Search Results (2,385)

Petal blight caused by Neopestalotiopsis clavispora infection in Rhododendron delavayi petals severely reduces their ornamental value; however, the metabolic and transcriptional responses of petals to this pathogen remain unclear. In this study, we integrated widely targeted metabolomic and transcriptomic analyses to systematically characterize the response mechanisms of R. delavayi petals at early (1 day post-infection), middle (2 days post-infection), and late (4 days post-infection) stages of N. clavispora infection. A total of 1251 metabolites were identified, and K-means clustering analysis revealed that the differentially accumulated metabolites (DAMs) in Subclass 1 were significantly enriched in flavonoid, phenylpropanoid, and glutathione metabolic pathways. Transcriptomic analysis identified 3744, 6986, and 5407 differentially expressed genes (DEGs) at early, middle and late stages, respectively. Weighted gene co-expression network analysis (WGCNA) indicated that the key hub genes at early, middle, and late stages were mainly involved in maintaining reactive oxygen species (ROS) homeostasis, plant–pathogen interaction signal transduction, and cell wall remodeling, respectively. Joint metabolomic and transcriptomic analysis showed that phenylpropanoid, flavonoid, and glutathione pathways were commonly and significantly enriched. In vitro antifungal assays demonstrated that 2000 mg/L phloretin significantly inhibited mycelial growth of N. clavispora and effectively alleviated petal infection. Collectively, R. delavayi petals exhibit stage-specific defense strategies against N. clavispora: in the early stage, by inducing H₂O₂ accumulation and ROS homeostasis; in the middle stage, by activating immune signaling pathways; and in the late stage, by enhancing cell wall remodeling and antioxidant capacity. This study provides a theoretical basis and a candidate compound for green control of petal blight. Full article

Pogostemon cablin (Blanco) Benth. cv. ‘Jing Huoxiang’, is a valuable medicinal plant widely studied for its aboveground tissues, which are rich in bioactive compounds such as patchouli alcohol. However, systematic investigations into the biosynthesis of sesquiterpenes in its underground parts (roots) remain limited, with several critical knowledge gaps: (1) the metabolic basis of root-specific accumulation of polycyclic sesquiterpenes is unclear; (2) key terpene synthase (TPS) gene resources remain underexplored; and (3) the regulatory network of terpenoid biosynthesis is poorly understood. Addressing these questions is essential for the rational design and efficient production of terpene synthases. In this study, we integrated metabolomic and transcriptomic approaches to systematically characterize terpenoid profiles across different tissues of P. cablin and elucidate their biosynthetic regulation. Using GC-MS analysis, we identified distinct terpenoid compositions in roots, stems, leaves, flowers, and glandular trichomes. Notably, patchouli alcohol and pogostone accounted for over 60% of the total volatile oil content, while roots specifically accumulated polycyclic sesquiterpenes such as β-caryophyllene and α-humulene. Through transcriptome sequencing and bioinformatic analysis, we comprehensively annotated the TPS gene family, revealing that the TPS-a subfamily (34 genes) was the most abundant in P. cablin, with several members exhibiting root-predominant expression. Co-expression network analysis further identified candidate genes encoding potential high-efficiency polycyclic sesquiterpene synthases and uncovered a β-caryophyllene/α-humulene-regulated tertiary metabolic pathway. Our findings not only fill a critical gap in understanding sesquiterpene biosynthesis in the underground tissues of P. cablin but also provide a foundation for synthetic biology-based optimization of terpenoid production. This research paves the way for the efficient biosynthesis of sesquiterpenes to meet industrial demands in pharmaceuticals, fragrances, and biofuels. Full article

