Key Pathways and Genes of Arabidopsis thaliana and Arabidopsis halleri Roots under Cadmium Stress Responses: Differences and Similarities

Cadmium (Cd) is among the world's major health concerns, as it renders soils unsuitable and unsafe for food and feed production. Phytoremediation has the potential to remediate Cd-polluted soils, but efforts are still needed to develop a deep understanding of the processes underlying it. In this study, we performed a comprehensive analysis of the root response to Cd stress in A. thaliana, which can phytostabilize Cd, and in A. halleri, which is a Cd hyperaccumulator. Suitable RNA-seq data were analyzed by WGCNA to identify modules of co-expressed genes specifically associated with Cd presence. The results evidenced that the genes of the hyperaccumulator A. halleri mostly associated with the Cd presence are finely regulated (up- and downregulated) and related to a general response to chemical and other stimuli. Additionally, in the case of A. thaliana, which can phytostabilize metals, the genes upregulated during Cd stress are related to a general response to chemical and other stimuli, while downregulated genes are associated with functions which, affecting root growth and development, determine a deep modification of the organ both at the cellular and physiological levels. Furthermore, key genes of the Cd-associated modules were identified and confirmed by differentially expressed gene (DEG) detection and external knowledge. Together, key functions and genes shed light on differences and similarities among the strategies that the plants use to cope with Cd and may be considered as possible targets for future research.

Zinc- and nickel-induced changes in fatty acid profiles in the zinc hyperaccumulator Arabidopsis halleri and non-accumulator Arabidopsis lyrata

This pilot study aimed at comparing zinc (Zn) and nickel (Ni) effects on the fatty acid (FA) profiles, oxidative stress and desaturase activity in the Zn hyperaccumulator Arabidopsis halleri and the excluder Arabidopsis lyrata to allow a better picture of the physiological mechanisms which may contribute to metal tolerance or acclimation. The most significant changes in the FA composition were observed in the shoots of the hyperaccumulator and in the roots of the excluder, and were not only metal-dependent, but also species-specific, since the most significant changes in the shoots of A. halleri were observed under Ni treatment, though Ni, in contrast to Zn, was accumulated mainly in its roots. Several FAs appeared in the roots and shoots of A. lyrata only upon metal exposure, whereas they were already found in control A. halleri. In both species, there was an increase in oleic acid under Ni treatment in both organs, whereas in Zn-treated plants the increase was shown only for the shoots. A rare conjugated α-parinaric acid was identified only in the shoots of metal-treated A. halleri. In the shoots of the hyperaccumulator, there was an increase in the content of saturated FAs and a decrease in the content of unsaturated FAs, while in the roots of the excluder, the opposite pattern was observed. These metal-induced changes in FA composition in the shoots of A. halleri can lead to a decrease in the fluidity of membranes, which could diminish the penetration of ROS into the membrane and thus maintain its stability.

Elemental bioimaging of Zn and Cd in leaves of hyperaccumulator Arabidopsis halleri using laser ablation-inductively coupled plasma-mass spectrometry and referencing strategies

The spatial distribution of Zn and Cd in leaves of the heavy metal hyperaccumulator species Arabidopsis halleri, a land plant in the Brassicaceae family of angiosperms, is determined by laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS). Detected intensities of nuclides of the environmental pollutants Zn and Cd are referenced to nuclides of the naturally abundant elements C, Mg, P, Ca, and Rb as internal standards, in order to compensate for widespread experimental issues in whole-leaf laser ablation. Referencing occurs by dividing the signal intensity of the analyte by the corresponding intensity of the internal standard. In order to avoid large quotients that occur during division by small numbers, quotients of pixels for which the internal standard is no higher than the background are set to zero. The effects of referencing on a loss of laser focus, overlapping layers of leaf tissue and cell damage within the imaged leaf tissue are addressed specifically. It is reported that referencing to ²⁵Mg, ³¹P, ⁴⁴Ca or ⁸⁵Rb can skew the results of Zn and Cd distribution because of their different ion mobility within leaves or other element-specific effects. This is particularly valid in the leaf venation and in regions of leaves where cell damage has occurred. Considering all aspects, ¹³C was found to be best suited among the investigated elements for referencing of leaves, because it stabilizes the resulting distributions of Zn and Cd even in samples affected by experimental issues.

Root and shoot biology of Arabidopsis halleri dissected by WGCNA: an insight into the organ pivotal pathways and genes of an hyperaccumulator

Arabidopsis halleri is a hyperaccumulating pseudo-metallophyte and an emerging model to explore molecular basis of metal tolerance and hyperaccumulation. In this regard, understanding of interacting genes can be a crucial aspect as these interactions regulate several biological functions at molecular level in response to multiple signals. In this current study, we applied a weighted gene co-expression network analysis (WGCNA) on root and shoot RNA-seq data of A. halleri to predict the related scale-free organ specific co-expression networks, for the first time. A total of 19,653 genes of root and 18,081 genes of shoot were grouped into 14 modules and subjected to GO and KEGG enrichment analysis. "Photosynthesis" and "photosynthesis-antenna proteins" were identified as the most enriched and common pathway to both root and shoot. Whereas "glucosinolate biosynthesis," "autophagy," and "SNARE interactions in vesicular transport" were specific to root, and "circadian rhythm" was found to be enriched only in shoot. Later, hub and bottleneck genes were identified in each module by using cytoHubba plugin based on Cytoscape and scoring the relevance of each gene to the topology of the network. The modules with the most significant differential expression pattern across control and treatment (Cd-Zn treatment) were selected and their hub and bottleneck genes were screened to validate their possible involvement in heavy metal stress. Moreover, we combined the analysis of co-expression modules together with protein-protein interactions (PPIs), confirming some genes as potential candidates in plant heavy metal stress and as biomarkers. The results from this analysis shed the light on the pivotal functions to the hyperaccumulative trait of A. halleri, giving perspective to new paths for future research on this species.

Phytoextraction of Zn and Cd with Arabidopsis halleri: a focus on fertilization and biological amendment as a means of increasing biomass and Cd and Zn concentrations

The current work aims to investigate the influence of fertilization (fertilizer) and fungal inoculation (Funneliformis mosseae and Serendipita indica (formerly Piriformospora indica), respectively arbuscular mycorrhizal (AMF) and endophytic fungi) on the phytoextraction potential of Arabidopsis halleri (L.) O'Kane & Al-Shehbaz (biomass yield and/or aboveground part Zn and Cd concentrations) over one life plant cycle. The mycorrhizal rates of A. halleri were measured in situ while the fungal inoculation experiments were carried out under controlled conditions. For the first time, it is demonstrated that the fertilizer used on A. halleri increased its biomass not only at the rosette stage but also at the flowering and fruiting stages. Fertilizer reduced the Zn concentration variability between developmental stages and increased the Cd concentration at fruiting stage. A. halleri roots did not show AMF colonization at any stage in our field conditions, neither in the absence nor in the presence of fertilizer, thus suggesting that A. halleri is not naturally mycorrhizal. Induced mycorrhization agreed with this result. However, S. indica has been shown to successfully colonize A. halleri roots under controlled conditions. This study confirms the benefit of using fertilizer to increase the phytoextraction potential of A. halleri. Overall, these results contribute to the future applicability of A. halleri in a phytomanagement strategy by giving information on its cultural itinerary.

