Physiological and molecular mechanisms of plant-root responses to iron toxicity

The chemical form and physiological activity of iron (Fe) in soil are dependent on soil pH and redox potential (Eh), and Fe levels in soils are frequently elevated to the point of causing Fe toxicity in plants, with inhibition of normal physiological activities and of growth and development. In this review, we describe how iron toxicity triggers important physiological changes, including nitric-oxide (NO)-mediated potassium (K+) efflux at the tips of roots and accumulation of reactive oxygen species (ROS) and reactive nitrogen (RNS) in roots, resulting in physiological stress. We focus on the root system, as the first point of contact with Fe in soil, and describe the key processes engaged in Fe transport, distribution, binding, and other mechanisms that are drawn upon to defend against high-Fe stress. We describe the root-system regulation of key physiological processes and of morphological development through signaling substances such as ethylene, auxin, reactive oxygen species, and nitric oxide, and discuss gene-expression responses under high Fe. We especially focus on studies on the physiological and molecular mechanisms in rice and Arabidopsis under high Fe, hoping to provide a valuable theoretical basis for improving the ability of crop roots to adapt to soil Fe toxicity.

A transcriptomic dataset for investigating the Arabidopsis Unfolded Protein Response under chronic, proteotoxic endoplasmic reticulum stress

The Unfolded Protein Response (UPR) is a retrograde, ER-to-nucleus, signalling pathway which is conserved across kingdoms. In plants, it contributes to development, reproduction, immunity and tolerance to abiotic stress. This RNA sequencing (RNA-seq) dataset was produced from 14-day-old Arabidopsis thaliana seedlings challenged by tunicamycin (Tm), an antibiotic inhibiting Asn-linked glycosylation in the endoplasmic reticulum (ER), causing an ER stress and eventually activating the UPR. Wild-type (WT) and a double mutant deficient for two main actors of the UPR (INOSITOL-REQUIRING ENZYME 1A and INOSITOL-REQUIRING ENZYME 1B) were used as genetic backgrounds in our experimental setup, allowing to distinguish among differentially-expressed genes (DEGs) which ones are dependent on or independent on IRE1s. Also, shoots and roots were harvested separately to determine organ-specific transcriptomic responses to Tm. Library and sequencing were performed using DNBseq™ technology by the Beijing Genomics Institute. Reads were mapped and quantified against the Arabidopsis genome. Differentially-expressed genes were identified using Rflomics upon filtering and normalization by the Trimmed Mean of M-value (TMM) method. While the genotype effect was weak under mock conditions (with a total of 182 DEGs in shoots and 195 DEGs in roots), the tunicamycin effect on each genotype was characterized by several hundred of DEGs in both shoots and roots. Among these genes, 872 and 563 genes were statistically up- and down-regulated in the shoot tissues of the double mutant when compared to those of WT, respectively. In roots of Tm-challenged seedlings, 425 and 439 genes were significantly up- and down-regulated in mutants with respect to WT. We believe that our dataset could be reused for investigating any biological questions linked to ER homeostasis and its role in plant physiology.

Contrasting shrub and grass hydraulic responses to experimental drought

Whole-plant hydraulics provide important information about responses to water limitation and can be used to understand how plant communities may change in a drier climate when measured on multiple species. Here, we measured above- and belowground hydraulic traits in Cornus drummondii, an encroaching shrub within North American tallgrass prairies, and Andropogon gerardii, a dominant C4 grass, to assess the potential hydraulic responses to future drought as this region undergoes woody expansion. Shelters that reduced precipitation by 50% and 0% were built over shrubs and grasses growing in sites that are burned at 1-year and 4-year frequencies. We then measured aboveground (Kshoot), belowground (Kroot), and whole-plant maximum hydraulic conductance (Kplant) in C. drummondii and Kroot in A. gerardii. We also measured vulnerability to embolism (P50) in C. drummondii stems. Overall, we show that: (1) A. gerardii had substantially greater Kroot than C. drummondii; (2) belowground hydraulic functioning was linked with aboveground processes; (3) above- and belowground C. drummondii hydraulics were not negatively impacted by the rainfall reductions imposed here. These results suggest that a multi-year drought will not ameliorate rates of woody expansion and highlight key differences in aboveground and belowground hydraulics for dominant species within the same ecosystem.

The structure and diversity of bacteria and fungi in the roots and rhizosphere soil of three different species of Geodorum

Shepherd's crook (Geodorum) is a genus of protected orchids that are valuable both medicinally and ornamentally. Geodorum eulophioides (GE) is an endangered and narrowly distributed species, and Geodorum densiflorum (GD) and Geodorum attenuatum (GA) are widespread species. The growth of orchids depend on microorganisms. However, there are few studies on the microbial structure in Geodorum, and little is known about the roles of microorganisms in the endangered mechanism of G. eulophioides. This study analyzed the structure and composition of bacterial and fungal communities in the roots and rhizosphere soil of GE, GD, and GA. The results showed that Delftia, Bordetella and norank_f_Xanthobacteraceae were the dominant bacteria in the roots of Geodorum, while norank_f_Xanthobacteraceae, Gaiella and norank_f_norank_o_Gaiellales were the dominant bacteria in the rhizosphere soil of Geodorum. In the roots, the proportion of Mycobacterium in GD_roadside was higher than that in GD_understory, on the contrary, the proportion of Fusarium, Delftia and Bordetella in GD_roadside was lower than that in GD_understory. Compared with the GD_understory, the roots of GD_roadside had lower microbial diversity. In the endangered species GE, Russula was the primary fungus in the roots and rhizosphere soil, with fungal diversity lower than in the more widespread species. Among the widespread species, the dominant fungal genera in the roots and rhizosphere soil were Neocosmospora, Fusarium and Coprinopsis. This study enhances our understanding of microbial composition and diversity, providing fundamental information for future research on microbial contributions to plant growth and ecosystem function in Geodorum.

Contrasting plant transcriptome responses between a pierce-sucking and a chewing herbivore go beyond the infestation site

BACKGROUND

Plants have acquired a repertoire of mechanisms to combat biotic stressors, which may vary depending on the feeding strategies of herbivores and the plant species. Hormonal regulation crucially modulates this malleable defense response. Jasmonic acid (JA) and salicylic acid (SA) stand out as pivotal regulators of defense, while other hormones like abscisic acid (ABA), ethylene (ET), gibberellic acid (GA) or auxin also play a role in modulating plant-pest interactions. The plant defense response has been described to elicit effects in distal tissues, whereby aboveground herbivory can influence belowground response, and vice versa. This impact on distal tissues may be contingent upon the feeding guild, even affecting both the recovery of infested tissues and those that have not suffered active infestation.

RESULTS

To study how phytophagous with distinct feeding strategies may differently trigger the plant defense response during and after infestation in both infested and distal tissues, Arabidopsis thaliana L. rosettes were infested separately with the chewing herbivore Pieris brassicae L. and the piercing-sucker Tetranychus urticae Koch. Moderate infestation conditions were selected for both pests, though no quantitative control of damage levels was carried out. Feeding mode did distinctly influence the transcriptomic response of the plant under these conditions. Though overall affected processes were similar under either infestation, their magnitude differed significantly. Plants infested with P. brassicae exhibited a short-term response, involving stress-related genes, JA and ABA regulation and suppressing growth-related genes. In contrast, T. urticae elicited a longer transcriptomic response in plants, albeit with a lower degree of differential expression, in particular influencing SA regulation. These distinct defense responses transcended beyond infestation and through the roots, where hormonal response, flavonoid regulation or cell wall reorganization were differentially affected.

CONCLUSION

These outcomes confirm that the existent divergent transcriptomic responses elicited by herbivores employing distinct feeding strategies possess the capacity to extend beyond infestation and even affect tissues that have not been directly infested. This remarks the importance of considering the entire plant's response to localized biotic stresses.

Mutation of AtPME2, a pH-Dependent Pectin Methylesterase, Affects Cell Wall Structure and Hypocotyl Elongation

Pectin methylesterases (PMEs) modify homogalacturonan's chemistry and play a key role in regulating primary cell wall mechanical properties. Here, we report on Arabidopsis AtPME2, which we found to be highly expressed during lateral root emergence and dark-grown hypocotyl elongation. We showed that dark-grown hypocotyl elongation was reduced in knock-out mutant lines as compared to the control. The latter was related to the decreased total PME activity as well as increased stiffness of the cell wall in the apical part of the hypocotyl. To relate phenotypic analyses to the biochemical specificity of the enzyme, we produced the mature active enzyme using heterologous expression in Pichia pastoris and characterized it through the use of a generic plant PME antiserum. AtPME2 is more active at neutral compared to acidic pH, on pectins with a degree of 55-70% methylesterification. We further showed that the mode of action of AtPME2 can vary according to pH, from high processivity (at pH8) to low processivity (at pH5), and relate these observations to the differences in electrostatic potential of the protein. Our study brings insights into how the pH-dependent regulation by PME activity could affect the pectin structure and associated cell wall mechanical properties.