Background: Flower color is a well-defined trait in Platycodon grandiflorus, whereas little is known about the effects of flower color variation on the metabolic profiles of reproductive organs. Triterpenoid saponins and flavonoids have common precursors upstream, suggesting a potential carbon flux trade-off. Methods: Untargeted UPLC-MS/MS metabolomics was performed on the reproductive organs of purple- and white-flowered P. grandiflorus at six stages of flower development. Mfuzz time-series clustering, PCA, and metabolite correlation networks were used for data analysis. Results: Six clusters were assigned to 25 metabolites (17 triterpenoid saponins and 8 flavonoids). Flavonoid glycosides were found to possess a conserved inverted V-shaped accumulation pattern in both germplasms. By contrast, saponins derived from triterpenoids showed strong germplasm-dependent accumulation patterns. White-flowered plants showed sustained accumulation, with a peak at the young fruit stage. In purple-flowered plants, accumulation peaked transiently at the withering stage, followed by a decline. PCA validated that metabolic divergence increased with developmental progression. Conclusions: Based on the metabolomic profiles, we hypothesize a putative trade-off model in which floral color divergence may change upstream carbon flux allocation between the triterpenoid saponin and flavonoid pathways. The young fruit stage of white-flowered plants is a candidate harvesting period for bioactive saponins. These conclusions are based only on the pattern of metabolite accumulation and need to be validated by multi-omics. Full article

Sorghum seeds accumulate substantial amounts of condensed tannins (CTs), which are also referred to as proanthocyanidins (PAs), contributing to their characteristic astringent taste. Flavan-3-ol polymers, known as PAs, are sequestered within plant vacuoles and become catalytically activated via laccase enzymes. However, the biological roles and regulatory pathways of laccases in sorghum are still largely unclear. Here, integrated transcriptomic and metabolomic profiling of developing sorghum seeds identified 7942 differentially expressed genes between low- and high-CT lines, with Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment revealing flavonoid biosynthesis as a key pathway; weighted gene co-expression network analysis (WGCNA) further pinpointed SbLAC14 as a hub gene within the module most strongly correlated with CT content. We then examined its regulation by microRNA397 (SbmiR397-5p). Dual-luciferase assays confirmed the binding of SbmiR397-5p to SbLAC14 in co-transformed tobacco leaves. Overexpressing SbLAC14 in transgenic Arabidopsis significantly increased CT accumulation while decreasing catechin and epicatechin levels. Furthermore, transgenic plants overexpressing miR397 (OEmiR397-5p) exhibited reduced CT content, accompanied by a lightening of seed color. Conversely, transgenic lines overexpressing a miR397-insensitive laccase transcript exhibited a reversed phenotypic outcome. Our findings indicate that SbmiR397-5p negatively regulates the expression of SbLAC14 in relation to CT biosynthesis, identifying it as a potential target for manipulating CT metabolism in sorghum. Those results provide a genetic entry point for metabolic engineering and breeding efforts aimed at modulating grain phenolic profiles. Full article

Understanding whether long-term vascular cambium vitality in ancient trees reflects progressive decline or adaptive reprogramming is central to grasping woody plant longevity. We performed an integrative analysis of functional traits, transcriptome profiles, and metabolomic landscapes of cambial zone enriched from 80-, 500-, and 1000-year-old Styphnolobium japonicum trees. With increasing tree age, the vascular cambium showed fewer cell layers, reduced thickness, and lower auxin, gibberellin, and IAA/ABA ratios, whereas bark thickness, malondialdehyde, abscisic acid, jasmonic acid, and salicylic acid contents increased. Transcriptomic and metabolomic analyses revealed that differentially expressed genes and metabolites were primarily enriched in the cell cycle, phytohormone signaling, and phenylpropanoid biosynthesis pathways. Specifically, genes associated with cell division were down-regulated in millennial trees, whereas phenolic acids, flavonoids, and lignin-related metabolites significantly accumulated. Piecewise structural equation modeling suggested associations among tree age, transcription factors, structural genes, metabolites, and cambial functional traits. These results indicate that cambial senescence is not a simple linear decay but a highly coordinated remodeling process, providing crucial evidence for delayed senescence in long-lived woody species. Full article

