Metabolomics and transcriptomics reveal defense mechanism of rice (Oryza sativa) grains under stress of 2,2',4,4'-tetrabromodiphenyl ether

Constructing mRNA-meth-miRNA single-sample networks to reveal the molecular interaction patterns induced by lunar orbital stressors in rice (Oryzasativa)

To explore the bio-effects during Moon exploration missions, we utilized the Chang'E 5 probe to carry the seeds of Oryza. Sativa L., which were later returned to Earth after 23 days in lunar orbit and planted in an artificial climate chamber. Compared to the control group, rice seeds that underwent spaceflight showed inhibited growth and development when planted on the ground. Then we collected samples and employed RNA sequencing (RNA-Seq) and whole-genome bisulfite sequencing (WGBS) in the tillering and heading stages of rice. To gain a comprehensive understanding of the dysregulation in molecular interaction patterns during Moon exploration, a bioinformatics pipeline based on mRNA-meth-miRNA Single-Sample Networks (SSNs) was developed. Specifically, we constructed four SSNs for each sample at the mRNA, DNA methylation (promoter and gene bodies), and miRNA levels. By combining with the Protein-Protein Interaction (PPI) network, SSNs can character individual-specific gene interaction patterns. Under spaceflight conditions, distinct interaction patterns emerge across various omics levels. However, the molecules driving changes at each omics level predominantly regulate consistent biological functions, such as metabolic processes, DNA damage and repair, cell cycle, developmental processes, etc. In the tillering stage, pathways such as ubiquitin mediated proteolysis, nucleotide excision repair, and nucleotide metabolism are significantly enriched. Moreover, we identified 18 genes that played key/hub roles in the dysregulation of multi-omics molecular interaction patterns, and observed their involvement in regulating the above biological processes. As aforementioned, our multi-omics SSNs method can reveal the molecular interaction patterns under deep space exploration.

Changes in the small-molecule fingerprints of rice planted near an industrial explosion site in Taiwan

A fire and explosion accident at a petrochemical complex sparked concerns over the rice health and production in nearby paddy fields. To unveil the potential effects, this study investigated small molecule changes in rice harvested in nearby counties using non-target analysis. Rice grains were harvested three, eight, 15, and 20 months after the accident from a total of ten townships. Small-molecule (m/z 70-1100) data in brown rice (n = 27) were acquired using high-resolution mass spectrometry (HRMS). Partial least squares discriminant analysis (PLS-DA) models were constructed to illustrate the temporal and spatial trends of rice's small-molecule fingerprints, and markers of production locations were identified. The small-molecule fingerprint in the rice directly exposed to the accident and harvested three months after the explosion differed significantly from those planted after the accident (PLS-DA model Q2 = 0.943, Q2/R2Y = 0.962), probably indicating the exclusion of long-term effects. Besides, in the rice directly exposed to the accident, the rice collected from near the explosion site (< 15 km) exhibited reduced jasmonic acid and increased imidacloprid levels (log2 fold change: -1.53 and 5.46, respectively), compared to that from farther locations. The result would suggest compromised disease defence in rice grown under the stress of explosion. In addition, lipid and amino acid metabolism perturbations are deemed relevant to plant development.

Polybrominated diphenyl ethers and polychlorinated biphenyls induced rice "diabetes" by disturbing the transport and decomposition of soluble sugars

Halogenated flame retardants in farmlands were observed to inhibit the growth of exposed crops. This study aimed to elucidate the mechanism of inhibition on rice by employing four representative polybrominated diphenyl ethers (PBDEs) and polychlorinated biphenyls (PCBs). The exposure to these contaminants at 200 nM led to a decrease of 0.63-0.95 fold in rice below-ground biomass and 0.49-0.66 fold in yield, and a corresponding 4%-10% increase in soluble sugars in leaves. PBDEs and PCBs were found to significantly disrupt the synthesis, decomposition, and transport of sugars in leaves, the three pivotal determinants of crop growth. Notably, these compounds promoted a 1.41- to 7.60-fold upregulation of the triose phosphate translocator, significantly enhancing soluble sugar synthesis. Conversely, a 0.45-0.97 fold downregulation was observed for sucrose transporters, thus impeding the leaf-to-shoot efflux of soluble sugars. Furthermore, PBDEs and PCBs were favorably bound to fructose-1,6-bisphosphate aldolase (FBA), inducing its substrate-specific dysfunction in fructose-1,6-diphosphate decomposition (3%-14%). Overall, PBDE and PCB exposure promoted a notable intracellular accumulation of soluble sugars in rice leaves, a typical symptom of plant diabetes, since the intensified synthesis of soluble sugars in leaves and the repressed decomposition and transportation of soluble sugars to other storage organs, thus impeding crop growth. This study provided an insightful understanding of the toxic effects and molecular mechanisms of halogenated flame retardants, highlighting their role in abnormal sugar accumulation and growth inhibition in crops and offering vital information for the risk assessment and administration of these compounds to guarantee the safety of agricultural products.

Improvement of plant quality by amino acid transporters: A comprehensive review

Amino acids serve as the primary means of transport and organic nitrogen carrier in plants, playing an essential role in plant growth and development. Amino acid transporters (AATs) facilitate the movement of amino acids within plants and have been identified and characterised in a number of species. It has been demonstrated that these amino acid transporters exert an influence on the quality attributes of plants, in addition to their primary function of transporting amino acid transport. This paper presents a summary of the role of AATs in plant quality improvement. This encompasses the enhancement of nitrogen utilization efficiency, root development, tiller number and fruit yield. Concurrently, AATs can bolster the resilience of plants to pests, diseases and abiotic stresses, thereby further enhancing the yield and quality of fruit. AATs exhibit a wide range of substrate specificity, which greatly optimizes the use of pesticides and significantly reduces pesticide residues, and reduces the risk of environmental pollution while increasing the safety of fruit. The discovery of AATs function provides new ideas and ways to cultivate high-quality crop and promote changes in agricultural development, and has great potential in the application of plant quality improvement.

Understanding the phytotoxic effects of organic contaminants on rice through predictive modeling with molecular descriptors: A data-driven analysis

The widespread introduction of organic compounds into environments poses significant risks to ecosystems. Assessing the adverse effects of organic contaminants on crops is crucial for ensuring food safety. However, laboratory research is often time-consuming and costly, and machine learning (ML) methods can offer a viable solution to address these challenges. This study aimed at developing a ML model that incorporates chemical descriptors to predict the phytotoxicity of organic contaminants on rice. A dataset was compiled by gathering published experimental data on the phytotoxicity of 60 organic compounds, with a focus on morphological inhibition, photosynthesis perturbation, and oxidative stress. Four ML models (RF, SVM, GBM, ANN) were developed using chemical molecular descriptors (CMD) and the Molecular ACCess System (MACCS) keys. RF-MACCS model demonstrated the highest fitness, achieving an R2 value of 0.79 and an RMSE of 0.14. Feature importance analysis highlighted nAtom, HBA, logKow, and TPSA as the most influential CMDs in our model. Additionally, substructures containing oxygen atoms, carbonyl group and carbon chains with nitrogen and oxygen atoms were identified as significant factors associated with phytotoxicity. This data-driven study could aid in predicting the phytotoxicity of organic contaminants on crops and evaluating the potential risks of emerging contaminants in agroecosystems.

Transcriptomics Combined with Physiology and Metabolomics Reveals the Mechanism of Tolerance to Lead Toxicity in Maize Seedling

Lead (Pb) exposure can induce molecular changes in plants, disrupt metabolites, and impact plant growth. Therefore, it is essential to comprehend the molecular mechanisms involved in Pb tolerance in plants to evaluate the long-term environmental consequences of Pb exposure. This research focused on maize as the test subject to study variations in biomass, root traits, genes, and metabolites under hydroponic conditions under Pb conditions. The findings indicate that high Pb stress significantly disrupts plant growth and development, leading to a reduction in catalase (CAT), superoxide dismutase (SOD), and peroxidase (POD) activities by 17.12, 5.78, and 19.38%, respectively. Conversely, Pb stress led to increase malondialdehyde (MDA) contents, ultimately impacting the growth of maize. The non-targeted metabolomics analysis identified 393 metabolites categorized into 12 groups, primarily consisting of organic acids and derivatives, organ heterocyclic compounds, lipids and lipid-like molecules and benzenoids. Further analysis indicated that Pb stress induced an accumulation of 174 metabolites mainly enriched in seven metabolic pathways, for example phenylpropanoid biosynthesis and flavonoid biosynthesis. Transcriptome analysis revealed 1933 shared differentially expressed genes (DEGs), with 1356 upregulated and 577 downregulated genes across all Pb treatments. Additionally, an integrated analysis identified several DEGs and differentially accumulated metabolites (DAMs), including peroxidase, alpha-trehalose, and D-glucose 6-phosphate, which were linked to cell wall biosynthesis. These findings imply the significance of this pathway in Pb detoxification. This comprehensive investigation, employing multiple methodologies, provides a detailed molecular-level insight into maize's response to Pb stress.

