Low pH, aluminum, and phosphorus coordinately regulate malate exudation through GmALMT1 to improve soybean adaptation to acid soils

GmSTOP1-3 regulates flavonoid synthesis to reduce ROS accumulation and enhance aluminum tolerance in soybean

Aluminum (Al) toxicity is a significant limiting factor for crop production in acid soils. The functions and regulatory mechanisms of transcription factor STOP1 (Sensitive to Proton Rhizotoxicity 1) family genes in Al-tolerance have been widely studied in many plant species, except for soybean. Here, expression of GmSTOP1-3 was significantly enhanced by Al stress in soybean roots. Overexpression of GmSTOP1-3 resulted in enhanced root elongation and decreased Al content, which was accompanied by increased antioxidant capacity under Al treatment. Furthermore, RNA-seq identified 498 downstream genes of GmSTOP1-3, including genes involved in flavonoid biosynthesis. Among them, the expression of chalcone synthase (GmCHS) and isoflavone synthase (GmIFS) were highly enhanced by GmSTOP1-3 overexpression. Further quantitative flavonoid metabolome analysis showed that overexpression of GmSTOP1-3 significantly increased the content of naringenin chalcone, naringenin, and genistein in soybean roots under Al treatment, which positively correlated with the expression level of the genes relative to flavonoid biosynthesis. Notably, genistein had a significant positive correlation with the expression levels of GmIFS. Combination of Dual Luciferase Complementation (LUC) and Electrophoretic Mobility Shift Assays (EMSA) revealed that GmSTOP1-3 directly bound to the promoters of GmCHS/GmIFS and activated both genes' transcription. Taken together, these results suggest that GmSTOP1-3 enhances soybean Al tolerance partially through regulating the flavonoid synthesis.

Physiological and comprehensive transcriptome analysis reveals distinct regulatory mechanisms for aluminum tolerance of Trifolium repens

It is estimated that up to 50 % of arable lands worldwide are acidic, and most crops are severely inhibited due to the high active aluminum (Al). Trifolium repens is an excellent legume forage with a certain acid tolerance, although it is affected by Al toxicity in acidic soil. In this study, physiological and transcriptomic responses of different white clover varieties were analyzed when exposed to a high-level of Al stress. The results revealed that Trifolium repens had a high level of Al toxicity tolerance, and accumulated nearly 70 % of Al3+ in its roots. Al toxicity significantly inhibited the root length and root activity, decreased the chlorophyll (Chl) content and photosynthetic pigments, while significantly increased the intercellular CO2 concentration (Ci). The content of malondialdehyde (MDA), electrolyte leakage (EL), proline and reactive oxygen species (ROS) were significantly accumulated under Al stress. Furthermore, a total of 27,480 differentially expressed genes (DEGs) were identified after the treatment. Gene ontology (GO) and Kyoto encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that most Al-responsive genes enriched to chloroplast thylakoid membrane, chloroplast stroma and photosynthesis in Haifa leaf while in MAG leaf highly enriched in response to regulation of defense response, which could induce the different tolerance of the two cultivars to Al stress. Besides, pectin methylesterase (PME), glycosyl transferases (GT1) and chalcone synthase genes associated with cell wall biosynthesis may improve the Al accumulation and enhance tolerance of Al toxicity. The results established here would help to understand the morphological structure, physiological and biochemical response, and molecular mechanism of white clover under Al tolerance.

Structural insight into the Arabidopsis vacuolar anion channel ALMT9 shows clade specificity

The Arabidopsis thaliana aluminum-activated malate transporter 9 (AtALMT9) functions as a vacuolar chloride channel that regulates the stomatal aperture. Here, we present the cryoelectron microscopy (cryo-EM) structures of AtALMT9 in three distinct states. AtALMT9 forms a dimer, and the pore is lined with four positively charged rings. The apo-AtALMT9 state shows a putative endogenous citrate obstructing the pore, where two W120 constriction residues enclose a gate with a pore radius of approximately 1.8 Å, representing an open state. Interestingly, channel closure is solely controlled by W120. Compared to wild-type plants, the W120A mutant exhibits more sensitivity to drought stress and is unable to restore the visual phenotype on leaves upon water recovery, reflecting persistent stomatal opening. Furthermore, notable variations are noted in channel gating and substrate recognition of Glycine max ALMT12, AtALMT9, and AtALMT1. In summary, our investigation enhances comprehension of the interplay between structure and function within the ALMT family.

Both hormones and energy-rich compounds play a role in the mitigation of elevated pH on aluminum toxicity in Citrus sinensis leaves

The contribution of plant hormones and energy-rich compounds and their metabolites (ECMs) in alleviating aluminum (Al) toxicity by elevated pH remains to be clarified. For the first time, a targeted metabolome was applied to identify Al-pH-interaction-responsive hormones and ECMs in Citrus sinensis leaves. More Al-toxicity-responsive hormones and ECMs were identified at pH 4.0 [4 (10) upregulated and 7 (17) downregulated hormones (ECMs)] than those at pH 3.0 [1 (9) upregulated and 4 (14) downregulated hormones (ECMs)], suggesting that the elevated pH improved the adaptation of hormones and ECMs to Al toxicity in leaves. The roles of hormones and ECMs in reducing leaf Al toxicity mediated by elevated pH might include the following aspects: (a) improved leaf growth by upregulating the levels of jasmonoyl-L-isoleucine (JA-ILE), 6-benzyladenosine (BAPR), N6-isopentenyladenosine (IPR), cis-zeatin-O-glucoside riboside (cZROG), and auxins (AUXs), preventing Al toxicity-induced reduction of gibberellin (GA) biosynthesis, and avoiding jasmonic acid (JA)-mediated defense; (b) enhanced biosynthesis and accumulation of tryptophan (TRP), as well as the resulting increase in biosynthesis of auxin, melatonin and secondary metabolites (SMs); (c) improved ability to maintain the homeostasis of ATP and other phosphorus (P)-containing ECMs; and (d) enhanced internal detoxification of Al due to increased organic acid (OA) and SM accumulation and elevated ability to detoxify reactive oxygen species (ROS) due to enhanced SM accumulation. To conclude, the current results corroborate the hypotheses that elevated pH reduces Al toxicity by upregulating the ability to maintain the homeostasis of ATP and other P-containing ECMs in leaves under Al toxicity and (b) hormones participate in the elevated pH-mediated alleviation of Al toxicity by positively regulating growth, the ability to detoxify ROS, and the internal detoxification of Al in leaves under Al toxicity. Our findings provide novel insights into the roles of hormones and ECMs in mitigating Al toxicity mediated by the elevated pH.

Identification and Analysis of Aluminum-Activated Malate Transporter Gene Family Reveals Functional Diversification in Orchidaceae and the Expression Patterns of Dendrobium catenatum Aluminum-Activated Malate Transporters

Aluminum-activated malate transporter (ALMT) genes play an important role in aluminum ion (Al3+) tolerance, fruit acidity, and stomatal movement. Although decades of research have been carried out in many plants, there is little knowledge about the roles of ALMT in Orchidaceae. In this study, 34 ALMT genes were identified in the genomes of four orchid species. Specifically, ten ALMT genes were found in Dendrobium chrysotoxum and D. catenatum, and seven were found in Apostasia shenzhenica and Phalaenopsis equestris. These ALMT genes were further categorized into four clades (clades 1-4) based on phylogenetic relationships. Sequence alignment and conserved motif analysis revealed that most orchid ALMT proteins contain conserved regions (TM1, GABA binding motif, and WEP motif). We also discovered a unique motif (19) belonging to clade 1, which can serve as a specifically identified characteristic. Comparison with the gene structure of AtALMT genes (Arabidopsis thaliana) showed that the gene structure of ALMT was conserved across species, but the introns were longer in orchids. The promoters of orchid ALMT genes contain many light-responsive and hormone-responsive elements, suggesting that their expression may be regulated by light and phytohormones. Chromosomal localization and collinear analysis of D. chrysotoxum indicated that tandem duplication (TD) is the main reason for the difference in the number of ALMT genes in these orchids. D. catenatum was chosen for the RT-qPCR experiment, and the results showed that the DcaALMT gene expression pattern varied in different tissues. The expression of DcaALMT1-9 was significantly changed after ABA treatment. Combining the circadian CO2 uptake rate, titratable total acid, and RT-qPCR data analysis, most DcaALMT genes were highly expressed at night and around dawn. The result revealed that DcaALMT genes might be involved in photosynthate accumulation. The above study provides more comprehensive information for the ALMT gene family in Orchidaceae and a basis for subsequent functional analysis.