Emilia sonchifolia (L.) DC is a medicinal and edible herb of Asteraceae with Lingnan characteristics. Flavonoids are its core pharmacodynamic substances, but the molecular regulation mechanism of differential accumulation of flavonoids in different organs of this species is still unclear. In this study, the molecular basis of tissue-specific synthesis of flavonoids was analyzed by integrating UPLC-MS broad-target metabolome and Illumina high-throughput transcriptome with four tissues of Emilia sonchifolia: root, stem, leaf, and flower. The results showed that a total of 73 flavonoid metabolites were identified in the metabolome, including naringenin chalcone, luteolin, quercitrin, and other pharmacologically active substances. Multi-omics joint analysis showed that the floral organ was the core tissue for the synthesis and enrichment of flavonoids, and there were specific characteristic flavonoid subtypes in different tissues. A total of 211 differentially expressed genes related to the flavonoid synthesis pathway were screened by transcriptome analysis, including 16 flavonol synthases, five cinnamic acid 4-hydroxylases, and five chalcone synthases. The WGCNA and gene–metabolite association network showed that the transcription levels of key enzyme genes such as CHS, C4H, F3′H, and F3H were highly positively correlated with the accumulation of downstream flavonols. The qRT-PCR quantitative verification showed that the expression patterns of CHS1, CHI4, F3′H5, F3H, FLS4, and GT in the four tissues were highly consistent with the transcriptome sequencing results, which confirmed that the transcriptome data were reliable. For the first time, this study revealed the molecular regulatory network of tissue-specific accumulation of flavonoids in Emilia sonchifolia, and clarified that the flower organ was the optimal medicinal harvesting site of flavonoids. It provided key theoretical support for the breeding of high-efficacy Emilia sonchifolia germplasm, the development of flavonoid active ingredients, and the study of secondary metabolic evolution of Compositae plants. Full article

Soil microbiomes are essential for nutrient cycling, plant health, stress resilience, and sustainable agriculture. Recent advances in high-throughput sequencing, multi-omics technologies, systems biology, and artificial intelligence (AI) have transformed our understanding of plant–microbiome interactions and enabled the development of innovative microbiome engineering strategies. This review provides a comprehensive overview of the mechanisms governing plant-associated soil microbiome assembly, microbial community functions, plant–microbe communication, and microbiome-mediated stress resistance in agricultural ecosystems. Current approaches to plant-associated soil microbiome manipulation and engineering, including microbial inoculants, synthetic microbial communities (SynComs), microbiome transplantation, rhizosphere steering, and synthetic biology-based interventions, are critically examined. The review further discusses the growing role of metagenomics, metabolomics, metatranscriptomics, machine learning (ML), and precision agriculture technologies in improving microbiome characterization, prediction, and management. Particular attention is given to the application of microbiome-based solutions for sustainable crop production, nutrient management, biological control, climate-smart agriculture, and ecosystem restoration. Despite significant progress, challenges related to field-scale variability, colonization stability, biosafety, regulatory frameworks, and data integration continue to limit large-scale implementation. Future advances in precision microbiome engineering are expected to combine ecological principles, multi-omics technologies, AI, and synthetic biology to develop predictive and resilient microbiome-based solutions for sustainable and climate-resilient agriculture. Full article

Pseudomonas sp. MUP55, isolated from rainfall water in Western Australia, was characterized by polyphasic taxonomy and functional assays. Whole-genome and 16S rRNA phylogeny placed Pseudomonas sp. MUP55 in the Pseudomonas fluorescens species group. Massetolide A/D was identified as the leading candidate bioactive compound(s), consistent with its biosynthetic gene cluster, GNPS library matching, and loss of activity in regulatory mutants. The strain showed broad-spectrum antimicrobial activity against bacterial (Escherichia coli and Xanthomonas campestris) and fungal (Fusarium oxysporum and Rhizoctonia solani) plant pathogens. GacA regulates Massetolide production: a P58L mutation abolished synthesis and reduced biocontrol efficacy. Metabolomic and transcriptomic analysis of a ΔpvfC mutant revealed that the pvf cluster regulates specialized metabolism while also contributing to secreted growth-inhibitory activity. The pvf cluster differentially regulates dual siderophore systems and uncouples the co-regulated small RNAs rsmY and rsmZ in the Gac/Rsm cascade. Deletion of pvfC partially reduced the growth-inhibitory activity of Pseudomonas sp. MUP55 supernatants against bacterial pathogens, indicating that pvfC also influences secreted antimicrobial activity beyond its global regulatory role. These findings establish Pseudomonas sp. MUP55 as a taxonomically novel, mechanistically characterized biocontrol agent with potential for sustainable agriculture. Full article

