Phosphatases are involved in modulating the TCA cycle in plants

Physiological and metabolomic insights into molecular mechanisms of root sensitivity to zinc toxicity in rice (Oryza sativa L.)

Zinc (Zn) is an essential micronutrient for plants, but excessive concentrations induce cytotoxicity. As one of the world's primary crops, rice's response mechanisms to Zn toxicity remain poorly understood. In this study, we characterized a rice mutant, NG3-6, which exhibited enhanced sensitivity to Zn toxicity compared to the wild type (WT). At Zn concentrations of 40 μM and above, NG3-6 displayed severe toxicity symptoms, including reduced primary root length, plant height, and dry weight, whereas the WT plants maintained normal growth until Zn concentrations exceeded 400 μM. The mutant demonstrated a higher Zn uptake capacity in roots, leading to increased Zn accumulation across all tissues. This higher Zn accumulation was correlated with elevated reactive oxygen species (ROS) production. Zn toxicity induced the accumulation of oxidative stress-related metabolites, such as L-proline, glutathione, and water-soluble sugars, in both the mutant and WT. However, NG3-6 showed distinct metabolic alterations in response to high Zn treatment, including significant accumulation of certain metabolites associated with the pentose phosphate pathway, amine biosynthesis, and benzoic acid-related pathways, concurrent with reduced flavonoid biosynthesis. These findings advance our understanding of the molecular mechanisms underlying root adaptive strategies to Zn toxicity in plants.

Synthetic crassulacean acid metabolism (SynCAM) for improving water-use efficiency in plants

The global climate crisis will continue to increase the frequency and duration of drought episodes in agricultural production areas worldwide. Hot and dry conditions create greater water-deficit stresses on crops, lowering their productivity. While multiple engineering strategies have been developed to improve the efficiency of photosynthesis, greater efforts are needed to improve the drought attenuation and water-use efficiency of crops. Crassulacean acid metabolism (CAM) is a naturally occurring elaboration of C3 photosynthesis that allows plants to occupy and thrive in hot and dry environments with limited or intermittent water supply. Creating synthetic versions of bioengineered CAM is one potentially fruitful approach to improving crop productivity while also reducing photorespiration and increasing water-use efficiency. We outline current efforts being undertaken to engineer CAM-like or synthetic versions of CAM (SynCAM) and future advances and strategies that might contribute to the optimization of SynCAM engineering in crops.This article is part of the theme issue 'Crops under stress: can we mitigate the impacts of climate change on agriculture and launch the 'Resilience Revolution'?'.

Pesticide-induced metabolic disruptions in crops: A global perspective at the molecular level

Pesticide pollution has emerged as a critical global environmental issue of pervasive concern. Although the application of pesticides has provided substantial benefits in controlling weeds, pests, and crop diseases, their indiscriminate use poses considerable challenges to soil health and food safety. Pesticides can be absorbed by crops through either foliar or root uptake, resulting in deleterious effects such as extensive tissue damage, growth inhibition, and reduced crop quality. Beside these visible effects, pesticides can alter gene expression and disrupt cellular signaling transduction, thereby interfering with essential metabolic processes even inducing toxic stress. Moreover, pesticides can interact intricately with biomolecules (e.g. proteins, nucleic acid) in crops, causing significant alterations in protein structure and physiological function. This review focuses on pesticide residues and their associated toxicity, emphasizing their pervasive influence on vital physiological and metabolic pathways, including carbohydrate metabolism, amino acid metabolism, and fatty acid metabolism. Particular attention is given to elucidating the molecular mechanisms underlying these disturbances, specifically regarding transcriptional regulation, cell signaling pathways, and biomolecular interactions. This review provides a comprehensive understanding of multifaceted effects of pesticides and to underscore the necessity for sustainable agricultural practices to safeguard crop yield and quality.

Activation of microbial community and enhancement of quality by inoculating Zygosaccharomyces rouxii during the post-fermentation stage of Doubanjiang

The prolonged post-fermentation stage of Doubanjiang imparts unique flavors but may reduce microbial vitality and increase contamination, affecting quality. This study investigated the effect of Zygosaccharomyces rouxii inoculation during post-fermentation. Results showed a 46.7% increase in amino nitrogen and a significant rise in volatile compounds like phenethyl alcohol, 3-methyl-1-butanol, and ethyl octanoate. The relative abundances of Staphylococcus and Pantoea increased among bacteria, while Pichia, Wickerhamiella, and Zygosaccharomyces increased among fungi. Redundancy analysis showed a positive correlation between these genera and the main volatiles. Microbial ecological network analysis showed that inoculating Z. rouxii increased nodes and edges, resulting in tighter inter-module connections and enhanced robustness. Key genera included Zygosaccharomyces, Staphylococcus, Kazachstania, and Weissella. Metaproteomic results demonstrated that upregulated proteins were predominantly enriched in pathways related to flavor formation, while downregulated proteins were associated with ribosome and DNA synthesis-related pathways. PICRUSt2 analysis results showed higher expression of enzymes related to volatiles in innoculated samples. Inoculating Z. rouxii during the post-fermentation could boost core microorganisms, curb foodborne pathogens, stabilize the microbial community, and enhance Doubanjiang quality.

