Proteomic Insights into Trichome Responses to Elevated Elemental Stress in Cation Exchanger (CAX) Mutants.

Research on elemental distribution in plants is crucial for understanding nutrient uptake, environmental adaptation, and optimizing agricultural practices for sustainable food production. Plant trichomes, with their self-contained structures and easy accessibility, offer a robust model system for investigating elemental repartitioning. Transport proteins, such as the four functional cation exchangers (CAXs) in Arabidopsis, are low-affinity, high-capacity transporters primarily located on the vacuole. Mutants in these transporters have been partially characterized, with one of the phenotypes of the CAX1 mutant being altered tolerance to low-oxygen conditions. A simple visual screen demonstrated trichome density and morphology in cax1 and quadruple CAX (cax1-4: qKO) mutants remained unaltered. Here we used SXRF (Synchrotron X-Ray Fluorescence) to show that trichomes in CAX-deficient lines accumulated high levels of chlorine, potassium, calcium, and manganese. Proteomic analysis on isolated Arabidopsis trichomes. showed changes in protein abundance in response to changes in element accumulation. The CAX mutants showed an increased abundance of plasma membrane ATPase and vacuolar H-pumping proteins, and proteins associated with water movement and endocytosis, while also showing changes in proteins associated with the regulation of plasmodesmata. These findings advance our understanding of the integration of CAX transport with elemental homeostasis within trichomes and shed light on how plants modulate protein abundance under conditions of altered elemental levels.

The evolution of the duckweed ionome mirrors losses in structural complexity.

BACKGROUND AND AIMS: The duckweeds (Lemnaceae) consist of 36 species exhibiting impressive phenotypic variation, including the progressive evolutionary loss of a fundamental plant organ, the root. Loss of roots and reduction of vascular tissues in recently derived taxa occur in concert with genome expansions of ≤14-fold. Given the paired loss of roots and reduction in structural complexity in derived taxa, we focus on the evolution of the ionome (whole-plant elemental contents) in the context of these fundamental changes in body plan. We expect that progressive vestigiality and eventual loss of roots might have both adaptive and maladaptive consequences that are hitherto unknown. METHODS: We quantified the ionomes of 34 accessions in 21 species across all duckweed genera, spanning 70 Myr in this rapidly cycling plant (doubling times are as rapid as ~24 h). We related both micro- and macroevolutionary ionome contrasts to body plan remodelling and showed nimble microevolutionary shifts in elemental accumulation and exclusion in novel accessions. KEY RESULTS: We observed a robust directional trend in calcium and magnesium levels, decreasing from the ancestral representative Spirodela genus towards the derived rootless Wolffia, with the latter also accumulating cadmium. We also identified abundant within-species variation and hyperaccumulators of specific elements, with this extensive variation at the fine (as opposed to broad) scale. CONCLUSIONS: These data underscore the impact of root loss and reveal the very fine scale of microevolutionary variation in hyperaccumulation and exclusion of a wide range of elements. Broadly, they might point to trade-offs not well recognized in ionomes.

Halophytes and heavy metals: A multi-omics approach to understand the role of gene and genome duplication in the abiotic stress tolerance of Cakile maritima.

PREMISE: The origin of diversity is a fundamental biological question. Gene duplications are one mechanism that provides raw material for the emergence of novel traits, but evolutionary outcomes depend on which genes are retained and how they become functionalized. Yet, following different duplication types (polyploidy and tandem duplication), the events driving gene retention and functionalization remain poorly understood. Here we used Cakile maritima, a species that is tolerant to salt and heavy metals and shares an ancient whole-genome triplication with closely related salt-sensitive mustard crops (Brassica), as a model to explore the evolution of abiotic stress tolerance following polyploidy. METHODS: Using a combination of ionomics, free amino acid profiling, and comparative genomics, we characterize aspects of salt stress response in C. maritima and identify retained duplicate genes that have likely enabled adaptation to salt and mild levels of cadmium. RESULTS: Cakile maritima is tolerant to both cadmium and salt treatments through uptake of cadmium in the roots. Proline constitutes greater than 30% of the free amino acid pool in C. maritima and likely contributes to abiotic stress tolerance. We find duplicated gene families are enriched in metabolic and transport processes and identify key transport genes that may be involved in C. maritima abiotic stress tolerance. CONCLUSIONS: These findings identify pathways and genes that could be used to enhance plant resilience and provide a putative understanding of the roles of duplication types and retention on the evolution of abiotic stress response.