Inhibition of microelement accumulation and disorder of saccharide and amino acid metabolism explain rice grain empty under dimethylarsinic acid stress

KEY MESSAGE

Metabolomic and transcriptomic analyses revealed an intensification of energy metabolism in rice grains under DMA stress, possibly causing the consumption of sugars or non-sugars and the development of unfilled grains Excessive dimethylarsinic acid (DMA) causes rice straighthead disease, a physiological disorder typically with erect panicle due to empty grain at maturity. Although the toxicity of DMA and its uptake and transport in rice are well recognized, the underlying mechanism of unfilled grains remains unclear. Therefore, a pot experiment was conducted using a susceptible variety (Ruanhuayou1179, RHY) and a resistant one (Nanjingxiangzhan, NJXZ) via the metabolomic and transcriptomic approaches to explore the mechanisms of empty grains in diseased rice under DMA stress. The results demonstrate an increase in total and methylated As in grains of RHY and NJXZ under DMA addition, with RHY containing higher levels of DMA. DMA addition increased the soluble sugar content in grains of RHY and NJXZ by 17.1% and 14.3% compared to the control, respectively, but significantly reduced the levels of amino acid, soluble protein, and starch. The decrease of grain Zn and B contents was also observed, and inadequate Zn might be a key factor limiting rice grain yield under DMA stress. Notably, DMA addition altered the expression levels of genes involved in the transport of sugar, amino acids, nitrates/peptides, and mineral ions. In sugar and amino acid metabolism, the reduction of metabolites and the upregulated expression of genes reflect positive regulation at the level of energy metabolism, implying that the reduction of grain starch and proteins might be ascribed to generate sufficient energy to resist the stress. This study provides a useful reference for understanding the molecular mechanism of grain emptying under DMA stress.

Coordinated responses of rice (Oryza sativa) to the stresses of benzotriazole ultraviolet stabilizers (BZT-UVs): Antioxidative system, photosynthetic activity, and metabolic regulation

Massive use of plastic products has caused their accumulation in soils, releasing large amounts of endogenous plastic additives (e.g., benzotriazole ultraviolet stabilizers, in short BZT-UVs) into terrestrial ecosystems. However, their plant toxicity is little known. Herein, we investigated the occurrence of BZT-UVs in contaminated farmland and selected three BZT-UV congeners to explore their toxic effects on the antioxidant, photosynthetic, and metabolic perturbation on rice (Oryza sativa). Results showed that the mean concentrations of ∑BZT-UVs in soil and plant samples were 180.7 ng/g dw and 156.4 ng/g dw, respectively. UV-P, UV-327 and UV-328 were the dominant BZT-UV congeners in both of soils and plants. Three BZT-UV congeners caused oxidative damages to rice in a dose-dependent manner, especially for UV-328. Functional genes involved in chlorophyll synthetases was inhibited by over 50 % under the stress of BZT-UVs, whereas those responsible for chlorophyll degradation were obviously promoted. The chlorophyll content was thus decreased, leading to a weakened photosynthesis system and an unbalanced carbon metabolism. The transcriptome and metabolome proved that the flux of carbohydrate metabolism and amino acid metabolism were obviously promoted in plants induced by BZT-UVs, which could inhibit the growth of rice. These findings offered insights into the coordinated responses of plants and advanced our understanding of potential ecological risks of BZT-UVs to terrestrial ecosystems.

Quinolone Antibiotics Inhibit the Rice Photosynthesis by Targeting Photosystem II Center Protein: Generational Differences and Mechanistic Insights

Soil antibiotic pollution profoundly influences plant growth and photosynthetic performance, yet the main disturbed processes and the underlying mechanisms remain elusive. This study explored the photosynthetic toxicity of quinolone antibiotics across three generations on rice plants and clarified the mechanisms through experimental and computational studies. Marked variations across antibiotic generations were noted in their impact on rice photosynthesis with the level of inhibition intensifying from the second to the fourth generation. Omics analyses consistently targeted the light reaction phase of photosynthesis as the primary process impacted, emphasizing the particular vulnerability of photosystem II (PS II) to the antibiotic stress, as manifested by significant interruptions in the photon-mediated electron transport and O2 production. PS II center D2 protein (psbD) was identified as the primary target of the tested antibiotics, with the fourth-generation quinolones displaying the highest binding affinity to psbD. A predictive machine learning method was constructed to pinpoint antibiotic substructures that conferred enhanced affinity. As antibiotic generations evolve, the positive contribution of the carbonyl and carboxyl groups on the 4-quinolone core ring in the affinity interaction gradually intensified. This research illuminates the photosynthetic toxicities of antibiotics across generations, offering insights for the risk assessment of antibiotics and highlighting their potential threats to carbon fixation of agroecosystems.

Comparative analysis of the effects of microplastics and nitrogen on maize and wheat: Growth, redox homeostasis, photosynthesis, and AsA-GSH cycle

Microplastics (MPs) pose a significant threat to the function of agro-ecosystems. At present, research on MPs has mainly focused on the effects of different concentrations or types of MPs on a crop, while ignoring other environmental factors. In agricultural production, the application of nitrogen (N) fertilizer is an important means to maintain the high yield of crops. The effects of MPs and N on growth parameters, photosynthetic system, active oxygen metabolism, nutrient content, and ascorbate-glutathione (AsA-GSH) cycle of maize and wheat were studied in order to explicit whether N addition could effectively alleviate the effects of MPs on maize and wheat. The results showed that MPs inhibited the plant height of both maize and wheat, and MPs effects on physiological traits of maize were more severe than those of wheat, reflecting in reactive oxygen metabolism and restriction of photosynthetic capacity. Under the condition of N supply, AsA-GSH cycle of two plants has different response strategies to MPs: Maize promoted enzyme activity and co-accumulation of AsA and GSH, while wheat tended to consume AsA and accumulate GSH. N application induced slight oxidative stress on maize, which was manifested as an increase in hydrogen peroxide and malonaldehyde contents, and activities of polyphenol oxidase and peroxidase. The antioxidant capacity of maize treated with the combination of MPs + N was better than that treated with N or MPs alone. N could effectively alleviate the adverse effects of MPs on wheat by improving the antioxidant capacity.

2,2',4,4'-Tetrabromodiphenyl Ether (BDE-47) at Environmental Levels Influenced Photosynthesis in the Mangrove Species Kandelia obovata

2,2',4,4'-tetra-bromodiphenytol ether (BDE-47) is one of the ubiquitous organic pollutants in mangrove sediments. To reveal the toxic effects of BDE-47 on mangrove plants, the mangrove species Kandelia obovate was used to investigate the photosynthetic capacity effects and the molecular mechanisms involved after BDE-47 exposure at environment-related levels (50, 500, and 5000 ng g-1 dw). After a 60-day exposure, the photosynthetic capacity was inhibited in K. obovata seedlings, and a decrease in the stomatal density and damage in the chloroplast ultrastructure in the leaves were found. Transcriptome sequencing showed that, following exposure to BDE-47, gene expression in photosynthesis-related pathways was predominantly suppressed in the leaves. The bioinformatics analysis indicated that BDE-47 exerts toxicity by inhibiting photosystem I activity and chlorophyll a/b-binding protein-related genes in the leaves of K. obovata. Thus, this study provides preliminary theoretical evidence for the toxic mechanism effect of BDE-47 on photosynthesis in mangrove species.

Effects of Foliar Spraying of Dicarboxylicdimethylammonium Chloride on Cadmium and Arsenic Accumulation in Rice Grains

A field experiment with double cropping rice was carried out to study the foliar application effects of dicarboxylicdimethylammonium chloride (DDAC) on cadmium (Cd) and arsenic (As) accumulation in rice grains. The results showed that the spraying of DDAC could significantly reduce the accumulation of Cd and As in rice grains. The highest reductions in Cd and As content were observed when 1.5 mmol L-1 DDAC was sprayed, with 49.1% and 27.4% reductions in Cd and As content in early rice grains and 56.5% and 28.1% reductions in Cd and As content in late rice grains, respectively. In addition, the content of calcium (Ca) in rice grains increased significantly after DDAC foliar application, which was also conducive to the synthesis of amino acids such as glutamate (Glu), glycine (Gly) and cysteine (Cys) in rice grains. The results indicated that the foliar spraying of DDAC can inhibit the absorption, transport, accumulation and toxicity of Cd and As in rice grains by increasing amino acid synthesis and regulating the absorption and transport of essential elements.

Sulfonamide-induced DNA hypomethylation disturbed sugar metabolism in rice (Oryza sativa L.)

DNA methylation is well-accepted as a bridge to unravel the complex interplay between genome and environmental exposures, and its alteration regulated the cellular metabolic responses towards pollutants. However, the mechanism underlying site-specific aberrant DNA methylation and metabolic disorders under pollutant stresses remained elusive. Herein, the multilevel omics interferences of sulfonamides (i.e., sulfadiazine and sulfamerazine), a group of antibiotics pervasive in farmland soils, towards rice in 14 days of 1 mg/L hydroponic exposure were systematically evaluated. Metabolome and transcriptome analyses showed that 57.1-71.4 % of mono- and disaccharides were accumulated, and the differentially expressed genes were involved in the promotion of sugar hydrolysis, as well as the detoxification of sulfonamides. Most differentially methylated regions (DMRs) were hypomethylated ones (accounting for 87-95 %), and 92 % of which were located in the CHH context (H = A, C, or T base). KEGG enrichment analysis revealed that CHH-DMRs in the promoter regions were enriched in sugar metabolism. To reveal the significant hypomethylation of CHH, multi-spectroscopic and thermodynamic approaches, combined with molecular simulation were conducted to investigate the molecular interaction between sulfonamides and DNA in different sequence contexts, and the result demonstrated that sulfonamides would insert into the minor grooves of DNA, and exhibited a stronger affinity with the CHH contexts of DNA compared to CG or CHG contexts. Computational modeling of DNA 3D structures further confirmed that the binding led to a pitch increase of 0.1 Å and a 3.8° decrease in the twist angle of DNA in the CHH context. This specific interaction and the downregulation of methyltransferase CMT2 (log2FC = -4.04) inhibited the DNA methylation. These results indicated that DNA methylation-based assessment was useful for metabolic toxicity prediction and health risk assessment.

