A transcriptomic (RNA-seq) analysis of genes responsive to both cadmium and arsenic stress in rice root

Unraveling tissue-specific molecular mechanisms orchestrating arsenic response processes in Pteris vittata through transcriptomic analysis

Pteris vittata remediates arsenic (As)-contaminated soils; however, the molecular mechanisms underlying the As management remain largely unknown. Therefore, in this study, we investigated As - related processes by conducting transcriptomic analysis on hydroponically grown P. vittata exposed to 500 ppb arsenate (AsV). Within 24 h, As was translocated to fronds, while As concentration among fronds differed (4.08-1323.35 µg/g-DW). Transcriptomic profiling of roots and fronds with high (PHAs) and low (PLAs) As concentrations revealed distinct As transport mechanisms. In the roots, the induction of PvPht1;3 and one PHO1 genes suggested the facilitation of AsV absorption, while ACR3 and POT genes were induced in both the roots and fronds. Notably, NRT2.5, NIP6;1, BOR2, and ABC transporter genes were specifically activated in PHAs, highlighting their potential roles in As hyperaccumulation. To our knowledge, this is the first report linking PHO1, POT, NRT2.5, NIP6;1, and BOR2 to As accumulation in P. vittata. Gene ontology enrichment analysis further emphasized a tissue-specific As response system. In the roots, differentially expressed genes (DEGs) associated with the activation of glutathione metabolic process, cell wall biogenesis, antioxidant response, and signal transduction pathways enabled a prompt response to As-derived stimuli, facilitating efficient As uptake and transport. In the fronds, DEGs related to cell wall modification, oxidative stress response, signal transduction, and active transport systems may contribute to As detoxification and hyperaccumulation. This study provides novel insights into the molecular basis of As uptake, transport, accumulation, and detoxification in P. vittata, providing valuable strategies for efficient phytoextraction via regulation of As metabolism.

Plant-microbiome interactions for enhanced crop production under cadmium stress: A review

Cadmium (Cd) is a toxic heavy metal that has detrimental effects on agriculture crops and human health. Both natural and anthropogenic processes release Cd into the environment, elevating its contents in soils. Under Cd stress, strong plant-microbiome interactions are important in improving crop production, but a systematic review is still missing. This review demonstrates the importance of microbiomes and their interactions with plants in mitigating Cd toxicity and promoting crop growth. Endogenous and exogenous microbiomes play a role to enhance plant's ability to respond to Cd stress. Specifically, the rhizosphere microbiome, which includes plant growth-promoting rhizobacteria and arbuscular mycorrhizal fungi, endosphere microbiome, and phyllosphere microbiome, are involved in Cd accumulation, immobilization, and translocation, and Cd-induced stress management. The mechanisms underlying these plant-microbiome interactions vary depending on the species and varieties of crops, composition and diversity of the microbiome, and level of Cd stress. Among the microbiome-mediated approaches, biosorption, bioprecipitation, and bioaccumulation are promising for Cd remediation in soil. Additionally, the endosphere microbiome, particularly Cd resistant endophytes, reduces Cd toxicity, increases the expression of Cd efflux genes, and enhances crop growth through regulating crops' antioxidant machinery and endogenous hormones. Furthermore, improved agricultural practices modulate the soil and plant microbiomes, thereby reducing Cd stress and increasing crop productivity.

GLABRA2 transcription factor integrates arsenic tolerance with epidermal cell fate determination

Arsenic poses a global threat to living organisms, compromising crop security and yield. Limited understanding of the transcriptional network integrating arsenic-tolerance mechanisms with plant developmental responses hinders the development of strategies against this toxic metalloid. Here, we conducted a high-throughput yeast one-hybrid assay using as baits the promoter region from the arsenic-inducible genes ARQ1 and ASK18 from Arabidopsis thaliana, coupled with a transcriptomic analysis, to uncover novel transcriptional regulators of the arsenic response. We identified the GLABRA2 (GL2) transcription factor as a novel regulator of arsenic tolerance, revealing a wider regulatory role beyond its established function as a repressor of root hair formation. Furthermore, we found that ANTHOCYANINLESS2 (ANL2), a GL2 subfamily member, acts redundantly with this transcription factor in the regulation of arsenic signaling. Both transcription factors act as repressors of arsenic response. gl2 and anl2 mutants exhibit enhanced tolerance and reduced arsenic accumulation. Transcriptional analysis in the gl2 mutant unveils potential regulators of arsenic tolerance. These findings highlight GL2 and ANL2 as novel integrators of the arsenic response with developmental outcomes, offering insights for developing safer crops with reduced arsenic content and increased tolerance to this hazardous metalloid.

Selenate simultaneously alleviated cadmium and arsenic accumulation in rice (Oryza sativa L.) via regulating transport genes

Cadmium (Cd) and arsenic (As) have contrasting biogeochemical behaviors in paddy soil, which posed an obstacle for reducing their accumulation in rice (Oryza sativa L.) simultaneously. In this study, selenate exhibited a more effective ability than selenite on simultaneous alleviation of Cd and As accumulation in rice under Cd-As co-exposure, and the mechanisms need to be further investigated. The results showed that selenate significantly decreased the root Cd and As contents by 59%-83% and 43%-72% compared to Cd-As compound exposure, respectively. Correspondingly, it significantly down-regulated the expression of uptake-related genes OsNramp5 (87.1%) and OsLsi1 (95.5%) in rice roots. Decreases in Cd (64.5%) and As (16.2%) contents in shoots were also found after selenate addition. Moreover, selenate may promoted the reduction of As(V) to As(Ⅲ) and As(III) efflux to the external medium, resulting in decreased As accumulation and As(Ⅲ) proportion in rice shoots and roots. In addition, selenate could promote the binding of Cd (by 14%-24%) and As (by 9%-15%) in the cell wall, and significantly reduced the oxidative stress by elevating levels of antioxidant enzymes (by 10%-105%) and thiol compounds (by 6%-210%). Additionally, selenate significantly down-regulated the expression of OsNramp1 (49.3%) and OsLsi2 (82.1%) associated with Cd and As transport in rice. These findings suggest selenate has the potential to be an effective material for the simultaneous reduction of Cd and As accumulation in rice under Cd-As co-contamination.

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

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

Unraveling the toxicity response and metabolic compensation mechanism of tannic acid-Cr(III) complex on alga Raphidocelis subcapitata

Due to their assembly properties and variable molecular weights, the potential biological toxicity effects of macromolecular organic ligand heavy metal complexes are more difficult to predict and their mechanisms are more complex. This study unraveled the toxicity response and metabolic compensation mechanism of tannic acid-Cr(III) (TA-Cr(III)) complex on alga Raphidocelis subcapitata using multi-omics approaches. Results showed TA-Cr(III) complex caused oxidative damage and photosystem disruption, destroying the cell morphology and inhibiting algal growth by >80 % at high exposure levels. TA-Cr(III) complex stress down-regulated proteins linked to proliferation, photosynthesis and antioxidation while upregulating carbon fixation, TCA cycle and amino acid metabolism. The increase of fumarate, citrate, isocitrate and semialdehyde succinate was validated by metabolomics analysis, which improved the TCA cycle, amino acid metabolism and carbon fixation. Activation of the above cellular processes somewhat compensated for the inhibition of algal photosynthesis by TA-Cr(III) complex exposure. In conclusion, physiological toxicity coupled with downstream metabolic compensation in response to Cr(III) complex of macromolecular was characterized in Raphidocelis subcapitata, unveiling the adaptive mechanism of algae under the stress of heavy metal complexes with macromolecular organic ligands.

Transporters and phytohormones analysis reveals differential regulation of ryegrass (Lolium perenne L.) in response to cadmium and arsenic stresses

Cadmium (Cd) and arsenic (As) are two highly toxic heavy metals and metalloids that coexist in many situations posing severe threats to plants. Our investigation was conducted to explore the different regulatory mechanisms of ryegrass (Lolium perenne L.) responding to individual and combined Cd and As stresses in hydroponics. Results showed that the ryegrass well-growth phenotype was not affected by Cd stress of 10 mg·L-1. However, As of 10 mg·L-1 caused rapid water loss, proline surge, and chlorosis in shoots, suggesting that ryegrass was highly sensitive to As. Transcriptomic analysis revealed that the transcription factor LpIRO2 mediated the upregulation of ZIP1 and YSL6 that played an important role in Cd tolerance. We found that the presence of As caused the overexpression of LpSWT12, a process potentially regulated by bHLH14, to mitigate hyperosmolarity. Indoleacetic acid (IAA) and abscisic acid (ABA) contents and expression of their signaling-related genes were significantly affected by As stress rather than Cd. We predict a regulatory network to illustrate the interaction between transporters, transcription factors, and signaling transduction, and explain the antagonism of Cd and As toxicity. This present work provides a research basis for plant protection from Cd and As pollution.