Adaptive physio-anatomical modulations and ionomics of Volkameria inermis L. in response to NaCl.

This study illustrates the salinity tolerance mechanisms in Volkameria inermis (a mangrove-associate), making it an ideal candidate for establishment in saline lands. The plant was exposed to 100, 200, 300, and 400 mM NaCl and the TI value indicates that the stress-imparting concentration was 400 mM. There was a decrease in biomass and tissue water, and a gradual increase in osmolytes like soluble sugars, proline, and free amino acids content was observed in plantlets with the increase in NaCl concentrations. Higher number of lignified cells in the vascular region of the plantlet's leaves treated with NaCl (400 mM) may influence the transport through the conducting tissues. SEM data reveals the presence of thick-walled xylem elements, an increased number of trichomes, and partially/fully closed stomata in the 400 mM NaCl-treated samples of V. inermis. In general, macro and micronutrient distribution tend to be affected in the NaCl-treated plantlets. However, Na content increased remarkably in plantlets treated with NaCl, and the highest accumulation was observed in roots (5.58-fold). Volkameria inermis can be a good option for phytodesalination in salt-affected areas since it is equipped with strong NaCl tolerance strategies and can be exploited for desalinization purpose of salt affected lands.

The phytodesalination potential of V. inermis was proved with the aid of physiochemical and anatomical studies, which was not yet revealed. The present study elucidated the level of NaCl tolerance in V. inermis and the development of associated adaptive responses.

Salivary elemental signature of dental caries: a systematic review and meta-analysis of ionomics studies.

Trace- and macro-chemical elements are crucial for cellular physiological functioning, and their alterations in biological fluids might be associated with an underlying pathological state. Hence, this study aimed to examine and summarize the published literature concerning the application of salivary ionomics for caries diagnosis. An extensive search of studies was conducted using PubMed, EMBASE, Web of Science, and Scopus, without any language and year restriction for answering the following PECO question: "In subjects (i.e., children, adolescents, or adults) with good systematic health, are there any variations in the salivary concentrations of trace- or macro-elements between caries-free (CF) individuals and caries-active (CA) subjects?" A modified version of the QUADOMICS tool was used to assess the quality of the included studies. The Review Manager Version 5.4.1. was used for data analyses. The analysis of salivary chemical elements that significantly differed between CF and CA subjects was also performed. Thirty-four studies were included, involving 2299 CA and 1669 CF subjects, having an age range from 3 to 64 years in over 16 countries. The meta-analysis revealed a statistically significant difference (p < 0.05) in the salivary levels of calcium, phosphorus, chloride, magnesium, potassium, sodium, and zinc between CA and CF subjects, suggesting higher levels of calcium, phosphorus, potassium, and sodium in CF subjects while higher levels of chloride, magnesium, and zinc in CA patients. Half of the included studies (17/34) were considered high quality, while the remaining half were considered medium quality. Only zinc and chloride ions were found to be higher significantly and consistent in CF and CA subjects, respectively. Conflicting outcomes were observed for all other salivary chemical elements including aluminum, bromine, calcium, copper, fluoride, iron, potassium, magnesium, manganese, sodium, ammonia, nitrite, nitrate, phosphorus, lead, selenium, and sulfate ions.

High-yield rice with rich nutrition and low toxicity can be obtained under potato-rice cropping system.

BACKGROUND: Rice is often rotated with dryland crops to produce sufficient foodstuff, as rice is the main food crop of humans. In order to verify whether under the intensive rice-based cropping system, high yield and good quality of rice can be achieved simultaneously to ensure food security. Five long-term paddy-upland rotations - wheat-rice (WR), rapeseed-rice (RR), garlic-rice (GR), broad beans-rice (BR) and potato-rice (PR) - were conducted from 2014 to investigate rice yield, along with the profiling of 24 elements in rice grain. RESULTS: Mg, Zn, Cu, As, Mo and Sb concentrations were highest in the aleurone layer, and Ag and Cd concentrations showed little variation among different parts of the rice grain. Al, Ti, V, Si, Fe and Tl concentrations in the endosperm under GR were higher, while the Se concentration under PR was the highest. Furthermore, the yield of GR and PR were higher than the other three rotations with N supplementation, and the sustainable yield index of PR and WR were larger than 0.8. CONCLUSION: When we consider the concentration of toxic (As, Cd and Pb) and nutrient elements (Ca, Fe, Zn, Se, Cu and Mg) in the endosperm and grain yields, PR can simultaneously achieve high yield, high nutrition and low toxicity with different nitrogen treatments. Here we provide novel insights regarding the selection of rice-based cropping systems, focused on producing nutritious and safe rice with high grain yield. © 2024 Society of Chemical Industry.

