Mobilization of Iron by Plant-Borne Coumarins

Engineering plant-microbe communication for plant nutrient use efficiency

Nutrient availability and efficient use are critical for crop productivity. Current agricultural practices rely on excessive chemical fertilizers, contributing to greenhouse gas emissions and environmental pollution. Rhizosphere microbes facilitate plant nutrient acquisition and contribute to nutrient use efficiency. Thus, engineering plant-microbe communication within the rhizosphere emerges as a promising and sustainable strategy to enhance agricultural productivity. Recent advances in plant engineering have enabled the development of plants capable of selectively enriching beneficial microbes through root exudates. At the same time, synthetic biology techniques have produced microbes capable of improving nutrient availability and uptake by plants. By engineering plant-microbe communication, researchers aim to harness beneficial soil microbes, thereby offering a targeted and efficient approach to optimizing plant nutrient use efficiency.

Exploring the Role of Debaryomyces hansenii as Biofertilizer in Iron-Deficient Environments to Enhance Plant Nutrition and Crop Production Sustainability

The European "Green Deal" policies are shifting toward more sustainable and environmentally conscious agricultural practices, reducing the use of chemical fertilizer and pesticides. This implies exploring alternative strategies. One promising alternative to improve plant nutrition and reinforce plant defenses is the use of beneficial microorganisms in the rhizosphere, such as "Plant-growth-promoting rhizobacteria and fungi". Despite the great abundance of iron (Fe) in the Earth's crust, its poor solubility in calcareous soil makes Fe deficiency a major agricultural issue worldwide. Among plant promoting microorganisms, the yeast Debaryomyces hansenii has been very recently incorporated, for its ability to induce morphological and physiological key responses to Fe deficiency in plants, under hydroponic culture conditions. The present work takes it a step further and explores the potential of D. hansenii to improve plant nutrition and stimulate growth in cucumber plants grown in calcareous soil, where ferric chlorosis is common. Additionally, the study examines D. hansenii's ability to induce systemic resistance (ISR) through a comparative relative expression study by qRT-PCR of ethylene (ET) biosynthesis (ACO1), or ET signaling (EIN2 and EIN3), and salicylic acid (SA) biosynthesis (PAL)-related genes. The results mark a significant milestone since D. hansenii not only enhances nutrient uptake and stimulates plant growth and flower development but could also amplify induced systemic resistance (ISR). Although there is still much work ahead, these findings make D. hansenii a promising candidate to be used for sustainable and environmentally friendly integrated crop management.

The activation of iron deficiency responses of grapevine rootstocks is dependent to the availability of the nitrogen forms

BACKGROUND

In viticulture, iron (Fe) chlorosis is a common abiotic stress that impairs plant development and leads to yield and quality losses. Under low availability of the metal, the applied N form (nitrate and ammonium) can play a role in promoting or mitigating Fe deficiency stresses. However, the processes involved are not clear in grapevine. Therefore, the aim of this study was to investigate the response of two grapevine rootstocks to the interaction between N forms and Fe uptake. This process was evaluated in a hydroponic experiment using two ungrafted grapevine rootstocks Fercal (Vitis berlandieri x V. vinifera) tolerant to deficiency induced Fe chlorosis and Couderc 3309 (V. riparia x V. rupestris) susceptible to deficiency induced Fe chlorosis.

RESULTS

The results could differentiate Fe deficiency effects, N-forms effects, and rootstock effects. Interveinal chlorosis of young leaves appeared earlier on 3309 C from the second week of treatment with NO3-/NH4+ (1:0)/-Fe, while Fercal leaves showed less severe symptoms after four weeks of treatment, corresponding to decreased chlorophyll concentrations lowered by 75% in 3309 C and 57% in Fercal. Ferric chelate reductase (FCR) activity was by trend enhanced under Fe deficiency in Fercal with both N combinations, whereas 3309 C showed an increase in FCR activity under Fe deficiency only with NO3-/NH4+ (1:1) treatment. With the transcriptome analysis, Gene Ontology (GO) revealed multiple biological processes and molecular functions that were significantly regulated in grapevine rootstocks under Fe-deficient conditions, with more genes regulated in Fercal responses, especially when both forms of N were supplied. Furthermore, the expression of genes involved in the auxin and abscisic acid metabolic pathways was markedly increased by the equal supply of both forms of N under Fe deficiency conditions. In addition, changes in the expression of genes related to Fe uptake, regulation, and transport reflected the different responses of the two grapevine rootstocks to different N forms.

CONCLUSIONS

Results show a clear contribution of N forms to the response of the two grapevine rootstocks under Fe deficiency, highlighting the importance of providing both N forms (nitrate and ammonium) in an appropriate ratio in order to ease the rootstock responses to Fe deficiency.

Nutrient availability and plant phenological stage influence the substrate microbiome in container-grown Impatiens walleriana 'Xtreme Red'

BACKGROUND

The microbiome plays a fundamental role in plant health and performance. Soil serves as a reservoir of microbial diversity where plants attract microorganisms via root exudates. The soil has an important impact on the composition of the rhizosphere microbiome, but greenhouse ornamental plants are commonly grown in soilless substrates. While soil microbiomes have been extensively studied in traditional agriculture to improve plant performance, health, and sustainability, information about the microbiomes of soilless substrates is still limited. Thus, we conducted an experiment to explore the microbiome of a peat-based substrate used in container production of Impatiens walleriana, a popular greenhouse ornamental plant. We investigated the effects of plant phenological stage and fertilization level on the substrate microbiome.

RESULTS

Impatiens plants grown under low fertilization rates were smaller and produced more flowers than plants grown under optimum and high fertilization. The top five bacterial phyla present in the substrate were Proteobacteria, Actinobacteria, Bacteriodota, Verrucomicrobiota, and Planctomycetota. We found a total of 2,535 amplicon sequence variants (ASV) grouped into 299 genera. The substrate core microbiome was represented by only 1.8% (48) of the identified ASV. The microbiome community composition was influenced by plant phenological stage and fertilizer levels. Phenological stage exhibited a stronger influence on microbiome composition than fertilizer levels. Differential abundance analysis using DESeq2 identified more ASVs significantly affected (enriched or depleted) in the high fertilizer levels at flowering. As observed for community composition, the effect of plant phenological stage on microbial community function was stronger than fertilizer level. Phenological stage and fertilizer treatments did not affect alpha-diversity in the substrate.

CONCLUSIONS

In container-grown ornamental plants, the substrate serves as the main microbial reservoir for the plant, and the plant and agricultural inputs (fertilization) modulate the microbial community structure and function of the substrate. The differences observed in substrate microbiome composition across plant phenological stage were explained by pH, total organic carbon (TOC) and fluoride, and across fertilizer levels by pH and phosphate (PO4). Our project provides an initial diversity profile of the bacteria occurring in soilless substrates, an underexplored source of microbial diversity.

Transcriptome analysis of iron over-accumulating Arabidopsis genotypes uncover putative novel regulators of systemic and retrograde signaling

On account of its competence to accept and donate electrons, iron (Fe) is an essential element across all forms of life, including plants. Maintaining Fe homeostasis requires precise orchestration of its uptake, trafficking, and translocation in order to meet the demand for Fe sinks such as plastids. Plants harboring defects in the systemic Fe transporter OPT3 (OLIGOPEPTIDE TRANSPORTER 3) display constitutive Fe deficiency responses and accumulate toxic levels of Fe in their leaves. Similarly, ectopic expression of IRONMAN (IMA) genes, encoding a family of phloem-localized signaling peptides, triggers the uptake and accumulation of Fe by inhibiting the putative Fe sensor BRUTUS. This study aims at elucidating the mechanisms operating between OPT3-mediated systemic Fe transport, activation of IMA genes in the phloem, and activation of Fe uptake in the root epidermis. Transcriptional profiling of opt3-2 mutant and IMA1/IMA3 overexpressing (IMA Ox) lines uncovered a small subset of genes that were consistently differentially expressed across all three genotypes and Fe-deficient control plants, constituting potential novel regulators of cellular Fe homeostasis. In particular, expression of the the F-box protein At1g73120 was robustly induced in all genotypes, suggesting a putative function in the posttranslational regulation of cellular Fe homeostasis. As further constituents of this module, two plastid-encoded loci that putatively produce transfer ribonucleic acid (tRNA)-derived small ribonucleic acids are possibly involved in retrograde control of root Fe uptake.