Molecular level toxicity effects of As(V) on Folsomia candida: Integrated transcriptomics and metabolomics analyses

Arsenic (As) is a widespread metalloid with well-known toxicity. To date, numerous studies have focused on individual level toxicity (e.g., growth and reproduction) of As to typical invertebrate springtails in soils, however, the molecular level toxicity and mechanism was poorly understood. Here, an integrated transcriptomics and metabolomics approach was used to reveal responses of Folsomia candida exposed to As(V) of 10 and 60 mg kg-1 at which the individual level endpoints were influenced. Transcriptomics identified 5349 and 4020 differentially expressed genes (DEGs) in low and high concentration groups, respectively, and the most DEGs were down-regulated. Enrichment analysis showed that low and high concentrations of As(V) significantly inhibited chromatin/chromosome-related biological processes (chromatin/chromosome organization, nucleosome assembly and organization, etc.) in springtails. At high concentration treatment, structural constituent of cuticle, chitin metabolic process and peptidase activity (serine-type peptidase activity, endopeptidase activity, etc.) were inhibited or disturbed. Moreover, the apoptosis pathway was significantly induced. Metabolomics analysis identified 271 differential changed metabolites (DCMs) in springtails exposed to high concentration of As. Steroid hormone biosynthesis was the most significantly affected pathway. Several DCMs that related to chitin metabolism could further support above transcriptomic results. These findings further extended the knowledge of As toxic mechanisms to soil fauna and offer important information for the environmental risk assessment.

From genes to ecosystems: Decoding plant tolerance mechanisms to arsenic stress

Arsenic (As), a metalloid of considerable toxicity, has become increasingly bioavailable through anthropogenic activities, raising As contamination levels in groundwater and agricultural soils worldwide. This bioavailability has profound implications for plant biology and farming systems. As can detrimentally affect crop yield and pose risks of bioaccumulation and subsequent entry into the food chain. Upon exposure to As, plants initiate a multifaceted molecular response involving crucial signaling pathways, such as those mediated by calcium, mitogen-activated protein kinases, and various phytohormones (e.g., auxin, methyl jasmonate, cytokinin). These pathways, in turn, activate enzymes within the antioxidant system, which combat the reactive oxygen/nitrogen species (ROS and RNS) generated by As-induced stress. Plants exhibit a sophisticated genomic response to As, involving the upregulation of genes associated with uptake, chelation, and sequestration. Specific gene families, such as those coding for aquaglyceroporins and ABC transporters, are key in mediating As uptake and translocation within plant tissues. Moreover, we explore the gene regulatory networks that orchestrate the synthesis of phytochelatins and metallothioneins, which are crucial for As chelation and detoxification. Transcription factors, particularly those belonging to the MYB, NAC, and WRKY families, emerge as central regulators in activating As-responsive genes. On a post-translational level, we examine how ubiquitination pathways modulate the stability and function of proteins involved in As metabolism. By integrating omics findings, this review provides a comprehensive overview of the complex genomic landscape that defines plant responses to As. Knowledge gained from these genomic and epigenetic insights is pivotal for developing biotechnological strategies to enhance crop As tolerance.

Comparison of Transcriptome Differences between Two Rice Cultivars Differing in Cadmium Translocation from Spike-Neck to Grain

At present, the mechanism of varietal differences in cadmium (Cd) accumulation in rice is not well understood. Two rice cultivars, ZZY (high translocation-high grain Cd) and SJ18 (low translocation-low grain Cd), were used to analyze transcriptome differences in the spike-neck tissue in field trials. The results showed that, compared with ZZY, 22,367 differentially expressed genes (DEGs) were identified in SJ18, including 2941 upregulated and 19,426 downregulated genes. GO analysis enriched 59 downregulated terms, concerning 24 terms enriched for more than 1000 DEGs, including cellular and metabolic processes, biological regulation, localization, catalytic activity, transporter activity, signaling, etc. KEGG enrichment identified 21 significant downregulated pathways, regarding the ribosome, metabolic pathways, biosynthesis of secondary metabolism, signaling transduction, cell membrane and cytoskeleton synthesis, genetic information transfer, amino acid synthesis, etc. Weighted gene co-expression network analysis (WGCNA) revealed that these DEGs could be clustered into five modules. Among them, the yellow module was significantly related to SJ18 with hub genes related to OsHMA and OsActin, whereas the brown module was significantly related to ZZY with hub genes related to mitogen-activated protein kinase (MAPK), CBS, and glutaredoxin. This suggests that different mechanisms are involved in the process of spike-neck-grain Cd translocation among varieties. This study provides new insights into the mechanisms underlying differences in Cd transport among rice varieties.

Nutrient and mycoremediation of a global menace 'arsenic': exploring the prospects of phosphorus and Serendipita indica-based mitigation strategies in rice and other crops

KEY MESSAGE

Serendipita indica induced metabolic reprogramming in colonized plants complements phosphorus-management in improving their tolerance to arsenic stress on multifaceted biological fronts. Restoration of the anthropic damage done to our environment is inextricably linked to devising strategies that are not only economically sound but are self-renewing and ecologically conscious. The dilemma of heavy metal (HM) dietary ingestion, especially arsenic (As), faced by humans and animals alike, necessitates the exploitation of such technologies and the cultivation of healthy and abundant crops. The remarkable symbiotic alliance between plants and 'mycorrhizas' has evolved across eons, benefiting growth/yield aspects as well as imparting abiotic/biotic stress tolerance. The intricate interdependence of Serendipita indica (S. indica) and rice plant reportedly reduce As accumulation, accentuating the interest of microbiologists, agriculturists, and ecotoxicological scientists apropos of the remediation mechanisms of As in the soil-AMF-rice system. Nutrient management, particularly of phosphorus (P), is also praised for mitigating As phytotoxicity by deterring the uptake of As molecules due to the rhizospheric cationic competition. Taking into consideration the reasonable prospects of success in minimizing As acquisition by rice plants, this review focuses on the physiological, metabolic, and transcriptional alterations underlying S. indica symbiosis, recuperation of As stress together with nutritional management of P by gathering case studies and presenting successful paradigms. Weaving together a volume of literature, we assess the chemical forms of As and related transport pathways, discuss As-P-rice interaction and the significance of fungi in As toxicity mitigation, predominantly the role of mycorrhiza, as well as survey of the multifaceted impacts of S. indica on plants. A potential strategy for simultaneous S. indica + P administration in paddy fields is proposed, followed by future research orientation to expand theoretic comprehension and encourage field-based implementation.

The Molecular Mechanism of the Response of Rice to Arsenic Stress and Effective Strategies to Reduce the Accumulation of Arsenic in Grain

Rice (Oryza sativa L.) is the staple food for more than 50% of the world's population. Owing to its growth characteristics, rice has more than 10-fold the ability to enrich the carcinogen arsenic (As) than other crops, which seriously affects world food security. The consumption of rice is one of the primary ways for humans to intake As, and it endangers human health. Effective measures to control As pollution need to be studied and promoted. Currently, there have been many studies on reducing the accumulation of As in rice. They are generally divided into agronomic practices and biotechnological approaches, but simultaneously, the problem of using the same measures to obtain the opposite results may be due to the different species of As or soil environments. There is a lack of systematic discussion on measures to reduce As in rice based on its mechanism of action. Therefore, an in-depth understanding of the molecular mechanism of the accumulation of As in rice could result in accurate measures to reduce the content of As based on local conditions. Different species of As have different toxicity and metabolic pathways. This review comprehensively summarizes and reviews the molecular mechanisms of toxicity, absorption, transport and redistribution of different species of As in rice in recent years, and the agronomic measures to effectively reduce the accumulation of As in rice and the genetic resources that can be used to breed for rice that only accumulates low levels of As. The goal of this review is to provide theoretical support for the prevention and control of As pollution in rice, facilitate the creation of new types of germplasm aiming to develop without arsenic accumulation or within an acceptable limit to prevent the health consequences associated with heavy metal As as described here.

