Distinct expression and function of three ammonium transporter genes (OsAMT1;1-1;3) in rice

Phytochrome B-mediated light signalling enhances rice resistance to saline-alkaline and sheath blight by regulating multiple downstream transcription factors

Light signalling regulates plant growth and stress resistance, whereas its mechanism in controlling saline-alkaline tolerance (SAT) remains largely unknown. This study identified that light signalling, primarily mediated by Phytochrome B (PhyB), inhibited ammonium transporter 1 (AMT1) to negatively regulate SAT. Our previous findings have shown that PhyB can impede the transcription factors indeterminate domain 10 (IDD10) and brassinazole resistant 1 (BZR1) to reduce NH4 + uptake, thereby modulating SAT and sheath blight (ShB) resistance in rice. However, inhibition of IDD10 and BZR1 in the phyB background did not fully suppress NH4 + uptake, suggesting that other signalling pathways regulated AMT1 downstream of PhyB. Further analysis revealed that PhyB interacted with Calcineurin B-like protein-interacting protein kinase 31 (CIPK31), which positively regulated AMT1 expression. CIPK31 also interacted with Teosinte Branched1/Cycloidea/PCF19 (TCP19), a key regulator of nitrogen use efficiency (NUE). However, PhyB neither degraded CIPK31 nor directly interacted with TCP19. Instead, PhyB inhibited the CIPK31-TCP19 interaction, releasing TCP19, which repressed AMT1;2 directly and AMT1;1 and AMT1;3 indirectly, thereby inhibiting NH4 + uptake and SAT while reducing ShB resistance. Additionally, Phytochrome Interacting Factor-Like 15 (PIL15) interacted with TCP19. Different from TCP19, PIL15 directly activated AMT1;2 to promote SAT, suggesting a balancing mechanism for NH4 + uptake downstream of PhyB. Furthermore, PIL15 interacted with IDD10 and BZR1 to form a transcriptional complex that collaboratively activated AMT1;2 expression. Overall, this study provides novel insights into how PhyB signalling regulates NH4 + uptake and coordinates SAT and ShB resistance in rice.

Ammonium Transporter 1 (AMT1) Gene Family in Pomegranate: Genome-Wide Analysis and Expression Profiles in Response to Salt Stress

Understanding the ammonium (NH4+) uptake and transport systems, particularly AMT1 genes, is important for plant growth and defense. However, there is a lack of research on identifying and analyzing AMT1 genes in pomegranate, emphasizing the need for further investigation in this area. Five AMT1 genes (PgAMT1-1 to PgAMT1-5) were identified, all of which contain the PF00909 domain, a feature of ammonium transporters. Various characteristics of these genes, including gene length, coding sequence length, and chromosomal locations, were examined. This study evaluated the isoelectric point, hydropathicity, conserved domains, motifs, and synteny of the PgAMT1 proteins. Phylogenetic analysis confirmed the homology of PgAMT1 genes with previously reported AMT in Arabidopsis and tomato. The tissue-specific expression analysis of PgAMT1 genes revealed distinct patterns: PgAMT1-1 and PgAMT1-2 were predominantly expressed in flowers, PgAMT1-3 exhibited notable expression in roots, leaves, and flowers, PgAMT1-4 was primarily expressed in leaf tissue, while the expression of PgAMT1-5 was detected in both leaves and roots. The impact of salt-induced stress on AMT1 gene expression was also examined, revealing that PgAMT1-1, PgAMT1-2, and PgAMT1-4 expression is reduced under increased salt stress. These expression modifications can help regulate NH4+ assimilation in conditions of elevated salinity, maintaining cellular homeostasis and ion balance. This study contributes to the comprehensive identification of the AMT1s gene family in pomegranate; however, further research on the functional characterization of the identified PgAMT1s is needed.

The Identification of AMT Family Genes and Their Expression, Function, and Regulation in Chenopodium quinoa

Quinoa (Chenopodium quinoa) is an Andean allotetraploid pseudocereal crop with higher protein content and balanced amino acid composition in the seeds. Ammonium (NH4+), a direct source of organic nitrogen assimilation, mainly transported by specific transmembrane ammonium transporters (AMTs), plays important roles in the development, yield, and quality of crops. Many AMTs and their functions have been identified in major crops; however, no systematic analyses of AMTs and their regulatory networks, which is important to increase the yield and protein accumulation in the seeds of quinoa, have been performed to date. In this study, the CqAMTs were identified, followed by the quantification of the gene expression, while the regulatory networks were predicted based on weighted gene co-expression network analysis (WGCNA), with the putative transcriptional factors (TFs) having binding sites on the promoters of CqAMTs, nitrate transporters (CqNRTs), and glutamine-synthases (CqGSs), as well as the putative TF expression being correlated with the phenotypes and activities of GSs, glutamate synthase (GOGAT), nitrite reductase (NiR), and nitrate reductase (NR) of quinoa roots. The results showed a total of 12 members of the CqAMT family with varying expressions in different organs and in the same organs at different developmental stages. Complementation expression analyses in the triple mep1/2/3 mutant of yeast showed that except for CqAMT2.2b, 11/12 CqAMTs restored the uptake of NH4+ in the host yeast. CqAMT1.2a was found to mainly locate on the cell membrane, while TFs (e.g., CqNLPs, CqG2Ls, B3 TFs, CqbHLHs, CqZFs, CqMYBs, CqNF-YA/YB/YC, CqNACs, and CqWRKY) were predicted to be predominantly involved in the regulation, transportation, and assimilation of nitrogen. These results provide the functions of CqAMTs and their possible regulatory networks, which will lead to improved nitrogen use efficiency (NUE) in quinoa as well as other major crops.