Genomic prediction for root and yield traits of barley under a water availability gradient: a case study comparing different spatial adjustments

BACKGROUND

In drought periods, water use efficiency depends on the capacity of roots to extract water from deep soil. A semi-field phenotyping facility (RadiMax) was used to investigate above-ground and root traits in spring barley when grown under a water availability gradient. Above-ground traits included grain yield, grain protein concentration, grain nitrogen removal, and thousand kernel weight. Root traits were obtained through digital images measuring the root length at different depths. Two nearest-neighbor adjustments (M1 and M2) to model spatial variation were used for genetic parameter estimation and genomic prediction (GP). M1 and M2 used (co)variance structures and differed in the distance function to calculate between-neighbor correlations. M2 was the most developed adjustment, as accounted by the Euclidean distance between neighbors.

RESULTS

The estimated heritabilities ([Formula: see text]) ranged from low to medium for root and above-ground traits. The genetic coefficient of variation ([Formula: see text]) ranged from 3.2 to 7.0% for above-ground and 4.7 to 10.4% for root traits, indicating good breeding potential for the measured traits. The highest [Formula: see text] observed for root traits revealed that significant genetic change in root development can be achieved through selection. We studied the genotype-by-water availability interaction, but no relevant interaction effects were detected. GP was assessed using leave-one-line-out (LOO) cross-validation. The predictive ability (PA) estimated as the correlation between phenotypes corrected by fixed effects and genomic estimated breeding values ranged from 0.33 to 0.49 for above-ground and 0.15 to 0.27 for root traits, and no substantial variance inflation in predicted genetic effects was observed. Significant differences in PA were observed in favor of M2.

CONCLUSIONS

The significant [Formula: see text] and the accurate prediction of breeding values for above-ground and root traits revealed that developing genetically superior barley lines with improved root systems is possible. In addition, we found significant spatial variation in the experiment, highlighting the relevance of correctly accounting for spatial effects in statistical models. In this sense, the proposed nearest-neighbor adjustments are flexible approaches in terms of assumptions that can be useful for semi-field or field experiments.

The nitrate transporter-sensor MtNPF6.8 regulates the branched chain amino acid/pantothenate metabolic pathway in barrel medic (Medicago truncatula Gaertn.) root tip

Nitrogen is the most limiting nutrient for plants, and it is preferentially absorbed in the form of nitrate by roots, which adapt to nitrate fluctuations by remodelling their architecture. Although core mechanisms of the response to nitrate availability are relatively well-known, signalling events controlling root growth and architecture have not all been identified, in particular in Legumes. However, the developmental effect of nitrate in Legumes is critical since external nitrate not only regulates root architecture but also N2-fixing nodule development. We have previously shown that in barrel medic (Medicago truncatula), the nitrate transporter MtNPF6.8 is required for nitrate sensitivity in root tip. However, uncertainty remains as to whether nitrogen metabolism itself is involved in the MtNPF6.8-mediated response. Here, we examine the metabolic effects of MtNPF6.8-dependent nitrate signalling using metabolomics and proteomics in WT and mtnpf6.8 root tips in presence or absence of nitrate. We found a reorchestration of metabolism due to the mutation, in favour of the branched chain amino acids/pantothenate metabolic pathway, and lipid catabolism via glyoxylate. That is, the mtnpf6.8 mutation was likely associated with a specific rerouting of acetyl-CoA production (glyoxylic cycle) and utilisation (pantothenate and branched chain amino acid synthesis). In agreement with our previous findings, class III peroxidases were confirmed as the main protein class responsive to nitrate, although in an MtNPF6.8-independent fashion. Our data rather suggest the involvement of other pathways within mtnpf6.8 root tips, such as Ca2+ signalling or cell wall methylation.

Unraveling differential characteristics and mechanisms of nitrogen uptake in wheat cultivars with varied nitrogen use efficiency

Nitrogen uptake is crucial to wheat nitrogen use efficiency (NUE). The study's findings indicate that both high- and low-NUE cultivars exhibited highest nitrogen uptake efficiency (NupE) under 0.2 mM nitrogen. Under 2 mM nitrogen, their NupEs decrease significantly, while uptakes to NO3- were notably higher than that of NH4+. Strikingly, high-NUE cultivars exhibited a significantly higher NH4+ uptake rate than low NUE cultivars, resulting in a marked improvement in their ability to take up nitrogen. The NUEs of the cultivars with 5 mM nitrogen were almost half that of 2 mM nitrogen. NO3- uptake primarily occurred in the mature zone of roots, while NH4+ uptake took place in the root tip meristem and elongation zones. Notably, the NH4+ uptake in root tip meristematic zone of high-NUE cultivar was significantly higher than that of low NUE cultivar. Furthermore, the NO3- uptake of high-NUE cultivar in the root mature zone was significantly higher than that of low-NUE cultivar under 2 mM nitrogen. These findings were consistent with the significantly higher expression levels of TaAMT in root tip and of TaNRT in root mature area of high-NUE cultivar compared to low-NUE cultivar, respectively, enabling efficient absorption of NO3- and NH4+ and transport of NO3- to shoot. The high-NUE cultivars showed elevated expression of amino acid transporters further promoting nitrogen uptake, and conversion of nitrogen into ureides and amino acids further facilitated inorganic nitrogen uptake by roots. The differential findings offer valuable insights into novel variety breeding of high NUE in the future.

Root transcriptomic provides insights on molecular mechanisms involved in the tolerance to water deficit in Pisum sativum inoculated with Pseudomonas sp

MAIN CONCLUSION

Root transcriptomics and biochemical analyses in water-stressed Pisum sativum plants inoculated with Pseudomonas spp. suggested preservation of ABA-related pathway and ROS detoxification, resulting in an improved tolerance to stress. Drought already affects agriculture in large areas of the globe and, due to climate change, these areas are predicted to become increasingly unsuitable for agriculture. For several years, plant growth-promoting bacteria (PGPB) have been used to improve legume yields, but many aspects of this interaction are still unclear. To elucidate the mechanisms through which root-associated PGPB can promote plant growth in dry environments, we investigated the response of pea plants inoculated with a potentially beneficial Pseudomonas strain (PK6) and subjected to two different water regimes. Combined biometric, biochemical, and root RNA-seq analyses revealed that PK6 improved pea growth specifically under water deficit, as inoculated plants showed an increased biomass, larger leaves, and longer roots. Abscisic acid (ABA) and proline quantification, together with the transcriptome analysis, suggested that PK6-inoculated plant response to water deficit was more diversified compared to non-inoculated plants, involving alternative metabolic pathways for the detoxification of reactive oxygen species (ROS) and the preservation of the ABA stress signaling pathway. We suggest that the metabolic response of PK6-inoculated plants was more effective in their adaptation to water deprivation, leading to their improved biometric traits. Besides confirming the positive role that PGPB can have in the growth of a legume crop under adverse conditions, this study offers novel information on the mechanisms regulating plant-bacteria interaction under varying water availability. These mechanisms and the involved genes could be exploited in the future for the development of legume varieties, which can profitably grow in dry climates.

Climate-dependent responses of root and shoot biomass to drought duration and intensity in grasslands-a meta-analysis

Understanding the effects of altered precipitation regimes on root biomass in grasslands is crucial for predicting grassland responses to climate change. Nonetheless, studies investigating the effects of drought on belowground vegetation have produced mixed results. In particular, root biomass under reduced precipitation may increase, decrease or show a delayed response compared to shoot biomass, highlighting a knowledge gap in the relationship between belowground net primary production and drought. To address this gap, we conducted a meta-analysis of nearly 100 field observations of grassland root and shoot biomass changes under experimental rainfall reduction to disentangle the main drivers behind grassland responses to drought. Using a response-ratio approach we tested the hypothesis that water scarcity would induce a decrease in total biomass, but an increase in belowground biomass allocation with increased drought length and intensity, and that climate (as defined by the aridity index of the study location) would be an additional predictor. As expected, meteorological drought decreased root and shoot biomass, but aboveground and belowground biomass exhibited contrasting responses to drought duration and intensity, and their interaction with climate. In particular, drought duration had negative effects on root biomass only in wet climates while more intense drought had negative effects on root biomass only in dry climates. Shoot biomass responded negatively to drought duration regardless of climate. These results show that long-term climate is an important modulator of belowground vegetation responses to drought, which might be a consequence of different drought tolerance and adaptation strategies. This variability in vegetation responses to drought suggests that physiological plasticity and community composition shifts may mediate how climate affects carbon allocation in grasslands, and thus ultimately carbon storage in soil.

Response to gallium (Ga) exposure and its distribution in rice plants

Root architecture is the temporal and spatial configuration of root system in the heterogeneous matrix of soil that is prone to chemical stresses. Gallium (Ga) is among the emerging chemical pollutants that are mostly associated with high-tech industries, specifically associated with semiconductors. In view of its potential risk and increasing distribution in the environment, this study was designed to evaluate the inhibition rate, Ga distribution in different tissues, and root architecture of rice seedlings under different concentrations of Ga. We observed that 2.59, 46.7, and 168.2 mg Ga/L were minimum (EC20), medium (EC50), and maximum (EC75) effective concentrations for rice plants that corresponded to the 20, 50, and 75% inhibition on the relative growth rate, respectively. Distribution of Ga in rice tissues showed that accumulation of Ga was much higher in roots than shoots of rice seedlings, and it increased with an increase in Ga doses. Evan blue staining technique reveals that the number of damaged/dead cell was dose-dependent on Ga. Moreover, several traits associated with root system architecture demonstrating that rice root system architecture altered in response to Ga stress. Collectively, the results reveal that Ga exposure inhibited the growth and development of rice plants. This study will enhance our understanding that how different concentrations of Ga in the environment can affect plants; however, more comprehensive studies are essential to further determine plant response against Ga stress.