Phytoextraction efficiency of Arabidopsis halleri is driven by the plant and not by soil metal concentration

The hyperaccumulation trait allows some plant species to allocate remarkable amounts of trace metal elements (TME) to their foliage without suffering from toxicity. Utilizing hyperaccumulating plants to remediate TME contaminated sites could provide a sustainable alternative to industrial approaches. A major hurdle that currently hampers this approach is the complexity of the plant-soil relationship. To better anticipate the outcome of future phytoremediation efforts, we evaluated the potential for soil metal-bioavailability to predict TME accumulation in two non-metallicolous and two metallicolous populations of the Zn/Cd hyperaccumulator Arabidopsis halleri. We also examined the relationship between a population's habitat and its phytoextraction efficiency. Total Zn and Cd concentrations were quantified in soil and plant material, and bioavailable fractions in soil were quantified via Diffusive Gradients in Thin-films (DGT). We found that shoot TME accumulation varied independent from both total and bioavailable soil TME concentrations in metallicolous individuals. In fact, hyperaccumulation patterns appear more plant- and less soil-driven: one non-metallicolous population proved to be as efficient in accumulating Zn on non-polluted soil as the metallicolous populations in their highly contaminated environment. Our findings demonstrate that in-situ information on plant phytoextraction efficiency is indispensable to optimize site-specific phytoremediation measures. If successful, hyperaccumulating plant biomass may provide valuable source material for application in the emerging field of green chemistry.

Comparative analysis identifies micro-RNA associated with nutrient homeostasis, development and stress response in Arabidopsis thaliana upon high Zn and metal hyperaccumulator Arabidopsis halleri

miRNAs have been found to be key players in mineral homeostasis, both in the control of nutrient balance and in the response to toxic trace elements. However, the effect of Zn excess on miRNAs has not been elucidated; moreover, no data are present regarding miRNAs in hyperaccumulator species, where metal homeostasis is tightly regulated. Therefore, expression levels of mature miRNAs were measured by RNA-Seq in Zn-sensitive Arabidopsis thaliana grown in control conditions and upon high Zn, in soil and in Zn-hyperaccumulator Arabidopsis halleri grown in control conditions. Differential expression of notable miRNAs and their targets was confirmed by real-time RT-PCR. The comparison in A. thaliana revealed a small subset modulated upon Zn treatment that is associated with stress response and nutrient homeostasis. On the other hand, a more consistent group of miRNAs was differentially expressed in A. halleri compared with A. thaliana, reflecting inherent differences in nutritional requirements and response to stresses and plant growth and development. Overall, these results confirm the involvement of miRNAs in Zn homeostasis and support the hypothesis of distinct regulatory pathways in hyperaccumulator species.

Between the devil and the deep blue sea: herbivory induces foraging for and uptake of cadmium in a metal hyperaccumulating plant

Plants have been shown to change their foraging behaviour in response to resource heterogeneity. However, an unexplored hypothesis is that foraging could be induced by environmental stressors, such as herbivory, which might increase the demand for particular resources, such as those required for herbivore defence. This study examined the way simulated herbivory affects both root foraging for and uptake of cadmium (Cd), in the metal-hyperaccumulating plant Arabidopsis halleri, which uses this heavy metal as herbivore defence. Simulated herbivory elicited enhanced relative allocation of roots to Cd-rich patches as well as enhanced Cd uptake, and these responses were exhibited particularly by plants from non-metalliferous origin, which have lower metal tolerance. By contrast, plants from a metalliferous origin, which are more tolerant to Cd, did not show any preference in root allocation, yet enhanced Cd sharing between ramets when exposed to herbivory. These results suggest that foraging for heavy metals, as well as their uptake and clonal-sharing, could be stimulated in A. halleri by herbivory impact. Our study provides first support for the idea that herbivory can induce not only defence responses in plants but also affect their foraging, resource uptake and clonal sharing responses.

Direct inhibition of photosynthesis by Cd dominates over inhibition caused by micronutrient deficiency in the Cd/Zn hyperaccumulator Arabidopsis halleri

This work reveals, by imaging in vivo measurements in the Cd/Zn hyperaccumulator Arabidopsis halleri, in how far Cd stress affects macronutrient (Ca, K) and micronutrient (Fe, Zn) distribution in the leaves. We directly correlate these changes with biophysics of the photosynthetic light reactions. Plants were grown for 2 months at 10 μM Zn (=control), and supplemented with 10, 15, 50 or 75 μM Cd. Direct imaging of OJIP transients revealed that bundle sheath cells were more sensitive to Cd toxicity than mesophyll cells further from the vein. Progressive inhibition of photosystem (PS) II reaction centres and decrease in quantum yield of electron transport between Q_A and Q_B and further to PSI acceptors was observed. This was correlated with the decreased dynamics of Q_A re-oxidation and lower operating efficiency of PSII. Analysis by a benchtop micro X-ray fluorescence device showed that Cd mostly accumulated in the veins, and restricted Fe and Zn distribution from the veins, especially in the 75 μM Cd, while K concentration increased in the whole leaf. Calcium distribution was apparently not affected by Cd, but Cd excess inhibited trichome formation and thereby diminished total Ca concentration in the leaves. The results point to differential tissue sensitivity to Cd, evident by heterogeneous inhibition of photosynthesis. Part of this may be a result of selective disturbances in the leaf nutrient homeostasis. The better photosynthetic performance away from the veins compared to the bundle sheath cells, however, indicates that direct inhibition of photosynthesis by Cd dominates over inhibition caused by micronutrient deficiency.

The two copies of the zinc and cadmium ZIP6 transporter of Arabidopsis halleri have distinct effects on cadmium tolerance

Plants have the ability to colonize highly diverse environments. The zinc and cadmium hyperaccumulator Arabidopsis halleri has adapted to establish populations on soils covering an extreme range of metal availabilities. The A. halleri ZIP6 gene presents several hallmarks of hyperaccumulation candidate genes: it is constitutively highly expressed in roots and shoots and is associated with a zinc accumulation quantitative trait locus. Here, we show that AhZIP6 is duplicated in the A. halleri genome. The two copies are expressed mainly in the vasculature in both A. halleri and Arabidopsis thaliana, indicative of conserved cis regulation, and acquired partial organ specialization. Yeast complementation assays determined that AhZIP6 is a zinc and cadmium transporter. AhZIP6 silencing in A. halleri or expression in A. thaliana alters cadmium tolerance, but has no impact on zinc and cadmium accumulation. AhZIP6-silenced plants display reduced cadmium uptake upon short-term exposure, adding AhZIP6 to the limited number of Cd transporters supported by in planta evidence. Altogether, our data suggest that AhZIP6 is key to fine-tune metal homeostasis in specific cell types. This study additionally highlights the distinct fates of duplicated genes in A. halleri.

Analysis of trace metal distribution in plants with lab-based microscopic X-ray fluorescence imaging

BACKGROUND

Many metals are essential for plants and humans. Knowledge of metal distribution in plant tissues in vivo contributes to the understanding of physiological mechanisms of metal uptake, accumulation and sequestration. For those studies, X-rays are a non-destructive tool, especially suited to study metals in plants.

RESULTS

We present microfluorescence imaging of trace elements in living plants using a customized benchtop X-ray fluorescence machine. The system was optimized by additional detector shielding to minimize stray counts, and by a custom-made measuring chamber to ensure sample integrity. Protocols of data recording and analysis were optimised to minimise artefacts. We show that Zn distribution maps of whole leaves in high resolution are easily attainable in the hyperaccumulator Noccaea caerulescens. The sensitivity of the method was further shown by analysis of micro- (Cu, Ni, Fe, Zn) and macronutrients (Ca, K) in non-hyperaccumulating crop plants (soybean roots and pepper leaves), which could be obtained in high resolution for scan areas of several millimetres. This allows to study trace metal distribution in shoots and roots with a wide overview of the object, and thus avoids making conclusions based on singular features of tiny spots. The custom-made measuring chamber with continuous humidity and air supply coupled to devices for imaging chlorophyll fluorescence kinetic measurements enabled direct correlation of element distribution with photosynthesis. Leaf samples remained vital even after 20 h of X-ray measurements. Subtle changes in some of photosynthetic parameters in response to the X-ray radiation are discussed.

