Comparative Transcriptome Analysis between Low- and High-Cadmium-Accumulating Genotypes of Pakchoi (Brassica chinensis L.) in Response to Cadmium Stress

Integration of comparative cytology, ionome, transcriptome and metabolome provide a basic framework for the response of foxtail millet to Cd stress

Apart from directly affecting the growth and development of crops, Cd in the soil can easily enter the human body through the food chain and pose a threat to human health. Therefore, understanding the toxicity of Cd to specific crops and the molecular mechanisms of their response to Cd is essential. In this study, hydroponic experiments were utilized to study the response of foxtail millet to Cd stress through phenotypic investigation, enzyme activity determination, ultrastructure, ionome, transcriptome and metabolome. With the increase in cadmium concentration, both the growth and photosynthetic capacity of foxtail millet seedlings are severely inhibited. The ultrastructure of cells is damaged, cells are deformed, chloroplasts swell and disappear, and cell walls thicken. Cd stress affects the absorption, transport, and redistribution of beneficial metal ions in the seedlings. Multi-omics analysis reveals the crucial roles of glycolysis, glutathione metabolism and phenylpropanoid and lignin biosynthesis pathways in Cd detoxification via energy metabolism, the antioxidant system and cell wall changes. Finally, a schematic diagram of foxtail millet in response to Cd stress was we preliminarily drew. This work provides a basic framework for further revealing the molecular mechanism of Cd tolerance in foxtail millet.

Sulfate-reducing bacteria block cadmium and lead uptake in rice by regulating sulfur metabolism

AIM

This study was dedicated to investigating the role of sulfur metabolic processes in sulfate-reducing bacteria in plant resistance to heavy metal contamination.

METHODS AND RESULTS

We constructed sulfate-reducing bacterial communities based on the functional properties of sulfate-reducing strains and then screened out the most effective sulfate-reducing bacterial community SYN1, that prevented Cd and Pb uptake in rice through a hydroponic experiment. This community lowered Cd levels in the roots and upper roots by 36.60% and 39.88%, respectively, and Pb levels by 35.96% and 51.54%. We also compared two treatment groups, inoculated with SYN1 and exogenously added GSH, and found that both enhanced the antioxidant response of the plants, increased the lignin and GSH contents and the expression of genes related to the phenylpropane biosynthesis pathway (OsCAD, Os4CL, OsCOMT, OsPOD, OsC3H, and OsPAL), and decreased the expression of heavy metal transporter genes (OsHMA2, OsIRT1) expression. There were no significant differences between the two treatments.

CONCLUSIONS

Sulfate-reducing bacteria produce GSH through the sulfur assimilation pathway, and GSH can directly chelate heavy metals or enhance plant antioxidant enzyme activities and regulate processes such as the uptake and translocation of heavy metals, thus enhancing plant resistance to heavy metal toxicity.

SpbZIP60 confers cadmium tolerance by strengthening the root cell wall compartmentalization in Sedum plumbizincicola

Cadmium (Cd) is a prominent heavy metal pollutant that inhibits plant growth and poses risks to human health. Sedum plumbizincicola, as a Cd/Zn/Pb hyperaccumulator species, exhibits robust resistance to heavy metals and effective enrichment capacities. In our previous study, overexpressing SpbZIP60 in Arabidopsis enhanced Cd tolerance; however, the underlying the molecular mechanism remains to be elucidated. Here, we identified SpbZIP60 as a representative Cd stress response factor with nuclear localization and transcriptional activation activity. SpbZIP60 underwent conservative splicing in response to endoplasmic reticulum (ER) stress, while its response to Cd stress is independent of the ER stress-mediated unfolded protein response pathway. Overexpression of SpbZIP60 in S. alfredii increased the Cd tolerance and antioxidant activity. Furthermore, SpbZIP60 increased the content of cell wall components and thickened cell wall under Cd stress. Transcriptome analysis indicated a significant enrichment of differentially expressed genes within the phenylpropanoid metabolism pathway. Besides, the binding of SpbZIP60 to the promoter region of SpBglu resulted in the activation of gene expression, thereby enhancing the process of lignin deposition. Collectively, our results elucidated a molecular regulatory model in which SpbZIP60 increased the thickness of the root cell wall to impede Cd entry into the cell, consequently improving Cd tolerance.

Unravelling the mechanisms of PFAS toxicity to submerged macrophytes and epiphytic biofilms at metabolic and molecular levels

Per- and poly-fluoroalkyl substances (PFAS) are an emerging class of persistent organic pollutants that are widespread in aquatic ecosystems and pose a serious threat to aquatic organisms. It is thus crucial to explore the toxicity mechanisms of PFAS to submerged macrophytes and biofilms. In this study, Vallisneria natans (V. natans) was exposed to environmentally relevant concentrations of perfluorooctanoic acid (PFOA) and perfluorooctane sulphonate (PFOS). Results showed that PFAS induced the excessive production of reactive oxygen species, triggering antioxidant responses. V. natans exhibited an improved stress tolerance by altering the biosynthesis of several plant secondary metabolites and the histidine, arginine, proline pathways in response to PFAS exposure. Moreover, PIP1-1, PIP2-2, SLAH1 and SLAH2 genes were upregulated, indicating the activation of aquaporins and slow-type anion channels. The uptake of PFOA and PFOS by V. natans was 41.74 % and 52.31 %, respectively. Notably, PFAS bound to functional proteins (GSTF10), promoting the detoxification of plants. Exposure to PFAS also altered the structure of biofilms by inducing the synthesis of large amounts of polysaccharides and proteins. The diversity and richness of the microbial community within periphytic biofilms changed significantly. These results provide a comprehensive description of the responses of aquatic plants and periphytic biofilms to PFAS and the removal mechanism of PFAS, contributing to the environmental risk assessments and removal of PFAS in aquatic ecosystems.

Mechanisms of Cadmium stress response in watermelon: Insights from physiological, transcriptomic, and metabolic analyses

Cadmium (Cd) contamination of soil may lead to Cd stress for plants, which significantly hinders plant growth and development, posing a risk to human health through the consumption of Cd-contaminated foods. Watermelon (Citrullus lanatus), a widely consumed fruit, is particularly affected by Cd stress globally, yet the mechanisms underlying its response are not well understood. Here, we subjected watermelon seedlings to simulated Cd stress treatment and explored the physiological, transcriptomic, and metabolic response. Our findings revealed that Cd stress treatment led to increased accumulation of reactive oxygen species (ROS) in watermelon leaves. Transcriptome sequencing unveiled a multitude of osmotic and oxidative stress-responsive genes, including peroxidase (POD), MYB, voltage-dependent anion channel (SLAC1), and ABC transporter. KEGG enrichment analysis highlighted the predominant enrichment of Cd stress-responsive genes in pathways such as glutathione (GSH) metabolism, MAPK signaling, and biosynthesis of secondary metabolites. Within the GSH metabolism pathway, several glutathione S-transferase (GST) genes were up-regulated, alongside phytochelatin synthetase (PCS) genes involved in phytochelatin synthesis. In the MAPK signaling pathway, genes associated with ABA and ethylene signal transduction showed up-regulation following Cd stress. Metabolomic analysis demonstrated that Cd stress enhanced the production of amino acids, phenolamines, and esters. Overall, our study elucidates that watermelon responds to Cd stress by activating its antioxidant system, GSH metabolism pathway, MAPK signal pathway, and biosynthesis of key metabolites. These findings offer valuable insights for the remediation of heavy metal pollution in soil affecting plant life.

The effect of cadmium on soil and plants, and the influence of Serendipita indica (Piriformospora indica) in mitigating cadmium stress

Due to environmental pollution, the risk of cadmium stress for crops is soaring, so researchers are exploring inexpensive solutions to enhance cultivated crops in contaminated soil. Using microorganisms to reduce cadmium risk has been one of the most effective strategies in recent decades. Serendipita indica (Piriformospora indica) is one of the best endophyte fungi that, in addition to reducing heavy metal stress for crops, can significantly reduce the threat of other abiotic stresses. As part of this research, cadmium in soil has been investigated, as well as its effects on plants' morphophysiological and biochemical characteristics. The present review has also attempted to identify the role of Serendipita indica in improving the growth and performance of crops, as well as its possible effect on reducing the risk of cadmium. The results showed that Serendipita indica enhance the growth and productivity of plants in contaminated environments by improving soil quality, reducing cadmium absorption, improving the activity of antioxidant enzymes and secondary metabolites, raising water and mineral absorption, and altering morphophysiological structures.

Association between plant microbiota and cadmium uptake under the influence of microplastics with different particle sizes

Plant microbiota are an important factor impacting plant cadmium (Cd) uptake. However, little is known about how plant microbiota affects the Cd uptake by plants under the influence of microplastics (MPs) with different particle sizes. In this study, bacterial structure and assembly in the rhizosphere and endosphere in pakchoi were analyzed by amplicon sequencing of 16S rRNA genes under the influence of different particle sizes of polystyrene microplastics (PS-MPs) combined with Cd treatments. Results showed that there were no significant differences observed in the shoot endophytes among different treatments. However, compared to Cd treatment, larger-sized PS-MPs (2 and 20 μm) significantly increased community diversity and altered the structural composition of rhizosphere bacteria and root endophytes, while smaller-sized PS-MPs (0.2 μm) did not. Under the treatment of larger-sized PS-MPs, the niche breadth of rhizosphere bacteria and root endophytes were significantly increased. And larger-sized PS-MPs also maintained stability and complexity of bacterial co-occurrence networks, while smaller-sized PS-MPs reduced them. Furthermore, compared to Cd treatment, the addition of larger particle size PS-MPs decreased the proportion of homogeneous section, while increased the proportion of drift in root endophytic bacterial community assembly. The role of larger-sized MPs in the community assembly of rhizosphere bacteria was opposite. Using random forest and structural equation models, the study found that larger-sized PS-MPs can promote the colonization of specific bacterial taxa, such as Brevundimonas, AKAU4049, SWB02, Ellin6055, Porphyrobacter, Sphingorhabdus, Rhodobacter, Erythrobacter, Devosia and some other bacteria belonging to Alphaproteobacteria, in the rhizosphere and root endosphere. The colonization of these taxa can may induce the formation of biofilms in the roots, immobilize heavy metals through oxidation processes, and promote plant growth, thereby reducing Cd uptake by pakchoi. The findings of this study provide important insights into the microbial mechanisms underlying the influence of MPs with different particle sizes on plant Cd uptake.