Uncovering the dominant role of root metabolism in shaping rhizosphere metabolome under drought in tropical rainforest plants

Plant-soil-microbe interactions are crucial for driving rhizosphere processes that contribute to metabolite turnover and nutrient cycling. With the increasing frequency and severity of water scarcity due to climate warming, understanding how plant-mediated processes, such as root exudation, influence soil organic matter turnover in the rhizosphere is essential. In this study, we used 16S rRNA gene amplicon sequencing, rhizosphere metabolomics, and position-specific 13C-pyruvate labeling to examine the effects of three different plant species (Piper auritum, Hibiscus rosa sinensis, and Clitoria fairchildiana) and their associated microbial communities on soil organic carbon turnover in the rhizosphere. Our findings indicate that in these tropical plants, the rhizosphere metabolome is primarily shaped by the response of roots to drought rather than direct shifts in the rhizosphere bacterial community composition. Specifically, the reduced exudation of plant roots had a notable effect on the metabolome of the rhizosphere of P. auritum, with less reliance on neighboring microbes. Contrary to P. auritum, H. rosa sinensis and C. fairchildiana experienced changes in their exudate composition during drought, causing alterations to the bacterial communities in the rhizosphere. This, in turn, had a collective impact on the rhizosphere's metabolome. Furthermore, the exclusion of phylogenetically distant microbes from the rhizosphere led to shifts in its metabolome. Additionally, C. fairchildiana appeared to be associated with only a subset of symbiotic bacteria under drought conditions. These results indicate that plant species-specific microbial interactions systematically change with the root metabolome. As roots respond to drought, their associated microbial communities adapt, potentially reinforcing the drought tolerance strategies of plant roots. These findings have significant implications for maintaining plant health and preference during drought stress and improving plant performance under climate change.

The exodermis: A forgotten but promising apoplastic barrier

The endodermis and exodermis are widely recognized as two important barriers in plant roots that play a role in regulating the movement of water and ions. While the endodermis is present in nearly all plant roots, the exodermis, characterized by Casparian strips and suberin lamellae is absent in certain plant species. The exodermis can be classified into three types: uniform, dimorphic, and inducible exodermis. Apart from its role in water and ion transport, the exodermis acts as a protective barrier against harmful substances present in the external environment. Furthermore, the exodermis is a complex barrier influenced by various environmental factors, and its resistance to water and ions varies depending on the type of exodermis and the maturity of the root. Therefore, investigations concerning the exodermis necessitate a plant-specific approach. However, our current understanding of the exodermal physiological functions and molecular mechanisms governing its development is limited due to the absence of an exodermis in the model plant Arabidopsis. Due to that, unfortunately, the exodermis has been largely overlooked until now. In this review, we aim to summarize the current fundamental knowledge regarding the exodermis in common research used crop species and propose suggestions for future research endeavors.

Benzophenone-3 sunscreen causes phytotoxicity and cytogenotoxicity in higher plants

The benzophenone-3 (BP-3) sunscreen is recurrently released into the environment from different sources, however, evaluations of its adverse effects on plants do not exist in the literature. In this study, BP-3 was evaluated, at concentrations 2; 20, and 200 µg/L, regarding phytotoxicity, based on germination and root elongation in seeds, in Lactuca sativa L., Cucumis sativus L. and Allium cepa L., and phytotoxicity, cytogenotoxicity and oxidative stress in A. cepa bulb roots. The BP-3 concentrations, except for the 200 µg/L concentration in L. sativa, caused no significant reduction in seed germination. All concentrations tested significantly reduced the elongation of roots from seeds and roots from bulbs. The 20 and 200 µg/L concentrations caused oxidation in cells, disturbances in the cell cycle, and alterations in prophase and metaphase, as well as the induction of micronuclei, in A. cepa root meristems. Furthermore, the three concentrations induced a high number of prophases in root tips. Such disorders were caused by excess H2O2 and superoxide produced in cells due to exposure to BP-3, which triggered significant phytotoxicity, cytotoxicity, and genotoxicity in root meristems. Thus, the recurrent contamination of agricultural and non-agricultural soils with BP-3, even at a concentration of 2 µg/L, represents an environmental risk for plants. These results point to the impending need to set limits for the disposal of this sunscreen into the environment since BP-3 has been used in industry for several decades.

Exogenous strigolactones alleviate drought stress in wheat (Triticum aestivum L.) by promoting cell wall biogenesis to optimize root architecture

Exogenous strigolactones (SLs, GR24) are widely used to alleviate drought stress in wheat. The physiological and biochemical mechanisms via which SLs help overcome drought stress in wheat shoots have been reported; however, the mechanisms in wheat roots are unclear. The present study explored the effects of the exogenous application of SLs on wheat roots' growth and molecular responses under drought stress using physiological analysis and RNA-seq. RNA-seq of roots showed that SLs mainly upregulated signal transduction genes (SIS8, CBL3, GLR2.8, LRK10L-2.4, CRK29, and CRK8) and transcription factors genes (ABR1, BHLH61, and MYB93). Besides, SLs upregulated a few downstream target genes, including antioxidant genes (PER2, GSTF1, and GSTU6), cell wall biogenesis genes (SUS4, ADF3, UGT13248, UGT85A24, UGT709G2, BGLU31, and LAC5), an aquaporin-encoding gene (TIP4-3), and dehydrin-encoding genes (DHN2, DHN3, and DHN4). As a result, SLs reduced oxidative damage, optimized root architecture, improved leaf-water relation, and alleviated drought damage. Thus, the present study provides novel insights into GR24-mediated drought stress management and a scientific basis for proposing GR24 application.

Roots Fuel Cell Produces and Stores Clean Energy

In recent years, extensive scientific efforts have been conducted to develop clean bioenergy technologies. A promising approach that has been under development for more than a hundred years is the microbial fuel cell (MFC) which utilizes exoelectrogenic bacteria as an electron source in a bioelectrochemical cell. The viability of bacteria in soil MFCs can be maintained by integrating plant roots, which release organic materials that feed the bacteria. In this work, we show that rather than organic compounds, roots also release redox species that can produce electricity in a biofuel cell. We first studied the reduction of the electron acceptor Cytochrome C by green onion roots. We integrate green onion roots into a biofuel cell to produce a continuous bias-free electric current for more than 24 h in the dark. This current is enhanced upon irradiation of the onion's leaves with light. We apply cyclic voltammetry and 2D-fluorescence measurements to show that NADH and NADPH act as major electron mediators between the roots and the anode, while their concentrations in the external root matrix are increased upon irradiation of the leaves. Finally, we show that roots can contribute to energy storage by charging a supercapacitor.

Differences of cadmium uptake and accumulation in roots of two maize varieties (Zea mays L.)

Different maize varieties respond differentially to cadmium (Cd) stress. As the first organ in contact with the soil, the response of the root is particularly important. However, the physiological mechanisms that determine the response are not well defined. Here, we compared the differences in Cd-induced related gene expression, ionic homeostasis, and ultrastructural changes in roots of Cd-tolerant maize variety (XR57) and Cd-sensitive maize variety (LY296), and assessed their effects on Cd uptake and accumulation. Our findings indicate that XR57 absorbed a significantly lower Cd than LY296 did, and that the expression levels of genes related to Cd uptake (ZmNRAMP5 and ZmZIP4) and efflux (ZmABCG4) in the root were consistent with the Cd absorption at the physiological levels. Compared with LY296, the lower Cd concentration in the roots of XR57 caused less interference with the ion balance. Transmission electron microscope images revealed that the roots from XR57 exposed to Cd had developed thicker cell walls than LY296. In addition, the large increase ZmABCC1 and ZmABCC2 expression levels in XR57 mediated the appearance of numerous electron-dense granules in the vacuoles present in the roots. As a result, the high Cd tolerance of XR57 is the result of a multi-level response that involves increased resistance to Cd uptake, a stronger capacity for vacuolar regionalization, and the formation of thicker cell walls. These findings may provide a theoretical basis for maize cultivation in Cd-contaminated areas.

Evaluation of phosphate rock as the only source of phosphorus for the growth of tall and semi-dwarf durum wheat and rye plants using digital phenotyping

Background

Phosphorus nutrition is important for obtaining high yields of crop plants. However, wheat plants are known to be almost incapable of taking up phosphorus from insoluble phosphate sources, and reduced height genes are supposed to decrease this ability further.

