and stomatal behaviour. Triticum dicoccoides showed a slight increase in SS and a pronounced increase in stomatal physiological responsiveness, whereas T. durum exhibited reduced SS and slower stomatal responses. These findings indicate distinct coordination between stomatal morphology and physiological control of gas exchange. Neither apparent Vc_max nor apparent J _max differed significantly between treatments, suggesting limited biochemical acclimation, whereas both subspecies displayed a significant increase in Φ_PSII under e[CO₂], implying improved photochemical efficiency. Wild T. dicoccoides exhibited higher stomatal responsiveness and greater WUE, while cultivated T. durum maintained more stable gas exchange and carbon assimilation. This suggests that the morphological and physiological traits conducive to high photosynthesis and stomatal optimization of WUE may be mutually exclusive.

Purple Light Steers Metabolic Flux Towards Sulforaphane in Flowering Chinese Cabbage Sprouts by Activating a BcHY5‐Mediated “Push‐Pull” Mechanism

Tue, 26 May 2026 00:46:13 -0700

ABSTRACT

Light quality is a powerful tool to modulate the chemistry of functional foods, yet the underlying molecular regulatory networks are poorly understood. This study reveals that purple light-emitting diode illumination engineers the metabolic flux in flowering Chinese cabbage sprouts to maximize the production of the anti-cancer agent sulforaphane. Compared to dark and white light controls, purple light treatment (center wavelength: 398 nm, half-width: 13 nm) resulted in a significant (6.84-fold) increase in sulforaphane content. Integrated metabolomic and transcriptomic analyses uncovered a “push-pull” mechanism: purple light “pushed” glucosinolate biosynthesis while “pulling” the metabolic stream towards sulforaphane by enhancing hydrolysis and suppressing the competing nitrile-forming pathway. We identified the transcription factor BcHY5 as the master regulator. Yeast one-hybrid and dual-luciferase assays confirmed BcHY5 directly binds to and activates promoters of key GSL biosynthetic genes (GSTU11, SUR1). These findings establish a novel light-regulatory framework, offering a practical strategy for the precision production of high-value phytochemicals in functional foods.

Genotype‐Dependent Modulation of Stomatal Function and Carbon Isotope Fractionation by Silicon in Common Bean Under Water Deficit

Tue, 26 May 2026 00:32:26 -0700

ABSTRACT

Silicon (Si) modulates plant responses to abiotic stress, but its role in legumes remains unclear. We investigated the effects of Si supply on drought responses in common bean genotypes contrasting in drought tolerance (BAT 477, tolerant; IAC Carioca 80 SH, susceptible), focusing on leaf gas exchange, carbon isotope discrimination (δ¹³C), leaf nitrogen (N), and C/N. Plants were grown under greenhouse upon different water regimes (80% and 40% of soil water holding capacity) and Si supply (0 and 200 mg dm⁻³). Silicon application increased intercellular CO₂ concentration (Ci) in both genotypes, regardless of water regime, suggesting changes in the balance between stomatal and non-stomatal limitations to photosynthesis. Effects on water-use efficiency (WUE) were genotype and stage-dependent, with increases observed only in the susceptible genotype under well-watered conditions. Leaf N increased with Si supply, particularly under drought in the tolerant genotype, while changes in the C/N reflected shifts in carbon-nitrogen balance associated with improved physiological performance. Despite higher Si accumulation in IAC Carioca 80 SH, this genotype did not exhibit superior drought tolerance, highlighting that Si accumulation per se does not determine physiological responsiveness. Multivariate analysis revealed coordinated associations among Si, WUE, δ¹³C, and C/N under drought, suggesting that Si modulates the balance between carbon assimilation, nutrient status, and water use. Our findings demonstrate that Si regulates integrated physiological responses rather than directly enhancing individual traits, with effects dependent on genotype and environment. These results highlight the potential of Si as a strategy to improve the physiological performance of legumes under drought.

A Nano‐SiO2‐Based Melatonin Delivery System Enhances Photosynthetic Carbon Metabolism and Yield of Soybean Under Saline‐Alkali Stress

Sun, 24 May 2026 16:30:05 -0700

ABSTRACT

Saline-alkali stress, a widespread abiotic stress worldwide, severely affects the growth, development, and yield formation of crops. Nanomaterials show great potential in regulating plant growth and improving stress resistance due to their unique physical and chemical characteristics. In this study, nano-silicon dioxide (nano-SiO₂) was prepared by the sol–gel method and used to construct a highly efficient melatonin delivery system. Soybean cultivars Hefeng 50 and Henong 95 were field-grown in saline-alkali soil and foliar-sprayed with 200 mg/L nano-SiO₂, 300 μM melatonin (MT), or their combination at the V3 stage. In the melatonin–nano-SiO₂ system, the encapsulation efficiency and drug-loading capacity of melatonin by nano-SiO₂ were 35% and 53%, respectively. The system can significantly enhance melatonin photostability. The melatonin–nano-SiO₂ treatment significantly enhanced the antioxidant enzyme activity and regulated glutathione levels in soybean plants and reduced the accumulation of reactive oxygen species. The results of physiology, RNA-seq, and qRT-PCR indicated that melatonin–nano-SiO₂ treatment can repair photosynthetic carbon metabolism damage induced by saline-alkali stress. Specifically, it increased leaf area, photosynthetic pigment content, photosystem II (PSII) efficiency, and gas exchange parameters of leaves. It also promoted the activities of sucrose phosphate synthase (SPS) and sucrose synthase (SuSy), while inhibiting the activities of α-amylase and β-amylase, thereby enhancing soluble sugar, sucrose, and starch accumulation. Ultimately, melatonin–nano-SiO₂ treatment significantly improved pod number per plant, seed number per plant, and 100-seed weight. Compared to saline-alkali stress, the per plant yield of HF50 and HN95 under melatonin–nano-SiO₂ treatment increased by 77.41% and 76.52%, respectively.

Multi‐Omics Reveals Mechanisms of Amino Acid Metabolism in Response to Saline–Alkali Stress in Oat Cultivars With Contrasting Tolerance

Lei Ling, Shuya Xing, Jia Li, Jiaxin Song, Yaoyue Zhang, Shutong Lu — Sun, 24 May 2026 16:19:18 -0700

ABSTRACT

Saline–alkali stress is a major factor limiting oat growth in various parts of the world. Amino acids, which are essential structural and metabolic compounds in plants, play a crucial role in enhancing salt tolerance. During abiotic stress, amino acids such as proline, arginine and asparagine are synthesised to serve as compatible osmotic regulators, precursors for secondary metabolites, or organic nitrogen storage compounds. In this study, we examined the effect of salt–alkali stress on amino acid metabolism in two oat varieties. Transcriptomic, proteomic and metabolomic analyses were performed to identify amino acid metabolism-related genes, proteins and metabolites in salt-sensitive and salt-tolerant oats after 6, 12, 24 and 48 h of saline–alkali stress. Saline–alkali stress significantly affected five groups of amino acids: oxaloacetate, glycerate, aromatic, pyruvate and α-ketoglutarate. Among the amino acids identified, phenylalanine and tyrosine showed relatively high expression levels at the transcriptome, proteome and metabolome levels. Genes related to amino acids, including cysK, SHMT, PAL and TDC (amino acid content regulators), were differentially expressed between the two oat varieties and amino acid metabolites such as L-glutamate, L-asparagine, L-aspartic acid, glutathione and betaine were differentially regulated. Key genes, including ASNS, serA, PRODH and cysK, were significantly differentially expressed in both varieties under stress, as validated by RT-qPCR. This study provides a comprehensive analysis of amino acid metabolism in two oat varieties with different salt tolerances and offers insights into the regulatory mechanisms of amino acid metabolism under abiotic stress.

Ecophysiological Characteristics of High‐Photosynthetic‐Efficiency Rice Varieties and Their Environmental Regulation

Miao Ye, Yuxin Mao, Rong Yuan, Zujian Zhang — Fri, 22 May 2026 01:01:05 -0700

ABSTRACT

Improving photosynthetic efficiency is considered to be one of the most promising approaches for further boosting rice yield. However, the ecophysiological characteristics of high-photosynthetic-efficiency rice varieties, whether at the leaf or canopy level, remain poorly understood. In this work, the ecophysiological characteristics of high-photosynthetic-efficiency rice varieties at leaf and canopy levels, as well as their regulation by environmental factors, were investigated. Furthermore, approaches for further improving rice photosynthesis were discussed. We concluded that high-photosynthetic-efficiency rice varieties are characterized by specific leaf traits, including high Rubisco and nitrogen content, high stomatal density with large stomata, large intercellular airspaces and high chloroplast coverage, and thin cell walls. They also exhibit high leaf vein density, large vein diameter, and large root surface area and root diameter. In addition, they have erect and dark green leaves, more leaves in the lower canopy, and a high degree of light-nitrogen matching in the canopy. Improving the response speed of rice photosynthesis to radiation changes, enhancing its adaptation to temperatures, increasing its tolerance to drought, and raising the CO₂ concentration can all effectively improve rice photosynthetic capacity. Increasing N input enhances high photosynthetic traits and promotes gas exchange. However, excessive N application decreases the N use efficiency (NUE) and causes a series of environmental problems. High NUE rice varieties should be bred to coordinately improve photosynthesis and protect the environment. This study provides a theoretical guidance for high-photosynthetic-efficiency rice breeding and cultivation.