Comparative transcriptome analysis of vegetable soybean grain discloses genes essential for grain quality

BACKGROUND

Vegetable soybean is an important vegetable crop in world. Seed size and soluble sugar content are considered crucial indicators of quality in vegetable soybean, and there is a lack of clarity on the molecular basis of grain quality in vegetable soybean.

RESULTS

In this context, we performed a comprehensive comparative transcriptome analysis of seeds between a high-sucrose content and large-grain variety (Zhenong 6, ZN6) and a low-sucrose content and small-grain variety (Williams 82, W82) at three developmental stages, i.e. stage R5 (Beginning Seed), stage R6 (Full Seed), and stage R7 (Beginning Maturity). The transcriptome analysis showed that 17,107 and 13,571 differentially expressed genes (DEGs) were identified in ZN6 at R6 (vs. R5) and R7 (vs. R6), respectively, whereas 16,203 and 16,032 were detected in W82. Gene expression pattern and DEGs functional enrichment proposed genotype-specific biological processes during seed development. The genes participating in soluble sugar biosynthesis such as FKGP were overexpressed in ZN6, whereas those responsible for lipid and protein metabolism such as ALDH3 were more enhanced in W82, exhibiting different dry material accumulation between two genotypes. Furthermore, hormone-associated transcriptional factors involved in seed size regulation such as BEH4 were overrepresented in ZN6, exhibiting different seed size regulation processes between two genotypes.

CONCLUSIONS

Herein, we not only discovered the differential expression of genes encoding metabolic enzymes involved in seed composition, but also identified a type of hormone-associated transcriptional factors overexpressed in ZN6, which may regulate seed size and soluble content. This study provides new insights into the underlying causes of differences in the soybean metabolites and appearance, and suggests that genetic data can be used to improve its appearance and textural quality.

Screening of low-Cd-accumulating and Cd-remediating oilseed rape varieties using a newly indicator system for risk management of Cd-contaminated agricultural land

Although oilseed rape is frequently used as an alternative planting crop in the phytoremediation of cadmium (Cd)-contaminated agricultural land, methods for screening excellent oilseed rape varieties in this regard are inadequate. Herein, we developed a screening method that incorporates Cd accumulation, distribution, and removal, economic output, adaptability to Cd-contaminated agricultural land, and trace element variation. A Cd-adaptability index (Cd-AI) based on 10 agronomic traits was used to measure the adaptability of varieties to Cd-contaminated agricultural land. Moreover, to simplify the evaluation of adaptability, yield, biomass, and pod number with high weightings were selected to construct a discriminant function for Cd-contaminated agricultural land adaptability (correctly classified 94.20%). In a 2 year field trial, we evaluated 225 oilseed rape varieties, among which we identified two promising low-Cd-accumulating and two Cd-remediating varieties. For the low-Cd-accumulating varieties (HuYou17 and DeXingYou558), we obtained grain bioaccumulation factor (BAF) values of 0.07 and 0.08, BAFsoil-stalk values of <1, and economic outputs of RMB 25,054 and 32,292 yuan hm-2, respectively. Similarly, the Cd-remediating varieties (ZaoZa8 and YuYou61) were characterized by BAFsoil-stalk values of 4.65 and 3.61, BAFsoil-grain values of 0.16 and 0.16, Cd removals of 69.02 and 58.25 g hm-2, and economic outputs of RMB 31,189 and 24,962 yuan hm-2, respectively. Compared with the control variety, we detected lower uptakes of multiple trace elements (3-43%) in the low-Cd-accumulating varieties, whereas the Cd-remediating varieties were characterized by 15.40% and 8.30% increases in the accumulation of magnesium and zinc, respectively. Our findings augment the evaluation indices used for evaluating oilseed rape varieties and provide valuable insights from the perspectives of varietal screening and promotional application. The effective varieties identified have application potential for safe production and the remediation of agricultural land without interrupting annual agricultural production, and provide an economically sustainable approach for the utilization of Cd-contaminated agricultural land.

Comparative transcriptome analysis between two different cadmium-accumulating genotypes of soybean (Glycine max) in response to cadmium stress

BACKGROUND

Cadmium (Cd) is extremely toxic and non-essential for plants. Different soybean varieties differ greatly in their Cd accumulation ability, but little is known about the underlying molecular mechanisms.

RESULTS

Here, we performed transcriptomic analysis using Illumina pair-end sequencing on root tissues from two soybean varieties (su8, high-Cd-accumulating (HAS) and su7, low Cd-accumulating (LAS)) grown with 0 or 50 μM CdSO4. A total of 18.76 million clean reads from the soybean root samples were obtained after quality assessment and data filtering. After Cd treatment, 739 differentially expressed genes (DEGs; 265 up and 474 down) were found in HAS; however, only 259 DEGs (88 up and 171 down) were found in LAS, and 64 genes were same between the two varieties. Pathway enrichment analysis suggested that after cadmium treatment, the DEGs between LAS and HAS were mainly enriched in glutathione metabolism and plant-pathogen interaction pathways. KEGG analysis showed that phenylalanine metabolism responding to cadmium stress in LAS, while ABC transporters responding to cadmium stress in HAS. Besides we found more differential expressed heavy metal transporters such as ABC transporters and zinc transporters in HAS than LAS, and there were more transcription factors differently expressed in HAS than LAS after cadmium treatment in two soybean varieties, eg. bHLH transcription factor, WRKY transcription factor and ZIP transcription factor.

CONCLUSIONS

Findings from this study will shed new insights on the underlying molecular mechanisms behind the Cd accumulation in soybean.

Enhancing soil health to minimize cadmium accumulation in agro-products: the role of microorganisms, organic matter, and nutrients

Agro-products accumulate Cd from the soil and are the main source of Cd in humans. Their use must therefore be minimized using effective strategies. Large soil beds containing low-to-moderate Cd-contamination are used to produce agro-products in many developing countries to keep up with the demand of their large populations. Improving the health of Cd-contaminated soils could be a cost-effective method for minimizing Cd accumulation in crops. In this review, the latest knowledge on the physiological and molecular mechanisms of Cd uptake and translocation in crops is presented, providing a basis for developing advanced technologies for producing Cd-safe agro-products. Inoculation of plant growth-promoting rhizobacteria and arbuscular mycorrhizal fungi, application of organic matter, essential nutrients, beneficial elements, regulation of soil pH, and water management are efficient techniques used to decrease soil Cd bioavailability and inhibiting the uptake and accumulation of Cd in crops. In combination, these strategies for improving soil health are environmentally friendly and practical for reducing Cd accumulation in crops grown in lightly to moderately Cd-contaminated soil.

Exploration the interaction of cadmium and copper toxic effects in pakchoi (Brassica chinensis L) roots through combinatorial transcriptomic and weighted gene co-expression network analysis

The interaction between cadmium(Cd) and copper(Cu) during combined pollution can lead to more complex toxic effects on humans and plants.However, there is still a lack of sufficient understanding regarding the types of interactions at the plant molecular level and the response strategies of plants to combined pollution. To assess this, we investigated the phenotypic and transcriptomic patterns of pakchoi (Brassica chinensis L) roots in response to individual and combined pollution of Cd and Cu. The results showed that compared to single addition, the translocation factor of heavy metals in roots significantly decreased (p < 0.05) under the combined addition, resulting in higher accumulation of Cd and Cu in the roots. Transcriptomic analysis of pakchoi roots revealed that compared to single pollution, there were 312 and 1926 differentially expressed genes (DEGs) specifically regulated in the Cd2Cu20 and Cd2Cu100 combined treatments, respectively. By comparing the expression of these DEGs among different treatments, we found that the combined pollution of Cd and Cu mainly affected the transcriptome of the roots in an antagonistic manner. Enrichment analysis indicated that pakchoi roots upregulated the expression of genes involved in glucosetransferase activity, phospholipid homeostasis, proton transport, and the biosynthesis of phenylpropanoids and flavonoids to resist Cd and Cu combined pollution. Using weighted gene co-expression network analysis (WGCNA), we identified hub genes related to the accumulation of Cd and Cu in the roots, which mainly belonged to the LBD, thaumatin-like protein, ERF, MYB, WRKY, and TCP transcription factor families. This may reflect a transcription factor-driven trade-off strategy between heavy metal accumulation and growth in pakchoi roots. Additionally, compared to single metal pollution, the expression of genes related to Nramp, cation/H+ antiporters, and some belonging to the ABC transporter family in the pakchoi roots was significantly upregulated under combined pollution. This could lead to increased accumulation of Cd and Cu in the roots. These findings provide new insights into the interactions and toxic mechanisms of multiple metal combined pollution at the molecular level in plants.