CONCLUSIONS

We show that using an optimized benchtop machine, with protocols for measurement and quantification tailored for plant analyses, trace metal distribution can be investigated in a reliable manner in intact, living plant leaves and roots. Zinc distribution maps showed higher accumulation in the tips and the veins of young leaves compared to the mesophyll tissue, while in the older leaves the distribution was more homogeneous.

Base-Pairing Requirements for Small RNA-Mediated Gene Silencing of Recessive Self-Incompatibility Alleles in Arabidopsis halleri

Small noncoding RNAs are central regulators of genome activity and stability. Their regulatory function typically involves sequence similarity with their target sites, but understanding the criteria by which they specifically recognize and regulate their targets across the genome remains a major challenge in the field, especially in the face of the diversity of silencing pathways involved. The dominance hierarchy among self-incompatibility alleles in Brassicaceae is controlled by interactions between a highly diversified set of small noncoding RNAs produced by dominant S-alleles and their corresponding target sites on recessive S-alleles. By controlled crosses, we created numerous heterozygous combinations of S-alleles in Arabidopsis halleri and developed an real-time quantitative PCR assay to compare allele-specific transcript levels for the pollen determinant of self-incompatibility (SCR). This provides the unique opportunity to evaluate the precise base-pairing requirements for effective transcriptional regulation of this target gene. We found strong transcriptional silencing of recessive SCR alleles in all heterozygote combinations examined. A simple threshold model of base pairing for the small RNA-target interaction captures most of the variation in SCR transcript levels. For a subset of S-alleles, we also measured allele-specific transcript levels of the determinant of pistil specificity (SRK), and found sharply distinct expression dynamics throughout flower development between SCR and SRK In contrast to SCR, both SRK alleles were expressed at similar levels in the heterozygote genotypes examined, suggesting no transcriptional control of dominance for this gene. We discuss the implications for the evolutionary processes associated with the origin and maintenance of the dominance hierarchy among self-incompatibility alleles.

Protein lysine methylation contributes to modulating the response of sensitive and tolerant Arabidopsis species to cadmium stress

The mechanisms underlying the response and adaptation of plants to excess of trace elements are not fully described. Here, we analysed the importance of protein lysine methylation for plants to cope with cadmium. We analysed the effect of cadmium on lysine-methylated proteins and protein lysine methyltransferases (KMTs) in two cadmium-sensitive species, Arabidopsis thaliana and A. lyrata, and in three populations of A. halleri with contrasting cadmium accumulation and tolerance traits. We showed that some proteins are differentially methylated at lysine residues in response to Cd and that a few genes coding KMTs are regulated by cadmium. Also, we showed that 9 out of 23 A. thaliana mutants disrupted in KMT genes have a tolerance to cadmium that is significantly different from that of wild-type seedlings. We further characterized two of these mutants, one was knocked out in the calmodulin lysine methyltransferase gene and displayed increased tolerance to cadmium, and the other was interrupted in a KMT gene of unknown function and showed a decreased capacity to cope with cadmium. Together, our results showed that lysine methylation of non-histone proteins is impacted by cadmium and that several methylation events are important for modulating the response of Arabidopsis plants to cadmium stress.

Urban soil phytomanagement for Zn and Cd in situ removal, greening, and Zn-rich biomass production taking care of snail exposure

The phytoextraction potential of Arabidopsis halleri (L.) O'Kane & Al Shehbaz and Salix viminalis L. to partially remove Zn and Cd in soil was investigated. In an urban field site, a very short rotation coppice of willows was implemented, and growth parameters were monitored for 3 years. A. halleri was cultivated in the same site with or without fertilizer to improve biomass yield and/or Zn and Cd aerial part concentrations. Effects of harvest and co-cultivation on these two parameters were measured. To determine if willows and A. halleri leaves were risky in case of consumption by a herbivorous invertebrate like the landsnail Cantareus aspersus, metal concentrations of snails fed with Zn- and Cd-enriched and low enriched leaves were compared. Willows and A. halleri grew well on the metal-contaminated soil (1.7 and 616 mg kg^-1 Cd and Zn, respectively). The A. halleri Zn foliar concentration reached the Zn hyperaccumulation threshold (> 10,000 mg kg^-1 DW) in the presence of NPK fertilizer and although the soil was alkaline (pH > 8.2). Cd concentration increased with harvest and fertilizer. Cd and Zn foliar concentrations of willows were far above baseline values. Laboratory snails exposure revealed that willow leaves ingestion caused a moderate increase of Cd, Pb, and Zn bioaccumulation in snails compared to the one caused by A. halleri ingestion. The soil and plant metal concentrations were reflected by field snail biomonitoring. This study confirmed the interest of selecting A. halleri and willows to partially remove Zn and Cd in the soil and emphasized their potential usefulness in greening urban contaminated area and producing raw materials for green chemistry while paying attention to the environmental pollutant transfer.

Response of Arabidopsis halleri to cesium and strontium in hydroponics: Extraction potential and effects on morphology and physiology

Stable isotopes of cesium (Cs) and strontium (Sr) as well as their radioactive isotopes are of serious environmental concern. The pollution of the biosphere, particularly soil and water has received considerable attention for removal of these contaminants in recent years. Arabidopsis halleri (A. halleri) is a hyperaccumulator plant species able to take up large amounts of several metals into its above ground organs without showing significant signs of toxicity. Therefore, we investigated responses, metal accumulation and element distribution in roots and leaves of A. halleri after treatment with stable Cs and Sr. Plants were hydroponically grown in different concentrations of cesium sulfate (between 0.002 and 20 mM) and strontium nitrate (between 0.001 and 100 mM). Uptake of Cs and Sr into leaves was analyzed from extracts by inductively coupled plasma mass spectrometry (ICP-MS). Although internal concentration of Cs and Sr increased with rising external concentrations, the amount of accumulated metal in relation to available metal decreased. Therefore, the potential of the plant to effectively transfer metals from growth medium to leaves occurred at low and moderate concentrations, whereas after that when the concentration of metal increased further the transfer factors were decreased. A. halleri accumulated Sr more efficiently than Cs. The transfer factors were higher for Sr (up to 184) than for Cs (up to 16). The results indicate positive correlation of Cs and Sr accumulation to K and Ca transport to leaves. The toxicity of Cs and Sr was assessed by measuring photosynthetic efficiency and growth parameters. In leaves, Cs and Sr affected the chlorophyll fluorescence at their low and high concentrations. Significant reduction of plant growth (dry weight of roots and leaves) was observed at Sr concentrations >0.01 mM. Cs-treated plants exhibited only decreased length of leaves at concentrations>0.02 mM. The distribution of the elements within the different tissues of leaves and roots was investigated by using Energy Dispersive X-Ray microanalysis (EDX) with a scanning electron microscope (SEM). EDX revealed that Cs and Sr were accumulated differently in root and leaf tissues. The hydroponic experiment showed a potential for A. halleri to treat hotspots with radioactive Cs and Sr.

Seasonal Stability and Dynamics of DNA Methylation in Plants in a Natural Environment

DNA methylation has been considered a stable epigenetic mark but may respond to fluctuating environments. However, it is unclear how they behave in natural environments. Here, we analyzed seasonal patterns of genome-wide DNA methylation in a single clone from a natural population of the perennial Arabidopsis halleri. The genome-wide pattern of DNA methylation was primarily stable, and most of the repetitive regions were methylated across the year. Although the proportion was small, we detected seasonally methylated cytosines (SeMCs) in the genome. SeMCs in the CHH context were detected predominantly at repetitive sequences in intergenic regions. In contrast, gene-body CG methylation (gbM) itself was generally stable across seasons, but the levels of gbM were positively associated with seasonal stability of RNA expression of the genes. These results suggest the existence of two distinct aspects of DNA methylation in natural environments: sources of epigenetic variation and epigenetic marks for stable gene expression.