The effects of Micro/Nano-plastics exposure on plants and their toxic mechanisms: A review from multi-omics perspectives

In recent years, plastic pollution has become a global environmental problem, posing a potential threat to agricultural ecosystems and human health, and may further exacerbate global food security problems. Studies have revealed that exposure to micro/nano-plastics (MPs/NPs) might cause various aspects of physiological toxicities, including plant biomass reduction, intracellular oxidative stress burst, photosynthesis inhibition, water and nutrient absorption reduction, cellular and genotoxicity, seed germination retardation, and that the effects were closely related to MP/NP properties (type, particle size, functional groups), exposure concentration, exposure duration and plant characteristics (species, tissue, growth stage). Based on a brief review of the physiological toxicity of MPs/NPs to plant growth, this paper comprehensively reviews the potential molecular mechanism of MPs/NPs on plant growth from perspectives of multi-omics, including transcriptome, metabolome, proteome and microbiome, thus to reveal the role of MPs/NPs in plant transcriptional regulation, metabolic pathway reprogramming, protein translational and post-translational modification, as well as rhizosphere microbial remodeling at multiple levels. Meanwhile, this paper also provides prospects for future research, and clarifies the future research directions and the technologies adopted.

Photosynthetic mechanisms of carbon fixation reduction in rice by cadmium and polycyclic aromatic hydrocarbons

Environmental pollutants interfere with plant photosynthesis, thus reduce the crop yield and carbon storage capacity of farmland. This study comparatively explored the effects and mechanisms of polycyclic aromatic hydrocarbons (PAHs, e.g., phenanthrene, pyrene, and benzo[a]pyrene) and cadmium (Cd) on the carbon fixation capacity of rice throughout the growth period. Cd posed severer inhibition on the net carbon fixation of rice than PAHs, with the inhibition rates of 1.40-14.8-fold over PAHs at the concentrations of 0.5 or 5 mg/kg soil. Ribulose diphosphate carboxylase/oxygenase (Rubisco) involved in the Calvin cycle was identified as the common target of these pollutants to inhibit the photosynthetic carbon fixation. Further investigation demonstrated that the different inhibitory effects of Cd and PAHs was resulted from their different interference on the dual catalysis function (carboxylation and oxygenation) of Rubisco. Cd disturbed the balance of the intercellular CO2/O2, thus promoting the oxygenation and inhibiting the carboxylation of the substrate of Rubisco. Under the stress of Cd, the downstream metabolites (e.g. glycolate, glyoxylate, and serine) of Rubisco oxygenation were upregulated by over 2.01-3.24-fold, whereas the carboxylation efficiency (Vcmax) was decreased by 5.58-29.3%. Comparatively, PAHs inhibited both the carboxylation and oxygenation by down-regulating the expression of Rubisco coding gene (OsRBCS2, Log2FC < -2). This study broadens the understanding of the mechanisms of different environmental pollutants on the carbon fixation, providing valuable information for the quantitative estimation of their impacts on the farmland carbon sink. The results would be constructive to develop strategies for eliminating the adverse effects of contaminants and assist the carbon-neutral programs.

Metabolome regulation and restoration mechanism of different varieties of rice (Oryza sativa L.) after lindane stress

There is a lack of studies on the ability of plants to metabolize chlorinated organic pollutants (COPs) and the dynamic expression changes of metabolic molecules during degradation. In this study, hybrid rice Chunyou 927 (CY) and Zhongzheyou 8 (ZZY), traditional rice subsp. Indica Baohan 1 (BH) and Xiangzaoxian 45 (XZX), and subsp. Japonica Yangjing 687 (YJ) and Longjing 31 (LJ) were stressed by a typical COPs of lindane and then transferred to a lindane-free culture to incubate for 9 days. The cumulative concentrations in the roots of BH, XZX, CY, ZZY, YJ and LJ were 71.46, 65.42, 82.06, 80.11, 47.59 and 56.10 mg·kg-1, respectively. And the degradation ratios on day 9 were 87.89 %, 86.92 %, 94.63 %, 95.49 %, 72.04 % and 82.79 %, respectively. On the 0 day after the release of lindane stress, the accumulated lindane inhibited the normal physiological activities of rice by affecting lipid metabolism in subsp. Indica BH, amino acid metabolism and synthesis and nucleotide metabolism in hybrid CY. Carbohydrate metabolism of subsp. Japonica YJ also was inhibited, but with low accumulation of lindane, YJ regulated amino acid metabolism to resist stress. With the degradation of lindane in rice, the amino acid metabolism of BH and CY, which had high degradation ratios on day 9, was activated to compound biomolecules required for the organism to recover from the damage. Amino acid metabolism and carbohydrate metabolism were disturbed and inhibited mainly in YJ with low degradation ratios. This study provides the difference of the metabolic capacity of the metabolic capacity of different rice varieties to lindane, and changes at the molecular level and metabolic response mechanism of rice during the metabolism of lindane.

A New Type of Quantum Fertilizer (Silicon Quantum Dots) Promotes the Growth and Enhances the Antioxidant Defense System in Rice Seedlings by Reprogramming the Nitrogen and Carbon Metabolism

To promote the growth and yield of crops, it is necessary to develop an effective silicon fertilizer. Herein, a new type of 2 nm silicon quantum dot (SiQD) was developed, and the phenotypic, biochemical, and metabolic responses of rice seedlings treated with SiQDs were investigated. The results indicated that the foliar application of SiQDs could significantly improve the growth of rice seedlings by increasing the uptake of nutrient elements and activating the antioxidative defense system. Furthermore, metabolomics revealed that the supply of SiQDs could significantly up-regulate several antioxidative metabolites (oxalic acid, maleic acid, glycine, lysine, and proline) by reprogramming the nitrogen- and carbon-related biological pathways. The findings provide a new strategy for developing an effective and promising quantum fertilizer in agriculture.

20 years of polybrominated diphenyl ethers on toxicity assessments

Polybrominated diphenyl ethers (PBDEs) serve as brominated flame retardants which continue to receive considerable attention because of their persistence, bioaccumulation, and potential toxicity. Although PBDEs have been restricted and phased out, large amounts of commercial products containing PBDEs are still in use and discarded annually. Consequently, PBDEs added to products can be released into our surrounding environments, particularly in aquatic systems, thus posing great risks to human health. Many studies and reviews have described the possible toxic effects of PBDEs, while few studies have comprehensively summarized and analyzed the global trends of their toxicity assessment. Therefore, this study utilizes bibliometrics to evaluate the worldwide scientific output of PBDE toxicity and analyze the hotspots and future trends of this field. Firstly, the basic information including the most contributing countries/institutions, journals, co-citations, influential authors, and keywords involved in PBDE toxicity assessment will be visualized. Subsequently, the potential toxicity of PBDE exposure to diverse systems, such as endocrine, reproductive, neural, and gastrointestinal tract systems, and related toxic mechanisms will be discussed. Finally, we conclude this review by outlining the current challenges and future perspectives in environmentally relevant PBDE exposure, potential carriers for PBDE transport, the fate of PBDEs in the environment and human bodies, advanced stem cell-derived organoid models for toxicity assessment, and promising omics technologies for obtaining toxic mechanisms. This review is expected to offer systematical insights into PBDE toxicity assessments and facilitate the development of PBDE-based research.

Tolerance mechanism of rice (Oryza sativa L.) seedings towards polycyclic aromatic hydrocarbons toxicity: The activation of SPX-mediated signal transduction to maintain P homeostasis

Plant tolerance to abiotic stress depends on fast molecular cascades involving stress perception, signal transduction, gene expression alterations, and metabolic rearrangement. This study sheds light on the tolerance mechanism of rice (Oryza sativa L.) towards the toxicity of the polycyclic aromatic hydrocarbons (PAHs), including phenanthrene (Phe), pyrene (Pyr), and benzo[a]pyrene (BaP). Results showed that three PAHs significantly activated the phosphoinositide signaling system involving the phosphorus (P) metabolism and homeostasis in rice roots. This activation increased phytic acid (IP6) levels to over 54.12% of the control (p < 0.05). Molecular docking verified that three PAHs occupied the IP6 binding site in SPX3, a negative regulatory factor of P homeostasis, where ARG229 interacted with PAHs via the van der Waals force. Moreover, the expression of gene encoding SPX3 was significantly downregulated 2.81-, 2.83-, and 2.18-fold under Phe, Pyr, and BaP stress, respectively, relative to the control. Conversely, the expression levels of the gene coding SDEL2 was significantly increased, promoting the degradation of SPX3. Ultimately, P absorption and nucleic acid synthesis were enhanced, alleviating the inhibition effect of PAHs on rice growth. Notably, Pyr demonstrated the strongest binding affinity for SPX3, confirming its critical interference with P homeostasis. These findings provide insight into the molecular mechanisms regulating plant responses to PAHs, and offer guidance for improving crop resistance against organic pollutants and protecting food security.