Cadmium induced changes in rhizosphere microecology to enhance Cd intake by Ligusticum sinense cv. Chuanxiong

As the most famous and widely used traditional Chinese medicine (TCM), Ligusticum sinense cv. Chuanxiong (L. Chuaniong) has been affected by cadmium (Cd) exceeding with high ability of Cd accumulation. There is relatively little research on Cd absorption and storage process in L. Chuanxiong, which is an important reason for the poor remediation efficiency. Hence, this study takes L. Chuanxiong as the point of penetration to explore how L. Chuanxiong affects rhizobacteria through root exudates to alter soil Cd intake, as well as to explore the migration and storage of Cd in its body with 0.10 (T0), 5.00 (T5), 10.00 (T10) mg/kg Cd contaminations. The results showed that the relative abundance of amino acids and phospholipids secreted from L. Chuanxiong root noticeably increased with increasing Cd levels, which directly activated soil Cd or extremely significantly (P < 0.01) recruited bacteria such as Bacillus, Arthrobacter to indirectly increase Cd availability. Under the interaction of root exudates and rhizobacteria, Cd bioavailability increased by 80.00% in rhizosphere soil and Cd accumulation in L. Chuanxiong increased 5.44-6.65 mg/kg. Cd subcellular distribution analysis demonstrated that Cd was mainly stored in the root (10-fold more than in the leaf), whose Cd content was cytoderm>cytoplasm>organelle in tissues. The sequential extraction results found that non-soluble phosphate and protein-chelated Cd dominated (85.00-90.00%) in the cell, while Cd cheated with alcohol soluble protein, amino acid salts, water-soluble organic acid in cell was minimal (5.50%). The phenomenon indicated that L. Chuanxiong fixed Cd in root (the medical part) with low translocation ability. This study can provide theoretical support for the high-quality production of L. Chuanxiong and other root medical plant in heavy metal influenced sites.

Physiological responses of low- and high-cadmium accumulating Robinia pseudoacacia-rhizobium symbioses to cadmium stress

The role of rhizobia in alleviating cadmium (Cd) stress in woody legumes is still unclear. Therefore, two types of black locust (Robinia pseudoacacia L.) with high and low Cd accumulation abilities were selected from 11 genotypes in China, and the effects of rhizobium (Mesorhizobium huakuii GP1T11) inoculation on the growth, CO2 and H2O gas exchange parameters, Cd accumulation, and the absorption of mineral elements of the high (SX) and low Cd-accumulator (HB) were compared. The results showed that rhizobium-inoculation significantly increased biomass, shoot Cd contents, Cd accumulation, root-to-shoot translocation factor (TF) and the absorption and accumulation of mineral elements in both SX and HB. Rhizobium-inoculation increased chlorophyll a and carotenoid contents, and the intercellular carbon dioxide concentrations in HB plants. Under Cd exposure, the high-accumulator SX exhibited a significant decrease in photosynthetic CO2 fixation (Pn) and an enhanced accumulation of Cd in leaves, but coped with Cd exposure by increasing chlorophyll synthesis, regulating stomatal aperture (Gs), controlling transpiration (Tr), and increasing the absorption and accumulation of mineral elements. In contrast, the low-accumulator HB was more sensitive to Cd exposure despite preferential accumulation of Cd in roots, with decreased chlorophyll and carotenoid contents, but significantly increased root biomass. Compared to the low-accumulator HB, non-inoculated Cd-exposed SX plants had higher chlorophyll contents, and rhizobium-inoculated Cd-exposed SX plants had higher Pn, Tr, and Gs as well as higher levels of P, K, Fe, Ca, Zn, and Cu. In conclusion, the high- and low-Cd-accumulator exhibited different physiological responses to Cd exposure. Overall, rhizobium-inoculation of black locust promoted the growth and heavy metal absorption, providing an effective strategy for the phytoremediation of heavy metal-contaminated soils by this woody legume.

Mechanisms of low cadmium accumulation in crops: A comprehensive overview from rhizosphere soil to edible parts

Cadmium (Cd) is a toxic heavy metal often found in soil and agricultural products. Due to its high mobility, Cd poses a significant health risk when absorbed by crops, a crucial component of the human diet. This absorption primarily occurs through roots and leaves, leading to Cd accumulation in edible parts of the plant. Our research aimed to understand the mechanisms behind the reduced Cd accumulation in certain crop cultivars through an extensive review of the literature. Crops employ various strategies to limit Cd influx from the soil, including rhizosphere microbial fixation and altering root cell metabolism. Additional mechanisms include membrane efflux, specific transport, chelation, and detoxification, facilitated by metalloproteins such as the natural resistance-associated macrophage protein (Nramp) family, heavy metal P-type ATPases (HMA), zinc-iron permease (ZIP), and ATP-binding cassette (ABC) transporters. This paper synthesizes differences in Cd accumulation among plant varieties, presents methods for identifying cultivars with low Cd accumulation, and explores the unique molecular biology of Cd accumulation. Overall, this review provides a comprehensive resource for managing agricultural lands with lower contamination levels and supports the development of crops engineered to accumulate minimal amounts of Cd.

Exogenous titanium dioxide nanoparticles alleviate cadmium toxicity by enhancing the antioxidative capacity of Tetrastigma hemsleyanum

Nanotechnology is one of the most recent approaches employed to defend plants against both biotic and abiotic stress including heavy metals such as Cadmium (Cd). In this study, we evaluated the effects of titanium dioxide (TiO2) nanoparticles (TiO2 NPs) in alleviating Cd stress in Tetrastigma hemsleyanum Diels et Gilg. Compared with Cd treatment, TiO2 NPs decreased leaf Cd concentration, restored Cd exposure-related reduction in the biomass to about 69% of control and decreased activities of antioxidative enzymes. Integrative analysis of transcriptome and metabolome revealed 325 differentially expressed genes associated with TiO2 NP treatment, most of which were enriched in biosynthesis of secondary metabolites. Among them, the flavonoid and phenylpropanoid biosynthetic pathways were significantly regulated to improve the growth of T. hemsleyanum when treated with Cd. In the KEGG Markup Language (KGML) network analysis, we found some commonly regulated pathways between Cd and Cd+TiO2 NP treatment, including phenylpropanoid biosynthesis, ABC transporters, and isoflavonoid biosynthesis, indicating their potential core network positions in controlling T. hemsleyanum response to Cd stress. Overall, our findings revealed a complex response system for tolerating Cd, encompassing the transportation, reactive oxygen species scavenging, regulation of gene expression, and metabolite accumulation in T. hemsleyanum. Our results indicate that TiO2 NP can be used to reduce Cd toxicity in T. hemsleyanum.

Role of microRNAs and their putative mechanism in regulating potato (Solanum tuberosum L.) life cycle and response to various environmental stresses

The exponentially increasing population and the demand for food is inextricably linked. This has shifted global attention to improving crop plant traits to meet global food demands. Potato (Solanum tuberosum L.) is a major non-grain food crop that is grown all over the world. Currently, some of the major global potato research work focuses on the significance of microRNAs (miRNAs) in potato. miRNAs are a type of non-coding RNAs that regulate the gene expression of their target mRNA genes by cleavage and/or their translational inhibition. This suggests an essential role of miRNAs in a multitude of plant biological processes, including maintenance of genome integrity, plant growth, development and maturation, and initiation of responses to various stress conditions. Therefore, engineering miRNAs to generate stress-resistant varieties of potato may result in high yield and improved nutritional qualities. In this review, we discuss the potato miRNAs specifically known to play an essential role in the various stages of the potato life cycle, conferring stress-resistant characteristics, and modifying gene expression. This review highlights the significance of the miRNA machinery in plants, especially potato, encouraging further research into engineering miRNAs to boost crop yields and tolerance towards stress.

Effects of different cellular and subcellular characteristics on the atmospheric Pb uptake, distribution and morphology in Tillandsia usneoides leaves

Lead (Pb) is a widespread highly toxic and persistent environmental pollutant. Plant leaves play a key role in accumulating atmospheric Pb, but its distribution in different cells and subcellular structures and the factors affecting it have been little studied. Here, Tillandsia usneoides, an indicator plant for atmospheric heavy metals, was treated with an aerosol generation device to analyze Pb contents in different cells (three types of cells in leaf surface scales, epidermal cells, mesophyll cells, vascular bundle cells), subcellular structures (cell wall, cell membrane, vacuoles, and organelles) and cell wall components (pectin, hemicellulose 1 and 2, and cellulose). Results show the different cells of T. usneoides leaves play distinct roles in the process of Pb retention. The outermost wing cells are structures that capture external pollutants, while mesophyll cells, as the aggregation site after material transport, ring cells, disc cells, epidermal cells, and vascular cells are material transporters. Pb was only detected in the cell wall and pectin, indicating the cell wall was the dominant subcellular structure for Pb retention, while pectin was the main component affecting Pb retention. FTIR analysis of cell wall components indicated the esterified carboxyl (CO) functional group in pectin may function in absorbing Pb. Pb entered leaf cells mainly in the form of low toxicity and activity to enhance its resistance.

