Contribution of proteomic studies towards understanding plant heavy metal stress response

Uptake, impact, adaptive mechanisms, and phytoremediation of heavy metals by plants: Role of transporters in heavy metal sequestration

Heavy metals (HMs) pose severe threats to both the environment and its inhabitants, leading to reduced crop productivity and hazardous impacts on human and animal health. Metallurgical activities in peri-urban areas are major contributors to the terrestrial deposition of various HMs. Upon entering plant the cells, HMs disrupt structural and physiological processes, inducing stress responses and triggering metabolic pathways for stress adaptations. The plants have evolved specialized transport systems to regulate the uptake, transport, and cellular concentrations of these metals. HMs often exploit transporters of essential nutrients, such as phosphate, hexose, and sulfate to gain entry into plant cells. Key players include zinc receptor transporter (ZRT1) and iron receptor transporter (IRT1), both part of the ZIP (Zinc Iron Permease) family, as well as heavy metal-associated ATPases (HMAs) and ATP binding cassette transporter C (ABCC-type transporters). Hyperaccumulating plants thrive in harsh environments with elevated concentrations of toxic ions, such as sodium, chloride, and heavy metals including arsenic (As), mercury (Hg), cadmium (Cd), lead (Pb), silicon (Si), boron (B), antimony (Sb), germanium (Ge), and tellurium (Te), by compartmentalizing these ions into vacuoles. The accumulation of heavy metals or metalloids like cadmium (Cd), lead (Pb), arsenic (As), chromium (Cr), nickel (Ni), manganese (Mn), zinc (Zn), thallium (Tl), cobalt (Co), cupper (Cu), and selenium (Se) has been extensively reported in various hyperaccumulating plant species. The halophytes, known for their inherent salinity tolerance, exhibit superior resilience to HM stress due to overlapping mechanisms of ion compartmentatlization and detoxification. This review provides an in-depth analysis on the effects of heavy metals on the metabolic processes, growth, and development of plants, emphasizing heavy tolerance mechanisms with a particular focus on halophytes. The role of HM transporters in metal sequestration and detoxification is discussed, along with the potential of hyperaccumulating halophytes for phytoremediation of HM-contaminated soils.

Advancing Chickpea Breeding: Omics Insights for Targeted Abiotic Stress Mitigation and Genetic Enhancement

Chickpea is a major source of proteins and is considered the most economically vital food legume. Chickpea production is threatened by several abiotic and biotic factors worldwide. The main constraints limiting worldwide chickpea production are abiotic conditions such as drought, heat, salinity, and cold. It is clear that chickpea is treasured for its nutritive value, in particular its high protein content, and hence study of problems like drought, cold and salinity stresses are very important concerning chickpeas. In this regard, several physiological, biochemical, and molecular mechanisms are reviewed to confer tolerance to abiotic stress. The most crippling economic losses in agriculture occur due to these abiotic stressors, which affect plants in many ways. All these abiotic stresses affect the water relations of the plant, both at the cellular level as well as the whole-plant level, causing both specific and non-specific reactions, damage and adaptation reactions. These stresses share common features. Breeding programs use a huge collection of over 100,000 chickpea accessions as their foundation. Significant advancements in conventional breeding, including mutagenesis, gene/allele introgression, and germplasm introduction, have been made through this method. Abiotic tolerance and yield component selection are made easier by creating unique DNA markers for the genus Cicer, which has been made possible by developments in high-throughput sequencing and molecular biology. Transcriptomics, proteomics, and metabolomics have also made it possible to identify particular genes, proteins, and metabolites linked to chickpea tolerance to abiotic stress. Chickpea abiotic stress tolerance has been directly and potentially improved by biotechnological applications, which are covered by all 'Omics' approaches. It requires information on the abiotic stress response at the different molecular levels, which comprises gene expression analysis for metabolites or proteins and its impact on phenotype. Studies on chickpea genome-wide expression profiling have been conducted to determine important candidate genes and their regulatory networks for abiotic stress response. This study aimed to offer a detailed overview of the diverse 'Omics' approaches for resilience's to abiotic stresses on chickpea plants.

Phosphorus and sulphur crosstalk in cereals: Unraveling the molecular interplay, agronomic impacts on yield and heavy metal tolerance

Phosphorus (P) and sulphur (S) are essential macronutrients for crop growth, playing critical roles in physiological and biochemical processes throughout the plant life cycle, as well as in mitigating heavy metal and metalloid toxicity. Therefore, the coordinated use of P and S is crucial for optimizing crop growth and reducing the accumulation of heavy metals and metalloids in plants. While P and S signaling pathways are often studied independently, our understanding of their interactions remains limited. A series of recent studies have revealed key components regulating P-S interactions in cereal crops such as rice, maize and wheat, providing new insights into the network that integrates the signaling pathways of P and S. However, the interaction between P and S in molecular regulatory pathways, crop yield improvement, and resistance to heavy metal stress has not yet been systematically summarized or hypothesized. Here, we summarize the latest advances in P-S interactions and propose potential working mechanisms that integrate these P-S interactive regulatory pathways in cereal crops. Furthermore, we discuss the regulatory mechanisms of P-S interactions in cereal crops that still need to be uncovered in the future.

Metabolomic Analysis of the Responses of Bryophyte Tortella tortuosa (Hedw.) Limpr. to Cadmium (Cd) Stress

In recent years, there have been many studies on the response of plants to heavy metal stress, but the metabolic changes in bryophytes, pioneer plants quickly responding to environmental changes, under exogenous cadmium (Cd) stress have yet to be explored. In this indoor experiment, the responses in the metabolome of bryophyte Tortella tortuosa (Hedw.) Limpr. to different Cd exposure levels (0 (CK), 5 (T1), and 10 (T2) mg·L-1) were analyzed. The results showed that the number of differentially accumulated metabolites (DAMs) secreted by T. tortuosa increased with the increase in the Cd concentration, and the biosynthesis of cofactors, D-Amino acid metabolism, Arginine biosynthesis, ATP-binding cassette transporters (ABC transporters), and biosynthesis of alkaloids derived from shikimate pathway were the main pathways enriched by DAMs. The relative abundances of malic acid, N-Formylkynurenine, L-Glutamine, L-Histidine, LL-2,6-Diaminopimelic acid, and fusaric acid in the T2 treatment increased by 16.06%, 62.51%, 14.51%, 11.92%, 21.37%, and 35.79%, respectively (p < 0.05), compared with those of the CK, and the correlation analysis results showed that the above DAMs were closely related to the changes in plant antioxidant enzyme activity and Cd concentration. These results indicate that the secretion of amino acid (N-Formylkynurenine, L-Histidine) and organic acids (isocitric acid, LL-2,6-Diaminopimelic acid, malic acid) through the metabolic pathways, including biosynthesis of amino acids, biosynthesis of cofactors, glyoxylate and dicarboxylate metabolism, and ABC transporters, is the metabolic mechanism of T. tortuosa to resist exogenous Cd stress. This study will provide a reference for the monitoring and remediation of heavy metal pollution.

Enhancing Cd and Pb tolerance of Robinia pseudoacacia (black locust) by regulating antioxidant defense system, macroelement uptake and microstructure

Woody plants have received considerable attention for the phytoremediation of heavy metal-contaminated soil. This study aimed to investigate the changes in antioxidant enzyme activity, macroelement uptake and microstructure of the woody plant Robinia pseudoacacia (black locust) for the phytoremediation of cadmium (Cd) and lead (Pb) co-contaminated soil based on dynamic sampling. The results show that black locust demonstrates strong tolerance in Cd and Pb co-contaminated soil. After 30-120 days of cultivation, the activities of superoxide dismutase, peroxidase and the macroelement (potassium [K] and calcium [Ca]) content in plant leaves significantly declined in response to Cd and Pb. However, after 160 d of cultivation, the antioxidant enzyme activities, chlorophyll, sulfhydryl and soluble protein contents, as well as Ca and magnesium content in plant leaves were returned to normal levels under the 40 mg kg-1 Cd and 1000 mg kg-1 Pb contaminated soil (CdPb3). Meanwhile, K content in plant leaves under the CdPb3 treatment was significantly (P < 0.05) increased by 68.9% compared with the control. Cadmium and Pb were primarily accumulated in black locust roots. Scanning electron microscope analysis indicated that the sieve tubes in the roots and stems of plant might block the transport of Cd and Pb. Transmission electron microscope analysis indicated that the number and volume of osmiophilic particles in plant leaves were increased and the cell walls were thickened in response to Cd and Pb stress. Path analysis further indicated that the growth of plant was related to macroelements uptake and physiological change (photosynthesis, antioxidant enzyme activity and chelation). Thus, black locust could effectively regulate the antioxidant defense system, macroelement absorption and microstructure to enhance plant tolerance to Cd and Pb stress. Moreover, black locust could maintain the normal urease, acid phosphatase and sucrase activities in the Cd and Pb co-contaminated soil. These findings suggest that black locust could be considered as a useful woody plant for the phytostabilization in Cd- and Pb-contaminated soil.