PDR9 allelic variation and MYB63 modulate nutrient-dependent coumarin homeostasis in Arabidopsis

Plant roots release phytochemicals into the soil environment to influence nutrient availability and uptake. Arabidopsis thaliana roots release phenylpropanoid coumarins in response to iron (Fe) deficiency, likely to enhance Fe uptake and improve plant health. This response requires sufficient phosphorus (P) in the root environment. Nonetheless, the regulatory interplay influencing coumarin production under varying availabilities of Fe and P is not known. Through genome-wide association studies, we have pinpointed the influence of the ABC transporter G family member, PDR9, on coumarin accumulation and trafficking (homeostasis) under combined Fe and P deficiency. We show that genetic variation in the promoter of PDR9 regulates its expression in a manner associated with coumarin production. Furthermore, we find that MYB63 transcription factor controls dedicated coumarin production by regulating both COUMARIN SYNTHASE (COSY) and FERULOYL-CoA 6'-HYDROXYLASE 1 (F6'H1) expression while orchestrating secretion through PDR9 genes under Fe and P combined deficiency. This integrated approach illuminates the intricate connections between nutrient signaling pathways in coumarin response mechanisms.

Root colonization by beneficial rhizobacteria

Rhizosphere microbes play critical roles for plant's growth and health. Among them, the beneficial rhizobacteria have the potential to be developed as the biofertilizer or bioinoculants for sustaining the agricultural development. The efficient rhizosphere colonization of these rhizobacteria is a prerequisite for exerting their plant beneficial functions, but the colonizing process and underlying mechanisms have not been thoroughly reviewed, especially for the nonsymbiotic beneficial rhizobacteria. This review systematically analyzed the root colonizing process of the nonsymbiotic rhizobacteria and compared it with that of the symbiotic and pathogenic bacteria. This review also highlighted the approaches to improve the root colonization efficiency and proposed to study the rhizobacterial colonization from a holistic perspective of the rhizosphere microbiome under more natural conditions.

A CYBDOM protein impacts iron homeostasis and primary root growth under phosphate deficiency in Arabidopsis

Arabidopsis primary root growth response to phosphate (Pi) deficiency is mainly controlled by changes in apoplastic iron (Fe). Upon Pi deficiency, apoplastic Fe deposition in the root apical meristem activates pathways leading to the arrest of meristem maintenance and inhibition of cell elongation. Here, we report that a member of the uncharacterized cytochrome b561 and DOMON domain (CYBDOM) protein family, named CRR, promotes iron reduction in an ascorbate-dependent manner and controls apoplastic iron deposition. Under low Pi, the crr mutant shows an enhanced reduction of primary root growth associated with increased apoplastic Fe in the root meristem and a reduction in meristematic cell division. Conversely, CRR overexpression abolishes apoplastic Fe deposition rendering primary root growth insensitive to low Pi. The crr single mutant and crr hyp1 double mutant, harboring a null allele in another member of the CYDOM family, shows increased tolerance to high-Fe stress upon germination and seedling growth. Conversely, CRR overexpression is associated with increased uptake and translocation of Fe to the shoot and results in plants highly sensitive to Fe excess. Our results identify a ferric reductase implicated in Fe homeostasis and developmental responses to abiotic stress, and reveal a biological role for CYBDOM proteins in plants.

Citrus sinensis manganese tolerance: Insight from manganese-stimulated secretion of root exudates and rhizosphere alkalization

We used manganese (Mn)-tolerant 'Xuegan' (Citrus sinensis) seedlings as materials and examined the characterization of Mn uptake and Mn-activated-release of root exudates under hydroponic conditions. We observed that root and shoot Mn bioaccumulation factor (BCF) reduced with the increase of Mn supply, and that Mn transfer factor (Tf) reduced greatly as Mn supply increased from 0 to 500 μM, beyond which Tf slightly increased with increasing Mn supply, suggesting that Mn supply reduced the ability to absorb and accumulate Mn in roots and shoots, as well as root-to-shoot Mn translocation. Without Mn, roots alkalized the solution pH from 5.0 to above 6.2, while Mn supply reduced root-induced alkalization. As Mn supply increased from 0 to 2000 μM, the secretion of root total phenolics (TPs) increased, while the solution pH decreased. Mn supply did not alter the secretion of root total free amino acids, total soluble sugars, malate, and citrate. Mn-activated-release of TPs was inhibited by low temperature and anion channel inhibitors, but not by protein biosynthesis inhibitor. Using widely targeted metabolome, we detected 48 upregulated [35 upregulated phenolic compounds + 13 other secondary metabolites (SMs)] and three downregulated SMs, and 39 upregulated and eight downregulated primary metabolites (PMs). These findings suggested that reduced ability to absorb and accumulate Mn in roots and shoots and less root-to-shoot Mn translocation in Mn-toxic seedlings, rhizosphere alkalization, and Mn-activated-release of root exudates (especially phenolic compounds) contributed to the high Mn tolerance of C. sinensis seedlings.

Stability of Coumarins and Determination of the Net Iron Oxidation State of Iron-Coumarin Complexes: Implications for Examining Plant Iron Acquisition Mechanisms

Coumarins are exuded into the soil environment by plant roots in response to iron (Fe) deficiency. Previous studies have shown that coumarins can increase the Fe solubility upon interaction with sparsely soluble Fe(III) (hydr)oxide. However, the chemical mechanisms of Fe(III) (hydr)oxide dissolution by coumarins remain unclear. The high redox instability of dissolved coumarins and the interference of coumarins in determining the Fe redox state hinder the quantitative and mechanistic investigation of coumarin-induced Fe mobilization. In this study, we investigated the oxidative stability of three coumarins that have been found in root exudates, esculetin, scopoletin, and fraxetin, over a broad pH range under oxic and anoxic conditions. Our results show that the oxidation of coumarins is irreversible under oxic conditions and that oxidative degradation rates increased with increasing pH under both oxic and anoxic conditions. However, the complexation of Fe protects coumarins from degradation in the circumneutral pH range even under oxic conditions. Furthermore, we observed that Ferrozine, which is commonly used for establishing Fe redox speciation, can facilitate the reduction of Fe(III) complexed by coumarins, even at circumneutral pH. Reduction rates increased with decreasing pH and were larger for fraxetin than for scopoletin and esculetin. Based on these observations, we optimized the Ferrozine method for determining the redox state of Fe complexed by coumarins. Understanding the stability of dissolved coumarins and using a precise analytical method to determine the redox state of Fe in the presence of coumarins are critical for investigating the mechanisms by which coumarins enhance the availability of Fe in the rhizosphere.

IMA peptides function in iron homeostasis and cadmium resistance

Iron (Fe), an essential micronutrient, participates in photosynthesis, respiration, and many other enzymatic reactions. Cadmium (Cd), by contrast, is a toxic element to virtually all living organisms. Both Fe deficiency and Cd toxicity severally impair crop growth and productivity, finally leading to human health issues. Understanding how plants control the uptake and homeostasis of Fe and combat Cd toxicity thus is mandatory to develop Fe-enriched but Cd-cleaned germplasms for human beings. Recent studies in Arabidopsis and rice have revealed that IRON MAN (IMA) peptides stand out as a key regulator to respond to Fe deficiency by competitively interacting with a ubiquitin E3 ligase, thus inhibiting the degradation of IVc subgroup bHLH transcription factors (TFs), mediated by 26 S proteasome. Elevated expression of IMA confers tolerance to Cd stress in both Arabidopsis and wheat by activating the iron deficiency response. Here, we discuss recent breakthroughs that IMA peptides function in the Fe-deficiency response to attain Fe homeostasis and combat Cd toxicity as a potential candidate for phytoremediation.

