Regulatory levels for the transport of ammonium in plant roots

Calcium-Regulated Phosphorylation Systems Controlling Uptake and Balance of Plant Nutrients

Essential elements taken up from the soil and distributed throughout the whole plant play diverse roles in different tissues. Cations and anions contribute to maintenance of intracellular osmolarity and the formation of membrane potential, while nitrate, ammonium, and sulfate are incorporated into amino acids and other organic compounds. In contrast to these ion species, calcium concentrations are usually kept low in the cytosol and calcium displays unique behavior as a cytosolic signaling molecule. Various environmental stresses stimulate increases in the cytosolic calcium concentration, leading to activation of calcium-regulated protein kinases and downstream signaling pathways. In this review, we summarize the stress responsive regulation of nutrient uptake and balancing by two types of calcium-regulated phosphorylation systems: CPK and CBL-CIPK. CPK is a family of protein kinases activated by calcium. CBL is a group of calcium sensor proteins that interact with CIPK kinases, which phosphorylate their downstream targets. In Arabidopsis, quite a few ion transport systems are regulated by CPKs or CBL-CIPK complexes, including channels/transporters that mediate transport of potassium (KAT1, KAT2, GORK, AKT1, AKT2, HAK5, SPIK), sodium (SOS1), ammonium (AMT1;1, AMT1;2), nitrate and chloride (SLAC1, SLAH2, SLAH3, NRT1.1, NRT2.4, NRT2.5), and proton (AHA2, V-ATPase). CPKs and CBL-CIPKs also play a role in C/N nutrient response and in acquisition of magnesium and iron. This functional regulation by calcium-dependent phosphorylation systems ensures the growth of plants and enables them to acquire tolerance against various environmental stresses. Calcium serves as the key factor for the regulation of membrane transport systems.

Molecular identification and functional characterization of GhAMT1.3 in ammonium transport with a high affinity from cotton (Gossypium hirsutum L.)

Ammonium (NH₄ ⁺ ) represents a primary nitrogen source for many plants, its effective transport into and between tissues and further assimilation in cells determine greatly plant nitrogen use efficiency. However, biological components involved in NH₄ ⁺ movement in woody plants are unclear. Here, we report kinetic evidence for cotton NH₄ ⁺ uptake and molecular identification of certain NH₄ ⁺ transporters (AMTs) from cotton (Gossypium hirustum). A substrate-influx assay using ¹⁵ N-isotope revealed that cotton possessed a high-affinity transport system with a K_m of 58 μM for NH₄ ⁺ . Sequence analysis showed that GhAMT1.1-1.3 encoded respectively a membrane protein containing 485, 509 or 499 amino acids. Heterologous functionality test demonstrated that GhAMT1.1-1.3 expression mediated NH₄ ⁺ permeation across the plasma membrane (PM) of yeast and/or Arabidopsis qko-mutant cells, allowing a growth restoration of both mutants on NH₄ ⁺ . Quantitative PCR measurement showed that GhAMT1.3 was expressed in roots and leaves and markedly up-regulated by N-starvation, repressed by NH₄ ⁺ resupply and regulated diurnally and age-dependently, suggesting that GhAMT1.3 should be a N-responsive gene. Importantly, GhAMT1.3 expression in Arabidopsis improved plant growth on NH₄ ⁺ and enhanced total nitrogen accumulation (∼50% more), conforming with the observation of 2-fold more NH₄ ⁺ absorption by GhAMT1.3-transformed qko plant roots during a 1-h root influx period. Together with its targeting to the PM and saturated transport kinetics with a K_m of 72 μM for NH₄ ⁺ , GhAMT1.3 is suggested to be a high-affinity NH₄ ⁺ permease that may play a significant role in cotton NH₄ ⁺ acquisition and utilization, adding a new member in the plant AMT family.

Ammonium and nitrate regulate NH4+ uptake activity of Arabidopsis ammonium transporter AtAMT1;3 via phosphorylation at multiple C-terminal sites

In plants, nutrient transporters require tight regulation to ensure optimal uptake in complex environments. The activities of many nutrient transporters are post-translationally regulated by reversible phosphorylation, allowing rapid adaptation to variable environmental conditions. Here, we show that the Arabidopsis root epidermis-expressed ammonium transporter AtAMT1;3 was dynamically (de-)phosphorylated at multiple sites in the cytosolic C-terminal region (CTR) responding to ammonium and nitrate signals. Under ammonium resupply rapid phosphorylation of a Thr residue (T464) in the conserved part of the CTR (CTRC) effectively inhibited AtAMT1;3-dependent NH4+ uptake. Moreover, phosphorylation of Thr (T494), one of three phosphorylation sites in the non-conserved part of the CTR (CRTNC), moderately decreased the NH4+ transport activity of AtAMT1;3, as deduced from functional analysis of phospho-mimic mutants in yeast, oocytes, and transgenic Arabidopsis. Double phospho-mutants indicated a role of T494 in fine-tuning the NH4+ transport activity when T464 was non-phosphorylated. Transient dephosphorylation of T494 with nitrate resupply closely paralleled a transient increase in ammonium uptake. These results suggest that T464 phosphorylation at the CTRC acts as a prime switch to prevent excess ammonium influx, while T494 phosphorylation at the CTRNC fine tunes ammonium uptake in response to nitrate. This provides a sophisticated regulatory mechanism for plant ammonium transporters to achieve optimal ammonium uptake in response to various nitrogen forms.

The Use of Nitrogen and Its Regulation in Cereals: Structural Genes, Transcription Factors, and the Role of miRNAs

Cereals and, especially, rice, maize, and wheat, are essential commodities, on which human nutrition is based. Expanding population and food demand have required higher production which has been achieved by increasing fertilization, and especially nitrogen supply to cereal crops. In fact, nitrogen is a crucial nutrient for the plant, but excessive use poses serious environmental and health issues. Therefore, increasing nitrogen use efficiency in cereals is of pivotal importance for sustainable agriculture. The main steps in the use of nitrogen are uptake and transport, reduction and assimilation, and translocation and remobilization. Many studies have been carried out on the genes involved in these phases, and on transcription factors regulating these genes. Lately, increasing attention has been paid to miRNAs responding to abiotic stress, including nutrient deficiency. Many miRNAs have been found to regulate transcription factors acting on the expression of specific genes for nitrogen uptake or remobilization. Recent studies on gene regulatory networks have also demonstrated that miRNAs can interact with several nodes in the network, functioning as key regulators in nitrogen metabolism.

Trading on the arbuscular mycorrhiza market: from arbuscules to common mycorrhizal networks

Arbuscular mycorrhiza (AM) symbiosis occurs between obligate biotrophic fungi of the phylum Glomeromycota and most land plants. The exchange of nutrients between host plants and AM fungi (AMF) is presumed to be the main benefit for the two symbiotic partners. In this review article, we outline the current concepts of nutrient exchanges within this symbiosis (mechanisms and regulation). First, we focus on phosphorus and nitrogen transfer from the fungal partner to the host plant, and on the reciprocal transfer of carbon compounds, with a highlight on a possible interplay between nitrogen and phosphorus nutrition during AM symbiosis. We further discuss potential mechanisms of regulation of these nutrient exchanges linked to membrane dynamics. The review finally addresses the common mycorrhizal networks formed AMF, which interconnect plants from similar and/or different species. Finally the best way to integrate this knowledge and the ensuing potential benefits of AM into sustainable agriculture is discussed.

TaAMT2;3a, a wheat AMT2-type ammonium transporter, facilitates the infection of stripe rust fungus on wheat

BACKGROUND

Ammonium transporters (AMTs), a family of proteins transporting ammonium salt and its analogues, have been studied in many aspects. Although numerous studies have found that ammonium affects the interaction between plants and pathogens, the role of AMTs remains largely unknown, especially that of the AMT2-type AMTs.