Insights into the reduction of methylmercury accumulation in rice grains through biochar application: Hg transformation, isotope fractionation, and transcriptomic analysis

Methylmercury (MeHg), a potent neurotoxin, easily moves from the soil into rice plants and subsequently accumulates within the grains. Although biochar can reduce MeHg accumulation in rice grains, the precise mechanism underlying biochar-mediated responses to mercury (Hg) stress, specifically regarding MeHg accumulation in rice, remains poorly understood. In the current study, we employed a 4% biochar amendment to remediate Hg-contaminated paddy soil, elucidate the impacts of biochar on MeHg accumulation through a comprehensive analysis involving Hg isotopic fractionation and transcriptomic analyses. The results demonstrated that biochar effectively lowered the levels of MeHg in paddy soils by decreasing bioavailable Hg and microbial Hg methylation. Furthermore, biochar reduced the uptake and translocation of MeHg in rice plants, ultimately leading to a reduction MeHg accumulation in rice grains. During the process of total mercury (THg) uptake, biochar induced a more pronounced negative isotope fractionation magnitude, whereas the effect was less pronounced during the upward transport of THg. Conversely, biochar caused a more pronounced positive isotope fractionation magnitude during the upward transport of MeHg. Transcriptomics analyses revealed that biochar altered the expression levels of genes associated with the metabolism of cysteine, glutathione, and metallothionein, cell wall biogenesis, and transport, which possibly enhance the sequestration of MeHg in rice roots. These findings provide novel insights into the effects of biochar application on Hg transformation and transport, highlighting its role in mitigating MeHg accumulation in rice.

Molecular-Assisted Breeding of Cadmium Pollution-Safe Cultivars

Cadmium (Cd) contamination in edible agricultural products, especially in crops intended for consumption, has raised worldwide concerns regarding food safety. Breeding of Cd pollution-safe cultivars (Cd-PSCs) is an effective solution to preventing the entry of Cd into the food chain from contaminated agricultural soil. Molecular-assisted breeding methods, based on molecular mechanisms for cultivar-dependent Cd accumulation and bioinformatic tools, have been developed to accelerate and facilitate the breeding of Cd-PSCs. This review summarizes the recent progress in the research of the low Cd accumulation traits of Cd-PSCs in different crops. Furthermore, the application of molecular-assisted breeding methods, including transgenic approaches, genome editing, marker-assisted selection, whole genome-wide association analysis, and transcriptome, has been highlighted to outline the breeding of Cd-PSCs by identifying critical genes and molecular biomarkers. This review provides a comprehensive overview of the development of Cd-PSCs and the potential future for breeding Cd-PSC using modern molecular technologies.

Cleaner production of Chinese cabbage by intercropping from Cd contaminated soil: Effects of hyperaccumulator variety and planting strip width

The utilization of Cd-contaminated soil in vegetable crop production can lighten the food crisis and improve the soil environmental resilience. Intercropping is a reliable technology in safety production from contaminated soil. A field-scale experiment was carried out to unravel how plant species and pattern affect the growth and Cd uptake of Chinese cabbage from Cd contaminated land. Among all the intercropping systems designed in this study, one row of Chinese cabbage intercropping with one row of Solanum nigrum L. is the best planting mode (high yields (2.78 kg/m2) and low Cd accumulation (0.02 mg/kg) of Chinese cabbage). Combined with the in-depth joint analysis of diverse soil physicochemical features (soil nutrient characteristics and microbial community structure), biomass yield and quality, and soil microbiological properties, we elaborated that two measures (screening hyperaccumulation types and controlling planting strip width) were the major factors in determining the growth of the aboveground and underground parts of Chinese cabbage respectively, thus directly regulating the application effectiveness of intercropping technology. The intertwined mechanisms (interspecific and intraspecific relationship) of different intercropping systems are summarized, which include better utilization of space, light and other resources in the aboveground part, bioavailability of nutrient, drive of soil bacteria and alleviated soil Cd stress in the underground part, etc. Our research outputs indicate the effectiveness and feasibility of intercropping can be improved by optimizing the streamline configuration and plant mode, which provide theory of reference and practical evidence for warranting the food safety and agricultural soil remediation simultaneously.

Transcriptomics combined with physiological analysis reveals the mechanism of cadmium uptake and tolerance in Ligusticum chuanxiong Hort. under cadmium treatment

Introduction

Ligusticum chuanxiong Hort. is a widely used medicinal plant, but its growth and quality can be negatively affected by contamination with the heavy metal cadmium (Cd). Despite the importance of understanding how L. chuanxiong responds to Cd stress, but little is currently known about the underlying mechanisms.

Methods

To address this gap, we conducted physiological and transcriptomic analyses on L. chuanxiong plants treated with different concentrations of Cd2+ (0 mg·L-1, 5 mg·L-1, 10 mg·L-1, 20 mg·L-1, and 40 mg·L-1).

Results

Our findings revealed that Cd stress inhibited biomass accumulation and root development while activating the antioxidant system in L. chuanxiong. Root tissues were the primary accumulation site for Cd in this plant species, with Cd being predominantly distributed in the soluble fraction and cell wall. Transcriptomic analysis demonstrated the downregulation of differential genes involved in photosynthetic pathways under Cd stress. Conversely, the plant hormone signaling pathway and the antioxidant system exhibited positive responses to Cd regulation. Additionally, the expression of differential genes related to cell wall modification was upregulated, indicating potential enhancements in the root cell wall's ability to sequester Cd. Several differential genes associated with metal transport proteins were also affected by Cd stress, with ATPases, MSR2, and HAM3 playing significant roles in Cd passage from the apoplast to the cell membrane. Furthermore, ABC transport proteins were found to be key players in the intravesicular compartmentalization and efflux of Cd.

Discussion

In conclusion, our study provides preliminary insights into the mechanisms underlying Cd accumulation and tolerance in L. chuanxiong, leveraging both physiological and transcriptomic approaches. The decrease in photosynthetic capacity and the regulation of plant hormone levels appear to be major factors contributing to growth inhibition in response to Cd stress. Moreover, the upregulation of differential genes involved in cell wall modification suggests a potential mechanism for enhancing root cell wall capabilities in isolating and sequestering Cd. The involvement of specific metal transport proteins further highlights their importance in Cd movement within the plant.

Multiple insights into lignin-mediated cadmium detoxification in rice (Oryza sativa)

Cadmium (Cd) is readily absorbed by rice and enters the food chain, posing a health risk to humans. A better understanding of the mechanisms of Cd-induced responses in rice will help in developing solutions to reduce Cd uptake in rice. Therefore, this research attempted to reveal the detoxification mechanisms of rice in response to Cd through physiological, transcriptomic and molecular approaches. The results showed that Cd stress restricted rice growth, led to Cd accumulation and H2O2 production, and resulted cell death. Transcriptomic sequencing revealed glutathione and phenylpropanoid were the major metabolic pathways under Cd stress. Physiological studies showed that antioxidant enzyme activities, glutathione and lignin contents were significantly increased under Cd stress. In response to Cd stress, q-PCR results showed that genes related to lignin and glutathione biosynthesis were upregulated, whereas metal transporter genes were downregulated. Further pot experiment with rice cultivars with increased and decreased lignin content confirmed the causal relationship between increased lignin and reduced Cd in rice. This study provides a comprehensive understanding of lignin-mediated detoxification mechanism in rice under Cd stress and explains the function of lignin in production of low-Cd rice to ensure human health and food safety.

Safe Production Strategies for Soil-Covered Cultivation of Morel in Heavy Metal-Contaminated Soils

Morel is a popular edible mushroom with considerable medicinal and economic value which has garnered global popularity. However, the increasing heavy metal (HM) pollution in the soil presents a significant challenge to morels cultivation. Given the susceptibility of morels to HM accumulation, the quality and output of morels are at risk, posing a serious food safety concern that hinders the development of the morel industry. Nonetheless, research on the mechanism of HM enrichment and mitigation strategies in morel remains scarce. The morel, being cultivated in soil, shows a positive correlation between HM content in its fruiting body and the HM content in the soil. Therefore, soil remediation emerges as the most practical and effective approach to tackle HM pollution. Compared to physical and chemical remediation, bioremediation is a low-cost and eco-friendly approach that poses minimal threats to soil composition and structure. HMs easily enriched during morels cultivation were examined, including Cd, Cu, Hg, and Pb, and we assessed soil passivation technology, microbial remediation, strain screening and cultivation, and agronomic measures as potential approaches for HM pollution prevention. The current review underscores the importance of establishing a comprehensive system for preventing HM pollution in morels.

Integrated biochemical and transcriptomic analysis reveals the effects of Burkholderia sp. SRB-1 on cadmium accumulating in Chrysopogon zizanioides L. under Cd stress

Application of plant growth-promoting rhizobacteria plays a vital role in enhancing phytoremediation efficiency. In this study, multiple approaches were employed to investigate the underlying mechanisms of Burkholderia sp. SRB-1 (SRB-1) on elevating Cd uptake and accumulation. Inoculation experiment indicated that SRB-1 could facilitate plant growth and Cd tolerance, as evidenced by the enhanced plant biomass and antioxidative enzymes activities. Cd content in plant shoots and roots increased about 36.56%-39.66% and 25.97%-130.47% assisted with SRB-1 when compared with control. Transcriptomics analysis revealed that SRB-1 upregulated expression of amiE, AAO1-2 and GA2-ox related to auxin and gibberellin biosynthesis in roots. Auxin and gibberellin, as hormone signals, regulated plant Cd tolerance and growth through activating hormone signal transduction pathways, which might also contribute to 67.94% increase of dry weight. The higher expression levels of ATP-binding cassette transporter subfamilies (ABCB, ABCC, ABCD and ABCG) in Chrysopogon zizanioides roots contributed to higher Cd uptake in Cd15 B (323.83 mg kg^-1) than Cd15 (136.28 mg kg^-1). Further, SRB-1 facilitated Cd migration from roots to shoots via upregulating the expression of Nramp, ZIP and HMA families. Our integrative analysis provided a molecular-scale perspective on Burkholderia sp. SRB-1 contributing to C. zizanioides performance.

