Metabolomic analysis reveals the molecular responses to copper toxicity in rice (Oryza sativa)

Small-scale heterogeneity of soil properties in farmland affected fava beans growth through rhizosphere differential metabolites and microorganisms

BACKGROUND

Soil heterogeneity has been acknowledged to influence plant growth, with the small-scale soil heterogeneity always being overlooked in practice. It remains unclear how rhizosphere soil biotics and abiotics respond to soil heterogeneity and how rhizosphere interactions influence crop growth.

RESULTS

In this study, we planted fava beans in a farmland around an e-waste dismantling site, and a distinct boundary (row spacing is 30 cm) was observed in the field during the flowering stage, which divided fava beans phenotypes into two distinct groups (Big vs Little) based on the differences in biomass and height. Soil total concentrations of As, B, Co, Cr, Cu, Pb, Sr, Zn, Ni, Cd and soil pH significantly differed in the rhizosphere of fava beans in the two adjacent rows, which were located on either side of the boundary, with a row-spacing of 30 cm. Random Forest analysis demonstrated that these differentiated soil properties (soil pH, total As, B, Cd, Co, Cr, Cu, Mo, Ni and Zn) substantially influenced fava beans growth (height and biomass). Metagenomic sequencing showed that microbial taxa were significantly enriched their abundance in rhizosphere soils between the two groups of fava beans, with eukaryotic taxa being more sensitively affected. A total of 20 metabolites including coniferyl alcohol, jasmonic acid, resveratrol, and L-aspartic acid, etc. were significantly correlated with fava beans growth. These metabolites were significantly enriched in 15 metabolic pathways (nucleotide metabolism, pyrimidine metabolism, purine metabolism, biosynthesis of plant secondary metabolites, lysine biosynthesis, etc.). Furthermore, 11 microbial genera involved in these metabolic pathways, and these genera were differentially enriched between the two groups and significantly correlated with fava beans growth.

CONCLUSIONS

Overall, the integrated analysis of multi-omics revealed that soil properties heterogeneity at small-scale altered the rhizosphere differential microorganisms and metabolites, which functionally influenced fava beans growth and tolerance to environmental stress. Notably, even soil heterogeneity at such a small spatial scale can cause significant differences in plant growth, and the comprehensive explorations utilizing multi-omics techniques provide novel insights to the field management, which is crucial for the survival and sustainable development of humanity.

Exogenous coumarin improves cell wall and plasma membrane stability and function by maintaining copper and calcium homeostasis in citrus roots under copper excess

Most citrus trees are planted in acidic soil with high availability of copper (Cu). Little is known about the mechanisms by which coumarin (COU) reduces Cu excess in plants. 'Xuegan' (Citrus sinensis) seedlings were treated with 0.5 (Cu0.5) or 400 (Cu excess or Cu400) CuCl2 and 0 (COU0) or 100 (COU100) μM COU for 24 weeks. COU100 alleviated Cu400-induced alterations in gene expression and metabolite profiles, cell wall (CW) materials (CWMs), CW components (CWCs), and Fourier transform infrared (FTIR) spectra of CWMs in roots; increase in Cu concentration in roots, root CWMs (RCWMs), root CWCs (RCWCs), Cu and Ca fractions in RCWMs, and Cu fraction in CW pectin; and decrease in Ca concentrations in roots, RCWMs, and RCWCs. In addition, COU100 mitigated Cu400-induced increase in electrolyte leakage and concentrations of total coumarins, total phenolics, total falvonoids, and nonstructural carbohydrates (NCs) and decrease in total free amino acid concentration in roots, as well as impairment in root system architecture (RSA) and root growth. Our results corroborated the hypothesis that the alleviation of root Cu excess by COU was caused by the combination of following several aspects: (a) reduced impairment to root growth and RSA; (b) upregulated ability to maintain CW and plasma membrane stability and function by maintaining Cu and calcium homeostasis; (c) elevated adaptability of primary metabolism to Cu excess; and (d) upregulated biosynthesis and catabolism (turnover) of secondary metabolites (SMs) and less upregulation of SMs. COU0-treated roots underwent some physiological and molecular adaptations to Cu excess.

The protective roles of boron against copper excess in citrus roots: Insights from physiology, transcriptome, and metabolome

Boron (B) deficiency and copper (Cu) excess are common problems in citrus orchard soils. Citrus sinensis seedlings were exposed to 25 (B25) or 2.5 (B2.5) μM H3BO3 and 0.5 (Cu0.5) or 350 (Cu350) μM CuCl3 for 24 weeks. Cu350 upregulated 2210 (1012) genes and 482 (341) metabolites and downregulated 3201 (695) genes and 175 (43) metabolites in roots at B2.5 (B25). Further analysis showed that the B-mediated mitigation of Cu toxicity in roots involved the coordination of the following aspects: (a) enhancing the ability to maintain cell wall and plasma membrane stability and function; (b) lowering the impairment of Cu350 to primary and secondary metabolisms and enhancing their adaptability to Cu350; and (c) alleviating Cu350-induced oxidative stress via the coordination of reactive oxygen species (ROS) and methylglyoxal detoxification systems. Cu350 upregulated the abundances of some saccharides, amino acids and derivatives, phospholipids, secondary metabolites, and vitamins, and the expression of several ROS detoxification-related genes in roots of B2.5-treated seedlings (RB2.5), but these adaptive responses did not prevent RB2.5 from Cu-toxicity (oxidative damage). The study identified some genes, metabolites, and metabolic processes/pathways possibly involved in root Cu tolerance. Additionally, the responses of gene expression and metabolite profiling to Cu-B treatments differed between leaves and roots. Therefore, this study provided novel information for B to reduce Cu toxicity in roots and might contribute to the development of soil amendments targeting Cu excess in citrus and other crops.