OsAMT1.1 knockout-induced decrease in cadmium absorption and accumulation by rice related to cadmium absorption-related gene downregulation

Cadmium (Cd) is a hazardous heavy metal that poses a serious risk to human health through the food chain, with rice being a significant vector because of its tendency to accumulate Cd. Nitrogen (N), an essential element for plant growth, also affects the Cd absorption and accumulation in crops. This study investigated the effects of N application on Cd absorption and accumulation in Cd-contaminated soils. Potting experiment showed that increasing N concentrations significantly increased the plant biomass and Cd contents in rice tissues. Ammonium (NH4+) transporter gene OsAMT1.1 knockout led to a substantial reduction in Cd absorption and accumulation in all rice tissues compared to that in the wild-type plants. Specifically, osamt1.1 mutants increased the Cd content in culm tissues, whereas it was reduced in brown rice. In addition, OsAMT1.1 knockout reduced Cd2+ influx in roots under NH4+-N addition, although OsAMT1.1 lacked Cd transport ability when expressed in yeast. Gene expression analysis revealed that OsAMT1.1 knockout reduced Cd absorption-related genes (OsIRT1, OsNRAMP1, and OsNRAMP5) expression levels. These finding highlight the critical role of N supply and OsAMT1.1 in regulating the Cd content in rice, offering insights into the molecular mechanisms of Cd transportation in plants.

Biological ammonium transporters: evolution and diversification

Although ammonium is the preferred nitrogen source for microbes and plants, in animal cells it is a toxic product of nitrogen metabolism that needs to be excreted. Thus, ammonium movement across biological membranes, whether for uptake or excretion, is a fundamental and ubiquitous biological process catalysed by the superfamily of the Amt/Mep/Rh transporters. A remarkable feature of the Amt/Mep/Rh family is that they are ubiquitous and, despite sharing low amino acid sequence identity, are highly structurally conserved. Despite sharing a common structure, these proteins have become involved in a diverse range of physiological process spanning all domains of life, with reports describing their involvement in diverse biological processes being published regularly. In this context, we exhaustively present their range of biological roles across the domains of life and after explore current hypotheses concerning their evolution to help to understand how and why the conserved structure fulfils diverse physiological functions.

A microscopic scenario on recovery mechanisms under waterlogging and submergence stress in rice

MAIN CONCLUSION

Adaptive traits in rice responding to flooding, a compound stress, are associated with morpho-anatomical and physiological changes which are regulated at the genetic level. Therefore, understanding submergence stress tolerance in rice will help development of adapted cultivars that can help mitigate agricultural losses. Rice is an important dietary component of daily human consumption and is cultivated as a staple crop worldwide. Flooding is a compound stress which imposes significant financial losses to farmers. Flood-affected rainfed rice ecosystems led to the development of various adaptive traits in different cultivars for their optimal growth and survival. Some cultivars can tolerate hypoxia by temporarily arresting elongation and conserving their energy sources, which they utilize to regrow after the stress conditions subside. However, few other cultivars rapidly elongate to escape hypoxia using carbohydrate resources. These contrasting characters are regulated at the genetic level through different quantitative trait loci that contain ERF transcription factors (TFs), Submergence and Snorkels. TFs can simultaneously activate the transcription of various genes involved in stress and development responses. These TFs are of prime importance because the introgressed and near-isogenic lines showed promising results with increased submergence tolerance without affecting yield or quality. However, the entire landscape of submergence tolerance is not entirely depicted, and further exploration in the field is necessary to understand the mechanism in rice completely. Therefore, this review will highlight the significant adaptive traits observed in flooded rice varieties and how they are regulated mechanistically.

Linking glucose signaling to nitrogen utilization by the OsHXK7-ARE4 complex in rice

How reciprocal regulation of carbon and nitrogen metabolism works is a long-standing question. In plants, glucose and nitrate are proposed to act as signaling molecules, regulating carbon and nitrogen metabolism via largely unknown mechanisms. Here, we show that the MYB-related transcription factor ARE4 coordinates glucose signaling and nitrogen utilization in rice. ARE4 is retained in the cytosol in complexing with the glucose sensor OsHXK7. Upon sensing a glucose signal, ARE4 is released, is translocated into the nucleus, and activates the expression of a subset of high-affinity nitrate transporter genes, thereby boosting nitrate uptake and accumulation. This regulatory scheme displays a diurnal pattern in response to circadian changes of soluble sugars. The are4 mutations compromise in nitrate utilization and plant growth, whereas overexpression of ARE4 increases grain size. We propose that the OsHXK7-ARE4 complex links glucose to the transcriptional regulation of nitrogen utilization, thereby coordinating carbon and nitrogen metabolism.

Varietal responses of root characteristics to low nitrogen application explain the differing nitrogen uptake and grain yield in two rice varieties

Rice root characteristics are tightly associated with high-efficient nitrogen uptake. To understand the relationship of root plastic responses with nitrogen uptake when reducing nitrogen application for green rice production, a hydroponic experiment and a soil pot experiment were conducted under high (HN) and low (LN) nitrogen applications, using two rice (Oryza sativa L.) varieties, NK57 and YD6, three nitrogen absorption traits (total nitrogen accumulation, net NH4 + influx on root surface, nitrogen uptake via apoplasmic pathway) and root characteristics were investigated. In comparison with HN, LN significantly reduced nitrogen absorption and grain yield in both varieties. Concomitantly, there was a decrease in total root length, root surface area, root number, root volume, and root cortical area under LN, while single root length, root aerenchyma area, and root lignin content increased. The expression of OsAMT1;1 and OsAMT1;2 down-regulated in both varieties. The findings revealed that YD6 had smaller reduction degree for the three nitrogen absorption traits and grain yield, accompanied by smaller reduction degree in total root length, root surface area, root cortical area, and expression of the two genes under LN. These root characteristics were significantly and positively correlated with the three nitrogen absorption traits and grain yield, especially under LN. These results indicate that a large root system, lower reduction degree in several root characters, and high expression of OsAMT genes in YD6 explains its high nitrogen accumulation and grain yield under reduced nitrogen application. The study may provide rationale for developing varieties with low nitrogen fertilizer requirements for enabling green rice production.