Phosphorus-induced restructuring of the ascorbate-glutathione cycle and lignin biosynthesis alleviates manganese toxicity in peach roots

Manganese (Mn) is indispensable for plant growth, but its excessive uptake in acidic soils leads to toxicity, hampering food safety. Phosphorus (P) application is known to mitigate Mn toxicity, yet the underlying molecular mechanism remains elusive. Here, we conducted physiological and transcriptomic analyses of peach roots response to P supply under Mn toxicity. Manganese treatment disrupted root architecture and caused ultrastructural damage due to oxidative injury. Notably, P application ameliorated the detrimental effects and improved the damaged roots by preventing the shrinkage of cortical cells, epidermis and endodermis, as well as reducing the accumulation of reactive oxygen species (ROS). Transcriptomic analysis revealed the differentially expressed genes enriched in phenylpropanoid biosynthesis, cysteine, methionine and glutathione metabolism under Mn and P treatments. Phosphorus application upregulated the transcripts and activities of core enzymes crucial for lignin biosynthesis, enhancing cell wall integrity. Furthermore, P treatment activated ascorbate-glutathione cycle, augmenting ROS detoxification. Additionally, under Mn toxicity, P application downregulated Mn uptake transporter while enhancing vacuolar sequestration transporter transcripts, reducing Mn uptake and facilitating vacuolar storage. Collectively, P application prevents Mn accumulation in roots by modulating Mn transporters, bolstering lignin biosynthesis and attenuating oxidative stress, thereby improving root growth under Mn toxicity. Our findings provide novel insights into the mechanism of P-mediated alleviation of Mn stress and strategies for managing metal toxicity in peach orchards.

The Role of Low-Molecular-Weight Organic Acids in Metal Homeostasis in Plants

Low-molecular-weight organic acids (LMWOAs) are essential O-containing metal-binding ligands involved in maintaining metal homeostasis, various metabolic processes, and plant responses to biotic and abiotic stress. Malate, citrate, and oxalate play a crucial role in metal detoxification and transport throughout the plant. This review provides a comparative analysis of the accumulation of LMWOAs in excluders, which store metals mainly in roots, and hyperaccumulators, which accumulate metals mainly in shoots. Modern concepts of the mechanisms of LMWOA secretion by the roots of excluders and hyperaccumulators are summarized, and the formation of various metal complexes with LMWOAs in the vacuole and conducting tissues, playing an important role in the mechanisms of metal detoxification and transport, is discussed. Molecular mechanisms of transport of LMWOAs and their complexes with metals across cell membranes are reviewed. It is discussed whether different endogenous levels of LMWOAs in plants determine their metal tolerance. While playing an important role in maintaining metal homeostasis, LMWOAs apparently make a minor contribution to the mechanisms of metal hyperaccumulation, which is associated mainly with root exudates increasing metal bioavailability and enhanced xylem loading of LMWOAs. The studies of metal-binding compounds may also contribute to the development of approaches used in biofortification, phytoremediation, and phytomining.

Diverse factors influence the amounts of carbon input to soils via rhizodeposition in plants: A review

Rhizodeposition encompasses the intricate processes through which plants generate organic compounds via photosynthesis, store these compounds within aboveground biomass and roots through top-down transport, and subsequently release this organic matter into the soil. Rhizodeposition represents one of the carbon (C) cycle in soils that can achieve long-term organic C sequestration. This function holds significant implications for mitigating the climate change that partly stems from the greenhouse effect associated with increased atmospheric carbon dioxide levels. Therefore, it is essential to further understand how the process of rhizodeposition allocates the photosynthetic C that plants create via photosynthesis. While many studies have explored the basic principles of rhizodeposition, along with the associated impact on soil C storage, there is a palpable absence of comprehensive reviews that summarize the various factors influencing this process. This paper compiles and analyzes the literature on plant rhizodeposition to describe how rhizodeposition influences soil C storage. Moreover, the review summarizes the impacts of soil physicochemical, microbial, and environmental characteristics on plant rhizodeposition and priming effects, and concludes with recommendations for future research.

Genome-wide identification of MATE and ALMT genes and their expression profiling in mungbean (Vigna radiata L.) under aluminium stress

The Multidrug and toxic compound extrusion (MATE) and aluminium activated malate transporter (ALMT) gene families are involved in response to aluminium (Al) stress. In this study, we identified 48 MATE and 14 ALMT gene families in Vigna radiata genome and classified into 5 (MATE) and 3 (ALMT) clades by phylogenetic analysis. All the VrMATE and VrALMT genes were distributed across mungbean chromosomes. Tandem duplication was the main driving force for evolution and expansion of MATE gene family. Collinearity of mungbean with soybean indicated that MATE gene family is closely linked to Glycine max. Eight MATE transporters in clade 2 were found to be associated with previously characterized Al tolerance related MATEs in various plant species. Citrate exuding motif (CEM) was present in seven VrMATEs of clade 2. Promoter analysis revealed abundant plant hormone and stress responsive cis-elements. Results from quantitative real time-polymerase chain reaction (qRT-PCR) revealed that VrMATE19, VrMATE30 and VrALMT13 genes were markedly up-regulated at different time points under Al stress. Overall, this study offers a new direction for further molecular characterization of the MATE and ALMT genes in mungbean for Al tolerance.

Investigating the involvement of potato (Solanum tuberosum L.) StPHR1 gene in the combined stress response to phosphorus deficiency and aluminum toxicity

Phosphorus deficiency and aluminum toxicity in acidic soils are important factors that limit crop yield. To further explore this issue, we identified 18 members of the StPHR gene family in the potato genome in this study. Through bioinformatics analysis, we found that the StPHR1 gene, an important member of this family, exhibited high expression levels in potato roots, particularly under conditions of phosphorus deficiency and aluminum toxicity stress. This suggested that the StPHR1 gene may play a crucial regulatory role in potato's resistance to phosphorus deficiency and aluminum toxicity. To validate this hypothesis, we conducted a series of experiments on the StPHR1 gene, including subcellular localization, GUS staining for tissue expression, heterologous overexpression, yeast two-hybrid hybridization, and bimolecular fluorescence complementation (BiFC). The results demonstrated that the StPHR1 gene is highly conserved in plants and is localized in the nucleus of potato cells. The heterologous overexpression of the gene in Arabidopsis plants resulted in a growth phenotype that exhibited resistance to both aluminum toxicity and phosphorus deficiency. Moreover, the heterologous overexpressing plants showed reduced aluminum content in the root system compared to the control group. Furthermore, we also identified an interaction between StPHR1 and StALMT6. These results highlight the potential application of regulating the expression of the StPHR1 gene in potato production to enhance its adaptation to the dual stress of phosphorus deficiency and high aluminum toxicity in acidic soils.

AcEXPA1, an α-expansin gene, participates in the aluminum tolerance of carpetgrass (Axonopus compressus) through root growth regulation

KEY MESSAGE

AcEXPA1, an aluminum (Al)-inducible expansin gene, is demonstrated to be involved in carpetgrass (Axonopus compressus) root elongation under Al toxicity through analyzing composite carpetgrass plants overexpressing AcEXPA1. Aluminum (Al) toxicity is a major mineral toxicity that limits plant productivity in acidic soils by inhibiting root growth. Carpetgrass (Axonopus compressus), a dominant warm-season turfgrass widely grown in acidic tropical soils, exhibits superior adaptability to Al toxicity. However, the mechanisms underlying its Al tolerance are largely unclear, and knowledge of the functional genes involved in Al detoxification in this turfgrass is limited. In this study, phenotypic variation in Al tolerance, as indicated by relative root elongation, was observed among seventeen carpetgrass genotypes. Al-responsive genes related to cell wall modification were identified in the roots of the Al-tolerant genotype 'A58' via transcriptome analysis. Among them, a gene encoding α-expansin was cloned and designated AcEXPA1 for functional characterization. Observed Al dose effects and temporal responses revealed that Al induced AcEXPA1 expression in carpetgrass roots. Subsequently, an efficient and convenient Agrobacterium rhizogenes-mediated transformation method was established to generate composite carpetgrass plants with transgenic hairy roots for investigating AcEXPA1 involvement in carpetgrass root growth under Al toxicity. AcEXPA1 was successfully overexpressed in the transgenic hairy roots, and AcEXPA1 overexpression enhanced Al tolerance in composite carpetgrass plants through a decrease in Al-induced root growth inhibition. Taken together, these findings suggest that AcEXPA1 contributes to Al tolerance in carpetgrass via root growth regulation.

Genome-wide characterization, transcriptome profiling, and functional analysis of the ALMT gene family in Medicago for aluminum resistance

Aluminum (Al) is the major limiting factor affecting plant productivity in acidic soils. Al3+ ions exhibit increased solubility at a pH below 5, leading to plant root tip toxicity. Alternatively, plants can perceive very low concentrations of Al3+, and Al triggers downstream signaling even at pH 5.7 without causing Al toxicity. The ALUMINUM-ACTIVATED-MALATE-TRANSPORTER (ALMT) family members act as anion channels, with some regulating the secretion of malate from root apices to chelate Al, which is a crucial mechanism for plant Al resistance. To date, the role of the ALMT gene family within the legume Medicago species has not been fully characterized. In this study, we investigated the ALMT gene family in M. sativa and M. truncatula and identified 68 MsALMTs and 18 MtALMTs, respectively. Phylogenetic analysis classified these genes into five clades, and synteny analysis uncovered genuine paralogs and orthologs. The real-time quantitative reverse transcription PCR (qRT-PCR) analysis revealed that MtALMT8, MtALMT9, and MtALMT15 in clade 2-2b are expressed in both roots and root nodules, and MtALMT8 and MtALMT9 are significantly upregulated by Al in root tips. We also observed that MtALMT8 and MtALMT9 can partially restore the Al sensitivity of Atalmt1 in Arabidopsis. Moreover, transcriptome analysis examined the expression patterns of these genes in M. sativa in response to Al at both pH 5.7 and pH 4.6, as well as to protons, and found that Al and protons can independently induce some Al-resistance genes. Overall, our findings indicate that MtALMT8 and MtALMT9 may play a role in Al resistance, and highlight the resemblance between the ALMT genes in Medicago species and those in Arabidopsis.