Elevated root nicotianamine concentrations are critical for Zn hyperaccumulation across diverse edaphic environments

The metallophyte Arabidopsis halleri thrives across an extremely broad edaphic range. Zn hyperaccumulation is found on soils differing in available Zn by up to six orders of magnitude, raising the question as to whether a common set of mechanisms confers this species-wide ability. Elevated root concentrations of the metal chelator nicotianamine due to strong constitutive expression of AhNAS2 are important for hyperaccumulation. In order to analyse the relevance of AhNAS2 under more natural conditions representing a range of metalliferous and nonmetalliferous habitats, we collected soil at eight different A. halleri sites and cultivated wild-type and AhNAS2-RNAi lines in these soils. AhNAS2 transcript abundance and root nicotianamine concentrations in wild-type plants were barely influenced by soil metal concentrations. The RNAi effect was fully expressed in different soils. Zn hyperaccumulation in AhNAS2-silenced lines was significantly reduced in seven soils. Root-to-shoot translocation of Cd, Mn, Cu, Ni, and Co was also affected by AhNAS2 silencing, albeit to a lower extent and less consistently. Leaf Fe levels were unaffected by AhNAS2 knockdown. Results demonstrate that elevated nicotianamine production in roots of A. halleri is a Zn hyperaccumulation factor regardless of the edaphic environment, that is, contributes to Zn hyperaccumulation in soils with contrasting Zn availability.

Real-time whole-plant dynamics of heavy metal transport in Arabidopsis halleri and Arabidopsis thaliana by gamma-ray imaging

Heavy metals such as zinc are essential for plant growth, but toxic at high concentrations. Despite our knowledge of the molecular mechanisms of heavy metal uptake by plants, experimentally addressing the real-time whole-plant dynamics of heavy metal uptake and partitioning has remained a challenge. To overcome this, we applied a high sensitivity gamma-ray imaging system to image uptake and transport of radioactive 65Zn in whole-plant assays of Arabidopsis thaliana and the Zn hyperaccumulator Arabidopsis halleri. We show that our system can be used to quantitatively image and measure uptake and root-to-shoot translocation dynamics of zinc in real time. In the metal hyperaccumulator Arabidopsis halleri, 65Zn uptake and transport from its growth media to the shoot occurs rapidly and on time scales similar to those reported in rice. In transgenic A. halleri plants in which expression of the zinc transporter gene HMA4 is suppressed by RNAi, 65Zn uptake is completely abolished.

Divergence in Glucosinolate Profiles between High- and Low-Elevation Populations of Arabidopsis halleri Correspond to Variation in Field Herbivory and Herbivore Behavioral Preferences

Variation in local herbivore pressure along elevation gradients is predicted to drive variation in plant defense traits. Yet, the extent of intraspecific variation in defense investment along elevation gradients, and its effects on both herbivore preference and performance, remain relatively unexplored. Using populations of Arabidopsis halleri (Brassicaceae) occurring at different elevations in the Alps, we tested for associations between elevation, herbivore damage in the field, and constitutive chemical defense traits (glucosinolates) assayed under common-garden conditions. Additionally, we examined the feeding preferences and performance of a specialist herbivore, the butterfly Pieris brassicae, on plants from different elevations in the Alps. Although we found no effect of elevation on the overall levels of constitutive glucosinolates in leaves, relative amounts of indole glucosinolates increased significantly with elevation and were negatively correlated with herbivore damage in the field. In oviposition preference assays, P. brassicae females laid fewer eggs on plants from high-elevation populations, although larval performance was similar on populations from different elevations. Taken together, these results support the prediction that species distributed along elevation gradients exhibit genetic variation in chemical defenses, which can have consequences for interactions with herbivores in the field.

CAX1 suppresses Cd-induced generation of reactive oxygen species in Arabidopsis halleri

The molecular analysis of metal hyperaccumulation in species such as Arabidopsis halleri offers the chance to gain insights into metal homeostasis and into the evolution of adaptation to extreme habitats. A prerequisite of metal hyperaccumulation is metal hypertolerance. Genetic analysis of a backcross population derived from Arabidopsis lyrata × A. halleri crosses revealed three quantitative trait loci for Cd hypertolerance. A candidate gene for Cdtol2 is AhCAX1, encoding a vacuolar Ca²⁺ /H⁺ antiporter. We developed a method for the transformation of vegetatively propagated A. halleri plants and generated AhCAX1-silenced lines. Upon Cd²⁺ exposure, several-fold higher accumulation of reactive oxygen species (ROS) was detectable in roots of AhCAX1-silenced plants. In accordance with the dependence of Cdtol2 on external Ca²⁺ concentration, this phenotype was exclusively observed in low Ca²⁺ conditions. The effects of external Ca²⁺ on Cd accumulation cannot explain the phenotype as they were not influenced by the genotype. Our data strongly support the hypothesis that higher expression of CAX1 in A. halleri relative to other Arabidopsis species represents a Cd hypertolerance factor. We propose a function of AhCAX1 in preventing a positive feedback loop of Cd-elicited ROS production triggering further Ca²⁺ -dependent ROS accumulation.

Both heavy metal-amendment of soil and aphid-infestation increase Cd and Zn concentrations in phloem exudates of a metal-hyperaccumulating plant

Plants that are able to hyperaccumulate heavy metals show increased concentrations of these metals in their leaf tissue. However, little is known about the concentrations of heavy metals and of organic defence metabolites in the phloem sap of these plants in response to either heavy metal-amendment of the soil or biotic challenges such as aphid-infestation. In this study, we investigated the effects of heavy metal-exposure and of aphid-infestation on phloem exudate composition of the metal hyperaccumulator species Arabidopsis halleri L. O'Kane & Al-Shehbaz (Brassicaceae). The concentrations of elements and of organic defence compounds, namely glucosinolates, were measured in phloem exudates of young and old (mature) leaves of plants challenged either by amendment of the soil with cadmium and zinc and/or by an infestation with the generalist aphid Myzus persicae. Metal-amendment of the soil led to increased concentrations of Cd and Zn, but also of two other elements and one indole glucosinolate, in phloem exudates. This enhanced defence in the phloem sap of heavy metal-hyperaccumulating plants can thus potentially act as effective protection against aphids, as predicted by the elemental defence hypothesis. Aphid-infestation also caused enhanced Cd and Zn concentrations in phloem exudates. This result provides first evidence that metal-hyperaccumulating plants can increase heavy metal concentrations tissue-specifically in response to an attack by phloem-sucking herbivores. Overall, the concentrations of most elements, including the heavy metals, and glucosinolates were higher in phloem exudates of young leaves than in those of old leaves. This defence distribution highlights that the optimal defence theory, which predicts more valuable tissue to be better defended, is applicable for both inorganic and organic defences.

Herbivore-Mediated Interaction Promotes the Maintenance of Trichome Dimorphism through Negative Frequency-Dependent Selection

Natural plant populations exhibit genetic variation in defense traits against herbivores. Despite a growing body of evidence for herbivore-mediated selection on plant defenses, we still know little about how genetic variation persists in antiherbivore defense traits. Here we present field and experimental evidence for herbivore-mediated frequency-dependent selection that promotes the maintenance of trichome-producing (hairy) and trichomeless (glabrous) plants of Arabidopsis halleri subsp. gemmifera. First, in a natural population where the specialist leaf beetle Phaedon brassicae was prevalent, hairy plants were damaged less when the frequency of neighboring glabrous plants increased. Furthermore, temporal variation in the frequency of the two plant morphs showed that rarer morphs increased in frequency at the scale of 1-m-diameter patches between survey years. Using a mesocosm experiment, we demonstrated a rare-morph advantage for defense (leaf damage and herbivore abundance) and reproduction (flower and clone production) between hairy and glabrous plants in the presence of P. brassicae. However, this rare-morph advantage was not detected when beetles were absent, with glabrous plants having higher reproduction than hairy plants under these conditions regardless of frequency conditions. These findings highlight the overlooked but potentially critical role of herbivore-mediated apparent interaction in maintaining plant defense polymorphism.