RESULTS

In the present study, we found that the concentration of ammonium in wheat leaves decreased after infection with Puccinia striiformis f. sp. tritici (Pst), the causal agent of stripe rust. Then, an AMT2-type ammonium transporter gene induced by Pst was identified and designated as TaAMT2;3a. Transient expression assays indicated that TaAMT2;3a was located to the cell and nuclear membranes. TaAMT2;3a successfully complemented the function of a yeast mutant defective in NH₄⁺ transport, indicating its ammonium transport capacity. Function of TaAMT2;3a in wheat-Pst interaction was further analyzed by barley stripe mosaic virus (BSMV)-induced gene silencing. Pst growth was significantly retarded in TaAMT2;3a-knockdown plants, in which ammonium in leaves were shown to be induced at the early stage of infection. Histological observation showed that the hyphal length, the number of hyphal branches and haustorial mother cells decreased in the TaAMT2;3a knockdown plants, leading to the impeded growth of rust pathogens.

CONCLUSIONS

The results clearly indicate that the induction of AMT2-type ammonium transporter gene TaAMT2;3a may facilitates the nitrogen uptake from wheat leaves by Pst, thereby contribute to the infection of rust fungi.

Exploring the adaptive mechanism of Passiflora edulis in karst areas via an integrative analysis of nutrient elements and transcriptional profiles

BACKGROUND

Passiflora edulis, known as passion fruit and native to South America, is now widely cultivated throughout southern China for its edible value, medicinal efficacy and ornamental properties. We have developed a cold-tolerant variety of P. edulis ('Pingtang 1') that can survive subzero temperatures and is highly adaptable in Karst areas. In this study, cuttings of 'Pingtang 1' were cultivated in a limestone (L) rocky desertification area and a sandy dolomite (D) rock desertification area. Changes in nutrient elements in both the soils and plants were revealed in the two plots. Moreover, RNA sequencing (RNA-Seq) was performed to profile the root transcriptomes for further exploration of nutrient adaptative mechanism of Passiflora edulis in Karst regions.

RESULTS

In this study, a total of, 244,705,162 clean reads were generated from four cDNA libraries and assembled into 84,198 unigenes, of which 56,962 were annotated by publicly available databases. Transcriptome profiles were generated, and 1314 unigenes (531 upregulated and 801 downregulated) were significantly differentially expressed between the L and D root cDNA libraries (L_R and D_R, respectively); these profiles provide a global overview of the gene expression patterns associated with P. edulis adaptability to Karst soils. Most unigenes including a number of differentially expressed genes (DEGs) were involved in nutrient element uptake, utilization, signal regulation. And DEGs enriched in KEGG pathways of plant hormone signal transduction, phenylpropanoid biosynthesis, and biosynthesis of unsaturated fatty acids were significantly expressed.

CONCLUSION

These results could contribute to better understanding the adaptation of this species to environmental stress and thus enhance the potential for successfully introducing and commercially deploying P. edulis.

Differential carbon allocation to nitrogen-rich patches in Poa annua precedes root proliferation but has no immediate benefit to N uptake

Nutrients are heterogeneously distributed in the soil environment. Plants have evolved a variety of mechanisms to maximise their ability to compete for limited resources, with differential root growth considered among the more important mechanisms. Despite the significant costs of root growth, little data is available regarding carbon (C) allocation to roots growing in heterogeneous conditions. Here, we investigate the allocation of recently assimilated C in Poa annua plants growing in uniform or heterogeneous nutrient conditions. In the first experiment we grew plants in split-root boxes, providing N either equally between the two chambers (0.5 mg/0.5 mg, 8 mg/8 mg) or with one side receiving more N (0.5 mg/8 mg, 8 mg/0.5 mg), and quantified C allocation and N uptake using ¹³CO₂ and K¹⁵NO₃. Where N was supplied equally to the two chambers, C was allocated equally to the roots irrespective of the total N supply. However, the ¹³C label was preferentially allocated (60:40) to high-N roots in the unequal treatments. N uptake was a function of local supply and was not affected by N supply to the roots in the other chamber. C allocation had no discernible effect on N uptake. In the second experiment, we tested whether differential N supply would lead to increased root growth in the high-N side. In this experiment, equal amounts of N were supplied to all plants as ammonium, with half receiving an equal distribution to the two root chambers (50/50), while the other half received an unequal supply (94/6). While no difference in root growth was noted in 50/50 plants, a 60:40 mass allocation was noted from day six onwards in plants receiving the 94/6 N supply. Despite increased root growth in the high-N side, the plants receiving the 94/6 treatment could not achieve the same shoot mass or N concentration as the 50/50 plants. No difference in total C allocation to the roots between treatments was noted in the first experiment, and no difference in total root mass between treatments was found in the second experiment, suggesting that root C supply was source-limited, while allocation to specific roots was strongly influenced by sink strength. Differential C allocation appears to be an important pre-requisite for increased root growth in N-rich patches.

Co-Application of Milk Tea Waste and NPK Fertilizers to Improve Sandy Soil Biochemical Properties and Wheat Growth

Desert soil is one of the most severe conditions which negatively affect the environment and crop growth production in arid land. The application of organic amendments with inorganic fertilizers is an economically viable and environmentally comprehensive method to develop sustainable agriculture. The aim of this study was to assess whether milk tea waste (TW) amendment combined with chemical fertilizer (F) application can be used to improve the biochemical properties of sandy soil and wheat growth. The treatments included control without amendment (T1), chemical fertilizers (T2), TW 2.5% + F (T3), TW 5% + F (T4) and TW 10% + F (T5). The results showed that the highest chlorophyll (a and b) and carotenoids, shoot and root dry biomass, and leaf area index (LAI) were significantly (p < 0.05) improved with all amendment treatments. However, the highest root total length, root surface area, root volume and diameter were recorded for T4 among all treatments. The greater uptake of N, P, and K contents for T4 increased for the shoot by 68.9, 58.3, and 57.1%, and for the root by 65.7, 34.3, and 47.4% compared to the control, respectively. Compared with the control, T5 treatment decreased the soil pH significantly (p < 0.05) and increased soil enzyme activities such as urease (95.2%), β-glucosidase (81.6%) and dehydrogenase (97.2%), followed by T4, T3, and T2. Our findings suggested that the integrated use of milk tea waste and chemical fertilizers is a suitable amendment method for improving the growth and soil fertility status of sandy soils.

The role of ammonium transporter (AMT) against salt stress in plants

Since NH₄⁺ is one of the most important limiting nitrogen sources for plant growth, ammonium uptake and transport system has particular attention. In plant cells, ammonium transporters (AMTs) are responsible for ammonium uptake and transport. In previous studies, we identified a PutAMT1;1 gene from Puccinellia tenuiflora, which is a monocotyledonous halophyte species that thrives in alkaline soil. The overexpression of PutAMT1;1 in Arabidopsis thaliana enhanced plant growth and increased plant susceptibility to toxic methylammonium (MeA). This transporter might be useful for improving the root to shoot mobilization of MeA (or NH₄⁺). Interestingly, in our other studies, it can be assumed that urease acts on urea to produce NH₄⁺, which may exacerbate salt stress. Overexpression of PutAMT1;1 promoted early root growth after seed germination in transgenic Arabidopsis under salt stress condition. These findings suggest that ammonium transport alleviates ammonia toxicity caused by salt stress. Subcellular localization revealed that PutAMT1;1 is mainly localized in the plasma membrane and the nuclear periphery and endomembrane system of yeast and plant cells. Here, we discuss these recent findings and speculate on the regular dynamic localization of PutAMT1;1 throughout the cell cycle, which may be related to intracellular activity.

Identification of candidate genes for leaf scorch in Populus deltoids by the whole genome resequencing analysis

Leaf scorch exists as a common phenomenon in the development of plant, especially when plants encounter various adversities, which leads to great losses in agricultural production. Both Jinhong poplar (JHP) and Caihong poplar (CHP) (Populus deltoids) are obtained from a bud sport on Zhonghong poplar. Compared with CHP, JHP always exhibits leaf scorch, poor growth, premature leaf discoloration, and even death. In this study, the candidate genes associated with leaf scorch between JHP and CHP were identified by the whole genome resequencing using Illumina HiSeqTM. There were 218,880 polymorphic SNPs and 46,933 indels between JHP and CHP, respectively. Among these, the candidate genes carrying non-synonymous SNPs in coding regions were classified into 6 groups. The expression pattern of these candidate genes was also explored in JHP and CHP among different sampling stages. Combined with the qRT-PCR analysis, the results showed that genes associated with transport of various nutritional elements, senescence and MYB transcription factor might play important roles during the process of leaf scorch in Populus deltoids. Four genes belonging to these three groups carried more than three SNPs in their coding sequence, which might play important roles in leaf scorch. The above results provided candidate genes involved in leaf scorch in Populus deltoids, and made us better understand the molecular regulation mechanism of leaf scorch in Populus deltoids.