Understanding how plants respond to polycyclic aromatic hydrocarbons (PAHs) stress is essential for evaluating ecological risks and improving phytoremediation strategies. PAHs are widespread and persistent environmental pollutants that exert toxic effects on plants at different developmental stages. Although Buchloe dactyloides (Nutt) Engelm shows potential for phytoremediation of PAHs contamination, its root defense mechanism against PAHs remains unclear. To this end, transcriptomics and non-targeted metabolomics were used to study the changes in gene expression and metabolite profiles in roots under PAHs stress. After 70 days of PAHs exposure, B. dactyloides roots exhibited increased activities of catalase (CAT) (from 1.955 to 6.436; ca. 3.29) and peroxidase (POD) (from 94.507 to 124.901; ca. 1.32), higher levels of ascorbate (AsA) (from 7976.69 to 18,950.09; ca. 2.38) and glutathione (GSH) (from 21.08 to 37.23; ca. 1.77), and accumulation of proline (from 40.585 to 66.671; ca. 1.64). Significant differences in genes and metabolites were observed between the treatment and control groups, with a total of 4083 differentially expressed genes (DEGs) and 100 differentially accumulated metabolites (DAMs). Further comprehensive analysis of transcriptomics and metabolomics revealed the potential role of multiple pathways in the defense response of B. dactyloides roots against PAHs stress, including amino acid synthesis, flavonoid biosynthesis, galactose metabolism, glycerophospholipid metabolism, and other pathways. These pathways may contribute to antioxidative defense under PAHs stress. In addition, increased trehalose and soluble sugar contents likely supplied energy and osmoprotective functions under stress. These findings provide insights into the mechanisms of root adaptation to PAHs and may support the long-term phytoremediation potential of B. dactyloides. Full article

Multiomics is increasingly valued as a strategy for investigating the regulatory mechanisms by which plants respond to adverse stress conditions. Currently, information on the molecular processes underlying plant responses to Pb stress, particularly those observed through an approach that combines proteomics and metabolomics, is lacking. Therefore, in this study, we aimed to explore functional correlations between Pb-responsive proteins and metabolites under Pb stress by performing label-free quantitative proteomics and untargeted metabolomics on the roots of the Pb hyperaccumulator Pogonatherum crinitum (Thunb.) Kunth. The selected Pb stress-responsive proteins were functionally verified using quantitative reverse transcription polymerase chain reaction (RT-qPCR) and parallel reaction monitoring (PRM). Under Pb stress, 397 upregulated and 431 downregulated proteins were identified through proteomic analysis. Metabolomic analysis identified 478 upregulated and 354 downregulated metabolites. Pathway enrichment analysis using the Kyoto Encyclopedia of Genes and Genomes revealed that differentially expressed proteins and metabolites were involved in pathways linked to heavy metal stress, such as starch and sucrose metabolism and plant hormone signal transduction. Through integrated proteomic and metabolomics analyses, we uncovered the coordinated regulatory interplay between glutathione (GSH) metabolism and jasmonic acid signaling. GSH reductase and 12-oxophytodienoate reductase drive the accumulation of GSH and jasmonic acid, respectively. The synergistic enhancement of these components is critical for maintaining cellular redox homeostasis and activating hormone-mediated defense signaling. These downstream metabolites were upregulated under Pb stress. RT-qPCR validation revealed that the transcriptional change trends were consistent with those of the proteomics analysis. Further quantitative validation of the target protein using PRM revealed significant upregulation under Pb stress. In conclusion, the P. crinitum root system upregulated the activity of key enzymes in the antioxidant system and plant hormone synthesis under Pb stress, thereby regulating the accumulation of GSH, glutamate, and metabolites for jasmonic acid synthesis. This integrated regulatory network provides promising candidate targets for breeding Pb-tolerant hyperaccumulators to remediate Pb-contaminated farmland and mining soil. Full article