Hexavalent chromium uptake in rice (Oryza sativa L.) mediated by sulfate and phosphate transporters OsSultr1;2 and OsPht1;1

Chromium (Cr) soil contamination is a critical global environmental concern, with hexavalent chromium (Cr[VI]) being especially perilous due to its high mobility, bioavailability, and phytotoxicity. This poses a significant threat to the cultivation of crops, particularly rice, where the mechanisms of Cr(VI) absorption remain largely unexplored. This study uncovered a competitive interaction between Cr(VI) and essential nutrients-sulfate and phosphate during the uptake process. Notably, deficiencies in sulfate and phosphate were associated with a marked increase in Cr(VI) accumulation in rice, reaching up to 76.5 % and 77.7 %, respectively. Employing q-PCR, this study identified significant up-regulation of the sulfate transporter gene, OsSultr1;2, and the phosphate transporter gene, OsPht1;1, in response to Cr(VI) stress. Genetic knockout studies have confirmed the crucial role of OsSultr1;2 in Cr(VI) uptake, with its deletion leading to a 36.1 % to 69.6 % decrease in Cr uptake by rice roots. Similarly, the knockout of OsPht1;1 resulted in an 18.1 % to 25.7 % decrease in root Cr accumulation. These findings highlight the key role of the sulfate transporter OsSultr1;2 in Cr(VI) uptake, with phosphate transporters also contributing significantly to the process. These insights are valuable for developing rice varieties with reduced Cr(VI) accumulation, ensuring the safety of rice grain production.

Untying arsenite tolerance mechanisms in contrasting maize genotypes attributed to NIPs-mediated controlled influx and root-to-shoot translocation, redox homeostasis and phytochelatin-mediated detoxification pathway

Contamination of ground water and soil with toxic metalloids like arsenic (As) poses a serious hazard to the global agricultural food production. One of the best ways to restrict entry of As into the food chain is selection of germplasms which accrue extremely low level of As in grains. Here, we screened diverse maize genotypes under high arsenite (100 μM AsIII) stress and identified PMI-PV-9 and PMI-PV-3 as AsIII-tolerant and -sensitive maize genotype respectively. Expression of genes associated with As uptake, vacuolar sequestration, biosynthesis of phytochelatins, root-to-shoot translocation, in vivo ROS generation, fine tuning of antioxidant defense system, DNA and membrane damage, H2O2 and superoxide anion (O2•-) levels were compared among the selected genotypes. PMI-PV-9 plants performed much better than PMI-PV-3 in terms of plant growth with no visible symptom of As toxicity. Susceptibility of PMI-PV-3 to AsIII stress may be attributed to comparatively low expression of genes involved in phytochelatins (PCs) biosynthesis. Concomitant decrease in ABCC1 expression might be another key factor for futile sequestration of AsIII into root vacuoles. Moreover, up-regulation of ZmNIP3;1 might contribute in high root-to-leaf As translocation. Substantial spike in H2O2, O2•- and MDA levels indicates that PMI-PV-3 plants have experienced more oxidative stress than PMI-PV-9 plants. Appearance of prominent deep brown and dark blue spots/stripes on leaves as revealed after DAB and NBT staining respectively suggest severe oxidative burst in PMI-PV-3 plants. Marked reduction in DHAR and MDAR activity rendered PMI-PV-3 cells to recycle ascorbate pool ineffectively, which might have exacerbated their susceptibility to AsIII stress. In a nutshell, incompetent PCs mediated detoxification system and disruption of cellular redox homeostasis owing to feeble antioxidant defence system resulting oxidative burst might be the prime reasons behind reduced performance of PMI-PV-3 plants under AsIII stress.

Rhizobium symbiosis improves amino acid and secondary metabolite biosynthesis of tungsten-stressed soybean (Glycine max)

The industrially important transition metal tungsten (W) shares certain chemical properties with the essential plant micronutrient molybdenum and inhibits the activity of molybdoenzymes such as nitrate reductase, impacting plant growth. Furthermore, tungsten appears to interfere with metabolic processes on a much wider scale and to trigger common heavy metal stress response mechanisms. We have previously found evidence that the tungsten stress response of soybeans (Glycine max) grown with symbiotically associated N2-fixing rhizobia (Bradyrhizobium japonicum) differs from that observed in nitrogen-fertilized soy plants. This study aimed to investigate how association with symbiotic rhizobia affects the primary and secondary metabolite profiles of tungsten-stressed soybean and whether changes in metabolite composition enhance the plant's resilience to tungsten. This comprehensive metabolomic and proteomic study presents further evidence that the tungsten-stress response of soybean plants is shaped by associated rhizobia. Symbiotically grown plants (N fix) were able to significantly increase the synthesis of an array of protective compounds such as phenols, polyamines, gluconic acid, and amino acids such as proline. This resulted in a higher antioxidant capacity, reduced root-to-shoot translocation of tungsten, and, potentially, also enhanced resilience of N fix plants compared to non-symbiotic counterparts (N fed). Taken together, our study revealed a symbiosis-specific metabolic readjustment in tungsten-stressed soybean plants and contributed to a deeper understanding of the mechanisms involved in the rhizobium-induced systemic resistance in response to heavy metals.

Phytochelatin-Mediated Cultivar-Dependent Cd Accumulations of Lactuca sativa and Implication for Cd Pollution-Safe Cultivars Screening

Cd pollution-safe cultivar (Cd-PSC) is a feasible strategy to minimize Cd contamination in leafy vegetables. The shoot Cd concentrations of 23 Lactuca sativa cultivars under Cd stress ranged from 0.124 to 2.155 mg·kg-1 with a maximum cultivar difference of 8 folds. Typical Cd-PSC C16 (L) and high-Cd-accumulating cultivar C13 (H) were screened to investigate the mechanisms of Cd accumulations in L. sativa through determining Cd concentrations, Cd subcellular distributions, phytochelatin profiles, and phytochelatin biosynthesis-related genes' expressions. Higher Cd distribution in a heat stable fraction in C13 (H) indicated that the high Cd accumulation trait of C13 (H) mainly depended on the Cd-phytochelatin complexes. Root phytochelatin concentrations were significantly elevated in C13 (H) (5.83 folds) than in C16 (L) (2.69 folds) (p < 0.05) under Cd stress. Significantly downregulated expressions of glutathione S-transferase rather than the regulation of phytochelatin synthesis genes in the root of C13 (H) might be responsible for sufficient glutathione supply for phytochelatins synthesis. These findings suggested that phytochelatin elevation in C13 (H) would favor the Cd root to shoot transportation, which provides new insights into the phytochelatin-related cultivar-dependent Cd accumulating characteristic in L. sativa.

Farmyard manure, a potential organic additive to reclaim copper and Macrophomina phaseolina stress responses in mash bean plants

In the era of global warming, stress combinations instead of individual stress are realistic threats faced by plants that can alter or trigger a wide range of plant responses. In the current study, the cumulative effect of charcoal rot disease caused by notorious fungal pathogen viz., Macrophomina phaseolina was investigated under toxic levels of copper (Cu) in mash bean, and farmyard manure (FYM) was employed to manage stress. Therefore, Cu-spiked soil (50 and 100 mg/kg) was inoculated with the pathogen, and amended with 2% FYM, to assess the effect of intricate interactions on mash bean plants through pot experiments. Results demonstrated that the individual stress of the pathogen or Cu was more severe for morpho-growth, physio-biochemical, and expression profiles of stress-related genes and total protein in mash bean plants as compared to stress combinations. Under single Cu stress, a significant amount of Cu accumulated in plant tissues, particularly in roots than in upper ground tissues, while, under stress combination less Cu accumulated in the plants. Nonetheless, 2% FYM in soil encountered the negative effect of stress responses provoked by the pathogen, Cu, or both by improving health markers (photosynthetic pigments, reducing sugar, total phenolics) and oxidative stress markers (catalase, peroxidase, and polyphenol oxidase), together with regulating the expression of stress-related genes (catalase, ascorbate peroxidase, and cytokinin-resistant genes), and proteins, besides decreasing Cu uptake in the plants. FYM worked better at lower concentrations (50 mg/kg) of Cu than at higher ones (100 mg/kg), hence could be used as a suitable option for better growth, yield, and crop performance under charcoal rot disease stress in Cu-contaminated soils.