How Can We Define "Optimal Microbiota?": A Comparative Review of Structure and Functions of Microbiota of Animals, Fish, and Plants in Agriculture

All multicellular organisms benefit from their own microbiota, which play important roles in maintaining the host nutritional health and immunity. Recently, the number of studies on the microbiota of animals, fish, and plants of economic importance is rapidly expanding and there are increasing expectations that productivity and sustainability in agricultural management can be improved by microbiota manipulation. However, optimizing microbiota is still a challenging task because of the lack of knowledge on the dominant microorganisms or significant variations between microbiota, reflecting sampling biases, different agricultural management as well as breeding backgrounds. To offer a more generalized view on microbiota in agriculture, which can be used for defining criteria of “optimal microbiota” as the goal of manipulation, we summarize here current knowledge on microbiota on animals, fish, and plants with emphasis on bacterial community structure and metabolic functions, and how microbiota can be affected by domestication, conventional agricultural practices, and use of antimicrobial agents. Finally, we discuss future tasks for defining “optimal microbiota,” which can improve host growth, nutrition, and immunity and reduce the use of antimicrobial agents in agriculture.

An integrated analysis of mRNA and sRNA transcriptional profiles in Coffea arabica L. roots: insights on nitrogen starvation responses

Coffea arabica L. is an important agricultural commodity, accounting for 60% of traded coffee worldwide. Nitrogen (N) is a macronutrient that is usually limiting to plant yield; however, molecular mechanisms of plant acclimation to N limitation remain largely unknown in tropical woody crops. In this study, we investigated the transcriptome of coffee roots under N starvation, analyzing poly-A+ libraries and small RNAs. We also evaluated the concentration of selected amino acids and N-source preferences in roots. Ammonium was preferentially taken up over nitrate, and asparagine and glutamate were the most abundant amino acids observed in coffee roots. We obtained 34,654 assembled contigs by mRNA sequencing, and validated the transcriptional profile of 12 genes by RT-qPCR. Illumina small RNA sequencing yielded 8,524,332 non-redundant reads, resulting in the identification of 86 microRNA families targeting 253 genes. The transcriptional pattern of eight miRNA families was also validated. To our knowledge, this is the first catalog of differentially regulated amino acids, N sources, mRNAs, and sRNAs in Arabica coffee roots.

Cell wall-bound silicon optimizes ammonium uptake and metabolism in rice cells

BACKGROUND AND AIMS

Turgor-driven plant cell growth depends on cell wall structure and mechanics. Strengthening of cell walls on the basis of an association and interaction with silicon (Si) could lead to improved nutrient uptake and optimized growth and metabolism in rice (Oryza sativa). However, the structural basis and physiological mechanisms of nutrient uptake and metabolism optimization under Si assistance remain obscure.

METHODS

Single-cell level biophysical measurements, including in situ non-invasive micro-testing (NMT) of NH4+ ion fluxes, atomic force microscopy (AFM) of cell walls, and electrolyte leakage and membrane potential, as well as whole-cell proteomics using isobaric tags for relative and absolute quantification (iTRAQ), were performed.

KEY RESULTS

The altered cell wall structure increases the uptake rate of the main nutrient NH4+ in Si-accumulating cells, whereas the rate is only half in Si-deprived counterparts.

CONCLUSIONS

Rigid cell walls enhanced by a wall-bound form of Si as the structural basis stabilize cell membranes. This, in turn, optimizes nutrient uptake of the cells in the same growth phase without any requirement for up-regulation of transmembrane ammonium transporters. Optimization of cellular nutrient acquisition strategies can substantially improve performance in terms of growth, metabolism and stress resistance.

Identification and characterization of two ammonium transporter genes in flowering Chinese cabbage (Brassica campestris)

Ammonium transporters (AMTs), which include AMT1 and AMT2 subfamilies, have been identified and partially characterized in many plants. In this study, two AMT2-type genes from Brassica campestris, namely BcAMT2 and BcAMT2like, were identified and characterized. BcAMT2 and BcAMT2like are 2666 bp and 2952 bp, encode proteins of 490 and 489 amino acids, respectively, and contain five exons and four introns. Transient expression of these proteins labelled with green fluorescence protein in onion epidermal cells indicated that both are located on the plasma membrane. When expressing BcAMT2 or BcAMT2like, the mutant yeast strain 31019b could grow on medium containing 2 mM ammonium as the only nitrogen source when expressing BcAMT2 or BcAMT2like, indicating that both are functional AMT genes. Quantitative PCR results showed that BcAMT2 and BcAMT2like were expressed in all tissues, but they displayed different expression patterns in the reproductive stages. BcAMT2s transcript levels in leaves were positively correlated with ammonium concentration and external pH. Moreover, the expression BcAMT2s responded to diurnal change. Furthermore, the uncharged form of ammonium, i.e., ammonia, might also be transported by BcAMT2s. These results provide new insights into the molecular mechanisms underlying ammonium absorption and transportation by the AMT2 subfamily in B. campestris.

Molecular cloning and expression analysis of ammonium transporters in tea plants (Camellia sinensis (L.) O. Kuntze) under different nitrogen treatments

Ammonium is a major inorganic nitrogen source for tea plant growth and is mainly taken up and transported by ammonium transporters (AMTs). Here, we analyzed the NH₄⁺ uptake kinetics of three tea cultivars, Longjing43 (LJ43), Zhongcha108 (ZC108) and Zhongcha302 (ZC302). The results revealed that ZC302 had a higher NH₄⁺ uptake efficiency than the other two cultivars. The full CDS sequences of three Camellia sinensis ammonium transporter (CsAMT) genes, i.e., CsAMT1.1, CsAMT1.2 and CsAMT3.1, were cloned. Analysis of tissue-specific expression showed that CsAMT1.2 followed a root-specific expression pattern, while transcripts of CsAMT1.1 and CsAMT3.1 were mainly accumulated in leaves. The temporal course experiment on gene expression levels showed CsAMT1.1 and CsAMT3.1 followed a reciprocal expression pattern in leaves as CsAMT1.1 was up-regulated by a short time (2 h, 6 h) nitrogen (N) supply both in the leaves and buds of LJ43 and ZC108; and the expression of CsAMT3.1 in leaves was increased by a long time (72 h) N supply, particularly in ZC302. Therefore, we inferred that CsAMT1.1 and CsAMT3.1 might play important roles in photorespiratory ammonium metabolism. The expression of CsAMT1.2 was extremely high in roots and can be greatly induced by N over a short period of time, especially in ZC302; thus, we concluded CsAMT1.2 might play an important role in ammonium uptake from soils in tea plant roots.

A tale of two mixotrophic chrysophytes: Insights into the metabolisms of two Ochromonas species (Chrysophyceae) through a comparison of gene expression

Ochromonas spp. strains CCMP1393 and BG-1 are phagotrophic phytoflagellates with different nutritional strategies. Strain CCMP1393 is an obligate phototroph while strain BG-1 readily grows in continuous darkness in the presence of bacterial prey. Growth and gene expression of strain CCMP1393 were investigated under conditions allowing phagotrophic, mixotrophic, or phototrophic nutrition. The availability of light and bacterial prey led to the differential expression of 42% or 45–59% of all genes, respectively. Data from strain CCMP1393 were compared to those from a study conducted previously on strain BG-1, and revealed notable differences in carbon and nitrogen metabolism between the 2 congeners under similar environmental conditions. Strain BG-1 utilized bacterial carbon and amino acids through glycolysis and the tricarboxylic acid cycle, while downregulating light harvesting and carbon fixation in the Calvin cycle when both light and bacteria were available. In contrast, the upregulation of genes related to photosynthesis, light harvesting, chlorophyll synthesis, and carbon fixation in the presence of light and prey for strain CCMP1393 implied that this species is more phototrophic than strain BG-1, and that phagotrophy may have enhanced phototrophy. Cellular chlorophyll a content was also significantly higher in strain CCMP1393 supplied with bacteria compared to those without prey. Our results thus point to very different physiological strategies for mixotrophic nutrition in these closely related chrysophyte species.