Microplastics meet invasive plants: Unraveling the ecological hazards to agroecosystems

The objective of this study was to assess the combined impact of environmental microplastic pollution and biological invasion which represent critical global eco-environmental challenges. The invasion of Solidago canadensis L. and soil microplastic contamination in the agroecosystem pose severe hazards to soil and plant ecology and human health. Oryza sativa L. (rice) was examined after individual and combined exposure to Solidago canadensis L. invasion (SI) and soil polyethylene microplastic contamination (MPc). Comparing the individual and combination treatments to the control, leaf biomass decreased, with varying changes in carbon, nitrogen, and phosphorus. Antioxidant enzyme activity and reactive oxygen species levels were significantly reduced following SI exposure and increased following the combined treatment (SI × MP). In contrast, ascorbate peroxidase and catalase activities were reduced after the combined treatment. Due to the confluence of various abiotic stressors, the combined treatment had a higher impact on leaf metabolites than the singular SI and MPc treatments. However, in comparison, the combined treatment significantly influenced the metabolic profile. In conclusion, the interaction between SI and MPc resulted in significant metabolic alterations. These changes were characterized by shifts in metabolite pools influenced by antioxidant enzyme activities and nutrient content, ultimately enhancing defense mechanisms within rice crops. Consequently, these stressors threaten the food safety, sustainability, and agricultural output of crops. The co-exposure of invasive plants and microplastics sheds light on the bio-ecological risks associated with microplastics in staple foods and offers valuable insights into the phytotoxicity of invasive plants in the presence of polyethylene microplastics.

Using regular and transcriptomic analyses to investigate the biotransformation mechanism and phytotoxic effects of 6:2 fluorotelomer carboxylic acid (6:2 FTCA) in pumpkin (Cucurbita maxima L.)

Although 6:2 fluorotelomer carboxylic acid (6:2 FTCA), which is one of the most popular substitutes for perfluorooctanoic acid (PFOA), has been widely distributed in environments, little is known about its biotransformation mechanism and phytotoxic effects in plants. Here, we showed that 6:2 FTCA could be taken up by pumpkin (Cucurbita maxima L.) roots from exposure solution and acropetally translocated to shoots. Biotransformation of 6:2 FTCA to different carbon chain perfluorocarboxylic acid (PFCA) metabolites (C2-C7) via α-and β-oxidation in pumpkin was observed, and perfluorohexanoic acid (PFHxA) was the major transformation product. The results of enzyme assays, enzyme inhibition experiments and gene expression analysis indicated that cytochrome P450 (CYP450), glutathione-S-transferase (GST) and ATP-binding cassette (ABC) transporters were involved in the metabolism of 6:2 FTCA in pumpkin. Plant-associated rhizobacteria and endophyte also contributed to 6:2 FTCA degradation through β-oxidation. The chlorophyll (Chl) content and genes involved in photosynthesis were significantly improved by 6:2 FTCA. The reductions of antioxidant and metabolic enzyme activities reflected the antioxidant defense system and detoxification system of pumpkin were both damaged, which were further confirmed by the down-regulating associated genes encoding phenylpropanoid biosynthesis, endoplasmic reticulum-related proteins, ascorbate-glutathione cycle and ABC transporters. This study is helpful to understand the environmental behaviors and toxicological molecular mechanisms of 6:2 FTCA in plants.

Benzotriazole Ultraviolet Stabilizers (BUVSs) as Potential Protein Kinase Antagonists in Rice

The ubiquitous occurrence of benzotriazole ultraviolet stabilizers (BUVSs) in the environment and organisms has warned of their potential ecological and health risks. Studies showed that some BUVSs exerted immune and chronic toxicities to animals by disturbing signaling transduction, yet limited research has investigated the toxic effects on crop plants and the underlying mechanisms of signaling regulation. Herein, a laboratory-controlled hydroponic experiment was conducted on rice to explore the phytotoxicity of BUVSs by integrating conventional biochemical experiments, transcriptomic analysis, competitive sorption assays, and computational studies. The results showed that BUVSs inhibited the growth of rice by 6.30-20.4% by excessively opening the leaf stomas, resulting in increased transpiration. BUVSs interrupted the transduction of abscisic acid (ABA) signal through competitively binding to Ca2+-dependent protein kinase (CDPK), weakening the CDPK phosphorylation and further inhibiting the downstream signaling. As structural analogues of ATP, BUVSs acted as potential ABA signaling antagonists, leading to physiological dysfunction in mediating stomatal closure under stresses. This is the first comprehensive study elucidating the effects of BUVSs on the function of key proteins and the associated signaling transduction in plants and providing insightful information for the risk evaluation and control of BUVSs.

Under flooding conditions, controlled-release fertiliser coated microplastics affect the growth and accumulation of cadmium in rice by increasing the fluidity of cadmium and interfering with metabolic pathways

The combined pollution of microplastics (MPs) and Cd can affect plant growth and development and Cd accumulation, with most studies focusing on dryland soil. However, the effects of polyurethane (PU) controlled-release fertiliser coated MPs (PU MPs), which widely exist in rice systems, coupled with Cd on plant growth and Cd accumulation under flooding conditions are still unknown. Therefore, in the present study, in situ techniques were used to systematically study the effects of PU MPs and Cd coupling on the physiological and biochemical performance, metabolomics characteristics, rhizosphere bacterial community, and Cd bioavailability of rice in different soil types (red soil/cinnamon soil). The results showed that the effects of PU MPs on rice growth and Cd accumulation were concentration-dependent, especially in red soil. High PU concentration (1 %) inhibited rice root growth significantly (44 %). The addition of PU MPs inhibited photosynthetically active radiation, net photosynthesis, and transpiration rate of rice, mainly with low concentration (0.1 %) in red soil and high concentration (1 %) in cinnamon soil. PU MPs can enhance the expression of Cd resistance genes (cadC and copA) in soil, enhance the mobility of Cd, and affect the metabolic pathways of metabolites in the rhizosphere soil (red soil: fatty acid metabolism; cinnamon soil: amino acid degradation, heterobiodegradation, and nucleotide metabolism) to promote Cd absorption in rice. Especially in red soil, Cd accumulation in the root and aboveground parts of rice after the addition of high concentration PU (1 %) was 1.7 times and 1.3 times, respectively, that of the control (p < 0.05). Simultaneously, microorganisms can affect rice growth and Cd bioavailability by affecting functional bacteria related to carbon, iron, sulfur, and manganese. The results of the present study provide novel insights into the potential effects of PU MPs coupled with Cd on plants, rhizosphere bacterial communities, and Cd bioavailability.

Interactions between sulfonamide homologues and glycosyltransferase induced metabolic disorders in rice (Oryza sativa L.)

Sulfadiazine and its derivatives (sulfonamides, SAs) could induce distinct biotoxic, metabolic and physiological abnormalities, potentially due to their subtle structural differences. This study conducted an in-depth investigation on the interactions between SA homologues, i.e. sulfadiazine (SD), sulfamerazine (SD1), and sulfamethazine (SD2), and the key metabolic enzyme (glycosyltransferase, GT) in rice (Oryza sativa L.). Untargeted screening of SA metabolites revealed that GT-catalyzed glycosylation was the primary transformation pathway of SAs in rice. Molecular docking identified that the binding sites of SAs on GT (D0TZD6) were responsible for transferring sugar moiety to synthesize polysaccharides and detoxify SAs. Specifically, amino acids in the GT-binding cavity (e.g., GLY487 and CYS486) formed stable hydrogen bonds with SAs (e.g., the sulfonamide group of SD). Molecular dynamics simulations revealed that SAs induced conformational changes in GT ligand binding domain, which was supported by the significantly decreased GT activity and gene expression level. As evidenced by proteomics and metabolomics, SAs inhibited the transfer and synthesis of sugar but stimulated sugar decomposition in rice leaves, leading to the accumulation of mono- and disaccharides in rice leaves. While the differences in the increased sugar content by SD (24.3%, compared with control), SD1 (11.1%), and SD2 (6.24%) can be attributed to their number of methyl groups (0, 1, 2, respectively), which determined the steric hindrance and hydrogen bonds formation with GT. This study suggested that the disturbances on crop sugar metabolism by homologues contaminants are determined by the interaction between the contaminants and the target enzyme, and are greatly dependent on the steric hindrance effects contributed by their side chains. The results are of importance to identify priority pollutants and ensure crop quality in contaminated fields.