Aluminium tolerance and stomata operation: Towards optimising crop performance in acid soil

Stomatal operation is crucial for optimising plant water and gas exchange and represents a major trait conferring abiotic stress tolerance in plants. About 56% of agricultural land around the globe is classified as acidic, and Al toxicity is a major limiting factor affecting plant performance in such soils. While most of the research work in the field discusses the impact of major abiotic stresses such as drought or salinity on stomatal operation, the impact of toxic metals and, specifically aluminium (Al) on stomatal operation receives much less attention. We aim to fill this knowledge gap by summarizing the current knowledge of the adverse effects of acid soils on plant stomatal development and operation. We summarised the knowledge of stomatal responses to both long-term and transient Al exposure, explored molecular mechanisms underlying plant adaptations to Al toxicity, and elucidated regulatory networks that alleviate Al toxicity. It is shown that Al-induced stomatal closure involves regulations of core stomatal signalling components, such as ROS, NO, and CO2 and key elements of ABA signalling. We also discuss possible targets and pathway to modify stomatal operation in plants grown in acid soils thus reducing the impact of Al toxicity on plant growth and yield.

Molecular and phylogenetic evidence of parallel expansion of anion channels in plants

Aluminum-activated malate transporters (ALMTs) and slow anion channels (SLACs) are important in various physiological processes in plants, including stomatal regulation, nutrient uptake, and in response to abiotic stress such as aluminum toxicity. To understand their evolutionary history and functional divergence, we conducted phylogenetic and expression analyses of ALMTs and SLACs in green plants. Our findings from phylogenetic studies indicate that ALMTs and SLACs may have originated from green algae and red algae, respectively. The ALMTs of early land plants and charophytes formed a monophyletic clade consisting of three subgroups. A single duplication event of ALMTs was identified in vascular plants and subsequent duplications into six clades occurred in angiosperms, including an identified clade, 1-1. The ALMTs experienced gene number losses in clades 1-1 and 2-1 and expansions in clades 1-2 and 2-2b. Interestingly, the expansion of clade 1-2 was also associated with higher expression levels compared to genes in clades that experienced apparent loss. SLACs first diversified in bryophytes, followed by duplication in vascular plants, giving rise to three distinct clades (I, II, and III), and clade II potentially associated with stomatal control in seed plants. SLACs show losses in clades II and III without substantial expansion in clade I. Additionally, ALMT clade 2-2 and SLAC clade III contain genes specifically expressed in reproductive organs and roots in angiosperms, lycophytes, and mosses, indicating neofunctionalization. In summary, our study demonstrates the evolutionary complexity of ALMTs and SLACs, highlighting their crucial role in the adaptation and diversification of vascular plants.

Characterization of SgALMT genes reveals the function of SgALMT2 in conferring aluminum tolerance in Stylosanthes guianensis through the mediation of malate exudation

Aluminum (Al) toxicity is the major constraint on plant growth and productivity in acidic soils. An adaptive mechanism to enhance Al tolerance in plants is mediated malate exudation from roots through the involvement of ALMT (Al-activated malate transporter) channels. The underlying Al tolerance mechanisms of stylo (Stylosanthes guianensis), an important tropical legume that exhibits superior Al tolerance, remain largely unknown, and knowledge of the potential contribution of ALMT genes to Al detoxification in stylo is limited. In this study, stylo root growth was inhibited by Al toxicity, accompanied by increases in malate and citrate exudation from roots. A total of 11 ALMT genes were subsequently identified in the stylo genome and named SgALMT1 to SgALMT11. Diverse responses to metal stresses were observed for these SgALMT genes in stylo roots. Among them, the expressions of 6 out of the 11 SgALMTs were upregulated by Al toxicity. SgALMT2, a root-specific and Al-activated gene, was selected for functional characterization. Subcellular localization analysis revealed that the SgALMT2 protein is localized to the plasma membrane. The function of SgALMT2 in mediating malate release was confirmed by analysis of the malate exudation rate from transgenic composite stylo plants overexpressing SgALMT2. Furthermore, overexpression of SgALMT2 led to increased root growth in transgenic stylo plants treated with Al through decreased Al accumulation in roots. Taken together, the results of this study suggest that malate secretion mediated by SgALMT2 contributes to the ability of stylo to cope with Al toxicity.

Harnessing root exudates for plant microbiome engineering and stress resistance in plants

A wide range of abiotic and biotic stresses adversely affect plant's growth and production. Under stress, one of the main responses of plants is the modulation of exudates excreted in the rhizosphere, which consequently leads to alterations in the resident microbiota. Thus, the exudates discharged into the rhizospheric environment play a preponderant role in the association and formation of plant-microbe interactions. In this review, we aimed to provide a synthesis of the latest and most pertinent literature on the diverse biochemical and structural compositions of plant root exudates. Also, this work investigates into their multifaceted role in microbial nutrition and intricate signaling processes within the rhizosphere, which includes quorum-sensing molecules. Specifically, it explores the contributions of low molecular weight compounds, such as carbohydrates, phenolics, organic acids, amino acids, and secondary metabolites, as well as the significance of high molecular weight compounds, including proteins and polysaccharides. It also discusses the state-of-the-art omics strategies that unveil the vital role of root exudates in plant-microbiome interactions, including defense against pathogens like nematodes and fungi. We propose multiple challenges and perspectives, including exploiting plant root exudates for host-mediated microbiome engineering. In this discourse, root exudates and their derived interactions with the rhizospheric microbiota should receive greater attention due to their positive influence on plant health and stress mitigation.

Unregulated GmAGL82 due to Phosphorus Deficiency Positively Regulates Root Nodule Growth in Soybean

Nitrogen fixation, occurring through the symbiotic relationship between legumes and rhizobia in root nodules, is crucial in sustainable agriculture. Nodulation and soybean production are influenced by low levels of phosphorus stress. In this study, we discovered a MADS transcription factor, GmAGL82, which is preferentially expressed in nodules and displays significantly increased expression under conditions of phosphate (Pi) deficiency. The overexpression of GmAGL82 in composite transgenic plants resulted in an increased number of nodules, higher fresh weight, and enhanced soluble Pi concentration, which subsequently increased the nitrogen content, phosphorus content, and overall growth of soybean plants. Additionally, transcriptome analysis revealed that the overexpression of GmAGL82 significantly upregulated the expression of genes associated with nodule growth, such as GmENOD100, GmHSP17.1, GmHSP17.9, GmSPX5, and GmPIN9d. Based on these findings, we concluded that GmAGL82 likely participates in the phosphorus signaling pathway and positively regulates nodulation in soybeans. The findings of this research may lay the theoretical groundwork for further studies and candidate gene resources for the genetic improvement of nutrient-efficient soybean varieties in acidic soils.

PlantPAN 4.0: updated database for identifying conserved non-coding sequences and exploring dynamic transcriptional regulation in plant promoters

PlantPAN 4.0 (http://PlantPAN.itps.ncku.edu.tw/) is an integrative resource for constructing transcriptional regulatory networks for diverse plant species. In this release, the gene annotation and promoter sequences were expanded to cover 115 species. PlantPAN 4.0 can help users characterize the evolutionary differences and similarities among cis-regulatory elements; furthermore, this system can now help in identification of conserved non-coding sequences among homologous genes. The updated transcription factor binding site repository contains 3428 nonredundant matrices for 18305 transcription factors; this expansion helps in exploration of combinational and nucleotide variants of cis-regulatory elements in conserved non-coding sequences. Additionally, the genomic landscapes of regulatory factors were manually updated, and ChIP-seq data sets derived from a single-cell green alga (Chlamydomonas reinhardtii) were added. Furthermore, the statistical review and graphical analysis components were improved to offer intelligible information through ChIP-seq data analysis. These improvements included easy-to-read experimental condition clusters, searchable gene-centered interfaces for the identification of promoter regions' binding preferences by considering experimental condition clusters and peak visualization for all regulatory factors, and the 20 most significantly enriched gene ontology functions for regulatory factors. Thus, PlantPAN 4.0 can effectively reconstruct gene regulatory networks and help compare genomic cis-regulatory elements across plant species and experiments.