Methods

We performed a pot experiment using Triticum durum Desf. tall spring variety LD222, its near-isogenic semidwarf line carrying Rht17 (Reduced height 17) gene, and winter rye (Secale cereale L.) variety Chulpan. The individual plants were grown in quartz sand. The phosphorus was provided either as phosphate rock powder mixed with sand, or as monopotassium phosphate solution (normal nutrition control) or was not supplemented at all (no-phosphorus control). Other nutrients were provided in soluble form. During experiment the plants were assessed using the TraitFinder (Phenospex Ltd., Heerlen, Netherlands) digital phenotyping system for a standard set of parameters. Double scan with 90 degrees turns of pots around vertical axis vs. single scan were compared for accuracy of phenotyping.

Results

The phenotyping showed that at least 20 days of growth after seedling emergence were necessary to get stable differences between genotypes. After this initial period, phenotyping confirmed poor ability of wheat to grow on substrate with phosphate rock as the only source of phosphorus compared to rye; however, Rht17 did not cause an additional reduction in growth parameters other than plant height under this variant of substrate. The agreement between digital phenotyping and conventionally measured traits was at previously reported level for grasses (R2 = 0.85 and 0.88 for digital biomass and 3D leaf area vs. conventionally measured biomass and leaf area, single scan). Among vegetation indices, only the normalized differential vegetation index (NDVI) and the green leaf index (GLI) showed significant correlations with manually measured traits, including the percentage of dead leaves area. The double scan improved phenotyping accuracy, but not substantially.

Wheat type one protein phosphatase promotes salt and osmotic stress tolerance in arabidopsis via auxin-mediated remodelling of the root system

The control of optimal root growth and plant stress responses depends largely on a variety of phytohormones among which auxin and brassinosteroids (BRs) are the most influential. We have previously reported that the durum wheat type 1 protein phosphatase TdPP1 participates in the control of root growth by modulating BR signaling. In this study, we pursue our understanding of how TdPP1 fulfills this regulatory function on root growth by evaluating the physiological and molecular responses of Arabidopsis TdPP1 over-expressing lines to abiotic stresses. Our results showed that when exposed to 300 mM Mannitol or 100 mM NaCl, the seedlings of TdPP1 over-expressors exhibit modified root architecture with higher lateral root density, and longer root hairs concomitant with a lower inhibition of the primary root growth. These lines also exhibit faster gravitropic response and a decrease in primary root growth inhibition when exposed to high concentrations of exogenous IAA. On another hand, a cross between TdPP1 overexpressors and DR5:GUS marker line was performed to monitor auxin accumulation in roots. Remarkably, the TdPP1 overexpression resulted in an enhanced auxin gradient under salt stress with a higher accumulation in primary and lateral root tips. Moreover, TdPP1 transgenics exhibit a significant induction of a subset of auxin-responsive genes under salt stress conditions. Therefore, our results reveal a role of PP1 in enhancing auxin signaling to help shape greater root plasticity thus improving plant stress resilience.

Interpreting water demands of forests and grasslands within a new Budyko formulation of evapotranspiration using percolation theory

The relationship between carbon cycle and water demand is key to understanding global climate change, vegetation productivity, and predicting the future of water resources. The water balance, which enumerates the relative fractions of precipitation P that run off, Q, or are returned to the atmosphere through evapotranspiration, ET, links drawdown of atmospheric carbon with the water cycle through plant transpiration. Our theoretical description based on percolation theory proposes that dominant ecosystems tend to maximize drawdown of atmospheric carbon in the process of growth and reproduction, thus providing a link between carbon and water cycles. In this framework, the only parameter is the fractal dimensionality d_f of the root system. Values of d_f appear to relate to the relative roles of nutrient and water accessibility. Larger values of d_f lead to higher ET values. Known ranges of grassland root fractal dimensions predict reasonably the range of ET(P) in such ecosystems as a function of aridity index. Forests with shallower root systems, should be characterized by a smaller d_f and, therefore, ET that is a smaller fraction of P. The prediction of ET/P using the 3D percolation value of d_f matches rather closely results deemed typical for forests based on a phenomenology already in common use. We test predictions of Q with P against data and data summaries for sclerophyll forests in southeastern Australia and the southeastern USA. Applying PET data from a nearby site constrains the data from the USA to lie between our ET predictions for 2D and 3D root systems. For the Australian site, equating cited "losses" with PET underpredicts ET. This discrepancy is mostly removed by referring to mapped values of PET in that region. Missing in both cases is local PET variability, more important for reducing data scatter in southeastern Australia, due to the greater relief.

High phytoremediation and translocation potential of an invasive weed species (Amaranthus retroflexus) in Europe in metal-contaminated areas

We demonstrated the metal accumulation potential of Amaranthus retorflexus, a European weed species, both in moderately and strongly metal-contaminated sites. Metal accumulation in roots, stems, and leaves were studied. We also calculated the bioaccumulation factor (BAF), and translocation factor (TF) values to quantify the metal accumulation, and translocation between plant organs. Our findings indicated that metal accumulation correlated with metal concentration; that is plant organs accumulated higher concentration of metals in the contaminated area than in the control one. We found that the concentrations of Ba, Mn, Sr and Zn were the highest in leaves, and Al, Cr, Cu, Fe and Pb in roots. High BAF value was found for Sr in all studied areas, indicating this metal's high accumulation potential of Amaranthus retorflexus. High TF values were found for Al, Ba, Cu, Fe, Mn, Sr and Zn; these metals were successfully transported to aboveground plant organs. We demonstrated that A. retroflexus, a fast-growing, rapidly spreading weed in Europe, was especially useful for heavy metal phytoremediation and phytoextraction.

Genetic Mapping of the Root Mycobiota in Rice and its Role in Drought Tolerance

BACKGROUND

Rice is the second most produced crop worldwide, but is highly susceptible to drought. Micro-organisms can potentially alleviate the effects of drought. The aim of the present study was to unravel the genetic factors involved in the rice-microbe interaction, and whether genetics play a role in rice drought tolerance. For this purpose, the composition of the root mycobiota was characterized in 296 rice accessions (Oryza sativa L. subsp. indica) under control and drought conditions. Genome wide association mapping (GWAS) resulted in the identification of ten significant (LOD > 4) single nucleotide polymorphisms (SNPs) associated with six root-associated fungi: Ceratosphaeria spp., Cladosporium spp., Boudiera spp., Chaetomium spp., and with a few fungi from the Rhizophydiales order. Four SNPs associated with fungi-mediated drought tolerance were also found. Genes located around those SNPs, such as a DEFENSIN-LIKE (DEFL) protein, EXOCYST TETHERING COMPLEX (EXO70), RAPID ALKALINIZATION FACTOR-LIKE (RALFL) protein, peroxidase and xylosyltransferase, have been shown to be involved in pathogen defense, abiotic stress responses and cell wall remodeling processes. Our study shows that rice genetics affects the recruitment of fungi, and that some fungi affect yield under drought. We identified candidate target genes for breeding to improve rice-fungal interactions and hence drought tolerance.

Microplastics occurrence and fate in full-scale treatment wetlands

Treatment wetlands (TWs) are an efficient technology for removing microplastics (MPs) from wastewater, according to previous studies. This study investigates the dynamics and fate of MPs in two wastewater treatment plants (WWTPs) using TWs, one with horizontal subsurface flow (HF) and another with a floating plant system (FS). Special attention is paid to the retention produced in the sludge and the role of macrophyte roots. The abundance of MPs in the influent to the WWTPs was on average 20.3 ± 0.85 MP/L and 8.4 ± 1.13 MP/L in HF and FS respectively, while the effluent had 0.58 ± 0.07 MP/L and 0.17 ± 0.06 MP/L, thus giving overall efficiencies of 97.42% and 98.13%, respectively. In the HF wetland, sludge samples near the inlet and the outlet were taken, distinguishing between sludge adhered to gravel and sludge attached to roots. In the floating macrophytes, sludge samples from secondary and tertiary treatments were taken. The results indicate that roots play a significant role in MPs retention. In the HF wetland, the complex formed by roots and gravel attached more MPs than gravel alone in the final zone of the wetland. In the FS, roots retained a significant quantity of MPs, both in the secondary and tertiary treatments, thus giving rise to a sludge less concentrated in MPs. This study aims to improve the knowledge of MPs behavior and fate in full-scale TWs, providing valuable information to enhance retention efficiency.

Root-Expressed Rice PAP3b Enhances Secreted APase Activity and Helps Utilize Organic Phosphate

Phosphate (Pi) deficiency leads to the induction of purple acid phosphatases (PAPs) in plants, which dephosphorylate organic phosphorus (P) complexes in the rhizosphere and intracellular compartments to release Pi. In this study, we demonstrate that OsPAP3b belongs to group III low-molecular weight PAP and is low Pi-responsive, preferentially in roots. The expression of OsPAP3b is negatively regulated with Pi resupply. Interestingly, OsPAP3b was found to be dual localized to the nucleus and secretome. Furthermore, OsPAP3b is transcriptionally regulated by OsPHR2 as substantiated by DNA-protein binding assay. Through in vitro biochemical assays, we further demonstrate that OsPAP3b is a functional acid phosphatase (APase) with broad substrate specificity. The overexpression (OE) of OsPAP3b in rice led to increased secreted APase activity and improved mineralization of organic P sources, which resulted in better growth of transgenics compared to the wild type when grown on organic P as an exogenous P substrate. Under Pi deprivation, OsPAP3b knock-down and knock-out lines showed no significant changes in total P content and dry biomass. However, the expression of other phosphate starvation-induced genes and the levels of metabolites were found to be altered in the OE and knock-down lines. In addition, in vitro pull-down assay revealed multiple putative interacting proteins of OsPAP3b. Our data collectively suggest that OsPAP3b can aid in organic P utilization in rice. The APase isoform behavior and nuclear localization indicate its additional role, possibly in stress signaling. Considering its important roles, OsPAP3b could be a potential target for improving low Pi adaptation in rice.