Integrated microbiome and multi-omics analysis reveal the molecular mechanisms of Eisenia fetida in response to biochar-derived dissolved and particulate matters

At present, most ecotoxicological studies are still confined to focusing on the harmful effects of biochar itself on soil fauna. However, the potential ecotoxicity of different components separated from biochar to terrestrial invertebrates remains poorly understood. In this study, the dissolved matter (DM) and particulate matter (PM) were separated from biochar (BC) and then introduced into the soil-earthworm system to investigate the response mechanism of earthworms at the molecular level. The results showed that BC and DM exposure caused an increase in the abundance of Proteobacteria in the cast bacterial community, suggesting the dysbiosis of intestinal microbiota. It was also observed that the cast bacterial communities were more sensitive to DM exposure than PM exposure. Transcriptomic analysis showed that BC and DM exposure induced significant enrichment of functional pathways related to infectious and neuropathic diseases. Metabolomic profiling manifested that DM exposure caused metabolic dysfunction, antioxidant and detoxification abilities recession. Furthermore, significant differences in the responses of earthworms at transcriptomic and metabolic levels confirmed that DM exhibited greater ecotoxicity than PM. This study highlighted the significant contributions of dissolved matter to the ecotoxicity of biochar from the perspective of transcriptomic and metabolomic profiles.

Molecular Defensive Mechanism of Echinacea purpurea (L.) Moench against PAH Contaminations

The understanding of the molecular defensive mechanism of Echinacea purpurea (L.) Moench against polycyclic aromatic hydrocarbon (PAH) contamination plays a key role in the further improvement of phytoremediation efficiency. Here, the responses of E. purpurea to a defined mixture of phenanthrene (PHE) and pyrene (PYR) at different concentrations or a natural mixture from an oilfield site with a history of several decades were studied based on transcriptomics sequencing and widely targeted metabolomics approaches. The results showed that upon 60-day PAH exposure, the growth of E. purpurea in terms of biomass (p < 0.01) and leaf area per plant (p < 0.05) was negatively correlated with total PAH concentration and significantly reduced at high PAH level. The majority of genes were switched on and metabolites were accumulated after exposure to PHE + PYR, but a larger set of genes (3964) or metabolites (208) showed a response to a natural PAH mixture in E. purpurea. The expression of genes involved in the pathways, such as chlorophyll cycle and degradation, circadian rhythm, jasmonic acid signaling, and starch and sucrose metabolism, was remarkably regulated, enhancing the ability of E. purpurea to adapt to PAH exposure. Tightly associated with transcriptional regulation, metabolites mainly including sugars and secondary metabolites, especially those produced via the phenylpropanoid pathway, such as coumarins, flavonoids, and their derivatives, were increased to fortify the adaptation of E. purpurea to PAH contamination. These results suggest that E. purpurea has a positive defense mechanism against PAHs, which opens new avenues for the research of phytoremediation mechanism and improvement of phytoremediation efficiency via a mechanism-based strategy.

Docosahexaenoic Acid Promotes Cd Excretion by Restoring the Abundance of Parabacteroides in Cd-Exposed Mice

As a common harmful pollutant, cadmium (Cd) can easily enter the human body through the food chain, posing a major threat to human health. Gut microbiota play a key role in Cd absorption. Docosahexaenoic acid (DHA) is thought to have a potential role in the treatment of Cd poisoning. This study investigated the therapeutic effect and mechanism of DHA in Cd-exposed mice from the perspective of the gut microbiota. The results showed that DHA significantly increased the Cd content in feces and decreased the Cd accumulation in the organs of mice. The gut microbiota results showed that DHA significantly restored the abundance of Parabacteroides in the gut microbiota of Cd-exposed mice. Parabacteroides distasonis (P. distasonis), a representative strain of the Parabacteroides, also showed Cd- and toxicity-reduction capabilities. P. distasonis significantly restored the gut damage caused by Cd exposure. At the same time, P. distasonis reduced the Cd content in the liver, spleen, lung, kidneys, gut, and blood to varying degrees and significantly increased the Cd content in feces. The succinic acid produced by P. distasonis plays an important role in promoting Cd excretion in Cd-exposed mice. Therefore, these results suggest that P. distasonis may have a potential role in DHA-mediated Cd excretion in Cd-exposed mice.

Dissolved organic matter transformation mechanisms and process optimization of wastewater sludge hydrothermal humification treatment for producing plant biostimulants

Understanding the composition, transformation and bioactivity of dissolved organic matter (DOM) at the molecular level is crucial for investigating the hydrothermal humification process of wastewater sludge and producing ecological fertilizers. In this study, DOM transformation pathways under alkali-thermal humification treatment (AHT) were characterized by Fourier transform-ion cyclotron resonance mass spectrometry (FT-ICR MS) in conjunction with molecular reaction network analysis. The effects of DOM on plant growth were examined using hydroponics and transcriptomic analysis. In the wastewater sludge humification process, AHT produced maximum amounts of protein (3260.56 mg/L) and humic acid (5788.24 mg/L) after 12 h. FT-ICR MS results indicated that protein-like structures were prone to continuous oxidation and were ultimately transformed into aromatic N-containing compounds resembling humic substances. Several reactive fragments (such as -C₂H₂O₂, -C₃H₄O₂, and -C₄H₆O₂) formed by the Maillard reaction (MR) were identified as potential precursors to humic acid (HA). In terms of biological effects, DOM_12h showed the highest rice germination and growth activity, whereas that produced by AHT for a longer period (> 12 h) displayed phytotoxicity owing to the accumulation of toxic substances. Plant biostimulants (such as amino acids and HAs) in DOM improved energy metabolism and carbohydrate storage in rice seedlings by upregulating the "starch and sucrose metabolism" pathways. Toxic substances (such as pyrrole, pyridine, and melanoidin) in DOM can activate cell walls formation to inhibit abiotic stimuli in rice seedlings through the biosynthesis of phenylpropanoid pathway. These findings provide a theoretical basis for optimizing sludge hydrothermal humification and recovering high-quality liquid fertilizers.

Inhibition of rice germination by ustiloxin A involves alteration in carbon metabolism and amino acid utilization

Ustiloxins are the main mycotoxin in rice false smut, a devastating disease caused by Ustilaginoidea virens. A typical phytotoxicity of ustiloxins is strong inhibition of seed germination, but the physiological mechanism is not clear. Here, we show that the inhibition of rice germination by ustiloxin A (UA) is dose-dependent. The sugar availability in UA-treated embryo was lower while the starch residue in endosperm was higher. The transcripts and metabolites responsive to typical UA treatment were investigated. The expression of several SWEET genes responsible for sugar transport in embryo was down-regulated by UA. Glycolysis and pentose phosphate processes in embryo were transcriptionally repressed. Most of the amino acids detected in endosperm and embryo were variously decreased. Ribosomal RNAs for growth were inhibited while the secondary metabolite salicylic acid was also decreased under UA. Hence, we propose that the inhibition of seed germination by UA involves the block of sugar transport from endosperm to embryo, leading to altered carbon metabolism and amino acid utilization in rice plants. Our analysis provides a framework for understanding of the molecular mechanisms of ustiloxins on rice growth and in pathogen infection.

Hemocytes in blue mussel Mytilus edulis adopt different energy supply modes to cope with different BDE-47 exposures

The energetic response of blue mussel Mytilus edulis when coping with tetrabromodiphenyl ether (BDE-47) exposure was evaluated from the perspective of alterations in energy supply mode, and the possible regulating mechanism was discussed based on a 21-day bioassay. The results showed that the energy supply mode changed with concentration: 0.1 μg/L BDE-47 decreased the activity of isocitrate dehydrogenase (IDH), succinate dehydrogenase (SDH), malate dehydrogenase and oxidative phosphorylation, suggesting inhibition of the tricarboxylic (TCA) acid cycle and aerobic respiration. The coincident increase in phosphofructokinase and the decrease in lactate dehydrogenase (LDH) indicated that glycolysis and anaerobic respiration were increased. When exposed to 1.0 μg/L BDE-47, M. edulis mainly utilized aerobic respiration, but lowered glucose metabolism as indicated by the decrease in glutamine and l-leucine was suggested to be involved in this process, which was differed from that in the control. The reoccurrence of IDH and SDH inhibition as well as LDH elevation indicated attenuation of aerobic and anaerobic respiration when the concentration increased to 10 μg/L, but severe protein damage was evidenced based on the elevation of amino acids and glutamine. Under the 0.1 μg/L BDE-47, activation of the AMPK-Hif-1a signaling pathway promoted the expression of glut1, which was the potential mechanism for the improvement of anaerobic respiration, and further activated glycolysis and anaerobic respiration. This study shows that the energy supply mode experienced a conversion from aerobic respiration under normal conditions to anaerobic mode in the low BDE-47 treatment and back to aerobic respiration with increasing BDE-47 concentrations, which may represent a potential mechanism for mussel physiological responses when faced with different levels of BDE-47 stress.

Exploring the impacts of service life of biological activated carbon on dissolved organic nitrogen removal

The biological activated carbon (BAC) process has been widely used in drinking water treatment to improve the removal of pollutants, including the precursors of nitrogenous disinfection byproducts (N-DBPs). Nevertheless, old BAC filter effluent DON concentration is heightened, increasing the highly toxic N-DBPs formation potential. Herein, the variation of dissolved organic nitrogen (DON) was comprehensively explored during one backwashing cycle, focusing on four BAC age (0.3, 2, 5, and 10 years) for BAC filters in drinking water. Comparatively, the removal rate of DON by four BAC followed the order 0.3-yr BAC (39.69%-66.96%) >2-yr BAC (10.10%-39.78%) >5-yr BAC (-4.18%-29.63%)>10-yr BAC (-20.88%-19.87%). When at day 7 after backwashing, 10-yr BAC filter effluent increased at least 13.71% of DON and considerably elevated the N-DBPs formation potential, which was attributed to the ultimate production of more various proteins/amino sugars-like compounds by microbes. In comparisons of microbial community between all BAC samples, Rhizobials were more prevalent in 10-yr BAC and could produce microbe-derived DON associated with amino acids. Moreover, microbes regulated metabolic pathways, including amino acid biosynthesis, TCA cycle, purine metabolism, and pyrimidine metabolism, to enhance the adaptive cellular machinery in response to environmental stressors, and therefore accelerated microbial secretion of microbe-derived DON. Structural equation model (SEM) analysis investigated that BAC age had bio-effects on N-DBPs formation potential, which were delivered via the linkage of " BAC age, microbial community, microbial metabolism, and DON molecular characteristics". Our findings demonstrate the necessity of reconsidering the feasibility of BAC filters for long-time operation, which has implications for future N-DBPs precursors control in drinking water.