Gene regulation and ionome homeostasis in rice plants in response to arsenite stress: potential connection between transcriptomics and ionomics.

Ionomics and transcriptomics were applied to demonstrate response of rice to arsenite [As(III)] stress in the current study. Rice plants were cultured in nutrient solutions treated with 0, 100 and 500 µg/L As(III) coded as CK, As1 and As5, respectively. The rice ionomes exhibited discriminatory response to environmental disturbances. Solid evidence of the effects of As(III) stress on binding, transport or metabolism of P, K, Ca, Zn and Cu was obtained in this work. Differentially expressed genes (DEGs) in the shoots were identified in three datasets: As1 vs CK, As5 vs CK and As5 vs As1. DEGs identified simultaneously in two or three datasets were selected for subsequent interaction and enrichment analyses. Upregulation of genes involved in protein kinase activity, phosphorus metabolic process and phosphorylation were detected in the rice treated with As(III), resulting in the maintenance of P homeostasis in the shoots. Zn and Ca binding genes were up-regulated since excess As inhibited the translocation of Zn and Ca from roots to shoots. Increased expression of responsive genes including HMA, WRKY, NAC and PUB genes conferred As tolerance in the rice plants to cope with external As(III) stress. The results suggested that As(III) stress could disturb the uptake and translocation of macro and essential elements by rice. Plants could regulate the expression of corresponding genes to maintain mineral nutrient homeostasis for essential metabolic processes.

Functional characterization of SLC39 family members ZIP5 and ZIP10 in overexpressing HEK293 cells reveals selective copper transport activity.

Zinc is the second most prevalent metal element present in living organisms, and control of its concentration is pivotal to physiology. The amount of zinc available to the cell cytoplasm is regulated by the activity of members of the SLC39 family, the ZIP proteins. Selectivity of ZIP transporters has been the focus of earlier studies which provided a biochemical and structural basis for the selectivity for zinc over other metals such as copper, iron, and manganese. However, several previous studies have shown how certain ZIP proteins exhibit higher selectivity for metal elements other than zinc. Sequence similarities suggest an evolutionary basis for the elemental selectivity within the ZIP family. Here, by engineering HEK293 cells to overexpress ZIP proteins, we have studied the selectivity of two phylogenetic clades of ZIP proteins, that is ZIP8/ZIP14 (previously known to be iron and manganese transporters) and ZIP5/ZIP10. By incubating ZIP over-expressing cells in presence of several divalent metals, we found that ZIP5 and ZIP10 are high affinity copper transporters with greater selectivity over other elements, revealing a novel substrate signature for the ZIP5/ZIP10 clade.

Rapid Prediction of Nutrient Concentration in Citrus Leaves Using Vis-NIR Spectroscopy.

The nutritional diagnosis of crops is carried out through costly foliar ionomic analysis in laboratories. However, spectroscopy is a sensing technique that could replace these destructive analyses for monitoring nutritional status. This work aimed to develop a calibration model to predict the foliar concentrations of macro and micronutrients in citrus plantations based on rapid non-destructive spectral measurements. To this end, 592 'Clementina de Nules' citrus leaves were collected during several months of growth. In these foliar samples, the spectral absorbance (430-1040 nm) was measured using a portable spectrometer, and the foliar ionomics was determined by emission spectrometry (ICP-OES) for macro and micronutrients, and the Kjeldahl method to quantify N. Models based on partial least squares regression (PLS-R) were calibrated to predict the content of macro and micronutrients in the leaves. The determination coefficients obtained in the model test were between 0.31 and 0.69, the highest values being found for P, K, and B (0.60, 0.63, and 0.69, respectively). Furthermore, the important P, K, and B wavelengths were evaluated using the weighted regression coefficients (BW) obtained from the PLS-R model. The results showed that the selected wavelengths were all in the visible region (430-750 nm) related to foliage pigments. The results indicate that this technique is promising for rapid and non-destructive foliar macro and micronutrient prediction.