Allene oxide synthase 1 contributes to limiting grain arsenic accumulation and seedling detoxification in rice

Arsenic (As) is a cancerogenic metalloid ubiquitously distributed in the environment, which can be easily accumulated in food crops like rice. Jasmonic acid (JA) and its derivatives play critical roles in plant growth and stress response. However, the role of endogenous JA in As accumulation and detoxification is still poorly understood. In this study, we found that JA biosynthesis enzymes Allene Oxide Synthases, OsAOS1 and OsAOS2, regulate As accumulation and As tolerance in rice. Evolutionary bioinformatic analysis indicated that AOS1 and AOS2 have evolved from streptophyte algae (e.g. the basal lineage Klebsormidium flaccidum) - sister clade of land plants. Compared to other two AOSs, OsAOS1 and OsAOS2 were highly expressed in all examined rice tissues and their transcripts were highly induced by As in root and shoot. Loss-of-function of OsAOS1 (osaos1-1) showed elevated As concentration in grains, which was likely attributed to the increased As translocation from root to shoot when the plants were subjected to arsenate [As(V)] but not arsenite [As (III)]. However, the mutation of OsAOS2 (osaos2-1) showed no such effect. Moreover, osaos1-1 and osaos2-1 increased the sensitivity of rice plants to both As(V) and As(III). Disrupted expression of genes involved in As accumulation and detoxification, such as OsPT4, OsNIP3;2, and OsOASTL-A1, was observed in both osaos1-1 and osaos2-1 mutant lines. In addition, a As(V)-induced significant decrease in Reactive Oxygen Species (ROS) production was observed in the root of osaos1-1 but not in osaos2-1. Taken together, our results indicate OsAOS1 modulates both As allocation and detoxification, which could be partially attributed to the altered gene expression profiling and ROS homeostasis in rice while OsAOS2 is important for As tolerance.

The protective role of tetraploidy and nanoparticles in arsenic-stressed rice: Evidence from RNA sequencing, ultrastructural and physiological studies

Genome doubling in plants induces physiological and molecular changes to withstand environmental stress. Diploid rice (D-2x) and its tetraploid (T-4x) plants were treated with 25 μM Arsenic (As) and 15 mg L-1 TiO2 nanoparticles (NPs), and results indicated decreased growth and photosynthetic activity with high accumulation of reactive oxygen species (ROS) due to the As-toxicity in rice lines, significantly in D-2x rice plants. The treatment of As-contaminated rice with TiO2 NPs resulted in increased root length (8.17%) and chlorophyll AB (13.28%) and decreased electrolyte leakage (21.76%) and H2O2 (17.65%) contents than its counterpart diploid rice. Moreover, TiO2 NPs improved the activity of peroxidase, catalase, glutathione, and superoxide dismutase and reduced lipid peroxidation due to lower ROS production in D-2x and T-4x under As toxicity. Transcriptome analysis revealed abrupt changes in the expression levels of key signaling heat shock proteins, tubulin, aquaporins, As, and metal transporters under As toxicity in T-4x and D-2x lines. The KEGG and GO studies highlighted the striking distinctions between rice lines under As-stress in glutathione metabolism, H2O2 catabolic process, MAPK signaling pathway, and carotenoid biosynthesis terms, revealing consistency between physiological and molecular results. Root cells from D-2x rice were significantly more distorted by As poisoning than those from 4x rice, and cell organelles, such as mitochondria and endoplasmic reticulum, were changed or deformed. These findings proved the superiority of tetraploid rice lines over their diploid counterpart in coping with As-stress.

Integrated transcriptomics and metabolomics reveal key metabolic pathway responses in Pistia stratiotes under Cd stress

Cadmium (Cd) can interfere with plant gene expression, change the content of metabolites and affect plant growth. In this study, untargeted metabolomics (LC-MS) and RNA-Seq sequencing were performed on root tissues of Pistia stratiotes exposed to Cd stress. The results showed that cadmium stress affected the accumulation and transport of cadmium in plants and increased the content of soluble sugar, the activities of ascorbate peroxidase (APX), and peroxidase (POD) by 34.89%, 41.45%, and 6.71% on average, and decreased the activity of superoxide dismutase (SOD) by 51.51% on average. At the same time, the contents of carotenoid, chlorophyll a, and chlorophyll b decreased by 29.52%, 20.11%, and 13.14%, respectively, Thus affecting the growth and development of plants. Metabolomic analysis showed that Cd stress affected eight metabolic pathways, involving 27 differentially expressed metabolites, mainly including unsaturated fatty acids, amino acids (phenylalanine), nucleotides, sulfur compounds, and flavonoids. By transcriptome analysis, a total of 3107 differentially expressed genes (DEGs, 2666 up-regulated genes, and 441 down-regulated genes) were identified, which were mainly involved in four pathways, among which glutathione metabolism and lignin biosynthesis were the key metabolic pathways. In conclusion, this study reveals the metabolic and transcriptional response mechanisms of P. stratiotes to Cd stress through multi-omics, providing the theoretical basis for the phytoremediation of water contaminated by Cd.

Pleiotropic melatonin-mediated responses on growth and cadmium phytoextraction of Brassica napus: A bioecological trial for enhancing phytoremediation of soil cadmium

Melatonin (MT) has recently gained significant scientific interest, though its mechanism of action in enhancing plant vigor, cadmium (Cd) tolerance, and Cd phytoremediation processes are poorly understood. Therefore, here we investigated the beneficial role of MT in improving growth and Cd remediation potential of rapeseed (Brassica napus). Plants, with or without MT (200 µM L^-1), were subjected to Cd stress (30 mg kg¹). Without MT, higher Cd accumulation (up to 99%) negatively affected plant growth and developmental feature as well as altered expression of several key genes (DEGs) involved in different molecular pathways of B. napus. As compared to only Cd-stressed counterparts, MT-treated plants exhibited better physiological performance as indicated by improved leaf photosynthetic and gaseous exchange processes (3-48%) followed by plant growth (up to 50%), fresh plant biomass (up to 45%), dry plant biomass (up to 32%), and growth tolerance indices (up to 50%) under Cd exposure. MT application enhanced Cd tolerance and phytoremediation capacity of B. napus by augmenting (1) Cd accumulation in plant tissues and its translocation to above-ground parts (by up to 45.0%), (2) Cd distribution in the leaf cell wall (by up to 42%), and (3) Cd detoxification by elevating phytochelatins (by up to 8%) and metallothioneins (by upto 14%) biosynthesis, in comparison to Cd-treated plants. MT played a protective role in stabilizing hydrogen peroxide and malondialdehyde levels in the tissue of the Cd-treated plants by enhancing the content of osmolytes (proline and total soluble protein) and activities of antioxidant enzymes (SOD, CAT, APX and GR). Transcriptomic analysis revealed that MT regulated 1809 differentially expressed genes (828 up and 981 down) together with 297 commonly expressed DEGs (CK vs Cd and Cd vs CdMT groups) involved in plant-pathogen interaction pathway, protein processing in the endoplasmic reticulum pathway, mitogen-activated protein kinase signaling pathway, and plant hormone signal transduction pathway which ultimately promoted plant growth and Cd remediation potential in the Cd-stressed plants. These results provide insights into the unexplored pleiotropic beneficial action of MT in enhancing in the growth and Cd phytoextraction potential of B. napus, paving the way for developing Cd-tolerant oilseed crops with higher remediation capacity as a bioecological trial for enhancing phytoremediation of hazardous toxic metals in the environment.

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.

Polyploidy and zinc oxide nanoparticles alleviated Cd toxicity in rice by modulating oxidative stress and expression levels of sucrose and metal-transporter genes

The Cd toxicity causes severe perturbations to the plant's growth and development. Here, polyploid and diploid rice lines were treated with zinc-oxide nanoparticles (ZnO-NPs) and Cd, and physiological, cytological and molecular changes were observed. The Cd toxicity significantly reduced plant's growth attributes (such as shoot length, biological yield, dry matter, and chlorophyll contents, which decreased by 19%, 18%, 16%, 19% in polyploid and 35%, 43%, 45% and 43% in diploid rice, respectively), and disturbed the sugar level through the production of electrolytes, hydrogen peroxide, and malondialdehyde. The application of ZnO-NPs significantly alleviated the Cd toxicity in both lines by improving the antioxidant enzymes activities and physiochemical attributes. Semi-thin sections and transmission electron microscope revealed more and different types of abnormalities in diploid rice compared to polyploid rice under Cd stress. Moreover, RNA-seq analysis identified several differentially expressed genes between polyploid and diploid rice, especially metal and sucrose transporter genes. The GO, COG, and KEGG analyses revealed ploidy-specific pathways associated with plant growth and development. In conclusion, ZnO-NPs application to both rice lines significantly improved plant growth and decreased Cd accumulation in plants. We inferred that polyploid rice is more resistant to Cd stress than diploid rice.