Genome-wide association study using specific-locus amplified fragment sequencing identifies new genes influencing nitrogen use efficiency in rice landraces

Nitrogen is essential for crop production. It is a critical macronutrient for plant growth and development. However, excessive application of nitrogen fertilizer is not only a waste of resources but also pollutes the environment. An effective approach to solving this problem is to breed rice varieties with high nitrogen use efficiency (NUE). In this study, we performed a genome-wide association study (GWAS) on 419 rice landraces using 208,993 single nucleotide polymorphisms (SNPs). With the mixed linear model (MLM) in the Tassel software, we identified 834 SNPs associated with root surface area (RSA), root length (RL), root branch number (RBN), root number (RN), plant dry weight (PDW), plant height (PH), root volume (RL), plant fresh weight (PFW), root fractal dimension (RFD), number of root nodes (NRN), and average root diameter (ARD), with a significant level of p < 2.39×10^-7. In addition, we found 49 SNPs that were correlated with RL, RBN, RN, PDW, PH, PFW, RFD, and NRN using genome-wide efficient mixed-model association (GEMMA), with a significant level of p < 1×10^-6. Additionally, the final results for eight traits associated with 193 significant SNPs by using multi-locus random-SNP-effect mixed linear model (mrMLM) model and 272 significant SNPs associated with 11 traits by using IIIVmrMLM. Within the linkage intervals of significantly associated SNP, we identified eight known related genes to NUE in rice, namely, OsAMT2;3, OsGS1, OsNR2, OsNPF7.4, OsPTR9, OsNRT1.1B, OsNRT2.3, and OsNRT2.2. According to the linkage disequilibrium (LD) decay value of this population, there were 75 candidate genes within the 150-kb regions upstream and downstream of the most significantly associated SNP (Chr5_29804690, Chr5_29956584, and Chr10_17540654). These candidate genes included 22 transposon genes, 25 expressed genes, and 28 putative functional genes. The expression levels of these candidate genes were measured by real-time quantitative PCR (RT-qPCR), and the expression levels of LOC_Os05g51700 and LOC_Os05g51710 in C347 were significantly lower than that in C117; the expression levels of LOC_Os05g51740, LOC_Os05g51780, LOC_Os05g51960, LOC_Os05g51970, and LOC_Os10g33210 were significantly higher in C347 than C117. Among them, LOC_Os10g33210 encodes a peptide transporter, and LOC_Os05g51690 encodes a CCT domain protein and responds to NUE in rice. This study identified new loci related to NUE in rice, providing new genetic resources for the molecular breeding of rice landraces with high NUE.

Genetic regulation of nitrogen use efficiency in Gossypium spp

Cotton (Gossypium spp.) is the most important fibre crop, with desirable characteristics preferred for textile production. Cotton fibre output relies heavily on nitrate as the most important source of inorganic nitrogen (N). However, nitrogen dynamics in extreme environments limit plant growth and lead to yield loss and pollution. Therefore, nitrogen use efficiency (NUE), which involves the utilisation of the 'right rate', 'right source', 'right time', and 'right place' (4Rs), is key for efficient N management. Recent omics techniques have genetically improved NUE in crops. We herein highlight the mechanisms of N uptake and assimilation in the vegetative and reproductive branches of the cotton plant while considering the known and unknown regulatory factors. The phylogenetic relationships among N transporters in four Gossypium spp. have been reviewed. Further, the N regulatory genes that participate in xylem transport and phloem loading are also discussed. In addition, the functions of microRNAs and transcription factors in modulating the expression of target N regulatory genes are highlighted. Overall, this review provides a detailed perspective on the complex N regulatory mechanism in cotton, which would accelerate the research toward improving NUE in crops.

Growth, nutrient uptake and transcriptome profiling of rice seedlings in response to mixed provision of ammonium- and nitrate-nitrogen

Nitrogen (N) is a principal macronutrient and plays a paramount role in mineral nutrition of rice plants. Mixed provision of ammonium- and nitrate-nitrogen (MPAN) at a moderate level could enhance N uptake and translocation and promote growth of rice, but current understanding of their molecular mechanisms is still insufficient. Two rice lines of W6827 and GH751, with contrasting ability of N uptake, were subjected to four levels of MPAN (NH₄⁺/NO₃^- = 100:0, 75:25, 50:50, 25:75) in hydroponic experiments. In terms of plant height, growth rate and shoot biomass, growth of GH751 tended to increase firstly and then decrease with enhancement in NO₃^--N ratio. It attained maximal level under 75:25 MPAN, with an 8.3% increase in shoot biomass. In general, W6827 was comparatively less responsive to MPAN. For GH751, the uptake rate of N, phosphor (P) and potassium (K) under 75:25 MPAN was enhanced by 21.1%, 20.8% and 16.1% in comparison with that of control (100:0 MPAN). Meanwhile, the translocation coefficient and content in shoots of N, P and K were all increased significantly. In contrast to transcriptomic profile under control, 288 differentially expressed genes (DEGs) were detected to be up-regulated and 179 DEGs down-regulated in transcription under 75:25 MPAN. Gene Ontology analysis revealed that some DEGs were up-regulated under 75:25 MPAN and they code for proteins mainly located in membrane and integral component of membrane and involved in metal ion binding, oxidoreductase activity and other biological processes. KEGG pathway enrichment analysis indicated that DEGs related to nitrogen metabolism, carbon fixation in photosynthetic organisms, photosynthesis, starch and sucrose metabolism, and zeatin biosynthesis were up- or down-regulated in transcription under 75:25 MPAN, and they are responsible for improved nutrient uptake and translocation and enhanced growth of seedlings.