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.

Comparison of the toxic effects of polystyrene and sulfonated polystyrene on wheat under cadmium stress

With advances in plastic resource utilization technologies, polystyrene (PS) and sulfonated polystyrene (SPS) microplastics continue to be produced and retained in environmental media, potentially posing greater environmental risks. These plastics, due to their different physicochemical properties, may have different environmental impacts when compounded with other pollutants. The objective of this study was to investigate the combined toxic effects of PS and SPS on wheat using cadmium (Cd) as a background contaminant. The results demonstrated that Cd significantly impeded the normal growth of wheat by disrupting root development. Both PS and SPS exhibited hormesis at low concentrations and promoted wheat growth. Under combined toxicity, PS reduced oxidative stress and promoted the uptake of essential metal elements in wheat. Additionally, KEGG pathway analysis revealed that PS facilitated the repair of Cd-induced blockage of the TCA cycle and glutathione metabolism. However, high concentrations of SPS in combined toxicity not only enhanced oxidative stress and interfered with the uptake of essential metal elements, but also exacerbated the blocked TCA cycle and interfered with pyrimidine metabolism. These differences are related to the different stability (Zeta potential, Hydrodynamic particle size) of the two microplastics in the aquatic environment and their ability to carry heavy metal ions, especially Cd. The results of this study provide important insights into understanding the effects of microplastics on crops in the context of Cd contamination and their environmental and food safety implications.

Melatonin confers tolerance to nitrogen deficiency through regulating MdHY5 in apple plants

Nitrogen (N) is an essential nutrient for crop growth and development, significantly influencing both yield and quality. Melatonin (MT), a known enhancer of abiotic stress tolerance, has been extensively studied. However, its relationship with nutrient stress, particularly N deficiency, and the underlying regulatory mechanisms of MT on N absorption remain unclear. In this study, exogenous MT treatment was found to improve the tolerance of apple plants to N deficiency. Apple plants overexpressing the MT biosynthetic gene N-acetylserotonin methyltransferase 9 (MdASMT9) were used to further investigate the effects of endogenous MT on low-N stress. Overexpression of MdASMT9 improved the light harvesting and heat transfer capability of apple plants, thereby mitigating the detrimental effects of N deficiency on the photosynthetic system. Proteomic and physiological data analyses indicated that MdASMT9 overexpression enhanced the trichloroacetic acid cycle and positively modulated amino acid metabolism to counteract N-deficiency stress. Additionally, both exogenous and endogenous MT promoted the transcription of MdHY5, which in turn bound to the MdNRT2.1 and MdNRT2.4 promoters and activated their expression. Notably, MT-mediated promotion of MdNRT2.1 and MdNRT2.4 expression through regulating MdHY5, ultimately enhancing N absorption. Taken together, these findings shed light on the association between MdASMT9-mediated MT biosynthesis and N absorption in apple plants under N-deficiency conditions.

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

Copper (Cu) is one of the essential microelements and widely participates in various pathways in plants, but excess Cu in plant cells could induce oxidative stress and harm plant growth. Rice (Oryza sativa) is a main crop food worldwide. The molecular mechanisms of rice in response to copper toxicity are still not well understood. In this study, two-week-old seedlings of the rice cultivar Nipponbare were treated with 100 μM Cu²⁺ (CuSO₄) in the external solution for 10 days. Physiological analysis showed that excess Cu significantly inhibited the growth and biomass of rice seedlings. After Cu treatment, the contents of Mn and Zn were significantly reduced in the roots and shoots, while the Fe content was significantly increased in the roots. Meanwhile, the activities of antioxidant enzymes including SOD and POD were dramatically enhanced after Cu treatment. Based on metabolomic analysis using liquid chromatography-tandem mass spectrometry (LC-MS/MS) methods, 695 metabolites were identified in rice roots. Among these metabolites, 123 metabolites were up-regulated and 297 were down-regulated, respectively. The differential metabolites (DMs) include carboxylic acids and derivatives, benzene and substituted derivatives, carbonyl compounds, cinnamic acids and derivatives, fatty acyls and organ nitrogen compounds. KEGG analysis showed that these DMs were mainly enriched in TCA cycle, purine metabolism and starch and sucrose metabolism pathways. Many intermediates in the TCA cycle and purine metabolism were down-regulated, indicating a perturbed carbohydrate and nucleic acid metabolism. Taken together, the present study provides new insights into the mechanism of rice roots to Cu toxicity.