Accumulation, transportation, and distribution of tetracycline and cadmium in rice

Co-exposure to heavy metal and antibiotic pollution might result in complexation and synergistic interactions, affecting rice growth and further exacerbating pollutant enrichment. Therefore, our study sought to clarify the influence of different Tetracycline (TC) and Cadmium(Cd) concentration ratios (both alone and combined) on rice growth, pollutant accumulation, and transportation during the tillering stage in hydroponic system. Surprisingly, our findings indicated that the interaction between TC and Cd could alleviate the toxic effects of TC/Cd on aerial rice structures and decrease pollutant burdens during root elongation. In contrast, TC and Cd synergistically promoted the accumulation of TC/Cd in rice roots. However, their interaction increased the accumulation of TC in roots while decreasing the accumulation of Cd when the toxicant doses increased. The strong affinity of rice to Cd promoted its upward transport from the roots, whereas the toxic effects of TC reduced TC transport. Therefore, the combined toxicity of the two pollutants inhibited their upward transport. Additionally, a low concentration of TC promoted the accumulation of Cd in rice mainly in the root tip. Furthermore, a certain dose of TC promoted the upward migration of Cd from the root tip. Laser ablation-inductively coupled plasma mass spectrometry demonstrated that Cd mainly accumulated in the epidermis and stele of the root, whereas Fe mainly accumulated in the epidermis, which inhibited the absorption and accumulation of Cd by the rice roots through the generation of a Fe plaque. Our findings thus provide insights into the effects of TC and Cd co-exposure on rice growth.

Generation of low-cadmium rice germplasms via knockout of OsLCD using CRISPR/Cas9

The OsLCD gene, which has been implicated in cadmium (Cd) accumulation in rice, might be a useful target for CRISPR/Cas9 editing. However, the effects of OsLCD gene editing on Cd accumulation, plant growth, and yield traits remain unknown. Here, we used CRISPR/Cas9 to generate oslcd single mutants from indica and japonica rice cultivars. We also generated osnramp5 single mutants and oslcd osnramp5 double mutants in the indica background. When grown in Cd-contaminated paddy soils, all oslcd single mutants accumulated less Cd than the wild types (WTs). Consistent with this, oslcd single mutants grown in Cd-contaminated hydroponic culture accumulated significantly less Cd in the shoots as compared to WTs. This decrease in accumulation probably resulted from the reduction of Cd translocation under Cd stress. Oxidative damage also decreased, and plant growth increased in all oslcd single mutant seedlings as compared to WTs in the presence of Cd. Plant growth and most yield traits, as well essential element concentrations in rice seedling shoots, brown rice, and rice straw, were similar between oslcd single mutants and WTs. In the presence of Cd, Cd concentrations in the brown rice and shoots of oslcd osnramp5 double mutants were significantly decreased compared with WTs as well as osnramp single mutants. Our results suggested that OsLCD knockout may reduce Cd accumulation alone or in combination with other knockout mutations in a variety of rice genotypes; unlike OsNramp5 mutations, OsLCD knockout did not reduce essential element contents. Therefore, OsLCD knockout might be used to generate low-Cd rice germplasms.

Comparative bioinformatics analysis and abiotic stress responses of expansin proteins in Cucurbitaceae members: watermelon and melon

Watermelon and melon are members of the Cucurbitaceae family including economically significant crops in the world. The expansin protein family, which is one of the members of the cell wall, breaks down the non-covalent bonds between cell wall polysaccharides, causing pressure-dependent cell expansion. Comparative bioinformatics and molecular characterization analysis of the expansin protein family were carried out in the watermelon (Citrullus lanatus) and melon (Cucumis melo) plants in the study. Gene expression levels of expansin family members were analyzed in leaf and root tissues of watermelon and melon under ABA, drought, heat, cold, and salt stress conditions by quantitative real-time PCR analysis. After comprehensive searches, 40 expansin proteins (22 ClaEXPA, 14 ClaEXPLA, and 4 ClaEXPB) in watermelon and 43 expansin proteins (19 CmEXPA, 15 CmEXPLA, 3 CmEXPB, and 6 CmEXPLB) in melon were identified. The greatest orthologous genes were identified with soybean expansin genes for watermelon and melon. However, the latest divergence time between orthologous genes was determined with poplar expansin genes for watermelon and melon expansin genes. ClaEXPA-04, ClaEXPA-09, ClaEXPB-01, ClaEXPB-03, and ClaEXPLA-13 genes in watermelon and CmEXPA-12, CmEXPA-10, and CmEXPLA-01 genes in melon can be involved in tissue development and abiotic stress response of the plant. The current study combining bioinformatics and experimental analysis can provide a detailed characterization of the expansin superfamily which has roles in growth and reaction to the stress of the plant. The study ensures detailed data for future studies examining gene functions including the roles in plant growth and stress conditions.

Comparative transcriptomic analysis reveals the important process in two rice cultivars with differences in cadmium accumulation

To date, Cd remains a major contaminant in rice production. An in-depth exploration of the mechanism that causes genotypic differences in Cd enrichment in rice is necessary to develop strategies to regulate Cd enrichment in rice. Here, two rice cultivars (low grain Cd, ZZ143; and high grain Cd, YX409) displayed different transcriptomic profile patterns when subjected to 100μmol/L Cd stress. In fact, 18,721(9833 upregulated and 8888 downregulated) and 16,403 (8366 upregulated and 8037 downregulated) differentially expressed genes (DEGs) were found in ZZ143 and YX409, respectively. Gene ontology (GO) classification revealed 28 and 26 terms enriched in ZZ143 and YX409, respectively. ZZ143 had more enriched DEGs than YX409, primarily in cellular processes, metabolic processes, binding terms, catalytic activity, etc. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that 21 and 24 pathways were significantly enriched in ZZ143 and YX409, respectively. Based on the DEGs, ZZ143 had a stronger ability for sulfur assimilation and Cys synthesis, whereas YX409 had a stronger ability to maintain cell wall stability. A series of DEGs involved in metabolic pathways, biosynthesis of secondary metabolites, plant hormone signal transduction pathways, and mitogen-activated protein kinase signaling pathways were identified, which maybe closely related to Cd resistance and the different Cd concentrations between cultivars. The above pathways and the greater number of identified DEGs in more than half of the GO terms and KEGG pathways suggest a higher absorption and stronger tolerance of the roots of ZZ143 than YX409 to Cd.

Transcriptomic mechanisms of reduced PM2.5-Pb retention in the leaves of the low-Pb-accumulation genotype of Chinese cabbage

Atmospheric fine particulate matter (PM_2.5) mainly contributes to Pb accumulation in the edible leaves of Chinese cabbage in North China. It was found that a low-Pb-accumulation (LPA) genotype of Chinese cabbage contained less Pb in leaves than high-Pb-accumulation (HPA) genotype exposed to PM_2.5-Pb. However, there are no data on the transcriptional regulatory mechanisms of foliar PM_2.5-Pb uptake by Chinese cabbage. The present study investigated the retention of PM_2.5-Pb in foliar apoplast and symplasm and the underlying molecular mechanisms of reduced Pb in LPA leaves. It appeared more Pb in apoplast and less Pb in symplasm of LPA leaves, whereas the pattern was opposite in HPA. There were 2646 and 3095 differentially expressed genes (DEGs) in LPA and HPA leaves under PM_2.5-Pb stress with clearly genotype-specific function, respectively. Furthermore, mRNA levels of XTH16 regulating cell wall thickening, PME2 and PME6 involved in cell wall remodification were significantly expressed in LPA, but not in HPA. Meanwhile, foliar PM_2.5-Pb stress downregulated expression of ZIP1, YSL1, and CNGC3 responsible for Pb influx to cell, and upregulated expression of ABCG36 regulated Pb efflux from symplasm in LPA leaves. These results improve our understanding to the mechanisms underlying foliar Pb uptake from PM_2.5-Pb at transcriptomic level.

Melatonin Alleviates Chromium Toxicity in Maize by Modulation of Cell Wall Polysaccharides Biosynthesis, Glutathione Metabolism, and Antioxidant Capacity

Melatonin, a pleiotropic regulatory molecule, is involved in the defense against heavy metal stress. Here, we used a combined transcriptomic and physiological approach to investigate the underlying mechanism of melatonin in mitigating chromium (Cr) toxicity in Zea mays L. Maize plants were treated with either melatonin (10, 25, 50 and 100 μM) or water and exposed to 100 μM K₂Cr₂O₇ for seven days. We showed that melatonin treatment significantly decreased the Cr content in leaves. However, the Cr content in the roots was not affected by melatonin. Analyses of RNA sequencing, enzyme activities, and metabolite contents showed that melatonin affected cell wall polysaccharide biosynthesis, glutathione (GSH) metabolism, and redox homeostasis. During Cr stress, melatonin treatment increased cell wall polysaccharide contents, thereby retaining more Cr in the cell wall. Meanwhile, melatonin improved the GSH and phytochelatin contents to chelate Cr, and the chelated complexes were then transported to the vacuoles for sequestration. Furthermore, melatonin mitigated Cr-induced oxidative stress by enhancing the capacity of enzymatic and non-enzymatic antioxidants. Moreover, melatonin biosynthesis-defective mutants exhibited decreased Cr stress resistance, which was related to lower pectin, hemicellulose 1, and hemicellulose 2 than wild-type plants. These results suggest that melatonin alleviates Cr toxicity in maize by promoting Cr sequestration, re-establishing redox homeostasis, and inhibiting Cr transport from the root to the shoot.