Comparative transcriptome analyses under individual and combined nutrient starvations provide insights into N/P/K interactions in rice

Crops often suffer from simultaneous limitations of multiple nutrients in soils, including nitrogen (N), phosphorus (P) and potassium (K), which are three major macronutrients essential for ensuring growth and yield. Although plant responses to individual N, P, and K deficiency have been well documented, our understanding of the responses to combined nutrient deficiencies and the crosstalk between nutrient starvation responses is still limited. Here, we compared the physiological responses in rice under seven kinds of single and multiple low nutrient stress of N, P and K, and used RNA sequencing approaches to compare their transcriptome changes. A total of 13,000 genes were found to be differentially expressed under all these single and multiple low N/P/K stresses, and 66 and 174 of them were shared by all these stresses in roots and shoots, respectively. Functional enrichment analyses of the DEGs showed that a group of biological and metabolic processes were shared by these low N/P/K stresses. Comparative analyses indicated that DEGs under multiple low nutrient stress was not the simple summation of single nutrient stress. N was found to be the predominant factor affecting the transcriptome under combined nutrient stress. N, P, or K availability exhibited massive influences on the transcriptomic responses to starvation of other nutrients. Many genes involved in nutrient transport, hormone signaling, and transcriptional regulation were commonly responsive to low N/P/K stresses. Some transcription factors were predicted to regulate the expression of genes that are commonly responsive to N, P, and K starvations. These results revealed the interactions between N, P, and K starvation responses, and will be helpful for further elucidation of the molecular mechanisms underlying nutrient interactions.

Analysis of the AMT gene family in chili pepper and the effects of arbuscular mycorrhizal colonization on the expression patterns of CaAMT2 genes

BACKGROUND

Ammonium (NH₄⁺) is a key nitrogen source supporting plant growth and development. Proteins in the ammonium transporter (AMT) family mediate the movement of NH₄⁺ across the cell membrane. Although several studies have examined AMT genes in various plant species, few studies of the AMT gene family have been conducted in chili pepper.

RESULTS

Here, a total of eight AMT genes were identified in chili pepper, and their exon/intron structures, phylogenetic relationships, and expression patterns in response to arbuscular mycorrhizal (AM) colonization were explored. Synteny analyses among chili pepper, tomato, eggplant, soybean, and Medicago revealed that the CaAMT2;1, CaAMT2.4, and CaAMT3;1 have undergone an expansion prior to the divergence of Solanaceae and Leguminosae. The expression of six AMT2 genes was either up-regulated or down-regulated in response to AM colonization. The expression of CaAMT2;1/2;2/2;3 and SlAMT2;1/2;2/2;3 was significantly up-regulated in AM fungi-inoculated roots. A 1,112-bp CaAMT2;1 promoter fragment and a 1,400-bp CaAMT2;2 promoter fragment drove the expression of the β-glucuronidase gene in the cortex of AM roots. Evaluation of AM colonization under different NH₄⁺ concentrations revealed that a sufficient, but not excessive, supply of NH₄⁺ promotes the growth of chili pepper and the colonization of AM. Furthermore, we demonstrated that CaAMT2;2 overexpression could mediate NH₄⁺ uptake in tomato plants.

CONCLUSION

In sum, our results provide new insights into the evolutionary relationships and functional divergence of chili pepper AMT genes. We also identified putative AMT genes expressed in AM symbiotic roots.

Bioengineering Techniques to Improve Nitrogen Transformation and Utilization: Implications for Nitrogen Use Efficiency and Future Sustainable Crop Production

Nitrogen (N) is crucial for plant growth and development, especially in physiological and biochemical processes such as component of different proteins, enzymes, nucleic acids, and plant growth regulators. Six categories, such as transporters, nitrate absorption, signal molecules, amino acid biosynthesis, transcription factors, and miscellaneous genes, broadly encompass the genes regulating NUE in various cereal crops. Herein, we outline detailed research on bioengineering modifications of N metabolism to improve the different crop yields and biomass. We emphasize effective and precise molecular approaches and technologies, including N transporters, transgenics, omics, etc., which are opening up fascinating opportunities for a complete analysis of the molecular elements that contribute to NUE. Moreover, the detection of various types of N compounds and associated signaling pathways within plant organs have been discussed. Finally, we highlight the broader impacts of increasing NUE in crops, crucial for better agricultural yield and in the greater context of global climate change.

Genome-Wide Identification and Characterization of Ammonium Transporter (AMT) Genes in Rapeseed (Brassica napus L.)