Weighted gene co-expression network analysis revealed the key pathways and hub genes of potassium regulating cotton root adaptation to salt stress

Soil salinization is one of the main abiotic stresses affecting cotton yield and planting area. Potassium application has been proven to be an important strategy to reduce salt damage in agricultural production. However, the mechanism of potassium regulating the salt adaptability of cotton has not been fully elucidated. In the present research, the appropriate potassium application rate for alleviating salt damage of cotton based on different K⁺/Na⁺ ratios we screened, and a gene co-expression network based on weighted gene co-expression network analysis (WGCNA) using the transcriptome data sets treated with CK (0 mM NaCl), S (150 mM NaCl), and SK8 (150 mM NaCl + 9.38 mM K₂SO₄) was constructed. In this study, four key modules that are highly related to potassium regulation of cotton salt tolerance were identified, and the mitogen-activated protein kinase (MAPK) signaling pathway, tricarboxylic acid (TCA) cycle and glutathione metabolism pathway were identified as the key biological processes and metabolic pathways for potassium to improve cotton root salt adaptability. In addition, 21 hub genes and 120 key candidate genes were identified in this study, suggesting that they may play an important role in the enhancement of salt adaptability of cotton by potassium. The key modules, key biological pathways and hub genes discovered in this study will provide a new understanding of the molecular mechanism of potassium enhancing salinity adaptability in cotton, and lay a theoretical foundation for the improvement and innovation of high-quality cotton germplasm.

Optimistic effects of galaxolide and polystyrene microplastic stress on the physio-biochemical characteristics and metabolic profiles of an ornamental plant

Galaxolide (HHCB) and polystyrene (PS) microplastics or nanoplastics have been widely recognized as emerging pollutants. However, very few efforts have been made to remove these contaminants from the environment using eco-friendly materials such as plant materials. Therefore, this study sought to investigate the physiological and biochemical effects and tolerance mechanisms of Mirabilis jalapa L. upon exposure to HHCB and PS. Our findings demonstrated that this ornamental plant was tolerant to HHCB and PS exposure. HHCB treatment increased antioxidant enzyme activity. However, superoxide dismutase (SOD) activity increased by 206.85% when the plants were treated with 0.5 mg L^-1 HHCB alone, whereas co-exposure to 0.5 mg L^-1 HHCB and 500 nm PS increased SOD activity by 93.82%. Contaminant exposure also affected photosynthetic parameters such as stomatal conductance and transpiration rate. In contrast, net photosynthetic rate and photosynthetic pigment content were not significantly affected. HHCB aggregated heavily in the roots of the plant. Moreover, 500 nm PS could be absorbed by the root and transported to the shoot, and 5 μm PS would be transferred to the shoot under the carrying effect of HHCB. Co-exposure to HHCB and PS significantly changed the glyoxylate and dicarboxylate metabolism, alanine, aspartate, and glutamate metabolism, and glycine, serine, and threonine metabolism pathways, thus affecting carbohydrate synthesis and energy metabolism in M. jalapa. These results provide a basis for the development of HHCB and PS remediation strategies using M. jalapa, an ornamental plant that is not only tolerant to organic contaminants but can also beautify the environment.

Multi-omics analysis reveals copper-induced growth inhibition mechanisms of earthworm (Eisenia fetida)

Exposure to high concentrations of copper can cause toxic effects on the growth and development of organisms, but the relevant toxic mechanisms are far from fully understood. This study investigated the changes of metabolites, genes, and gut microorganisms in earthworms (Eisenia fetida) exposed to 0 (control), 67.58 (low), 168.96 (medium), and 337.92 (high) mg/kg of Cu in soil for 60 days. Differentially expressed genes (DEGs) and differential metabolites (DMs) at the low-, medium-, and high-level Cu exposure groups were identified and introduced into Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Integrated metabolomic and transcriptomic analysis revealed that amino acid metabolism, lipid metabolism, and carbohydrate metabolism are the major metabolic pathways disturbed by Cu exposure. Furthermore, Cu exposure significantly decreased the diversity of the intestinal bacterial community and affected the relative abundance (increased or decreased) of intestinal colonizing bacteria. This resulted in high energy expenditure, inhibited nutrient absorption and fatty acid synthesis, and weakened antioxidant and detoxification abilities, ultimately inhibiting the growth of E. fetida. These findings offer important clues and evidence for understanding the mechanism of Cu-induced growth and development toxicity in E. fetida and provide further data for risk assessment in terrestrial ecosystems.

Metabolomic analysis reveals the impact of ketoprofen on carbon and nitrogen metabolism in rice (Oryza sativa L.) seedling leaves

Pharmacologically active compounds (PACs) are becoming common pollutants in the natural environment, posing potential risks to crop quality; however, the toxic effects and metabolic changes that they cause in agricultural plants remain unclear. Here, we investigated the effects of ketoprofen on respiration rate, ATP synthesis, carbon and nitrogen metabolism, and metabolomics in rice seedling leaves. The results showed that ketoprofen treatment adversely affected the respiration rate, ATP content, H⁺-ATPase activity and induced changes in the contents of carbon assimilation products (soluble sugar, reducing sugar, sucrose, and starch) and the activities of key enzymes in carbon metabolism (sucrose synthase (SS), sucrose phosphate synthase (SPS), and sucrose invertase (InV)). The contents of nitrate, ammonium, and free amino acids, and the activities of key enzymes involved in nitrogen metabolism (nitrate reductase (NR), nitrite reductase (NiR), glutamine synthetase (GS), glutamate synthase (GOGAT), and glutamate dehydrogenase (GDH)) were also affected in a concentration-dependent manner. Metabolomics analysis showed that ketoprofen disturbed the type and content of metabolites (amino acids, carbohydrates, and secondary metabolites) to varying degrees and perturbed key metabolic pathways (substance synthesis and energy metabolism), ultimately resulting in the reduction of rice seedling biomass. This study provides important information and a useful reference for the accurate assessment of the environmental risks of PACs.

Effects of biochar on the phytotoxicity of polyvinyl chloride microplastics

Polyvinyl chloride microplastics (PVC-MPs) are toxic to crops, resulting in economic losses during agricultural production. Owing to its strong adsorption capacity, biochar can effectively remove MPs from water. It is presumed that biochar can alleviate the phytotoxicity of PVC-MPs. To verify this hypothesis, the effects of different concentrations of corncob biochar (CCBC) on the phytotoxicity of PVC-MPs were investigated using hydroponic experiments. The results showed that PVC-MPs attached to lettuce roots substantially inhibited the growth and quality of lettuce. The tested CCBC adsorbed the PVC-MPs. At appropriate concentrations, CCBC alleviated the inhibitory effect of PVC-MPs on lettuce yield; however, it decreased some quality indicators. The single PVC-MPs induced oxidative damage to lettuce, as demonstrated by the increased hydrogen peroxide (H2O2) and malondialdehyde (MDA) content. Addition of CCBC considerably decreased the contents of H2O2 and MDA in the lettuce shoots but increased the H2O2 content in the roots. These findings indicate that CCBC may alleviate the adverse effects caused by PVC-MPs to the lettuce shoots but aggravate the toxic effects on the lettuce roots. This study provides a basis for understanding the removal of the phytotoxicity of MPs.

Effects of Exogenous Chlorinated Amino Acetic Acid on Cadmium and Mineral Elements in Rice Seedlings

To explore the effect of exogenous application of chlorinated amino acetic acid on cadmium (Cd) transport characteristics in rice seedlings, X24 and Z35 rice were taken as the research objects to carry out hydroponics experiments, and the changes of Cd content in rice seedlings, rice mineral elements and amino acid content in rice were analyzed. The results showed that exogenous application of 1.2 mmol·L^-1 chlorinated amino acetic acid inhibited cadmium in shoots and roots of rice seedlings; Cd content in shoots and roots were reduced by up to 62.19% and 45.61%, respectively. The majority of cadmium was in the cell wall of shoots and roots; this decreased with the increase of the concentration of chlorinated acetic acid. In addition, the Mn content in shoots and Ca content in roots of rice seedlings increased significantly after the application of chlorinated amino acetic acid. The results of amino acid analysis showed that the contents of aspartic acid, glutamic acid and cystine in rice seedlings were increased. These results indicate that exogenous application of chlorinated amino acetic acid is beneficial to the synthesis of aspartic acid, glutamic acid and cysteine in rice seedlings, increases the content of Mn in shoots and Ca in roots of rice seedlings, and significantly alleviates cadmium stress in seedlings. This provides a theoretical basis for the development of an environmentally friendly Cd-lowering foliar fertilizer for rice.