Drought research on quinoa has focused almost exclusively on the shoots, leaving the roots, the organ that first senses soil drying, largely unexamined, and its recovery dynamics are still poorly characterized. Here, we show that in the Chilean coastal quinoa ecotype AZ1, recovery from drought is governed belowground, and the root regains hydraulic and metabolomic competence well before the stomata reopen. After 72 h of soil drying, stomatal conductance (g_s) decreased by 98%, whole-plant transpiration declined biphasically (~92% of the loss within the first two hours), and water potential decreased steeply at the soil–root interface (with soil and root water potential declining approximately 10- and 20-fold relative to well-watered plants), while the stem remained near-stable, pinpointing the root as the dominant hydraulic bottleneck. Twenty-four hours after rewatering, root system and whole-plant water potential, osmotic root hydraulic conductance (Lp_rOS), root anatomy, and the polar metabolome were largely restored, yet g_s remained statistically indistinguishable from droughted plants. Strikingly, hydraulic recovery proceeded without rebuilding the osmotic sugar pool; instead, normalization of TCA-cycle intermediates points to an energy-powered and possible aquaporin-mediated transport route that bypasses still-suberized apoplastic barriers. Root system metabolomics, led by GABA and L-alanine, which overshot the control, tracked root rehydration but correlated negatively with g_s, suggesting that nitrogen-rich solutes may act as candidate belowground cues restraining stomatal reopening. These findings suggest that the quinoa root system acts as a pacemaker for drought recovery. Full article

Background: Anthocyanin accumulation is a developmentally regulated trait shaped by complex interactions between metabolic and transcriptional networks. However, dissecting the regulatory mechanisms underlying anthocyanin biosynthesis is often complicated by confounding variation in plant growth and environmental conditions. Methods: Here, we used a time-resolved multi-omics approach to investigate anthocyanin accumulation in maize seedlings by comparing an anthocyanin-rich inbred line PH19401 with an anthocyanin-deficient line YPX across five developmental stages. Results: Untargeted metabolomic and transcriptomic profiling revealed progressive divergence between the two lines beginning at early development stages. Using a dual-line, intersection-based filtering strategy, we identified a refined set of metabolites and genes closely associated with anthocyanin accumulation. These candidates were enriched in pathways related to phenylpropanoid metabolism, energy metabolism, and redox regulation. Weighted gene co-expression network analysis (WGCNA) identified two transcriptional modules that showed opposing associations with anthocyanin content. The positively associated module was centered on MYB transcription factors, consistent with canonical regulation of flavonoid biosynthesis, whereas the negatively associated module was enriched in genes involved in primary metabolism and signaling. Integration of transcriptomic and metabolomic datasets further revealed coordinated relationships between MYB hub genes and flavonoid intermediates, linking transcriptional regulation with metabolic output. Together, these results support a model in which anthocyanin accumulation is associated with activation of MYB-centered transcriptional programs and broader metabolic reprogramming that enhances precursor supply and redox balance, while competing transcriptional programs favor primary metabolism. Conclusions: This study provides a systems-level perspective on anthocyanin biosynthesis in maize seedlings and establishes an analytical framework for dissecting developmentally regulated metabolic traits. Full article