Polystyrene nanoplastics' accumulation in roots induces adverse physiological and molecular effects in water spinach Ipomoea aquatica Forsk

The ubiquity of plastic pollution has emerged as a perplexing issue for aquatic and terrestrial plants. To assess the toxic effects of polystyrene NPs (PS-NPs, 80 nm), we conducted a hydroponic experiment in which water spinach (Ipomoea aquatica Forsk) was subjected to low (0.5 mg/L), medium (5 mg/L), and high (10 mg/L) concentrations of fluorescent PS-NPs for 10 days to examine their accumulation and transportation in water spinach and associated impacts on growth, photosynthesis, antioxidant defense systems. Laser confocal scanning microscopy (LCSM) observations at 10 mg/L PS-NPs exposure indicated that PS-NPs only adhered to the root surface of water spinach and were not transported upward, indicating that short-term exposure to high concentrations of PS-NPs (10 mg/L) did not cause the internalization of PS-NPs in the water spinach. However, this high concentration of PS-NPs (10 mg/L) discernibly inhibited the growth parameters (fresh weight, root length and shoot length), albeit failed to induce any significant impact on chlorophyll a and chlorophyll b concentrations. Meanwhile, high concentration of PS-NPs (10 mg/L) significantly decreased the SOD and CAT activities in leaves (p < 0.05). At the molecular level, low and medium concentrations of PS-NPs (0.5, 5 mg/L) significantly promoted the expression of photosynthesis (PsbA and rbcL) and antioxidant-related (SIP) genes in leaves (p < 0.05), and high concentration of PS-NPs (10 mg/L) significantly increased the transcription levels of antioxidant-related (APx) genes (p < 0.01). Our results imply that PS-NPs accumulate in the roots of water spinach, compromising the upward transport of water and nutrients and undermining the antioxidant defense system of the leaves at the physiological and molecular levels. These results provide a fresh perspective to examine the implications of PS-NPs on edible aquatic plants, and future efforts should be focused intensively on the impacts of PS-NPs on agricultural sustainability and food security.

Maize transcription factor ZmNAC2 enhances osmotic stress tolerance in transgenic Arabidopsis

Osmotic stress seriously limits crop yield and quality. Among plant-specific transcription factors families, the NAC family of transcription factors is extensively involved in various growth, development and stress responses. Here we identified a maize NAC family transcription factor ZmNAC2 with inducible gene expression in response to osmotic stress. The subcellular localization showed that it was localized in the nucleus and overexpression of ZmNAC2 in Arabidopsis significantly promoted seed germination and elevated cotyledon greening under osmotic stress. ZmNAC2 also enhanced stomatal closure and decreased water loss in transgenic Arabidopsis. Overexpression of ZmNAC2 activated ROS scavenging and the transgenic lines accumulated less MDA and developed more lateral roots with drought or mannitol treatment. Further RNA-seq and qRT-PCR analysis showed that ZmNAC2 up-regulated a number of genes related to osmotic stress resistance, as well as plant hormone signaling genes. All together, ZmNAC2 enhances osmotic stress tolerance by regulating multiple physiological processes and molecular mechanisms, and exhibits potential as the target gene in crop breeding to increase osmotic stress resistance.

CRISPR/Cas9-Engineered Large Fragment Deletion Mutations in Arabidopsis CEP Peptide-Encoding Genes Reveal Their Role in Primary and Lateral Root Formation

C-TERMINALLY ENCODED PEPTIDEs (CEPs) are post-translationally modified peptides that play essential roles in root and shoot development, nitrogen absorption, nodule formation and stress resilience. However, it has proven challenging to determine biological activities of CEPs because of difficulties in obtaining loss-of-function mutants for these small genes. To overcome this challenge, we thus assembled a collection of easily detectable large fragment deletion mutants of Arabidopsis CEP genes through the clustered regularly interspaced short palindromic repeat/CRISPR-associated protein 9-engineered genome editing. This collection was then evaluated for the usability by functionally analyzing the Arabidopsis growth and development with a focus on the root. Most cep mutants displayed developmental defects in primary and lateral roots showing an increased primary root length and an enhanced lateral root number, demonstrating that the genetic resource provides a useful tool for further investigations into the roles of CEPs.

Expansion Microscopy of Plant Cells (PlantExM)

Expansion microscopy (ExM) achieves super-resolution imaging without the need for sophisticated super-resolution microscopy hardware through a combination of physical and optical magnification. Samples are fixed, stained, and embedded in a swellable gel. Following cross-linking of fluorophores to the gel matrix, the components of the sample are digested away and the gel expanded in water. Labeled objects which are too close to be resolved by diffraction-limited microscopy are moved far enough apart that these can now be resolved as individual objects on a standard confocal. Originally developed for animal cells and tissues, ExM for plants requires the additional consideration of cell wall digestion. Super-resolution can be limited in plants due to the size of cells, light scattering of tissues, and variations in refractive index. By removing the components which cause these limitations, ExM opens up the possibility of super-resolution at depth within plant tissues for the first time. Here we describe our method for PlantExM which is optimized for cytoskeleton resolution, which, when also coupled with compatible optical super-resolution technologies, can produce images of the plant cytoskeleton in unprecedented detail.

Characteristics of nitrogen distribution and its response to microecosystem changes in green infrastructure with different woody plants

With the acceleration of urbanization, N pollution in rainfall runoff has become the primary cause of eutrophication. In order to control N pollution in rainfall runoff, green infrastructure (GI) has been widely implemented. However, little is known about the process through which plants, especially woody plants, affect N distribution and the microecosystem in GI. Limited information suggests that woody plants mainly affect N distribution and alter the microecosystem through the influence of their roots. Therefore, laboratory tests were conducted to investigate the roles of the taproot plant Sophora japonica and the fibrous root plant Malus baccata and the resultant changes at the microecosystem level regarding N removal in a column-scale GI. After one year of growth, analysis of the morphological traits of the roots revealed that the average root length and diameter of S. japonica were approximately 2.3 and 1.8 times greater than those of M. baccata, respectively. An investigation of microbial diversity revealed that in comparison to the control GI system without plants, the GI systems with S. japonica and M. baccata hosted 45.68% and 59.88% more Actinobacteria, respectively. Further, the soil urease (S-UE) activities in the GI systems with S. japonica and M. baccata were 13.6% and 98.8% higher than that in the control, respectively, and the soil acid protease (S-ALPT) activities were 20.5% and 25.4% higher than that in the control, respectively. Compared to the control and the S. japonica GI system, the NH₃-N content in the soil of the M. baccata GI was 94.4% and 15.2% lower, respectively, and the NO₃-N content was 57.3% and 12.7% lower, respectively. The M. baccata GI system had the lowest NH₃-N and NO₃-N contents because it was most abundant in Actinobacteria and Arthrobacter and had the highest S-UE and S-ALPT activities. The results may be useful for improving N removal in GI containing different woody plants, and by extension for improving control of N pollution from rainfall runoff.

Organ-specific expression of genes associated with the UDP-glucose metabolism in sugarcane (Saccharum spp. hybrids)

BACKGROUND

The importance of uridine 5'-diphosphate glucose (UDP-G) synthesis and degradation on carbon (C) partitioning has been indicated in several studies of plant systems, whereby the kinetic properties and abundance of involved enzymes had a significant effect upon the volume of C moving into the hemicellulose, cellulose and sucrose pools. In this study, the expression of 136 genes belonging to 32 gene families related to UDP-G metabolism was studied in 3 major sugarcane organs (including leaf, internode and root) at 6 different developmental stages in 2 commercial genotypes.

RESULTS

Analysis of the genes associated with UDP-G metabolism in leaves indicated low expression of sucrose synthase, but relatively high expression of invertase genes, specifically cell-wall invertase 4 and neutral acid invertase 1-1 and 3 genes. Further, organs that are primarily responsible for sucrose synthesis or bioaccumulation, i.e., in source organs (mature leaves) and storage sink organs (mature internodes), had very low expression of sucrose, cellulose and hemicellulose synthesis genes, specifically sucrose synthase 1 and 2, UDP-G dehydrogenase 5 and several cellulose synthase subunit genes. Gene expression was mostly very low in both leaf and mature internode samples; however, leaves did have a comparatively heightened invertase and sucrose phosphate synthase expression. Major differences were observed in the transcription of several genes between immature sink organs (roots and immature internodes). Gene transcription favoured utilisation of UDP-G toward insoluble and respiratory pools in roots. Whereas, there was comparatively higher expression of sucrose synthetic genes, sucrose phosphate synthase 1 and 4, and comparatively lower expression of many genes associated with C flow to insoluble and respiratory pools including myo-Inositol oxygenase, UDP-G dehydrogenase 4, vacuolar invertase 1, and several cell-wall invertases in immature internodes.