Integrated transcriptome and metabonomic analysis of key metabolic pathways in response to cadmium stress in novel buckwheat and cultivated species

INTRODUCTION

Buckwheat (Fagopyrum tataricum), an important food crop, also has medicinal uses. It is widely planted in Southwest China, overlapping with planting areas remarkably polluted by cadmium (Cd). Therefore, it is of great significance to study the response mechanism of buckwheat under Cd stress and further develop varieties with excellent Cd tolerance.

METHODS

In this study, two critical periods of Cd stress treatment (days 7 and 14 after Cd treatment) of cultivated buckwheat (Pinku-1, named K33) and perennial species (F. tatari-cymosum Q.F. Chen) (duoku, named DK19) were analyzed using transcriptome and metabolomics.

RESULTS

The results showed that Cd stress led to changes in reactive oxygen species (ROS) and the chlorophyll system. Moreover, Cd-response genes related to stress response, amino acid metabolism, and ROS scavenging were enriched or activated in DK19. Transcriptome and metabolomic analyses highlighted the important role of galactose, lipid (glycerophosphatide metabolism and glycerophosphatide metabolism), and glutathione metabolism in response to Cd stress in buckwheat, which are significantly enriched at the gene and metabolic levels in DK19.

DISCUSSION

The results of the present study provide valuable information for a better understanding of the molecular mechanisms underlying Cd tolerance in buckwheat and useful clues for the genetic improvement of drought tolerance in buckwheat.

Site-specific ecological effect assessment at community level for polymetallic contaminated soil

Current ecological risk assessment (ERA) is based more on book-keeping than on science especially for terrestrial ecosystems due to the lack of relevance to real field. Accordingly, site-specific ecological effect assessment is critical for ERA, especially at high tiers. This study developed procedures to assess ecological effect at community level based on field data. As a case study, we assessed ecological effect of polymetallic contamination in soil in the surrounding of an abandoned mining and smelting site in Hunan, China. Firstly, Zn was identified as the dominant contaminant in soil and slope gradient (SG) and pH as environmental impact factors using distance-based redundancy analysis(db-RDA). Secondly, sensitive endpoints were screened using correlation analysis between Zn and parameters of plant community composition and functional traits. Thirdly, exposure-effect curves between Zn and screened endpoints were developed by taking SG and pH as covariates using Bayesian kernel machine regression analysis (BKMR), based on which half-effect concentrations (EC₅₀s) and 10 %-effect concentrations (EC₁₀s) of soil Zn for each endpoint were calculated. Finally, site-specific hazardous concentrations (HC₅₀s) of Zn were estimated. It was revealed site-specific EC₅₀s and EC₁₀s for soil Zn ranged 80.5-201 mg kg^-1 and 342-893 mgkg^-1, respectively, and HC₅₀s based on EC₁₀s and EC₅₀s ranged 104-110 mg kg^-1 and 595-612 mg kg^-1, respectively, which are more specific and inclusive than those obtained based on crop and vegetable seed germination and seedling growth toxicity experiments.

Shoot-root signal circuit: Phytoremediation of heavy metal contaminated soil

High concentrations of heavy metals in the environment will cause serious harm to ecosystems and human health. It is urgent to develop effective methods to control soil heavy metal pollution. Phytoremediation has advantages and potential for soil heavy metal pollution control. However, the current hyperaccumulators have the disadvantages of poor environmental adaptability, single enrichment species and small biomass. Based on the concept of modularity, synthetic biology makes it possible to design a wide range of organisms. In this paper, a comprehensive strategy of "microbial biosensor detection - phytoremediation - heavy metal recovery" for soil heavy metal pollution control was proposed, and the required steps were modified by using synthetic biology methods. This paper summarizes the new experimental methods that promote the discovery of synthetic biological elements and the construction of circuits, and combs the methods of producing transgenic plants to facilitate the transformation of constructed synthetic biological vectors. Finally, the problems that should be paid more attention to in the remediation of soil heavy metal pollution based on synthetic biology were discussed.

Bioaccumulation of industrial heavy metals and interactive biochemical effects on two tropical medicinal plant species

Concentrations of heavy metals (Cr, Cu, Fe, Mn, Ni, Pb, and Zn) accumulation were studied in the leaves of two medicinal plant species, namely Holarrhena pubescens and Wrightia tinctoria, from two industrial areas and a control area. Our comparison study revealed that industrialization significantly increased the accumulation of heavy metals in both plant species. A comparison study in control and industrial areas exhibited that heavy metal accumulation was higher in the industrially affected area than in the control area. Heavy metal concentration exceeded the permissible limit recommended by the WHO in both species of two industrial areas. However, both species accumulated the least heavy metal concentration in the control area. Biochemical investigation specifies that in response to heavy metal accumulation, both species increased the activity of hydrogen peroxide (H₂O₂), malondialdehyde content, the activity of enzymatic (superoxide dismutase and peroxidase) and nonenzymatic (ascorbic acid) antioxidant, but decreased the primary (soluble carbohydrate and total protein), secondary metabolites (phenol and flavonoid) content and free radical scavenging (DPPH) activity. This study indicates that industrialization potentially harms medicinal plants by reducing the efficacy of their medicinal property.

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

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

Reprisal of Schima superba to Mn stress and exploration of its defense mechanism through transcriptomic analysis

One of the most diverse protein families, ATP-binding cassette (ABC) transporters, play a role in disease resistance, heavy metal tolerance, and food absorption.Differentially expressed genes contribute in the investigation of plant defense mechanisms under varying stress conditions. To elucidate the molecular mechanisms involved in Mn metal stress, we performed a transcriptomic analysis to explore the differential gene expression in Schima superba with the comparison of control. A total of 79.84 G clean data was generated and 6558 DEGs were identified in response to Mn metal stress. Differentially expressed genes were found to be involved in defense, signaling pathways, oxidative burst, transcription factors and stress responses. Genes important in metal transport were more expressive in Mn stress than control plants. The investigation of cis-acting regions in the ABC family indicated that these genes might be targeted by a large variety of trans-acting elements to control a variety of stress circumstances. Moreover, genes involved in defense responses, the mitogen-activated protein kinase (MAPK) signaling and signal transduction in S. superba were highly induced in Mn stress. Twenty ABC transporters were variably expressed on 1st, 5th, and 10th day of Mn treatment, according to the qRT PCR data. Inclusively, our findings provide an indispensable foundation for an advanced understanding of the metal resistance mechanisms. Our study will enrich the sequence information of S. superba in a public database and would provide a new understanding of the molecular mechanisms of heavy metal tolerance and detoxification.

Proteomic and Genomic Studies of Micronutrient Deficiency and Toxicity in Plants

Micronutrients are essential for plants. Their growth, productivity and reproduction are directly influenced by the supply of micronutrients. Currently, there are eight trace elements considered to be essential for higher plants: Fe, Zn, Mn, Cu, Ni, B, Mo, and Cl. Possibly, other essential elements could be discovered because of recent advances in nutrient solution culture techniques and in the commercial availability of highly sensitive analytical instrumentation for elemental analysis. Much remains to be learned about the physiology of micronutrient absorption, translocation and deposition in plants, and about the functions they perform in plant growth and development. With the recent advancements in the proteomic and molecular biology tools, researchers have attempted to explore and address some of these questions. In this review, we summarize the current knowledge of micronutrients in plants and the proteomic/genomic approaches used to study plant nutrient deficiency and toxicity.

A Comprehensive Review on Chickpea (Cicer arietinum L.) Breeding for Abiotic Stress Tolerance and Climate Change Resilience

Chickpea is one of the most important pulse crops worldwide, being an excellent source of protein. It is grown under rain-fed conditions averaging yields of 1 t/ha, far from its potential of 6 t/ha under optimum conditions. The combined effects of heat, cold, drought, and salinity affect species productivity. In this regard, several physiological, biochemical, and molecular mechanisms are reviewed to confer tolerance to abiotic stress. A large collection of nearly 100,000 chickpea accessions is the basis of breeding programs, and important advances have been achieved through conventional breeding, such as germplasm introduction, gene/allele introgression, and mutagenesis. In parallel, advances in molecular biology and high-throughput sequencing have allowed the development of specific molecular markers for the genus Cicer, facilitating marker-assisted selection for yield components and abiotic tolerance. Further, transcriptomics, proteomics, and metabolomics have permitted the identification of specific genes, proteins, and metabolites associated with tolerance to abiotic stress of chickpea. Furthermore, some promising results have been obtained in studies with transgenic plants and with the use of gene editing to obtain drought-tolerant chickpea. Finally, we propose some future lines of research that may be useful to obtain chickpea genotypes tolerant to abiotic stress in a scenario of climate change.