Capturing Early‐Stage Chilling Response in Field‐Grown Sorghum and Maize by Integrating Aerial Phenotyping and Metabolomic Signatures

Thu, 21 May 2026 01:30:54 -0700

ABSTRACT

Early-season chilling limits sorghum establishment in temperate environments, yet the metabolic basis of this sensitivity remains poorly understood. We combined temporal spectral reflectance with untargeted metabolomics to characterize species and genotype-level responses to early planting conditions. Normalized Difference Vegetative Index (NDVI) and Normalized Difference Red-Edge (NDRE) index revealed consistently faster seedling development and greater early-season greenness in maize compared with sorghum, with chilling-tolerant sorghum genotypes exhibiting intermediate reflectance patterns. Principal component analysis of metabolite profiles separated maize and sorghum along a dominant species axis, while planting date effects and genotype-specific metabolic stability were captured along secondary axes. Untargeted metabolomics identified 144 differentially accumulated metabolites (DAMs) between maize and sorghum and 56 DAMs between early- and optimum-planted sorghum. Early planting induced marked metabolic reorganization in sorghum, characterized by the accumulation of phenylpropanoid intermediates (chlorogenic acid, 4-hydroxybenzoic acid), osmoprotective sugars and polyols (galactinol, mannitol), amino acid derivatives (pipecolic acid, O-acetylserine), and aromatic amino acids, accompanied by depletion of central carbon metabolites including sucrose, fructose, sorbitol, and 3-phosphoglycerate. Pathway enrichment analysis indicated chilling-induced suppression of starch and sucrose metabolism, fructose–mannose pathways, and amino sugar metabolism, alongside activation of phenylpropanoid, terpenoid, aromatic amino acid, glucosinolate, and cyanoamino acid biosynthesis in sorghum compared with maize. The results of the current study demonstrate that early-season chilling constrains carbon turnover in sorghum and promotes diversion of metabolic flux toward antioxidative and osmoprotective pathways. The spectral metabolomic framework presented here identifies biochemical signatures associated with chilling sensitivity and provides targets for improving early-season vigor in sorghum.

SlTCP14 Positively Regulates Low‐Light Tolerance by Increasing Antioxidant Activity and BR Biosynthesis in Tomato

Thu, 21 May 2026 01:22:19 -0700

ABSTRACT

Tomato (Solanum lycopersicum L.) often experiences low-light stress during winter greenhouse cultivation. TCPs are unique transcription factors in higher plants and are involved in plant development and the response to abiotic stress. However, the molecular mechanisms through which TCP transcription factors regulate low-light tolerance in crops are unclear. In this study, we elucidated the molecular regulatory mechanism through which SlTCP14, a class I TCP transcription factor, positively regulates low-light tolerance in tomatoes. Compared with the wild type plants, the OE-SlTCP14 plants presented increased chlorophyll content, photosynthetic capacity, and antioxidant enzyme activity but reduced ROS accumulation, whereas the opposite effects were detected for the CR-SlTCP14 plants (SlTCP14 silencing). SlTCP14 binds to the promoter region of the peroxidase gene SlPER10. Additionally, the levels of brassinosteroids (BRs) and BR biosynthetic intermediates significantly increased in OE-SlTCP14 plants, suggesting that the BR biosynthesis pathway may be involved in the induction of chlorophyll biosynthesis through SlTCP14. The results of this study elucidated the mechanism by which SlTCP14 improves low-light tolerance in tomatoes by increasing antioxidant activity and promoting BR synthesis. Our findings provide a reliable basis for further research on the mechanism underlying low-light tolerance and the selection of low-light-tolerant varieties in tomato.

The Protein Response Mechanism of Adventitious Root Formation About Scaly Branches in Platycladus orientalis

Wed, 20 May 2026 02:53:22 -0700

ABSTRACT

Platycladus orientalis (P. orientalis) is a monoecious and evergreen tree. It is not only one of the most common ornamental species, but also has some pratical value. Cutting propagation is a common technique used to preserve excellent P. orientalis resources. But the rooting rate is influenced by both internal and external factors. In this study, we used our new cultivar “Liye” as the material to design experiment. We detected the determination of physiological indicators including soluble protein, peroxidase (POD), polyphenol oxidase (PPO), and indole acetic acid oxidase (IAAO). Meanwhile, the content of indole-3-acetic acid (IAA), zeatin riboside (ZR), abscisic acid (ABA), and gibberellin 3 (GA₃) were detected after indole-3-butyric acid (IBA) treatment. According to the data on phenotypic changes, we analyzed some proteins related with hormones by isobaric tag for relative absolute quantitation (iTRAQ). We found IAA is a key endogenous hormone that induced the formation of adventitious root in young branches of P. orientalis. Besides, the content of ZR, ABA, and GA₃ showed the different trends of change. We found 136 differential expression proteins related to hormones, and selected two proteins related to cytokinin, three proteins related to auxin, and one protein related to abscisic acid based on the changing trends of hormone content at different stages. The results provided a more holistic view of cellular processes and laid a theoretical foundation for the production of uniform and high quality seedlings in P. orientalis.

Synergistic Application of Humic Acid and Bacillus mobilis IJL Mitigates Nickel‐Induced Stress in Soybean Through Modulation of the ABA Pathway

Mon, 18 May 2026 20:47:00 -0700

ABSTRACT

This study investigated the synergistic effects of plant growth–promoting rhizobacteria (PGPR) and humic acid in mitigating nickel-induced stress in soybean. Bacterial isolates were obtained from the Pohang beach environment, among which the Bacillus mobilis IJL strain demonstrated particularly promising performance under in vitro conditions. To further evaluate the combined effects of B. mobilis IJL and humic acid, a pot experiment was established with four treatments: control (water only), IJL, humic acid (100 mg kg⁻¹), and IJL + humic acid, under both normal and nickel-stress conditions (50 mg kg⁻¹). A comprehensive set of plant physiological, biochemical, antioxidant, and computational parameters was assessed. The IJL + humic acid treatment significantly improved plant growth, chlorophyll content, leaf spectral indices, antioxidant capacity, and nutrient uptake under both normal and Ni-stressed conditions. Additionally, endogenous abscisic acid (ABA) levels were markedly reduced in IJL + humic acid–treated plants. Computational analyses indicated that metabolites produced by IJL and humic acid may inhibit two key enzymes in the ABA biosynthetic pathway, 9-cis-epoxycarotenoid dioxygenase (NCED3) and abscisic aldehyde oxidase (AAO3), thereby contributing to lower ABA. These findings provide novel insight into how the synergistic application of humic acid and IJL mitigates Ni-induced stress in soybean by modulating the ABA-mediated stress signaling pathway. The results suggested that the potential of B. mobilis IJL combined with humic acid can be used as an organic tool to enhance plant performance and nutrient uptake in nickel-contaminated soil.

Harnessing the Power of Phenolic Compounds for Boosted Crop Resilience and Health

Sun, 17 May 2026 23:24:13 -0700

ABSTRACT

Phenolic compounds are secondary metabolites synthesized by plants that play crucial roles in plant defense, growth, and adaptation to environmental stresses. These compounds are primarily derived from the shikimate pathway and are classified based on their carbon skeleton into simple phenolics (C6, C6–Cn, and C6–Cn–C6) and complex phenolics, such as flavonoids, lignans, stilbenes and tannins. Phenolic compounds act as signaling molecules in plant-microbe interactions, including legume-rhizobia symbiosis and arbuscular mycorrhization. They also contribute to plant defense against biotic and abiotic stressors through direct antimicrobial activity, structural reinforcement and modulation of plant immune responses. Phenolic compounds are synthesized via the shikimate/phenylpropanoid or polyketide acetate/malonate pathways, resulting in a diverse array of compounds with distinct biological activities. Recent advances in biotechnology, including elicitation, genetic transformation, and metabolic engineering, have enabled the enhanced production of valuable phenolic compounds in plants. However, challenges remain in optimizing phenolic biosynthesis for improved crop resilience due to the complexity of the regulatory networks and potential trade-offs with plant growth and ecological interactions. Future research should focus on integrating systems biology, multi-omics approaches, and precision breeding to harness the potential of phenolic compounds for sustainable agriculture and crop improvement in the face of increasing biotic and abiotic stress.