CONCLUSION

This study represents the first effort to quantify the expression of gene families associated with UDP-G metabolism in sugarcane. Transcriptional analysis displayed the likelihood that C partitioning in sugarcane is closely related to the transcription of genes associated with the UDP-G metabolism. The data presented may provide an accurate genetic reference for future efforts in altering UDP-G metabolism and in turn C partitioning in sugarcane.

An Experimental Rhizobox System for the Integrative Analysis of Root Development and Abiotic Stress Responses Under Water-Deficit Conditions

The study of root growth and plasticity in situ is rendered difficult by the opacity and mechanical barrier of soil substrates. Therefore, for the analysis of developmental processes and abiotic stress and development relationships, it is essential to set up cultivation systems that overcome these hindrances in a non-invasive and non-destructive manner. For this purpose, we have developed a useful and powerful rhizobox culture system, where the roots are separated from the soil substrate by a porous membrane with a mesh of such width that allows the exchange of water and solutes without allowing the roots to penetrate the soil. This system provides direct, easy, and quick access to the roots and allows to follow root growth and development, root system architecture, and root system plasticity at different stages of plant development and under various environmental conditions. Moreover, these rhizoboxes provide clean and intact roots that can be easily harvested to perform further physiological, biochemical, and molecular analyses at different stages of development and in response to various environmental constraints. This rhizobox method was validated by assessing root response plasticity of drought-stressed Arabidopsis and pea plants grown in soil displaying water content alterations. This rhizobox system is suitable for many types of abiotic stress-development studies, including the comparison of different stress intensities or of various mutants and genotypes.

Measuring of water transport selectively along the plant root plasmodesmata using gradient nuclear magnetic resonance with paramagnetic doping

In this study, we measured translational water diffusion selectively along symplast pathway through plasmodesmata in maize roots, and the effective plasmodesmata permeability coefficient (P) was determined using a nuclear magnetic resonance (NMR) spin echo method. Measuring of water transport selectively along the plant root plasmodesmata was achieved with paramagnetic complexes (PCs) of high relaxation efficiency. PCs penetrate into the intercellular space of root tissue, but not into cells, and accelerate the magnetic relaxation processes of intercellular water, thereby excluding the contribution of intercellular water to the registered NMR diffusion echo attenuation. In result, NMR control of translational diffusion can be applied to the signal of the water moving along the symplast pathway through plasmodesmata, where the PCs do not penetrate. Diethylenetriaminepentaacetic acid (GdDTPA), Mn²⁺-trans-1,2-diaminocyclohexane-N,N,N',N'-tetraacetic acid (MnDCTA), and GdCl₃ were used as PCs. An increase in the PCs concentration led to a side effect in the form of a varying decrease in diffusive water transport in the roots. The P was determined by extrapolating the concentration dependence to zero concentration of PCs. Among the PCs studied, MnDCTA had the least side effects on the water transport when the concentration dependence was linear. When MnDCTA was used, the P accounted for 30-35% of the total cell water permeability (by transmembrane and symplast pathways). The rate of water flow along the plasmodesmata in the approximation of the piston mode of flow along the linear cell chain was estimated to range from 4.5 × 10^-7 to 8.8 × 10^-7 m/s.

Assay of Fe(III) Chelate Reductase Activity in Arabidopsis thaliana Root

A sensitive FerroZine assay is used to measure the membrane-bound ferric-chelate reductase activity in the Arabidopsis thaliana roots. In Arabidopsis, FRO2 (FERRIC CHELATE REDUCTASE 2) encodes the Fe(III) chelate reductase and its expression is induced by iron deficiency. As FRO2 reduces Fe(III) to soluble Fe(II), the resulting Fe(II) forms a purple-colored complex with the dye FerroZine. The concentration of the Fe(II)-FerroZine is directly proportional to the absorbance at 562 nm.

The assessment of the soil-plant-animal transport of the risk elements at the locations affected by brown coal mining

The North Bohemian Brown Coal Basin (Czech Republic) is suggested as a source of significant pollution in the surrounding environment with various pollutants, including risk elements. A total of 53 sampling points were selected within the North Bohemian region. The selected sampling points represented either the basin areas (affected by the coal mining and related activities) or the mountain areas (an area unaffected by the coal mining but characterized by the geogenic sources of the risk elements). At each of the sampling points, soils and respective dominant indigenous plant samples were collected. A suite of ecological indices, namely, individual pollution index (Ii), Nemerow index (PN), bioaccumulation factor (BAF), translocation factor (TF), and hazard quotient (HQ), were applied to estimate the environmental risk of As, Be, Cd, and Zn levels in soils, potential soil-plant transfer, and soil-plant-animal transport of these stated elements. The results from Ii showed that the maximum values of As, Be, Cd, and Zn in the investigated soils exceeded the preventive values, where the Ii value was up to 58 for As in the mountain areas, indicating severe pollution. At the same time, mild pollution was recorded in the case of Cd. For Be in the researched soils, its Ii assessment result was a wide range, varying between a clean environment and severe pollution. Whereas As and Be uptake by plants was limited and these elements were retained in the plant's roots, relatively high mobility and soil to plant shoots transport ability of Cd were recorded and documented by the TF values. The HQs calculated for selected herbivorous mammals in the area showed that the potential health risk of As and Be was limited to only plant roots in the hotspots with extreme As and Be contents. In comparison, substantial health risk of Cd was observed in the aboveground biomass of plants. Therefore, the potential remediation of the coal mining areas should be focused on (i) identification of the As and Be hotspots and (ii) to reduce the mobility and plant availability of Cd in the whole investigated area.

Root system response to salt stress in grapevines (Vitis spp.): A link between root structure and salt exclusion

Accessing freshwater resources for agriculture becomes more complex due to increasing demands and declining water quality. Alternative water sources, such as saline water, require ad hoc solutions. Therefore, understanding roots' response to saline water is crucial for future agriculture. We examined the response of three grapevine rootstocks (Paulsen 1103, Richter 110 and SO4) to salt stress. The rootstocks were subjected to two salinity treatments: 10 mM and 30 mM NaCl (EC = 2 and 4 ds/m, respectively). Root and shoot samples were taken at the end of the experiment for morphologic and ionomic analyses. The specific root area (SRA) increased in response to salinity for all three rootstocks due to root tissue density and average root diameter reductions. Salinity also led to increased root Na⁺ and Cl^- contents and reduced root K⁺/Na⁺ ratio, parallel to increased leaf Cl^- but not Na⁺ contents. SO4 showed improved chloride and sodium exclusion, concomitant with its highest SRA, resulting from the increase in its thin roots' contribution to the total root system surface area. We suggest that enhanced SRA combined with decreased root tissue density and diameter may improve grapevines' salt exclusion by less salt uptake from the soil.

Native multispecies and fast-growing forest root biomass increase C and N stocks in a reclaimed bauxite mining area

This study is aimed at evaluating C and N stocks in fractions of soil organic matter (SOM) in an area of bauxite mining under recovery with tree species. We have analyzed the long-term recovery of C and N stocks of organic matter fractions from five types of forest cover (Eucalyptus, Anadenanthera peregrina, mixed plantation of 16 native species, a mined area without vegetation cover as a control site, and a natural forest cover as a reference site). The total organic C (TOC) and N (TN) stocks and also organic matter fractions, particulate organic matter (POM), mineral-associated organic matter (MAOM), microbial biomass (MB), and labile C (LC), were determined, as well as the C/N ratio and the carbon management index (CMI). Although the stocks of TOC and LC, CMI, and MB did not differ between the types of forest cover in the 0-60 cm layer, they were lower than the values in the native forest. Forest cover increases the stocks of TOC, LC, MB, and CMI in the area of bauxite mining compared to the control site. In addition, we found that the TOC C and TN stocks and also SOM fractions (LC, C-MAOM, C-POM, N-MAOM, and N-POM) are positively correlated (r ≥ 0.71 for all cases) with volume of roots larger than 2 mm. Therefore, Eucalyptus, A. peregrina, and a mixed of 16 native trees contribute for restoring stocks of soil C and N following bauxite mining in the Brazilian Atlantic Forest.

Inter-Kingdom Networks of Canola Microbiome Reveal Bradyrhizobium as Keystone Species and Underline the Importance of Bulk Soil in Microbial Studies to Enhance Canola Production

The subterranean microbiota of plants is of great importance for plant growth and health, as root-associated microbes can perform crucial ecological functions. As the microbial environment of roots is extremely diverse, identifying keystone microorganisms in plant roots, rhizosphere, and bulk soil is a necessary step towards understanding the network of influence within the microbial community associated with roots and enhancing its beneficial elements. To target these hot spots of microbial interaction, we used inter-kingdom network analysis on the canola growth phase of a long-term cropping system diversification experiment conducted at four locations in the Canadian Prairies. Our aims were to verify whether bacterial and fungal communities of canola roots, rhizosphere, and bulk soil are related and influenced by diversification of the crop rotation system; to determine whether there are common or specific core fungi and bacteria in the roots, rhizosphere, and bulk soil under canola grown in different environments and with different levels of cropping system diversification; and to identify hub taxa at the inter-kingdom level that could play an important ecological role in the microbiota of canola. Our results showed that fungi were influenced by crop diversification, which was not the case on bacteria. We found no core microbiota in canola roots but identified three core fungi in the rhizosphere, one core mycobiota in the bulk soil, and one core bacterium shared by the rhizosphere and bulk soil. We identified two bacterial and one fungal hub taxa in the inter-kingdom networks of the canola rhizosphere, and one bacterial and two fungal hub taxa in the bulk soil. Among these inter-kingdom hub taxa, Bradyrhizobium sp. and Mortierella sp. are particularly influential on the microbial community and the plant. To our knowledge, this is the first inter-kingdom network analysis utilized to identify hot spots of interaction in canola microbial communities.