Integrating Multi-Omics Analysis Reveals the Regulatory Mechanisms of White-Violet Mutant Flowers in Grape Hyacinth (Muscari latifolium).

Grape hyacinth (Muscari spp.) is a famous bulbous blue flower; however, few bicolor varieties are available in the market. Therefore, the discovery of bicolor varieties and understanding of their mechanisms are crucial to the breeding of new varieties. In this study, we report a significant bicolor mutant with white upper and violet lower portions, with both parts belonging to a single raceme. Ionomics showed that pH and metal element contents were not responsible for the bicolor formation. Targeted metabolomics illustrated that the content of the 24 color-related compounds was significantly lower in the upper part than that in the lower part. Moreover, full-length transcriptomics combined with second-generation transcriptomics revealed 12,237 differentially expressed genes in which anthocyanin synthesis gene expression of the upper part was noted to be significantly lower than that of the lower part. Transcription factor differential expression analysis was used to describe the presence of a pair of MaMYB113a/b sequences, with low levels of expression in the upper part and high expression in the lower part. Furthermore, tobacco transformation confirmed that overexpression of MaMYB113a/b can promote anthocyanin accumulation in tobacco leaves. Accordingly, the differential expression of MaMYB113a/b contributes the formation of a bicolor mutant in Muscari latifolium.

Ionome profiling and arsenic speciation provide evidence of arsenite detoxification in rice by phosphate and arsenite-oxidizing bacteria.

Arsenite (As(III)) as the most toxic and mobile form is the dominant arsenic (As) species in flooded paddy fields, resulting in higher accumulation of As in paddy rice than other terrestrial crops. Mitigation of As toxicity to rice plant is an important way to safeguard food production and safety. In the current study, As(III)-oxidizing bacteria Pseudomonas sp. strain SMS11 was inoculated with rice plants to accelerate conversion of As(III) into lower toxic arsenate (As(V)). Meanwhile, additional phosphate was supplemented to restrict As(V) uptake by the rice plants. Growth of rice plant was significantly inhibited under As(III) stress. The inhibition was alleviated by the introduction of additional P and SMS11. Arsenic speciation showed that additional P restricted As accumulation in the rice roots via competing common uptake pathways, while inoculation with SMS11 limited As translocation from root to shoot. Ionomic profiling revealed specific characteristics of the rice tissue samples from different treatment groups. Compared to the roots, ionomes of the rice shoots were more sensitive to environmental perturbations. Both extraneous P and As(III)-oxidizing bacteria SMS11 could alleviate As(III) stress to the rice plants through promoting growth and regulating ionome homeostasis.

1,135 ionomes reveal the global pattern of leaf and seed mineral nutrient and trace element diversity in Arabidopsis thaliana.

Soil is a heterogeneous reservoir of essential elements needed for plant growth and development. Plants have evolved mechanisms to balance their nutritional needs based on availability of nutrients. This has led to genetically based variation in the elemental composition, the 'ionome', of plants, both within and between species. We explore this natural variation using a panel of wild-collected, geographically widespread Arabidopsis thaliana accessions from the 1001 Genomes Project including over 1,135 accessions, and the 19 parental accessions of the Multi-parent Advanced Generation Inter-Cross (MAGIC) panel, all with full-genome sequences available. We present an experimental design pipeline for high-throughput ionomic screenings and analyses with improved normalisation procedures to account for errors and variability in conditions often encountered in large-scale, high-throughput data collection. We report quantification of the complete leaf and seed ionome of the entire collection using this pipeline and a digital tool, Ion Explorer, to interact with the dataset. We describe the pattern of natural ionomic variation across the A. thaliana species and identify several accessions with extreme ionomic profiles. It forms a valuable resource for exploratory genetic mapping studies to identify genes underlying natural variation in leaf and seed ionome and genetic adaptation of plants to soil conditions.

Construction and analysis of a Noccaea caerulescens TILLING population.