A citrate efflux transporter important for manganese distribution and phosphorus uptake in rice

The plant citrate transporters, functional in mineral nutrient uptake and homeostasis, usually belong to the multidrug and toxic compound extrusion transporter family. We identified and functionally characterized a rice (Oryza sativa) citrate transporter, OsCT1, which differs from known plant citrate transporters and is structurally close to rice silicon transporters. Domain analysis depicted that OsCT1 carries a bacterial citrate-metal transporter domain, CitMHS. OsCT1 showed citrate efflux activity when expressed in Xenopus laevis oocytes and is localized to the cell plasma membrane. It is highly expressed in the shoot and reproductive tissues of rice, and its promoter activity was visible in cells surrounding the vasculature. The OsCT1 knockout (KO) lines showed a reduced citrate content in the shoots and the root exudates, whereas overexpression (OE) line showed higher citrate exudation from their roots. Further, the KO and OE lines showed variations in the manganese (Mn) distribution leading to changes in their agronomical traits. Under deficient conditions (Mn-sufficient conditions followed by 8 days of 0 μm MnCl2  · 4H2 O treatment), the supply of manganese towards the newer leaf was found to be obstructed in the KO line. There were no significant differences in phosphorus (P) distribution; however, P uptake was reduced in the KO and increased in OE lines at the vegetative stage. Further, experiments in Xenopus oocytes revealed that OsCT1 could efflux citrate with Mn. In this way, we provide insights into a mechanism of citrate-metal transport in plants and its role in mineral homeostasis, which remains conserved with their bacterial counterparts.

Proteomic response to phosphorus deficiency and aluminum stress of three aluminum-tolerant phosphobacteria isolated from acidic soils

Aluminum (Al)-tolerant phosphobacteria enhance plant growth in acidic soils by improving Al complexing and phosphorus (P) availability. However, the impact of Al stress and P deficiency on bacterial biochemistry and physiology remains unclear. We investigated the single and mutual effects of Al stress (10 mM) and P deficiency (0.05 mM) on the proteome of three aluminum-tolerant phosphobacteria: Enterobacter sp. 198, Enterobacter sp. RJAL6, and Klebsiella sp. RCJ4. Cultivated under varying conditions, P deficiency upregulated P metabolism proteins while Al exposure downregulated iron-sulfur and heme-containing proteins and upregulated iron acquisition proteins. This demonstrated that Al influence on iron homeostasis and bacterial central metabolism. This study offers crucial insights into bacterial behavior in acidic soils, benefiting the development of bioinoculants for crops facing Al toxicity and P deficiency. This investigation marks the first proteomic study on the interaction between high Al and P deficiency in acid soils-adapted bacteria.

Harnessing the power of exogenous factors to enhance plant resistance to aluminum toxicity; a critical review

Aluminum (Al) is the most prevalent element in the earth crust and is toxic to plants in acidic soils. However, plants can address Al toxicity through external exclusion (which prevents Al from entering roots) and internal detoxification (which counterbalances the toxic-Al absorbed by roots). Nowadays, certain categories of exogenously added regulatory factors (EARF), such as nutritional elements, organic acids, amino acids, phytohormones, or biochar, etc. play a critical role in reducing the bioavailability/toxicity of Al in plants. Numerous studies suggest that regulating factors against Al toxicity mediate the expression of Al-responsive genes and transcription factors, thereby regulating the secretion of organic acids, alkalizing rhizosphere pH, modulating cell wall (CW) modifications, improving antioxidant defense systems, and promoting the compartmentalization of non-toxic Al within intracellular. This review primarily discusses recent and older published papers to demonstrate the basic concepts of Al phytotoxicity. Furthermore, we provide a comprehensive explanation of the crucial roles of EARF-induced responses against Al toxicity in plants. This information may serve as a foundation for improving plant resistance to Al and enhancing the growth of susceptible species in acidic soils. And this review holds significant theoretical significance for EARF to improve the quality of acidic soils cultivated land, increase crop yield and quality, and ensure food security.

Recent Updates on ALMT Transporters' Physiology, Regulation, and Molecular Evolution in Plants

Aluminium toxicity and phosphorus deficiency in soils are the main interconnected problems of modern agriculture. The aluminium-activated malate transporters (ALMTs) comprise a membrane protein family that demonstrates various physiological functions in plants, such as tolerance to environmental Al3+ and the regulation of stomatal movement. Over the past few decades, the regulation of ALMT family proteins has been intensively studied. In this review, we summarise the current knowledge about this transporter family and assess their involvement in diverse physiological processes and comprehensive regulatory mechanisms. Furthermore, we have conducted a thorough bioinformatic analysis to decipher the functional importance of conserved residues, structural components, and domains. Our phylogenetic analysis has also provided new insights into the molecular evolution of ALMT family proteins, expanding their scope beyond the plant kingdom. Lastly, we have formulated several outstanding questions and research directions to further enhance our understanding of the fundamental role of ALMT proteins and to assess their physiological functions.

Pan-transcriptomic Profiling Demarcates Serendipita Indica-Phosphorus Mediated Tolerance Mechanisms in Rice Exposed to Arsenic Toxicity

Inadvertent accumulation of arsenic (As) in rice (Oryza sativa L.) is a concern for people depending on it for their subsistence, as it verily causes epigenetic alterations across the genome as well as in specific cells. To ensure food safety, certain attempts have been made to nullify this highest health hazard encompassing physiological, chemical and biological methods. Albeit, the use of mycorrhizal association along with nutrient reinforcement strategy has not been explored yet. Mechanisms of response and resistance of two rice genotypes to As with or without phosphorus (P) nutrition and Serendipita indica (S. indica; S.i) colonization were explored by root transcriptome profiling in the present study. Results revealed that the resistant genotype had higher auxin content and root plasticity, which helped in keeping the As accumulation and P starvation response to a minimum under alone As stress. However, sufficient P supply and symbiotic relationship switched the energy resources towards plant's developmental aspects rather than excessive root proliferation. Higher As accumulating genotype (GD-6) displayed upregulation of ethylene signaling/biosynthesis, root stunting and senescence related genes under As toxicity. Antioxidant defense system and cytokinin biosynthesis/signaling of both genotypes were strengthened under As + S.i + P, while the upregulation of potassium (K) and zinc (Zn) transporters depicted underlying cross-talk with iron (Fe) and P. Differential expression of phosphate transporters, peroxidases and GSTs, metal detoxification/transport proteins, as well as phytohormonal metabolism were responsible for As detoxification. Taken together, S. indica symbiosis fortified with adequate P-fertilizer can prove to be effective in minimizing As acquisition and accumulation in rice plants.

PP2C.D phosphatase SAL1 positively regulates aluminum resistance via restriction of aluminum uptake in rice

Aluminum (Al) toxicity represents a primary constraint for crop production in acidic soils. Rice (Oryza sativa) is a highly Al-resistant species; however, the molecular mechanisms underlying its high Al resistance are still not fully understood. Here, we identified SAL1 (SENSITIVE TO ALUMINUM 1), which encodes a plasma membrane (PM)-localized PP2C.D phosphatase, as a crucial regulator of Al resistance using a forward genetic screen. SAL1 was found to interact with and inhibit the activity of PM H+-ATPases, and mutation of SAL1 increased PM H+-ATPase activity and Al uptake, causing hypersensitivity to internal Al toxicity. Furthermore, knockout of NRAT1 (NRAMP ALUMINUM TRANSPORTER 1) encoding an Al uptake transporter in a sal1 background rescued the Al-sensitive phenotype of sal1, revealing that coordination of Al accumulation in the cell, wall and symplasm is critical for Al resistance in rice. By contrast, we found that mutations of PP2C.D phosphatase-encoding genes in Arabidopsis (Arabidopsis thaliana) enhanced Al resistance, which was attributed to increased malate secretion. Our results reveal the importance of PP2C.D phosphatases in Al resistance and the different strategies used by rice and Arabidopsis to defend against Al toxicity.

An Oxalate Transporter Gene, AtOT, Enhances Aluminum Tolerance in Arabidopsis thaliana by Regulating Oxalate Efflux

Secretion and efflux of oxalic acid from roots is an important aluminum detoxification mechanism for various plants; however, how this process is completed remains unclear. In this study, the candidate oxalate transporter gene AtOT, encoding 287 amino acids, was cloned and identified from Arabidopsis thaliana. AtOT was upregulated in response to aluminum stress at the transcriptional level, which was closely related to aluminum treatment concentration and time. The root growth of Arabidopsis was inhibited after knocking out AtOT, and this effect was amplified by aluminum stress. Yeast cells expressing AtOT enhanced oxalic acid resistance and aluminum tolerance, which was closely correlated with the secretion of oxalic acid by membrane vesicle transport. Collectively, these results underline an external exclusion mechanism of oxalate involving AtOT to enhance oxalic acid resistance and aluminum tolerance.

Aluminum in plant: Benefits, toxicity and tolerance mechanisms

Aluminum (Al) is the third most ubiquitous metal in the earth's crust. A decrease in soil pH below 5 increases its solubility and availability. However, its impact on plants depends largely on concentration, exposure time, plant species, developmental age, and growing conditions. Although Al can be beneficial to plants by stimulating growth and mitigating biotic and abiotic stresses, it remains unknown how Al mediates these effects since its biological significance in cellular systems is still unidentified. Al is considered a major limiting factor restricting plant growth and productivity in acidic soils. It instigates a series of phytotoxic symptoms in several Al-sensitive crops with inhibition of root growth and restriction of water and nutrient uptake as the obvious symptoms. This review explores advances in Al benefits, toxicity and tolerance mechanisms employed by plants on acidic soils. These insights will provide directions and future prospects for potential crop improvement.