Ammonium transporters (AMTs) are plasma membrane proteins mediating ammonium uptake and transport. As such, AMTs play vital roles in ammonium acquisition and mobilization, plant growth and development, and stress and pathogen defense responses. Identification of favorable AMT genotypes is a prime target for crop improvement. However, to date, systematic identification and expression analysis of AMT gene family members has not yet been reported for rapeseed (Brassica napus L.). In this study, 20 AMT genes were identified in a comprehensive search of the B. napus genome, 14 members of AMT1 and 6 members of AMT2. Tissue expression analyses revealed that the 14 AMT genes were primarily expressed in vegetative organs, suggesting that different BnaAMT genes might function in specific tissues at the different development stages. Meanwhile, qRT-PCR analysis found that several BnaAMTs strongly respond to the exogenous N conditions, implying the functional roles of AMT genes in ammonium absorption in rapeseed. Moreover, the rapeseed AMT genes were found to be differentially regulated by N, P, and K deficiency, indicating that crosstalk might exist in response to different stresses. Additionally, the subcellular localization of several BnaAMT proteins was confirmed in Arabidopsis protoplasts, and their functions were studied in detail by heterologous expression in yeast. In summary, our studies revealed the potential roles of BnaAMT genes in N acquisition or transportation and abiotic stress response and could provide valuable resources for revealing the functionality of AMTs in rapeseed.

Signaling pathways underlying nitrogen transport and metabolism in plants

Nitrogen (N) is an essential macronutrient required for plant growth and crop production. However, N in soil is usually insufficient for plant growth. Thus, chemical N fertilizer has been extensively used to increase crop production. Due to negative effects of N rich fertilizer on the environment, improving N usage has been a major issue in the field of plant science to achieve sustainable production of crops. For that reason, many efforts have been made to elucidate how plants regulate N uptake and utilization according to their surrounding habitat over the last 30 years. Here, we provide recent advances focusing on regulation of N uptake, allocation of N by N transporting system, and signaling pathway controlling N responses in plants. [BMB Reports 2023; 56(2): 56-64].

Physio-biochemical, agronomical, and gene expression analysis reveals different responsive approach to low nitrogen in contrasting rice cultivars for nitrogen use efficiency

BACKGROUND

Nitrogen (N) is an essential macronutrient for plant growth and development as it is an essential constituent of biomolecules. Its availability directly impacts crop yield. Increased N application in crop fields has caused environmental and health problems, and decreasing nitrogen inputs are in demand to maintain crop production sustainability. Understanding the molecular mechanism of N utilization could play a crucial role in improving the nitrogen use efficiency (NUE) of crop plants.

METHODS AND RESULTS

In the present study, the effect of low N supply on plant growth, physio-biochemical, chlorophyll fluorescence attributes, yield components, and gene expression analysis were measured at six developmental stages in rice cultivars. Two rice cultivars were grown with a supply of optimium (120 kg ha^-1) and low N (60 kg ha^-1). Cultivar Vikramarya excelled Aditya at low N supply, and exhibits enhanced plant growth, physiological efficiency, agronomic efficiency, and improved NUE due to higher N uptake and utilization at low N treatment. Moreover, plant biomass, leaf area, and photosynthetic rate were significantly higher in cv. Vikramarya than cv. Aditya at different growth stages, under low N treatment. In addition, enzymatic activities in cultivar Vikramarya were higher than cultivar Aditya under low nitrogen, indicating its greater potential for N metabolism. Gene expression analysis was carried out for the most important nitrogen assimilatory enzymes, such as nitrate reductase (NR), nitrite reductase (NiR), glutamine synthetase (GS), and glutamate synthase (GOGAT). Expression levels of these genes at different growth stages were significantly higher in cv. Vikramarya compared to cv. Aditya at low N supply. Our findings suggest that improving NUE needs specific revision in N metabolism and physiological assimilation.

CONCLUSION

Overall differences in plant growth, physiological efficiency, biochemical activities, and expression levels of N metabolism genes in N-efficient and N-inefficient rice cultivars need a specific adaptation to N metabolism. Regulatory genes may separately or in conjunction, enhance the NUE. These results provide a platform for selecting crop cultivars for nitrogen utilization efficiency at low N treatment.

Ectopic Expression of Sugarcane ScAMT1.1 Has the Potential to Improve Ammonium Assimilation and Grain Yield in Transgenic Rice under Low Nitrogen Stress

In China, nitrogen (N) fertilizer is excessively used in sugarcane planting areas, while the nitrogen use efficiency (NUE) of sugarcane is relatively low. Mining and identifying the key genes in response to low N stress in sugarcane can provide useful gene elements and a theoretical basis for developing sugarcane varieties with high NUE. In our study, RNA-Seq combined with qRT-PCR analysis revealed that the ScAMT1.1 gene responded positively to low N stress, resulting in the stronger low N tolerance and high NUE ability of sugarcane cultivar ROC22. Then, ScAMT1.1 was cloned from sugarcane. The full-length cDNA of the ScAMT1.1 gene is 1868 bp, containing a 1491 bp open reading frame (ORF), and encoding 496 amino acids. ScAMT1.1 belongs to the AMT superfamily and shares 91.57% homologies with AMT1.1 from Oryza sativa. Furthermore, it was stably overexpressed in rice (O. sativa). Under low N treatment, the plant height and the fresh weight of the ScAMT1.1-overexpressed transgenic rice were 36.48% and 51.55% higher than that of the wild-type, respectively. Both the activity of ammonium assimilation key enzymes GS and GDH, and the expression level of ammonium assimilation key genes, including GS1.1, GS1.2, GDH, Fd-GOGAT, and NADH-GOGAT2 in the transgenic plants, were significantly higher than that of the wild-type. The grain number and grain yield per plant in the transgenic rice were 6.44% and 9.52% higher than that of the wild-type in the pot experiments, respectively. Taken together, the sugarcane ScAMT1.1 gene has the potential to improve ammonium assimilation ability and the yield of transgenic rice under low N fertilizer conditions. This study provided an important functional gene for improving sugarcane varieties with high NUE.