Beneficial Microbes in Plant Salinity Stress Responses: Integrating Correlative Evidence With Mechanistic Frameworks

Arka Chakrovarty, Ashish Kumar Singh, Akhilesh Kumar Pandey — Sun, 17 May 2026 16:24:41 -0700

ABSTRACT

Salinity disrupts ionic balance, osmotic regulation, redox homeostasis, and hormone signaling, thereby constraining plant growth and metabolism. Plants employ adaptive responses to salinity stress, including ion transport regulation, compatible solute accumulation, antioxidant defenses, and signaling reprogramming; however, these mechanisms are often insufficient under high salinity. Beneficial microbes, including plant growth-promoting rhizobacteria, endophytes, fungi, and halotolerant taxa, are increasingly associated with improved plant performance under saline conditions. These associations are consistently linked with changes in ion homeostasis, osmotic adjustments, redox balance, hormone signaling, and root architecture. Importantly, most available evidence derives from transcriptomic, biochemical, and physiological observations, which do not establish direct mechanistic regulation. This review critically evaluates microbial contributions to plant salinity responses by explicitly distinguishing between experimentally validated mechanisms, correlative associations, and hypothesis-driven models. We integrate insights from molecular genetics, biochemistry, and multi-omics approaches while highlighting their limitations in establishing causality. Particular emphasis is placed on experimental strategies required to establish causal mechanisms, including isotope tracing, genetic perturbation, and synthetic community approaches.

The bHLH Transcription Factor DkLHW Is a Positive Regulator of Plant Height in Persimmon

Fri, 15 May 2026 06:06:22 -0700

ABSTRACT

Dwarfism is an important agronomic trait in perennial fruit trees, although its molecular regulatory mechanism in persimmon remains poorly understood. In this study, we identified a bHLH transcription factor, DkLHW, which functions as a positive regulator of plant height in persimmon. Yeast two-hybrid (Y2H), bimolecular fluorescence complementation (BiFC), and pull-down assays demonstrated that DkLHW interacts with DkMYB117. Electrophoretic mobility shift (EMSA) assays showed that DkLHW enhances the DNA-binding ability of DkMYB117 to the DkGA2ox2 promoter. Dual-luciferase reporter assays further demonstrated that this enhanced binding leads to stronger transcriptional repression of DkGA2ox2. Heterologous overexpression of DkLHW in tobacco resulted in increased plant height, longer internodes, and elevated levels of active GAs. Similarly, transient overexpression of DkLHW in persimmon leaves down-regulated DkGA2ox2 expression and increased active GA content. Expression analysis showed that DkLHW transcript levels were significantly lower in the dwarf cultivar ‘Nantongxiaofangshi’ (Diospyros kaki Linn.cv. Nantongxiaofangshi) compared with standard cultivars. These results indicate that DkLHW positively regulates persimmon plant height by forming a functional module with DkMYB117 to repress DkGA2ox2 expression and modulate gibberellin homeostasis. Our findings provide new insights into the transcriptional network controlling dwarfism in persimmon and identify DkLHW as a potential target for molecular breeding of plant architecture.

Roles of Genetic Networks, Environmental Responses and Hormonal Regulation in the Maintenance and Differentiation of Tree Stem Cells

Shasha Wang, Jin Li, Shanchen Zhong, Kai Cui — Thu, 14 May 2026 05:01:19 -0700

ABSTRACT

Tree stem cells are primarily localized in the apical meristems, including the shoot apical meristem (SAM) and the root apical meristem (RAM), as well as in the lateral meristems, specifically the vascular cambium. Through continuous division and differentiation, these stem cells drive both vertical and radial growth in trees. This review systematically examines recent research progress on tree stem cells, with a focus on their structural organization and characteristics, mechanisms of maintenance and regulation, and potential applications. Structurally, tree stem cells exhibit pronounced tissue specificity and clear functional differentiations. With respect to regulatory mechanisms, their maintenance and differentiation are coordinately controlled by genetic networks such as CLV–WUS, WOX and HD-ZIP III/KANADI, environmental factors such as drought, salinity and extreme temperatures, and plant hormones, including auxins, cytokinins, abscisic acid and gibberellins. In terms of applications, research on tree stem cells provides key technological support for in vitro cell culture, large-scale production of bioactive compounds from forest products, and sustainable wood utilization. This paper summarizes recent domestic and international research on tree stem cells, highlighting their regulatory mechanisms, physiological characteristics, and application prospects. Furthermore, it discusses current challenges and future directions in this field, with the aim of informing efforts in forest genetic improvement and the sustainable development of tree resources.

PLS‐PM Modeling Reveals Biochar‐AMF Synergy on Salinity Tolerance in Suaeda salsa Through Ion Homeostasis and Oxidative Stress Alleviation

Thu, 14 May 2026 04:40:27 -0700

ABSTRACT

Soil salinization imposes severe ionic and osmotic stress on plants, threatening ecosystem sustainability. Biochar (BC) and arbuscular mycorrhizal fungi (AMF) have shown potential to alleviate salinity stress, but their interactive effects on the soil–plant-microbe continuum have not been fully elucidated. This study utilized partial least squares path modeling (PLS-PM) to assess the individual and combined contributions of BC and AMF to sodium (Na⁺) homeostasis in Suaeda salsa. Results indicate that BC primarily acted as a soil conditioner, reducing Na⁺ bioavailability by 49.19% (compared to the unamended saline control) (as indicated by the soil Na⁺/K⁺ ratio) through enhanced adsorption and cation exchange, thereby contributing to improved soil health (including an 87.23% increase in SOC). In contrast, AMF elicited a plant physiological response, characterized by the upregulation of antioxidant enzymes (such as a 114.85% increase in catalase) and osmotic regulators (e.g., a 90.22% increase in soluble sugars), which collectively mitigated oxidative stress and promoted vacuolar sequestration of Na⁺. A strong synergistic effect (E > 0) was observed. The PLS-PM model quantitatively delineated the causal pathways, revealing that BC and AMF function through complementary soil–soil solution-root-leaf-vacuole transport routes. This study reveals the mechanism underlying the interaction between biochar and AMF, while quantifying the pathways through which they synchronously regulate the rhizosphere chemical environment and internal detoxification in plants, providing new insights into how halophytes cope with environmental stress challenges.

Wheat Dwarf Virus as a Modulator of Multi‐Stress Responses in Wheat

Jana Asszonyi — Wed, 13 May 2026 04:27:24 -0700

ABSTRACT

Wheat dwarf virus (WDV) is an emerging constraint to cereal production whose epidemiological significance has intensified under climate change. Rising temperatures, extended vector activity, and the expansion of Psammotettix alienus into new regions have increased both the frequency and severity of WDV outbreaks. Beyond its direct effects on plant development, WDV acts as a powerful regulator of host physiology, functioning as a host signalling hub that reprograms hormonal signalling, alters source-sink relationships, disrupts redox homeostasis, and modulates responses to both abiotic and biotic stress. Recent molecular studies have revealed how viral proteins manipulate the cell cycle, transcriptional machinery, and RNA silencing pathways to optimise viral replication while attenuating defence responses. These processes intersect with core stress-response networks, particularly those governed by abscisic acid, gibberellins, cytokinins, and auxin, positioning WDV as a model system for investigating hormonal crosstalk under combined stress. Despite advances in genomics, transcriptomics, and vector biology, major knowledge gaps persist regarding WDV interactions with co-occurring fungal pathogens, its impact on the plant microbiome, and its role in shaping cereal resilience under drought, heat, or nutrient limitations. This review synthesises current understanding of WDV biology from the molecular to the ecological scale, highlights mechanisms underpinning stress integration, and outlines future research priorities essential for developing sustainable management strategies in a changing climate.

Alternative Splicing: A New Regulatory Mechanism for Plants Responds to Biotic and Abiotic Stresses

Yuxia Yao, Yushi Lu, Yuna Pan, Wenjin Yu, Changxia Li — Wed, 13 May 2026 03:08:34 -0700

ABSTRACT

Alternative splicing (AS) is an important post-transcriptional regulation method in eukaryotes. AS has been shown to play an important role in plant responses to biotic and abiotic stresses. This paper summarizes the main types of AS events and the pathways and regulatory mechanisms of AS in plants' response to biotic and abiotic stresses. We hope to provide a reference for further understanding of the stress response mechanism in plant AS and a theoretical basis for breeding resistant varieties.

Synergistic Regulation of Codonopsis pilosula Growth and Metabolism by Trichoderma, Salicylic Acid, and Methyl Jasmonate

Tue, 12 May 2026 20:25:55 -0700

ABSTRACT

Endophytic fungi can mediate salicylic acid (SA) and methyl jasmonate (MeJA)-related signaling in medicinal plants, thereby influencing metabolite synthesis, stress resistance, and growth development. Experimental groups comprised control, Trichoderma longibrachiatum inoculation (FG), FG + SA (FS), FG + MeJA (FM), FG + SA + MeJA (FSM), and corresponding inhibitor treatments (FSI, FMI, FSMI), with I indicating inhibitor application. Morphological traits, photosynthetic parameters, nitrogen metabolism enzyme activities, antioxidant defense indices, and signaling-related molecules in Codonopsis pilosula were measured at 15, 30, and 50 days. Non-targeted metabolomic analysis was conducted to identify differential metabolites and enriched pathways. The results showed that the FSM treatment markedly promoted root development and biomass accumulation in C. pilosula, increased chlorophyll content and photosynthetic rate, and enhanced antioxidant capacity, as reflected by increased CAT and GR activities. Meanwhile, endogenous SA and JA levels were markedly altered, and nitric oxide (NO) levels exhibited treatment-dependent dynamics, suggesting that NO may participate in broader hormone-associated signaling responses during the Trichoderma–SA/MeJA interaction. Metabolomic analysis revealed that FSM notably regulated steroid and brassinolide biosynthesis pathways, with key metabolites such as 6-deoxotyphasterol upregulated and 4,4-dimethyl-5alpha-cholesta-8,14,24-trien-3beta-ol downregulated. Inhibitor treatments reduced enzyme activities, increased malondialdehyde accumulation, and suppressed growth and photosynthetic efficiency. Overall, the combined SA and MeJA treatment together with fungal inoculation was associated with the strongest promotion of growth and stress resistance in C. pilosula. This study reveals the metabolic reprogramming features of microbe–hormone interactions in medicinal plants and provides theoretical support for the quality cultivation of C. pilosula.