Unraveling plant adaptation to single and combined nutrient deficiencies in a dicotyledonous and a monocotyledonous plant species

Nutrient deficiencies considerably limit agricultural production worldwide. However, while single deficiencies are widely studied, combined deficiencies are poorly addressed. Hence, the aim of this paper was to study single and combined deficiencies of iron (Fe) and phosphorus (P) in barley (Hordeum vulgare) and tomato (Solanum lycopersicum). Plants were grown in hydroponics and root exudation was measured over the growing period. At harvest, root morphology and root and shoot ionome was assessed. Shoot-to-root-ratio decreased in both species and in all nutrient deficiencies, besides in -Fe tomato. Barley root growth was enhanced in plants subjected to double deficiency behaving similarly to -P, while tomato reduced root morphology parameters in all treatments. To cope with the nutrient deficiency barley exuded mostly chelants, while tomato relied on organic acids. Moreover, tomato exhibited a slight exudation increase over time not detected in barley. Overall, in none of the species the double deficiency caused a substantial increase in root exudation. Multivariate statistics emphasized that all the treatments were significantly different from each other in tomato, while in barley only -Fe was statistically different from the other treatments. Our findings highlight that the response of the studied plants in double deficiencies is not additive but plant specific.

NO Is Not the Same as GSNO in the Regulation of Fe Deficiency Responses by Dicot Plants

Iron (Fe) is abundant in soils but with a poor availability for plants, especially in calcareous soils. To favor its acquisition, plants develop morphological and physiological responses, mainly in their roots, known as Fe deficiency responses. In dicot plants, the regulation of these responses is not totally known, but some hormones and signaling molecules, such as auxin, ethylene, glutathione (GSH), nitric oxide (NO) and S-nitrosoglutathione (GSNO), have been involved in their activation. Most of these substances, including auxin, ethylene, GSH and NO, increase their production in Fe-deficient roots while GSNO, derived from GSH and NO, decreases its content. This paradoxical result could be explained with the increased expression and activity in Fe-deficient roots of the GSNO reductase (GSNOR) enzyme, which decomposes GSNO to oxidized glutathione (GSSG) and NH3. The fact that NO content increases while GSNO decreases in Fe-deficient roots suggests that NO and GSNO do not play the same role in the regulation of Fe deficiency responses. This review is an update of the results supporting a role for NO, GSNO and GSNOR in the regulation of Fe deficiency responses. The possible roles of NO and GSNO are discussed by taking into account their mode of action through post-translational modifications, such as S-nitrosylation, and through their interactions with the hormones auxin and ethylene, directly related to the activation of morphological and physiological responses to Fe deficiency in dicot plants.

Beyond iron-storage pool: functions of plant apoplastic iron during stress

Iron (Fe) is an essential micronutrient for plants, and its storage in the apoplast represents an important Fe pool. Plants have developed various strategies to reutilize this apoplastic Fe pool to adapt to Fe deficiency. In addition, growing evidence indicates that the dynamic changes in apoplastic Fe are critical for plant adaptation to other stresses, including ammonium stress, phosphate deficiency, and pathogen attack. In this review, we discuss and scrutinize the relevance of apoplastic Fe for plant behavior changes in response to stress cues. We mainly focus on the relevant components that modulate the actions and downstream events of apoplastic Fe in stress signaling networks.

ELONGATED HYPOCOTYL 5 regulates BRUTUS and affects iron acquisition and homeostasis in Arabidopsis thaliana

Iron (Fe) is an essential micronutrient for both plants and animals. Fe-limitation significantly reduces crop yield and adversely impacts on human nutrition. Owing to limited bioavailability of Fe in soil, plants have adapted different strategies that not only regulate Fe-uptake and homeostasis but also bring modifications in root system architecture to enhance survival. Understanding the molecular mechanism underlying the root growth responses will have critical implications for plant breeding. Fe-uptake is regulated by a cascade of basic helix-loop-helix (bHLH) transcription factors (TFs) in plants. In this study, we report that HY5 (Elongated Hypocotyl 5), a member of the basic leucine zipper (bZIP) family of TFs, plays an important role in the Fe-deficiency signaling pathway in Arabidopsis thaliana. The hy5 mutant failed to mount optimum Fe-deficiency responses, and displayed root growth defects under Fe-limitation. Our analysis revealed that the induction of the genes involved in Fe-uptake pathway (FIT-FER-LIKE IRON DEFICIENCY-INDUCED TRANSCRIPTION FACTOR, FRO2-FERRIC REDUCTION OXIDASE 2 and IRT1-IRON-REGULATED TRANSPORTER1) is reduced in the hy5 mutant as compared with the wild-type plants under Fe-deficiency. Moreover, we also found that the expression of coumarin biosynthesis genes is affected in the hy5 mutant under Fe-deficiency. Our results also showed that HY5 negatively regulates BRUTUS (BTS) and POPEYE (PYE). Chromatin immunoprecipitation followed by quantitative polymerase chain reaction revealed direct binding of HY5 to the promoters of BTS, FRO2 and PYE. Altogether, our results showed that HY5 plays an important role in the regulation of Fe-deficiency responses in Arabidopsis.

4-methylumbelliferone (4-MU) enhances drought tolerance of apple by regulating rhizosphere microbial diversity and root architecture

The dwarfing rootstocks-mediated high-density apple orchard is becoming the main practice management. Currently, dwarfing rootstocks are widely used worldwide, but their shallow root system and drought sensitivity necessitate high irrigation requirements. Here, the root transcriptome and metabolome of dwarfing (M9-T337, a drought-sensitive rootstock) and vigorous rootstocks (Malus sieversii, a drought-tolerant species, is commonly used as a rootstock) showed that a coumarin derivative, 4-Methylumbelliferon (4-MU), was found to accumulate significantly in the roots of vigorous rootstock under drought condition. When exogenous 4-MU was applied to the roots of dwarfing rootstock under drought treatment, the plants displayed increased root biomass, higher root-to-shoot ratio, greater photosynthesis, and elevated water use efficiency. In addition, diversity and structure analysis of the rhizosphere soil microbial community demonstrated that 4-MU treatment increased the relative abundance of putatively beneficial bacteria and fungi. Of these, Pseudomonas, Bacillus, Streptomyces, and Chryseolinea bacterial strains and Acremonium, Trichoderma, and Phoma fungal strains known for root growth, or systemic resistance against drought stress, were significantly accumulated in the roots of dwarfing rootstock after 4-MU treatment under drought stress condition. Taken together, we identified a promising compound-4-MU, as a useful tool, to strengthen the drought tolerance of apple dwarfing rootstock.