Protein Hydrolysate Stimulates Growth in Tomato Coupled With N-Dependent Gene Expression Involved in N Assimilation

Plant-derived protein hydrolysates (PHs) have received increased attention in the last decade because of their potential to improve yield, nutritional quality as well as tolerance to abiotic stressors. The current study investigated the effects and the molecular mechanisms of a legume-derived PH under optimal and sub-optimal nitrogen (N) concentrations (112 and 7 mg L^-1, respectively) in tomato (Solanum lycopersicum L.). Growth and mineral composition of tomato plants treated with PHs by foliar spray or substrate drench were compared to untreated plants. In addition, the expression was determined of genes encoding ammonium and nitrate transporters and seven enzymes involved in N metabolism: nitrate reductase (NR), nitrite reductase (NiR), glutamine synthetase 1 (GS1), glutamine synthetase 2 (GS2), ferredoxin-dependent glutamate synthase (GLT), NADH-dependent glutamate synthase (GLS), and glutamate dehydrogenase (GDH). The root and total plant dry weight, SPAD index and leaf nitrogen content were higher by 21, 17, 7, and 6%, respectively, in plants treated by a substrate drench in comparison to untreated tomato plants, whereas foliar application of PH gave intermediate values. PH-treated plants grown with lower N availability showed reduced expression of NR and NiR as well as of nitrate and ammonium transporter transcripts in both leaf and root tissues in comparison with untreated plants; this was especially pronounced after application of PH by substrate drench. Conversely, the transcript level of an amino acid transporter gene was up-regulated in comparison with untreated plants. At high N regime, the transcript levels of the ammonium and amino acid transporters and also NR, NiR, and GLT were significantly up-regulated in root after PH foliar and substrate drench applications compared with untreated plants. An up-regulation was also observed for GS1, GS2, and GDH transcripts in leaf after substrate drench. These results highlighted the potential benefits of using legume PH in vegetable production systems to increase growth and N-nutritional status of plants.

Foxtail Millet [Setaria italica (L.) Beauv.] Grown under Low Nitrogen Shows a Smaller Root System, Enhanced Biomass Accumulation, and Nitrate Transporter Expression

Foxtail millet (FM) [Setaria italica (L.) Beauv.] is a grain and forage crop well adapted to nutrient-poor soils. To date little is known how FM adapts to low nitrogen (LN) at the morphological, physiological, and molecular levels. Using the FM variety Yugu1, we found that LN led to lower chlorophyll contents and N concentrations, and higher root/shoot and C/N ratios and N utilization efficiencies under hydroponic culture. Importantly, enhanced biomass accumulation in the root under LN was in contrast to a smaller root system, as indicated by significant decreases in total root length; crown root number and length; and lateral root number, length, and density. Enhanced carbon allocation toward the root was rather for significant increases in average diameter of the LN root, potentially favorable for wider xylem vessels or other anatomical alterations facilitating nutrient transport. Lower levels of IAA and CKs were consistent with a smaller root system and higher levels of GA may promote root thickening under LN. Further, up-regulation of SiNRT1.1, SiNRT2.1, and SiNAR2.1 expression and nitrate influx in the root and that of SiNRT1.11 and SiNRT1.12 expression in the shoot probably favored nitrate uptake and remobilization as a whole. Lastly, more soluble proteins accumulated in the N-deficient root likely as a result of increases of N utilization efficiencies. Such "excessive" protein-N was possibly available for shoot delivery. Thus, FM may preferentially transport carbon toward the root facilitating root thickening/nutrient transport and allocate N toward the shoot maximizing photosynthesis/carbon fixation as a primary adaptive strategy to N limitation.

Regulatory Role of Silicon in Mediating Differential Stress Tolerance Responses in Two Contrasting Tomato Genotypes Under Osmotic Stress

Previous studies have shown the role of silicon (Si) in mitigating the adverse effect of drought stress in different crop species. However, data are lacking on a comparison of drought tolerant and drought sensitive crop cultivars in response to Si nutrition. Therefore, the aim of this study was to elucidate the mechanism (s) by which two contrasting tomato genotypes respond to Si nutrition under osmotic stress condition. Two tomato lines contrasting in their response to drought stress were hydroponically grown under polyethylene glycol (PEG, 6000) and two regimes of Si (0 and 1.5 mM). Metabolite profiling was performed in two lines. Growth and relevant physiological parameters, and expression levels of selected genes were also measured. Si application resulted in improved osmotic stress tolerance in both drought tolerant line LA0147 and drought sensitive line FERUM. In the drought tolerant line, Si enhanced uptake of sulfur (S) and ammonium ( NH 4 + ) which led to a significantly higher production of amino acids arginine, methionine, serine, and glycine. While in the drought sensitive line, Si significantly increased production of amino acids proline and GABA which further lowered the level of GSSG to GSH ratio and thus balanced the redox homeostasis under osmotic stress. The higher significant production of amino acids arginine, methionine, GABA, and proline enhanced production of free polyamines putrescine and spermidine and improved osmotic stress tolerance. Therefore, we conclude that Si distinctively regulated osmotic stress tolerance in two contrasting tomato genotypes by differential accumulation of relevant amino acids which eventually led to enhanced polyamine metabolism.

A Critical Role of AMT2;1 in Root-To-Shoot Translocation of Ammonium in Arabidopsis

Ammonium uptake in plant roots is mediated by AMT/MEP/Rh-type ammonium transporters. Out of five AMTs being expressed in Arabidopsis roots, four AMT1-type transporters contribute to ammonium uptake, whereas no physiological function has so far been assigned to the only homolog belonging to the MEP subfamily, AMT2;1. Based on the observation that under ammonium supply, the transcript levels of AMT2;1 increased and its promoter activity shifted preferentially to the pericycle, we assessed the contribution of AMT2;1 to xylem loading. When exposed to ¹⁵N-labeled ammonium, amt2;1 mutant lines translocated less tracer to the shoots and contained less ammonium in the xylem sap. Moreover, in an amt1;1 amt1;2 amt1;3 amt2;1 quadruple mutant (qko), co-expression of AMT2;1 with either AMT1;2 or AMT1;3 significantly enhanced ¹⁵N translocation to shoots, indicating a cooperative action between AMT2;1 and AMT1 transporters. Under N deficiency, proAMT2;1-GFP lines showed enhanced promoter activity predominantly in cortical root cells, which coincided with elevated ammonium influx conferred by AMT2;1 at millimolar substrate concentrations. Our results indicate that in addition to contributing moderately to root uptake in the low-affinity range, AMT2;1 functions mainly in root-to-shoot translocation of ammonium, depending on its cell-type-specific expression in response to the plant nutritional status and to local ammonium gradients.

Wheat Ammonium Transporter (AMT) Gene Family: Diversity and Possible Role in Host-Pathogen Interaction with Stem Rust

Ammonium transporter (AMT) proteins have been reported in many plants, but no comprehensive analysis was performed in wheat. In this study, we identified 23 AMT members (hereafter TaAMTs) using a protein homology search in wheat genome. Tissue-specific expression analysis showed that TaAMT1;1a, TaAMT1;1b, and TaAMT1;3a were relatively more highly expressed in comparison with other TaAMTs. TaAMT1;1a, TaAMT1;1b, and TaAMT1;3a-GFP were localized in the plasma membrane in tobacco leaves, and TaAMT1;1a, TaAMT1;1b, and TaAMT1;3a successfully complemented a yeast 31019b strain in which ammonium uptake was deficient. In addition, the expression of TaAMT1;1b in an Arabidopsis AMT quadruple mutant (qko) successfully restored [Formula: see text] uptake ability. Resupply of [Formula: see text] rapidly increased cellular [Formula: see text] contents and suppressed expression of TaAMT1;3a, but not of TaAMT;1;1a and TaAMT1;1b expressions. Expression of TaAMT1;1a, TaAMT1;1b, and TaAMT1;3a was not changed in leaves after [Formula: see text] resupply. In contrast, nitrogen (N) deprivation induced TaAMT1;1a, TaAMT1;1b, and TaAMT1;3a gene expressions in the roots and leaves. Expression analysis in the leaves of the stem rust-susceptible wheat line "Little Club" and the rust-tolerant strain "Mini 2761" revealed that TaAMT1;1a, TaAMT1;1b, and TaAMT1;3a were specifically induced in the former but not in the latter. Rust-susceptible wheat plants grown under N-free conditions exhibited a lower disease index than plants grown with [Formula: see text] as the sole N source in the medium after infection with Puccinia graminis f. sp. tritici, suggesting that [Formula: see text] and its transport may facilitate the infection of wheat stem rust disease. Our findings may be important for understanding the potential function TaAMTs in wheat plants.