Deciphering ABA Receptor PYL Gene Family in Sugar Beet: Evolutionary Analysis and Drought Stress Response

Erxuan Shang, Wenjing Qiu, Yingxiao He, Jiaming Zhu, Yu Tian, Bing Yu — Mon, 11 May 2026 23:45:23 -0700

ABSTRACT

Abscisic acid (ABA) receptors (PYL) play a pivotal role in plant responses to abiotic stress. However, functional characterization of PYL genes in sugar beet response to stresses remains unexplored. Here, 11 BvPYL genes were identified in the sugar beet genome, and they were classified into three subgroups. A comprehensive analysis of their gene structures, sequence features, chromosomal distributions, and promoter cis-elements was conducted. Furthermore, their evolutionary relationships, predicted interaction networks, and expression patterns under drought stress were investigated. qRT-PCR and transcriptomics data revealed expression profiles of the BvPYL family from two perspectives: short-term response and long-term adaptation to drought. Most BvPYL members were up-regulated under both conditions. Subcellular localization analysis showed that BvPYL8 is nuclear-localized. Protein interaction screening and molecular docking predicted that BvPYL8 interacts with multiple PP2C proteins (e.g., PP2C8, PP2C24, PP2C37, PP2C50, PP2C51 and PP2C56) through hydrogen bonding with a key asparagine residue (ASN-148), and their interaction was experimentally verified using the Y2H and BiFC assay. A molecular mechanism for the BvPYL8-PP2Cs-BvSnRK2s-TFs pathway in the ABA signaling pathway under drought stress was proposed. These results may serve as a springboard for further functional exploration of the BvPYL gene family in sugar beet and its related species, and provide important target genes for improving crop drought tolerance through genetic engineering and molecular breeding.

Editing of SlMYB60 Reveals a Role in Cuticle Formation in Tomato

Sun, 10 May 2026 18:40:34 -0700

ABSTRACT

Under climate change, yield stability depends heavily on the ability to develop resilient crops, better adapted to water scarcity. Studies in model systems have uncovered molecular pathways and genes that potentiate the plant response to environmental stress. CRISPR-based editing technologies enable the precise and rapid transfer of beneficial traits from model species to crops. Previous work identified Solanum lycopersicon MYB60 (SlMYB60) as the functional ortholog of the Arabidopsis guard cell-related AtMYB60 transcription factor. Loss of AtMYB60 function results in reduced stomatal opening and enhanced stress resistance, providing a valuable target for crop improvement. Here, we report the CRISPR-mediated exploitation of SlMYB60 in two tomato commercial varieties. Unexpectedly, editing of SlMYB60 did not result in reduced stomatal opening and enhanced stress resistance. Independent edited lines showed increased stomatal size, enhanced leaf water loss, and cuticle permeability. RNAseq analyses revealed that the expression of genes involved in cell wall and cuticle metabolism was altered in the edited lines. Scanning electron microscope analysis of leaf epidermis revealed defects in cuticle deposition and in the formation of outer cuticle ledges. As opposed to the guard cell-specific activity of the AtMYB60 promoter, we found that the SlMYB60 promoter was active in both stomata and epidermal cells. Our findings indicate functional divergence between AtMYB60 and SlMYB60, providing valuable insights into species-specific regulatory mechanisms and emphasizing the complexities of translating gene-editing strategies across plant systems.

The Evolutionarily Conserved Jasmonate Pathway Positively Affects Desiccation Tolerance on Syntrichia caninervis by Boosting Antioxidant Capacity

Sun, 10 May 2026 18:19:35 -0700

ABSTRACT

Syntrichia caninervis (S. caninervis) serves as a model organism for desiccation tolerance research because of its exceptional capacity to withstand 98% cellular water loss. Although jasmonic acid (JA) biosynthesis and signaling genes have been well characterized in vascular plants, their functional and evolutionary roles in bryophytes remain poorly understood. This study demonstrated that exogenous JA treatment significantly delayed the reduction in absolute water content (AWC) and the optimal photochemical efficiency of photosystem II (Fv/Fm) during dehydration in S. caninervis, while mitigating reactive oxygen species (ROS) accumulation through enhanced antioxidant enzyme activity. Multi-omics analyses revealed the upregulation of JA pathway genes during early dehydration, coinciding with JA pathway protein accumulation. Notably, the genes involved in JA biosynthesis undergo phosphorylation and acetylation during dehydration. Genome-wide analysis identified 34 JA pathway genes in S. caninervis that were uniformly distributed across chromosomes without sex chromosome association. Collinearity analysis confirmed the conservation of the JA pathway genes between S. caninervis and Physcomitrella patens (P. patens). Multiple stress- and phytohormone-responsive cis-elements were enriched in JA pathway genes, highlighting their regulatory adaptation to environmental stresses. In addition, RT-qPCR analysis revealed that JA pathway genes responded to dehydration, salt, cold, and heat stress. Overall, these findings provide compelling evidence for the evolutionary conservation of JA pathway in terrestrial plants and advance our understanding of their functional mechanisms in desiccation tolerance.

Functional Characterization of MeJA‐Induced OjTIFY2 in Mediating Salt Stress Tolerance in Oenanthe javanica

Sat, 09 May 2026 00:20:44 -0700

ABSTRACT

The plant-specific transcription factor TIFY plays key roles in plant growth and development, including seed germination, signal transduction, and responses to environmental stimuli and plant hormones. However, few studies have investigated the function of the TIFY family in responding to salinity stress in water dropwort (Oenanthe javanica (Blume) D.C). Here, a total of 24 OjTIFY genes, named OjTIFY1-OjTIFY24, were identified in water dropwort. And their phylogenetic relationships, gene structure, chromosomal distribution, promoter regions, and collinearity patterns were comprehensively analyzed. We further identified a member, OjTIFY2, located in the nucleus and positively upregulated by exogenous MeJA. Meanwhile, we found that exogenous MeJA could alleviate the sensitivity of water dropwort to salt stress by regulating the activity of antioxidant enzymes and the content of osmotic regulatory substances. A transient overexpression experiment in water dropwort showed that OjTIFY2 enhanced its tolerance to salt stress. The qRT-PCR analysis showed that OjSOS1, OjSOS3, OjKAT1, OjP5CS, and OjHKT1 were significantly upregulated when OjTIFY2-overexpressing lines were subjected to salt stress. Then, the transgenic Arabidopsis overexpressing OjTIFY2 also exhibited tolerance to salt stress by increasing the activities of SOD, POD, and CAT, and the contents of proline and chlorophyll, and by reducing the contents of MDA and H₂O₂. We also found that OjTIFY2 positively regulates the expression of salt-stress-related genes AtSOS1, AtSOS3, AtKAT1, AtP5CS, and AtHKT1. These results suggest that OjTIFY2 acts as a positive regulator of salt tolerance in water dropwort by modulating ROS scavenging and the expression of salt-related genes.

Editorial: Special Issue “Methodologies to Assess Crop Stress Resilience”

Christos Bazakos, Michal Lieberman‐Lazarovich, Hélène S. Robert — Sat, 09 May 2026 00:00:22 -0700

Physiologia Plantarum, Volume 178, Issue 3, May/June 2026.

Evaluation of Bna.SCT and Bna.REF1 as Target Genes to Reduce Sinapine in Rapeseed Using a Protoplast‐Based CRISPR RNP Approach

Fri, 08 May 2026 06:52:24 -0700

ABSTRACT

Rapeseed is a major oil crop worldwide, producing both oil and a high amount of protein. However, the use of its seed meal as a protein source for animal feed is limited by antinutritional factors, such as sinapine, which reduces nutrient absorption and affects the palatability. Efforts to reduce sinapine levels through conventional breeding have had limited success. Given the challenges of a changing climate and a growing global population, maximising crop utility, particularly the value of seed meal as a byproduct, is increasingly important. Genetic modification has been successfully used to reduce sinapine in rapeseed, but regulatory restrictions limit its commercial adoption in some regions. CRISPR-Cas gene editing, which is gaining broader global acceptance, offers a promising alternative to directly produce transgene-free mutants. In this study, we build on our previous work by generating transgene-free rapeseed mutants using protoplast-based CRISPR RNP gene editing. We successfully targeted the Bna.SCT and Bna.REF1 genes with editing efficiencies of 22%–63%, frequently achieving mutations in all four alleles of the target genes in T₂ plants with a single sgRNA. Seed sinapine content was reduced by up to 38% in Bna.SCT mutants and 77% in Bna.REF1 mutants, with no observed effects on plant growth or development. These findings suggest that Bna.REF1 is the most effective target for sinapine reduction in transgene-free mutants among the genes tested in our lab.