Hydrogen sulfide alleviates chromium toxicity by promoting chromium sequestration and re-establishing redox homeostasis in Zea mays L

Hydrogen sulfide (H₂S) is a multifunctional gaseous signaling molecule involved in the regulation of Cr stress responses. In the present study, we combined transcriptomic and physiological analyses to elucidate the mechanism underlying the mitigation of Cr toxicity by H₂S in maize (Zea mays L.). We showed that treatment with sodium hydrosulfide (NaHS, a donor of H₂S) partially alleviated Cr-induced growth inhibition. However, Cr uptake was not affected. RNA sequencing suggested that H₂S regulates the expression of many genes involved in pectin biosynthesis, glutathione metabolism, and redox homeostasis. Under Cr stress, NaHS treatment significantly increased pectin content and pectin methylesterase activity; thus, more Cr was retained in the cell wall. NaHS application also increased the content of glutathione and phytochelatin, which chelate Cr and transport it into vacuoles for sequestration. Furthermore, NaHS treatment mitigated Cr-induced oxidative stress by enhancing the capacity of enzymatic and non-enzymatic antioxidants. Overall, our results strongly support that H₂S alleviates Cr toxicity in maize by promoting Cr sequestration and re-establishing redox homeostasis rather than by reducing Cr uptake from the environment.

Microbial extracellular polymeric substances alleviate cadmium toxicity in rice (Oryza sativa L.) by regulating cadmium uptake, subcellular distribution and triggering the expression of stress-related genes

Cadmium (Cd) accumulation in crops causes potential risks to human health. Microbial extracellular polymeric substances (EPS) are a complex mixture of biopolymers that can bind various heavy metals. The present work examined the alleviating effects of EPS on Cd toxicity in rice and its detoxification mechanism. The 100 μM Cd stress hampered the overall plant growth and development, damaged the ultrastructures of both leaf and root cells, and caused severe lipid peroxidation in rice plants. However, applying EPS at a concentration of 100 mg/L during Cd stress resulted in increased biomass, reduced Cd accumulation and transport, and minimized the oxidative damage. EPS application also enhanced Cd retention in the shoot cell walls and root vacuoles, and actively altered the expression of genes involved in cell wall formation, antioxidant defense systems, transcription factors, and hormone metabolism. These findings provide new insights into EPS-mediated mitigation of Cd stress in plants and help us to develop strategies to improve crop yield in Cd-contaminated soils in the future.

Effects of cadmium and copper mixtures on antibiotic resistance genes in rhizosphere soil

The evolvement and development of antibiotic resistance in microorganisms may be influenced by metals; however, it is still unclear how cadmium (Cd) and copper (Cu) combined affect the distribution and presence of antibiotic-resistance genes (ARGs) in rhizosphere soil. The aims of this research were to (1) compare the distribution patterns of bacterial communities and ARGs in response to the effects of Cd and Cu both separately and combined; (2) explore the possible mechanisms underlying the variation in soil bacterial communities and ARGs in addition to the combined effects of Cd, Cu, and various environmental variables (nutrients, pH, etc.); and (3) provide a reference for assessing the risks of metals (Cd and Cu) and ARGs. The findings showed that the multidrug resistance genes acrA and acrB and the transposon gene intI-1 were present in high relative abundance in bacterial communities. Cadmium and Cu had a substantial interaction effect on the abundance of acrA, whereas Cu had a notable main effect on the abundance of intI-1. According to the network analysis, the strong links between bacterial taxa and specific ARGs revealed that most ARGs were hosted by Proteobacteria, Actinobacteria, and Bacteroidetes. According to structural equation modeling, Cd had a larger effect on ARGs than Cu. Compared to previous analyses of ARGs, bacterial community diversity had little effect on ARGs in this study. Overall, the results may have important consequences for determining the possible hazard of soil metals and extend the understanding of how Cd and Cu co-select ARGs in rhizosphere soils.

Differentially-expressed genes related to glutathione metabolism and heavy metal transport reveals an adaptive, genotype-specific mechanism to Hg2+ exposure in rice (Oryza sativa L.)

Rice consumption is an essential cause of mercury (Hg) exposure for humans in Asia. However, the mechanism of Hg transport and accumulation in rice plants (Oryza sativa L.) remains unclear. Here, rice genotypes with contrasting Hg uptake and translocation abilities, i.e. H655 (high Hg-accumulator) and H767 (low Hg-accumulator), were selected from 261 genotypes. Through comparative physiological and transcriptome analyses, we investigated the processes responsible for the relationship between Hg accumulation, transport and tolerance. The results showed significant stimulation of antioxidative metabolism, particularly glutathione (GSH) accumulation, and up-regulated expression of regulatory genes of glutathione metabolism for H655, but not for H767. In addition, up-regulated expression of GSH S-transferase (GST) and OsPCS1 in H655 that catalyzes the binding of Hg and GSH, enhances the Hg detoxification capacity, while high-level expression of YSL2 in H655 enhances the transport ability for Hg. Conclusively, Hg accumulation in rice is a consequence of enhanced expression of genes related to Hg binding with GSH and Hg transport. With these results, the present study contributes to the selection of rice genotypes with limited Hg accumulation and to the mitigation of Hg migration in food chains thereby enhancing nutritional safety of Hg-polluted rice fields.

Transcriptomic analysis reveals key genes and pathways corresponding to Cd and Pb in the hyperaccumulator Arabis paniculata

Soil and water are increasingly at risk of contamination from the toxic heavy metals lead (Pb) and cadmium (Cd). Arabis paniculata (Brassicaceae) is a hyperaccumulator of heavy metals (HMs) found widely distributed in areas impacts by mining activities. However, the mechanism by which A. paniculata tolerates HMs is still uncharacterized. For this experiment, we employed RNA sequencing (RNA-seq) in order to find Cd (0.25 mM)- and Pb (2.50 mM)-coresponsive genes A. paniculata. In total, 4490 and 1804 differentially expressed genes (DEGs) were identified in root tissue, and 955 and 2209 DEGs were identified in shoot tissue, after Cd and Pb exposure, respectively. Interestingly in root tissue, gene expression corresponded similarly to both Cd and Pd exposure, of which 27.48% were co-upregulated and 41.00% were co-downregulated. Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) analyses showed that the co-regulated genes were predominantly involved in transcription factors (TFs), cell wall biosynthesis, metal transport, plant hormone signal transduction, and antioxidant enzyme activity. Many critical Pb/Cd-induced DEGs involved in phytohormone biosynthesis and signal transduction, HM transport, and transcription factors were also identified. Especially the gene ABCC9 was co-downregulated in root tissues but co-upregulated in shoot tissues. The co-downregulation of ABCC9 in the roots prevented Cd and Pb from entering the vacuole rather than the cytoplasm for transporting HMs to shoots. While in shoots, the ABCC9 co-upregulated results in vacuolar Cd and Pb accumulation, which may explain why A. paniculata is a hyperaccumulator. These results will help to reveal the molecular and physiological processes underlying tolerance to HM exposure in the hyperaccumulator A. paniculata, and aid in future efforts to utilize this plant in phytoremediation.

Morphophysiological, proteomic and metabolomic analyses reveal cadmium tolerance mechanism in common wheat (Triticum aestivum L.)

Soil cadmium (Cd) contamination can reduce wheat yield and quality, thus threatening food security and human health. Herein, morphological physiology, Cd accumulation and distribution, proteomic and metabolomic analyses were performed (using wheat cultivars 'Luomai23' (LM, Cd-sensitive) and 'Zhongyu10' (ZY, Cd-tolerant) at the seedling stage with sand culture) to reveal Cd tolerance mechanism. Cd inhibited wheat growth, caused oxidative stress, hindered carbon and nitrogen metabolism, and altered the quantity and composition of root exudates. The root Cd concentration was lower in ZY than in LM by about 35% under 15 μM Cd treatments. ZY reduced Cd uptake through root exudation of amino acids and alkaloids. ZY also reduced Cd accumulation through specific up-regulation (twice) of major facilitator superfamily (MFS) proteins. Furthermore, ZY enhanced Cd cell wall fixation and vacuolar compartmentalization by increasing pectin contents, hemicellulose1 contents, and adenosine triphosphate binding cassette subfamily C member 1 (ABCC1) transporter expression, thus reducing the Cd organelle fraction of ZY by about 12% and 44% in root and shoot, respectively, compared with LM. Additionally, ZY had enhanced resilience to Cd due to increased antioxidant capacity, plasma membrane stability, nitrogen metabolism, and endoplasmic reticulum homeostasis, indicating that the increased Cd tolerance could be because of multi-level coordination. These findings provide a reference for exploring the molecular mechanism of Cd tolerance and accumulation, providing a basis for safe utilization of Cd-contaminated soil by breeding Cd-tolerant and low Cd-accumulating wheat varieties.