Exogenous application of Bradyrhizobium japonicum AC20 enhances soybean tolerance to atrazine via regulating rhizosphere soil microbial community and amino acid, carbohydrate metabolism related genes expression

Atrazine is used to control broad-leaved weeds in farmland and has negative impacts on soybean growth. Legume-rhizobium symbiosis plays an important role in regulating abiotic stress tolerance of plants, however, the mechanisms of rhizobia regulate the tolerance of soybean to atrazine based on the biochemical responses of the plant-soil system are limited. In this experiment, Glycine max (L.) Merr. Dongnong 252, planted in 20 mg kg^-1 of atrazine-contaminated soil, was inoculated with Bradyrhizobium japonicum AC20, and the plant growth, rhizosphere soil microbial diversity and the expression of the genes related to soybean carbon and nitrogen metabolism were assessed. The results indicated that strain AC20 inoculation alleviated atrazine-induced growth inhibition via increasing the contents of leghemoglobin and total nitrogen in soybean seedlings. The psbA gene expression level of the soybean seedlings that inoculated strain AC20 was 1.4 times than that of no rhizobium inoculating treatments. Moreover, the inoculated AC20 increased the abundance of Acidobacteria and Actinobacteria in soybean rhizosphere. Transcriptome analysis demonstrated that strain AC20 regulated the genes expression of amino acid metabolism and carbohydrate metabolism of soybean seedlings. Correlation analysis between 16S rRNA and transcriptome showed that strain AC20 reduced Planctomycetes abundance so as to down-regulated the expression of genes Glyma. 13G087800, Glyma. 12G005100 and Glyma.12G098900 involved in starch synthesis pathway of soybean leaves. These results provide available information for the rhizobia application to enhance the atrazine tolerate in soybean seedlings.

Overexpression of the Phosphoserine Phosphatase-Encoding Gene (AtPSP1) Promotes Starch Accumulation in Lemna turionifera 5511 under Sulfur Deficiency

Duckweeds are well known for their high accumulation of starch under stress conditions, along with inhibited growth. The phosphorylation pathway of serine biosynthesis (PPSB) was reported as playing a vital role in linking the carbon, nitrogen, and sulfur metabolism in this plant. The overexpression of AtPSP1, the last key enzyme of the PPSB pathway in duckweed, was found to stimulate the accumulation of starch under sulfur-deficient conditions. The growth- and photosynthesis-related parameters were higher in the AtPSP1 transgenic plants than in the WT. The transcriptional analysis showed that the expression of several genes in starch synthesis, TCA, and sulfur absorption, transportation, and assimilation was significantly up- or downregulated. The study suggests that PSP engineering could improve starch accumulation in Lemna turionifera 5511 by coordinating the carbon metabolism and sulfur assimilation under sulfur-deficient conditions.

Leymus chinensis Adapts to Degraded Soil Environments by Changing Metabolic Pathways and Root Exudate Components

Phytoremediation is a promising remediation strategy for degraded soil restoration. Root exudates are the main carrier substances for information communication and energy transfer between plant roots and soil, which play non-negligible roles in the restoration process. This work investigated the adaptation of Leymus chinensis root exudates to different degraded levels of soil and the mechanism of rhizosphere restoration in a 3-year degraded soil field study. We found that the soil quality at each degradation level significantly increased, with the soil organic matter (SOM) content slightly increasing by 1.82%, moderately increasing by 3.27%, and severely increasing by 3.59%, and there were significant increases in the contents of available nutrients such as available phosphorus (AP), ammonia nitrogen (AN), and nitrate nitrogen (NN). The physiological activities indicated that root tissue cells also mobilize oxidative stress to respond to the soil environment pressure. A total of 473 main components were obtained from root exudates by gas chromatography-time-of-flight mass spectrometry (GC-TOFMS), including acids, alcohols, carbohydrates, and other major primary metabolites. OPLS-DA revealed that soil degradation exerted an important influence on the metabolic characteristics of root exudates, and the numbers of both up- and downregulated metabolic characteristic peaks increased with the increase in the degree of degradation. Forty-three metabolites underwent clear changes, including some defense-related metabolites and osmotic adjustment substances that were significantly changed. These changes mainly mobilized a series of lipid metabolism pathways to maintain the fluidity of membrane function and help plants adapt to unfavorable soil environmental conditions. The PPP energy metabolism pathway was mobilized in response to slight degradation, and TCA energy pathways responded to the environmental pressure of severe soil degradation.