Crop management shapes the diversity and activity of DNA and RNA viruses in the rhizosphere

BACKGROUND

The rhizosphere is a hotspot for microbial activity and contributes to ecosystem services including plant health and biogeochemical cycling. The activity of microbial viruses, and their influence on plant-microbe interactions in the rhizosphere, remains undetermined. Given the impact of viruses on the ecology and evolution of their host communities, determining how soil viruses influence microbiome dynamics is crucial to build a holistic understanding of rhizosphere functions.

RESULTS

Here, we aimed to investigate the influence of crop management on the composition and activity of bulk soil, rhizosphere soil, and root viral communities. We combined viromics, metagenomics, and metatranscriptomics on soil samples collected from a 3-year crop rotation field trial of oilseed rape (Brassica napus L.). By recovering 1059 dsDNA viral populations and 16,541 ssRNA bacteriophage populations, we expanded the number of underexplored Leviviricetes genomes by > 5 times. Through detection of viral activity in metatranscriptomes, we uncovered evidence of "Kill-the-Winner" dynamics, implicating soil bacteriophages in driving bacterial community succession. Moreover, we found the activity of viruses increased with proximity to crop roots, and identified that soil viruses may influence plant-microbe interactions through the reprogramming of bacterial host metabolism. We have provided the first evidence of crop rotation-driven impacts on soil microbial communities extending to viruses. To this aim, we present the novel principal of "viral priming," which describes how the consecutive growth of the same crop species primes viral activity in the rhizosphere through local adaptation.

CONCLUSIONS

Overall, we reveal unprecedented spatial and temporal diversity in viral community composition and activity across root, rhizosphere soil, and bulk soil compartments. Our work demonstrates that the roles of soil viruses need greater consideration to exploit the rhizosphere microbiome for food security, food safety, and environmental sustainability. Video Abstract.

Structural characterization and immunoregulatory activity of a neutral polysaccharide from the roots of Apocynum venetum L

The structural characteristics and immunoregulatory activities of neutral heteropolysaccharide (AVRP-N) separated from the roots of Apocynum venetum L. were extensively investigated. The results showed that the weight average molecular mass (Mw) of AVRP-N was 6.430 × 10³ Da. Moreover, the backbone is composed of natural acetylated (1 → 4)-β-D-Man and (1 → 5)-α-L-Ara domains. The mannan is composed of →4)-β-D-Manp-(1→, →4)-β-D-Glcp-(1→, and the terminal group α-D-Galp-(1→ attached to →4,6)-β-D-Manp-(1→ at O-6. Araban is composed of →5)-α-L-Araf-(1→; the terminal group α-L-Araf-(1→attached to→2,3,5)-α-L-Araf-(1→ at O-2, O-3 and →3,5)-α-L-Araf-(1→ at O-3. In addition, the senior structure shows that AVRP-N has a triple-helix conformation. Furthermore, AVRP-N exhibited immunomodulatory effects, which could significantly regulate the proliferation of mouse splenic lymphocytes by enhancing the secretion of the cytokines (IFN-γ, IL-2, IL-4, and IL-10). Our results provide new structural and immunoregulatory information for natural polysaccharides derived from Apocynum venetum L.

Can As concentration in crop be controlled by Se fertilization? A meta-analysis and outline of As sequestration mechanisms

Arsenic (As) is a pollutant with a strong toxic effect on animals, plants and human beings. Exogenous selenium (Se) has been suggested to reduce the accumulation of As in crops, but contradictory results were found in the published literature. In order to clarify the possible processes, we collected the literature that reports on the effects of Se application on As uptake and accumulation in crops, analyzed the data by meta-analysis, and tested the effects of different factors on As accumulation by meta-regression model and subgroup analysis. The results highlighted a significant dose-dependent reduction of As content in crops after Se addition. Exogenous Se can significantly reduce As concentrations in grains by 18.76%. The reduction was dose-dependent for rice grains under aerobic soil conditions but not for rice grains under anoxic soil conditions. Se-enriched soils (greater than 0.5 mg kg^-1) significantly reduced As concentrations in grains. Selenium significantly decreased the transfer factor of As from root to shoot. Moreover, selenite had a stronger inhibiting effect on the transport of As from root to shoot than selenate. The inhibition of selenium fertilization on As concentrations seems to take place in root and soil, while physiological processes in rice may be involved in restricting uptake and transport from root to shoot. These findings provide new ideas for effectively alleviating the transfer of As to the human body through the food chain.

Genomic and physiological evaluation of two root associated Pseudomonas from Coffea arabica

Many Pseudomonas species promote plant growth and colonize a wide range of environments. The annotation of a Coffea arabica ESTs database revealed a considerable number of Pseudomonas sequences. To evaluate the genomic and physiology of Pseudomonas that inhabit coffee plants, fluorescent Pseudomonas from C. arabica root environment were isolated. Two of them had their genomes sequenced; one from rhizospheric soil, named as MNR3A, and one from internal part of the root, named as EMN2. In parallel, we performed biochemical and physiological experiments to confirm genomic analyses results. Interestingly, EMN2 has achromobactin and aerobactin siderophore receptors, but does not have the genes responsible for the production of these siderophores, suggesting an interesting bacterial competition strategy. The two bacterial isolates were able to degrade and catabolize plant phenolic compounds for their own benefit. Surprisingly, MNR3A and EMN2 do not contain caffeine methylases that are responsible for the catabolism of caffeine. In fact, bench experiments confirm that the bacteria did not metabolize caffeine, but were resistant and chemically attracted to it. Furthermore, both bacteria, most especially MNR3A, were able to increase growth of lettuce plants. Our results indicate MNR3A as a potential plant growth promoting bacteria.

Could ammonium nutrition increase plant C-sink strength under elevated CO2 conditions?

Atmospheric carbon dioxide (CO₂) is increasing, and this affects plant photosynthesis and biomass production. Under elevated CO₂ conditions (eCO₂), plants need to cope with an unbalanced carbon-to-nitrogen ratio (C/N) due to a limited C sink strength and/or the reported constrains in leaf N. Here, we present a physiological and metabolic analysis of ammonium (NH₄⁺)-tolerant pea plants (Pisum sativum L., cv. snap pea) grown hydroponically with moderate or high NH₄⁺ concentrations (2.5 or 10 mM), and under two atmospheric CO₂ concentrations (400 and 800 ppm). We found that the photosynthetic efficiency of the NH₄⁺ tolerant pea plants remain intact under eCO₂ thanks to the capacity of the plants to maintain the foliar N status (N content and total soluble proteins), and the higher C-skeleton requirements for NH₄⁺ assimilation. The capacity of pea plants grown at 800 ppm to promote the C allocation into mobile pools of sugar (mainly sucrose and glucose) instead of starch contributed to balancing plant C/N. Our results also support previous observations: plants exposed to eCO₂ and NH₄⁺ nutrition can increase of stomatal conductance. Considering the C and N source-sink balance of our plants, we call for exploring a novel trait, combining NH₄⁺ tolerant plants with a proper NH₄⁺ nutrition management, as a way for a better exploitation of eCO₂ in C3 crops.

Molecular mechanisms for pH-mediated amelioration of aluminum-toxicity revealed by conjoint analysis of transcriptome and metabolome in Citrus sinensis roots

Little is known about the effects of pH-aluminum (Al) interactions on gene expression and/or metabolite profiles in plants. Eleven-week-old seedlings of Citrus sinensis were fertilized with nutrient solution at an Al level of 0 or 1 mM and a pH of 3.0 or 4.0 for 18 weeks. Increased pH mitigated Al-toxicity-induced accumulation of callose, an Al-sensitive marker. In this study, we identified more differentially expressed genes and differentially abundant metabolites in pH 4.0 + 1 mM Al-treated roots (P4AR) vs pH 4.0 + 0 mM Al-treated roots (P4R) than in pH 3.0 + 1 mM Al-treated roots (P3AR) vs pH 3.0 + 0 mM Al-treated roots (P3R), suggesting that increased pH enhanced root metabolic adaptations to Al-toxicity. Further analysis indicated that increased pH-mediated mitigation of root Al-toxicity might be related to several factors, including: enhanced capacity to maintain the homeostasis of phosphate and energy and the balance between generation and scavenging of reactive oxygen species and aldehydes; and elevated accumulation of secondary metabolites such as polyphenol, proanthocyanidins and phenolamides and adaptations of cell wall and plasma membrane to Al-toxicity.