Molecular insights into lignin biosynthesis on cadmium tolerance: Morphology, transcriptome and proteome profiling in Salix matsudana

Soil pollution caused by cadmium (Cd) is a serious concern. Phytoremediation is a popular technology in the remediation of Cd-contaminated soil. Salix matsudana var. matsudana f. umbraculifera Rehd. has been characterized as a high Cd-accumulating and tolerant willow (HCW). Here, transcriptome and proteome profiling, along with morphology analyses were performed to explore molecular cross-talk involved in Cd tolerance. Our results showed that 73%- 83% of the Cd in roots accumulated in the cell walls and root xylem cell walls were significantly thickened. From transcriptome and proteome analysis, a total of 153 up-regulated differentially-expressed genes and 655 up-regulated differentially-expressed proteins were found in common between two comparison groups (1 d and 4 d vs. respective control). Furthermore, phenylpropanoid biosynthesis was identified as a key pathway in response to Cd stress. In this pathway, lignin biosynthesis genes or proteins were significantly up-regulated, and lignin content increased significantly in roots under Cd stress. Two Cd-induced genes cinnamoyl-CoA reductase 1 (SmCCR1) and cinnamyl alcohol dehydrogenase 7 (SmCAD7) from HCW increased the lignin content and enhanced Cd tolerance in transgenic poplar calli. These results lay the foundation for further clarifying the molecular mechanisms of Cd tolerance in woody plants.

Transcriptome alterations of radish shoots exposed to cadmium can be interpreted in the context of leaf senescence

Till now few transcriptome studies have described shoot responses of heavy metal (HM)-sensitive plants to excess Cd and still a unifying model of Cd action is lacking. Using RNA-seq technique, the transcriptome responses of radish (Raphanus sativus L.) leaves to Cd stress were investigated in plants raised hydroponically under control and 5.0 mg L^-1 Cd. The element was mainly accumulated in roots and led to declined biomass and photosynthetic pigments, increased H₂O₂ and lipid peroxidation, and the accumulation of sugars, protein thiols, and phytochelatins. Out of 524 differentially expressed genes (DEGs), 244 and 280 upregulated and downregulated ones were assigned to 82 and 115 GO terms, respectively. The upregulated DEGs were involved in osmotic regulation, protein metabolism, chelators, and carbohydrate metabolisms, whereas downregulated DEGs were related to photosynthesis, response to oxidative stress, glucosinolate, and secondary metabolite biosynthesis. Our transcriptome data suggest that Cd triggers ROS production and photosynthesis decline associated with increased proteolysis through ubiquitin-proteasome system (UPS)- and chloroplast-proteases and in this way brings about re-mobilization of N and C stores into amino acids and sugars. Meanwhile, declined glucosinolate metabolism in favor of chelator synthesis and upregulation of dehydrins as inferred from transcriptome analysis confers shoots some tolerance to the HM-derived ionic/osmotic imbalances. Thus, the induction of leaf senescence might be a major long-term response of HM-sensitive plants to Cd toxicity.

Rhizospheric microbiomics integrated with plant transcriptomics provides insight into the Cd response mechanisms of the newly identified Cd accumulator Dahlia pinnata

Phytoremediation that depends on excellent plant resources and effective enhancing measures is important for remediating heavy metal-contaminated soils. This study investigated the cadmium (Cd) tolerance and accumulation characteristics of Dahlia pinnata Cav. to evaluate its Cd phytoremediation potential. Testing in soils spiked with 5-45 mg kg-1 Cd showed that D. pinnata has a strong Cd tolerance capacity and appreciable shoot Cd bioconcentration factors (0.80-1.32) and translocation factors (0.81-1.59), indicating that D. pinnata can be defined as a Cd accumulator. In the rhizosphere, Cd stress (45 mg kg-1 Cd) did not change the soil physicochemical properties but influenced the bacterial community composition compared to control conditions. Notably, the increased abundance of the bacterial phylum Patescibacteria and the dominance of several Cd-tolerant plant growth-promoting rhizobacteria (e.g., Sphingomonas, Gemmatimonas, Bryobacter, Flavisolibacter, Nocardioides, and Bradyrhizobium) likely facilitated Cd tolerance and accumulation in D. pinnata. Comparative transcriptomic analysis showed that Cd significantly induced (P < 0.001) the expression of genes involved in lignin synthesis in D. pinnata roots and leaves, which are likely to fix Cd2+ to the cell wall and inhibit Cd entry into the cytoplasm. Moreover, Cd induced a sophisticated signal transduction network that initiated detoxification processes in roots as well as ethylene synthesis from methionine metabolism to regulate Cd responses in leaves. This study suggests that D. pinnata can be potentially used for phytoextraction and improves our understanding of Cd-response mechanisms in plants from rhizospheric and molecular perspectives.

Dissection of the response mechanism of alfalfa under phosphite stress based on metabolomic and transcriptomic data

Phosphite, a reduced form of phosphate, inhibits the growth and even has toxic effect on plants. To learn more about the mechanism of alfalfa responses to phosphite, the morphological and physiological characteristics, and the metabolites and transcript levels were comprehensively analyzed following the exposure of alfalfa seedlings to phosphite and phosphate under greenhouse conditions. The results showed that phosphite inhibited seedling growth and photosynthesis. However, the absorption efficiency of phosphite was higher than that of phosphate in roots, which was supported by increased total phosphorus concentration of 16.29% and 52.30% on days 8 and 12. Moreover, phosphite stress affected the synthesis of lipids and carbohydrates, which were reflected in enhanced glycolipid and sulfolipid in roots and amylose in shoots. Phosphite stress resulted in a decrease in indole acetic acid (IAA) in the whole plant and zeatin in the shoots, which could enable alfalfa to adapt to the phosphite environment. Some genes involved in phosphate starvation response included SPX, phosphate response regulator2, and inorganic phosphate transporter 1-4 (PHT1;4) in roots were affected by phosphite stress. In addition, some genes that are involved in stress responses and DNA repair were induced by phosphite stress. These observations together suggest that alfalfa responds to phosphite stress by inhibiting growth, regulating the genes induced by phosphate starvation, improving oxidative protection, promoting DNA repair, and adjusting the IAA and zeatin signaling transductions. Our findings provide novel insights into the molecular response to phosphite stress in alfalfa.

Integrated eco-physiological, biochemical, and molecular biological analyses of selenium fortification mechanism in alfalfa

Foliar Se (IV) application at 100 mg/kg can act as a positive bio-stimulator of redox, photosynthesis, and nutrient metabolism in alfalfa via phenotypes, nutritional compositions, biochemistry, combined with transcriptome analysis. Selenium (Se) is an essential element for mammals, and plants are the primary source of dietary Se. However, Se usually has dual (beneficial/toxic) effects on the plant itself. Alfalfa (Medicago sativa L.) is one of the most important forage resources in the world due to its high nutritive value. In this study, we have investigated the effects of sodium selenite (Se (IV)) (0, 100, 200, 300, and 500 mg/kg) on eco-physiological, biochemical, and transcriptional mechanisms in alfalfa. The phenotypic and nutritional composition alterations revealed that lower Se (IV) (100 mg/kg) levels positively affected alfalfa; it enhanced the antioxidant activity, which may contribute to redox homeostasis and chloroplast function. At 100 mg/kg Se (IV) concentration, the H₂O_2, and malondialdehyde (MDA) contents decreased by 36.72% and 22.62%, respectively, whereas the activity of glutathione peroxidase (GPX) increased by 31.10%. Se supplementation at 100 mg/kg increased the plant pigments contents, the light-harvesting capacity of PSII (Fv/Fm) and PSI (ΔP700max), and the carbon fixation efficiency, which was demonstrated by enhanced photosynthesis (37.6%). Furthermore, alfalfa shifted carbon flux to protein synthesis to improve quality at 100 mg/kg of Se (IV) by upregulating carbohydrate and amino acid metabolic genes. On the contrary, at 500 mg/kg, Se (IV) became toxic. Higher Se (IV) disordered the plant antioxidant system, increasing H₂O₂ and MDA by 14.2 and 4.3%, respectively. Moreover, photosynthesis was inhibited by 20.2%, and more structural substances, such as lignin, were synthesized. These results strongly suggest that Se (IV) at a concentration of 100 mg/kg act as the positive bio-stimulator of redox metabolism, photosynthesis, and nutrient in alfalfa.

Transcriptional memory of gene expression across generations participates in transgenerational plasticity of field pennycress in response to cadmium stress

Transgenerational plasticity (TGP) occurs when maternal environments influence the expression of traits in offspring, and in some cases may increase fitness of offspring and have evolutionary significance. However, little is known about the extent of maternal environment influence on gene expression of offspring, and its relationship with trait variations across generations. In this study, we examined TGP in the traits and gene expression of field pennycress (Thlaspi arvense) in response to cadmium (Cd) stress. In the first generation, along with the increase of soil Cd concentration, the total biomass, individual height, and number of seeds significantly decreased, whereas time to flowering, superoxide dismutase (SOD) activity, and content of reduced glutathione significantly increased. Among these traits, only SOD activity showed a significant effect of TGP; the offspring of Cd-treated individuals maintained high SOD activity in the absence of Cd stress. According to the results of RNA sequencing and bioinformatic analysis, 10,028 transcripts were identified as Cd-responsive genes. Among them, only 401 were identified as transcriptional memory genes (TMGs) that maintained the same expression pattern under normal conditions in the second generation as in Cd-treated parents in the first generation. These genes mainly participated in Cd tolerance-related processes such as response to oxidative stress, cell wall biogenesis, and the abscisic acid signaling pathways. The results of weighted correlation network analysis showed that modules correlated with SOD activity recruited more TMGs than modules correlated with other traits. The SOD-coding gene CSD2 was found in one of the modules correlated with SOD activity. Furthermore, several TMGs co-expressed with CSD2 were hub genes that were highly connected to other nodes and critical to the network's topology; therefore, recruitment of TMGs in offspring was potentially related to TGP. These findings indicated that, across generations, transcriptional memory of gene expression played an important role in TGP. Moreover, these results provided new insights into the trait evolution processes mediated by phenotypic plasticity.