Understanding the Phytoremediation Mechanisms of Potentially Toxic Elements: A Proteomic Overview of Recent Advances

Potentially toxic elements (PTEs) such as cadmium (Cd), lead (Pb), chromium (Cr), and arsenic (As), polluting the environment, pose a significant risk and cause a wide array of adverse changes in plant physiology. Above threshold accumulation of PTEs is alarming which makes them prone to ascend along the food chain, making their environmental prevention a critical intervention. On a global scale, current initiatives to remove the PTEs are costly and might lead to more pollution. An emerging technology that may help in the removal of PTEs is phytoremediation. Compared to traditional methods, phytoremediation is eco-friendly and less expensive. While many studies have reported several plants with high PTEs tolerance, uptake, and then storage capacity in their roots, stem, and leaves. However, the wide application of such a promising strategy still needs to be achieved, partly due to a poor understanding of the molecular mechanism at the proteome level controlling the phytoremediation process to optimize the plant's performance. The present study aims to discuss the detailed mechanism and proteomic response, which play pivotal roles in the uptake of PTEs from the environment into the plant's body, then scavenge/detoxify, and finally bioaccumulate the PTEs in different plant organs. In this review, the following aspects are highlighted as: (i) PTE's stress and phytoremediation strategies adopted by plants and (ii) PTEs induced expressional changes in the plant proteome more specifically with arsenic, cadmium, copper, chromium, mercury, and lead with models describing the metal uptake and plant proteome response. Recently, interest in the comparative proteomics study of plants exposed to PTEs toxicity results in appreciable progress in this area. This article overviews the proteomics approach to elucidate the mechanisms underlying plant's PTEs tolerance and bioaccumulation for optimized phytoremediation of polluted environments.

Identification and functional analysis of cation-efflux transporter 1 from Brassica juncea L

BACKGROUND

Brassica juncea behaves as a moderate-level accumulator of various heavy metal ions and is frequently used for remediation. To investigate the roles of metal ion transporters in B. juncea, a cation-efflux family gene, BjCET1, was cloned and functionally characterized.

RESULTS

BjCET1 contains 382 amino acid residues, including a signature motif of the cation diffusion facilitator protein family, six classic trans-membrane-spanning structures and a cation-efflux domain. A phylogenetic analysis showed that BjCET1 has a high similarity level with metal tolerance proteins from other Brassica plants, indicating that this protein family is highly conserved in Brassica. BjCET1 expression significantly increased at very early stages during both cadmium and zinc treatments. Green fluorescence detection in transgenic tobacco leaves revealed that BjCET1 is a plasma membrane-localized protein. The heterologous expression of BjCET1 in a yeast mutant increased the heavy-metal tolerance and decreased the cadmium or zinc accumulations in yeast cells, suggesting that BjCET1 is a metal ion transporter. The constitutive expression of BjCET1 rescued the heavy-metal tolerance capability of transgenic tobacco plants.

CONCLUSIONS

The data suggest that BjCET1 is a membrane-localized efflux transporter that plays essential roles in heavy metal ion homeostasis and hyper-accumulation.

Integrative analysis of transcriptome and proteome provides insights into adaptation to cadmium stress in Sedum plumbizincicola

Sedum plumbizincicola, a cadmium (Cd) hyperaccumulating herbaceous plant, can accumulate large amounts of Cd in the above-ground tissues without being poisoned. However, the molecular mechanisms regulating the processes are not fully understood. In this study, Transcriptional and proteomic analyses were integrated to investigate the response of S. plumbizincicola plants to Cd stress and to identify key pathways that are potentially responsible for Cd tolerance and accumulation. A total of 630 DAPs (differentially abundant proteins, using fold change >1.5 and adjusted p-value <0.05) were identified from Tandem Mass Tag (TMT)- based quantitative proteomic profiling, which were enriched in processes including phenylpropanoid biosynthesis, protein processing in endoplasmic reticulum, and biosynthesis of secondary metabolites. Combined with the previous transcriptomic study, 209 genes and their corresponding proteins showed the identical expression pattern. The identified genes/proteins revealed the potential roles of several metabolism pathways, including phenylpropanoid biosynthesis, oxidative phosphorylation, phagosome, and glutathione metabolism, in mediating Cd tolerance and accumulation. Lignin staining and Cd accumulation assay of the transgenic lines over-expressing a selected Cd up-regulated gene SpFAOMT (Flavonoid 3',5'-methyltransferase) showed its functions in adapting to Cd stress, and provided insight into its role in lignin biosynthesis and Cd accumulation in S. plumbizincicola during Cd stress.

Impact of CuO nanoparticles on maize: Comparison with CuO bulk particles with special reference to oxidative stress damages and antioxidant defense status

The present study aimed to systematically investigate the particle size effects of copper (II) oxide [CuO nanoparticles (<50 nm) and CuO bulk particles (<10 μm)] on maize (Zea mays L.). Bioaccumulation of Cu, in vivo ROS generation, membrane damage, transcriptional modulation of antioxidant genes, cellular redox status of glutathione and ascorbate pool, expression patterns of COPPER TRANSPORTER 4 and stress responsive miRNAs (miR398a, miR171b, miR159f-3p) with their targets were investigated for better understanding of the underlying mechanisms and the extent of CuO nanoparticles and CuO bulk particles induced oxidative stress damages. More restricted seedling growth, comparatively higher membrane injury, marked decline in the levels of chlorophylls and carotenoids and severe oxidative burst were evident in CuO bulk particles challenged leaves. Dihydroethidium and CM-H2DCFDA staining further supported elevated reactive oxygen species generation in CuO bulk particles stressed roots. CuO bulk particles exposed seedlings accumulated much higher amount of Cu in roots as compared to CuO nanoparticles stressed plants with low root-to-shoot Cu translocation. Moderately high GR expression with maintenance of a steady GSH-GSSG ratio in CuO nanoparticles challenged leaves might be accountable for their rather improved performance under stressed condition. miR171b-mediated enhanced expression of SCARECROW 6 might participate in the marked decline of chlorophyll content in CuO bulk particles exposed leaves. Ineffective recycling of AsA pool is another decisive feature of inadequate performance of CuO bulk particles stressed seedlings in combating oxidative stress damages. Taken together, our findings revealed that toxicity of CuO bulk particles was higher than CuO nanoparticles and the adverse effects of CuO bulk particles on maize seedlings might be due to higher Cu ions dissolution.

Recent advances in physiological and molecular mechanisms of heavy metal accumulation in plants

Among abiotic stress, the toxicity of metals impacts negatively on plants' growth and productivity. This toxicity promotes various perturbations in plants at different levels. To withstand stress, plants involve efficient mechanisms through the implication of various signaling pathways. These pathways enhance the expression of many target genes among them gene coding for metal transporters. Various metal transporters which are localized at the plasma membrane and/or at the tonoplast are crucial in metal stress response. Furthermore, metal detoxification is provided by metal-binding proteins like phytochelatins and metallothioneins. The understanding of the molecular basis of metal toxicities signaling pathways and tolerance mechanisms is crucial for genetic engineering to produce transgenic plants that enhance phytoremediation. This review presents an overview of the recent advances in our understanding of metal stress response. Firstly, we described the effect of metal stress on plants. Then, we highlight the mechanisms involved in metal detoxification and the importance of the regulation in the response to heavy metal stress. Finally, we mentioned the importance of genetic engineering for enhancing the phytoremediation technique. In the end, the response to heavy metal stress is complex and implicates various components. Thus, further studies are needed to better understand the mechanisms involved in response to this abiotic stress.

Biochemical and Metabolic Plant Responses toward Polycyclic Aromatic Hydrocarbons and Heavy Metals Present in Atmospheric Pollution

Heavy metals (HMs) and polycyclic aromatic hydrocarbons (PAHs) are toxic components of atmospheric particles. These pollutants induce a wide variety of responses in plants, leading to tolerance or toxicity. Their effects on plants depend on many different environmental conditions, not only the type and concentration of contaminant, temperature or soil pH, but also on the physiological or genetic status of the plant. The main detoxification process in plants is the accumulation of the contaminant in vacuoles or cell walls. PAHs are normally transformed by enzymatic plant machinery prior to conjugation and immobilization; heavy metals are frequently chelated by some molecules, with glutathione, phytochelatins and metallothioneins being the main players in heavy metal detoxification. Besides these detoxification mechanisms, the presence of contaminants leads to the production of the reactive oxygen species (ROS) and the dynamic of ROS production and detoxification renders different outcomes in different scenarios, from cellular death to the induction of stress resistances. ROS responses have been extensively studied; the complexity of the ROS response and the subsequent cascade of effects on phytohormones and metabolic changes, which depend on local concentrations in different organelles and on the lifetime of each ROS species, allow the plant to modulate its responses to different environmental clues. Basic knowledge of plant responses toward pollutants is key to improving phytoremediation technologies.