The AMT1 family genes from Malus robusta display differential transcription features and ammonium transport abilities

Ammonium is an important nitrogen sources for plant growth. In this study, we report on the gene characterization of the ammonium transporter AMT1 subfamily in the apple rootstock Malus robusta Rehd. Thirteen AMT genes were comprehensively evaluated from the apple genome (version 1.0). Then the gene features and expression patterns of five AMT1 members from M. robusta were analyzed. These genes fell into four clusters in the AMT phylogenetic tree: clade I (MrAMT1;1 and MrAMT1;3), clade II (MrAMT1;4), clade III (MrAMT1;2), and clade IV (MrAMT1;5). All the AMT1s, apart from MrAMT1;4, were expressed in vegetative organs and strongly responded to nitrogen concentration changes. For example, MrAMT1;2 and MrAMT1;3 had high transcript accumulation levels in the leaves and roots, respectively. Finally, the functions of these AMT1s were studied in detail by heterologous expression in yeast. These genes allowed strain 31019b to assimilate nitrogen, but their ¹⁵NH₄⁺ uptake kinetics varied. These results revealed the functional roles of AMT1 during ammonium absorption in the AMT-defective mutant yeast system.

Isolation and functional characterization of an ammonium transporter gene, PyAMT1, related to nitrogen assimilation in the marine macroalga Pyropia yezoensis (Rhodophyta)

Ammonium and nitrate are the primary nitrogen sources in natural environments, and are essential for growth and development in photosynthetic eukaryotes. In this study, we report on the isolation and characterization of an ammonium transporter gene (PyAMT1) which performs a key function in nitrogen (N) metabolism of Pyropia yezoensis thalli. The predicted length of PyAMT1 was 483 amino acids (AAs). The AA sequence included 11 putative transmembrane domains and showed approximately 33-44% identity to algal and plant AMT1 AA sequences. Functional complementation in an AMT-defective yeast mutant indicated that PyAMT1 mediated ammonium transport across the plasma membrane. Expression analysis showed that the PyAMT1 mRNA level was strongly induced by N-deficiency, and was more highly suppressed by resupply of inorganic-N than organic-N. These results suggest that PyAMT1 plays important roles in the ammonium transport system, and is highly regulated in response to external/internal N-status.

Nitrate and Nitrogen Oxides: Sources, Health Effects and Their Remediation

Increased use of nitrogenous (N) fertilizers in agriculture has significantly altered the global N-cycle because they release nitrogenous gases of environmental concerns. The emission of nitrous oxide (N2O) contributes to the global greenhouse gas accumulation and the stratospheric ozone depletion. In addition, it causes nitrate leaching problem deteriorating ground water quality. The nitrate toxicity has been reported in a number of studies showing the health hazards like methemoglobinemia in infants and is a potent cause of cancer. Despite these evident negative environmental as well as health impacts, consumption of N fertilizer cannot be reduced in view of the food security for the teeming growing world population. Various agronomic and genetic modifications have been practiced to tackle this problem. Some agronomic techniques adopted include split application of N, use of slow-release fertilizers, nitrification inhibitors and encouraging the use of organic manure over chemical fertilizers. As a matter of fact, the use of chemical means to remediate nitrate from the environment is very difficult and costly. Particularly, removal of nitrate from water is difficult task because it is chemically non-reactive in dilute aqueous solutions. Hence, the use of biological means for nitrate remediation offers a promising strategy to minimize the ill effects of nitrates and nitrites. One of the important goals to reduce N-fertilizer application can be effectively achieved by choosing N-efficient genotypes. This will ensure the optimum uptake of applied N in a balanced manner and exploring the molecular mechanisms for their uptake as well as metabolism in assimilatory pathways. The objectives of this paper are to evaluate the interrelations which exist in the terrestrial ecosystems between the plant type and characteristics of nutrient uptake and analyze the global consumption and demand for fertilizer nitrogen in relation to cereal production, evaluate the various methods used to determine nitrogen use efficincy (NUE), determine NUE for the major cereals grown across large agroclimatic regions, determine the key factors that control NUE, and finally analyze various strategies available to improve the use efficiency of fertilizer nitrogen.

Evaluation of buffers toxicity in tobacco cells: Homopiperazine-1,4-bis (2-ethanesulfonic acid) is a suitable buffer for plant cells studies at low pH

Low pH is an important environmental stressor of plant root cells. Understanding the mechanisms of stress and tolerance to acidity is critical; however, there is no widely accepted pH buffer for studies of plant cells at low pH. Such a buffer might also benefit studies of Al toxicity, in which buffering at low pH is also important. The challenge is to find a buffer with minimal cellular effects. We examined the cytotoxicity and possible metabolic disturbances of four buffers that have adequate pKa values and potential use for studies in the pH range of 4.0-5.0. These were homopipes (homopiperazine-1,4-bis (2-ethanesulfonic acid); pKa1 4.4), 3,3-dimethylglutaric acid (pKa1 3.73), β-alanine (pKa1 3.70) and potassium biphthalate (pKa1 2.95; pKa2 5.41). First, tobacco BY-2 cells were grown in a rich medium containing 10 mM of each buffer or MES (2-(N-morpholino) ethanesulfonic acid) as a control, with the pH initially adjusted to 5.7. β-alanine was clearly toxic and dimethylgluturate and biphthalate were found to be cytostatic, in which no culture growth occurred but cell viability was either unaffected or decreased only after 5 days. Only homopipes allowed normal culture growth and cell viability. Homopipes (10 mM) was then tested in cell cultures with an initial pH of 4.3 ± 0.17 in minimal medium to examine whether its undissociated species (H2A) displayed any cellular effects and no cytotoxic effects were observed. It is possible to conclude that among tested buffers, homopipes is the most suitable for studies at low pH, and may be especially useful for aluminum toxicity experiments.

Transcriptome and metabolite analysis identifies nitrogen utilization genes in tea plant (Camellia sinensis)

Applied nitrogen (N) fertilizer significantly increases the leaf yield. However, most N is not utilized by the plant, negatively impacting the environment. To date, little is known regarding N utilization genes and mechanisms in the leaf production. To understand this, we investigated transcriptomes using RNA-seq and amino acid levels with N treatment in tea (Camellia sinensis), the most popular beverage crop. We identified 196 and 29 common differentially expressed genes in roots and leaves, respectively, in response to ammonium in two tea varieties. Among those genes, AMT, NRT and AQP for N uptake and GOGAT and GS for N assimilation were the key genes, validated by RT-qPCR, which expressed in a network manner with tissue specificity. Importantly, only AQP and three novel DEGs associated with stress, manganese binding, and gibberellin-regulated transcription factor were common in N responses across all tissues and varieties. A hypothesized gene regulatory network for N was proposed. A strong statistical correlation between key genes’ expression and amino acid content was revealed. The key genes and regulatory network improve our understanding of the molecular mechanism of N usage and offer gene targets for plant improvement.

Controlling the Hydrolysis and Loss of Nitrogen Fertilizer (Urea) by using a Nanocomposite Favors Plant Growth

Urea tends to be hydrolyzed by urease and then migrate into the environment, which results in a low utilization efficiency and severe environmental contamination. To solve this problem, a network-structured nanocomposite (sodium humate-attapulgite-polyacrylamide) was fabricated and used as an excellent fertilizer synergist (FS) that could effectively inhibit the hydrolysis, reduce the loss, and enhance the utilization efficiency of nitrogen. Additionally, the FS exerted significant positive effects on the expression of several nitrogen-uptake-related genes, ion flux in maize roots, the growth of crops, and the organic matter in soil. The FS could modify the microbial community in the soil and increase the number of bacteria involved in nitrogen metabolism, organic matter degradation, the iron cycle, and photosynthesis. Importantly, this technology displayed a high biosafety and has a great potential to reduce nonpoint agricultural pollution. Therefore, this work provides a promising approach to manage nitrogen and to promote the sustainable development of agriculture and the environment.