BACKGROUND: Metals such as Zn or Cd are toxic to plant and humans when they are exposed in high quantities through contaminated soil or food. Noccaea caerulescens, an extraordinary Zn/Cd/Ni hyperaccumulating species, is used as a model plant for metal hyperaccumulation and phytoremediation studies. Current reverse genetic techniques to generate mutants based on transgenesis is cumbersome due to the low transformation efficiency of this species. We aimed to establish a mutant library for functional genomics by a non-transgenic approach, to identify mutants with an altered mineral profiling, and to screen for mutations in bZIP19, a regulator of Zn homeostasis in N. caerulescens. RESULTS: To generate the N. caerulescens mutant library, 3000 and 5000 seeds from two sister plants of a single-seed recurrent inbred descendant of the southern French accession Saint-Félix-de-Pallières (SF) were mutagenized respectively by 0.3 or 0.4% ethyl methane sulfonate (EMS). Two subpopulations of 5000 and 7000 M2 plants were obtained after 0.3 or 0.4% EMS treatment. The 0.4% EMS treatment population had a higher mutant frequency and was used for TILLING. A High Resolution Melting curve analysis (HRM) mutation screening platform was optimized and successfully applied to detect mutations for NcbZIP19, encoding a transcription factor controlling Zn homeostasis. Of four identified point mutations in NcbZIP19, two caused non-synonymous substitutions, however, these two mutations did not alter the ionome profile compared to the wild type. Forward screening of the 0.4% EMS treatment population by mineral concentration analysis (ionomics) in leaf material of each M2 plant revealed putative mutants affected in the concentration of one or more of the 20 trace elements tested. Several of the low-Zn mutants identified in the ionomic screen did not give progeny, illustrating the importance of Zn for the species. The mutant frequency of the population was evaluated based on an average of 2.3 knockout mutants per tested monogenic locus. CONCLUSIONS: The 0.4% EMS treatment population is effectively mutagenized suitable for forward mutant screens and TILLING. Difficulties in seed production in low Zn mutants, obtained by both forward and reverse genetic approach, hampered further analysis of the nature of the low Zn phenotypes.

Impacts of heavy metal pollution on the ionomes and transcriptomes of Western mosquitofish (Gambusia affinis).

Our understanding of the mechanisms mediating the resilience of organisms to environmental change remains lacking. Heavy metals negatively affect processes at all biological scales, yet organisms inhabiting contaminated environments must maintain homeostasis to survive. Tar Creek in Oklahoma, USA, contains high concentrations of heavy metals and an abundance of Western mosquitofish (Gambusia affinis), though several fish species persist at lower frequency. To test hypotheses about the mechanisms mediating the persistence and abundance of mosquitofish in Tar Creek, we integrated ionomic data from seven resident fish species and transcriptomic data from mosquitofish. We predicted that mosquitofish minimize uptake of heavy metals more than other Tar Creek fish inhabitants and induce transcriptional responses to detoxify metals that enter the body, allowing them to persist in Tar Creek at higher density than species that may lack these responses. Tar Creek populations of all seven fish species accumulated heavy metals, suggesting mosquitofish cannot block uptake more efficiently than other species. We found population-level gene expression changes between mosquitofish in Tar Creek and nearby unpolluted sites. Gene expression differences primarily occurred in the gill, where we found upregulation of genes involved with lowering transfer of metal ions from the blood into cells and mitigating free radicals. However, many differentially expressed genes were not in known metal response pathways, suggesting multifarious selective regimes and/or previously undocumented pathways could impact tolerance in mosquitofish. Our systems-level study identified well characterized and putatively new mechanisms that enable mosquitofish to inhabit heavy metal-contaminated environments.

Desert dust deposition supplies essential bioelements to Red Sea corals.