Ammonium Uptake, Mediated by Ammonium Transporters, Mitigates Manganese Toxicity in Duckweed, Spirodela polyrhiza

Nitrogen is an essential nutrient that affects all aspects of the growth, development and metabolic responses of plants. Here we investigated the influence of the two major sources of inorganic nitrogen, nitrate and ammonium, on the toxicity caused by excess of Mn in great duckweed, Spirodela polyrhiza. The revealed alleviating effect of ammonium on Mn-mediated toxicity, was complemented by detailed molecular, biochemical and evolutionary characterization of the species ammonium transporters (AMTs). Four genes encoding AMTs in S. polyrhiza, were classified as SpAMT1;1, SpAMT1;2, SpAMT1;3 and SpAMT2. Functional testing of the expressed proteins in yeast and Xenopus oocytes clearly demonstrated activity of SpAMT1;1 and SpAMT1;3 in transporting ammonium. Transcripts of all SpAMT genes were detected in duckweed fronds grown in cultivation medium, containing a physiological or 50-fold elevated concentration of Mn at the background of nitrogen or a mixture of nitrate and ammonium. Each gene demonstrated an individual expression pattern, revealed by RT-qPCR. Revealing the mitigating effect of ammonium uptake on manganese toxicity in aquatic duckweed S. polyrhiza, the study presents a comprehensive analysis of the transporters involved in the uptake of ammonium, shedding a new light on the interactions between the mechanisms of heavy metal toxicity and the regulation of the plant nitrogen metabolism.

Mutation of phytochrome B promotes resistance to sheath blight and saline-alkaline stress via increasing ammonium uptake in rice

Phytochrome B (PhyB), a red-light receptor, plays important roles in diverse biological processes in plants; however, its function in NH₄ ⁺ uptake and stress responses of plants is unclear. Here, we observed that mutation in indeterminate domain 10 (IDD10), which encodes a key transcription factor in NH₄ ⁺ signaling, led to NH₄ ⁺ -sensitive root growth in light but not in the dark. Genetic combinations of idd10 and phy mutants demonstrated that phyB, but not phyA or phyC, suppressed NH₄ ⁺ -sensitive root growth of idd10. PhyB mutants and PhyB overexpressors (PhyB OXs) accumulated more and less NH₄ ⁺ , respectively, compared with wild-type plants. Real time quantitative polymerase chain reaction (RT-qPCR) revealed that PhyB negatively regulated NH₄ ⁺ -mediated induction of Ammonium transporter 1;2 (AMT1;2). AMT1 RNAi plants with suppressed AMT1;1, AMT1;2, and AMT1;3 expression exhibited shorter primary roots under NH₄ ⁺ conditions. This suggested that NH₄ ⁺ uptake might be positively associated with root growth. Further, PhyB interacted with and inhibited IDD10 and brassinazole-resistant 1 (BZR1). IDD10 interacted with BZR1 to activate AMT1;2. NH₄ ⁺ uptake is known to promote resistance of rice (Oryza sativa) to sheath blight (ShB) and saline-alkaline stress. Inoculation of Rhizoctonia solani demonstrated that PhyB and IDD10 negatively regulated and AMT1 and BZR1 positively regulated resistance of rice to ShB. In addition, PhyB negatively regulated and IDD10 and AMT1 positively regulated resistance of rice to saline-alkaline stress. This suggested that PhyB-IDD10-AMT1;2 signaling regulates the saline-alkaline response, whereas the PhyB-BZR1-AMT1;2 pathway modulates ShB resistance. Collectively, these data prove that mutation in the PhyB gene enhances the resistance of rice to ShB and saline-alkaline stress by increasing NH₄ ⁺ uptake.

Genome-Wide Comprehensive Analysis of the Nitrogen Metabolism Toolbox Reveals Its Evolution and Abiotic Stress Responsiveness in Rice (Oryza sativa L.)

Nitrogen metabolism (NM) plays an essential role in response to abiotic stresses for plants. Enzyme activities have been extensively studied for nitrogen metabolism-associated pathways, but the knowledge of nitrogen metabolism-associated genes involved in stress response is still limited, especially for rice. In this study, we performed the genome-wide characterization of the genes putatively involved in nitrogen metabolism. A total of 1110 potential genes were obtained to be involved in nitrogen metabolism from eight species (Arabidopsis thaliana (L.) Heynh., Glycine max (L.) Merr., Brassica napus L., Triticum aestivum L., Sorghum bicolor L., Zea mays L., Oryza sativa L. and Amborella trichopoda Baill.), especially 104 genes in rice. The comparative phylogenetic analysis of the superfamily revealed the complicated divergence of different NM genes. The expression analysis among different tissues in rice indicates the NM genes showed diverse functions in the pathway of nitrogen absorption and assimilation. Distinct expression patterns of NM genes were observed in rice under drought stress, heat stress, and salt stress, indicating that the NM genes play a curial role in response to abiotic stress. Most NM genes showed a down-regulated pattern under heat stress, while complicated expression patterns were observed for different genes under salt stress and drought stress. The function of four representative NM genes (OsGS2, OsGLU, OsGDH2, and OsAMT1;1) was further validated by using qRT-PCR analysis to confirm their responses to these abiotic stresses. Based on the predicted transcription factor binding sites (TFBSs), we built a co-expression regulatory network containing transcription factors (TFs) and NM genes, of which the constructed ERF and Dof genes may act as the core genes to respond to abiotic stresses. This study provides novel sights to the interaction between nitrogen metabolism and the response to abiotic stresses.