Pichia manshurica (P. manshurica), a gas-producing spoilage yeast prevalent in fermented foods, causes package swelling, off-flavor formation, and quality deterioration, thereby shortening shelf life and reducing commercial value. Carvacrol, a natural phenolic compound from plant essential oils, has broad-spectrum antimicrobial activity, but its mechanism for inhibiting P. manshurica’s gas production is unclear. In this study, in vitro and in situ experiments confirmed that carvacrol significantly inhibits gas production by P. manshurica in a concentration-dependent manner. Transcriptomic analysis identified 374 differentially expressed genes (DEGs), which were mainly enriched in biological processes such as nitrogen compound metabolism, lipid metabolism, and organic substance biosynthesis, as well as cellular components including the cell membrane, mitochondrion, and endoplasmic reticulum. Metabolomic analysis screened a total of 440 differentially accumulated metabolites (DAMs), primarily involving carboxylic acids, phospholipids, fatty acids, and amino acids. Integrated transcriptome–metabolome analysis revealed that carvacrol disrupts cell membrane integrity, blocks the tricarboxylic acid cycle and oxidative phosphorylation, and interferes with energy, lipid, and amino acid metabolism in P. manshurica, thereby suppressing its gas production. This study elucidates the molecular mechanism by which carvacrol inhibits gas production by P. manshurica, providing a theoretical basis for the development and application of carvacrol as a natural preservative in fermented foods. Full article

This study evaluated the effects of dietary Zanthoxylum armatum DC. ‘Jiuyeqing’ leaf extract (ZBLE) in laying hens. A total of 1024 healthy 41-week-old Lohmann Pink layers were assigned to four treatments with eight replicates of 32 hens and fed diets containing 0, 2, 4, or 6 g ZBLE/kg for 8 weeks. The results showed that laying rate significantly increased linearly during weeks 1–4 and 1–8 (p = 0.009 and 0.005, respectively), and the 6 g/kg group had a higher laying rate than the control group (CON) over weeks 1–8 (p = 0.026). Yolk color score increased (p < 0.001), and serum immunoglobulin M concentration increased significantly (p = 0.007), whereas serum biochemical parameters remained unchanged. Serum total antioxidant capacity and total superoxide dismutase activity and hepatic total antioxidant capacity and catalase activity increased significantly, whereas serum malondialdehyde decreased. Intestinal responses were segment-specific, with increased duodenal villus height, alongside greater jejunal crypt depth and a lower jejunal villus-to-crypt ratio at 6 g/kg. Hepatic metabolomic comparison between the CON and 6 g/kg groups indicated that glycerophospholipid metabolism was the most strongly enriched pathway. Overall, 6 g ZBLE/kg produced the most favorable response among the tested levels and may serve as a plant-based feed additive for laying hens. Full article

Trichoderma species are widely investigated and commercially applied as eco-friendly biocontrol agents in sustainable agriculture. These filamentous fungi protect plants through multiple complementary mechanisms, including mycoparasitism, antibiosis, competition for nutrients and ecological niches, and induction of systemic resistance in host plants. These activities are mediated by a diverse array of secondary metabolites, hydrolytic enzymes, and signaling pathways that collectively suppress pathogens and enhance plant health. Beyond disease control, selected Trichoderma strains promote plant growth by improving nutrient acquisition, modulating phytohormone signaling, and increasing tolerance to abiotic stresses. This review summarizes recent advances in the mechanisms underlying Trichoderma spp. mediated biocontrol, with particular emphasis on secondary metabolites, formulation strategies, commercialization, and field applications. Commercial products are available in various formulations, including wettable powders, granules, and liquid preparations, and have demonstrated efficacy against several economically important plant diseases under field conditions. However, their performance remains highly dependent on strain characteristics, host species, environmental conditions and agricultural practices, resulting in inconsistent efficacy across agroecosystems. Recent progress in genomics, transcriptomics, and metabolomics has substantially improved our understanding of Trichoderma–plant–pathogen interactions and revealed considerable strain-specific variation in biocontrol and plant growth-promoting traits. Future research should prioritize strain-specific optimization, formulation stability, microbiome-informed applications, and improved field predictability. Overall, Trichoderma spp. Represents a valuable component of integrated disease management, offering an effective and sustainable alternative to synthetic pesticides. Full article