Climate change-related increase in seawater temperature has become a leading cause of coral bleaching and mortality. However, corals from the northern Red Sea show high thermal tolerance and no recorded massive bleaching event. This specific region is frequently subjected to intense dust storms, coming from the surrounding arid deserts, which are expected to increase in frequency and intensity in the future. The aerial dust deposition supplies essential bioelements to the water column. Here, we investigated the effect of dust deposition on the physiology of a Red Sea coral, Stylophora pistillata. We measured the modifications in coral and Symbiodiniaceae metallome (cellular metal content), as well as the changes in photosynthesis and oxidative stress status of colonies exposed during few weeks to dust deposition. Our results show that 1 mg L-1 of dust supplied nanomolar amounts of nitrate and other essential bioelements, such as iron, manganese, zinc and copper, rapidly assimilated by the symbionts. At 25°C, metal bioaccumulation enhanced the chlorophyll concentration and photosynthesis of dust-exposed corals compared to control corals. These results suggest that primary production was limited by metal availability in seawater. A 5°C increase in seawater temperature enhanced iron assimilation in both control and dust-enriched corals. Temperature rise increased the photosynthesis of control corals only, dust-exposed ones having already reached maximal photosynthesis rates at 25°C. Finally, we observed a combined effect of temperature and bioelement concentration on the assimilation of molybdenum, cadmium, manganese and copper, which were in higher concentrations in symbionts of dust-exposed corals maintained at 30°C. All together these observations highlight the importance of dust deposition in the supply of essential bioelements, such as iron, to corals and its role in sustaining coral productivity in Red Sea reefs.

Macro and trace elements signature of periodontitis in saliva: A systematic review with quality assessment of ionomics studies.

OBJECTIVES: The present systematic review examined the available evidence on distinctive salivary ion profile in periodontitis compared to periodontal health and provided a qualitative assessment of the literature. BACKGROUND: Macro and trace elements are essential for cellular physiology, and their changes in biological fluids can be revelatory of an underlying pathological status. METHODS: Data from relevant studies identified from PubMed, Embase, and Scopus databases were retrieved to answer the following PECO question: "In systemically healthy individuals, are there any differences in any salivary macro or trace element concentration between periodontally healthy subjects (H) and patients with periodontitis (P)?" Quality of included studies was rated using a modified version of the QUADOMICS tool. A consistency analysis was performed to identify significantly discriminant chemical elements. RESULTS: After the screening of 873 titles, 13 studies were included reporting data on 22 different elements. Among them, levels of sodium and potassium were consistently and significantly higher in P compared to H. Conflicting results were found for all the other elements, despite concentration of calcium, copper, and manganese mostly increased in saliva of P. Levels of magnesium were found higher in P than in H in 2 studies but lower in 3. Zinc resulted significantly increased in saliva from H compared to P individuals in 2 studies, but one study reported opposite results. Four studies were considered as high quality, while reporting of operative protocols and statistical analysis was a major limitation for the others. Due to high methodologic heterogeneity, meta-analysis was not performed. CONCLUSIONS: Levels of macro or trace elements were differentially identified in saliva across diverse periodontal conditions, having a major potential for investigation of oral homeostasis and for high-resolution periodontal diagnosis. Products of inflammatory physiologic cellular impairment, such as sodium and potassium, were the most consistently associated with periodontitis (PROSPERO CRD42021235744).

State-of-the-art OMICS strategies against toxic effects of heavy metals in plants: A review.

Environmental pollution of heavy metals (HMs), mainly due to anthropogenic activities, has received growing attention in recent decades. HMs, especially the non-essential carcinogenic ones, including chromium (Cr), cadmium (Cd), mercury (Hg), aluminum (Al), lead (Pb), and arsenic (As), have appeared as the most significant air, water, and soil pollutants, which adversely affect the quantity, quality, and security of plant-based food all over the world. Plants exposed to HMs could experience significant decline in growth and yield. To avoid or tolerate the toxic effects of HMs, plants have developed complicated defense mechanisms, including absorption and accumulation of HMs in cell organelles, immobilization by forming complexes with organic chelates, extraction by using numerous transporters, ion channels, signalling cascades, and transcription elements, among others. OMICS strategies have developed significantly to understand the mechanisms of plant transcriptomics, genomics, proteomics, metabolomics, and ionomics to counter HM-mediated stress stimuli. These strategies have been considered to be reliable and feasible for investigating the roles of genomics (genomes), transcriptomic (coding), mRNA transcripts (non-coding), metabolomics (metabolites), and ionomics (metal ions) to enhance stress resistance or tolerance in plants. The recent developments in the mechanistic understandings of the HMs-plant interaction in terms of their absorption, translocation, and toxicity invasions at the molecular and cellular levels, as well as plants' response and adaptation strategies against these stressors, are summarized in the present review. Transcriptomics, genomics, metabolomics, proteomics, and ionomics for plants against HMs toxicities are reviewed, while challenges and future recommendations are also discussed.