Molecular fundamentals of nitrogen uptake and transport in trees

Nitrogen (N) is frequently a limiting factor for tree growth and development. Because N availability is extremely low in forest soils, trees have evolved mechanisms to acquire and transport this essential nutrient along with biotic interactions to guarantee its strict economy. Here we review recent advances in the molecular basis of tree N nutrition. The molecular characteristics, regulation, and biological significance of membrane proteins involved in the uptake and transport of N are addressed. The regulation of N uptake and transport in mycorrhized roots and transcriptome-wide studies of N nutrition are also outlined. Finally, several areas of future research are suggested.

Post-translational regulation of nitrogen transporters in plants and microorganisms

For microorganisms and plants, nitrate and ammonium are the main nitrogen sources and they are also important signaling molecules controlling several aspects of metabolism and development. Over the past decade, numerous studies revealed that nitrogen transporters are strongly regulated at the transcriptional level. However, more and more reports are now showing that nitrate and ammonium transporters are also subjected to post-translational regulations in response to nitrogen availability. Phosphorylation is so far the most well studied post-translational modification for these transporters and it affects both the regulation of nitrogen uptake and nitrogen sensing. For example, in Arabidopsis thaliana, phosphorylation was shown to activate the sensing function of the root nitrate transporter NRT1.1 and to switch the transport affinity. Also, for ammonium transporters, a phosphorylation-dependent activation/inactivation mechanism was elucidated in recent years in both plants and microorganisms. However, despite the fact that these regulatory mechanisms are starting to be thoroughly described, the signaling pathways involved and their action on nitrogen transporters remain largely unknown. In this review, we highlight the inorganic nitrogen transporters regulated at the post-translational level and we compare the known mechanisms in plants and microorganisms. We then discuss how these mechanisms could contribute to the regulation of nitrogen uptake and/or nitrogen sensing.

Nitrogen use efficiency in crops: lessons from Arabidopsis and rice

Application of chemical fertilizers, especially nitrogen (N), to crops has increased dramatically in the last half century and therefore developing crop varieties with improved N use efficiency (NUE) is urgent for sustainable agriculture. N utilization procedures generally can be divided into uptake, transport, and assimilation. Transporters for nitrate or ammonium acquisition and enzymes for assimilation are among the essential components determining NUE, and many transcription factors also play a pivotal role in regulating N use-associated genes, thereby contributing to NUE. Although some efforts in improving NUE have been made in various plants, the regulatory mechanisms underlying NUE are still elusive, and NUE improvement in crop breeding is very limited. In this review, the crucial components involved in N utilization and the candidates with the potential for NUE improvement in dicot Arabidopsis and monocot rice are summarized. In addition, strategies based on new techniques which can be used for dissecting regulatory mechanisms of NUE and also the possible ways in which NUE can be improved in crops are discussed.

Genome-wide identification, classification and transcriptional analysis of nitrate and ammonium transporters in Coffea

Nitrogen (N) is quantitatively the main nutrient required by coffee plants, with acquisition mainly by the roots and mostly exported to coffee beans. Nitrate (NO3-) and ammonium (NH4+) are the most important inorganic sources for N uptake. Several N transporters encoded by different gene families mediate the uptake of these compounds. They have an important role in source preference for N uptake in the root system. In this study, we performed a genome-wide analysis, including in silico expression and phylogenetic analyses of AMT1, AMT2, NRT1/PTR, and NRT2 transporters in the recently sequenced Coffea canephora genome. We analyzed the expression of six selected transporters in Coffea arabica roots submitted to N deficiency. N source preference was also analyzed in C. arabica using isotopes. C. canephora N transporters follow the patterns observed for most eudicots, where each member of the AMT and NRT families has a particular role in N mobilization, and where some of these are modulated by N deficiency. Despite the prevalence of putative nitrate transporters in the Coffea genome, ammonium was the preferential inorganic N source for N-starved C. arabica roots. This data provides an important basis for fundamental and applied studies to depict molecular mechanisms involved in N uptake in coffee trees.

Transcription Factor OsDOF18 Controls Ammonium Uptake by Inducing Ammonium Transporters in Rice Roots

Nitrogen is one of the most important mineral elements for plant growth. We studied the functional roles of Oryza sativa DNA BINDING WITH ONE FINGER 18 (OsDOF18) in controlling ammonium uptake. The growth of null mutants of OsDOF18 was retarded in a medium containing ammonium as the sole nitrogen source. In contrast, those mutants grew normally in a medium with nitrate as the sole nitrogen source. The gene expression was induced by ammonium but not by nitrate. Uptake of ammonium was lower in osdof18 mutants than in the wild type, while that of nitrate was not affected by the mutation. This indicated that OsDOF18 is involved in regulating ammonium transport. Among the 10 ammonium transporter genes examined here, expression of OsAMT1;1, OsAMT1;3, OsAMT2;1, and OsAMT4;1 was reduced in osdof18 mutants, demonstrating that the ammonium transporter genes function downstream of OsDOF18. Genes for nitrogen assimilation were also affected in the mutants. These results provide evidence that OsDOF18 mediates ammonium transport and nitrogen distribution, which then affects nitrogen use efficiency.

Addressing Challenges to Enhance the Bioactives of Withania somnifera through Organ, Tissue, and Cell Culture Based Approaches

Withania somnifera is a highly valued medicinal plant in traditional home medicine and is known for a wide range of bioactivities. Its commercial cultivation is adversely affected by poor seed viability and germination. Infestation by various pests and pathogens, survival under unfavourable environmental conditions, narrow genetic base, and meager information regarding biosynthesis of secondary metabolites are some of the other existing challenges in the crop. Biotechnological interventions through organ, tissue, and cell culture provide promising options for addressing some of these issues. In vitro propagation facilitates conservation and sustainable utilization of the existing germplasms and broadening the genetic base. It would also provide means for efficient and rapid mass propagation of elite chemotypes and generating uniform plant material round the year for experimentation and industrial applications. The potential of in vitro cell/organ cultures for the production of therapeutically valuable compounds and their large-scale production in bioreactors has received significant attention in recent years. In vitro culture system further provides distinct advantage for studying various cellular and molecular processes leading to secondary metabolite accumulation and their regulation. Engineering plants through genetic transformation and development of hairy root culture system are powerful strategies for modulation of secondary metabolites. The present review highlights the developments and sketches current scenario in this field.

Related to ABI3/VP1-Like 1 (RAVL1) regulates brassinosteroid-mediated activation of AMT1;2 in rice (Oryza sativa)

The promotive effects of brassinosteroids (BRs) on plant growth and development have been widely investigated; however, it is not known whether BRs directly affect nutrient uptake. Here, we explored the possibility of a direct relationship between BRs and ammonium uptake via AMT1-type genes in rice (Oryza sativa). BR treatment increased the expression of AMT1;1 and AMT1;2, whereas in the mutant d61-1, which is defective in the BR-receptor gene BRI1, BR-dependent expression of these genes was suppressed. We then employed Related to ABI3/VP1-Like 1 (RAVL1), which is involved in BR homeostasis, to investigate BR-mediated AMT1 expression and its effect on NH4+ uptake in rice roots. AMT1;2 expression was lower in the ravl1 mutant, but higher in the RAVL1-overexpressing lines. EMSA and ChIP analyses showed that RAVL1 activates the expression of AMT1;2 by directly binding to E-box motifs in its promoter. Moreover, 15NH4+ uptake, cellular ammonium contents, and root responses to methyl-ammonium strongly depended on RAVL1 levels. Analysing AMT1;2 expression levels in different crosses between BRI1 and RAVL1 mutant and overexpression lines indicated that RAVL1 acts downstream of BRI1 in the regulation of AMT1;2. Thus, the present study shows how BRs may be involved in the transcriptional regulation of nutrient transporters to modulate their uptake capacity.