Molecular and Biochemical Insights Into Early Responses of Hemp to Cd and Zn Exposure and the Potential Effect of Si on Stress Response

With the intensification of human activities, plants are more frequently exposed to heavy metals (HM). Zinc (Zn) and cadmium (Cd) are frequently and simultaneously found in contaminated soils, including agronomic soils contaminated by the atmospheric fallout near smelters. The fiber crop Cannabis sativa L. is a suitable alternative to food crops for crop cultivation on these soils. In this study, Cd (20 μM) and Zn (100 μM) were shown to induce comparable growth inhibition in C. sativa. To devise agricultural strategies aimed at improving crop yield, the effect of silicon (Si; 2 mM) on the stress tolerance of plants was considered. Targeted gene expression and proteomic analysis were performed on leaves and roots after 1 week of treatment. Both Cd- and Zn-stimulated genes involved in proline biosynthesis [pyrroline-5-carboxylate reductase (P5CR)] and phenylpropanoid pathway [phenylalanine ammonia-lyase (PAL)] but Cd also specifically increased the expression of PCS1-1 involved in phytochelatin (PC) synthesis. Si exposure influences the expression of numerous genes in a contrasting way in Cd- and Zn-exposed plants. At the leaf level, the accumulation of 122 proteins was affected by Cd, whereas 47 proteins were affected by Zn: only 16 proteins were affected by both Cd and Zn. The number of proteins affected due to Si exposure (27) alone was by far lower, and 12 were not modified by heavy metal treatment while no common protein seemed to be modified by both CdSi and ZnSi treatment. It is concluded that Cd and Zn had a clear different impact on plant metabolism and that Si confers a specific physiological status to stressed plants, with quite distinct impacts on hemp proteome depending on the considered heavy metal.

Activation of biochar through exoenzymes prompted by earthworms for vermibiochar production: A viable resource recovery option for heavy metal contaminated soils and water

The industrial revolution and indiscriminate usage of a wide spectrum of agrochemicals account for the dumping of heavy metals in the environment. In-situ/ex-situ physical, chemical, and bioremediation strategies with pros and cons have been adopted for recovering metal contaminated soils and water. Therefore, there is an urgent requirement for a cost-effective and environment-friendly technique to combat metal pollution. Biochar combined with earthworms and vermifiltration is a suitable emerging technique for the remediation of metal-polluted soils and water. The chemical substances (e.g., sodium hydroxide, zinc chloride, potassium hydroxide, and phosphoric acid) have been used to activate biochar, which also faces several shortcomings. Studies reveal that extracellular enzymes have been used to activate biochar which is produced by earthworms and microbes that can alter the surface of the biochar. The present review focuses on the global scenario of metal pollution and its remediation through biochar activation using earthworms. The earthworms and biochar can produce "vermibiochar" which is capable of reducing the metal ions from contaminated water and soils. The vermifiltration can be a suitable technology for metal removal from wastewater/effluent. Thus, the biochar has a trick of producing entirely new options at a time when vermifiltration and other technologies are least expected. Further attention to the biochar-assisted vermifiltration of different sources of wastewater is required to be explored for the large-scale utilization of the process.

Biochemical and metabolic responses of the deep-sea mussel Bathymodiolus platifrons to cadmium and copper exposure

Greater interest in commercial deep-sea mining has been accompanied by mounting environmental concerns, including metal contamination resulting from mining activities. However, little is known about the toxic effects of metal exposure on deep-sea life. Given its ability to accumulate metals from the surrounding environment, its wide distribution at both vents and seeps, and its high abundance, the deep-sea mussel Bathymodiolus platifrons could serve as an ideal model to investigate the toxicological responses of deep-sea organisms to metal exposure. Here, we evaluated metal accumulation, traditional metal-related biomarkers, namely acid phosphatase (ACP), alkaline phosphatase (AKP), superoxide dismutase, catalase, reduced glutathione, metallothioneins, and malondialdehyde, as well as metabolic profiles in the gills of B. platifrons after a 7-day exposure to copper (100 μg/L), cadmium (500 μg/L), or copper-plus-cadmium treatments (100 μg/L Cu and 500 μg/L Cd). Metal exposure concentrations selected in this study can be found in deep-sea hydrothermal environments. Metal exposure resulted in significant metal accumulation in the gills of the mussel, indicating that B. platifrons has promise for use as an indicator of deep-sea metal pollution levels. Traditional biomarkers (AKP, ACP, and measured antioxidants) revealed cellular injury and oxidative stress in mussels following metal exposure. Metabolic responses in the three treatment groups indicated that metal exposure perturbed osmoregulation, energy metabolism, and nucleotide metabolism in mussels, in a response marked by differentially altered levels of amino acids, hypotaurine, betaine, succinate, glucose 6-phosphate, fructose 6-phosphate, guanosine, guanosine 5'-monophosphate, and inosine. Nevertheless, several uniquely altered metabolites were found in each treatment exposure group, suggesting dissimilar modes of toxicity between the two metal types. In the Cd-exposed group, the monosaccharide D-allose, which is involved in suppressing mitochondrial ROS production, was downregulated, a response consistent with oxidative stress in Cd-exposed B. platifrons. In the Cu-exposed group, the detected alterations in dopamine, dopamine-related, and serotonin-related metabolites together suggest disturbed neurotransmission in Cu-exposed B. platifrons. In the Cu-plus-Cd group, we detected a decline in fatty acid levels, implying that exposure to both metals jointly exerted a negative influence on the physiological functioning of the mussel. To the best of our knowledge, this is the first study to investigate changes in metabolite profiles in Bathymodiolus mussels exposed to metal. The findings reported here advance our understanding of the adverse impact of metal exposure on deep-sea life and can inform deep-sea mining assessments through the use of multiple biomarkers.

Genomic patterns of structural variation among diverse genotypes of Sorghum bicolor and a potential role for deletions in local adaptation

Genomic structural mutations, especially deletions, are an important source of variation in many species and can play key roles in phenotypic diversification and evolution. Previous work in many plant species has identified multiple instances of structural variations (SVs) occurring in or near genes related to stress response and disease resistance, suggesting a possible role for SVs in local adaptation. Sorghum [Sorghum bicolor (L.) Moench] is one of the most widely grown cereal crops in the world. It has been adapted to an array of different climates as well as bred for multiple purposes, resulting in a striking phenotypic diversity. In this study, we identified genome-wide SVs in the Biomass Association Panel, a collection of 347 diverse sorghum genotypes collected from multiple countries and continents. Using Illumina-based, short-read whole-genome resequencing data from every genotype, we found a total of 24,648 SVs, including 22,359 deletions. The global site frequency spectrum of deletions and other types of SVs fit a model of neutral evolution, suggesting that the majority of these mutations were not under any types of selection. Clustering results based on single nucleotide polymorphisms separated the genotypes into eight clusters which largely corresponded with geographic origins, with many of the large deletions we uncovered being unique to a single cluster. Even though most deletions appeared to be neutral, a handful of cluster-specific deletions were found in genes related to biotic and abiotic stress responses, supporting the possibility that at least some of these deletions contribute to local adaptation in sorghum.

Metallothionein dependent-detoxification of heavy metals in the agricultural field soil of industrial area: Earthworm as field experimental model system

Earthworms are known to reclaim soil contamination and maintain soil health. In the present study, the concentration of DTPA extractable heavy metals, Cd, Cu, Cr, Pb, and Zn in vermicasts and tissues of the earthworms (anecic: Lampito mauritii; epigeic: Drawida sulcata) collected from the soils of four different industrial sites, Site-I (Sago industry), Site-II (Chemplast industry), Site-III (Dairy industry) and Site-IV (Dye industry) have been studied. The heavy metals in industrial soils recorded were 0.01-326.42 mg kg^-1 with higher Cu, Cr, and Zn contents while the vermicasts showed lower heavy metal loads with improved physicochemical properties and elevated humic substances. The higher humic substances dramatically decreased the heavy metals in the soil. The bioaccumulation factors of heavy metals (mg kg^-1) are in the order: Zn (54.50) > Cu (17.43) > Cr (4.54) > Pb (2.24) > Cd (2.12). The greatest amount of metallothionein protein (nmol g^-1) was recorded in earthworms from Site-IV (386.76) followed by Site-III (322.14), Site-II (245.82), and Site-I (232.21). Drawida sulcata can produce a considerable amount of metallothionein protein than Lampito mauritii as the metallothionein production is dependent upon the presence of pollutants. The molecular docking analysis indicates a binding score of 980 for Cd, Cr and Cu, and 372 for Zn. Pb may bind with a non-metallothionein protein of earthworms and bio-accumulated in the internal chloragogenous tissues. Metallothionein neutralizes the metal toxicity and controls the ingestion of essential elements.