The Response of Leaf Tissues of the C4 Euhalophyte Suaeda altissima (L.) Pall. To Salinity Stress

Lyudmila Khalilova, Elena Shuyskaya, Maria Prokofieva, Yurii Balnokin — Thu, 07 May 2026 02:04:07 -0700

ABSTRACT

Impact of long-term (17-day) exposure to growth-stimulating (250 mM) and growth-inhibitory (750 mM) NaCl concentrations on biochemical characteristics related to C₄ pathway, anatomy and ultrastructure of chloroplasts of leaf tissues in the euhalophyte S. altissima was investigated. Immunological and biochemical studies identified C₄ enzymes, phosphoenol pyruvate carboxylase (PEPC), NAD-malic enzyme (NAD-ME), and NAD-malate dehydrogenase (NAD-MDH). Anatomical studies revealed Kranz anatomy with mesophyll (MCs) and Kranz cells (KCs) at the leaf periphery. Water-storage cells (WSCs) and vascular bundle chlorenchyma cells (VBCCs), both located in the leaf middle, contained chloroplasts, as did MCs and KCs. Electron microscopy revealed granal chloroplasts containing starch granules, while immunogold labeling revealed Rubisco in chloroplasts of all chlorophyllous tissues. The highest Rubisco content was found in KC chloroplasts. These results are consistent with the notion that S. altissima is a C₄ plant; however, they do not exclude its belonging to an intermediate C₃-C₄ form. The growth-stimulating NaCl concentration increased Rubisco content in all chlorophyllous tissues and activity of NAD-ME in leaves activating, probably, the C₄ pathway. In contrast, the growth-inhibitory NaCl concentration reduced Rubisco content, decreasing it below the level observed in the absence of NaCl. An increase in cell size was observed in the chlorophyllous tissues in response to both the growth-stimulating and growth-inhibitory salinity, leading to an increase in leaf succulence. The greatest increase in size was observed in WSCs. Chloroplasts from different tissues differed in their ability to maintain native structure and robustness of Rubisco-chloroplast binding under salinity, suggesting chloroplast heterogeneity and different Rubisco sensitivities to NaCl.

SCL15 Promotes Seed Longevity Acquisition in Arabidopsis thaliana by Enhancing Antioxidant and Repair Mechanisms During Maturation

Wed, 06 May 2026 20:29:58 -0700

ABSTRACT

To ensure seed longevity and successful germination, orthodox seeds acquire protective and repair mechanisms during the late stage of seed development to counteract the detrimental effects of desiccation and subsequent rehydration, processes often associated with oxidative stress. SCARECROW-LIKE 15 (SCL15) was identified as a key regulator of seed longevity acquisition through transcriptomic profiling of maturing seeds from Arabidopsis thaliana wild type (Col-0), an SCL15 mutant, and transgenic lines overexpressing SCL15 under the seed-specific Napin promoter. SCL15 influences pathways associated with reactive oxygen species (ROS) detoxification, chlorophyll degradation, DNA and protein repair, and the accumulation of protective molecules, including late embryo abundant proteins, heat shock proteins, raffinose family oligosaccharides, and 12S globulins during seed maturation. Loss of SCL15 function impaired seed vigor and storability, accompanied by elevated ROS levels, chlorophyll retention, and reduced antioxidant capacity during seed maturation and dry storage. In contrast, SCL15 overexpression enhanced antioxidant activity, chlorophyll breakdown, and the accumulation of protective and repair factors. Together, these findings indicate that SCL15 contributes to maintaining seed viability by coordinating antioxidant defenses with protective and reparative systems during seed maturation, thereby promoting desiccation tolerance and the acquisition of longevity. In addition, the present results, together with our previous work, suggest that SCL15 may participate in integrating hormonal and circadian pathways to balance dormancy release with the acquisition of seed longevity.

Environmental Factors Shape Terpenoid Accumulation and Predicted Bioactivity in Houttuynia cordata

Tue, 05 May 2026 02:18:23 -0700

ABSTRACT

Houttuynia cordata is a traditional medicinal plant with various bioactivities mainly caused by its terpenoids. However, the effects of geography, environment, biosynthesis, and multiple pharmacological targets of these compounds are still not well understood. We used UPLC-MS/MS and GC–MS metabolomics to analyze terpenoids in accession 7# grown across six regions in China (Yunnan, Guangxi, Hubei, Chongqing, Guizhou, and Sichuan) and identified key environmental factors linked through random forest analysis. Network pharmacology identified potential targets and pathways for differentially accumulated terpenoids, further validated by molecular docking. Transcriptome sequencing identified terpenoid biosynthetic genes. A total of 502 terpenoid metabolites were detected, and chemotypic diversity was strongly shaped by geographical origin. Altitude (bio21) and annual precipitation (bio12) emerged as the primary environmental factors associated with 58 and 18 differential metabolites, respectively. Network analysis of 39 terpenoids revealed 239 potential targets, with 23 core targets (e.g., ESR1, STAT3, BCL2, AR) enriched in cancer, endocrine resistance, and hormone-related pathways. Docking confirmed stable interactions between key terpenoids (byzantionoside B, ursonic Acid) and core targets (ESR1, AR, BCL2) with binding energies < −7.5 kcal mol⁻¹. Transcriptomic analysis uncovered 103 differentially expressed genes in the MVA and MEP pathways, with several (e.g., AACT, FPPS, HMGR, DXS) showing strong correlations with core terpenoid accumulation. This multi-omics study provides insights into substantial geospatial variation in H. cordata terpenoids, identifies altitude and precipitation as major environmental factors associated with terpenoid accumulation, and offers a predictive framework for the biosynthetic network and multi-target pharmacological potential, especially anticancer. It offers a theoretical basis for quality control and optimized cultivation.

Transcriptomic Signatures of Nitrate Response in Rapeseed Genotypes With Distinct Root System Sizes

Tue, 05 May 2026 01:46:11 -0700

ABSTRACT

Nitrogen fertilization remains a cornerstone of modern agriculture, yet its excessive use contributes to environmental degradation. Rapeseed (Brassica napus L.) is notably inefficient in N uptake, highlighting the importance of root traits that enhance soil exploration and nutrient acquisition. This study investigated root transcriptomic responses to nitrate availability across rapeseed genetic diversity. A panel of 40 lines was screened on vertical agar plates, revealing substantial variation in root morphology, strong heritability, and genetic control. Low nitrate supply increased the root-to-shoot biomass ratio and stimulated lateral root proliferation. Transcriptomic profiling was then conducted on three genotype pairs selected to represent distinct root system sizes. Hydroponically grown plants were exposed to two divergent nitrate levels for 24 h, and root tissues were harvested for RNA sequencing. Differential expression analysis identified over a 1000 genes significantly induced or repressed by nitrate treatment, with only 10% shared across genotypes. Gene ontology enrichment analysis revealed a central nitrate-responsive transcriptional program, accompanied by distinct molecular signatures associated with root size. Co-expression network analysis identified regulatory modules that integrate nitrate transporters with auxin signaling and energy metabolism. These modules also uncovered roles for glucosinolate biosynthesis and aquaporin-mediated water transport. This study provides a set of candidate genes and regulatory networks that represent promising targets for breeding rapeseed varieties with optimized root traits for sustainable agriculture.

Weighted Gene Co‐Expression Network Analysis Reveals Hub Genes Associated With Response to Low‐Phosphorus Stress in Pueraria lobata

Yanhua Tang, Shuwei Zhang, Yi Xi, Lili Zhao, Chao Chen — Mon, 04 May 2026 21:24:51 -0700

ABSTRACT

Phosphorus is an essential element for plant growth, and its deficiency severely limits crop productivity. To explore genetic resources for improving phosphorus use efficiency, this study investigated the differential low-phosphorus tolerance mechanisms of two kudzu (Pueraria lobata) germplasms from Australia (tolerant) and Jiangsu, China (sensitive) using hydroponics, RNA-seq, and WGCNA. The results showed that the Australian germplasm exhibited superior low-phosphorus tolerance through root morphological plasticity, which was characterized by increased root length and tip number under low phosphorus (0.05 mmol L⁻¹ KH₂PO₄); enhanced reactive oxygen species scavenging, with higher peroxidase and catalase activities under extremely low phosphorus (0.005 mmol L⁻¹ KH₂PO₄), and extensive transcriptome reprogramming, including 8896 upregulated genes in response to phosphorus deficiency. In contrast, the Jiangsu germplasm showed limited adaptive responses, with reduced root hairs and biomass under stress. WGCNA partitioned 21,734 expressed genes into 20 co-expression modules, among which the turquoise and light green modules showed significant correlations with phosphorus treatments and phenotypic traits. Genes in the turquoise module were primarily enriched in oxidative phosphorylation and phenylpropanoid biosynthesis pathways, whereas the light green module was significantly enriched in ribosome-related pathways. Five hub genes, ABCG5, TALDO, VAMP7B, EEF1AS, and RPLP0, were identified as core components of these modules. Collectively, these findings establish the Australian kudzu as a valuable germplasm resource for improving phosphorus use efficiency in crops and provide key molecular targets for precision breeding.