Comparative Transcriptome Analysis Reveals Complex Physiological Response and Gene Regulation in Peanut Roots and Leaves under Manganese Toxicity Stress

Excess Manganese (Mn) is toxic to plants and reduces crop production. Although physiological and molecular pathways may drive plant responses to Mn toxicity, few studies have evaluated Mn tolerance capacity in roots and leaves. As a result, the processes behind Mn tolerance in various plant tissue or organ are unclear. The reactivity of peanut (Arachis hypogaea) to Mn toxicity stress was examined in this study. Mn oxidation spots developed on peanut leaves, and the root growth was inhibited under Mn toxicity stress. The physiological results revealed that under Mn toxicity stress, the activities of antioxidases and the content of proline in roots and leaves were greatly elevated, whereas the content of soluble protein decreased. In addition, manganese and iron ion content in roots and leaves increased significantly, but magnesium ion content decreased drastically. The differentially expressed genes (DEGs) in peanut roots and leaves in response to Mn toxicity were subsequently identified using genome-wide transcriptome analysis. Transcriptomic profiling results showed that 731 and 4589 DEGs were discovered individually in roots and leaves, respectively. Furthermore, only 310 DEGs were frequently adjusted and controlled in peanut roots and leaves, indicating peanut roots and leaves exhibited various toxicity responses to Mn. The results of qRT-PCR suggested that the gene expression of many DEGs in roots and leaves was inconsistent, indicating a more complex regulation of DEGs. Therefore, different regulatory mechanisms are present in peanut roots and leaves in response to Mn toxicity stress. The findings of this study can serve as a starting point for further research into the molecular mechanism of important functional genes in peanut roots and leaves that regulate peanut tolerance to Mn poisoning.

Aluminum stress signaling, response, and adaptive mechanisms in plants

Over 40% of arable land in the world is acidic. Al stress has become a global agricultural problem affecting plant growth and limiting crop production in acidic soils. Plants have evolved different regulatory mechanisms of adaptation to exogenous environmental challenges, such as Al stress, by altering their growth patterns. In the past decades, several key genes involved in plant response to Al stress and the mechanism of Al detoxification have been revealed. However, the signaling pathways of plant response to Al stress and the regulatory mechanism of plant Al tolerance remain poorly understood. In this review, we summarized the findings of recent studies on the plant Al tolerance mechanism and the molecular regulation mechanism of phytohormones in response to Al stress. This review improves our understanding of the regulatory mechanisms of plants in response to Al stress and provides a reference for the breeding of Al-tolerant crops.

Finger millet RNA-seq reveals differential gene expression associated with tolerance to aluminum toxicity and provides novel genomic resources

Eleusine coracana, finger millet, is a multipurpose crop cultivated in arid and semi-arid regions of Africa and Asia. RNA sequencing (RNA-seq) was used in this study to obtain valuable genomic resources and identify genes differentially expressed between Al-tolerant and Al-susceptible genotypes. Two groups of finger millet genotypes were used: Al-tolerant (215836, 215845, and 229722) and Al-susceptible (212462, 215804 and 238323). The analysis of the RNA-seq data resulted in 198,546 unigenes, 56.5% of which were annotated with significant hits in one or more of the following six databases: NR (48.8%), GO (29.7%), KEGG (45%), PlantTFDB (19.0%), Uniprot (49.2%), and NT (46.2%). It is noteworthy that only 220 unigenes in the NR database had significant hits against finger millet sequences suggesting that finger millet's genomic resources are scarce. The gene expression analysis revealed that 322 genes were significantly differentially expressed between the Al-tolerant and Al-susceptible genotypes, of which 40.7% were upregulated while 59.3% were downregulated in Al-tolerant genotypes. Among the significant DEGs, 54.7% were annotated in the GO database with the top hits being ATP binding (GO:0005524) and DNA binding (GO:0003677) in the molecular function, DNA integration (GO:0015074) and cell redox homeostasis in the biological process, as well as cellular anatomical entity and intracellular component in the cellular component GO classes. Several of the annotated DEGs were significantly enriched for their corresponding GO terms. The KEGG pathway analysis resulted in 60 DEGs that were annotated with different pathway classes, of which carbohydrate metabolism and signal transduction were the most prominent. The homologs of a number of significant DEGs have been previously reported as being associated with Al or other abiotic stress responses in various crops, including carboxypeptidase SOL1, HMA3, AP2, bZIP, C3H, and WRKY TF genes. A more detailed investigation of these and other DEGs will enable genomic-led breeding for Al tolerance in finger millet. RNA-seq data analysis also yielded 119,073 SNP markers, the majority of which had PIC values above 0.3, indicating that they are highly informative. Additionally, 3,553 single-copy SSR markers were identified, of which trinucleotide SSRs were the most prevalent. These genomic resources contribute substantially to the enrichment of genomic databases for finger millet, and facilitate future research on this crop.

Cloning, Expression Analysis, and Functional Characterization of Candidate Oxalate Transporter Genes of HbOT1 and HbOT2 from Rubber Tree (Hevea brasiliensis)

Secretion of oxalic acid from roots is an important aluminum detoxification mechanism for many plants such as Hevea brasiliensis (rubber tree). However, the underlying molecular mechanism and oxalate transporter genes in plants have not yet been reported. In this study, the oxalate transporter candidate genes HbOT1 and HbOT2 from the rubber tree were cloned and preliminarily identified. It was found that HbOT1 had a full length of 1163 bp with CDS size of 792 bp, encoding 263 amino acids, and HbOT2 had a full length of 1647 bp with a CDS region length of 840 bp, encoding 279 amino acid residues. HbOT1 and HbOT2 were both stable hydrophobic proteins with transmembrane structure and SNARE_assoc domains, possibly belonging to the SNARE_assoc subfamily proteins of the SNARE superfamily. qRT-PCR assays revealed that HbOT1 and HbOT2 were constitutively expressed in different tissues, with HbOT1 highly expressed in roots, stems, barks, and latex, while HbOT2 was highly expressed in latex. In addition, the expressions of HbOT1 and HbOT2 were up-regulated in response to aluminum stress, and they were inducible by metals, such as copper and manganese. Heterologous expression of HbOT1 and HbOT2 in the yeast mutant AD12345678 enhanced the tolerance to oxalic acid and high concentration aluminum stress, which was closely correlated with the secretion of oxalic acid. This study is the first report on oxalate transporter genes in plants, which provides a theoretical reference for the study on the molecular mechanism of oxalic acid secretion to relieve aluminum toxicity and on aluminum-tolerance genetic engineering breeding.

Integrating transcriptomic and metabolomic analysis in roots of wild soybean seedlings in response to low-phosphorus stress

INTRODUCTION

Plants undergo divergent adaptations to form different ecotypes when exposed to different habitats. Ecotypes with ecological adaptation advantages are excellent germplasm resources for crop improvement.

METHODS

his study comprehensively compared the differences in morphology and physiological mechanisms in the roots of two different ecotypes of wild soybean (Glycine soja) seedlings under artificially simulated low-phosphorus (LP) stress.

RESULT

The seedlings of barren-tolerant wild soybean (GS2) suffered less damage than common wild soybean (GS1). GS2 absorbed more phosphorus (P) by increasing root length. In-depth integrated analyses of transcriptomics and metabolomics revealed the formation process of the ecological adaptability of the two different ecotypes wild soybean from the perspective of gene expression and metabolic changes. This study revealed the adaptation process of GS2 from the perspective of the adaptation of structural and molecular metabolism, mainly including: (1) Enhancing the metabolism of phenolic compounds, lignin, and organic acid metabolism could activate unavailable soil P; (2) Up-regulating genes encoding pectinesterase and phospholipase C (PLC) specifically could promote the reuse of structural P; (3) Some factors could reduce the oxidative damage to the membranes caused by LP stress, such as accumulating the metabolites putrescine and ascorbate significantly, up-regulating the genes encoding SQD2 (the key enzyme of sulfolipid substitution of phospholipids) substantially and enhancing the synthesis of secondary antioxidant metabolite anthocyanins and the AsA-GSH cycle; (4) enhancing the uptake of soil P by upregulating inorganic phosphate transporter, acid phosphatase ACP1, and purple acid phosphatase genes; (5) HSFA6b and MYB61 are the key TFs to resist LP stress.

DISCUSSION

In general, GS2 could resist LP stress by activating unavailable soil P, reusing plant structural P, rebuilding membrane lipids, and enhancing the antioxidant membrane protection system. Our study provides a new perspective for the study of divergent adaptation of plants.