The transcription factor MYC1 interacts with FIT to negatively regulate iron homeostasis in Arabidopsis thaliana

Iron (Fe) is an indispensable trace mineral element for the normal growth of plants, and it is involved in different biological processes; Fe shortage in plants can induce chlorosis and yield loss. The objective of this research is to identify novel genes that participated in the regulation of Fe-deficiency stress in Arabidopsis thaliana. A basic helix-loop-helix (bHLH) transcription factor (MYC1) was identified to be interacting with the FER-LIKE IRON DEFICIENCY-INDUCED TRANSCRIPTION FACTOR (FIT) using a yeast-two-hybrid assay. Transcript-level analysis showed that there was a decrease in MYC1 expression in Arabidopsis to cope with Fe-deficiency stress. Functional deficiency of MYC1 in Arabidopsis leads to an increase in Fe-deficiency tolerance and Fe-accumulation, whereas MYC1-overexpressing plants have an enhanced sensitivity to Fe-deficiency stress. Additionally, MYC1 inhibited the formation of FIT and bHLH38/39 heterodimers, which suppressed the expressed level for Fe acquisition genes FRO2 and IRT1 during Fe-deficiency stress. These results showed that MYC1 functions as a negative modulator of the Fe-deficiency stress response by inhibiting the formation of FIT and bHLH38/39 heterodimers, thereby suppressing the binding of FIT and bHLH38/39 heterodimers to the promoters of FRO2 and IRT1 to modulate Fe intake during Fe-deficiency stress. Overall, the findings of this study elucidated the role of MYC1 in coping with Fe-deficiency stress, and provided potential targets for the developing of crop varieties resistant to Fe-deficiency stress.

Understanding the plant-microbe interactions in environments exposed to abiotic stresses: An overview

Abiotic stress poses a severe danger to agriculture since it negatively impacts cellular homeostasis and eventually stunts plant growth and development. Abiotic stressors like drought and excessive heat are expected to occur more frequently in the future due to climate change, which would reduce the yields of important crops like maize, wheat, and rice which may jeopardize the food security of human populations. The plant microbiomes are a varied and taxonomically organized microbial community that is connected to plants. By supplying nutrients and water to plants, and regulating their physiology and metabolism, plant microbiota frequently helps plants develop and tolerate abiotic stresses, which can boost crop yield under abiotic stresses. In this present study, with emphasis on temperature, salt, and drought stress, we describe current findings on how abiotic stresses impact the plants, microbiomes, microbe-microbe interactions, and plant-microbe interactions as the way microorganisms affect the metabolism and physiology of the plant. We also explore crucial measures that must be taken in applying plant microbiomes in agriculture practices faced with abiotic stresses.

Spatial profiling of microbial communities by sequential FISH with error-robust encoding

Spatial analysis of microbiomes at single cell resolution with high multiplexity and accuracy has remained challenging. Here we present spatial profiling of a microbiome using sequential error-robust fluorescence in situ hybridization (SEER-FISH), a highly multiplexed and accurate imaging method that allows mapping of microbial communities at micron-scale. We show that multiplexity of RNA profiling in microbiomes can be increased significantly by sequential rounds of probe hybridization and dissociation. Combined with error-correction strategies, we demonstrate that SEER-FISH enables accurate taxonomic identification in complex microbial communities. Using microbial communities composed of diverse bacterial taxa isolated from plant rhizospheres, we apply SEER-FISH to quantify the abundance of each taxon and map microbial biogeography on roots. At micron-scale, we identify clustering of microbial cells from multiple species on the rhizoplane. Under treatment of plant metabolites, we find spatial re-organization of microbial colonization along the root and alterations in spatial association among microbial taxa. Taken together, SEER-FISH provides a useful method for profiling the spatial ecology of complex microbial communities in situ.

Entomopathogenic Fungi-Mediated Solubilization and Induction of Fe Related Genes in Melon and Cucumber Plants

Endophytic insect pathogenic fungi have a multifunctional lifestyle; in addition to its well-known function as biocontrol agents, it may also help plants respond to other biotic and abiotic stresses, such as iron (Fe) deficiency. This study explores M. brunneum EAMa 01/58-Su strain attributes for Fe acquisition. Firstly, direct attributes include siderophore exudation (in vitro assay) and Fe content in shoots and in the substrate (in vivo assay) were evaluated for three strains of Beauveria bassiana and Metarhizium bruneum. The M. brunneum EAMa 01/58-Su strain showed a great ability to exudate iron siderophores (58.4% surface siderophores exudation) and provided higher Fe content in both dry matter and substrate compared to the control and was therefore selected for further research to unravel the possible induction of Fe deficiency responses, Ferric Reductase Activity (FRA), and relative expression of Fe acquisition genes by qRT-PCR in melon and cucumber plants.. In addition, root priming by M. brunneum EAMa 01/58-Su strain elicited Fe deficiency responses at transcriptional level. Our results show an early up-regulation (24, 48 or 72 h post inoculation) of the Fe acquisition genes FRO1, FRO2, IRT1, HA1, and FIT as well as the FRA. These results highlight the mechanisms involved in the Fe acquisition as mediated by IPF M. brunneum EAMa 01/58-Su strain.

Identification of a Novel Coumarins Biosynthetic Pathway in the Endophytic Fungus Fusarium oxysporum GU-7 with Antioxidant Activity

Coumarins are generally considered to be produced by natural plants. Fungi have been reported to produce coumarins, but their biosynthetic pathways are still unknown. In this study, Fusarium oxysporum GU-7 and GU-60 were isolated from Glycyrrhiza uralensis, and their antioxidant activities were determined to be significantly different. Abundant dipeptide, phenolic acids, and the plant-derived coumarins fraxetin and scopoletin were identified in GU-7 by untargeted metabolomics, and these compounds may account for its stronger antioxidant activity compared to GU-60. Combined with metabolome and RNA sequencing analysis, we identified 24 potentially key genes involved in coumarin biosynthesis and 6 intermediate metabolites. Interestingly, the best hit of S8H, a key gene involved in hydroxylation at the C-8 position of scopoletin to yield fraxetin, belongs to a plant species. Additionally, nondestructive infection of G. uralensis seeds with GU-7 significantly improved the antioxidant activity of seedlings compared to the control group. This antioxidant activity may depend on the biological characteristics of endophytes themselves, as we observed a positive correlation between the antioxidant activity of endophytic fungi and that of their nondestructively infected seedlings. IMPORTANCE Plant-produced coumarins have been shown to play an important role in assembly of the plant microbiomes and iron acquisition. Coumarins can also be produced by some microorganisms. However, studies on coumarin biosynthesis in microorganisms are still lacking. We report for the first time that fraxetin and scopoletin were simultaneously produced by F. oxysporum GU-7 with strong free radical scavenging abilities. Subsequently, we identified intermediate metabolites and key genes in the biosynthesis of these two coumarins. This is the first report on the coumarin biosynthesis pathway in nonplant species, providing new strategies and perspectives for coumarin production and expanding research on new ways for plants to obtain iron.

The diversity of iron acquisition strategies of calcifuge plant species from dry acidic grasslands

Although the calcifuge plant species existing in dry acidic grasslands are believed to be prone to iron (Fe)-dependent limitations, little is known about their susceptibility and reaction to pH-dependent Fe starvation. Therefore, the present study examines the effects of contrasting soils (acidic Podzol vs alkaline Rendzina) and Fe supplementation (Fe-HBED) on alkaline substratum (5 and 25 μmol Fe-HBED kg^-1 soil). Five calcifuge dicotyledonous plant species (Alyssum montanum L., Antennaria dioica (L.) Gaertn., Hypochaeris radicata L., Jasione montana L. and Potentilla arenaria Borkh.) were tested in a pot experiment under field conditions. Chlorosis, chlorophyll content, growth and chlorophyll a fluorescence were measured. The elemental composition (contents of Ca, Mg, Fe, Mn, Zn and Cu) of the roots and shoots were analyzed, as well as their specialized metabolites. Two studied species (A. dioica d and J. montana) were susceptible to pH-dependent chlorosis, and this deficiency was successfully diminished by the application of Fe-HBED. Almost all the studied species (except A. montanum) preferred the acidic soil. Fe-HBED treatments were not sufficient for supporting the growth of H. radicata and J. montana in alkaline soil to the same degree as in acidic soil, which suggests additional non-Fe-dependent limitations. Both Fe starvation and Fe over-supplementation caused species-specific changes in chlorophyll a fluorescence. The disturbed Fe acquisition in the alkaline soil was not the sole source of the observed limitations, as the chlorosis-susceptible species demonstrated a complex interaction between Fe, Mn and Zn. The species resistant to lime chlorosis contained greater amounts of specialized metabolites than the susceptible plants. Our findings do not support hypothesis that all calcifuges are susceptible to Fe-dependent chlorosis: calcifuge plant species from dry acidic grasslands appear to have diverse Fe requirements and acquisition strategies.