Metabolic Regulations of Glycine max Induced by Potassium Nanoparticles Under Simulated Salinity Conditions: A Comparative Morpho‐Physiological Aspect

Mon, 04 May 2026 02:48:27 -0700

ABSTRACT

Crop productivity is a major concern in modern agriculture due to fluctuating environmental conditions, such as salinity. This study aims to explore the green-synthesized potassium nanoparticles (K-NPs) mediated metabolic regulations, including improved ion homeostasis, photosynthetic efficiency, and antioxidative defense mechanisms in soybean (Glycine max var. Soygold) under salinity stress. The K-NPs were green synthesized using the leaf extract of Cordia myxa L. and then characterized using UV–Vis spectroscopy, high-resolution transmission electron microscopy (HRTEM), and zeta potential. Soybean seedlings were treated with 0, 30, 60, and 90 mg L⁻¹ of K-NPs along with salinity stress of 30, 60, and 90 mg L⁻¹ NaCl at 3, 7, and 14 days of plant growth. After the treatments, morphological, biochemical and antioxidant activities were measured. The plant root/shoot lengths were enhanced by 9% and 59%, respectively, while the number of leaves was increased by 32%, fresh biomass by 84%, and dry weight by 105% under K-NPs treatments compared to control. K-NPs at 30 and 60 mg L⁻¹showed non-significant results under 60 and 90 mg L⁻¹ NaCl concentrations, but highly significant results were observed at 90 mg L⁻¹ K-NPs under 30 and 90 mg L⁻¹ NaCl concentrations. The 90 mg L⁻¹ K-NP concentration improved the root/shoot lengths of soybean seedlings by 33% and 132%, respectively. The number of leaves were increased by 38%, the plant fresh biomass by 22%, and dry weight by 133% as compared to lower concentrations under salinity stress. Furthermore, phenolic contents, secondary metabolites, and ionic homeostasis were also increased in the presence of 90 mg L⁻¹ K-NPs under 90 mg L⁻¹ NaCl salinity stress. When exposed to salt stress, K-NPs treatment increased antioxidant enzymes (SOD, CAT, and POX) more than the salt stressed control. Taken together, these results suggest that K-NPs are effective nanomaterials for plant growth enhancement by regulating the defense mechanisms of soybean to cope with salt stress conditions. The findings could help in the designing and optimization of nanomaterial-based fertilizers in order to achieve sustainable agriculture.

Integrated Multivariate and Univariate Analysis of Circadian Metabolomic Signatures in Yerba Mate Clones in a Semi‐Hydroponic System

Mon, 04 May 2026 02:19:37 -0700

ABSTRACT

This study presents an integrated multivariate and univariate analysis of circadian metabolomic signatures in Ilex paraguariensis (yerba mate) clones cultivated under semi-hydroponic conditions. Using repeated measures ANOVA–Simultaneous Component Analysis (RM-ASCA+) and hierarchical clustering on principal components (HCPC), we explored clone-specific and photoperiod-dependent metabolic responses across light and dark phases, complemented by high-resolution timepoint sampling (HRS) and targeted screening. Clone EC21 exhibited elevated levels of sugars, amino acids, and organic acids, suggesting a metabolic strategy adapted to saline stress and nocturnal energy demands. Photoperiod effects revealed circadian regulation of central carbon metabolites (e.g., glucose, fructose, maltose) and phenylpropanoid intermediates linked to bioactive compounds such as caffeoyl-quinic acids. Interaction effects highlighted metabolic plasticity, particularly in nitrogen assimilation, with compounds like 2-oxo-glutaric acid, glutamine, and ornithine showing clone-specific temporal patterns. Caffeine, a heritable and physiologically relevant metabolite, displayed distinct circadian profiles. EC24 accumulated caffeine during the day, while EC21 peaked at night. This dynamic distribution, supported by allantoin patterns in caffeine catabolism, suggests divergent nitrogen turnover strategies between clones. These findings underscore the importance of genotype selection and temporal regulation in optimizing yerba mate performance under semi-hydroponic systems. The combined use of RM-ASCA+ and univariate analysis proved to be a powerful approach for profiling metabolomic rhythms, offering valuable insights for breeding programs targeting bioactive compound enhancement, stress resilience, and metabolic efficiency.

Comprehensive Genome Identification Analysis of WOX Gene Family and Its Expression in Protopanaxatriol Ginsenosides Under MeJA Treatment in Ginseng

Fri, 01 May 2026 03:03:10 -0700

ABSTRACT

Panax ginseng is an important medicinal plant, and its major bioactive components are ginsenosides. The WOX gene family is a plant-specific transcription factor family involved in the regulation of multiple biological processes, including stem cell maintenance, embryonic development, lateral organ development, and organogenesis. In this study, we screened and identified members of the PgWOX gene family using an established ginseng transcriptome and genome database. Subsequently, a comprehensive analysis was performed, including phylogenetic analysis, gene structure characterization, conserved motif identification, cis-acting element prediction, expression pattern analysis, and chromosomal localization analysis. In addition, gene ontology (GO) functional annotation and co-expression network analysis were conducted for PgWOX genes, in which the co-expression correlations between PgWOX genes and the previously published key enzyme genes involved in ginsenoside biosynthesis were investigated. Furthermore, ginseng adventitious roots were treated with methyl jasmonate (MeJA) to study the expression responses of three PgWOX genes that clustered with the known key ginsenoside biosynthesis-related enzyme genes in the co-expression network. The results showed that all three PgWOX genes exhibited distinct expression responses to MeJA. Finally, the contents of five protopanaxatriol-type ginsenosides (Re, Rf, Rg1, Rg2, and Rh1) were determined in ginseng adventitious roots treated with MeJA at various time points, focusing on three PgWOX genes (PgWOX21, PgWOX35, and PgWOX36). The results demonstrated that Re content showed the most significant variation among all detected ginsenosides. This study provides valuable data for subsequent research on members of the WOX gene family in P. ginseng and offers an experimental reference for verifying the functions of these family members in the MeJA signaling pathway.

Fungal Pathogen Activity and Stress‐Dependent Responses of Grapevine Wood to Esca and Drought

Fri, 01 May 2026 00:11:17 -0700

ABSTRACT

Biotic and abiotic stresses alter the physiology of perennial plants, with consequences for fungal endophytes and disease expression. In grapevine, drought inhibits esca disease expression, but the underlying molecular interactions between the plant and fungi are unknown. We combined wood metatranscriptomics, metabolomics, and metabarcoding to investigate these interactions in 30-year-old grapevines and eight wood-pathogenic fungi under conditions of drought or esca leaf symptom expression. Both esca and drought decreased grapevine transpiration, but with different underlying mechanisms that induced specific transcriptomic and metabolic signatures. Similar pathways were also activated, including the phenylpropanoid and stilbenoid synthesis pathways. These stress responses could potentially confer cross-tolerance and elicit different fungal molecular responses. Across all fungi, the total level of putative virulence factors increased significantly under both stresses. Under drought, only the relative abundance of Phaeomoniella chlamydospora and gene expression involved in anti-oxidative mechanisms, growth, and reproduction increased. Under esca expression conditions, only the relative abundance of Fomitiporia mediterranea and gene expression involved in wood degradation, competition, detoxification, and growth increased. Under drought, induced grapevine defenses and reduced transpiration, together with the low abundance and putatively weak virulence of F. mediterranea may account for the inhibition of esca leaf symptom.

Endophytic Biostimulant Pyrroloquinoline Quinone Enhances Banana Growth and Primes Immunity Against Fusarium Wilt

Thu, 30 Apr 2026 21:00:45 -0700

ABSTRACT

Pyrroloquinoline quinone (PQQ) is a redox cofactor derived from prokaryotes that participates in various biological processes involving dehydrogenase enzymes. Previous field trials identified a PQQ-producing endophyte, Burkholderia seminalis 869T2, which enhances banana growth and reduces Fusarium wilt incidence from 24.5% to 3.4%. While more recent studies have confirmed its agricultural benefits across multiple plant species, the underlying molecular mechanisms remain unclear. Here, integrated omics and imaging mass spectrometry were employed to investigate the role of PQQ in planta. Our results indicate that PQQ achieves these outcomes by modulating key aspects of plant energy metabolism, including the tricarboxylic acid (TCA) cycle, oxidative phosphorylation, and NAD/NADP pathways. In addition, PQQ appears to influence phytohormone signalling pathways and trigger systemic plant resistance. Consistent with these molecular responses, exogenous PQQ enhanced root and shoot development and improved resistance to Fusarium infection. Collectively, these findings indicate that the endophyte functions as a biostimulant through PQQ production, coordinating plant metabolism and defence to counter pathogen invasion. This study provides mechanistic insight into plant–endophyte mutualism and highlights the potential of both PQQ and PQQ-producing endophytes as biostimulants for sustainable agricultural applications.