Metabolomic analysis to study the effect of foliar copper supplementation on sulfur-containing compounds of garlic bulb by LC-MS

INTRODUCTION

Garlic (Allium sativum L.) is renowned for its health-promoting properties, largely due to its sulfur-rich compounds. While copper is essential for plant growth and metabolism, excessive levels can disrupt cellular processes and lead to oxidative stress.

OBJECTIVES

This study aims to investigate the impact of copper supplementation on the metabolic profile of garlic, with a particular focus on changes in sulfur metabolism.

METHODS

Ito garlic cloves were harvested in 2020 on Red-Yellow Latosol soil. Copper chelate fertilizer was applied foliarly at 300 mL/ha, 30, 20, and 10 days before harvest. After harvesting, cloves were refrigerated and analyzed. Using LC-MS metabolomics, the metabolic profile of garlic was analyzed after copper supplementation to assess changes, specifically in sulfur-containing compounds.

RESULTS

Copper supplementation led to a significant reduction in key sulfur-containing metabolites critical for the health-promoting properties of garlic, including allicin (FC = 0.0947), alliin (FC = 0.0147), and γ-glutamyl-S-allylcysteine (FC = 0.0076). Enrichment analysis identified alterations in pathways related to glutamine, glutamate, alanine, and aspartate metabolism. Additionally, precursors of glutathione (GSH) were depleted, likely as a result of GSH sparing efforts to counteract copper-induced oxidative stress. This redirection may increase susceptibility to ferroptosis, a form of cell death linked to oxidative damage.

CONCLUSION

The metabolomic analysis of copper-supplemented Ito garlic cloves showed a significant reduction in sulfur compounds allicin, alliin, and γ-glutamyl-S-allylcysteine, important for organoleptic and medicinal properties. This decrease indicates a metabolic shift towards antioxidant defenses, with glutathione being redirected to defense pathways rather than secondary metabolites. Future studies should explore oxidative stress and ferroptosis markers, and lipidomics for a deeper understanding of garlic response to copper exposure.

Impact of Abiotic Stress on Rice and the Role of DNA Methylation in Stress Response Mechanisms

With the intensification of global climate change and the increasing complexity of agricultural environments, the improvement of rice stress tolerance is an important focus of current breeding research. This review summarizes the current knowledge on the impact of various abiotic stresses on rice and the associated epigenetic responses (DNA methylation). Abiotic stress factors, including high temperature, drought, cold, heavy metal pollution, and high salinity, have a negative impact on crop productivity. Epigenetic changes are key regulatory factors in plant stress responses, and DNA methylation is one of the earliest discovered and thoroughly studied mechanisms in these epigenetic regulatory mechanisms. The normal growth of rice is highly dependent on the environment, and changes in the environment can lead to rice sterility and severe yield loss. Changes in the regulation of the DNA methylation pathway are involved in rice's response to stress. Various DNA methylation-regulating protein complexes that function during rice development have been identified. Significant changes in DNA methylation occur in numerous stress-responsive genes, particularly those in the abscisic acid signaling pathway. These findings underscore the complex mechanisms of the abiotic stress response in rice. We propose the effective improvement of tolerance traits by regulating the epigenetic status of rice and emphasize the role of DNA methylation in abiotic stress tolerance, thereby addressing global climate change and ensuring food security.

Metabolite responses of cucumber on copper toxicity in presence of fullerene C60 derivatives

Copper (Cu) toxicity in crops is a result of excessive release of Cu into environment. Little is known about mitigation of Cu toxicity through the application of carbon-based nanomaterials including water-soluble fullerene C60 derivatives. Two derivatives of fullerene were examined: polyhydroxylated C60 (fullerenol) and arginine C60 derivative. In order to study the response of Cu-stressed plants (Cucumis sativus L.) to these nanomaterials, metabolomics analysis by gas chromatography-mass spectrometry (GC-MS) was performed. Excess Cu (15 μM) caused substantial increase in xylem sap Cu, retarded dry biomass and leaf chlorosis of hydroponically grown cucumber. In Cu-stressed leaves, metabolomes was disturbed towards suppression metabolism of nitrogen (N) compounds and activation metabolism of hexoses. Also, upregulation of some metabolites involving in antioxidant defense system, such as ascorbic acid, tocopherol and ferulic acid, was occurred in Cu-stressed leaves. Hydroponically added fullerene adducts decreased the xylem sap Cu and alleviated Cu toxicity with effectiveness has been most pronounced for arginine C60 derivative. Metabolic responses of plants subjected to high Cu with fullerene derivatives were opposite to that observed under Cu alone. Fatty acids up-regulation (linolenic acid) and antioxidant molecules (tocopherol) down-regulation might indicate that arginine C60 adduct can alleviate Cu induced oxidative stress. Although fullerenol slightly improved cucumber growth, its effect on metabolic state of Cu-stressed plants was not statistically significant. We suggest that tested fullerene C60 adducts have a potential to prevent Cu toxicity in plants through a mechanism associated with their capability to restrict xylem transport of Cu from roots to shoot, and to maintain antioxidative properties of plants.