Transcriptomics and metabolomics reveal tolerance new mechanism of rice roots to Al stress

The prevalence of soluble aluminum (Al) ions is one of the major limitations to crop production worldwide on acid soils. Therefore, understanding the Al tolerance mechanism of rice and applying Al tolerance functional genes in sensitive plants can significantly improve Al stress resistance. In this study, transcriptomics and metabolomics analyses were performed to reveal the mechanism of Al tolerance differences between two rice landraces (Al-tolerant genotype Shibanzhan (KR) and Al-sensitive genotype Hekedanuo (MR) with different Al tolerance. The results showed that DEG related to phenylpropanoid biosynthesis was highly enriched in KR and MR after Al stress, indicating that phenylpropanoid biosynthesis may be closely related to Al tolerance. E1.11.1.7 (peroxidase) was the most significant enzyme of phenylpropanoid biosynthesis in KR and MR under Al stress and is regulated by multiple genes. We further identified that two candidate genes Os02g0770800 and Os06g0521900 may be involved in the regulation of Al tolerance in rice. Our results not only reveal the resistance mechanism of rice to Al stress to some extent, but also provide a useful reference for the molecular mechanism of different effects of Al poisoning on plants.

Polybrominated diphenyl ethers interact with the key protein involved in carbohydrate metabolism in rice

Rice exposed to organic pollutants such as polybrominated diphenyl ethers (PBDEs) usually experiences reduced biomass and increased soluble sugar content. This study showed that 2, 2', 4, 4'-tetrabromodiphenyl ether (BDE-47) led to increased glucose, fructose, and sucrose in rice leaves, accompanied by decreased photosynthetic rate and biomass. In order to identify the key enzyme that BDE-47 interacted with, a diazirine-alkynyl photoaffinity probe was designed, and photoaffinity labeling based chemoproteomics was conducted. Among all differentially expressed proteins, fructose-1, 6-bisphosphate aldolase (FBA) involved in carbohydrate metabolism was most likely the target protein of BDE-47. Spectral techniques and molecular docking analysis further revealed that the pollutant-protein interaction was driven by hydrophobic force. BDE-47 inhibited FBA catalytic efficiency by competing with its substrate, fructose-1, 6-diphosphate (F-1, 6-P), leading to soluble sugar accumulation, photosynthetic rate decline and biomass reduction. This study unraveled the influencing mechanism of PBDEs on rice by combining the novel photoaffinity labeling-based chemoproteomics with conventional proteomics. The improved knowledge on direct interaction between organic pollutants and proteins will help alleviate the harmful effects of soil pollution on plants.

Negative impacts of nanoplastics on the purification function of submerged plants in constructed wetlands: Responses of oxidative stress and metabolic processes

Constructed wetlands (CWs) are an important barrier to prevent nanoplastics (NPs) and microplastics (MPs) from entering receiving streams. However, little is known about how the accumulation of NPs affects the growth, photosynthesis, oxidative stress responses, and metabolism of plants, especially submerged plants that are widely used in CWs for water purification. Herein, we adopted Utricularia vulgaris (U. vulgaris), a typical submerged macrophyte as the model plant to address the above knowledge gaps under exposure to polystyrene NPs (PS-NPs, 500 nm, 0∼10 mg·L^-1). Results showed that PS-NPs were absorbed by insect traps and further transported to stems and leaves of U. vulgaris, which limited plant height (6.8∼72.9%), relative growth rate (7.4∼17.2%), and photosynthesis (3.7∼28.2%). U. vulgaris suffered from oxidative stresses, as evidenced by the increase in malondialdehyde, antioxidant enzymes (catalase, peroxidase, and superoxide dismutase), and H₂O₂, especially under 1 and 10 mg·L^-1. Abundances of 548 metabolites were quantified, and 291 metabolites were detected with altered levels after exposure, in which 25∼34% metabolites were up-regulated, and 32∼40% metabolites were down-regulated in metabolite expression. Metabolic pathways of the tricarboxylic acid cycle and amino acid were disrupted, in which citric acid, threonine, and adenine decreased, while amino acids (like serine, phenylalanine, histidine, etc.) increased first and then decreased with increasing PS-NPs concentrations. Moreover, PS-NPs reduced the removal efficiency of total nitrogen and phosphorus from water by U. vulgaris, bringing potential risks to aquatic ecosystems. These findings have greatly enhanced our understanding of the metabolic mechanisms and interactions of aquatic macrophytes that are heavily used in CWs in response to NPs stress, as well as the impact of NPs on CWs functioning.

Photosynthetic, antioxidative, and metabolic adjustments of a crop plant to elevated levels of La and Ce exposure

Rare earth elements (REEs) have been widely applied as fertilizers in farmland of China for decades to improve the yield and quality of crops. Unfortunately, adverse effects on plants have been observed due to overdosing with REEs. Until now, the toxicology of REEs was mainly evaluated based on phenotypic responses, but knowledge gaps still exist concerning their metabolic effects. Here, the physiological responses and nontargeted metabolomics studies were combined to systematically explore the potential effects of La and Ce on a crop plant, wheat Triticum aestivum. It was observed that REEs accumulated in the shoots of wheat, with significant reduction of the shoot biomass at higher exposure doses. The disturbance of photosynthesis and induced oxidative stress were identified by analyzing indicators of the photosynthetic (chlorophyll a/b, carotenoid and rubisco) and antioxidant systems (POD, CAT, SOD, GSH and MDA). Furthermore, the global metabolic profiles of REEs treatment groups and the non-exposed control group were screened and compared, and the metabolomic disturbance of REEs was dose-dependent. A high overlap of significantly changed metabolites and matched disturbed biological pathways was found between La and Ce treatments, indicating similarity of their toxicity mechanism in wheat shoots. Generally, the perturbed metabolomic pathways were mainly related to carbohydrate, amino acid and nucleotide/side metabolism, suggesting a disturbance of carbon and nitrogen metabolism, which finally affected the growth of wheat. We thus proved the potential adverse effect of inappropriate application of REEs in crop plants and postulated metabolomics as a feasible tool to identify the underlying toxicological mechanisms.

Combining Proteomics and Metabolomics to Analyze the Effects of Spaceflight on Rice Progeny

Spaceflight is a special abiotic stress, the biological effect mechanism of which on contemporary rice has been clarified, However, its effect on offspring rice was still unclear. In order to understand the response mechanism of F2 generation plants to space flight, this study used SJ-10 recoverable satellite to carry DN423 rice seeds for 12.5 days in orbit flight. After returning to the ground, the plants were then planted to F2 generation to explore the biological effect mechanism. Our research showed that in the F2 generation of TLS, the rice plant height of the space flight group increased by 33.8%, the ear length and thousand-grain weight decreased by 9.7 and 4.6%, respectively, and the grain number per panicle increased by 6.5%. Moreover, related proteins that control changes in agronomic traits have been identified. The changes of MDA, H2O2, soluble sugar, electron leakage and antioxidant enzyme activity confirmed the stress response in F2 generation plants. ITRAQ and LC-MS technology were used to reveal the change pattern of protein levels and metabolite levels in F2 generation plants, 389 and 405 proteins were identified as differentially abundant proteins in TLS and TS, respectively. In addition, there were 124 and 125 metabolites that changed during these two periods. The proteome and metabolome result further confirmed that the F2 generation plants still retained the memory of space flight stress, and retained the memory of space flight stress through genome instability. Oxidative stress signals activated sugar signals to rebuild metabolic networks to adapt to space flight stress. The reconstruction of energy metabolism, amino acid metabolism, phenylalanine metabolism, and flavonoid metabolism played an important role in the process of adapting to space flight stress. The results of this study broaden the perspective of space biological effects and provide a basis for studying the effects of abiotic stress on plant progeny.

Metabolomic analysis of Scenedesmus obliquus reveals new insights into the phytotoxicity of imidazolium nitrate ionic liquids

Due to the persistence of ionic liquids (ILs) in aquatic environments, it is necessary to reveal their ecological risk to aquatic organisms. Herein, the biotoxicity of two alkyl-methylimidazolium nitrate ILs ([C₁₀mim]NO₃ and [C₁₂mim]NO₃) against Scenedesmus obliquus were studied. Results showed that the growth inhibition of S. obliquus increased with increasing concentrations of ILs, maximum values of 94.61% at 4 mg/L of [C₁₀mim]NO₃ and 97.34% at 0.8 mg/L of [C₁₂min]NO₃ were observed. The fluorescence parameters of photosystem II, such as light quantum yield and electron transfer rate, showed a negative relationship with the exposure dose. [C₁₂mim]NO₃ had a more significant effect than [C₁₀mim]NO₃. Moreover, the redox homeostasis of algae was disrupted; the accumulation of reactive oxygen species, leading to obvious inhibition of superoxide dismutase and catalase activities was observed. A metabolomic analysis indicated that the contents of most metabolites were reduced significantly, and fructose and galactose decreased significantly by 42.3% and 88.6%, respectively, in the [C₁₀mim]NO₃ treatment compared to those in the control. The inhibition of amino acid biosynthesis and glyoxylate and dicarboxylate metabolism explained the more serious biotoxicity of [C₁₂mim]NO₃ than that of [C₁₀mim]NO₃. This study facilitates a better understanding of the environmental safety and ecological risks of ILs.