Plant Recovery after Metal Stress-A Review

Contamination of the environment with metals, their adverse impact on plant performance and transmission to the human food chain through crops and vegetables are important concerns worldwide. Although the literature on metal contamination, toxicity and plant response to this stress factor is quite abundant, there are very limited reports on the phenomenon of plant recovery after metal stress. The present article reviews available literature on the recovery process examined in various plant species, in response to several metals (Al, Cd, Cu, Ni, Pb, Zn), applied at different concentrations and treatment duration. The reviewed studies have been carried out in laboratory conditions. However, it should be highlighted that although metal stress is not as transient as most of other stress factors (e.g., drought, heat, chilling), metal concentration in the soil may still decrease due to, e.g., leaching to lower soil layers or uptake by organisms. Thus, in natural conditions, plants may be subjected to post-metal-stress conditions. The review also discusses the mechanism behind efficient recovery and the impact of post metal stress on future plant performance-possible acquisition of stress memory, adaptation to unfavorable conditions and cross-tolerance towards other stress factors.

Biotechnological strategies for enhancing heavy metal tolerance in neglected and underutilized legume crops: A comprehensive review

Contamination of agricultural land and water by heavy metals due to rapid industrialization and urbanization including various natural processes have become one of the major constraints to crop growth and productivity. Several studies have reported that to counteract heavy metal stress, plants should be able to maneuver various physiological, biochemical and molecular processes to improve their growth and development under heavy metal stress. With the advent of modern biotechnological tools and techniques it is now possible to tailor legume and other plants overexpressing stress-induced genes, transcription factors, proteins, and metabolites that are directly involved in heavy metal stress tolerance. This review provides an in-depth overview of various biotechnological approaches and/or strategies that can be used for enhancing detoxification of the heavy metals by stimulating phytoremediation processes. Synthetic biology tools involved in the engineering of legume and other crop plants against heavy metal stress tolerance are also discussed herewith some pioneering examples where synthetic biology tools that have been used to modify plants for specific traits. Also, CRISPR based genetic engineering of plants, including their role in modulating the expression of several genes/ transcription factors in the improvement of abiotic stress tolerance and phytoremediation ability using knockdown and knockout strategies has also been critically discussed.

Regulation mechanisms of humic acid on Pb stress in tea plant (Camellia sinensis L.)

Though the interaction between humic acid (HA) and heavy metals has been widely reported, the effects of HA on the toxicity of heavy metals to plants are still in debate. In this study, the regulation mechanisms of HA on Pb stress in tea plant (Camellia sinensis L.) was investigated through hydroponic experiments, and the experimental results were explained by using transmission electron microscope (TEM), scanning transmission X-ray microscopes (STXM) and isobaric tags for relative and absolute quantitation (iTRAQ) differential proteomics. Significant alleviation of Pb stress was found with HA coexistence. TEM results showed that HA greatly mitigated the damage of cells caused by Pb stress. Compared with sole Pb treatment, the addition of HA increased the contents of pectin and pectic acid in the cell wall by 10.5% and 30.5%, while arabinose (Ara) and galactose (Gal) decreased by 20.5% and 15.9%, respectively, which were beneficial for increasing Pb adsorption capacity of the cell wall and promoting cell elongation. Moreover, iTRAQ differential proteomics analysis proved that HA strengthened the antioxidant system, promoted the synthesis of cell wall, and stabilized protein and sulfur-containing substance metabolism in molecular level. Notably, the concentration of calcium (Ca) in the cell wall of HA coexistence treatment was 47.4% higher than Pb treatment. STXM results also indicated that the distribution of Ca in the cell wall was restored with the presence of HA. This might promote the formation of the egg-box model, thus alleviating Pb stress in cells. Our results reveal the regulation mechanisms of HA on Pb detoxification in plants and provide useful information for improving the safety of agricultural products.

Genotoxic effects and proteomic analysis on Allium cepa var. agrogarum L. root cells under Pb stress

Ionic lead (Pb) in the environment has accumulated due to anthropogenic activities, causing a potential threat to plants and plant consumers. We conducted this study to reveal the molecular mechanism of Pb stress response in plants. The effects of Pb (5.0 and 15.0 μM) on mitosis, DNA replication, gene expression and proteins in root-tip cells of Allium cepa var. agrogarum L. were addressed. The results indicated that root growth was inhibited dramatically in Pb treatment groups. Chromosomal aberrations were observed and the mitotic index decreased during Pb treatments at different concentrations. The accumulation of reactive oxygen species (ROS) in onion roots was induced by Pb stress. Pb increased DNA damage and suppressed cell cycle progression. The above toxic effects got more serious with increasing Pb concentration and prolonging exposure time. A total of 17 proteins were expressed differentially between control and Pb exposure groups. Under Pb treatment, the decreased expression of Anx D1 indicated decreased defensive response; the decreased expression of SHMT1 indicated decreased respiration; the decreased expression of COMT2 indicated decreased response of other funtions; the increased expression of NDPK indicated increased transcription and protein synthesis; the increased expression of PR1 and CHI1 indicated increased pathogen invasion; the increased expression of ORC5 and MPK5 indicated the reduced DNA replicating activity; the decreased expression of POLD1 indicated the reduced DNA repair activity. Our results provide new insights at the proteomic level into the Pb-induced responses, defensive responses and toxic effects, and provide new molecular markers of the early events of plant responses to Pb toxicity.

Variable protein expression in marine-derived filamentous fungus Penicillium chrysogenum in response to varying copper concentrations and salinity

Copper is one of the essential trace dietary minerals for all living organisms, but is potentially toxic at higher concentrations, mainly due to the redox reactions in its transition state. Tolerance of microbes towards copper is primarily attributed to chelation and biosorption. In this study, marine-derived filamentous fungi were evaluated for their ability to remove Cu(ii) from a culture medium. Further, the cellular response of a select isolate to salinity stress (0, 35 and 100 PSU) and Cu(ii) stress (0, 100, and 500 ppm) was studied using the peptide mass fingerprinting technique, which revealed expression of 919 proteins, of which 55 proteins were commonly expressed across all conditions. Housekeeping proteins such as citrate synthase, pyruvate carboxylase, ribosomal proteins, ATP synthases, and more were expressed across all conditions. Reactive oxygen species scavenging proteins such as glutaredoxin, mitochondrial peroxiredoxins and thioredoxins were expressed under Cu(ii) and salinity stresses individually as well as in combination. Up-regulation of glutaredoxin under Cu(ii) stress with fold change values of 18.3 and 13.9 under 100 ppm and 500 ppm of Cu(ii) indicated active scavenging of free radicals to combat oxidative damage. The common mechanisms reported were enzymatic scavenging of free radicals, activation of DNA damage and repair proteins and probable intracellular metal chelation. This indicated multiple stress mechanisms employed by the isolate to combat the singular and synergistic effects of Cu(ii) and salinity stress.

Impact of Pb on Chlamydomonas reinhardtii at Physiological and Transcriptional Levels

Trace elements stress is one of the most damaging abiotic stresses in environment. Nevertheless, the defense mechanism in microalgae remains poorly understood. In this study, physiological and molecular methods were performed to analyze the defense responses in green alga Chlamydomonas reinhardtii. It was speculated that the defense responses might mainly be due to the regulation of hormone signaling, indicating its potential role in alleviating the Pb toxicity besides other physiological and molecular defense responses like decrease in growth rate, chlorophyll content and photosynthesis efficiency, intensification of antioxidative mechanisms, regulation of transcription factors, trace elements chelation, and sequestration into vacuole via trace elements transporters. The sole differentially expressed ATP-binding cassette (ABC) transporters indicated that ABC transporters might play a very important role in the transport and relocation of Pb in C. reinhardtii. Additionally, our data provide the required knowledge for future investigations regarding Pb toxicity and defense mechanisms in algae, and detection of trace elements pollution in environment.

Assessment of ZnO-NPs toxicity in maize: An integrative microRNAomic approach

Rapid expansion of nanotechnology and indiscriminate discharge of metal oxide nanoparticles (NPs) into the environment pose a serious hazard to the ecological receptors including plants. To better understand the role of miRNAs in ZnO-NPs stress adaptation, two small RNA libraries were prepared from control and ZnO-NPs (800 ppm, <50 nm particle size) stressed maize leaves. Meager performance of ZnO-NPs treated seedlings was associated with elevated tissue zinc accumulation, enhanced ROS generation, loss of root cell viability, increased foliar MDA content, decrease in chlorophyll and carotenoids contents. Deep sequencing identified 3 (2 known and 1 novel) up- and 77 (73 known and 4 novel) down-regulated miRNAs from ZnO-NPs challenged leaves. GO analysis reveals that potential targets of ZnO-NPs responsive miRNAs regulate diverse biological processes viz. plant growth and development (miR159f-3p, zma_18), ROS homeostasis (miR156b, miR166l), heavy metal transport and detoxification (miR444a, miR167c-3p), photosynthesis (miR171b) etc. Up-regulation of SCARECROW 6 in ZnO-NPs treated leaves might be responsible for suppression of chlorophyll biosynthesis leading to yellowing of leaves. miR156b.1 mediated up-regulation of CALLOSE SYNTHASE also does not give much protection against ZnO-NPs treatment. Taken together, the findings shed light on the miRNA-guided stress regulatory networks involved in plant adaptive responses to ZnO-NPs stress.