Transcriptomics, proteomics, and metabolomics interventions prompt crop improvement against metal(loid) toxicity

The escalating challenges posed by metal(loid) toxicity in agricultural ecosystems, exacerbated by rapid climate change and anthropogenic pressures, demand urgent attention. Soil contamination is a critical issue because it significantly impacts crop productivity. The widespread threat of metal(loid) toxicity can jeopardize global food security due to contaminated food supplies and pose environmental risks, contributing to soil and water pollution and thus impacting the whole ecosystem. In this context, plants have evolved complex mechanisms to combat metal(loid) stress. Amid the array of innovative approaches, omics, notably transcriptomics, proteomics, and metabolomics, have emerged as transformative tools, shedding light on the genes, proteins, and key metabolites involved in metal(loid) stress responses and tolerance mechanisms. These identified candidates hold promise for developing high-yielding crops with desirable agronomic traits. Computational biology tools like bioinformatics, biological databases, and analytical pipelines support these omics approaches by harnessing diverse information and facilitating the mapping of genotype-to-phenotype relationships under stress conditions. This review explores: (1) the multifaceted strategies that plants use to adapt to metal(loid) toxicity in their environment; (2) the latest findings in metal(loid)-mediated transcriptomics, proteomics, and metabolomics studies across various plant species; (3) the integration of omics data with artificial intelligence and high-throughput phenotyping; (4) the latest bioinformatics databases, tools and pipelines for single and/or multi-omics data integration; (5) the latest insights into stress adaptations and tolerance mechanisms for future outlooks; and (6) the capacity of omics advances for creating sustainable and resilient crop plants that can thrive in metal(loid)-contaminated environments.

Metabolic Responses to Manganese Toxicity in Soybean Roots and Leaves

Soybean is one of the most crucial beans in the world. Although Mn (manganese) is a kind of important nutritive element helpful to plant growth and health, excess Mn is harmful to crops. Nevertheless, the effect of Mn toxicity on soybean roots and leaves metabolism is still not clear. To explore this, water culture experiments were conducted on the development, activity of enzyme, and metabolic process of soybeans under varying levels of Mn treatment (5 and 100 μM). Compared with the control, the soybeans under Mn stress showed inhibited growth and development. Moreover, the activity of superoxide dismutase (SOD), catalase (CAT), peroxidase (POD), ascorbate peroxidase (APX), and the soluble protein content in leaves and roots of soybean were all increased. However, soluble sugar and proline contents in soybean roots and leaves showed the opposite trend. In addition, the Mg (magnesium) and Fe (iron) ion contents in soybean leaves significantly decreased, and the Mn ion content greatly increased. In roots, the Mn and Fe ion content increased, whereas the Mg ion content decreased. Furthermore, the metabolomic analysis based on nontargeted liquid chromatography-mass spectrometry identified 136 and 164 differential metabolites (DMs) that responded to Mn toxicity in roots and leaves of soybean, respectively. These DMs might participate in five different primary metabolic pathways in soybean leaves and roots, suggesting that soybean leaves and roots demonstrate different kinds of reactions in response to Mn toxicity. These findings indicate that Mn toxicity will result in enzymes activity being changed and the metabolic pathway being seriously affected, hence inhibiting the development of soybean.

Multi-Omics Revealed Peanut Root Metabolism Regulated by Exogenous Calcium under Salt Stress

High salinity severely inhibits plant seedling root development and metabolism. Although plant salt tolerance can be improved by exogenous calcium supplementation, the metabolism molecular mechanisms involved remain unclear. In this study, we integrated three types of omics data (transcriptome, metabolome, and phytohormone absolute quantification) to analyze the metabolic profiles of peanut seedling roots as regulated by exogenous calcium under salt stress. (1) exogenous calcium supplementation enhanced the allocation of carbohydrates to the TCA cycle and plant cell wall biosynthesis rather than the shikimate pathway influenced by up-regulating the gene expression of antioxidant enzymes under salt stress; (2) exogenous calcium induced further ABA accumulation under salt stress by up-regulating the gene expression of ABA biosynthesis key enzymes AAO2 and AAO3 while down-regulating ABA glycosylation enzyme UGT71C5 expression; (3) exogenous calcium supplementation under salt stress restored the trans-zeatin absolute content to unstressed levels while inhibiting the root cis-zeatin biosynthesis.