Characteristics of NH4+ and NO3- fluxes in tea (Camellia sinensis) roots measured by scanning ion-selective electrode technique

As a vital beverage crop, tea has been extensively planted in tropical and subtropical regions. Nitrogen (N) levels and forms are closely related to tea quality. Based on different N levels and forms, we studied changes in NO3- and NH4+ fluxes in tea roots utilizing scanning ion-selective electrode technique. Our results showed that under both single and mixed N forms, influx rates of NO3- were much lower than those of NH4+, suggesting a preference for NH4+ in tea. With the increase in N concentration, the influx rate of NO3- increased more than that of NH4+. The NH4+ influx rates in a solution without NO3- were much higher than those in a solution with NO3-, while the NO3- influx rates in a solution without NH4+ were much lower than those in a solution with NH4+. We concluded that (1) tea roots showed a preference for NH4+, (2) presence of NO3- had a negative effect on NH4+ influx, and (3) NH4+ had a positive effect on NO3- influx. Our findings not only may help advance hydroponic tea experiments but also may be used to develop efficient fertilization protocols for soil-grown tea in the future.

The OsAMT1.1 gene functions in ammonium uptake and ammonium-potassium homeostasis over low and high ammonium concentration ranges

Rice (Oryza sativa) grown in paddy fields is an ammonium (NH₄⁺)-preferring crop; however, its AMT-type NH₄⁺ transporters that mediate root N acquisition have not been well characterized yet. In this study, we analyzed the expression pattern and physiological function of the OsAMT1.1 gene of the AMT1 subfamily in rice. OsAMT1.1 is located in the plasma membrane and is mainly expressed in the root epidermis, stele and mesophyll cells. Disruption of the OsAMT1.1 gene decreased the uptake of NH₄⁺, and the growth of roots and shoots under both low NH₄⁺ and high NH₄⁺ conditions. OsAMT1.1 contributed to the short-term (5 min) ¹⁵NH₄⁺ influx rate by approximately one-quarter, irrespective of the NH₄⁺ concentration. Knockout of OsAMT1.1 significantly decreased the total N transport from roots to shoots under low NH₄⁺ conditions. Moreover, compared with the wild type, the osamt1.1 mutant showed an increase in the potassium (K) absorption rate under high NH₄⁺ conditions and a decrease under low NH₄⁺ conditions. The mutants contained a significantly high concentration of K in both the roots and shoots at a limited K (0.1 mmol/L) supply when NH₄⁺ was replete. Taken together, the results indicated that OsAMT1.1 significantly contributes to the NH₄⁺ uptake under both low and high NH₄⁺ conditions and plays an important role in N-K homeostasis in rice.

Take a Trip Through the Plant and Fungal Transportome of Mycorrhiza

Soil nutrient acquisition and exchanges through symbiotic plant-fungus interactions in the rhizosphere are key features for the current agricultural and environmental challenges. Improved crop yield and plant mineral nutrition through a fungal symbiont has been widely described. In return, the host plant supplies carbon substrates to its fungal partner. We review here recent progress on molecular players of membrane transport involved in nutritional exchanges between mycorrhizal plants and fungi. We cover the transportome, from the transport proteins involved in sugar fluxes from plants towards fungi, to the uptake from the soil and exchange of nitrogen, phosphate, potassium, sulfate, and water. Together, these advances in the comprehension of the mycorrhizal transportome will help in developing the future engineering of new agro-ecological systems.

Gene characterization and transcription analysis of two new ammonium transporters in pear rootstock (Pyrus betulaefolia)

Ammonium is the primarily nitrogen source for plant growth, but the molecular basis of ammonium acquisition in fruit species remains poorly understood. In this study, we report on the characterization of two new ammonium transporters (AMT) in the perennial tree Pyrus betulaefolia. In silico analyses and yeast complementation assays revealed that both PbAMT1;3 and PbAMT1;5 can be classified in the AMT1 sub-family. The specific expression of PbAMT1;3 in roots and of PbAMT1;5 in leaves indicates that they have diverse functions in ammonium uptake or transport in P. betulaefolia. Their expression was strongly influenced by ammonium availability. In addition, the transcript level of PbAMT1;5 was significantly affected by the diurnal cycle and senescence hormones. They conferred the ability to uptake nitrogen to the yeast strain 31019b; however, the (15)NH4 (+) uptake kinetics of PbAMT1;3 were different from those of PbAMT1;5. Indeed, PbAMT1;3 had a higher affinity for (15)NH4 (+), and pH changes were associated with this substrates' transport in yeast. The present study provides basic gene features and transcriptional information for the two new members of the AMT1 sub-family in P. betulaefolia and will aid in decoding the precise roles of AMTs in P. betulaefolia physiology.

Transcriptome Analysis of Gelatin Seed Treatment as a Biostimulant of Cucumber Plant Growth

The beneficial effects of gelatin capsule seed treatment on enhanced plant growth and tolerance to abiotic stress have been reported in a number of crops, but the molecular mechanisms underlying such effects are poorly understood. Using mRNA sequencing based approach, transcriptomes of one- and two-week-old cucumber plants from gelatin capsule treated and nontreated seeds were characterized. The gelatin treated plants had greater total leaf area, fresh weight, frozen weight, and nitrogen content. Pairwise comparisons of the RNA-seq data identified 620 differentially expressed genes between treated and control two-week-old plants, consistent with the timing when the growth related measurements also showed the largest differences. Using weighted gene coexpression network analysis, significant coexpression gene network module of 208 of the 620 differentially expressed genes was identified, which included 16 hub genes in the blue module, a NAC transcription factor, a MYB transcription factor, an amino acid transporter, an ammonium transporter, a xenobiotic detoxifier-glutathione S-transferase, and others. Based on the putative functions of these genes, the identification of the significant WGCNA module and the hub genes provided important insights into the molecular mechanisms of gelatin seed treatment as a biostimulant to enhance plant growth.

Genetic approaches to enhancing nitrogen-use efficiency (NUE) in cereals: challenges and future directions

Over 100million tonnes of nitrogen (N) fertiliser are applied globally each year to maintain high yields in agricultural crops. The rising price of N fertilisers has made them a major cost for farmers. Inefficient use of N fertiliser leads to substantial environmental problems through contamination of air and water resources and can be a significant economic cost. Consequently, there is considerable need to improve the way N fertiliser is used in farming systems. The efficiency with which crops use applied N fertiliser - the nitrogen-use efficiency (NUE) - is currently quite low for cereals. This is the case in both high yielding environments and lower yielding environments characteristic of cereal growing regions of Australia. Multiple studies have attempted to identify the genetic basis of NUE, but the utility of the results is limited because of the complex nature of the trait and the magnitude of genotype by environment interaction. Transgenic approaches have been applied to improve plant NUE but with limited success, due, in part, to a combination of the complexity of the trait but also due to lack of accurate phenotyping methods. This review documents these two approaches and suggests future directions in improving cereal NUE with a focus on the Australian cereal industry.

Switching substrate specificity of AMT/MEP/ Rh proteins

In organisms from all kingdoms of life, ammonia and its conjugated ion ammonium are transported across membranes by proteins of the AMT/Rh family. Efficient and successful growth often depends on sufficient ammonium nutrition. The proteins mediating this transport, the so called Ammonium Transporter (AMT) or Rhesus like (Rh) proteins, share a very similar trimeric overall structure and a high sequence similarity even throughout the kingdoms. Even though structural components of the transport mechanism, like an external substrate recruitment site, an essential twin histidine pore motif, a phenylalanine gate and the hydrophobic pore are strongly conserved and have been analyzed in detail by molecular dynamic simulations and mutational studies, the substrate(s), which pass the central pores of the AMT/Rh subunits, NH4(+), NH3 + H(+), NH4(+) + H(+) or NH3, are still a matter of debate for most proteins, including the best characterized AmtB protein from Escherichia coli. The lack of a robust expression system for functional analysis has hampered proof of structural and mutational studies, although the NH3 transport function for Rh-like proteins is rarely disputed. In plant transporters belonging to the subfamily AMT1, transport is associated with electrical currents, while some plant transporters, notably of the AMT2 type, were suggested to transport NH3 across the membrane, without associated ionic currents. Here we summarize data in favor of each substrate for the distinct AMT/Rh classes, discuss mutants and how they differ in structure and functionality. A common mechanism with deprotonation and subsequent NH3 transport through the central subunit pore is suggested.