The Role of Histone Modifications in Plant Priming and Their Analysis by Chromatin Immunoprecipitation

Aslihan Temel, Nihal Gören‐Sağlam — Thu, 30 Apr 2026 03:47:49 -0700

ABSTRACT

Plants are frequently exposed to adverse conditions. Priming, also known as acclimation or hardening, induces stress memory and prepares plants for future challenges by activating defense and protective mechanisms. For this reason, priming is an effective means to maintain plant yield in the face of climate change. Memory behind the priming is mainly based on epigenetic modifications, for example, histone posttranslational modifications (PTMs) on the priming-related genes. While histone PTMs are the most diverse group of epigenetic modifications and regulate gene expression via addition of chemical groups to histone amino acids, their characterization is challenging. Chromatin immunoprecipitation (ChIP) is an essential method for the characterization of histone PTMs; however, subject to many challenges, especially in plant samples. This review discusses the current understanding of histone modifications in plant stress and priming and the ChIP methodology and troubleshooting. Yield losses resulting from climate change necessitate the use of priming as an agricultural practice. In order to apply priming, an in-depth analysis of stress- or priming-induced histone PTMs is essential. ChIP has been extensively used in plant stress studies and has undergone numerous improvements. Although there are more sophisticated methods, ChIP is still regarded as a standard method for the characterization of chromatin profiles. This review aims to support researchers in the utilization of ChIP, particularly, for plant stress and/or priming studies.

Correction to “Phloem Proteomics to Identify Small Open Reading Frame (sORF)‐encoded Peptides With a Putative Role in the Control of Flowering Time in Arabidopsis”

Wed, 29 Apr 2026 01:45:41 -0700

Physiologia Plantarum, Volume 178, Issue 3, May/June 2026.

Genome Editing of a Carotenogenic Gene for Lycopene Enhancement Increases Heavy Metal Stress Susceptibility in Tomato (Solanum lycopersicum L.)

Wed, 29 Apr 2026 00:02:09 -0700

ABSTRACT

Improving the nutritional quality and abiotic stress tolerance of crop plants is essential for sustainable agriculture and global food security. Recent advances in genome editing, particularly the CRISPR/Cas9 system, have enabled precise modification of metabolic pathways to enhance valuable traits such as carotenoid accumulation. The present study aimed to enhance fruit lycopene content and assess associated stress responses in tomato (Solanum lycopersicum L.) through targeted genome editing of the lycopene beta cyclase (β-LCY, EC 5.5.1.19) gene, encoding for a key enzyme in the carotenoid biosynthetic pathway. A Csy4-based multiplex CRISPR/Cas9 approach was applied to edit β-LCY in three tomato genotypes, including two cultivated varieties and the wild species S. peruvianum L. Genotypic analysis revealed significant genotype-dependent differences in editing efficiency. The β-LCY knockout lines exhibited markedly increased lycopene accumulation in fruits, resulting in enhanced pigmentation. However, when subjected to cadmium stress, these lines showed greater susceptibility than wild-type plants, with pronounced wilting and stress symptoms. Physiological, biochemical, and metabolomic analyses confirmed disruption of stress-response mechanisms associated with carotenoid pathway modification. These findings demonstrate that while genome editing can successfully enhance desirable metabolic traits, it may also impair abiotic stress tolerance. This study provides new insight into the complex interplay between the carotenoid biosynthetic pathway and stress adaptation in tomato.

Untargeted Metabolomics Coupled With Machine Learning Unravels Crop‐Specific Versus Generalized Effects of Biostimulants in Cucumber, Pepper, and Tomato

Hajar Salehi, Pascual García‐Pérez, Luigi Lucini — Tue, 28 Apr 2026 23:46:31 -0700

ABSTRACT

In recent years, agricultural practices have shifted toward sustainability, aiming to reduce the use of agrochemicals and rely more on bio-based solutions. However, the effectiveness of these latter suffers from inconsistency. Understanding how different crops respond to biostimulants, instead of referring to a specific trial or crop, is a challenge in this field. This study attempts to identify common metabolite signatures associated with different commercial biostimulants across three crops, moving from trial-specific to more generalized effects in horticultural crops. To this aim, advanced metabolomics data integration and supervised statistical methods have been used. Advanced multivariate analyses included analysis of variance (ANOVA)-multiblock orthogonal partial least squares (AMOPLS), and Data Integration Analysis for Biomarker discovery using Latent variable approaches for Omics studies (DIABLO). HCA and AMOPLS revealed differences in metabolic profiles among the biostimulant treatments, while confirming crop-specific responses. Data integration indicated that three metabolites, betaine, N-caffeoylputrescine, and 2-amino-4-hydroxypyrimidine-5-carboxylic acid, were consistently modulated across all three crops treated by the multi-component biostimulant containing osmolytes and zeatin. Notably, these metabolites are known to be involved in plant growth and adaptation to different abiotic stresses. Overall, the applied analytical approach enabled the identification of putative markers within complex metabolic datasets that included different crop species. The use of independent validation methods increases confidence in these markers and supports the integration of complementary datasets in biostimulant studies.

Effect of the Antibiotic Norfloxacin on Volatile Organic Compound Emissions From the Cyanobacteria Microcystis aeruginosa

Tue, 28 Apr 2026 20:16:38 -0700

ABSTRACT

Cyanobacterial volatile organic compounds (VOCs) play important roles in aquatic ecosystems and toxicology. To uncover the promoting mechanisms of norfloxacin on cyanobacterial VOC emissions, the cell growth, reactive oxygen species (ROS) content, photosynthetic performance, and VOC emissions in Microcystis aeruginosa were investigated upon exposure to 10, 30, and 60 μM norfloxacin, and related gene expression was analyzed under the concentration (60 μM) with maximum promotion on the emission. Norfloxacin inhibited cell growth by reducing photosynthetic performance, causing ROS accumulation, and altering normal metabolic processes by changing related gene expression. Seven main compound types were found in M. aeruginosa VOCs, mainly including alcohols, sulfocompounds, benzenes, aldehydes, terpenoids, hydrocarbons, and esters. For almost all VOC components (except β-cyclocitral), norfloxacin promoted their emission by up-regulating related genes, including seven genes in sulfocompound biosynthesis, seven genes in benzene biosynthesis, four genes in terpene biosynthesis, and four genes in fatty acid derivative (aldehydes, alcohols, hydrocarbons, and esters) formation. For β-cyclocitral, its increased emission under norfloxacin stress might result from the accumulated ROS rupturing the C7C8 double bonds of β-carotene. These findings demonstrated that antibiotics could improve VOC emissions from cyanobacteria by up-regulating related genes and increasing ROS accumulation (only for β-cyclocitral), which might intensify water odor, promote cyanobacteria dominating eutrophicated waters, and facilitate atmospheric chemical reactions above the waters.

The bZIP Transcription Factor PjbZIP1 Enhances Resistance to Powdery Mildew in Paeonia jishanensis by Directly Activating PjICS Involved in the SA Pathway

Mon, 27 Apr 2026 23:48:15 -0700

ABSTRACT

Paeonia jishanensis is a wild tree peony germplasm resource in China that has strong resistance to powdery mildew. Domesticated peony varieties exhibit compromised immunity to powdery mildew pathogens. The present study investigated the function of PjbZIP1 through expression analysis, virus-induced gene silencing (VIGS), and overexpression in Arabidopsis. Structural analysis identified a canonical basic region/leucine zipper (bZIP) motif at the C-terminal region of PjbZIP1. In P. jishanensis plants, PjbZIP1 expression was upregulated under powdery mildew infection, exogenous salicylic acid (SA) treatment, and methyl jasmonate exposure. Gene-silenced PjbZIP1 plants exhibited increased susceptibility to powdery mildew, whereas transgenic PjbZIP1 overexpression enhanced resistance. In addition, VIGS and overexpression of PjbZIP1 affected SA synthesis and the induction of genes associated with the plant defense signaling pathway. Among the candidate genes involved in SA-regulated defense responses, PjbZIP1 significantly upregulated the expression of PjICS, which encodes a key enzyme for SA biosynthesis. Yeast one-hybrid, firefly luciferase complementation imaging, and electrophoretic mobility shift assays demonstrated in vitro and in vivo that PjbZIP1 interacts with PjICS. Transcription of PjICS was induced in P. jishanensis infected with powdery mildew and was significantly enhanced in overexpressed PjbZIP1 plants. These findings establish that PjbZIP1 enhances powdery mildew resistance in tree peony by regulating the PjICS-mediated SA signaling defense pathway. These findings establish PjbZIP1 as a critical regulator of SA-mediated resistance to powdery mildew in P. jishanensis, providing genetic tools for breeding disease-resistant cultivars.