Molecular response and evolution of plant anion transport systems to abiotic stress

We propose that anion channels are essential players for green plants to respond and adapt to the abiotic stresses associated changing climate via reviewing the literature and analyzing the molecular evolution, comparative genetic analysis, and bioinformatics analysis of the key anion channel gene families. Climate change-induced abiotic stresses including heatwave, elevated CO₂, drought, and flooding, had a major impact on plant growth in the last few decades. This scenario could lead to the exposure of plants to various stresses. Anion channels are confirmed as the key factors in plant stress responses, which exist in the green lineage plants. Numerous studies on anion channels have shed light on their protein structure, ion selectivity and permeability, gating characteristics, and regulatory mechanisms, but a great quantity of questions remain poorly understand. Here, we review function of plant anion channels in cell signaling to improve plant response to environmental stresses, focusing on climate change related abiotic stresses. We investigate the molecular response and evolution of plant slow anion channel, aluminum-activated malate transporter, chloride channel, voltage-dependent anion channel, and mechanosensitive-like anion channel in green plant. Furthermore, comparative genetic and bioinformatic analysis reveal the conservation of these anion channel gene families. We also discuss the tissue and stress specific expression, molecular regulation, and signaling transduction of those anion channels. We propose that anion channels are essential players for green plants to adapt in a diverse environment, calling for more fundamental and practical studies on those anion channels towards sustainable food production and ecosystem health in the future.

A zinc finger protein SlSZP1 protects SlSTOP1 from SlRAE1-mediated degradation to modulate aluminum resistance

In acidic soils, aluminum (Al) toxicity is the main factor inhibiting plant root development and reducing crops yield. STOP1 (SENSITIVE TO PROTON RHIZOTOXICITY 1) was a critical factor in detoxifying Al stress. Under Al stress, STOP1 expression was not induced, although STOP1 protein accumulated, even in the presence of RAE1 (STOP1 DEGRADATION E3-LIGASE). How the Al stress triggers and stabilises the accumulation of STOP1 is still unknown. Here, we characterised SlSTOP1-interacting zinc finger protein (SlSZP1) using a yeast-two-hybrid screening, and generated slstop1, slszp1 and slstop1/slszp1 knockout mutants using clustered regularly interspaced short palindromic repeats (CRISPR) in tomato. SlSZP1 is induced by Al stress but it is not regulated by SlSTOP1. The slstop1, slszp1 and slstop1/slszp1 knockout mutants exhibited hypersensitivity to Al stress. The expression of SlSTOP1-targeted genes, such as SlRAE1 and SlASR2 (ALUMINUM SENSITIVE), was inhibited in both slstop1 and slszp1 mutants, but not directly regulated by SlSZP1. Furthermore, the degradation of SlSTOP1 by SlRAE1 was prevented by SlSZP1. Al stress increased the accumulation of SlSTOP1 in wild-type (WT) but not in slszp1 mutants. The overexpression of either SlSTOP1 or SlSZP1 did not enhance plant Al resistance. Altogether, our results show that SlSZP1 is an important factor for protecting SlSTOP1 from SlRAE1-mediated degradation.

Rhizosheath: An adaptive root trait to improve plant tolerance to phosphorus and water deficits?

Drought and nutrient limitations adversely affect crop yields, with below-ground traits enhancing crop production in these resource-poor environments. This review explores the interacting biological, chemical and physical factors that determine rhizosheath (soil adhering to the root system) development, and its influence on plant water uptake and phosphorus acquisition in dry soils. Identification of quantitative trait loci for rhizosheath development indicate it is genetically determined, but the microbial community also directly (polysaccharide exudation) and indirectly (altered root hair development) affect its extent. Plants with longer and denser root hairs had greater rhizosheath development and increased P uptake efficiency. Moreover, enhanced rhizosheath formation maintains contact at the root-soil interface thereby assisting water uptake from drying soil, consequently improving plant survival in droughted environments. Nevertheless, it can be difficult to determine if rhizosheath development is a cause or consequence of improved plant adaptation to dry and nutrient-depleted soils. Does rhizosheath development directly enhance plant water and phosphorus use, or do other tolerance mechanisms allow plants to invest more resources in rhizosheath development? Much more work is required on the interacting genetic, physical, biochemical and microbial mechanisms that determine rhizosheath development, to demonstrate that selection for rhizosheath development is a viable crop improvement strategy.

Tolerance to soil acidity of soybean (Glycine max L.) genotypes under field conditions Southwestern Ethiopia

Soil acidity with associated low nutrient availability is one of the major constraints to soybean production in southwestern Ethiopia. Integrated use of lime and acid-tolerant crops is believed to reduce soil acidity and improve crop production. The experiment was conducted in the field condition of Mettu, southwestern Ethiopia during the 2017/18 main cropping season. The experiment comprised fifteen soybean genotypes and two soil amendment (lime and unlimed) treatments arranged in a split-plot design with three replications. For each treatment, four rows were planted per plot; data related to growth, root, nodule, and yield of the crop were collected at a necessary stage for each. Liming and genotype interaction had significantly (P = 0.01) affected all parameters considered except for hundred seed weight and root volume and were affected only by the main effects of genotypes and liming. A significant reduction for most parameters was found on lime-untreated soil than treated soil. Though some genotypes showed higher performance for root, growth parameters, and yield components under unlimed soils; however, gave higher yield and yield components, when grown on lime-untreated with an average yield reduction of 13.7%, due to soil acidity. The maximum grain yield of (1943.93 kg ha-1) was obtained under lime treated acid soil from PI567046A genotype; while the lowest (510.49 kg ha-1) were recorded from SCS-1genotype under the lime untreated acid soil. Genotype BRS268 showed higher yield (1319.83 kg ha-1) under lime untreated acid soil than lime treated acid soil (1143.47 kg ha-1) and showed less reduction percentage for a number of the nodules, root weight, and number of seeds per plant; while PI567046A showed high reduction percentage for yield, biomass, number of pod and seed per plant. A high difference was observed among the soybean genotypes for soil acidity tolerance, which might be further exploited by breeders for the genetic improvement of soybean. Genotype BRS268 had performed better than other tested genotypes under increased soil acidity. selection would be effective to improve soybean genotypes performance on acid soils and identify low Phosphorus tolerant genotype that helps smallholder farmers optimize soybean productivity on acid soils in the study area. HAWASSA-04 variety is the most tolerant among the tested materials. However, further study is required by considering additional genotypes to reach a conclusive recommendation

Multi-omics analysis of the regulatory effects of low-phosphorus stress on phosphorus transport in soybean roots

The regulatory effects of uneven phosphorus supplies on phosphorus transport in soybean roots are still unclear. To further analyze the regulatory effects of low-phosphorus stress on phosphorus transport in soybean roots and the effects of uneven phosphorus application on the physiological mechanism of phosphorus transport in soybean roots, dual-root soybean plants were prepared via grafting, and a sand culture experiment was performed. From the unfolded cotyledon stage to the initial flowering stage, one side of each dual-root soybean system was irrigated with a low-phosphorus-concentration solution (phosphorus-application [P+] side), and the other side was irrigated with a phosphorus-free nutrient solution (phosphorus-free [P-] side); this setup allowed the study of the effects of different phosphorus supply levels on the expression of genes and proteins and the accumulation of metabolites in soybean roots on the P- side to clarify the method through which phosphorus transport is regulated in soybean roots and to provide a theoretical basis for improving the use rate of phosphorus fertilizer. The results revealed that the unilateral supply of low-concentration phosphorus promoted the uptake of phosphorus by soybean roots and the transport of phosphorus from the P+ side to the P- side. Compared with the normal concentration of phosphorus supply and the phosphorus-free supply, the low concentration phosphorus supply affected the regulation of the metabolic pathways involved in starch and sucrose metabolism, glycolysis, fructose, and mannose metabolism, etc., thereby affecting soybean root phosphorus transport. The low-phosphorus stress inhibited fructose synthesis and sucrose synthase synthesis in the soybean roots and the synthesis of hexokinase (HK) and fructose kinase, which catalyzes the conversion of fructose to fructose-6-phosphate. Low-phosphorus stress promoted the synthesis of sucrose invertase and the conversion of sucrose into maltose by the activity of starch synthase (StS) and stimulated the synthesis of UDPG pyrophosphorylase (UGP) and phosphoglucose isomerase (GP1), which is involved in the conversion of UDP-glucose to glucose-6-phosphate. The phosphorus transport pathway of soybean roots was then affected, which promoted phosphorus allocation to UTP and glucose-6-phosphate. Additionally, low-phosphorus stress hastened glycolysis in the soybean roots and inhibited the synthesis of malic acid, thereby promoting the transport of phosphorus in the roots. In addition, low-phosphorus stress inhibited the synthesis of fructose, mannose, and mannose-1-phosphate and the synthesis of other enzymes involved in phosphorus transport as well as invertase, thereby inhibiting the transport and synthesis of several organic phosphorus-containing compounds.