Low-level cadmium exposure induced hormesis in peppermint young plant by constantly activating antioxidant activity based on physiological and transcriptomic analyses

As one of the most toxic environmental pollutants, cadmium (Cd) has lastingly been considered to have negative influences on plant growth and productivity. Recently, increasing studies have shown that low level of Cd exposure could induce hormetic effect which benefits to plants. However, the underlying mechanisms of Cd-triggered hormesis are poorly understood. In this study, we found that Cd stress treatment showed a hormetic effect on peppermint and Cd treatment with 1.6 mg L-1 concertation manifested best stimulative effects. To explore the hormesis mechanisms of Cd treatment, comparative transcriptome analysis of peppermint young plants under low (1.6 mg L-1) and high (6.5 mg L-1) level of Cd exposure at 0 h, 24 h and 72 h were conducted. Twelve of differentially expressed genes (DEGs) were selected for qRT-PCR validation, and the expression results confirmed the credibility of transcriptome data. KEGG analysis of DEGs showed that the phenylpropanoid biosynthesis and photosynthesis were important under both low and high level of Cd treatments. Interestingly, GO and KEGG analysis of 99 DEGs specifically induced by low level of Cd treatment at 72 h indicated that these DEGs were mainly involved in the pathway of phenylpropanoid biosynthesis and their functions were associated with antioxidant activity. The expression pattern of those genes in the phenylpropanoid biosynthesis pathway and encoding antioxidant enzymes during 72 h of Cd exposure showed that low level of Cd treatment induced a continuation in the upward trend but high level of Cd treatment caused an inverted V-shape. The changes of physiological parameters during Cd exposure were highly consistent with gene expression pattern. These results strongly demonstrate that low level of Cd exposure constantly enhanced antioxidant activity of peppermint to avoid oxidative damages caused by Cd ion, while high level of Cd stress just induced a temporary increase in antioxidant activity which was insufficient to cope with lasting Cd toxicity. Overall, the results presented in this study shed a light on the underlying mechanisms of the Cd-mediated hormesis in plant. Moreover, our study provided a safe method for the efficient utilization of mild Cd-contaminated soil as peppermint is an important cash plant.

Transcriptome analysis reveals the molecular mechanisms of Phragmites australis tolerance to CuO-nanoparticles and/or flood stress induced by arbuscular mycorrhizal fungi

The molecular mechanism of arbuscular mycorrhizal fungi (AMF) in vertical flow constructed wetlands (VFCWs) for the purification of copper oxide nanoparticles (CuO-NPs) contaminated wastewater remains unclear. In this study, transcriptome analysis was used to explore the effect of AMF inoculation on the gene expression profile of Phragmites australis roots under different concentrations of CuO-NPs and/or flood stress. 551, 429 and 2281 differentially expressed genes (DEGs) were specially regulated by AMF under combined stresses of CuO-NPs and flood, single CuO-NPs stress and single flood stress, respectively. Based on the results of DEG function annotation and enrichment analyses, AMF inoculation under CuO-NPs and/or flood stress up-regulated the expression of a number of genes involved in antioxidant defense systems, cell wall biosynthesis and transporter protein, which may contribute to plant tolerance. The expression of 30 transcription factors (TFs) was up-regulated by AMF inoculation under combined stresses of CuO-NPs and flood, and 44 and 44 TFs were up-regulated under single CuO-NPs or flood condition, respectively, which may contribute to the alleviating effect of symbiosis on CuO-NPs and/or flood stress. These results provided a theoretical basis for enhancing the ecological restoration function of wetland plants for metallic nanoparticles (MNPs) by mycorrhizal technology in the future.

Identification of arsenic-tolerant varieties and candidate genes of tolerance in spring wheat (Triticum aestivum L.)

Despite the growing concerns about arsenic toxicity, information on tolerance and responsible genetic factors in wheat remains elusive. To address that, the present study aimed to screen the wheat varieties against arsenic based on growth parameters, yield, grain accumulation, and associated genes. A total of 110 wheat varieties were grown in arsenic-contaminated regions to record physio-morphological traits. The wheat 90K Infinium iSelect SNP array was used for the genome-wide association model to identify genomic regions. Wheat varieties such as Punjab-81, AARI-11, and Daman showed arsenic concentrations >45 μg/kg in similar conditions as well as the impact on grain yield, chlorophyll, Thousand Kernel Weight, and plant height. Contrastingly, varieties like Kohistan-97, As-2002, Barani-70, and Pari-73 showed grain concentrations <5 μg/kg grown under highly contaminated conditions. Three significant loci associated with arsenic accumulation in grain were identified on chromosomes 6A (qASG1-6A) and 6B (qASG3-6B and qASG4-6B). Annotation at these loci identified 39 wheat genes among which several were important for growth and tolerance against stress. The candidate gene (TraesCS6B02G429400) responsible for Glutathione-S-transferase was identified in the present study and must be investigated further using a transcriptomic approach. The present study provided background information for breeding prospects to improve wheat yield and tolerance against arsenic.

Widespread bacterial responses and their mechanism of bacterial metallogenic detoxification under high concentrations of heavy metals

Microbial mineralization is increasingly used in bioremediation of heavy metal pollution, but better mechanistic understanding of the processes involved and how they are regulated are required to improve the practical application of microorganisms in bioremediation. We used a combination of morphological (TEM) and analytical (XRD, XPS, FTIR) methods, together with novel proteomic analyses, to investigate the detoxification mechanisms, used by a range of bacteria, including the strains Bacillus velezensis LB002, Escherichia coli DH5α, B. subtilis 168, Pseudomonas putida KT2440, and B. licheniformis MT-1, exposed to elevated concentrations of Cd²⁺ and combinations of Cd²⁺, Pb²⁺, Cu²⁺, and Zn²⁺, in the presence and absence of added CaCl₂. Common features of detoxification included biomineralization, including the production of biological vaterite, up-regulation of proteins involved in flagellar movement and chemotaxis, biofilm synthesis, transmembrane transport of small molecules and organic matter decomposition. The putative roles of differentially expressed proteins in detoxification are discussed in relation to chemical and morphological data and together provide important tools to improve screening, selection, and practical application of bacterial isolates in bioremediation of polluted environments.

Genomics and transcriptomics to protect rice (Oryza sativa. L.) from abiotic stressors: -pathways to achieving zero hunger

More over half of the world's population depends on rice as a major food crop. Rice (Oryza sativa L.) is vulnerable to abiotic challenges including drought, cold, and salinity since it grown in semi-aquatic, tropical, or subtropical settings. Abiotic stress resistance has bred into rice plants since the earliest rice cultivation techniques. Prior to the discovery of the genome, abiotic stress-related genes were identified using forward genetic methods, and abiotic stress-tolerant lines have developed using traditional breeding methods. Dynamic transcriptome expression represents the degree of gene expression in a specific cell, tissue, or organ of an individual organism at a specific point in its growth and development. Transcriptomics can reveal the expression at the entire genome level during stressful conditions from the entire transcriptional level, which can be helpful in understanding the intricate regulatory network relating to the stress tolerance and adaptability of plants. Rice (Oryza sativa L.) gene families found comparatively using the reference genome sequences of other plant species, allowing for genome-wide identification. Transcriptomics via gene expression profiling which have recently dominated by RNA-seq complements genomic techniques. The identification of numerous important qtl,s genes, promoter elements, transcription factors and miRNAs involved in rice response to abiotic stress was made possible by all of these genomic and transcriptomic techniques. The use of several genomes and transcriptome methodologies to comprehend rice (Oryza sativa, L.) ability to withstand abiotic stress have been discussed in this review.

Phenotypic and transcriptomic responses of cultivated sunflower seedlings (Helianthus annuus L.) to four abiotic stresses

Plants encounter and respond to numerous abiotic stresses during their lifetimes. These stresses are often related and could therefore elicit related responses. There are, however, relatively few detailed comparisons between multiple different stresses at the molecular level. Here, we investigated the phenotypic and transcriptomic response of cultivated sunflower (Helianthus annuus L.) seedlings to three water-related stresses (i.e., dry-down, an osmotic challenge, and salt stress), as well as a generalized low-nutrient stress. All four stresses negatively impacted seedling growth, with the nutrient stress having a more divergent response from control as compared to the water-related stresses. Phenotypic responses were consistent with expectations for growth in low-resource environments, including increased (i.e., less negative) carbon fractionation values and leaf C:N ratios, as well as increased belowground biomass allocation. The number of differentially expressed genes (DEGs) under stress was greater in leaf tissue, but roots exhibited a higher proportion of DEGs unique to individual stresses. Overall, the three water-related stresses had a more similar transcriptomic response to each other vs. nutrient stress, though this pattern was more pronounced in root vs. leaf tissue. In contrast to our DEG analyses, co-expression network analysis revealed that there was little indication of a shared response between the four stresses in despite the majority of DEGs being shared between multiple stresses. Importantly, osmotic stress, which is often used to simulate drought stress in experimental settings, had little transcriptomic resemblance to true water limitation (i.e., dry-down) in our study, calling into question its utility as a means for simulating drought.