The Role of Mathematical Modeling in Plant Abiotic Stress Biology: Current Trends and Future Prospects

Mon, 27 Apr 2026 23:19:43 -0700

ABSTRACT

Plant responses to abiotic stress are governed by complex interactions operating across physiological, biochemical, and molecular levels, which remain difficult to interpret using experimental approaches alone. Increasing frequency and intensity of stresses such as drought, salinity, and heat further highlight the need for integrative tools that can capture these dynamics and support predictive understanding. Mathematical modeling has therefore become an important approach for analyzing plant stress responses across multiple scales. This review examines the range of modeling frameworks applied in plant abiotic stress biology, including empirical, statistical, mechanistic, and process-based models, along with emerging machine learning approaches. Their capacity to represent plant responses from cellular processes to whole-plant and crop-level behavior is discussed, with particular attention to their application under single and combined stress conditions. Recent developments in integrating physiological knowledge with omics-driven data and data-driven modeling approaches are also considered. Current applications in crop improvement, stress assessment, and climate-resilient agricultural planning are evaluated, alongside key limitations such as parameter uncertainty, scale integration, and representation of interacting stresses. The review further identifies directions for developing more robust and biologically grounded modeling frameworks that can improve predictive capability under variable environmental conditions. By synthesizing existing approaches and highlighting current gaps, this article aims to support the advancement of modeling strategies in plant abiotic stress research.

Is There a Relationship Between Secondary Metabolites of Leaves and the Growth of Eucalyptus Species?

Mon, 27 Apr 2026 16:59:43 -0700

ABSTRACT

Flavonoids are essential molecules that affect plant growth and development and act as defense mechanisms against biotic and abiotic factors. This study aimed to assess whether the content of flavonoids in different species of Eucalyptus is related to tree growth. The objective of the work is (i) to identify whether there is a relationship between flavonoids, height and diameter among Eucalyptus species and (ii) to identify differences in flavonoid content between species. The experimental design was randomized blocks with three replicates, with 20 plants in each experimental plot. The treatments consisted of six Eucalyptus species: Eucalyptus camaldulensis, E. saligna, E. grandis, E. urophylla, C. citriodora and a GG100 clone (hybrid clone of E. urophylla × E. grandis). This study measured plant diameter at breast height (DBH) and height (HC). Leaf samples were taken from the species in their respective repetitions for flavonoid evaluation, and subsequent separation and quantification of the isoflavones, daidzein (D1), daidzin (D2), genistein (G1), genistin (G2), using liquid chromatography. In general, the E. grandis species showed the best results for DAP and AP. D1 was higher than what? for C. citriodora and E. saligna. D2 was higher than what? for E. camaldulensis. The principal component analysis demonstrated a negative relationship among the variables AP and DAP with D1, D2, G1, and G2. With the results of this study, it can be inferred that there is no relationship between height, diameter, and flavonoids among the Eucalyptus species evaluated since the species with the lowest concentrations of isoflavones had the highest growth and diameter.

Transcriptome Analysis Reveals Far‐Red Light's Effect on the Seedling Leaf Angle of Rice (Oryza sativa L.)

Sun, 26 Apr 2026 19:34:49 -0700

ABSTRACT

Far-red light significantly affects plant growth, including seedling development, root growth, and leaf angle, but the regulatory mechanisms underlying the positioning of the rice leaf angle remain unclear. In this study, eight light quality treatments were applied: white light (W), white light with far-red (W + Fr), red light (R), red light with far-red (R + Fr), blue light (B), blue light with far-red (B + Fr), red-blue light (RB), and red-blue light with far-red (RB + Fr). Additionally, six far-red light ratios (0%, 7.5%, 15%, 30%, 60%, 100%) were used to investigate the molecular mechanisms by which far-red light modulates leaf angles in rice seedlings. Compared to treatments without far-red light, supplemental far-red light significantly increased leaf angle and markedly decreased plant height, enhanced seedling quality, increased specific leaf weight, promoted root growth and photosynthetic capacity, and overall improved seedling performance. Moreover, far-red light markedly increased the leaf angle of rice seedlings. As the far-red proportion increased, leaf angle first increased and then decreased, a pattern consistent with the anatomical observations. Transcriptome analysis and WGCNA identified RPL5 as a key candidate gene involved in leaf angle regulation. However, the functional role of RPL5 and its regulatory mechanisms on leaf angles require further experimental validation. This study provides a theoretical basis for understanding how light and auxin signals coordinate to regulate rice leaf angles in response to far-red light.

Clearing the Noise: Seasonal Dynamics of Endophytic Bacteria in Fagus sylvatica Leaves Revealed by Application of PNA Clamps

Sun, 26 Apr 2026 19:05:03 -0700

ABSTRACT

The characterization of the seasonal dynamics of endophytic bacteria in beech leaves can be hindered by co-amplification of chloroplast and mitochondrial plant DNA. This study applies established peptide nucleic acid (PNA) clamps to suppress host-derived amplification while resolving bacterial succession across the vegetative season. Chloroplast- and mitochondrion-specific PNAs inverted the proportion of host to bacterial reads, enabled the recovery of bacterial sequence variants, and increased alpha diversity accordingly. Beta-diversity analyses showed that, once host contamination was removed, samples displayed a clear seasonal trajectory. Early-season leaves contained high abundances of Pseudomonas together with taxa likely introduced through plant–insect–microbe interactions. As leaves matured, the microbiome shifted toward a more stable composition dominated by well-established genera. The transition from early transient taxa to the later enrichment of phyllosphere-adapted and nutrient-cycling genera demonstrates that beech leaves host a temporally structured microbiome shaped by leaf development and seasonal environmental stress.

Issue Information

Wed, 22 Apr 2026 20:25:30 -0700

Physiologia Plantarum, Volume 178, Issue 3, May/June 2026.

Coordinated Regulation of Iron Homeostasis, Antioxidant Defenses and Hormone Signaling Underlies Pepper Responses to Iron Deficiency and Excess

Mingrui Xu, Yuefei Ma, Xiaoxia Zhou, Yali Yang, Fengfeng Dang, Ying Sun — Wed, 22 Apr 2026 20:24:05 -0700

ABSTRACT

Iron availability strongly influences crop performance, yet the mechanisms in non-model horticultural species remain unclear. We combined morphological, physiological, and root transcriptome analyses to dissect the response of Capsicum annuum L. cultivar CA#8 to iron deficiency, low iron, and excess iron. Seedlings grown hydroponically under four iron supplies (0, 5, 25, and 150 μM EDTA–Fe) showed distinct shoot and root phenotypes: iron deficiency caused interveinal chlorosis and strong inhibition of root growth, excess iron induced leaf wrinkling with white spots and reduced root development, whereas low iron had milder effects. Under deficiency, rhizosphere pH decreased and ferric chelate reductase activity increased sharply, supporting activation of a Strategy I-type acquisition system. Shoot and root iron contents declined in deficient and low-iron plants but increased under excess iron, while manganese accumulated mainly in deficient shoots and zinc remained largely unchanged. Iron stress altered multiple hormones and triggered transient increases in superoxide dismutase, peroxidase, and catalase activities, consistent with regulated adjustments of the reactive oxygen species homeostasis. Root RNA-seq at two days identified 1822, 436, and 1211 differentially expressed genes under deficiency, low iron, and excess iron, respectively. Enrichment and co-expression analyses highlighted a coordinated induction or repression of iron transporters and regulators, including IRT- and NRAMP-like uptake components, YSL- and VTL-like transporters, and transcription factors and hormone-related genes linked to iron and oxidative signaling. Research indicates that pepper plants maintain iron homeostasis by integrating proton extrusion, reduction capacity, metal transport, vacuolar sequestration, and antioxidant defense mechanisms to limit damage under both iron deficiency and excess.

A Self‐Cleavage–Dependent Activation Mechanism of the Effector RipBH Associated With Bacterial Wilt and Tuber Rot in Potato

Wed, 22 Apr 2026 20:19:43 -0700

ABSTRACT

Homeostatic regulation of proteolytic activity is fundamental to plant cellular physiology, and dysregulated protease-like activities are frequently associated with cytotoxic or stress-induced cell death. Here, we identify RipBH, a previously uncharacterized type III-secreted protein from Ralstonia solanacearum, as an intracellular self-cleaving protease-like effector with the capacity to perturb host physiological balance. RipBH harbors a papain-like catalytic core and multiple ankyrin repeats; structural mutagenesis showed that conserved catalytic residues (C135, H244, D268, and N117) are indispensable for self-processing and cell death–inducing activity. RipBH undergoes auto-cleavage inside plant cells, producing smaller fragments that are detectable in both the cytoplasm and nucleus. Truncation of ankyrin repeats altered cleavage behavior and abolished cell-death induction, supporting the idea that ankyrin-mediated structural constraints function as a regulatory module required for activation. Importantly, RipBH-induced necrosis occurred largely independently of the tested canonical ETI-related signaling components, suggesting a physiology-centered disruption pathway rather than immune receptor-mediated recognition. We propose that RipBH operates as a pathogen-encoded proteolytic switch that destabilizes intracellular homeostasis, providing a potential mechanistic link between effector auto-processing and necrosis-like physiological collapse under biotic stress. Our findings contribute to the conceptual framework of proteolysis-associated plant cell dysfunction and highlight pathogen-driven interference with core physiological processes.