Advances in Iron Retrograde Signaling Mechanisms and Uptake Regulation in Photosynthetic Organisms

Iron (Fe) is an essential metal for the growth and development of different organisms, including plants and algae. This metal participates in different biological processes, among which are cellular respiration and photosynthesis. Fe is found associated with heme groups and as part of inorganic Fe-S groups as cofactors of numerous cellular proteins. Although Fe is abundant in soils, it is often not bioavailable due to soil pH. For this reason, photosynthetic organisms have developed different strategies for the uptake, the sensing of Fe intracellular levels but also different mechanisms that maintain and regulate adequate concentrations of this metal in response to physiological needs. This work focuses on discussing recent advances in the characterization of the mechanisms of Fe homeostasis and Fe retrograde signaling in photosynthetic organisms.

Evaluation of eleven kiwifruit genotypes for bicarbonate tolerance and characterization of two tolerance-contrasting genotypes

Screening bicarbonate-tolerant genotypes is an environmentally-friendly and long-term effective strategy to cope with bicarbonate-induced chlorosis in fruit crops grown on calcareous soils. We investigated eleven genotypes from four kiwifruit species (Actinidia chinensis, A. macrosperma, A. polygama, and A. valvata) for differences in bicarbonate tolerance. We also characterized the physiological and molecular differences in two contrasting genotypes of this group. In the first experiment, bicarbonate-treated plantlets were irrigated with 3.0 g L^-1 CaCO₃ and 5.04 g L^-1 NaHCO₃ in peat and perlite medium culture. Based on principal component analysis, weight-based membership function method and cluster analysis, the tested genotypes were classified into three groups: (1) tolerant, including YX, Av-1, Acd, Ap, Av-2, and QM; (2) moderately tolerant, including Av-3, Am, Av-4, and HWD; and (3) sensitive, including only QH. In the second experiment, QH (bicarbonate-sensitive) and YX (bicarbonate-tolerant) were grown in sand culture with 4.0 g L^-1 CaCO₃ and 0.84 g L^-1 or 1.26 g L^-1 NaHCO₃. Compared with QH, YX showed a better ability to take up iron (Fe) by roots and to transport Fe from roots to shoots in the bicarbonate treatments, probably due to a better capacity to protect from oxidative damage and to excrete protons, and a differential expression of genes associated with Fe uptake and translocation, including HA8, IRT1, YSL3 and NRAMP3. The results can facilitate identifying potential resources for bicarbonate tolerance and breeding new rootstocks, and contribute to the elucidation of the bicarbonate tolerance mechanisms in the genus Actinidia.

Mechanisms underlying cereal/legume intercropping as nature-based biofortification: A review

The deficiencies of micronutrients known as hidden hunger are severely affecting more than one-half of the world’s population, which is highly related to low bioavailability of micronutrients, poor quality diets, and consumption of cereal-based foods in developing countries. Although numerous experiments proved biofortification as a paramount approach for improving hidden hunger around the world, its effectiveness is highly related to various soil factors, climate conditions, and the adoption rates of biofortified crops. Furthermore, agronomic biofortification may result in the sedimentation of heavy metals in the soil that pose another detrimental effect on plants and human health. In response to these challenges, several studies suggested intercropping as one of the feasible, eco-friendly, low-cost, and short-term approaches for improving the nutritional quality and yield of crops sustainable way. Besides, it is the cornerstone of climate-smart agriculture and the holistic solution for the most vulnerable area to solve malnutrition that disturbs human healthy catastrophically. Nevertheless, there is meager information on mechanisms and processes related to soil-plant interspecific interactions that lead to an increment of nutrients bioavailability to tackle the crisis of micronutrient deficiency in a nature-based solution. In this regard, this review tempted to (1) explore mechanisms and processes that can favor the bioavailability of Zn, Fe, P, etc. in soil and edible parts of crops, (2) synthesize available information on the benefits and synergic role of the intercropping system in food and nutritional security, and (3) outline the bottlenecks influencing the effectiveness of biofortification for promoting sustainable agriculture in sub-Saharan Africa (SSA). Based on this review SSA countries are malnourished due to limited access to diverse diets, supplementation, and commercially fortified food; hence, I suggest integrated research by agronomists, plant nutritionists, and agroecologist to intensify and utilize intercropping systems as biofortification sustainably alleviating micronutrient deficiencies.

Graphical Abstract

Trace metals at the frontline of pathogen defence responses in non-hyperaccumulating plants

Metal hyperaccumulation is an exclusive evolutionary trait contributing to efficient plant defence against biotic stress. The defence can be based on direct metal toxicity or the joint effects of accumulated metal and organic compounds, the latter being based on integrated signalling networks. While the role of metals in biotic stress defence of hyperaccumulators has been intensively studied, their role in the pathogen immunity of non-accumulator plants is far less understood. New findings show that in metal non-hyperaccumulating plants, localized hot spots of zinc, manganese, and iron increase plant immunity, while manipulation of nutrient availability may be used for priming against subsequent pathogen attack. Recent findings on the role of metals in plant-pathogen interactions are discussed considering the narrow line between deficiency and toxicity, host-pathogen nutrient competition and synergistic effects of simultaneous metal and biotic stress. We discuss the suitability of the direct-defence and joint-effects hypotheses in non-hyperaccumulating plants, and the involvement of metals as active centres of immunity-related enzymes. We also consider future challenges in revealing the mechanisms underlying metal-mediated plant immunity.

MbHY5-MbYSL7 mediates chlorophyll synthesis and iron transport under iron deficiency in Malus baccata

Iron (Fe) plays an important role in cellular respiration and catalytic reactions of metalloproteins in plants and animals. Plants maintain iron homeostasis through absorption, translocation, storage, and compartmentalization of iron via a cooperative regulative network. Here, we showed different physiological characteristics in the leaves and roots of Malus baccata under Fe sufficiency and Fe deficiency conditions and propose that MbHY5 (elongated hypocotyl 5), an important transcription factor for its function in photomorphogenesis, participated in Fe deficiency response in both the leaves and roots of M. baccata. The gene co-expression network showed that MbHY5 was involved in the regulation of chlorophyll synthesis and Fe transport pathway under Fe-limiting conditions. Specifically, we found that Fe deficiency induced the expression of MbYSL7 in root, which was positively regulated by MbHY5. Overexpressing or silencing MbYSL7 influenced the expression of MbHY5 in M. baccata.

Chemical Constituents and Their Production in Mexican Oaks (Q. Rugosa, Q. Glabrescens and Q. Obtusata)

Mexico is considered one of the main regions of diversification of the genus Quercus (oaks). Oak species are one of the most important tree groups, particularly in temperate forests, due to its diversity and abundance. Some studies have shown that oak contains specialized metabolites with medicinal importance. In this work, the acetonic extract from leaves of three Mexican oaks (Quercus rugosa, Q. glabrescens, and Q. obtusata) was separated using thin-layer chromatography and column chromatography. Chemical identification of the major compounds was determined using high-performance liquid chromatography and nuclear magnetic resonance. Nineteen compounds were identified, three belonging to the terpenoid family (ursolic acid, β-amyrin, and β-sitosterol) and 16 from the phenolic family. Of the isolated compounds, seven are new reports for oak species (scopoletin, ursolic acid, β-amyrin, luteolin-7-O-glucoside, kaempferol-3-O-sophoroside, kaempferol-3-O-glucoside, and kaempferol-3-O-sambubioside). More compounds were identified in Q. rugosa followed by Q. glabrescens and then Q. obtusata. The characterization of specialized metabolites in oak species is relevant, from both phytocentric and anthropocentric perspectives.