Nitric Oxide Participates in Aluminum-Stress-Induced Pollen Tube Growth Inhibition in Tea (Camelliasinensis) by Regulating CsALMTs

Nitric oxide (NO), as a signal molecule, is involved in the mediation of heavy-metal-stress-induced physiological responses in plants. In this study, we investigated the effect of NO on Camellia sinensis pollen tubes exposed to aluminum (Al) stress. Exogenous application of the NO donor decreased the pollen germination rate and pollen tube length and increased the malondialdehyde (MDA) content and antioxidant enzyme activities under Al stress. Simultaneously, the NO donor effectively increased NO content in pollen tube of C. sinensis under Al stress and could aggravate the damage of Al³⁺ to C. sinensis pollen tubes by promoting the uptake of Al³⁺. In addition, application of the NO-specific scavenger significantly alleviated stress damage in C. sinensis pollen tube under Al stress. Moreover, 18 CsALMT members from a key Al-transporting gene family were identified, which could be divided into four subclasses. Pearson correlation analysis showed the expression level of CsALMT8 showed significant positive correlation with the Al³⁺ concentration gradient and NO levels, but a significant negative correlation with pollen germination rate and pollen tube length. The expression level of CsALMT5 was negatively correlated with the Al³⁺ concentration gradient and NO level, and positively correlated with pollen germination rate and pollen tube length. The expression level of CsALMT17 showed a significant negative correlation with Al³⁺ concentration and NO content in pollen tubes, but significant positive correlation with pollen germination rate and pollen tube length. In conclusion, a complex signal network regulated by NO-mediated CsALMTs revealed that CsALMT8 was regulated by environmental Al³⁺ and NO to assist Al³⁺ entry into pollen tubes; CsALMT5 might be influenced by the Al³⁺ signal, stimulate malate efflux in vacuoles and chelate with Al³⁺ to detoxify Al in C. sinensis pollen tube.

The root apoplastic pH as an integrator of plant signaling

Plant nutrition, growth, and response to environmental stresses are pH-dependent processes that are regulated at the apoplastic and subcellular levels. The root apoplastic pH is especially sensitive to external cues and can also be modified by intracellular inputs, such as hormonal signaling. Optimal crosstalk of the mechanisms involved in the extent and span of the apoplast pH fluctuations promotes plant resilience to detrimental biotic and abiotic factors. The fact that variations in local pHs are a standard mechanism in different signaling pathways indicates that the pH itself can be the pivotal element to provide a physiological context to plant cell regions, allowing a proportional reaction to different situations. This review brings a collective vision of the causes that initiate root apoplastic pHs variations, their interaction, and how they influence root response outcomes.

A Berberine Bridge Enzyme-Like Protein, GmBBE-like43, Confers Soybean's Coordinated Adaptation to Aluminum Toxicity and Phosphorus Deficiency

Phosphorus (P) deficiency and aluminum (Al) toxicity often coexist and are two major limiting factors for crop production in acid soils. The purpose of this study was to characterize the function of GmBBE-like43, a berberine bridge enzyme-like protein-encoding gene, in soybean (Glycine max) adaptation to Al and low P stresses. Present quantitative real-time PCR (qRT-PCR) assays confirmed the phosphate (Pi)-starvation enhanced and Al-stress up-regulated expression pattern of GmBBE-like43 in soybean roots. Meanwhile, the expression of a GmBBE-like43-GFP chimera in both common bean hairy roots and tobacco leaves demonstrated its cell wall localization. Moreover, both transgenic Arabidopsis and soybean hairy roots revealed the function of GmBBE-like43 in promoting root growth under both Al and low P stresses. GmBBE-like43-overexpression also resulted in more H₂O₂ production on transgenic soybean hairy root surface with oligogalacturonides (OGs) application and antagonized the effects of Al on the expression of two SAUR-like genes. Taken together, our results suggest that GmBBE-like43 might be involved in the soybean's coordinated adaptation to Al toxicity and Pi starvation through modulation of OGs-oxidation in the cell wall.

Identification of two chickpea multidrug and toxic compound extrusion transporter genes transcriptionally upregulated upon aluminum treatment in root tips

Aluminum (Al) toxicity poses a significant challenge for the yield improvement of chickpea, which is an economically important legume crop with high nutritional value in human diets. The genetic basis of Al-tolerance in chickpea remains unclear. Here, we assessed the Al-tolerance of 8 wild Cicer and one cultivated chickpea (PBA Pistol) accessions by measuring the root elongation in solution culture under control (0 μM Al³⁺) and Al treatments (15, 30 μM Al³⁺). Compared to PBA Pistol, the wild Cicer accessions displayed both tolerant and sensitive phenotypes, supporting wild Cicer as a potential genetic pool for Al-tolerance improvement. To identify potential genes related to Al-tolerance in chickpea, genome-wide screening of multidrug and toxic compound extrusion (MATE) encoding genes was performed. Fifty-six MATE genes were identified in total, which can be divided into 4 major phylogenetic groups. Four chickpea MATE genes (CaMATE1-4) were clustered with the previously characterized citrate transporters MtMATE66 and MtMATE69 in Medicago truncatula. Transcriptome data showed that CaMATE1-4 have diverse expression profiles, with CaMATE2 being root-specific. qRT-PCR analyses confirmed that CaMATE2 and CaMATE4 were highly expressed in root tips and were up-regulated upon Al treatment in all chickpea lines. Further measurement of carboxylic acids showed that malonic acid, instead of malate or citrate, is the major extruded acid by Cicer spp. root. Protein structural modeling analyses revealed that CaMATE2 has a divergent substrate-binding cavity from Arabidopsis AtFRD3, which may explain the different acid-secretion profile for chickpea. Pangenome survey showed that CaMATE1-4 have much higher genetic diversity in wild Cicer than that in cultivated chickpea. This first identification of CaMATE2 and CaMATE4 responsive to Al³⁺ treatment in Cicer paves the way for future functional characterization of MATE genes in Cicer spp., and to facilitate future design of gene-specific markers for Al-tolerant line selection in chickpea breeding programs.

Identification of aluminum-activated malate transporters (ALMT) family genes in hydrangea and functional characterization of HmALMT5/9/11 under aluminum stress

Hydrangea (Hydrangea macrophylla (Thunb.) Ser.) is a famous ornamental plant species with high resistance to aluminum (Al). The aluminum-activated malate transporter (ALMT) family encodes anion channels, which participate in many physiological processes, such as Al tolerance, pH regulation, stomatal movement, and mineral nutrition. However, systematic studies on the gene family have not been reported in hydrangea. In this study, 11 candidate ALMT family members were identified from the transcriptome data for hydrangea, which could be divided into three clusters according to the phylogenetic tree. The protein physicochemical properties, phylogeny, conserved motifs and protein structure were analyzed. The distribution of base conservative motifs of HmALMTs was consistent with that of other species, with a highly conserved WEP motif. Furthermore, tissue-specific analysis showed that most of the HmALMTs were highly expressed in the stem under Al treatment. In addition, overexpression of HmALMT5, HmALMT9 and HmALMT11 in yeasts enhanced their tolerance to Al stress. Therefore, the above results reveal the functional role of HmALMTs underlying the Al tolerance of hydrangea. The present study provides a reference for further research to elucidate the functional mechanism and expression regulation of the ALMT gene family in hydrangea.

Genome Editing Targets for Improving Nutrient Use Efficiency and Nutrient Stress Adaptation

In recent years, the development of RNA-guided genome editing (CRISPR-Cas9 technology) has revolutionized plant genome editing. Under nutrient deficiency conditions, different transcription factors and regulatory gene networks work together to maintain nutrient homeostasis. Improvement in the use efficiency of nitrogen (N), phosphorus (P) and potassium (K) is essential to ensure sustainable yield with enhanced quality and tolerance to stresses. This review outlines potential targets suitable for genome editing for understanding and improving nutrient use (NtUE) efficiency and nutrient stress tolerance. The different genome editing strategies for employing crucial negative and positive regulators are also described. Negative regulators of nutrient signalling are the potential targets for genome editing, that may improve nutrient uptake and stress signalling under resource-poor conditions. The promoter engineering by CRISPR/dead (d) Cas9 (dCas9) cytosine and adenine base editing and prime editing is a successful strategy to generate precise changes. CRISPR/dCas9 system also offers the added advantage of exploiting transcriptional activators/repressors for overexpression of genes of interest in a targeted manner. CRISPR activation (CRISPRa) and CRISPR interference (CRISPRi) are variants of CRISPR in which a dCas9 dependent transcription activation or interference is achieved. dCas9-SunTag system can be employed to engineer targeted gene activation and DNA methylation in plants. The development of nutrient use efficient plants through CRISPR-Cas technology will enhance the pace of genetic improvement for nutrient stress tolerance of crops and improve the sustainability of agriculture.

GmWRKY81 Encoding a WRKY Transcription Factor Enhances Aluminum Tolerance in Soybean

Aluminum (Al) toxicity is an essential factor that adversely limits soybean (Glycine max (L.) Merr.) growth in acid soils. WRKY transcription factors play important roles in soybean responses to abiotic stresses. Here, GmWRKY81 was screened from genes that were differentially expressed under Al treatment in Al-tolerant soybean Baxi10 and Al-sensitive soybean Bendi2. We found that GmWRKY81 was significantly induced by 20 μM AlCl3 and upregulated by AlCl3 treatment for 2 h. In different tissues, the expression of GmWRKY81 was differentially induced. In 0-1 cm root tips, the expression of GmWRKY81 was induced to the highest level. The overexpression of GmWRKY81 in soybean resulted in higher relative root elongation, root weight, depth, root length, volume, number of root tips and peroxidase activity but lower root average diameter, malonaldehyde and H2O2 contents, indicating enhanced Al tolerance. Moreover, RNA-seq identified 205 upregulated and 108 downregulated genes in GmWRKY81 transgenic lines. Fifteen of these genes that were differentially expressed in both AlCl3-treated and GmWRKY81-overexpressing soybean had the W-box element, which can bind to the upstream-conserved WRKY domain. Overall, the combined functional analysis indicates that GmWRKY81 may improve soybean Al tolerance by regulating downstream genes participating in Al3+ transport, organic acid secretion and antioxidant reactions.