Fine-scale frequency differentiation along a herbivory gradient in the trichome dimorphism of a wild Arabidopsis

Geographic variation is commonly observed in plant resistance traits, where plant species might experience different selection pressure across a heterogeneous landscape. Arabidopsis halleri subsp. gemmifera is dimorphic for trichome production, generating two morphs, trichome-producing (hairy) and trichomeless (glabrous) plants. Trichomes of A. halleri are known to confer resistance against the white butterfly, cabbage sawfly, and brassica leaf beetle, but not against flea beetles. We combined leaf damage, microclimate, and microsatellite loci data of 26 A. halleri populations in central Japan, to explore factors responsible for fine-scale geographic variation in the morph frequency. We found that hairy plants were less damaged than glabrous plants within populations, but the among-site variation was the most significant source of variation in the individual-level damage. Fixation index (Gst″) of a putative trichome locus exhibited a significant divergence along population-level damage with an exception of an outlier population, inferring the local adaptation to herbivory. Notably, this outlier was a population wherein our previous study reported a balancing role of the brassica leaf beetle Phaedon brassicae on the morph frequency. This differentiation of the trichome locus was unrelated to neutral genetic differentiation (evaluated by Gst″ of microsatellite loci) and meteorological factors (including temperature and solar radiation). The present findings, combined with those of our previous work, provide suggestive evidence that herbivore-driven divergence and occasional outbreak of a specific herbivore have jointly contributed to the ecogeographic pattern in the frequency of two morphs.

Estimating genomic diversity and population differentiation - an empirical comparison of microsatellite and SNP variation in Arabidopsis halleri

BACKGROUND

Microsatellite markers are widely used for estimating genetic diversity within and differentiation among populations. However, it has rarely been tested whether such estimates are useful proxies for genome-wide patterns of variation and differentiation. Here, we compared microsatellite variation with genome-wide single nucleotide polymorphisms (SNPs) to assess and quantify potential marker-specific biases and derive recommendations for future studies. Overall, we genotyped 180 Arabidopsis halleri individuals from nine populations using 20 microsatellite markers. Twelve of these markers were originally developed for Arabidopsis thaliana (cross-species markers) and eight for A. halleri (species-specific markers). We further characterized 2 million SNPs across the genome with a pooled whole-genome re-sequencing approach (Pool-Seq).

RESULTS

Our analyses revealed that estimates of genetic diversity and differentiation derived from cross-species and species-specific microsatellites differed substantially and that expected microsatellite heterozygosity (SSR-H e) was not significantly correlated with genome-wide SNP diversity estimates (SNP-H e and θ Watterson) in A. halleri. Instead, microsatellite allelic richness (A r) was a better proxy for genome-wide SNP diversity. Estimates of genetic differentiation among populations (F ST) based on both marker types were correlated, but microsatellite-based estimates were significantly larger than those from SNPs. Possible causes include the limited number of microsatellite markers used, marker ascertainment bias, as well as the high variance in microsatellite-derived estimates. In contrast, genome-wide SNP data provided unbiased estimates of genetic diversity independent of whether genome- or only exome-wide SNPs were used. Further, we inferred that a few thousand random SNPs are sufficient to reliably estimate genome-wide diversity and to distinguish among populations differing in genetic variation.

CONCLUSIONS

We recommend that future analyses of genetic diversity within and differentiation among populations use randomly selected high-throughput sequencing-based SNP data to draw conclusions on genome-wide diversity patterns. In species comparable to A. halleri, a few thousand SNPs are sufficient to achieve this goal.

Between-species differences in gene copy number are enriched among functions critical for adaptive evolution in Arabidopsis halleri

Background

Gene copy number divergence between species is a form of genetic polymorphism that contributes significantly to both genome size and phenotypic variation. In plants, copy number expansions of single genes were implicated in cultivar- or species-specific tolerance of high levels of soil boron, aluminium or calamine-type heavy metals, respectively. Arabidopsis halleri is a zinc- and cadmium-hyperaccumulating extremophile species capable of growing on heavy-metal contaminated, toxic soils. In contrast, its non-accumulating sister species A. lyrata and the closely related reference model species A. thaliana exhibit merely basal metal tolerance.

Results

For a genome-wide assessment of the role of copy number divergence (CND) in lineage-specific environmental adaptation, we conducted cross-species array comparative genome hybridizations of three plant species and developed a global signal scaling procedure to adjust for sequence divergence. In A. halleri, transition metal homeostasis functions are enriched twofold among the genes detected as copy number expanded. Moreover, biotic stress functions including mostly disease Resistance (R) gene-related genes are enriched twofold among genes detected as copy number reduced, when compared to the abundance of these functions among all genes.

Conclusions

Our results provide genome-wide support for a link between evolutionary adaptation and CND in A. halleri as shown previously for Heavy metal ATPase4. Moreover our results support the hypothesis that elemental defences, which result from the hyperaccumulation of toxic metals, allow the reduction of classical defences against biotic stress as a trade-off.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-3319-5) contains supplementary material, which is available to authorized users.

RNA-Seq reveals virus-virus and virus-plant interactions in nature

As research on plant viruses has focused mainly on crop diseases, little is known about these viruses in natural environments. To understand the ecology of viruses in natural systems, comprehensive information on virus-virus and virus-host interactions is required. We applied RNA-Seq to plants from a natural population of Arabidopsis halleri subsp. gemmifera to simultaneously determine the presence/absence of all sequence-reported viruses, identify novel viruses and quantify the host transcriptome. By introducing the criteria of read number and genome coverage, we detected infections by Turnip mosaic virus (TuMV), Cucumber mosaic virus and Brassica yellows virus Active TuMV replication was observed by ultramicroscopy. De novo assembly further identified a novel partitivirus, Arabidopsis halleri partitivirus 1 Interestingly, virus reads reached a maximum level that was equivalent to that of the host's total mRNA, although asymptomatic infection was common. AhgAGO2, a key gene in host defence systems, was upregulated in TuMV-infected plants. Multiple infection was frequent in TuMV-infected leaves, suggesting that TuMV facilitates multiple infection, probably by suppressing host RNA silencing. Revealing hidden plant-virus interactions in nature can enhance our understanding of biological interactions and may have agricultural applications.

Phylogeography of Arabidopsis halleri (Brassicaceae) in mountain regions of Central Europe inferred from cpDNA variation and ecological niche modelling

The present study aimed to investigate phylogeographical patterns present within A. halleri in Central Europe. 1,281 accessions sampled from 52 populations within the investigated area were used in the study of genetic variation based on chloroplast DNA. Over 500 high-quality species occurrence records were used in ecological niche modelling experiments. We evidenced the presence of a clear phylogeographic structure within A. halleri in Central Europe. Our results showed that two genetically different groups of populations are present in western and eastern part of the Carpathians. The hypothesis of the existence of a glacial refugium in the Western Carpathians adn the Bohemian Forest cannot be rejected from our data. It seems, however, that the evidence collected during the present study is not conclusive. The area of Sudetes was colonised after LGM probably by migrants from the Bohemian Forest.