Mechanisms of ammonium assimilation by Chlorella vulgaris F1068: Isotope fractionation and proteomic approaches

Removal of ammonium (NH4(+)-N) by microalgae has evoked interest in wastewater treatment, however, the detailed mechanisms of ammonium assimilation remain mysterious. This study investigated the effects of NH4(+)-N concentration on the removal and biotransformation efficiency by Chlorella vulgaris F1068, and explored the mechanisms by (15)N isotope fractionation and proteome approaches. The results showed NH4(+)-N was efficiently removed (84.8%) by F1068 at 10mgL(-1) of NH4(+)-N. The isotope enrichment factor (ε=-2.37±0.08‰) of (15)N isotope fractionation revealed 47.6% biotransformation at above condition, while 7.0% biotransformation at 4mgL(-1) of NH4(+)-N (ε=-1.63±0.06‰). This was due to the different expression of glutamine synthetase, a key enzyme in ammonium assimilation, which was up-regulated 6.4-fold at proteome level and 18.0-fold at transcription level. The results will provide a better mechanistic understanding of ammonium assimilation by microalgae and this green technology is expected to reduce the burden of NH4(+)-N removal for municipal sewage treatment plants.

Overexpressing of OsAMT1-3, a High Affinity Ammonium Transporter Gene, Modifies Rice Growth and Carbon-Nitrogen Metabolic Status

AMT1-3 encodes the high affinity NH₄⁺ transporter in rice roots and is predominantly expressed under nitrogen starvation. In order to evaluate the effect of AMT1-3 gene on rice growth, nitrogen absorption and metabolism, we generated AMT1-3-overexpressing plants and analyzed the growth phenotype, yield, carbon and nitrogen metabolic status, and gene expression profiles. Although AMT1-3 mRNA accumulated in transgenic plants, these plants displayed significant decreases in growth when compared to the wild-type plants. The nitrogen uptake assay using a 15N tracer revealed poor nitrogen uptake ability in AMT1-3-overexpressing plants. We found significant decreases in AMT1-3-overexpressing plant leaf carbon and nitrogen content accompanied with a higher leaf C/N ratio. Significant changes in soluble proteins and carbohydrates were also observed in AMT1-3-overexpressing plants. In addition, metabolite profile analysis demonstrated significant changes in individual sugars, organic acids and free amino acids. Gene expression analysis revealed distinct expression patterns of genes that participate in carbon and nitrogen metabolism. Additionally, the correlation between the metabolites and gene expression patterns was consistent in AMT1-3-overexpressing plants under both low and high nitrogen growth conditions. Therefore, we hypothesized that the carbon and nitrogen metabolic imbalance caused by AMT1-3 overexpressing attributed to the poor growth and yield of transgenic plants.

The rice OsAMT1;1 is a proton-independent feedback regulated ammonium transporter

Functional identification of a relatively lower affinity ammonium transporter, OsAMT1;1, which is a proton-independent feedback regulated ammonium transporter in rice. Rice genome contains at least 12 ammonium transporters, though their functionality has not been clearly resolved. Here, we demonstrate the functional properties of OsAMT1;1 applying functional complementation and (15)NH4 (+) uptake determination in yeast cells in combination with electrophysiological measurements in Xenopus oocytes. Our results show that OsAMT1;1 is a NH4 (+) transporter with relatively lower affinity to NH4 (+) (110-129 μM in oocytes and yeast cells, respectively). Under our experimental conditions, OsAMT1;1-mediated NH4 (+) uptake or current is not significantly modulated by extra- or intracellular pH gradient, suggesting that this transporter probably functions as a NH4 (+) uniporter. Inhibition of yeast growth or currents elicited from oocytes by ammonium assimilation inhibitor L-methionine sulfoximine indicates that NH4 (+) transport by OsAMT1;1 is likely feedback regulated by accumulation of the substrate. In addition, effects of phosphorylation inhibitors imply that NH4 (+) uptake by OsAMT1;1 is also modulated by tyrosine-specific protein kinase or calcium-regulated serine/threonine-specific protein phosphatase involved phosphorylation processes.

Integration of trap- and root-derived nitrogen nutrition of carnivorous Dionaea muscipula

Carnivorous Dionaea muscipula operates active snap traps for nutrient acquisition from prey; so what is the role of D. muscipula's reduced root system? We studied the capacity for nitrogen (N) acquisition via traps, and its effect on plant allometry; the capacity of roots to absorb NO₃(-), NH₄(+) and glutamine from the soil solution; and the fate and interaction of foliar- and root-acquired N. Feeding D. muscipula snap traps with insects had little effect on the root : shoot ratio, but promoted petiole relative to trap growth. Large amounts of NH₄(+) and glutamine were absorbed upon root feeding. The high capacity for root N uptake was maintained upon feeding traps with glutamine. High root acquisition of NH₄(+) was mediated by 2.5-fold higher expression of the NH₄(+) transporter DmAMT1 in the roots compared with the traps. Electrophysiological studies confirmed a high constitutive capacity for NH₄(+) uptake by roots. Glutamine feeding of traps inhibited the influx of (15)N from root-absorbed (15)N/(13)C-glutamine into these traps, but not that of (13)C. Apparently, fed traps turned into carbon sinks that even acquired organic carbon from roots. N acquisition at the whole-plant level is fundamentally different in D. muscipula compared with noncarnivorous species, where foliar N influx down-regulates N uptake by roots.

Sequence and expression analysis of the AMT gene family in poplar

Ammonium transporters (AMTs) are plasma membrane proteins that exclusively transport ammonium/ammonia. These proteins are encoded by an ancient gene family with many members. The molecular characteristics and evolutionary history of AMTs in woody plants are still poorly understood. We comprehensively evaluated the AMT gene family in the latest release of the Populus trichocarpa genome (version 3.0; Phytozome 9.0), and identified 16 AMT genes. These genes formed four clusters; AMT1 (7 genes), AMT2 (2 genes), AMT3 (2 genes), and AMT4 (5 genes). Evolutionary analyses suggested that the Populus AMT gene family has expanded via whole-genome duplication events. Among the 16 AMT genes, 15 genes are located on 11 chromosomes of Populus. Expression analyses showed that 14 AMT genes were vegetative organs expressed; AMT1;1/1;3/1;6/3;2 and AMT1;1/1;2/2;2/3;1 had high transcript accumulation level in the leaves and roots, respectively and strongly changes under the nitrogen-dependent experiments. The results imply the functional roles of AMT genes in ammonium absorption in poplar.

Involvement of indole-3-acetic acid produced by Azospirillum brasilense in accumulating intracellular ammonium in Chlorella vulgaris

Accumulation of intracellular ammonium and activities of the enzymes glutamine synthetase (GS) and glutamate dehydrogenase (GDH) were measured when the microalgae Chlorella vulgaris was immobilized in alginate with either of two wild type strains of Azospirillum brasilense or their corresponding indole-3-acetic acid (IAA)-attenuated mutants. After 48 h of immobilization, both wild types induced higher levels of intracellular ammonium in the microalgae than their respective mutants; the more IAA produced, the higher the intracellular ammonium accumulated. Accumulation of intracellular ammonium in the cells of C. vulgaris followed application of four levels of exogenous IAA reported for A. brasilense and its IAA-attenuated mutants, which had a similar pattern for the first 24 h. This effect was transient and disappeared after 48 h of incubation. Immobilization of C. vulgaris with any bacteria strain induced higher GS activity. The bacterial strains also had GS activity, comparable to the activity detected in C. vulgaris, but weaker than when immobilized with the bacteria. When net activity was calculated, the wild type always induced higher GS activity than IAA-attenuated mutants. GDH activity in most microalgae/bacteria interactions resembled GS activity. When complementing IAA-attenuated mutants with exogenous IAA, GS activity in co-immobilized cultures matched those of the wild type A. brasilense immobilized with the microalga. Similarity occurred when the net GS activity was measured, and was higher with greater quantities of exogenous IAA. It is proposed that IAA produced by A. brasilense is involved in ammonium uptake and later assimilation by C. vulgaris.