Silicon regulates the expression of vacuolar H+-pyrophosphatase 1 and decreases cadmium accumulation in rice (Oryza sativa L.)

Deciphering the mechanism of Cd accumulation in crops is imperative for minimizing soil-to-plant transfer of Cd to improve safe food production. Hydroponic experiments were performed examining Cd accumulation, growth performance and protein characteristics of two rice genotypes, Xiushui817 and Zheda821, with low and high grain Cd accumulation, respectively, under Cd stress and in the presence of Si. Xiushui817 had lower root-to-shoot Cd translocation and was more sensitive to Cd stress than Zheda821. Si reduced the shoot Cd content in both genotypes but more efficacy in Zheda821. Tandem mass tags (TMT)-based proteomic analysis identified 25 proteins associated with low grain Cd accumulation, including vacuolar H⁺-pyrophosphatase 1 (OVP1) that was up-regulated after Si addition in Zheda821. The sequence comparison of OVP1 showed one nucleotide difference in Xiushui817 relative to Zheda821 resulting in one amino acid. Overexpression of OVP1 reduced shoot Cd concentration and improved the growth of rice compared with WT under both control and Cd treatment. The results highlight the significant roles of OVP1 in both Cd accumulation and the Si-induced Cd reduction in rice. Our findings provide valuable insights into the molecular mechanism of low Cd accumulation and Si-induced decrease in Cd accumulation in rice. OVP1 could be used for transgenic overexpression in rice or other cereals for safe food production.

Variations in Growth, Physiology, and Antioxidative Defense Responses of Two Tomato (Solanum lycopersicum L.) Cultivars after Co-Infection of Fusarium oxysporum and Meloidogyne incognita

The soil-borne fungus Fusarium oxysporum (Fo) and the nematode Meloidogyne incognita (Mi) are destructive pathogens that cause substantial yield losses to tomato (Solanum lycopersicum L.) crops worldwide. The present study sought to elucidate the physiological, biochemical, and cytological responses of tomato cultivars (Gailing maofen 802 and Zhongza 09) by root invasion of Fo (1 × 105 CFUmL−1) and Mi (1500 second-stage juveniles (J2) alone and in combination after 14 days. Results revealed that combined inoculation of Fo and Mi significantly increased disease intensity, electrolyte leakage, and hydrogen peroxide and malondialdehyde contents; and decreased photosynthetic capacity and enzyme activity in both cultivars as compared to their solo inoculation. Increasing the disease intensity reduced the maximum morphological traits, such as shoot length, total dry weight, and total chlorophyll contents, in G. maofen 802 (by 32%, 54.2%, and 52.3%, respectively) and Zhongza 09 (by 18%, 32%, and 21%, respectively) as compared to the control. Others factors were also reduced in G. maofen 802 and Zhongza 09, such as photosynthetic capacity (by 70% and 57%, respectively), stomatal conductance (by 86% and 70%, respectively), photochemical quantum yield of photosystem II (YII) (by 36.6% and 29%, respectively), and electron transport rate (by 17.7% and 10%, respectively), after combined inoculation of Fo and Mi. Furthermore, the combined infestation of Fo and Mi resulted in reduced activity of plant-defense-related antioxidants in G. maofen 802 compared with their single application or control. However, these antioxidants were highly up-regulated in Zhongza 09 (by 59%–93%), revealing the induction of tolerance against studied pathogens. The transmission electron microscopy (TEM) results further demonstrated that root cells of Zhongza 09 had unique tetrahedral crystal-like structures in the membrane close to mitochondria under all treatments except control. Therefore, it is concluded that Mi caused severe root damage, suppressed plant growth, depleted antioxidants, and caused high generation of ROS in the presence of Fo as compared to its solo inoculation. Tolerant cultivars adopted different mechanistic strategies at the structural and cellular levels to tolerate the Mi and Fo stresses.

Identification and Characterization of an OSH1 Thiol Reductase from Populus Trichocarpa

Interferon gamma-induced lysosomal thiol reductase (GILT) is abundantly expressed in antigen-presenting cells and participates in the treatment and presentation of antigens by major histocompatibility complex II. Also, GILT catalyzes the reduction of disulfide bonds, which plays an important role in cellular immunity. (1) Background: At present, the studies of GILT have mainly focused on animals. In plants, GILT homologous gene (Arabidopsis thalianaOSH1: AtOSH1) was discovered in the forward screen of mutants with compromised responses to sulphur nutrition. However, the complete properties and functions of poplar OSH1 are unclear. In addition, CdCl2 stress is swiftly engulfing the limited land resources on which humans depend, restricting agricultural production. (2) Methods: A prokaryotic expression system was used to produce recombinant PtOSH1 protein, and Western blotting was performed to identify its activity. In addition, a simplified version of the floral-dip method was used to transform A. thaliana. (3) Results: Here, we describe the identification and characterization of OSH1 from Populus trichocarpa. The deduced PtOSH1 sequence contained CQHGX2ECX2NX4C and CXXC motifs. The transcript level of PtOSH1 was increased by cadmium (Cd) treatment. In addition, recombinant PtOSH1 reduced disulfide bonds. A stress assay showed that PtOSH1-overexpressing (OE) A. thaliana lines had greater resistance to Cd than wild-type (WT) plants. Also, the activities of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) in PtOSH1-OE plants were significantly higher than those in WT A. thaliana. These results indicate that PtOSH1 likely plays an important role in the response to Cd by regulating the reactive oxygen species (ROS)-scavenging system. (4) Conclusions: PtOSH1 catalyzes the reduction of disulfide bonds and behaves as a sulfhydryl reductase under acidic conditions. The overexpression of PtOSH1 in A. thaliana promoted root development, fresh weight, and dry weight; upregulated the expression levels of ROS scavenging-related genes; and improved the activity of antioxidant enzymes, enhancing plant tolerance to cadmium (Cd) stress. This study aimed to provide guidance that will facilitate future studies of the function of PtOSH1 in the response of plants to Cd stress.

Influence of PGPB Inoculation on HSP70 and HMA3 Gene Expression in Switchgrass under Cadmium Stress

This study aimed to evaluate the gene expression of HSP70 and HMA3 in the switchgrass inoculated with plant-growth-promoting-bacteria (PGPB) under cadmium (Cd) stress and to observe the benefit of PGPB in plant growth and development. Plants were grown in hydroponic culture and treated with PGPB inoculants: Pseudomonas grimontii, Pantoea vagans, Pseudomonas veronii, and Pseudomonas fluorescens with the strains Bc09, So23, E02, and Oj24, respectively. The experimental results revealed that HSP70 and HMA3 genes expressed highly in the PGPB-inoculated plants under Cd stress. In addition, the expression of HSP70 and HMA3 genes was considerably higher in the first two days after successive four-day exposure of Cd in plants compared to the last two days of exposure. Increased biomass and indole-3-acetic-acid production with reduced Cd accumulation were observed in the PGPB-inoculated plants under Cd stress compared to the Cd-control plants. These PGPB, with their beneficial mechanisms, protect plants by modifying the gene expression profile that arises during Cd-toxic conditions and increased the healthy biomass of switchgrass. This demonstrates there is a correlation among the growth parameters under Cd stress. The PGPB in this study may help to intensify agriculture by triggering mechanisms to encourage plant growth and development under heavy metal stress.

Identification and Allelopathy of Green Garlic (Allium sativum L.) Volatiles on Scavenging of Cucumber (Cucumis sativus L.) Reactive Oxygen Species

Garlic and formulations containing allicin are used widely as fungicides in modern agriculture. However, limited reports are available on the allelopathic mechanism of green garlic volatile organic compounds (VOCs) and its component allelochemicals. The aim of this study was to investigate VOCs of green garlic and their effect on scavenging of reactive oxygen species (ROS) in cucumber. In this study, green garlic VOCs were collected by HS-SPME, then analyzed by GS-MS. Their biological activity were verified by bioassays. The results showed that diallyl disulfide (DADS) is the main allelochemical of green garlic VOCs and the DADS content released from green garlic is approximately 0.08 mg/g. On this basis, the allelopathic effects of green garlic VOCs in vivo and 1 mmol/L DADS on scavenging of ROS in cucumber seedlings were further studied. Green garlic VOCs and DADS both reduce superoxide anion and increase the accumulation of hydrogen peroxide of cucumber seedlings. They can also regulate active antioxidant enzymes (SOD, CAT, POD), antioxidant substances (MDA, GSH and ASA) and genes (CscAPX, CsGPX, CsMDAR, CsSOD, CsCAT, CsPOD) responding to oxidative stress in cucumber seedlings.