Fate of cadmium in the rhizosphere of Arabidopsis halleri grown in a contaminated dredged sediment

In regions impacted by mining and smelting activities, dredged sediments are often contaminated with metals. Phytotechnologies could be used for their management, but more knowledge on the speciation of metals in the sediment and on their fate after colonization by plant roots is needed. This work was focused on a dredged sediment from the Scarpe river (North of France), contaminated with Zn and Cd. Zn, Cd hyperaccumulating plants Arabidopsis halleri from metallicolous and non-metallicolous origin were grown on the sediment for five months in a pot experiment. The nature and extent of the modifications in Cd speciation with or without plant were determined by electron microscopy, micro X-ray fluorescence and bulk and micro X-ray absorption spectroscopy. In addition, changes in Cd exchangeable and bioavailable pools were evaluated, and Cd content in leachates was measured. Finally, Cd plant uptake and plant growth parameters were monitored. In the original sediment, Cd was present as a mixed Zn, Cd, Fe sulfide. After five months, although pots still contained reduced sulfur, Cd-bearing sulfides were totally oxidized in vegetated pots, whereas a minor fraction (8%) was still present in non-vegetated ones. Secondary species included Cd bound to O-containing groups of organic matter and Cd phosphates. Cd exchangeability and bioavailability were relatively low and did not increase during changes in Cd speciation, suggesting that Cd released by sulfide oxidation was readily taken up with strong interactions with organic matter and phosphate ligands. Thus, the composition of the sediment, the oxic conditions and the rhizospheric activity (regardless of the plant origin) created favorable conditions for Cd stabilization. However, it should be kept in mind that returning to anoxic conditions may change Cd speciation, so the species formed cannot be considered as stable on the long term.

Zinc triggers a complex transcriptional and post-transcriptional regulation of the metal homeostasis gene FRD3 in Arabidopsis relatives

In Arabidopsis thaliana, FRD3 (FERRIC CHELATE REDUCTASE DEFECTIVE 3) plays a central role in metal homeostasis. FRD3 is among a set of metal homeostasis genes that are constitutively highly expressed in roots and shoots of Arabidopsis halleri, a zinc hyperaccumulating and hypertolerant species. Here, we examined the regulation of FRD3 by zinc in both species to shed light on the evolutionary processes underlying the evolution of hyperaccumulation in A. halleri. We combined gene expression studies with the use of β-glucuronidase and green fluorescent protein reporter constructs to compare the expression profile and transcriptional and post-transcriptional regulation of FRD3 in both species. The AtFRD3 and AhFRD3 genes displayed a conserved expression profile. In A. thaliana, alternative transcription initiation sites from two promoters determined transcript variants that were differentially regulated by zinc supply in roots and shoots to favour the most highly translated variant under zinc-excess conditions. In A. halleri, a single transcript variant with higher transcript stability and enhanced translation has been maintained. The FRD3 gene thus undergoes complex transcriptional and post-transcriptional regulation in Arabidopsis relatives. Our study reveals that a diverse set of mechanisms underlie increased gene dosage in the A. halleri lineage and illustrates how an environmental challenge can alter gene regulation.

Intraspecific variability of cadmium tolerance and accumulation, and cadmium-induced cell wall modifications in the metal hyperaccumulator Arabidopsis halleri

Certain molecular mechanisms of Cd tolerance and accumulation have been identified in the model species Arabidopsis halleri, while intraspecific variability of these traits and the mechanisms of shoot detoxification were little addressed. The Cd tolerance and accumulation of metallicolous and non-metallicolous A. halleri populations from different genetic units were tested in controlled conditions. In addition, changes in shoot cell wall composition were investigated using Fourier transform infrared spectroscopy. Indeed, recent works on A. halleri suggest Cd sequestration both inside cells and in the cell wall/apoplast. All A. halleri populations tested were hypertolerant to Cd, and the metallicolous populations were on average the most tolerant. Accumulation was highly variable between and within populations, and populations that were non-accumulators of Cd were identified. The effect of Cd on the cell wall composition was quite similar in the sensitive species A. lyrata and in A. halleri individuals; the pectin/polysaccharide content of cell walls seems to increase after Cd treatment. Nevertheless, the changes induced by Cd were more pronounced in the less tolerant individuals, leading to a correlation between the level of tolerance and the extent of modifications. This work demonstrated that Cd tolerance and accumulation are highly variable traits in A. halleri, suggesting adaptation at the local scale and involvement of various molecular mechanisms. While in non-metallicolous populations drastic modifications of the cell wall occur due to higher Cd toxicity and/or Cd immobilization in this compartment, the increased tolerance of metallicolous populations probably involves other mechanisms such as vacuolar sequestration.

Evidence of various mechanisms of Cd sequestration in the hyperaccumulator Arabidopsis halleri, the non-accumulator Arabidopsis lyrata, and their progenies by combined synchrotron-based techniques

Arabidopsis halleri is a model plant for Zn and Cd hyperaccumulation. The objective of this study was to determine the relationship between the chemical forms of Cd, its distribution in leaves, and Cd accumulation and tolerance. An interspecific cross was carried out between A. halleri and the non-tolerant and non-hyperaccumulating relative A. lyrata providing progenies segregating for Cd tolerance and accumulation. Cd speciation and distribution were investigated using X-ray absorption spectroscopy and microfocused X-ray fluorescence. In A. lyrata and non-tolerant progenies, Cd was coordinated by S atoms only or with a small contribution of O groups. Interestingly, the proportion of O ligands increased in A. halleri and tolerant progenies, and they were predominant in most of them, while S ligands were still present. Therefore, the binding of Cd with O ligands was associated with Cd tolerance. In A. halleri, Cd was mainly located in the xylem, phloem, and mesophyll tissue, suggesting a reallocation process for Cd within the plant. The distribution of the metal at the cell level was further discussed. In A. lyrata, the vascular bundles were also Cd enriched, but the epidermis was richer in Cd as compared with the mesophyll. Cd was identified in trichomes of both species. This work demonstrated that both Cd speciation and localization were related to the tolerance character of the plant.

Contrasting effects of nicotianamine synthase knockdown on zinc and nickel tolerance and accumulation in the zinc/cadmium hyperaccumulator Arabidopsis halleri

Elevated nicotianamine synthesis in roots of Arabidopsis halleri has been established as a zinc (Zn) hyperaccumulation factor. The main objective of this study was to elucidate the mechanism of nicotianamine-dependent root-to-shoot translocation of metals. Metal tolerance and accumulation in wild-type (WT) and AhNAS2-RNA interference (RNAi) plants were analysed. Xylem exudates were subjected to speciation analysis and metabolite profiling. Suppression of root nicotianamine synthesis had no effect on Zn and cadmium (Cd) tolerance but rendered plants nickel (Ni)-hypersensitive. It also led to a reduction of Zn root-to-shoot translocation, yet had the opposite effect on Ni mobility, even though both metals form coordination complexes of similar stability with nicotianamine. Xylem Zn concentrations were positively, yet nonstoichiometrically, correlated with nicotianamine concentrations. Two fractions containing Zn coordination complexes were detected in WT xylem. One of them was strongly reduced in AhNAS2-suppressed plants and coeluted with (67) Zn-labelled organic acid complexes. Organic acid concentrations were not responsive to nicotianamine concentrations and sufficiently high to account for complexing the coordinated Zn. We propose a key role for nicotianamine in controlling the efficiency of Zn xylem loading and thereby the formation of Zn coordination complexes with organic acids, which are the main Zn ligands in the xylem but are not rate-limiting for Zn translocation.

Zinc and cadmium hyperaccumulation act as deterrents towards specialist herbivores and impede the performance of a generalist herbivore

Extraordinarily high leaf metal concentrations in metal hyperaccumulator plants may serve as an elemental defence against herbivores. However, mixed results have been reported and studies using comparative approaches are missing. We investigated the deterrent and toxic potential of metals employing the hyperaccumulator Arabidopsis halleri. Effects of zinc (Zn) and cadmium (Cd) on the preferences of three Brassicaceae specialists were tested in paired-choice experiments using differently treated plant material, including transgenic plants. In performance tests, we determined the toxicity and joint effects of both metals incorporated in an artificial diet on the survival of a generalist. Feeding by all specialists was significantly reduced by metal concentrations from above 1000 μg Zn g(-1) DW and 18 μg Cd g(-1) DW. By contrast, metals did not affect oviposition. Generalist survival decreased with increasing concentrations of individual metals, whereby the combination of Zn and Cd had an additive toxic effect even at the lowest applied concentrations of 100 μg Zn g(-1) and 2 μg Cd g(-1) . Metal hyperaccumulation protects plants from herbivory resulting from deterrence and toxicity against a wide range of herbivores. The combination of metals exacerbates toxicity through joint effects and enhances elemental defence. Thus, metal hyperaccumulation is ecologically beneficial for plants.