Metallophenolomics: A Novel Integrated Approach to Study Complexation of Plant Phenolics with Metal/Metalloid Ions

Plant adaptive strategies have been shaped during evolutionary development in the constant interaction with a plethora of environmental factors, including the presence of metals/metalloids in the environment. Among adaptive reactions against either the excess of trace elements or toxic doses of non-essential elements, their complexation with molecular endogenous ligands, including phenolics, has received increasing attention. Currently, the complexation of phenolics with metal(loid)s is a topic of intensive studies in different scientific fields. In spite of the numerous studies on their chelating capacity, the systemic analysis of phenolics as plant ligands has not been performed yet. Such a systematizing can be performed based on the modern approach of metallomics as an integral biometal science, which in turn has been differentiated into subgroups according to the nature of the bioligands. In this regard, the present review summarizes phenolics–metal(loid)s’ interactions using the metallomic approach. Experimental results on the chelating activity of representative compounds from different phenolic subgroups in vitro and in vivo are systematized. General properties of phenolic ligands and specific properties of anthocyanins are revealed. The novel concept of metallophenolomics is proposed, as a ligand-oriented subgroup of metallomics, which is an integrated approach to study phenolics–metal(loid)s’ complexations. The research subjects of metallophenolomics are outlined according to the methodology of metallomic studies, including mission-oriented biometal sciences (environmental sciences, food sciences and nutrition, medicine, cosmetology, coloration technologies, chemical sciences, material sciences, solar cell sciences). Metallophenolomics opens new prospects to unite multidisciplinary investigations of phenolic–metal(loid) interactions.

Rahnella aquatilis JZ-GX1 alleviates iron deficiency chlorosis in Cinnamomum camphora by secreting desferrioxamine and reshaping the soil fungal community

Plant growth-promoting rhizobacteria are important for improving plant iron nutrition, but the interactions among inoculants, host plants and soil microorganisms have not been greatly explored. Rahnella aquatilis JZ-GX1 was applied to treat the increasingly serious iron deficiency chlorosis in Cinnamomum camphora, and the resulting improvement in chlorosis was determined by assessing the contents of chlorophyll, active iron, Fe²⁺ and antioxidant enzymes in leaves, the effects on the soil microbial community and the metabolism in the rhizosphere by high-throughput sequencing techniques and liquid chromatography-mass spectrometry (LC-MS). The results showed that inoculation with JZ-GX1 significantly increased the chlorophyll content of C. camphora, which promoted the redistribution of active iron in roots and leaves, increased the activities of superoxide dismutase (SOD), peroxidase (POD), catalase (CAT) and ascorbate peroxidase (APX), and thus reduced membrane damage in iron-deficient C. camphora caused by reactive oxygen species. According to genome prediction and ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) analysis, the JZ-GX1 strain could secrete desferrioxamine (DFO), and the concentration of DFO in C. camphora rhizosphere was 21-fold higher than that in uninoculated soil. The exogenous application of DFO increased the SPAD and Fe²⁺ contents in leaves. In addition, the inoculant affected the fungal community structure and composition in the C. camphora rhizosphere soil and increased the abundances of specific taxa, such as Glomus, Mortierella, Trichoderma, and Penicillium. Therefore, R. aquatilis JZ-GX1 application promoted iron absorption in C. camphora trees by secreting DFO and alleviated iron deficiency chlorosis through interactions with the local fungal community.

Emerging roles of protein phosphorylation in plant iron homeostasis

Remarkable progress has been made in dissecting the molecular mechanisms involved in iron (Fe) homeostasis in plants, especially the identification of key transporter and transcriptional regulatory networks. But how the protein activity of these master players is regulated by Fe status remains underexplored. Recent studies show that major players toggle switch their properties by protein phosphorylation under different Fe conditions and consequently control the signaling cascade and metabolic adjustment. Moreover, Fe deficiency causes changes of multiple kinases and phosphatases. Here, we discuss how these findings highlight the emergence of the protein phosphorylation-dependent regulation for rapid and precise responses to Fe status to attain Fe homeostasis. Further studies will be needed to fully understand the regulation of these intricate networks.

Physiological and Transcriptome Analyses Revealed the Mechanism by Which Deferoxamine Promotes Iron Absorption in Cinnamomum camphora

Iron deficiency causes chlorosis and growth inhibition in Cinnamomum camphora, an important landscaping tree species. Siderophores produced by plant growth-promoting rhizobacteria have been widely reported to play an indispensable role in plant iron nutrition. However, little to date has been determined about how microbial siderophores promote plant iron absorption. In this study, multidisciplinary approaches, including physiological, biochemical and transcriptome methods, were used to investigate the role of deferoxamine (DFO) in regulating Fe availability in C. camphora seedlings. Our results showed that DFO supplementation significantly increased the Fe²⁺ content, SPAD value and ferric-chelate reductase (FCR) activity in plants, suggesting its beneficial effect under Fe deficiency. This DFO-driven amelioration of Fe deficiency was further supported by the improvement of photosynthesis. Intriguingly, DFO treatment activated the metabolic pathway of glutathione (GSH) synthesis, and exogenous spraying reduced glutathione and also alleviated chlorosis in C. camphora. In addition, the expression of some Fe acquisition and transport-related genes, including CcbHLH, CcFRO6, CcIRT2, CcNramp5, CcOPT3 and CcVIT4, was significantly upregulated by DFO treatment. Collectively, our data demonstrated an effective, economical and feasible organic iron-complexing agent for iron-deficient camphor trees and provided new insights into the mechanism by which siderophores promote iron absorption in plants.

News about amino acid metabolism in plant-microbe interactions

Plants constantly come into contact with a diverse mix of pathogenic and beneficial microbes. The ability to distinguish between them and to respond appropriately is essential for plant health. Here we review recent progress in understanding the role of amino acid sensing, signaling, transport, and metabolism during plant-microbe interactions. Biochemical pathways converting individual amino acids into active compounds have recently been elucidated, and comprehensive large-scale approaches have brought amino acid sensors and transporters into focus. These findings show that plant central amino acid metabolism is closely interwoven with stress signaling and defense responses at various levels. The individual biochemical mechanisms and the interconnections between the different processes are just beginning to emerge and might serve as a foundation for new plant protection strategies.

Plant-Microbiota Interactions in Abiotic Stress Environments

Abiotic stress adversely affects cellular homeostasis and ultimately impairs plant growth, posing a serious threat to agriculture. Climate change modeling predicts increasing occurrences of abiotic stresses such as drought and extreme temperature, resulting in decreasing the yields of major crops such as rice, wheat, and maize, which endangers food security for human populations. Plants are associated with diverse and taxonomically structured microbial communities that are called the plant microbiota. Plant microbiota often assist plant growth and abiotic stress tolerance by providing water and nutrients to plants and modulating plant metabolism and physiology and, thus, offer the potential to increase crop production under abiotic stress. In this review, we summarize recent progress on how abiotic stress affects plants, microbiota, plant-microbe interactions, and microbe-microbe interactions, and how microbes affect plant metabolism and physiology under abiotic stress conditions, with a focus on drought, salt, and temperature stress. We also discuss important steps to utilize plant microbiota in agriculture under abiotic stress.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Carbonate-Induced Chemical Reductants Are Responsible for Iron Acquisition in Strategy I Wild Herbaceous Plants Native to Calcareous Grasslands