The Formation of Hollow Trait in Cucumber (Cucumis sativus L.) Fruit Is Controlled by CsALMT2

The hollow trait is crucial for commercial quality of cucumber (Cucumis sativus L.) fruit, and its molecular regulatory mechanism is poorly understood due to its environmental sensitivity. In the previous research, we obtained the hollow and the non-hollow materials of ecotype cucumbers of South China, which were not easily affected by the external environment through a systematic breeding method. In this study, first, we proposed to use the percentage of the hollow area as the criterion to compare the hollow characteristics between two materials, and to analyze the formation mechanism of early hollow trait from the perspective of cytology. The results showed that the hollow trait occurred in the early stage of fruit development, and formed with the opening of carpel ventral zipped bi-cell layer, which formed rapidly from 2 to 4 days, and then slowed to a constant rate from 14 to 16 days. Meanwhile, the different genetic populations were constructed using these materials, and fine mapping was performed by bulked segregant analysis (BSA) and kompetitive allele specific PCR (KASP) method. The Csa1G630860 (CsALMT2), encoding protein ALMT2, was determined as a candidate gene for regulating the hollow trait in fruit. Furthermore, the expression profile of CsALMT2 was analyzed by qRT-PCR and fluorescence in situ hybridization. The expression of CsALMT2 had obvious tissue specificity, and it was abundantly expressed in the ovule development zone inside the fruit. In the hollow material of cucumber fruit, the expression of CsALMT2 was significantly downregulated. The subcellular localization in tobacco leaves indicated that CsALMT2 was distributed on the plasma membrane. In conclusion, in this study, for the first time, we found the regulatory gene of hollow trait in cucumber fruit, which laid the foundation for subsequent research on the molecular mechanism of hollow trait formation in cucumber fruit, and made it possible to apply this gene in cucumber breeding.

Impact of the Arbuscular Mycorrhizal Fungus Funneliformis mosseae on the Physiological and Defence Responses of Canna indica to Copper Oxide Nanoparticles Stress

Copper oxide nanoparticles (nano-CuO) are recognized as an emerging pollutant. Arbuscular mycorrhizal fungi (AMF) can mitigate the adverse impacts of various pollutants on host plants. However, AMF's mechanism for alleviating nano-CuO phytotoxicity remains unclear. The goal of this study was to evaluate how AMF inoculations affect the physiological features of Canna indica seedlings exposed to nano-CuO stress. Compared with the non-AMF inoculated treatment, AMF inoculations noticeably improved plant biomass, mycorrhizal colonization, leaf chlorophyll contents, and the photosynthetic parameters of C. indica under nano-CuO treatments. Moreover, AMF inoculation was able to significantly mitigate nano-CuO stress by enhancing antioxidant enzyme activities and decreasing ROS levels in the leaves and roots of C. indica, thus increasing the expression of genes involved in the antioxidant response. In addition, AMF inoculation reduced the level of Cu in seedlings and was associated with an increased expression of Cu transport genes and metallothionein genes. Furthermore, AMF inoculations increased the expression levels of organic acid metabolism-associated genes while facilitating organic acid secretion, thus reducing the accumulation of Cu. The data demonstrate that AMF-plant symbiosis is a feasible biocontrol approach to remediate nano-CuO pollution.

Mechanisms Underlying Soybean Response to Phosphorus Deficiency through Integration of Omics Analysis

Low phosphorus (P) availability limits soybean growth and yield. A set of potential strategies for plant responses to P deficiency have been elucidated in the past decades, especially in model plants such as Arabidopsis thaliana and rice (Oryza sativa). Recently, substantial efforts focus on the mechanisms underlying P deficiency improvement in legume crops, especially in soybeans (Glycine max). This review summarizes recent advances in the morphological, metabolic, and molecular responses of soybean to phosphate (Pi) starvation through the combined analysis of transcriptomics, proteomics, and metabolomics. Furthermore, we highlight the functions of the key factors controlling root growth and P homeostasis, base on which, a P signaling network in soybean was subsequently presumed. This review also discusses current barriers and depicts perspectives in engineering soybean cultivars with high P efficiency.

Nanobiochar-rhizosphere interactions: Implications for the remediation of heavy-metal contaminated soils

Soil heavy metal contamination has increasingly become a serious environmental issue globally, nearing crisis proportions. There is an urgent need to find environmentally friendly materials to remediate heavy-metal contaminated soils. With the continuing maturation of research on using biochar (BC) for the remediation of contaminated soil, nano-biochar (nano-BC), which is an important fraction of BC, has gradually attracted increasing attention. Compared with BC, nano-BC has unique and useful properties for soil remediation, including a high specific surface area and hydrodynamic dispersivity. The efficacy of nano-BC for immobilization of non-degradable heavy-metal contaminants in soil systems, however, is strongly affected by plant rhizosphere processes, and there is very little known about the role that nano-BC play in these processes. The rhizosphere represents a dynamically complex soil environment, which, although having a small thickness, drives potentially large materials fluxes into and out of plants, notably agricultural foodstuffs, via large diffusive gradients. This article provides a critical review of over 140 peer-reviewed papers regarding nano-BC-rhizosphere interactions and the implications for the remediation of heavy-metal contaminated soils. We conclude that, when using nano-BC to remediate heavy metal-contaminated soil, the relationship between nano-BC and rhizosphere needs to be considered. Moreover, the challenges to extending our knowledge regarding the environmental risk of using nano-BC for remediation, as well as further research needs, are identified.

Transcriptome Analysis Revealed the Mechanisms Involved in Ultrasonic Seed Treatment-Induced Aluminum Tolerance in Peanut

Ultrasonic (US) treatment is an efficient method to induce crop tolerance against heavy metal toxicity; however, US-induced aluminum (Al) tolerance in peanuts was rarely studied. This study was comprised of two treatments, namely, CK, without ultrasonic treatment, and US, an ultrasonic seed treatment, for 15 min. Both treated and non-treated treatments were applied with Al in the form of AlCl3.18H2O at 5 mmol L-1 in Hoagland solution at one leaf stage. Results depicted that plant height, main root length, and number of lateral roots increased significantly under US treatment. Transcriptome analysis revealed that plant hormone signal transduction and transcription factors (TFs) were significantly enriched in the differentially expressed genes (DEGs) in US treatment, and the plant hormones were measured, including salicylic acid (SA) and abscisic acid (ABA) contents, were substantially increased, while indole acetic acid (IAA) and jasmonic acid (JA) contents were decreased significantly in US treatment. The TFs were verified using quantitative real-time (qRT)-PCR, and it was found that multiple TFs genes were significantly upregulated in US treatment, and ALMT9 and FRDL1 genes were also significantly upregulated in US treatment. Overall, the US treatment induced the regulation of hormone content and regulated gene expression by regulating TFs to improve Al tolerance in peanuts. This study provided a theoretical rationale for US treatment to improve Al tolerance in peanuts.

Research Advances in the Mutual Mechanisms Regulating Response of Plant Roots to Phosphate Deficiency and Aluminum Toxicity

Low phosphate (Pi) availability and high aluminum (Al) toxicity constitute two major plant mineral nutritional stressors that limit plant productivity on acidic soils. Advances toward the identification of genes and signaling networks that are involved in both stresses in model plants such as Arabidopsis thaliana and rice (Oryza sativa), and in other plants as well have revealed that some factors such as organic acids (OAs), cell wall properties, phytohormones, and iron (Fe) homeostasis are interconnected with each other. Moreover, OAs are involved in recruiting of many plant-growth-promoting bacteria that are able to secrete both OAs and phosphatases to increase Pi availability and decrease Al toxicity. In this review paper, we summarize these mutual mechanisms by which plants deal with both Al toxicity and P starvation, with emphasis on OA secretion regulation, plant-growth-promoting bacteria, transcription factors, transporters, hormones, and cell wall-related kinases in the context of root development and root system architecture remodeling that plays a determinant role in improving P use efficiency and Al resistance on acidic soils.

Structural basis of ALMT1-mediated aluminum resistance in Arabidopsis

The plant aluminum (Al)-activated malate transporter ALMT1 mediates the efflux of malate to chelate the Al in acidic soils and underlies the plant Al resistance. Here we present cryo-electron microscopy (cryo-EM) structures of Arabidopsis thaliana ALMT1 (AtALMT1) in the apo, malate-bound, and Al-bound states at neutral and/or acidic pH at up to 3.0 Å resolution. The AtALMT1 dimer assembles an anion channel and each subunit contains six transmembrane helices (TMs) and six cytosolic α-helices. Two pairs of Arg residues are located in the center of the channel pore and contribute to malate recognition. Al binds at the extracellular side of AtALMT1 and induces conformational changes of the TM1-2 loop and the TM5-6 loop, resulting in the opening of the extracellular gate. These structures, along with electrophysiological measurements, molecular dynamic simulations, and mutagenesis study in Arabidopsis, elucidate the structural basis for Al-activated malate transport by ALMT1.