Photosynthetic Toxicity of Enrofloxacin on Scenedesmus obliquus in an Aquatic Environment

Aquaculture facilities are a potential source of antibiotics in aquatic environments, having adverse effects on the algae species. In this study, the toxicity induced by enrofloxacin (ENR) on the algae Scenedesmus obliquus was evaluated. The uptake of ENR and the change in the growth and photosynthesis of algae were analyzed. At the exposure doses of 10-300 μg/L, the accumulated levels of ENR in algae were 10.61-18.22 μg/g and 12.09-18.34 μg/g after 48 h and 96 h of treatment, respectively. ENR inhibited the growth of algae, with a concentration for 50% effect of 119.74 μg/L, 53.09 μg/L, 64.37 μg/L, and 52.64 μg/L after 24 h, 48 h, 72 h and 96 h of treatment, respectively, indicating the self-protection and repair ability of algae in a short period of time. Furthermore, the chlorophyll contents decreased in all treatment groups, and the photosynthetic system Ⅱ parameters decreased in a dose-dependent manner under ENR stress, suggesting that ENR caused a disorder in the electron transport of the photosynthesis of algae, and the carbon fixation and assimilation processes were thus damaged. These results indicate that ENR poses a considerable risk to aquatic environments, affects the carbon sinks, and even has an adverse effect on human health.

Toxicity Effects of Combined Mixtures of BDE-47 and Nickel on the Microalgae Phaeodactylum tricornutum (Bacillariophyceae)

Nickel and 2,2’,4,4’-tetrabromodiphenyl ether (BDE-47) are two environmental pollutants commonly and simultaneously present in aquatic systems. Nickel and BDE-47 are individually toxic to various aquatic organisms. However, their toxicity mechanisms are species-dependent, and the toxic effects of combined mixtures of BDE-47 and nickel have not yet been investigated. The present study investigated the toxic effects of combined mixtures of BDE-47 and nickel in the diatom Phaeodactylum tricornutum. BDE-47 and nickel mixtures significantly decreased cell abundance and photosynthetic efficiency, while these cells’ reactive oxygen species (ROS) production significantly increased. The EC₅₀-72 h for BDE-47 and mixtures of BDE-47 and nickel were 16.46 ± 0.93 and 1.35 ± 0.06 mg/L, respectively. Thus, combined mixtures of the two pollutants enhance their toxic effects. Interactions between BDE-47 and nickel were evaluated, revealing synergistic interactions that contributed to toxicity in P. tricornutum. Moreover, transcriptomic analyses revealed photosynthesis, nitrogen metabolism, the biosynthesis of amino acids, the biosynthesis of secondary metabolites, oxoacid metabolism, organic acid metabolism, carboxylic acid metabolism, and oxidation-reduction processes were considerably affected by the mixtures. This study provides evidence for the mechanisms of toxicity from combined BDE-47 and nickel exposure while also improving our understanding of the ecological risks of toxic chemicals on microalgae.

Integrative Transcriptome and Metabolome Profiles Reveal Common and Unique Pathways Involved in Seed Initial Imbibition Under Artificial and Natural Salt Stresses During Germination of Halophyte Quinoa

Salt stress is a major environmental factor that seriously restricts quinoa seed germination. However, the key regulatory mechanisms underlying the effect of salt stress on the initial imbibition stage of quinoa seeds are unclear. In this study, dry seeds (0 h) and imbibed (8 h) seeds with 450 mM NaCl (artificial salt) and 100% brackish water of Yellow River Estuary (BW, natural salt) were used to assess the key salt responses based on germination, transcriptome, and metabolome analyses. The results indicated that the capacity of germinating seeds to withstand these two salt stresses was similar due to the similarities in the germination percentage, germination index, mean germination time, and germination phenotypes. Combined omics analyses revealed that the common and unique pathways were induced by NaCl and BW. Starch and sucrose metabolism were the only commonly enriched pathways in which the genes were significantly changed. Additionally, amino sugar and nucleotide sugar metabolism, and ascorbate and aldarate metabolism were preferably enriched in the NaCl group. However, glutathione metabolism tended to enrich in the BW group where glutathione peroxidase, peroxiredoxin 6, and glutathione S-transferase were significantly regulated. These findings suggest that the candidates involved in carbohydrate metabolism and antioxidant defense can regulate the salt responses of seed initial imbibition, which provide valuable insights into the molecular mechanisms underlying the effect of artificial and natural salt stresses.

Effect of application of iron (Fe) and α-ketoglutaric acid on growth, photosynthesis, and Fe content in fragrant rice seedlings

At a three-leaf stage, two Fe treatments [0 mg kg-1 (Fe-) and 20 mg·kg-1 (Fe+) in the form of FeCl3] were used in the soil of the pot and then two concentrations of α-ketoglutaric acid [0 mg L-1 (A-) and 50 mg L-1 (A+)] were sprayed to the rice plants of Meixiangzhan and Yuxiangyouzhan cultivars. We showed that seedlings exhibited an increased length and fresh and dry mass of shoots and roots with treatments Fe+A- and Fe-A+, as well as the Fe content increased greatly. Both treatments increased the morphological characteristic values of roots and promoted photosynthesis. Interestingly, Fe+A+ notably affected the photosynthesis of fragrant rice seedlings; however, it exerted no significant differences on other parameters. Overall, Fe and α-ketoglutaric acid had the potential for improving the growth of fragrant rice seedlings. The interaction between Fe and α-ketoglutaric acid regulated photosynthesis in seedling leaves, which provided evidence for further improvement of rice cultivation.

The phytotoxicity of exposure to two polybrominated diphenyl ethers (BDE47 and BDE209) on photosynthesis and the response of the hormone signaling and ROS scavenging system in tobacco leaves

To reveal the response and adaptative mechanism of plants to the organic pollutants PBDEs, physiological and transcriptomic techniques were used to study the effects of exposure to BDE47 and BDE209 on tobacco (Nicotiana tabacum L.) plant growth, physiological function and response of key genes. Exposure to both BDE47 and BDE209 inhibited the growth of tobacco plants. The number of down-regulated DEGs following exposure to BDE47 was significantly higher than that following exposure to BDE209. Enrichment analysis using the KEGG showed that BDE47 and BDE209 primarily affected tobacco leaf photosynthesis-antenna proteins, photosynthesis, plant hormone signal transduction and α-linolenic acid metabolism. BDE47 primarily inhibits the synthesis of Chl a, and BDE209 has a more significant impact on Chl b. Most photosynthesis-related DEGs were concentrated in PSII and PSI; the number of down-regulated DEGs in PSI was significantly higher than that in PSII, and the range in which the PSI activity was reduced was also higher than that of PSII, i.e., PSII and PSI (particularly PSI) were sensitive to the effects of exposure to BDE47 and BDE209 on photosynthesis. The increase of the ratio of regulatory energy dissipation played an important protective role in alleviating the photoinhibition of PSII. Exposure to BDE47 and BDE209 can lead to the accumulation of ROS in tobacco leaves, but correspondingly, the activities of antioxidant enzymes SOD, POD, CAT, APX and GPX and the up-regulated expression of their coding genes play an important role in preventing excessive oxidative damage. Exposure to BDE47 and BDE209 promoted the up-regulation of gene expression related to Pro synthesis. In particular, the Pro synthetic process of the Orn pathway was promoted. Exposure to BDE47 and BDE209 induced the up-regulated expression of genes related to the synthesis of ABA and JA, promoted the synthesis of ABA and JA, and activated ABA and JA signal transduction pathways. In conclusion, both BDE47 and BDE209 inhibit the synthesis of chlorophyll and hinder the process of light energy capture and electron transfer in tobacco leaves. BDE47 was more toxic than BDE209. However, tobacco leaves can also adapt to BDE47 and BDE209 by regulating the antioxidant system, accumulating Pro and initiating the hormone signal transduction process. The results of this study provide a theoretical basis for the phytotoxicity mechanism of PBDEs.

Defining key metabolic roles in osmotic adjustment and ROS homeostasis in the recretohalophyte Karelinia caspia under salt stress

The recretohalophyte Karelinia caspia is of forage and medical value and can remediate saline soils. We here assess the contribution of primary/secondary metabolism to osmotic adjustment and ROS homeostasis in Karelinia caspia under salt stress using multi-omic approaches. Computerized phenomic assessments, tests for cellular osmotic changes and lipid peroxidation indicated that salt treatment had no detectable physical effect on K. caspia. Metabolomic analysis indicated that amino acids, saccharides, organic acids, polyamine, phenolic acids, and vitamins accumulated significantly with salt treatment. Transcriptomic assessment identified differentially expressed genes closely linked to the changes in above primary/secondary metabolites under salt stress. In particular, shifts in carbohydrate metabolism (TCA cycle, starch and sucrose metabolism, glycolysis) as well as arginine and proline metabolism were observed to maintain a low osmotic potential. Chlorogenic acid/vitamin E biosynthesis was also enhanced, which would aid in ROS scavenging in the response of K. caspia to salt. Overall, our findings define key changes in primary/secondary metabolism that are coordinated to modulate the osmotic balance and ROS homeostasis to contribute to the salt tolerance of K. caspia.