Genome-wide analysis of sulfur-encoding biosynthetic genes in rice (Oryza sativa L.) with Arabidopsis as the sulfur-dependent model plant

Sulfur is an essential element required for plant growth and development, physiological processes and stress responses. Sulfur-encoding biosynthetic genes are involved in the primary sulfur assimilation pathway, regulating various mechanisms at the gene, cellular and system levels, and in the biosynthesis of sulfur-containing compounds (SCCs). In this study, the SCC-encoding biosynthetic genes in rice were identified using a sulfur-dependent model plant, the Arabidopsis. A total of 139 AtSCC from Arabidopsis were used as reference sequences in search of putative rice SCCs. At similarity index > 30%, the similarity search against Arabidopsis SCC query sequences identified 665 putative OsSCC genes in rice. The gene synteny analysis showed a total of 477 syntenic gene pairs comprised of 89 AtSCC and 265 OsSCC biosynthetic genes in Arabidopsis and rice, respectively. Phylogenetic tree of the collated (AtSCCs and OsSCCs) SCC-encoding biosynthetic genes were divided into 11 different clades of various sizes comprised of branches of subclades. In clade 1, nearing equal representation of OsSCC and AtSCC biosynthetic genes imply the most ancestral lineage. A total of 25 candidate Arabidopsis SCC homologs were identified in rice. The gene ontology enrichment analysis showed that the rice-Arabidopsis SCC homologs were significantly enriched in the following terms at false discovery rate (FDR) < 0.05: (i) biological process; sulfur compound metabolic process and organic acid metabolic processes, (ii) molecular function; oxidoreductase activity, acting on paired donors with incorporation or reduction of molecular oxygen and (iii) KEGG pathway; metabolic pathways and biosynthesis of secondary metabolites. At less than five duplicated blocks of separation, no tandem duplications were observed among the SCC biosynthetic genes distributed in rice chromosomes. The comprehensive rice SCC gene description entailing syntenic events with Arabidopsis, motif distribution and chromosomal mapping of the present findings offer a foundation for rice SCC gene functional studies and advanced strategic rice breeding.

Arsenic and cadmium induced macronutrient deficiencies trigger contrasting gene expression changes in rice

Arsenic (As) and cadmium (Cd), two major carcinogenic heavy metals, enters into human food chain by the consumption of rice or rice-based food products. Both As and Cd disturb plant-nutrient homeostasis and hence, reduces plant growth and crop productivity. In the present study, As/Cd modulated responses were studied in non-basmati (IR-64) and basmati (PB-1) rice varieties, at physiological, biochemical and transcriptional levels. At the seedling stage, PB-1 was found more sensitive than IR-64, in terms of root biomass; however, their shoot phenotype was comparable under As and Cd stress conditions. The ionomic data revealed significant nutrient deficiencies in As/Cd treated-roots. The principal component analysis identified NH₄⁺ as As-associated key macronutrient; while, NH₄⁺/NO₃^- and K⁺ was majorly associated with Cd mediated response, in both IR-64 and PB-1. Using a panel of 21 transporter gene expression, the extent of nutritional deficiency was ranked in the order of PB-1(As)<IR-64(As)<PB-1(Cd)<IR-64(Cd). A feed-forward model is proposed to explain nutrient deficiency induced de-regulation of gene expression, as observed under Cd-treated IR-64 plants, which was also validated at the level of sulphur metabolism related enzymes. Using urea supplementation, as nitrogen-fertilizer, significant mitigation was observed under As stress, as indicated by 1.018- and 0.794-fold increase in shoot biomass in IR-64 and PB-1, respectively compared to that of control. However, no significant amelioration was observed in response to supplementation of urea under Cd or potassium under As/Cd stress conditions. Thus, the study pinpointed the relative significance of various macronutrients in regulating As- and Cd-tolerance and will help in designing suitable strategies for mitigating As and/or Cd stress conditions.

Antioxidants as modulators of arsenic-induced oxidative stress tolerance in plants: An overview

Arsenic (As) is a highly toxic contaminant in the environment. Although both inorganic and organic types of arsenic exist in the environment, the most common inorganic forms of As that adversely affect plants are arsenite (As III) and arsenate (As V). Despite no evidence for As being essential for plant growth, exposure of roots to this element can cause its uptake primarily via transporters responsible for the transport of essential mineral nutrients. Arsenic exposure even at low concentrations disturbs the plant normal functioning via excessive generation of reactive oxygen species, a condition known as oxidative stress leading to an imbalance in the redox system of the plant. This is associated with considerable damage to the cell components thereby impairing normal cellular functions and activation of several cell survival and cell death pathways. To counteract this oxidative disorder, plants possess natural defense mechanisms such as chemical species and enzymatic antioxidants. This review considers how different types of antioxidants participate in the oxidative defense mechanism to alleviate As stress in plants. Since the underlying phenomena of oxidative stress tolerance are not yet fully elucidated, the potential for "Omics" technologies to uncover molecular mechanisms are discussed. Various strategies to improve As-induced oxidative tolerance in plants such as exogenous supplementation of effective growth regulators, protectant chemicals, transgenic approaches, and genome editing are also discussed thoroughly in this review.

The protective role of MdATG10-mediated autophagy in apple plant under cadmium stress

Autophagy is a conserved degradation pathway in plants, which plays an important role in plant cellular homeostasis during abiotic stress. Although various abiotic stressors have been reported to induce autophagic activity in plants, the specific role of autophagy in plant cadmium (Cd) tolerance remains undiscovered. In this study, we treated three MdATG10-overexpressing apple lines with hydroponic Cd stress and found the enhanced Cd tolerance in transgenic plants. Transgenic apple plants exhibited less growth limitation and reduced Cd damage on the photosynthetic system. That was accompanied by higher antioxidant enzymes activity and lower harmful ROS accumulation in apple leaves under Cd stress. The higher autophagic activity led to a more active metabolic system of Pro, His, and Arg in transgenic plants under Cd stress, which was closely related to the plant Cd tolerance. In addition, the transcriptional activities of several Cd transport and detoxification-related genes were regulated by MdATG10-overexpression in response to Cd stress. This study is the first to demonstrate the protective role of autophagy in the Cd tolerance of plants.

Cadmium Exposure Alters Rhizospheric Microbial Community and Transcriptional Expression of Vetiver Grass

Vetiver grass (Chrysopogon zizanioides L.) has been used to remediate cadmium (Cd)-contaminated soil, while there have been few studies on the influence of Cd exposure on the rhizospheric microbial community and transcriptional expression of C. zizanioides. In this study, we investigated the response of the rhizospheric microbial community and transcriptional expression of C. zizanioides in 20 mg/kg Cd-contaminated soil. The results showed that Cd levels in the roots and shoots of C. zizanioides reached 250.80 and 73.40 mg/kg, respectively. The Cd exposure changed the rhizospheric bacterial community, resulting in the significant enrichment of Sphingomonas, Lysobacter, and Gemmatimonadetes in Cd-contaminated soil. In addition, 880 and 3,419 differentially expressed genes were identified in the plant roots and shoots, respectively, in response to Cd stress. Among these, the overexpressed genes associated with redox homeostasis, glutathione (GSH) metabolism, cell wall biosynthesis, and transmembrane transport pathways were found to participate in Cd detoxification in C. zizanioides. These findings could be useful for understanding the selective variation of the rhizospheric microbial community and the detoxification mechanisms of C. zizanioides in Cd phytoremediation.

Comparative Transcriptomic Analysis of Root Cadmium Responses in Two Chinese Rice Cultivars Yuzhenxiang and Xiangwanxian 12

Cadmium (Cd) pollution in paddy soil is an increasingly serious issue in rice production. It has been reported that there is a higher or lower grain Cd accumulation in the rice cultivars Yuzhenxiang (YZX) or Xiangwanxian 12 (XWX), respectively. To better manage the Cd pollution problem, the genes that might play vital roles in governing the difference in root Cd responses between these two rice cultivars were examined. In this study, the results of RNA sequencing (RNA-seq) showed that there were 341 and 161 differentially expressed genes in the roots of YZX and XWX after Cd exposure, respectively. Among these genes, 7 genes, such as Os06g0196300 (OsJ_019618), Os07g0570700 (OsJ_24808), ADI1, GDCSH, HSFB2C, PEX11-4, and CLPB1, possessed higher degree nodes with each other, through interaction analysis by the STRING (search tool for the retrieval of interacting genes/proteins) software, suggesting that they might play vital roles in Cd response. Based on GO enrichment analysis, 41 differently expressed genes after Cd treatment in YZX or XWX were identified to be related to Cd response. Through comparative transcriptomic analysis, 257 genes might be associated with the root Cd response difference between YZX and XWX. Furthermore, we supposed that ADI1, CFBP1, PEX11-4, OsJ_019618, OsJ_24808, GDCSH, CLPB1, LAC6, and WNK3 might be implicated in Cd response based on the combined analysis of RT-qPCR, interaction, and GO annotation analysis. In conclusion, the numerous genes that might be related to Cd stress response and root Cd response difference between YZX and XWX at the booting stage may be of benefit for the development of rice varieties with low Cd consumption.