Quantitative proteomic analysis of tomato genotypes with differential cadmium tolerance

This is a report on comprehensive characterization of cadmium (Cd)-exposed root proteomes in tomato using label-free quantitative proteomic approach. Two genotypes differing in Cd tolerance, Pusa Ruby (Cd-tolerant) and Calabash Rouge (Cd-sensitive), were exposed during 4 days to assess the Cd-induced effects on root proteome. The overall changes in both genotypes in terms of differentially accumulated proteins (DAPs) were mainly associated to cell wall, redox, and stress responses. The proteome of the sensitive genotype was more responsive to Cd excess, once it presented higher number of DAPs. Contrasting protein accumulation in cellular component was observed: Cd-sensitive enhanced intracellular components, while the Cd-tolerant increased proteins of extracellular and envelope regions. Protective and regulatory mechanisms were different between genotypes, once the tolerant showed alterations of various protein groups that lead to a more efficient system to cope with Cd challenge. These findings could shed some light on the molecular basis underlying the Cd stress response in tomato, providing fundamental insights for the development of Cd-safe cultivars. Graphical abstract.

Comparative proteomic study of phytotoxic effects of silver nanoparticles and silver ions on tobacco plants

Widespread application of silver nanoparticles (AgNPs), due to their antibacterial and antifungal properties, increases their release into the environment and potential detrimental impact on living organisms. Plants may serve as a potential pathway for AgNPs bioaccumulation and a route into the food chain, hence investigation of AgNP phytotoxic effects are of particular importance. Since proteins are directly involved in stress response, studies of their abundance changes can help elucidate the mechanism of the AgNP-mediated phytotoxicity. In this study, we investigated proteomic changes in tobacco (Nicotiana tabacum) exposed to AgNPs and ionic silver (AgNO3). A high overlap of differently abundant proteins was found in root after exposure to both treatments, while in leaf, almost a half of the proteins exhibited different abundance level between treatments, indicating tissue-specific responses. Majority of the identified proteins were down-regulated in both tissues after exposure to either AgNPs or AgNO3; in roots, the most affected proteins were those involved in response to abiotic and biotic stimuli and oxidative stress, while in leaf, both treatments had the most prominent effect on photosynthesis-related proteins. However, since AgNPs induced higher suppression of protein abundance than AgNO3, we conclude that AgNP effects can, at least partially, be attributed to nanoparticle form.

iTRAQ-Based Quantitative Analysis of Responsive Proteins Under PEG-Induced Drought Stress in Wheat Leaves

Drought is an important abiotic stress that seriously restricts crop productivity. An understanding of drought tolerance mechanisms offers guidance for cultivar improvement. In order to understand how a well-known wheat genotype Jinmai 47 responds to drought, we adopted the iTRAQ and LC/MS approaches and conducted proteomics analysis of leaves after exposure to 20% of polyethylene glycol-6000 (PEG)-induced stress for 4 days. The study identified 176 differentially expressed proteins (DEPs), with 65 (36.5%) of them being up-regulated, and 111 (63.5%) down-regulated. DEPs, located in cellular membranes and cytosol mainly, were involved in stress and redox regulation (51), carbohydrate and energy metabolism (36), amino acid metabolism (24), and biosynthesis of other secondary metabolites (20) primarily. Under drought stress, TCA cycle related proteins were up-regulated. Antioxidant system, signaling system, and nucleic acid metabolism etc. were relatively weakened. In comparison, the metabolism pathways that function in plasma dehydration protection and protein structure protection were strongly enhanced, as indicated by the improved biosynthesis of 2 osmolytes, sucrose and Proline, and strongly up-regulated protective proteins, LEA proteins and chaperones. SUS4, P5CSs, OAT, Rab protein, and Lea14-A were considered to be important candidate proteins, which deserve to be further investigated.

Molecular Mechanisms of Tungsten Toxicity Differ for Glycine max Depending on Nitrogen Regime

Tungsten (W) finds increasing application in military, aviation and household appliance industry, opening new paths into the environment. Since W shares certain chemical properties with the essential plant micronutrient molybdenum (Mo), it is proposed to inhibit enzymatic activity of molybdoenzymes [e.g., nitrate reductase (NR)] by replacing the Mo-ion bound to the co-factor. Recent studies suggest that W, much like other heavy metals, also exerts toxicity on its own. To create a comprehensive picture of tungsten stress, this study investigated the effects of W on growth and metabolism of soybean (Glycine max), depending on plant nitrogen regime [nitrate fed (N fed) vs. symbiotic N2 fixation (N fix)] by combining plant physiological data (biomass production, starch and nutrient content, N2 fixation, nitrate reductase activity) with root and nodule proteome data. Irrespective of N regime, NR activity and total N decreased with increasing W concentrations. Nodulation and therefore also N2 fixation strongly declined at high W concentrations, particularly in N fix plants. However, N2 fixation rate (g N fixed g-1 nodule dwt) remained unaffected by increasing W concentrations. Proteomic analysis revealed a strong decline in leghemoglobin and nitrogenase precursor levels (NifD), as well as an increase in abundance of proteins involved in secondary metabolism in N fix nodules. Taken together this indicates that, in contrast to the reported direct inhibition of NR, N2 fixation appears to be indirectly inhibited by a decrease in nitrogenase synthesis due to W induced changes in nodule oxygen levels of N fix plants. Besides N metabolism, plants exhibited a strong reduction of shoot (both N regimes) and root (N fed only) biomass, an imbalance in nutrient levels and a failure of carbon metabolic pathways accompanied by an accumulation of starch at high tungsten concentrations, independent of N-regime. Proteomic data (available via ProteomeXchange with identifier PXD010877) demonstrated that the response to high W concentrations was independent of nodule functionality and dominated by several peroxidases and other general stress related proteins. Based on an evaluation of several W responsive proteotypic peptides, we identified a set of protein markers of W stress and possible targets for improved stress tolerance.

Biochar amendment improves crop production in problem soils: A review

Problem soils are referred to as those with poor physical, chemical, and biological properties that inhibit or prevent plant growth. These poor properties may be a result of soil formation processes but are largely due to inappropriate farming practices or anthropogenic pollution. The world has lost a third of its arable land due to erosion and pollution in the past 40 years. Thus, there is an urgent need for improving and remediating problem soils. As a novel multifunctional carbon material, biochar has been widely used as a soil amendment for improving soil quality. Previous reviews have summarized the characteristics of biochar, the interactions with various soil contaminants, and the effects on soil quality, soil productivity, and carbon sequestration. Relatively limited attention has been focused on the effects of biochar amendment on plant growth in problem soils. As a result, a comprehensive review of literature in the Web of Science was conducted with a focus on the effects of biochar amendment on plant growth in problems soils. The review is intended to present an overview about problem soils, biochars as functional materials for soil amendment, how amended biochars interact with soils, soil microbes, and plant roots in remediation of problem soil and improve plant growth. Additionally, existing knowledge gaps and future directions are discussed. Information gathered from this review suggests that biochar amendment is a viable way of improving the quality of problem soils and enhancing crop production. It is anticipated that further research on biochar amendment will increase our understanding on the interactions of biochar with components of problem soils, speed up our effort on soil remediation, and improve crop production in problem soils.

Long- and short-term protective responses of rice seedling to combat Cr(VI) toxicity

In India, rice is the principal crop and is the staple diet of majority of the population. Widespread use of hexavalent chromium [Cr(VI)] in leather processing, wood preservatives, stainless-steel manufacture, and electroplating industries has resulted in contamination of paddy fields and poses a great challenge to the society be it crops, animals, or human beings. Cr(VI) toxicity results in growth inhibition and leading to changes in components of antioxidant systems as well as secondary metabolites. We evaluated the comparative short and long term effects of Cr(VI) stress on rice plants to explore the plant defense responses against Cr stress. Different assays including the phenolic and flavonoid content evaluation, malondialdehyde (MDA), proline, antioxidant enzyme analysis, and DPPH assay were performed to understand the plant response against the Cr(VI) stress. Total phenols and flavonoids were significantly higher in Cr stressed plants as compared to control groups. Under Cr(VI) exposure, significant higher accumulation of proline was observed. Similarly, high levels of MDA content were also observed after 7 days of Cr stress. In addition, the antioxidant activities such as GST, APX, and SOD including DPPH radical scavenging were also markedly increased during Cr(VI) stress. Further identification and quantification of phenols were done spectrophotometrically to view the whole spectrum of phenolics. HPLC analysis showed gallic acid as the main contributor to abiotic defense response. Our study showed that Cr stress imposes serious toxic effects and plant phenolics have a protective role against metal stress.