Synergistic effects of nitrogen metabolites on auxin regulating plant growth and development

Nitrogen is one of the important nutrients required for plant growth and development. There is increasing evidences that almost all types of nitrogen metabolites affect, at least to some extent, auxin content and/or signaling in plants, which in turn affects seed germination, plant root elongation, gravitropism, leaf expansion and floral transition. This opinion focuses on the roles of nitrogen metabolites, NO 3 - , NH 4 + , tryptophan and NO and their synergistic effects with auxin on plant growth and development. Nitrate reductase (NR) converts nitrate into nitrite, and was roughly positive-correlated with the root auxin level, suggesting a crosstalk between nitrate signaling and auxin signaling. Abscisic Acid Responsive Element Binding Factor 3 (AFB3) and Tryptophan Aminotransferase of Arabidopsis 1 (TAA1) are also the key enzymes involved in nitrogen metabolite-regulated auxin biosynthesis. Recent advances in the crosstalk among NO 3 - , NH 4 + , tryptophan and NO in regulation to NR, AFB3 and TAA1 are also summarized.

OsCSLD1 Mediates NH4+-Dependent Root Hair Growth Suppression and AMT1;2 Expression in Rice (Oryza sativa L.)

Root hairs play crucial roles in the roots, including nutrient uptake, water assimilation, and anchorage with soil, along with supporting rhizospheric microorganisms. In rice, ammonia uptake is mediated by a specialized ammonium transporter (AMT). AMT1;1, AMT1;2, and AMT1;3 have been extensively studied in relation to nitrogen signaling. Cellulose synthase-like D1 (CSLD1) is essential for cell expansion and is highly specific to root hair cells. csld1 mutants showed successful initiation but failed to elongate. However, when nitrogen was depleted, csld1 root hairs resumed elongation. Further experiments revealed that in the presence of ammonium (NH4+), csld1 roots failed to elongate. csld1 elongated normally in the presence of nitrate (NO3−). Expression analysis showed an increase in root hair-specific AMT1;2 expression in csld1. CSLD1 was positively co-expressed with AMT1;2 changing nitrogen concentration in the growth media. CSLD1 showed increased expression in the presence of both ammonium and nitrate. Methylammonium (MeA) treatment of CSLD1 overexpression lines suggests that CSLD1 does not directly participate in nitrogen transport. Further studies on the root hair elongation mutant sndp1 showed that nitrogen assimilation is unlikely to depend on root hair length. Therefore, these results suggest that CSLD1 is closely involved in nitrogen-dependent root hair elongation and regulation of AMT1;2 expression in rice roots.

Glutamine synthetase plays an important role in ammonium tolerance of Myriophyllum aquaticum

High-strength ammonium (NH₄⁺), the main characteristic of swine wastewater, poses a significant threat to the rural ecological environment. As a novel phytoremediation technology, Myriophyllum aquaticum wetlands have high tolerance and removal rate of NH₄⁺. Glutamine synthetase (GS), a pivotal enzyme in nitrogen (N) metabolism, is hypothesized to play an important role in the tolerance of M. aquaticum to high NH₄⁺. Herein, the responses of M. aquaticum to GS inhibition by 0.1 mM methionine sulfoximine (MSX) under 15 mM NH₄⁺ were investigated. After 5 days, visible NH₄⁺ toxicity symptoms were observed in MSX-treated plants. Compared with the control, the NH₄⁺ accumulation in the leaves increased by 20.99 times, while that of stems and roots increased by 3.27 times and 47.76 %, suggesting that GS inhibition had a greater impact on the leaves. GS inhibition decreased pigments in the leaves by 8.64 %-41.06 %, triggered oxidative stress, and affected ions concentrations in M. aquaticum. The concentrations of glutamine (Gln) and asparagine decreased by 63.46 %-97.43 % and 12.37 %-76.41 %, respectively, while the concentrations of most other amino acids increased after 5 days of MSX treatment, showing that GS inhibition reprogrammed the amino acids synthesis. A decrease in Gln explains the regulations of N-related genes, including increased expression of AMT in roots and decreased expression of GS, GOGAT, GDH, and AS, which would cause further NH₄⁺ accumulation via promoting NH₄⁺ uptake and decreasing NH₄⁺ assimilation in M. aquaticum. This study revealed for the first time that GS inhibition under high NH₄⁺ condition can lead to phytotoxicity in M. aquaticum due to NH₄⁺ accumulation. The physiological and molecular responses of the leaves, stems, and roots confirmed the importance of GS in the high NH₄⁺ tolerance of M. aquaticum. These findings provide new insights into NH₄⁺ tolerance mechanisms in M. aquaticum and a theoretical foundation for the phytoremediation of high NH₄⁺-loaded swine wastewater.

Improving Nitrogen Use Efficiency in Rice for Sustainable Agriculture: Strategies and Future Perspectives

Nitrogen (N) is an important nutrient for the growth and development of rice. The application of N fertilizer has become one of the inevitable ways to increase rice yield due to insufficient soil N content. However, in order to achieve stable and high yield, farmers usually increase N fertilizer input without hesitation, resulting in a series of problems such as environmental pollution, energy waste and low production efficiency. For sustainable agriculture, improving the nitrogen use efficiency (NUE) to decrease N fertilizer input is imperative. In the present review, we firstly demonstrate the role of N in mediating root architecture, photosynthesis, metabolic balance, and yield components in rice. Furthermore, we further summarize the current agronomic practices for enhancing rice NUE, including balanced fertilization, the use of nitrification inhibitors and slow-release N fertilizers, the split application of N fertilizer, root zone fertilization, and so on. Finally, we discuss the recent advances of N efficiency-related genes with potential breeding value. These genes will contribute to improving the N uptake, maintain the N metabolism balance, and enhance the NUE, thereby breeding new varieties against low N tolerance to improve the rice yield and quality. Moreover, N-efficient varieties also need combine with precise N fertilizer management and advanced cultivation techniques to realize the maximum exploitation of their biological potential.