Environmental conditions and plant physiology modulate Cu phytotoxicity in field-contaminated soils.

Foliar Cu concentration has been widely used as a biomarker of plant growth in phytotoxicity bioassays. This relation has helped find plant processes altered by Cu in dose-response experiments (a bivariate approach). However, when plants are grown in field conditions, their responses can vary in function of multiple variables, such as the environment, plant physiology, and other elements in plant (plant ionome). These sources of variability are commonly unreported, which could limit bioassays' utility. Thus, the present study aimed to assess and integrate the mentioned sources of variability on Cu phytotoxicity. Lettuce was used as plant model. Lettuces were grown in growth chambers with contrasting light and air humidity conditions and on two different field-contaminated soils (sandy and loamy soils). Results showed that environmental conditions significantly affected foliar Cu and plant growth, but this effect differed in the two studied soils. Foliar Cu was not a good biomarker of plant growth. In contrast, integrating the potential phytotoxicity effect with the plant's nutritional status allowed a better understanding of plant growth. We remarked on using a structural equation modeling approach (SEM) to integrate plant physiology and plant ionome as moderators of plant growth. Results showed that plant growth was primarily related to plant nutritional status rather than Cu phytotoxicity. Also, the foliar Cu concentration would affect plant nutritional status due to photosynthesis-related plant processes and cation balance. Finally, this research invites to state and include sources of variability when assessing phytotoxicity. This way, it is possible to advance toward understanding complex linked processes occurring in field conditions.

IonFlow: a galaxy tool for the analysis of ionomics data sets.

INTRODUCTION: Inductively coupled plasma mass spectrometry (ICP-MS) experiments generate complex multi-dimensional data sets that require specialist data analysis tools. OBJECTIVE: Here we describe tools to facilitate analysis of the ionome composed of high-throughput elemental profiling data. METHODS: IonFlow is a Galaxy tool written in R for ionomics data analysis and is freely accessible at https://github.com/wanchanglin/ionflow . It is designed as a pipeline that can process raw data to enable exploration and interpretation using multivariate statistical techniques and network-based algorithms, including principal components analysis, hierarchical clustering, relevance network extraction and analysis, and gene set enrichment analysis. RESULTS AND CONCLUSION: The pipeline is described and tested on two benchmark data sets of the haploid S. Cerevisiae ionome and of the human HeLa cell ionome.

Maghemite nano-fertilization promotes fluoride tolerance in rice by restoring grain yield and modulating the ionome and physiome.

The present manuscript elucidated the ameliorative potential of nano-maghemite (FeNPs) against the hazardous effects of fluoride toxicity in the sensitive rice cultivar, IR-64. Fluoride pollution triggered bioaccumulation in root, shoot and spikelets which inhibited reproduction, agronomic development and mineral uptake. Suppressed activity of enzymatic antioxidants and excessive cobalt translocation manifested severe ROS-induced oxidative injuries. Seedling priming with FeNPs reduced fluoride bioaccumulation and promoted efficient uptake of macroelements and micronutrients like potassium, calcium, iron, zinc, copper, nickel, manganese, selenium and vanadium and reduced the translocation of cobalt in mature seedlings during stress. This altogether triggered growth and activated the enzymes like SOD, CAT, APX and GPOX. High accumulation of non-enzymatic antioxidants like proline, anthocyanins, flavonoids, phenolics along with stimulated GSH synthesis (determined from high GR, GST and GPX activity) and glyoxalase activity enabled FeNP-pulsed plants to efficiently scavenge ROS, O2-, H2O2 and methylglyoxal, and mitigate oxidative injuries. The ROS production was also lowered due to suppressed NADPH oxidase activity. This ensured subsequent revitalization of Hill activity and the level of photosynthetic pigments. Due to reduced fluoride partitioning and improved nutritional sink, the grain and panicle development in FeNP-primed, stressed seedlings were more stimulated than even control sets. Overall, our findings supported by statistical modelling established the potential of iron-nanotechnology in promoting safe rice cultivation even in fluoride-polluted environments.