Significant progress has been made in understanding Strategy I iron (Fe) acquisition using crop/model plants under controlled conditions in laboratories. However, plant species native to calcareous soils may have evolved unique strategies for adaptation to high carbonate/pH-induced Fe deficiency. Until now, little information is available on the Fe acquisition mechanisms in these plants. Here, we explored the Fe acquisition mechanisms in wild dicot species native to calcareous grasslands, by monitoring the Fe nutrition-related rhizosphere processes in field and greenhouse conditions. Most of these wild species displayed comparable shoot Fe concentration to those of crops, and some dicots actually accumulated very high shoot Fe. However, these species did not exhibit ferric reductase oxidase (FRO)-dependent Strategy I responses to Fe deficiency, including visual rhizosphere acidification and increased Fe3+ reduction. In contrast, chemical reductants exuded by roots of dicots were responsible for Fe3+ reduction in these wild plants. These features were not observed in the FRO-dependent Strategy I crop plant cucumber. Neither leaf chlorophyll nor shoot/root Fe was depressed by 10% CaCO3 application in all the examined wild species. Furthermore, their root exudation was significantly activated by CaCO3, leading to an increased Fe3+ reduction. We show that chemical reductant-mediated Fe3+ reduction occurs preferentially in these wild dicots and that these mechanisms are not sensitive to high soil carbonate/pH. Our findings support that Fe acquisition in Strategy I wild plants native to calcareous soils is substantially different from the enzyme-dependent system of Strategy I plants.

Targeted Metabolomics With a Chemometric Study of Oxygenated Heterocyclic Aglycones as a Tool for Preliminary Authenticity Assessment of Orange and Grapefruit Juices

Profiles of citrus juice oxygenated heterocyclic aglycones (OHAs), which are notable marker secondary metabolites, were used to assess the authenticity of sweet orange and grapefruit juices in situations where mandarin and pomelo juices might be adulterants. Thirty-nine known OHAs, including 10 methoxyflavones, 13 coumarins, and 16 furanocoumarins, as well as 13 tentatively screened OHAs, were analyzed in orange, mandarin, grapefruit and pomelo juices using our newly developed high-resolution HPLC-UV and fluorescence detection method. Quantitative OHA profiles from 158 pure juice samples were obtained to establish a purity discriminant model using an omics strategy. Reduction of OHA variables showed that three important methoxyflavones, i.e. isosinensetin, tangeretin and sinensetin provided the best discrimination ability between sweet orange and mandarin juices. There are two subtypes of pomelos, Shatianyou Group and Wendan Group, of which juices should be separately compared to grapefruit juice. Five OHAs, namely meranzin, 3,5,6,7,8,3',4'-heptamethoxyflavone, osthole, 6',7'-epoxybergamottin, and bergamottin were found to discriminate Shatianyou Group of pomelo juice from grapefruit juice; whereas three OHAs, namely bergaptol, isomeranzin, and 6',7'-dihydroxybergamottin were able to discriminate Wendan Group of pomelo juice from grapefruit juice. The established partial least squares discriminant analysis (PLS-DA) models were capable of detecting as little as 10% mandarin juice in sweet orange juice and 10% pomelo juice in grapefruit juice, allowing for fast prescreening of excess addition with good reliability (root mean square error of prediction, RMSEP < 5%).

Genome-Wide Association Analysis Reveals the Genetic Basis of Iron-Deficiency Stress Tolerance in Maize

Iron (Fe) is an essential trace element for almost all organisms and is often the major limiting nutrient for normal growth. Fe deficiency is a worldwide agricultural problem, which affects crop productivity and product quality. Understanding the Fe-deficiency response in plants is necessary for improving both plant health and the human diet. In this study, Fe-efficient (Ye478) and Fe-inefficient maize inbred lines (Wu312) were used to identify the genotypic difference in response to low Fe stress during different developmental stages and to further determine the optimal Fe-deficient Fe(II) supply level which leads to the largest phenotypic difference between Ye478 and Wu312. Then, genome-wide association analysis was performed to further identify candidate genes associated with the molecular mechanisms under different Fe nutritional statuses. Three candidate genes involved in Fe homeostasis of strategy II plants (strategy II genes) were identified, including ZmDMAS1, ZmNAAT1, and ZmYSL11. Furthermore, candidate genes ZmNAAT1, ZmDMAS1, and ZmYSL11 were induced in Fe-deficient roots and shoots, and the expression of ZmNAAT1 and ZmDMAS1 responded to Fe deficiency more in shoots than in roots. Beyond that, several genes that may participate in Fe homeostasis of strategy I plants (strategy I genes) were identified, which were either encoding Fe transporters (ZmIRT1 and ZmZIP4), or acting as essential ethylene signal transducers (ZmEBF1). Interestingly, ZmIRT1, ZmZIP4, and ZmEBF1 were significantly upregulated under low Fe stress, suggesting that these genes may be involved in Fe-deficiency tolerance in maize which is considered as strategy II plant. This study demonstrates the use of natural variation in the association population to identify important genes associated with Fe-deficiency tolerance and may further provide insights for understanding the molecular mechanism underlying the tolerance to Fe-deficiency stress in maize.

OsbHLH061 links TOPLESS/TOPLESS-RELATED repressor proteins with POSITIVE REGULATOR OF IRON HOMEOSTASIS 1 to maintain iron homeostasis in rice

As excess iron (Fe) is toxic, uptake of this essential micronutrient must be tightly controlled. Previous studies have shown that Oryza sativa (rice) POSITIVE REGULATOR OF IRON HOMEOSTASIS1 (OsPRI1) acts upstream of the iron-related transcription factor 2 (OsIRO2) and OsIRO3 to positively regulate root-to-shoot Fe translocation. However, as expression of OsPRI1 is constitutive it is unclear how the Fe-deficiency response is turned off to prevent toxicity when Fe is sufficient. The bHLH transcription factor OsbHLH061 interacts with OsPRI1, and this study used molecular, genetics, biochemical and physiological approaches to functionally characterise OsbHLH061 and how it affects Fe homeostasis. OsbHLH061 knockout or overexpression lines increase or decrease Fe accumulation in shoots respectively. Mechanistically, OsbHLH061 expression is upregulated by high Fe, and physically interacts with OsPRI1, the OsbHLH061-OsPRI1 complex recruits TOPLESS/TOPLESS-RELATED (OsTPL/TPR) co-repressors to repress OsIRO2 and OsIRO3 expression. The OsbHLH061 ethylene-responsive element-binding factor-associated amphiphilic repression (EAR) motif is required for this transcriptional repression activity. These results define a functional OsTPL/TPR-OsbHLH061-OsPRI1-OsIRO2/3 module that negatively controls long-distance transport of Fe in plants for adaptation to changing Fe environments and maintain Fe homeostasis in rice.

Siderophores: an alternative bioremediation strategy?

Siderophores are small molecular weight iron scavengers that are mainly produced by bacteria, fungi, and plants. Recently, they have attracted increasing attention because of their potential role in environmental bioremediation. Although siderophores are generally considered to exhibit high specificity for iron, they have also been reported to bind to various metal and metalloid ions. This unique ability allows siderophores to solubilise and mobilise heavy metals and metalloids from soil, thereby facilitating their bioremediation. In addition, because of their redox nature, they can mediate the production of reactive oxygen species (ROS), and thus promote the biodegradation of organic contaminants. The aim of this review is to summarise the existing knowledge on the developed strategies of siderophore-assisted bioremediation of metals, metalloids, and organic contaminants. Additionally, this review also includes the biosynthesis and classification of microbial and plant siderophores.