Plant Defensin type 1 (PDF1): protein promiscuity and expression variation within the Arabidopsis genus shed light on zinc tolerance acquisition in Arabidopsis halleri

Plant defensins are recognized for their antifungal properties. However, a few type 1 defensins (PDF1s) were identified for their cellular zinc (Zn) tolerance properties after a study of the metal extremophile Arabidopsis halleri. In order to investigate whether different paralogues would display specialized functions, the A. halleri PDF1 family was characterized at the functional and genomic levels. Eleven PDF1s were isolated from A. halleri. Their ability to provide Zn tolerance in yeast cells, their activity against Fusarium oxysporum f. sp. melonii, and their level of expression in planta were compared with those of the seven A. thaliana PDF1s. The genomic organization of the PDF1 family was comparatively analysed within the Arabidopsis genus. AhPDF1s and AtPDF1s were able to confer Zn tolerance and AhPDF1s also displayed antifungal activity. PDF1 transcripts were constitutively more abundant in A. halleri than in A. thaliana. Within the Arabidopsis genus, the PDF1 family is evolutionarily dynamic, in terms of gain and loss of gene copy. Arabidopsis halleri PDF1s display no superior abilities to provide Zn tolerance. A constitutive increase in AhPDF1 transcript accumulation is proposed to be an evolutionary innovation co-opting the promiscuous PDF1 protein for its contribution to Zn tolerance in A. halleri.

Cell type-specific transcriptome of Brassicaceae stigmatic papilla cells from a combination of laser microdissection and RNA sequencing

Pollination is an early and critical step in plant reproduction, leading to successful fertilization. It consists of many sequential processes, including adhesion of pollen grains onto the surface of stigmatic papilla cells, foot formation to strengthen pollen-stigma interaction, pollen hydration and germination, and pollen tube elongation and penetration. We have focused on an examination of the expressed genes in papilla cells, to increase understanding of the molecular systems of pollination. From three representative species of Brassicaceae (Arabidopsis thaliana, A. halleri and Brassica rapa), stigmatic papilla cells were isolated precisely by laser microdissection, and cell type-specific gene expression in papilla cells was determined by RNA sequencing. As a result, 17,240, 19,260 and 21,026 unigenes were defined in papilla cells of A. thaliana, A. halleri and B. rapa, respectively, and, among these, 12,311 genes were common to all three species. Among the17,240 genes predicted in A. thaliana, one-third were papilla specific while approximately half of the genes were detected in all tissues examined. Bioinformatics analysis revealed that genes related to a wide range of reproduction and development functions are expressed in papilla cells, particularly metabolism, transcription and membrane-mediated information exchange. These results reflect the conserved features of general cellular function and also the specific reproductive role of papilla cells, highlighting a complex cellular system regulated by a diverse range of molecules in these cells. This study provides fundamental biological knowledge to dissect the molecular mechanisms of pollination in papilla cells and will shed light on our understanding of plant reproduction mechanisms.

The current status of the elemental defense hypothesis in relation to pathogens

Metal hyperaccumulating plants are able to accumulate exceptionally high concentrations of metals, such as zinc, nickel, or cadmium, in their aerial tissues. These metals reach concentrations that would be toxic to most other plant species. This trait has evolved multiple times independently in the plant kingdom. Recent studies have provided new insight into the ecological and evolutionary significance of this trait, by showing that some metal hyperaccumulating plants can use high concentrations of accumulated metals to defend themselves against attack by pathogenic microorganisms and herbivores. Here, we review the evidence that metal hyperaccumulation acts as a defensive trait in plants, with particular emphasis on plant-pathogen interactions. We discuss the mechanisms by which defense against pathogens might have driven the evolution of metal hyperaccumulation, including the interaction of this trait with other forms of defense. In particular, we consider how physiological adaptations and fitness costs associated with metal hyperaccumulation could have resulted in trade-offs between metal hyperaccumulation and other defenses. Drawing on current understanding of the population ecology of metal hyperaccumulator plants, we consider the conditions that might have been necessary for metal hyperaccumulation to be selected as a defensive trait, and discuss the likelihood that these were fulfilled. Based on these conditions, we propose a possible scenario for the evolution of metal hyperaccumulation, in which selective pressure for resistance to pathogens or herbivores, combined with gene flow from non-metallicolous populations, increases the likelihood that the metal hyperaccumulating trait becomes established in plant populations.

Taxonomy and systematics are key to biological information: Arabidopsis, Eutrema (Thellungiella), Noccaea and Schrenkiella (Brassicaceae) as examples

Taxonomy and systematics provide the names and evolutionary framework for any biological study. Without these names there is no access to a biological context of the evolutionary processes which gave rise to a given taxon: close relatives and sister species (hybridization), more distantly related taxa (ancestral states), for example. This is not only true for the single species a research project is focusing on, but also for its relatives, which might be selected for comparative approaches and future research. Nevertheless, taxonomical and systematic knowledge is rarely fully explored and considered across biological disciplines. One would expect the situation to be more developed with model organisms such as Noccaea, Arabidopsis, Schrenkiella and Eutrema (Thellungiella). However, we show the reverse. Using Arabidopsis halleri and Noccaea caerulescens, two model species among metal accumulating taxa, we summarize and reflect past taxonomy and systematics of Arabidopsis and Noccaea and provide a modern synthesis of taxonomic, systematic and evolutionary perspectives. The same is presented for several species of Eutrema s. l. and Schrenkiella recently appeared as models for studying stress tolerance in plants and widely known under the name Thellungiella.

Control of Zn uptake in Arabidopsis halleri: a balance between Zn and Fe

Zinc (Zn) is an essential plant micronutrient but is toxic in excess. To cope with excess Zn, plant species possess a strict metal homeostasis mechanism. The Zn hyperaccumulator Arabidopsis halleri has developed various adaptive mechanisms involving uptake, chelation, translocation and sequestration of Zn. In this mini review, we broadly discuss the different Zn tolerance mechanisms and then focus on controlled Zn uptake in A. halleri. Members of the ZRT/IRT-like protein (ZIP) family of metal transporters are mainly regulated by Zn and are involved in Zn uptake. A few members of the ZIP family, such as IRT1 and IRT2, are regulated by iron (Fe) and can transport multi-metals, including Zn, Fe, Mn, Cd, and Co. This mini-review also discusses the differential expression of multiple metal ZIP transporters in A. halleri and A. thaliana, a non-hyperaccumulator, with Zn exposure as well as Fe deficiency and their role in controlled Zn uptake and tolerance.

Zinc uptake and radial transport in roots of Arabidopsis thaliana: a modelling approach to understand accumulation

BACKGROUND AND AIMS

Zinc uptake in roots is believed to be mediated by ZIP (ZRT-, IRT-like proteins) transporters. Once inside the symplast, zinc is transported to the pericycle, where it exits by means of HMA (heavy metal ATPase) transporters. The combination of symplastic transport and spatial separation of influx and efflux produces a pattern in which zinc accumulates in the pericycle. Here, mathematical modelling was employed to study the importance of ZIP regulation, HMA abundance and symplastic transport in creation of the radial pattern of zinc in primary roots of Arabidopsis thaliana.