Comparative physiological and transcriptomic analyses illuminate common mechanisms by which silicon alleviates cadmium and arsenic toxicity in rice seedlings

The inessential heavy metal/loids cadmium (Cd) and arsenic (As), which often co-occur in polluted paddy soils, are toxic to rice. Silicon (Si) treatment is known to reduce Cd and As toxicity in rice plants. To better understand the shared mechanisms by which Si alleviates Cd and As stress, rice seedlings were hydroponically exposed to Cd or As, then treated with Si. The addition of Si significantly ameliorated the inhibitory effects of Cd and As on rice seedling growth. Si supplementation decreased Cd and As translocation from roots to shoots, and significantly reduced Cd- and As-induced reactive oxygen species generation in rice seedlings. Transcriptomics analyses were conducted to elucidate molecular mechanisms underlying the Si-mediated response to Cd or As stress in rice. The expression patterns of the differentially expressed genes in Cd- or As-stressed rice roots with and without Si application were compared. The transcriptomes of the Cd- and As-stressed rice roots were similarly and profoundly reshaped by Si application, suggesting that Si may play a fundamental, active role in plant defense against heavy metal/loid stresses by modulating whole genome expression. We also identified two novel genes, Os01g0524500 and Os06g0514800, encoding a myeloblastosis (MYB) transcription factor and a thionin, respectively, which may be candidate targets for Si to alleviate Cd and As stress in rice, as well as for the generation of Cd- and/or As-resistant plants. This study provides valuable resources for further clarification of the shared molecular mechanisms underlying the Si-mediated alleviation of Cd and As toxicity in rice.

Interactions between pyrene and heavy metals and their fates in a soil-maize (Zea mays L.) system: Perspectives from the root physiological functions and rhizosphere microbial community

The co-occurrence of polycyclic aromatic hydrocarbons (PAHs) and heavy metals in agricultural soils has become a worldwide food crop security concern. Pot experiments, rhizosphere microbial metagenomic sequencing, and root metatranscriptomic sequencing were performed to investigate the interactions among pyrene, Cu, and Cd in a soil-maize (Zea mays L.) system. This study provided direct evidence that the co-presence of PAHs and heavy metals changed the root physiological functions and the rhizosphere microbial community, which subsequently influenced the fate of the contaminants. Co-contamination at low levels tended to enhance the uptake potential and biodegradation performance of the plant, whereas increased contaminant concentrations produced opposite effects. The co-presence of 1000 mg/kg Cu decreased the abundance of Mycobacterium in the rhizosphere and reduced pyrene degradation by 12%-16%. The presence of 400-750 mg/kg pyrene altered the metabolic processes, molecular binding functions, and catalytic activity of enzymes in the maize roots, thus impeding the phytoextraction of Cu and Cd. Competitive absorption between Cu and Cd was observed for the 800-1000 mg/kg Cu and 50-100 mg/kg Cd co-treatment, in which Cu showed a competitive advantage, enhancing its root-to-shoot translocation. These findings provide important information for the production of safe crops and for the development of phytoremediation technologies.

A transcriptomic view of cadmium retention in roots of cadmium-safe rice line (Oryza sativa L.)

A better understanding of the mechanisms controlling cadmium (Cd) accumulation in rice will benefit the development of strategies to minimize Cd accumulation in grains. A Cd-safe rice line designated D62B accumulated less than 0.2 mg Cd kg^-1 in brown rice due to its strong capacity for Cd retention in roots. Here transcriptomic was used to clarify the underlying mechanisms of Cd response in roots of D62B compared with a high Cd-accumulating line (Wujin4B). There were 777, 1058 differentially expressed genes (DEGs) in D62B and Wujin4B, respectively, when exposed to Cd. The functions of DEGs were clearly line-specific. Cell wall biosynthesis responded more intensively to Cd stress in D62B, facilitating Cd restriction. Meanwhile, more glutathione (GSH) and phytochelatins synthesized in D62B with the upregulation of sulphur and GSH metabolism. Besides, membrane proteins played critical roles in Cd response in D62B, whereas 18 terms involved in regulation were enriched in Wujin4B. Exogenous GSH further induced the expression of genes related to GSH metabolism and cell wall biosynthesis, leading to the retention of more Cd. Great responsiveness of cell wall biosynthesis and GSH metabolism could be considered the most important specific mechanisms for Cd retention in the roots of Cd-safe rice line.

Physiological, anatomical, and transcriptional responses of mulberry (Morus alba L.) to Cd stress in contaminated soil

Mulberry has been widely studied for its capacity to tolerate heavy metals. However, the anatomical and molecular response mechanisms of Cd detoxification and transportation in mulberry have not been fully elucidated. In this study, the anatomical characteristics, Cd and mineral element uptake and transport, and transcriptome profiling of mulberry were studied under Cd stress. The results showed that mulberry possessed strong detoxification and self-protection abilities against Cd stress. The growth and photosynthetic pigment contents of mulberry were only slightly affected when the soil Cd content was less than 37.0 mg/kg, while the Ca and Mg contents in the mulberry roots were clearly (p < 0.05) increased by 37.85%-40.87% and 36.63%-53.06% in 37.0-55.4 mg/kg Cd-contaminated soil. Meanwhile, the relationships between antioxidant enzyme activities, such as peroxidase, catalase, and ascorbate peroxidase, and Cd content in plants were positive. Furthermore, the structures of leaf cells, root and stem tissues were largely intact; simultaneously, the increase in osmiophilic particles and the dissolution of starch granules in mulberry leaves significantly responded to Cd stress. Clusters of Orthologous Groups of proteins (COG) and Gene Ontology (GO) classification analysis indicated that mulberry can enhance the catalytic activity, regulate the transport and metabolism of inorganic ions, and strengthen its antioxidant enzyme activity and defense mechanism to decrease Cd intoxication. Large numbers of differentially expressed genes associated with cell wall biosynthesis, antioxidant enzyme activities, glutathione metabolism, chelation, plant hormone signal transduction, and the mitogen-activated protein kinase (MAPK) signaling pathway were upregulated under Cd stress. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis indicated that plant hormone signal transduction was significantly (p < 0.05) enriched in roots, stems, and leaves of mulberry, and abscisic acid and ethylene can mediate MAPK signaling pathways to increase plant tolerance to Cd stress. The results suggested that the physiological, cellular and tissue, and transcriptional regulation of mulberry can facilitate its stress adaptation in Cd-contaminated soil.

An update on redox signals in plant responses to biotic and abiotic stress crosstalk: insights from cadmium and fungal pathogen interactions

Complex signalling pathways are involved in plant protection against single and combined stresses. Plants are able to coordinate genome-wide transcriptional reprogramming and display a unique programme of transcriptional responses to a combination of stresses that differs from the response to single stresses. However, a significant overlap between pathways and some defence genes in the form of shared and general stress-responsive genes appears to be commonly involved in responses to multiple biotic and abiotic stresses. Reactive oxygen and nitrogen species, as well as redox signals, are key molecules involved at the crossroads of the perception of different stress factors and the regulation of both specific and general plant responses to biotic and abiotic stresses. In this review, we focus on crosstalk between plant responses to biotic and abiotic stresses, in addition to possible plant protection against pathogens caused by previous abiotic stress. Bioinformatic analyses of transcriptome data from cadmium- and fungal pathogen-treated plants focusing on redox gene ontology categories were carried out to gain a better understanding of common plant responses to abiotic and biotic stresses. The role of reactive oxygen and nitrogen species in the complex network involved in plant responses to changes in their environment is also discussed.