Increasing media pH contribute to the absorption of boron via roots to promote the growth of citrus

Low pH is an important limiting factor for plant development in the south of China due to problems of acid red soil and boron (B) deficiency. Whereas, there is very limited information on the relationship between media pH and B distribution in plant, the physiological process changed by the interaction of pH and B in citrus growth also unclear. This experiment was conducted on trifoliate rootstock by employing two different concentrations of B (0 or 10 μM B) under three pH levels: pH 4, pH 5, and pH 6. Our results illustrate that low pH inhibite plant growth and cause oxidative stress in the roots, resulting in cell membrane injury. The increase of pH and B addition reduce the accumulation of ROS (O₂^.- and H₂O₂) by regulating the activity of Class Ⅲ peroxidases (CIII Prxs). Moreover, increased pH improves the internal circulation of B in plants and decrease the content of lignin and cellulose in cell wall (CW). In summary, our investigation demonstrated that the increase of pH in nutrient solution can accelerate the re-distribution of B by roots to promote citrus growth. The accumulation of B in roots can protect plants from the damage of ROS by regulating the activity of CIII Prxs as well as decrease the content of lignin and cellulose are to promotes roots elongation.

The lexical status of verbs among typical and dyslexic native Arabic readers: a developmental model

The goal of this study was to investigate the development of mental lexicon organization among typical and dyslexic native Arabic readers. The participants included 271 students, divided into dyslexic readers, age-matched typical readers, and typical readers 2 years younger. The lexical status of root and pattern morphemes was examined using two priming paradigms: masked priming and the cross-modal immediate repetition task. We conducted two visual lexical decision tasks (Experiment 1 for verb pattern, Experiment 3 for verb roots), and two auditory decision tasks (Experiment 2 for verb pattern, Experiment 4 for verb roots). In the visual tasks, the participants were asked to decide whether a visual stimulus was a real word or not by pressing the laptop keyboard's "yes" or "no" button. The auditory experiments were conducted similarly to the visual experiments, except that the stimuli were auditory, to clarify the locus of the morphological deficit observed in the visual test of the dyslexic students, should there be such failures. Analysis of Experiment 1 showed that verb patterns are not lexical entities with a role in organizing the mental lexicon among typical and dyslexic readers of different ages. However, Experiment 3 indicated that roots do indeed constitute lexical entities with a role in organizing the mental lexicon among normal and dyslexic readers of different ages. In Experiment 2, the auditory-morpho priming effect in the word pattern test was stronger among dyslexic and young readers than among more skilled readers, and contributed to speeding up lexical decisions more than its quality, among all research groups. In Experiment 4, the auditory-morpho priming effect in the root test was stronger than the visual effect among all participants, and contributed to hastening lexical decisions and improving the quality of the answers (success percentage). The results showed that roots contribute to the reading process. However, their contribution is different among dyslexic readers. Its construction is slower and different from that of typical readers, whereas word patterns have no lexical representation among the three reader groups that are likely to facilitate lexical decisions. The results are discussed with reference to the latest research literature on morpheme type (root or pattern).

Length and colonization rates of roots associated with arbuscular or ectomycorrhizal fungi decline differentially with depth in two northern hardwood forests

Ectomycorrhizal (EM) and arbuscular mycorrhizal (AM) fungi are often studied independently, and thus little is known regarding differences in vertical distribution of these two groups in forests where they co-occur. We sampled roots at two soil depths in two northern hardwood stands in Bartlett, New Hampshire, co-dominated by tree species that associate with AM or EM fungi. Root length of both groups declined with depth. More importantly, root length of EM plant species exceeded that of AM plants at 0-10-cm depth, while AM exceeded EM root length at 30-50-cm depth. Colonization rates were similar between mineral and organic portions of the shallow (0-10 cm) samples for EM and AM fungi and declined dramatically with depth (30-50 cm). The ratio of EM to AM fungal colonization declined with depth, but not as much as the decline in root length with depth, resulting in greater dominance by EM fungi near the surface and by AM fungi at depth. The depth distribution of EM and AM roots may have implications for soil carbon accumulation as well as for the success of the associated tree species.

Genome-wide identification and expression analysis of the GRAS gene family in response to drought stress in chickpea (Cicer arietinum L.)

The GRAS (gibberellic acid insensitive, repressor of GAI and scarecrow) transcription factors (TFs) regulate diverse biological processes involved in plant growth and development. These TFs are also known to regulate gene expression in response to various abiotic stress factors like cold, drought, etc. In chickpea one of the most devastating abiotic stress factors is terminal drought. The GRAS TF family has not been characterized in chickpea (Cicer arietinum L.) until now. In this study, we report 46 GRAS TF genes (CaGRAS genes) in the chickpea genome. The CaGRAS proteins were categorized into nine subfamilies based on their phylogenetic relationship with known GRAS members of Arabidopsis and soybean. The PAT subfamily was the largest consisting of ten CaGRAS members whereas the LAS subfamily was the smallest with only one member. Gene duplication analysis revealed that segmental duplication was the primary reason for the expansion of this gene family within the chickpea genome. The gene expression levels of CaGRAS genes were analysed using two different chickpea varieties contrasting for drought tolerance trait, i.e., ICC 4958 (drought tolerant) and ICC 1882 (drought sensitive). On exposure to drought stress, the two chickpea genotypes, exhibited differential drought response, which was quantified and estimated in terms of differences in leaf relative water content (RWC). The well-watered or control plants of the drought tolerant variety were able to maintain a higher leaf RWC by the end of the drought stress period, whereas the control plants of the drought sensitive variety continued to show a decline in leaf RWC. The two genotypes also differed in their root morphologies, under well-watered and drought stress conditions. The gene expression analysis revealed a potential role of PAT, SCR, SCL3 and SHR GRAS members in the regulation of differential response to drought, in the root tissues, for both the genotypes. CaGRAS 12 (SCR) was identified as a drought-responsive GRAS TF gene, which could serve as a potential candidate gene for utilization in developing chickpea varieties with improved drought tolerance. This study demonstrates the drought-responsive expression of CaGRAS genes in chickpea and also describes the morpho-physiological response of chickpea plants to drought stress conditions.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-03104-z.

Unravelling the treasure trove of drought-responsive genes in wild-type peanut through transcriptomics and physiological analyses of root

Peanut is one of the most valuable legumes, grown mainly in arid and semi-arid regions, where its production may be hindered by the lack of water. Therefore, breeding drought tolerant varieties is of great importance for peanut breeding programs around the world. Unlike cultivated peanuts, wild peanuts have greater genetic diversity and are an important source of alleles conferring tolerance/resistance to abiotic and biotic stresses. To decipher the transcriptome changes under drought stress, transcriptomics of roots of highly tolerant Arachis duranensis (ADU) and moderately susceptible A. stenosperma (AST) genotypes were performed. Transcriptome analysis revealed an aggregate of 1465 differentially expressed genes (DEGs), and among the identified DEGs, there were 366 single nucleotide polymorphisms (SNPs). Gene ontology and Mapman analyses revealed that the ADU genotype had a higher number of transcripts related to DNA methylation or demethylation, phytohormone signal transduction and flavonoid production, transcription factors, and responses to ethylene. The transcriptome analysis was endorsed by qRT-PCR, which showed a strong correlation value (R² = 0.96). Physio-biochemical analysis showed that the drought-tolerant plants produced more osmolytes, ROS phagocytes, and sugars, but less MDA, thus attenuating the effects of drought stress. In addition, three SNPs of the gene encoding transcription factor NFAY (Aradu.YE2F8), expansin alpha (Aradu.78HGD), and cytokinin dehydrogenase 1-like (Aradu.U999X) exhibited polymorphism in selected different genotypes. Such SNPs could be useful for the selection of drought-tolerant genotypes.

Putting Plant Roots at Light: Temporal Imaging of Plant Roots and Soil Water with a Light Transmission Technique for Linking Water and Root Observations to Soil-Plant Models

Estimating how the "hidden half" of plants, that is the roots, take up water or the influences of root system architecture or root physiological properties (such as root hydraulic conductance) on efficiency of water uptake is of prime importance for improving crops against water deficits. To unravel soil-root interactions for water, we describe a system that enables a dynamic imaging of the soil water content and of the root system, from the single root to the whole root system scales.This system uses plants grown in rhizotrons filled with sandy soil and is based on the variable attenuation of the intensity of light transmitted through the rhizotron with soil water content (the rhizotron is nearly translucent when saturated and becomes darker as soil water content decreases). Images of the transmitted light during plant water uptake (or exudation) phases are recorded with a camera, showing a qualitative pattern of water content variations. The gray levels of the image pixels are then quantitatively related to water content with a calibration.This system is affordable and can be easily implemented without specific equipment. It is scalable and quick to allow the phenotyping of a range of plant genotypes relative to their water uptake pattern. This pattern can be then related with root system properties (soil colonization, root architecture ) at different plant stages. In combination with modeling , imaging results help in obtaining physiological parameters such as root hydraulic conductivity, distributed root water uptake rates or root xylem water potential. Combination of modeling and experiment further helps in testing biological and physiological assumptions and in predicting the uptake behavior of plants in the field.