METHODS

A comprehensive one-dimensional dynamic model of radial zinc transport in roots was developed and used to conduct simulations. The model accounts for the structure of the root consisting of symplast and apoplast and includes effects of water flow, diffusion and cross-membrane transport via transporters. It also incorporates the radial geometry and varying porosity of root tissues, as well as regulation of ZIP transporters.

KEY RESULTS

Steady-state patterns were calculated for various zinc concentrations in the medium, water influx and HMA abundance. The experimentally observed zinc gradient was reproduced very well. An increase of HMA or decrease in water influx led to loss of the gradient. The dynamic behaviour for a change in medium concentration and water influx was also simulated showing short adaptation times in the range of seconds to minutes. Slowing down regulation led to oscillations in expression levels, suggesting the need for rapid regulation and existence of buffering agents.

CONCLUSIONS

The model captures the experimental findings very well and confirms the hypothesis that low abundance of HMA4 produces a radial gradient in zinc concentration. Surprisingly, transpiration was found also to be a key parameter. The model suggests that ZIP regulation takes place on a comparable timescale as symplastic transport.

Differential expression and regulation of iron-regulated metal transporters in Arabidopsis halleri and Arabidopsis thaliana--the role in zinc tolerance

To avoid zinc (Zn) toxicity, plants have developed a Zn homeostasis mechanism to cope with Zn excess in the surrounding soil. In this report, we uncovered the difference of a cross-homeostasis system between iron (Fe) and Zn in dealing with Zn excess in the Zn hyperaccumulator Arabidopsis halleri ssp. gemmifera and nonhyperaccumulator Arabidopsis thaliana. Arabidopsis halleri shows low expression of the Fe acquisition and deficiency response-related genes IRT1 and IRT2 compared with A. thaliana. In A. thaliana, lowering the expression of IRT1 and IRT2 through the addition of excess Fe to the medium increases Zn tolerance. Excess Zn induces significant Fe deficiency in A. thaliana and reduces Fe accumulation in shoots. By contrast, the accumulation of Fe in shoots of A. halleri was stable under various Zn treatments. Root ferric chelate reductase (FRO) activity and expression of FIT are low in A. halleri compared with A. thaliana. Overexpressing a ZIP family member IRT3 in irt1-1, rescues the Fe-deficient phenotype. A fine-tuned Fe homeostasis mechanism in A. halleri maintains optimum Fe level by Zn-regulated ZIP transporters and prevents high Zn uptake through Fe-regulated metal transporters, and in part be responsible for Zn tolerance.

Heavy metal specificity of cellular tolerance in two hyperaccumulating plants, Arabidopsis halleri and Thlaspi caerulescens

•  The cellular tolerance to nickel (Ni), zinc (Zn) and cadmium (Cd) of two poly-hyperaccumulators, Arabidopsis halleri and Thlaspi caerulescens, was investigated in order to compare their cellular phenotypes toward various metal ion exposures. •  Protoplasts were kept for 24 h on solutions containing increasing concentrations of the metal ions, and a viability test was performed. Zinc loading of the protoplasts was investigated with Arabidopsis lyrata and A. halleri protoplasts using the Zn fluorescent indicator Newport green diacetate. •  Only T. caerulescens protoplasts showed a clear tolerance to Ni. On the other hand, protoplasts from both hyperaccumulators displayed a very high and constitutive Zn tolerance and an inducible Cd tolerance. The vacuolar storage of Zn was confirmed, but no Zn accumulation at all was observed in A. halleri protoplasts after Zn exposure. •  Specific metal tolerances were found at the cellular level in the hyperaccumulating plants, highlighting that specific adaptations to metal ions exist in the cells as well as in the whole plants.

Does zinc protect the zinc hyperaccumulator Arabidopsis halleri from herbivory by snails?

•  Hyperaccumulation of metals has been proposed to be a defence against herbivores. Here we investigated whether snails discriminated between plants of Arabidopsis halleri, and the F2 of the cross between A. halleri and A. petraea, on the basis of their internal Zn concentration •  A. halleri and F2 plants were grown in four different Zn concentrations. Snails preferred F2 plants to A. halleri plants, and preferred plants that had been grown under low external Zn concentrations, but there was no evidence that they discriminated on the basis of internal Zn concentration •  F2 plants were germinated on Zn contaminated soil and snails were allowed to eat the seedlings for a range of different time periods. The survivors were grown on, and tested for, Zn accumulation under standard conditions. No difference was found between the different time periods, indicating that the snails had eaten seedlings randomly •  The results do not support a hypothesis that high internal Zn concentration protects seedlings from predation or herbivory by snails.

Do Arabidopsis halleri from nonmetallicolous populations accumulate zinc and cadmium more effectively than those from metallicolous populations?

•  The ability of metallicolous and nonmetallicolous populations of Arabidopsis halleri to accumulate zinc (Zn), cadmium (Cd) and lead (Pb) is compared here in order to explore the extent and variability of this trait in wild A. halleri plants. •  Aerial plant parts and the soil around the harvested plants were collected and analysed for metal concentrations or total and extractable metal concentrations, respectively, for 20 metallicolous and 13 nonmetallicolous populations. •  Results show that metallicolous and nonmetallicolous populations have the same ability to accumulate Zn and Cd but that neither population type is able to accumulate Pb. Between populations within type, an homogenous accumulating response is observed for Zn, whereas the ability to accumulate Cd is variable. •  Zn and Cd accumulation to very high concentrations is a constitutive property of the species. The Zn and Cd hyperaccumulator trait of A. halleri from contaminated sites was confirmed. Interestingly, nonmetallicolous plants are Zn and Cd hyperaccumulators. The possibility of using A. halleri in phytoremediation is discussed.

Within and between population genetic variation for zinc accumulation in Arabidopsis halleri

•  Hyperaccumulator plants in the field show significant variation in the metal concentration in their aerial parts, but little is known of the causes of this variation. This paper investigates the role of soil zinc (Zn) concentration and genetic variation in causing between and within population variation in Zn accumulation in Arabidopsis halleri. •  Seed from 17 populations of A. halleri collected in central Europe were grown under standard conditions at three external Zn concentrations and tested for Zn concentration in the leaves. •  Between population variation was highest at low external zinc concentrations. At 10 µm Zn some plants had very low leaf Zn concentrations, and were indistinguishable from nonaccumulators. However, at higher Zn concentrations, all plants showed hyperaccumulation. There were no differences in the accumulating abilities of populations from sites with different degrees of contamination. •  Heritability of accumulation, determined for individual families from three populations, was quite high (25-50%), indicating that selection for increased accumulating ability should be possible, although selection would be easier at low external Zn concentrations. The Zn concentration of field collected plants was affected partly by plant genotype but not by the total soil Zn around their roots.

Zinc tolerance and accumulation in metallicolous and nonmetallicolous populations of Arabidopsis halleri (Brassicaceae)

Zinc tolerance was investigated in five populations of Arabidopsis halleri (syn.: Cardaminopsis halleri) raised from seeds collected from contaminated and uncontaminated sites. Tolerance was measured by determining the concentration which inhibited root growth (EC₁₀₀ ). A. halleri populations from contaminated and uncontaminated sites were found to be Zn-tolerant compared with the Zn-nontolerant species Arabidopsis thaliana and A. lyrata subsp. petraea. At very high Zn concentrations, populations of A. halleri from uncontaminated sites were slightly less Zn-tolerant than those from contaminated sites. These observations support the hypothesis that in A. halleri, Zn tolerance is largely a constitutive property. One population from an uncontaminated site and one population from a contaminated site were studied for Zn uptake. Zinc content was measured in shoots and roots using a colorimetric test under laboratory conditions. The results showed that whatever their origin, individuals from both populations are Zn accumulators compared with the nonaccumulator species A. thaliana. Moreover, the population from the uncontaminated area accumulated Zn in its shoots and roots more quickly than the population from the contaminated site. These results suggest that, in A. halleri, Zn accumulation to very high concentration is a constitutive property.