Integrated mRNA and microRNA expression analysis of root response to phosphate deficiency in Medicago sativa

The deficiency of available phosphate significantly limits plant growth and development. This study sought to investigate how alfalfa (Medicago sativa), a high-yielding and high-quality forage widely cultivated worldwide, responds to phosphate deficiency stress by integrating transcriptional and post-transcriptional data. In this study, 6,041 differentially expressed genes (DEGs) were identified in alfalfa roots under phosphate deficiency conditions. Furthermore, psRNATarget, RNAhybrid, and TargetFinder were used to predict the target genes of 137 differentially expressed miRNAs (DEMs) in the root. In total, 3,912 DEGs were predicted as target genes. Pearson correlation analysis revealed 423 pairs of miRNA-mRNA regulatory relationships. MiRNA negatively regulates mRNA involved in regulatory pathways of phosphate deficiency responses in alfalfa. miR156e targeted squamosa promoter-binding-like protein 13A (SPL13), miR160c targeted auxin response factor 18 (ARF18), and miR2587a controlled glycolysis and citrate cycle via Phosphoenolpyruvate carboxykinase (ATP) (PCKA). Novel-miR27 regulated SPX domain-containing protein that controls phosphate transport in alfalfa root, novel-miR3-targeted sulfoquinovosyl transferase SQD2 controlled sulfolipid synthesis and glutathione S-transferase (GST; mediated by miR169j/k and novel-miR159) regulated glutathione metabolism. miR399l regulated auxin-responsive protein SAUR72 involved in IAA signal transduction, while abscisic acid receptor PYL4 (regulated by novel-miR205 and novel-miR83) participated in ABA signal transduction. Combined miRNA-mRNA enrichment analysis showed that most miRNAs regulate the phosphate starvation response of alfalfa by modulating target genes involved in carbohydrate metabolism, sulfolipid metabolism, glutathione metabolism, and hormone signal transduction. Therefore, this study provides new insights into the post-transcriptional regulation mechanism of phosphate deficiency responses and new perspectives on phosphate assimilation pathways in alfalfa and other legumes.

Heavy metal and metalloid toxicity in horticultural plants: Tolerance mechanism and remediation strategies

Heavy metal/metalloids (HMs) are among the primary soil pollutants that limit crop production worldwide. Plants grown in HM contaminated soils exhibit reduced growth and development, resulting in a decrease in crop production. The exposure to HMs induces plant oxidative stress due to the formation of free radicals, which alter plant morphophysiological and biochemical mechanisms at cellular and tissue levels. When exposed to HM toxicity, plants evolve sophisticated physiological and cellular defense strategies, such as sequestration and transportation of metals, to ensure their survival. Plants also have developed efficient strategies by activating signaling pathways, which induce the expression of HM transporters. Plants either avoid the uptake of HMs from the soil or activate the detoxifying mechanism to tolerate HM stress, which involves the production of antioxidants (enzymatic and non-enzymatic) for the scavenging of reactive oxygen species. The metal-binding proteins including phytochelatins and metallothioneins also participate in metal detoxification. Furthermore, phytohormones and their signaling pathways also help to regulate cellular activities to counteract HM stress. The excessive levels of HMs in the soil can contribute to plant morpho-physiological, biochemical, and molecular alterations, which have a detrimental effect on the quality and productivity of crops. To maintain the commercial value of fruits and vegetables, various measures should be considered to remove HMs from the metal-polluted soils. Bioremediation is a promising approach that involves the use of tolerant microorganisms and plants to manage HMs pollution. The understanding of HM toxicity, signaling pathways, and tolerance mechanisms will facilitate the development of new crop varieties that help in improving phytoremediation.

Transcriptome Analysis Reveals the Stress Tolerance to and Accumulation Mechanisms of Cadmium in Paspalum vaginatum Swartz

Cadmium (Cd) is a non-essential heavy metal and high concentrations in plants causes toxicity of their edible parts and acts as a carcinogen to humans and animals. Paspalum vaginatum is widely cultivating as turfgrass due to its higher abiotic stress tolerance ability. However, there is no clear evidence to elucidate the mechanism for heavy metal tolerance, including Cd. In this study, an RNA sequencing technique was employed to investigate the key genes associated with Cd stress tolerance and accumulation in P. vaginatum. The results revealed that antioxidant enzyme activities catalase (CAT), peroxidase (POD), superoxide dismutase (SOD), and glutathione S-transferase GST) were significantly higher at 24 h than in other treatments. A total of 6820 (4457/2363, up-/down-regulated), 14,038 (9894/4144, up-/down-regulated) and 17,327 (7956/9371, up-/down-regulated) differentially expressed genes (DEGs) between the Cd1 vs. Cd0, Cd4 vs. Cd0, and Cd24 vs. Cd0, respectively, were identified. The GO analysis and the KEGG pathway enrichment analysis showed that DEGs participated in many significant pathways in response to Cd stress. The response to abiotic stimulus, the metal transport mechanism, glutathione metabolism, and the consistency of transcription factor activity were among the most enriched pathways. The validation of gene expression by qRT-PCR results showed that heavy metal transporters and signaling response genes were significantly enriched with increasing sampling intervals, presenting consistency to the transcriptome data. Furthermore, over-expression of PvSnRK2.7 can positively regulate Cd-tolerance in Arabidopsis. In conclusion, our results provided a novel molecular mechanism of the Cd stress tolerance of P. vaginatum and will lay the foundation for target breeding of Cd tolerance in turfgrass.

Integrative chemical and omics analyses reveal copper biosorption and tolerance mechanisms of Bacillus cereus strain T6

A comprehensive understanding of the cellular response of microbes to metal stress is necessary for the rational development of microbe-based biosorbents for metal removal. The present study investigated the copper (Cu) sorption and resistance mechanism of Bacillus cereus strain T6, a newly isolated Cu-resistant bacterium, by integrative analyses of physiochemistry, genomics, transcriptomics, and metabolomics. The growth inhibition assay and biosorption determination showed that this bacterium exhibited high tolerance to Cu, with a minimum inhibitory concentration of 4.0 mM, and accumulated Cu by both extracellular adsorption and intracellular binding. SEM microscopic images and FTIR spectra showed significant cellular surface changes at the high Cu level but not at low, and the involvement of surface functional groups in the biosorption of Cu, respectively. Transcriptomic and untargeted metabolomic analyses detected 362 differentially expressed genes and 60 significantly altered metabolites, respectively. Integrative omics analyses revealed that Cu exposure dramatically induced a broad spectrum of genes involved in Cu transport and iron homeostasis, and suppressed the denitrification pathway, leading to significant accumulation of metabolites for metal transporter synthesis, membrane remolding, and antioxidant activities. The results presented here provide a new perspective on the intricate regulatory network of Cu homeostasis in bacteria.

Nitric oxide enhances resistance of Pleurotus eryngii to cadmium stress by alleviating oxidative damage and regulating of short-chain dehydrogenase/reductase family

The function and mechanism of nitric oxide (NO) in regulating Pleurotus eryngii biological response to cadmium (Cd) stress was evaluated by using anti-oxidation and short-chain dehydrogenase/reductase (SDR) family analysis. The fresh biomass of P. eryngii mycelia sharply decreased after treatment with 50 µM Cd; the lipid peroxidation and H₂O₂ accumulation in P. eryngii were found responsible for it. Proper exogenous supply of NO (150 µM SNP) alleviated the oxidative damage induced by Cd stress in P. eryngii, which reduced the accumulation of thiobarbituric acid reactive substances (TBARS) and H₂O₂. The activities of antioxidant enzymes (superoxide dismutase, peroxidase) were significantly increased to deal with Cd stress when treated with SNP (150 µM), and the content of proline was also closely related to NO-mediated reduction of Cd toxicity. Moreover, SDR family members were widely involved in the response to Cd stress, especially PleSCH70 gene was observed for the first time in participating in NO-mediated enhancement of Cd tolerance in P. eryngii. Taken together, this study provides new insights in understanding the tolerance mechanisms of P. eryngii to heavy metal and lays a foundation for molecular breeding of P. eryngii to improve its tolerance to environmental stress.

Pieces of evidence of enhanced cellulose biosynthesis in the low-Cd cultivar and high expression level of transportation genes in the high-Cd cultivar of Lactuca sativa

To investigate the molecular mechanism of Cd-accumulating difference between Lactuca sativa cultivars, full-length transcriptome comparison, as well as biochemical validation, have been conducted between Cd pollution-safe cultivar (Cd-PSC, cv. LYDL) and high-Cd-accumulating cultivar (cv. HXDWQ). The full-length transcriptome of L. sativa cultivars was achieved for the first time. The results showed high Cd compartmentalization in the cell wall of cv. LYDL was ascribed to the enhanced cell wall biosynthesis under Cd stress, which was consistent with the high cellular debris Cd level (32.10-43.58%). The expression levels of transporter genes in cv. HXDWQ were about 1.19 to 1.21-fold higher than those in cv. LYDL, which was in accordance with the high ratio of easy migrative Cd chemical forms (68.59-81.98%), indicating the high Cd accumulation in the shoot of cv. HXDWQ was ascribed to the higher transportation capacity in cv. HXDWQ. Moreover, the Cd-induced endoplasmic reticulum (ER) stress was associated with the higher Cd detoxification and tolerance in cv. HXDWQ rather than in cv. LYDL. The study provides new insights into the Cd-induced transcriptomic difference between L. sativa cultivars and further contributes to the molecular breeding of L. sativa Cd-PSC.