An amiRNA screen uncovers redundant CBF and ERF34/35 transcription factors that differentially regulate arsenite and cadmium responses

Arsenic stress causes rapid transcriptional responses in plants. However, transcriptional regulators of arsenic-induced gene expression in plants remain less well known. To date, forward genetic screens have proven limited for dissecting arsenic response mechanisms. We hypothesized that this may be due to the extensive genetic redundancy present in plant genomes. To overcome this limitation, we pursued a forward genetic screen for arsenite tolerance using a randomized library of plants expressing >2,000 artificial microRNAs (amiRNAs). This library was designed to knock-down diverse combinations of homologous gene family members within sub-clades of transcription factor and transporter gene families. We identified six transformant lines showing an altered response to arsenite in root growth assays. Further characterization of an amiRNA line targeting closely homologous CBF and ERF transcription factors show that the CBF1,2 and 3 transcription factors negatively regulate arsenite sensitivity. Furthermore, the ERF34 and ERF35 transcription factors are required for cadmium resistance. Generation of CRISPR lines, higher-order T-DNA mutants and gene expression analyses, further support our findings. These ERF transcription factors differentially regulate arsenite sensitivity and cadmium tolerance.

Metal and Metalloid Toxicity in Plants: An Overview on Molecular Aspects

Worldwide, the effects of metal and metalloid toxicity are increasing, mainly due to anthropogenic causes. Soil contamination ranks among the most important factors, since it affects crop yield, and the metals/metalloids can enter the food chain and undergo biomagnification, having concomitant effects on human health and alterations to the environment. Plants have developed complex mechanisms to overcome these biotic and abiotic stresses during evolution. Metals and metalloids exert several effects on plants generated by elements such as Zn, Cu, Al, Pb, Cd, and As, among others. The main strategies involve hyperaccumulation, tolerance, exclusion, and chelation with organic molecules. Recent studies in the omics era have increased knowledge on the plant genome and transcriptome plasticity to defend against these stimuli. The aim of the present review is to summarize relevant findings on the mechanisms by which plants take up, accumulate, transport, tolerate, and respond to this metal/metalloid stress. We also address some of the potential applications of biotechnology to improve plant tolerance or increase accumulation.

Arsenic uptake and toxicity in wheat (Triticum aestivum L.): A review of multi-omics approaches to identify tolerance mechanisms

Arsenic (As) due to its widespread has become a primary concern for sustainable food production, especially in Southeast Asian countries. In that context, the present review presented a comprehensive detail of the available literature marking an assortment of As-induced impacts on wheat. The conclusive findings of past research suggest that As tends to grossly affect the germination, elongation, biomass, grain yield, and induce oxidative stress. Several human studies are suggestive of higher cancer risks (>1 × 10^-6) due to the ingestion of wheat grains. However, the body of proof is limited and the scarcity of information limited understanding about tolerance mechanism in wheat against As. Therefore, the paper provided a reference from tolerance mechanism based studies in other crops like rice and maize. The generated knowledge of arsenomics would pave the way for plant breeders to develop resistant varieties for As to ensure sustainable food production.

A meta-analysis of transcriptomic profiles reveals molecular pathways response to cadmium stress of Gramineae

As a non-essential heavy metal, cadmium (Cd) is toxic to plants. In the last 15 years, over 70 transcriptome studies have been published to decipher the molecular response mechanism against Cd stress in different plants. To extract generalization results from transcriptomic data across different plants and obtain some hub genes that respond to Cd stress, we carried out a meta-analysis of 32 published datasets. Cluster analysis revealed that plant species played a more decisive role than the media used and exposure time in the transcriptome patterns of plant roots response to Cd. The datasets from a Gramineae-like (GL) group were closer in clustering. 838 DEGs were commonly Cd-regulated in at least nine of 18 GL datasets. Gene ontology and KEGG pathway analyses revealed that oxidative stress-related terms and lignin synthesis-related terms were significantly enriched. Mapman analysis revealed that these common DEGs were mainly involved in regulation, cellular response, secondary metabolism, transport, cell wall and lipid metabolism. In Oryza sativa, 15 DEGs were up-regulated in at least four of five HM (As, Cr, Cd, Hg and Pb) groups, such as Os10g0517500 (methionine gamma-lyase) and Os01g0159800 (bHLH107). Moreover, our datasets can be used to retrieve log2FC value of specific genes across 29 studies (48 datasets), which provides data reference for the subsequent selection of HM-related genes. Our results provide the basis for further understanding of Cd tolerance mechanisms in plants.

A Visual Leaf Zymography Technique for the In Situ Examination of Plant Enzyme Activity under the Stress of Environmental Pollution

This study established a high-efficiency fluorescence quenching approach for the in situ visualization and modeling of the spatial distribution of xylanase, β-glucosidase, and phosphatase activities in plant leaves under pollution stress (namely, the leaf zymography technique, LZT). In the LZT, a membrane saturated with an enzyme-specific fluorescent substrate on the leaf surface was incubated and the fluorescence image generated on the membrane under ultraviolet light was recorded. An image-based modeling method for restoring the morphological traits of the true image by reducing noise was developed to ensure the accurate estimation of enzyme activities. The LZT could simultaneously measure 48 samples within 2 h, with good reproducibility. The results obtained by the LZT were comparable to those obtained by a conventional biochemical analysis method and presented low-cost and convenient advantages. This paper explains the theoretical basis required to investigate the realistic application of the LZT for assessing ecotoxicity in large-scale monitoring.

Whole-transcriptome sequencing (RNA-seq) study of the ZFL zebrafish liver cell line after acute exposure to Cd2+ ions

Cadmium (Cd) is a non-essential metal with no known biological function and a broad range of toxic effects in biological systems. We used whole-transcriptome sequencing (RNA-seq) to study the effects of Cd²⁺ toxicity in zebrafish liver cells, ZFL. The results of an RNA-Seq analysis of ZFL cells exposed to 5, 10 or 20 μM Cd²⁺ for 4- or 24-h. The differentially expressed genes affected by Cd²⁺ were analyzed by using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis to study the regulated pathways. Cd²⁺ regulated the expression of genes associated with cellular Cu, Zn, and Fe homeostasis, DNA replication leading to cell cycle arrest and apoptosis, and glutathione metabolism. Cd²⁺ boosted up the amino acid synthesis, possibly to support the glutathione metabolism for tackling the oxidative stress generated from Cd²⁺. Cd²⁺ stimulation was similar to heat or xenobiotics, based on the responses from ZFL such as endoplasmic reticulum stress and protein folding. We linked also those finding of gene activations relating to carcinogenesis of Cd. This paper provides a comprehensive analysis of the expression profiles induced by Cd²⁺ exposure in ZFL cells, as well as useful insights into the specific toxic effects.

Transcriptome analysis provides molecular evidences for growth and adaptation of plant roots in cadimium-contaminated environments

Cadmium (Cd) is a detrimental element that can be toxic to plants. The physiological and biochemical responses of plants to Cd stress have been extensively studied, but the molecular mechanisms remain unclear. The present study showed that Cd severely inhibited the growth of roots and shoots and reduced plant biomass of mung bean seedlings. To further investigate the gene profiles and molecular processes in response Cd stress, transcriptome analyses of mung bean roots exposed to 100 μM Cd for 1, 5, and 9 days were performed. Cd treatment significantly decreased global gene expression levels at 5 and 9 d compared with the control. A total of 6737, 10279, and 9672 differentially expressed genes (DEGs) were identified in the 1-, 5-, and 9-day Cd-treated root tissues compared with the controls, respectively. Based on the analysis of DEG function annotation and enrichment, a pattern of mung bean roots response to Cd stress was proposed. The processes detoxification and antioxidative defense were involved in the early response of mung bean roots to Cd. Cd stress downregulated the expressions of a series of genes involved in cell wall biosynthesis, cell division, DNA replication and repair, and photosynthesis, while genes involved in signal transduction and regulation, transporters, secondary metabolisms, defense systems, and mitochondrial processes were upregulated in response to Cd, which might be contributed to the improvement of plant tolerance. Our results provide some novel insights into the molecular processes for growth and adaption of mung bean roots in response to Cd and many candidate genes for further biotechnological manipulations to improve plant tolerance to heavy metals.

Dual-Functional Redox-Responsive Nanocarriers for Loading Phytohormone and Complexation with Heavy Metal Ions

This work focused on designing a novel redox-responsive nanocarrier synthesized from carboxymethyl-β-cyclodextrin-modified nanosilica, which could load and release plant hormones, such as salicylic acid (SA), in plant cells. When the SA-loaded nanoparticles cross the plant cell wall, the disulfide bond can be broken to form sulfhydryl groups under the action of reduced glutathione (GSH), thus releasing SA. Meanwhile, the resulting thiol groups exhibited strong affinity toward several heavy metal ions, mercury ions in particular, thus playing a role similar to phytochelatins for detoxification. The results of SA release in vitro proved that the release proceeded much faster in GSH-rich than in GSH-free environments. The adsorption behaviors of the redox-responsive nanoparticles toward heavy metal ions, after phytohormones release, were systematically investigated. Moreover, the synergetic effects on sustained release and metal ion capture enable the redox-responsive cyclodextrin-modified silica to be an effective and dual-functional nanocarrier that has great potential for agricultural applications.