Ensuring future food security and resource sustainability: insights into the rhizosphere

Feeding the world’s growing population requires continuously increasing crop yields with less fertilizers and agrochemicals on limited land. Focusing on plant belowground traits, especially root-soil-microbe interactions, holds a great promise for overcoming this challenge. The belowground root-soil-microbe interactions are complex and involve a range of physical, chemical, and biological processes that influence nutrient-use efficiency, plant growth and health. Understanding, predicting, and manipulating these rhizosphere processes will enable us to harness the relevant interactions to improve plant productivity and nutrient-use efficiency. Here, we review the recent progress and challenges in root-soil-microbe interactions. We also highlight how root-soil-microbe interactions could be manipulated to ensure food security and resource sustainability in a changing global climate, with an emphasis on reducing our dependence on fertilizers and agrochemicals.

Plant iron nutrition: the long road from soil to seeds

Iron (Fe) is an essential plant micronutrient since many cellular processes including photosynthesis, respiration, and the scavenging of reactive oxygen species depend on adequate Fe levels; however, non-complexed Fe ions can be dangerous for cells, as they can act as pro-oxidants. Hence, plants possess a complex homeostatic control system for safely taking up Fe from the soil and transporting it to its various cellular destinations, and for its subcellular compartmentalization. At the end of the plant's life cycle, maturing seeds are loaded with the required amount of Fe needed for germination and early seedling establishment. In this review, we discuss recent findings on how the microbiota in the rhizosphere influence and interact with the strategies adopted by plants to take up iron from the soil. We also focus on the process of seed-loading with Fe, and for crop species we also consider its associated metabolism in wild relatives. These two aspects of plant Fe nutrition may provide promising avenues for a better comprehension of the long pathway of Fe from soil to seeds.

Micronutrient homeostasis in plants for more sustainable agriculture and healthier human nutrition

The provision of sustainable, sufficient, and nutritious food to the growing population is a major challenge for agriculture and the plant research community. In this respect, the mineral micronutrient content of food crops deserves particular attention. Micronutrient deficiencies in cultivated soils and plants are a global problem that adversely affects crop production and plant nutritional value, as well as human health and well-being. In this review, we call for awareness of the importance and relevance of micronutrients in crop production and quality. We stress the need for better micronutrient nutrition in human populations, not only in developing but also in developed nations, and describe strategies to identify and characterize new varieties with high micronutrient content. Furthermore, we explain how adequate nutrition of plants with micronutrients impacts metabolic functions and the capacity of plants to express tolerance mechanisms against abiotic and biotic constraints. Finally, we provide a brief overview and a critical discussion on current knowledge, future challenges, and specific technological needs for research on plant micronutrient homeostasis. Research in this area is expected to foster the sustainable development of nutritious and healthy food crops for human consumption.

How Plants Recalibrate Cellular Iron Homeostasis

Insufficient iron supply poses severe constraints on plants, restricting species with inefficient iron uptake mechanisms from habitats with low iron availability and causing yield losses in agricultural ecosystems. Iron deficiency also poses a severe threat on human health. Anemia resulting from insufficient iron intake is affecting one of four people in the world. It is, therefore, imperative to understand the mechanisms by which plants acquire iron against a huge soil-cell gradient and how iron is distributed within the plant to develop strategies that increase its concentration in edible plant parts. Research into the processes that are employed by plants to adjust cellular iron homeostasis revealed an astonishingly complex puzzle of signaling nodes and circuits, which are intertwined with the perception and communication of other environmental cues such as pathogens, light, nutrient availability and edaphic factors such as pH. In a recent Spotlight issue in this journal, a collection of review articles summarized the state-of-the-art in plant iron research, covering the most active and, debatably, most important topics in this field. Here, we highlight breakthroughs that were reported after the publication date of this review collection, focusing on exciting and potentially influential studies that have changed our understanding of plant iron nutrition.

Root exudates impact plant performance under abiotic stress

Plant root exudates serve pivotal roles in supporting plant development and interactions with the physicochemical and biological factors in the rhizosphere. Under stress conditions, root exudation is involved in enhancing plant resource-use efficiency and facilitating the crosstalk between plant and soil microbes to ameliorate stress. Although there are a large number of root exudates that remain to be characterized, recent technological advancements have allowed for the function of many exudate compounds to be elucidated. In this review, we discuss current knowledge about the key root exudates that modulate plant resource-use efficiency under various abiotic stresses including drought, aluminum toxicity, phosphorus, nitrogen, and iron deficiency. The role that key root exudates play in shaping microbial communities in the rhizosphere under stress conditions is also an important consideration addressed in this review.

Challenges and opportunities to regulate mineral transport in rice

Iron (Fe) is an essential mineral for plants, and its deficiency as well as toxicity severely affects plant growth and development. Although Fe is ubiquitous in mineral soils, its acquisition by plants is difficult to regulate particularly in acidic and alkaline soils. Under alkaline conditions, where lime is abundant, Fe and other mineral elements are sparingly soluble. In contrast, under low pH conditions, especially in paddy fields, Fe toxicity could occur. Fe uptake is complicated and could be integrated with copper (Cu), manganese (Mn), zinc (Zn), and cadmium (Cd) uptake. Plants have developed sophisticated mechanisms to regulate the Fe uptake from soil and its transport to root and above-ground parts. Here, we review recent developments in understanding metal transport and discuss strategies to effectively regulate metal transport in plants with a particular focus on rice.

Mining Fiskeby III and Mandarin (Ottawa) Expression Profiles to Understand Iron Stress Tolerant Responses in Soybean

The soybean (Glycine max L. merr) genotype Fiskeby III is highly resistant to a multitude of abiotic stresses, including iron deficiency, incurring only mild yield loss during stress conditions. Conversely, Mandarin (Ottawa) is highly susceptible to disease and suffers severe phenotypic damage and yield loss when exposed to abiotic stresses such as iron deficiency, a major challenge to soybean production in the northern Midwestern United States. Using RNA-seq, we characterize the transcriptional response to iron deficiency in both Fiskeby III and Mandarin (Ottawa) to better understand abiotic stress tolerance. Previous work by our group identified a quantitative trait locus (QTL) on chromosome 5 associated with Fiskeby III iron efficiency, indicating Fiskeby III utilizes iron deficiency stress mechanisms not previously characterized in soybean. We targeted 10 of the potential candidate genes in the Williams 82 genome sequence associated with the QTL using virus-induced gene silencing. Coupling virus-induced gene silencing with RNA-seq, we identified a single high priority candidate gene with a significant impact on iron deficiency response pathways. Characterization of the Fiskeby III responses to iron stress and the genes underlying the chromosome 5 QTL provides novel targets for improved abiotic stress tolerance in soybean.

Genome-Wide Analysis of the UDP-Glycosyltransferase Family Reveals Its Roles in Coumarin Biosynthesis and Abiotic Stress in Melilotus albus

Coumarins, natural products abundant in Melilotus albus, confer features in response to abiotic stresses, and are mainly present as glycoconjugates. UGTs (UDP-glycosyltransferases) are responsible for glycosylation modification of coumarins. However, information regarding the relationship between coumarin biosynthesis and stress-responsive UGTs remains limited. Here, a total of 189 MaUGT genes were identified from the M. albus genome, which were distributed differentially among its eight chromosomes. According to the phylogenetic relationship, MaUGTs can be classified into 13 major groups. Sixteen MaUGT genes were differentially expressed between genotypes of Ma46 (low coumarin content) and Ma49 (high coumarin content), suggesting that these genes are likely involved in coumarin biosynthesis. About 73.55% and 66.67% of the MaUGT genes were differentially expressed under ABA or abiotic stress in the shoots and roots, respectively. Furthermore, the functions of MaUGT68 and MaUGT186, which were upregulated under stress and potentially involved in coumarin glycosylation, were characterized by heterologous expression in yeast and Escherichia coli. These results extend our knowledge of the UGT gene family along with MaUGT gene functions, and provide valuable findings for future studies on developmental regulation and comprehensive data on UGT genes in M. albus.