Comparative Analysis of Italian Lettuce (Lactuca sativa L. var. ramose) Transcriptome Profiles Reveals the Molecular Mechanism on Exogenous Melatonin Preventing Cadmium Toxicity

Cadmium (Cd) accumulation in lettuce causes a large amount of yield loss during industry. Although many studies report that exogenous melatonin helps to alleviate the Cd stress of lettuce, the molecular mechanism for how plant tissue responds to Cd treatment is unclear. Herein, we applied both PacBio and Illumina techniques for Italian lettuce under different designed treatments of Cd and melatonin, aiming to reveal the potential molecular pathway of the response to Cd stress as well as the how the pre-application of exogenous melatonin affect this process. This result reveals that the root has the biggest expression pattern shift and is a more essential tissue to respond to both Cd and melatonin treatments than leaves. We reveal the molecular background of the Cd stress response in prospects of antioxidant and hormone signal transduction pathways, and we found that their functions are diverged and specifically expressed in tissues. We also found that candidate genes related to melatonin detoxify during Cd stress. Our study sheds new light for future research on how melatonin improves the cadmium resistance of lettuce and also provide valuable data for lettuce breeding.

Important Roles of Thiols in Methylmercury Uptake and Translocation by Rice Plants

The bioaccumulation of the neurotoxin methylmercury (MeHg) in rice is a significant concern due to its potential risk to humans. Thiols have been known to affect MeHg bioavailability in microorganisms, but how thiols influence MeHg accumulation in rice plants remains unknown. Here, we investigated effects of common low-molecular-weight thiols, including cysteine (Cys), glutathione (GSH), and penicillamine (PEN), on MeHg uptake and translocation by rice plants. Results show that rice roots can rapidly take up MeHg, and this process is influenced by the types and concentrations of thiols in the system. The presence of Cys facilitated MeHg uptake by roots and translocation to shoots, while GSH could only promote MeHg uptake, but not translocation, by roots. Conversely, PEN significantly inhibited MeHg uptake and translocation to shoots. Using labeled ¹³Cys assays, we also found that MeHg uptake was coupled with Cys accumulation in rice roots. Moreover, analyses of comparative transcriptomics revealed that key genes associated with metallothionein and SULTR transporter families may be involved in MeHg uptake. These findings provide new insights into the uptake and translocation of MeHg in rice plants and suggest potential roles of thiol attributes in affecting MeHg bioavailability and bioaccumulation in rice.

Transcriptomic analyses of sweet potato in response to Cd exposure and protective effects of K on Cd-induced physiological alterations

We aimed to understand the molecular mechanism of differential cadmium (Cd) accumulation in two cultivars of sweet potato and to clarify the effects of potassium (K) supply on Cd accumulation. Comparative transcriptomes were employed to identify key genes and pathways using a low-Cd (N88) and a high-Cd cultivar (X16) in a pot experiment. The antioxidant capacity and cell wall components of root tips were analyzed to account for the effect of K regulating Cd accumulation in N88 via a hydroponic experiment. Transcriptome analysis revealed that 29 and 20 genes were differentially expressed in N88 and X16, respectively, when comparing the control with the two Cd treatments. X16 had more differentially expressed genes (DEGs), including 2649 common up-regulated and 3173 common down-regulated than N88 in any treatment. GO and KEGG analyses showed that the DEGs were assigned and enriched in different pathways. Some critical DEGs such as PDR, HMA3, COPT5, CAX3, GAUT, CCR, AUX1, CAT, SOD, GSR, and GST were identified. The DEGs were involved in pathways including heavy metal transport or detoxification, cell wall biosynthesis, plant hormone signal transduction, and glutathione metabolism. Additionally, K supply substantially decreased Cd accumulation and reactive oxygen species production and promoted the production of cellulose, pectin and lignin in the root tips when exposed to Cd. Several critical DEGs associated with heavy metal transport and cell wall biosynthesis were responsible for the difference of Cd accumulation between the two cultivars. Application of K could help decrease Cd accumulation in sweet potato.

Unraveling Cadmium Toxicity in Trifolium repens L. Seedling: Insight into Regulatory Mechanisms Using Comparative Transcriptomics Combined with Physiological Analyses

Trifolium repens (T. repens) can accumulate significant amounts of heavy metal ions, and has strong adaptability to wide environmental conditions, and relatively large biomass, which is considered a potential plant for phytoremediation. However, the molecular mechanisms of T. repens involved in Cd tolerance have not yet been studied in detail. This study was conducted to examine the integrative responses of T. repens exposed to a high-level CdCl₂ by investigating the physiological and transcriptomic analyses. The results suggested that T. repens seedlings had a high degree of tolerance to Cd treatment. The roots accumulated higher Cd concentration than leaves and were mainly distributed in the cell wall. The content of MDA, soluble protein, the relative electrolyte leakage, and three antioxidant enzymes (POD, SOD, and APX) was increased with the Cd treatment time increasing, but the CAT enzymes contents were decreased in roots. Furthermore, the transcriptome analysis demonstrated that the differentially expressed genes (DEGs) mainly enriched in the glutathione (GSH) metabolism pathway and the phenylpropanoid biosynthesis in the roots. Overexpressed genes in the lignin biosynthesis in the roots might improve Cd accumulation in cell walls. Moreover, the DEGs were also enriched in photosynthesis in the leaves, transferase activity, oxidoreductase activity, and ABA signal transduction, which might also play roles in reducing Cd toxicity in the plants. All the above, clearly suggest that T. repens employ several different mechanisms to protect itself against Cd stress, while the cell wall biosynthesis and GSH metabolism could be considered the most important specific mechanisms for Cd retention in the roots of T. repens.

Transcriptomic Analysis of Cadmium Stressed Tamarix hispida Revealed Novel Transcripts and the Importance of Abscisic Acid Network

Cadmium (Cd) pollution is widely detected in soil and has been recognized as a major environmental problem. Tamarix hispida is a woody halophyte, which can form natural forest on the desert and soil with 0.5 to 1% salt content, making it an ideal plant for the research on response to abiotic stresses. However, no systematic study has investigated the molecular mechanism of Cd tolerance in T. hispida. In the study, RNA-seq technique was applied to analyze the transcriptomic changes in T. hispida treated with 150 μmol L^-1 CdCl₂ for 24, 48, and 72 h compared with control. In total, 72,764 unigenes exhibited similar sequences in the Non-redundant nucleic acid database (NR database), while 36.3% of all these unigenes may be new transcripts. In addition, 6,778, 8,282, and 8,601 DEGs were detected at 24, 48, and 72 h, respectively. Functional annotation analysis indicated that many genes may be involved in Cd stress response, including ion bonding, signal transduction, stress sensing, hormone responses and ROS metabolism. A ThUGT gene from the abscisic acid (ABA) signaling pathway can enhance Cd resistance ability of T. hispida by regulating the production of ROS under Cd stress and inhibit absorption of Cd. The new transcriptome resources and data that we present in this study for T. hispida may facilitate investigation of molecular mechanisms governing Cd resistance.

AetSRG1 contributes to the inhibition of wheat Cd accumulation by stabilizing phenylalanine ammonia lyase

Cadmium (Cd) is a toxic heavy metal that poses a serious threat to crop safety, productivity, and human health. Aegilops tauschii is the D genome donor of common wheat and shows abundant genetic variation. However, the tolerance of Ae. tauschii toward Cd at the molecular level is poorly understood. In this study, key factors involved in the Cd stress response of Ae. tauschii were investigated by RNA sequencing. Differentially expressed genes (DEGs) under Cd stress were identified in Ae. tauschii roots and shoots. A Fe(II)/2-oxoglutarate dependent dioxygenase (designated as AetSRG1), with an unknown function in Cd stress, was of particular interest. The open reading frame of AetSRG1 was cloned and overexpressed in wheat, which resulted in reduced Cd accumulation along with a lower Cd²⁺ flux, decreased electrolyte leakage, and higher reactive oxygen species production. The protein of AetSRG1 interacted with phenylalanine ammonia lyase (PAL). Finally, we found that AetSRG1 stabilizes PAL and promotes the synthesis of endogenous salicylic acid. This study provides novel insights into the molecular mechanisms underlying the response of Ae. tauschii toward Cd stress. The key genes identified in this work serve as potential targets for developing low cadmium wheat.

Temporal and tissue-specific transcriptome analyses reveal mechanistic insights into the Solidago canadensis response to cadmium contamination

Understanding the cellular mechanisms mediating invasive plant adaptation to excessive cadmium (Cd) in environments is crucial for designing phytoremediation strategies for Cd-contaminated soils. Here we performed RNA sequencing on the root and leaf tissues of Solidago canadensis stressed by Cd for 0, 12, 24, and 48 h. Tissue-specific gene expression was notably significant, i.e., 76% (1667) of differentially expressed unigenes in the root and 78% (1856) in the leaf were exclusive to each tissue. Distinctive enrichment of gene functions was further observed in each tissue's response. In detail, adaptation of the root to Cd stress involved the up-regulation of genes encoding molecular chaperones (mainly heat shock proteins) and induction of some antioxidants, which may help cells scavenge reactive oxygen species (ROS). In comparison, leaf exposure to Cd ramped up the expression of genes associated with secondary metabolism, comprised mainly of cytochrome P450, but slowed down its photosynthetic functions, which seems to conserve energy for survival. Moreover, we highlighted candidate gene modules that are highly linked to physiological traits. Collectively, these observations suggest that S. canadensis may adopt a multipronged approach to actively cope with Cd stress, with both management of ROS accumulation and metabolic adjustment to optimize energy metabolism.