Synergistic Interaction between Copper and Nitrogen-Uptake, Translocation, and Distribution in Rice Plant

Interactions among nutrients have been widely recognized in plants and play important roles in crop growth and yield formation. However, the interplay of Cu and N in rice plants is not yet clear. In this study, rice plants were grown with different combinations of Cu and N supply. The effects of Cu-N interaction on the growth, yield production, Cu and N transport, and gene expression levels were analyzed. The results showed that the effect of N supply on rice growth and yield formation was more pronounced than that of Cu supply. The Cu supply significantly improved the uptake of N (by 9.52-30.64%), while the N supply significantly promoted the root-to-shoot translocation of Cu (by 27.28-38.45%) and distributed more Cu (1.85-19.16%) into the shoots and leaves. The results of qRT-PCR showed that +Cu significantly up-regulated the expression levels of both NO₃^- and NH₄⁺ transporter genes OsNRTs and OsAMTs, including OsNRT1.1B, OsNRT2.1, OsNRT2.3a, OsNRT2.4, OsAMT1.2, OsAMT1.3, and OsAMT3.1. Meanwhile, +N significantly up-regulated the expression levels of Cu transporter genes OsHMA5 and OsYSL16. In addition, the supply of Cu up-regulated the expression levels of OsGS1;2, OsGS2, and OsNADH-GOGAT to 12.61-, 6.48-, and 6.05-fold, respectively. In conclusion, our study demonstrates a synergistic effect between Cu and N in rice plants. It is expected that our results would be helpful to optimize the application of N and Cu fertilizers in agriculture.

A Koshihikari X Oryza rufipogon Introgression Line with a High Capacity to Take up Nitrogen to Maintain Growth and Panicle Development under Low Nitrogen Conditions

Nitrogen (N) is an important macronutrient for plant growth and development. Currently, N fertilizers are required for the efficient production of modern crops such as rice due to their limited capacity to take up N when present at low concentrations. Wild rice represents a useful genetic resource for improving crop responses to low nutrient stress. Here, we describe the isolation and characterization of an introgression line, KRIL37, that carries a small region of the Oryza rufipogon genome in the Oryza sativa L. cv Koshihikari (KH) background. This line was found to grow better under low N conditions and have similar or lower C/N ratios in aerial portions compared to those in the parental KH cultivar, suggesting that KRIL37 has a higher capacity to take up and assimilate N when present at low concentrations. KRIL37 performance in the field was also better than that of KH cultivated without N and fertilizer (-F). Transcriptome analyses of 3-week-old seedlings based on RNA-sequencing revealed that KH induced a wider suite of genes than the tolerant line KRIL37 in response to low N conditions. Some ammonium transporters and N assimilation genes were found to be induced under low N in KRIL37, but not in KH. Our findings suggest that the superior growth performance of KRIL37 under limited N conditions could be due to the expression of wild alleles influencing N uptake and assimilation. Our study demonstrates the potential to use wild rice genomes to improve modern crops for low nutrient tolerance.

Superior Haplotypes for Early Root Vigor Traits in Rice Under Dry Direct Seeded Low Nitrogen Condition Through Genome Wide Association Mapping

Water and land resources have been aggressively exploited in the recent decades to meet the growing demands for food. The changing climate has prompted rice scientists and farmers of the tropics and subtropics to adopt the direct seeded rice (DSR) system. DSR system of rice cultivation significantly reduces freshwater consumption and labor requirements, while increasing system productivity, resource use efficiency, and reducing greenhouse gas emissions. Early root vigor is an essential trait required in an ideal DSR system of rice cultivation to ensure a good crop stand, adequate uptake of water, nutrients and compete with weeds. The aus subpopulation which is adapted for DSR was evaluated to understand the biology of early root growth under limited nitrogen conditions over two seasons under two-time points (14 and 28 days). The correlation study identified a positive association between shoot dry weight and root dry weight. The genome-wide association study was conducted on root traits of 14 and 28 days with 2 million single-nucleotide polymorphisms (SNPs) using an efficient mixed model. QTLs over a significant threshold of p < 0.0001 and a 10% false discovery rate were selected to identify genes involved in root growth related to root architecture and nutrient acquisition from 97 QTLs. Candidate genes under these QTLs were explored. On chromosome 4, around 30 Mbp are two important peptide transporters (PTR5 and PTR6) involved in mobilizing nitrogen in the root during the early vegetative stage. In addition, several P transporters and expansin genes with superior haplotypes are discussed. A novel QTL from 21.12 to 21.46 Mb on chromosome 7 with two linkage disequilibrium (LD) blocks governing root length at 14 days were identified. The QTLs/candidate genes with superior haplotype for early root vigor reported here could be explored further to develop genotypes for DSR conditions.

Impact of microplastics from polyethylene and biodegradable mulch films on rice (Oryza sativa L.)

Extensive use of plastic film mulch has resulted in accumulation of a large amount of residual plastic, which will eventually fragment into microplastics in agricultural soils. However, it is unclear how microplastics from plastic mulch film affect crops. To address this issue, rice plants exposed to microplastics derived from poly(butyleneadipate-co-terephthalate) (PBAT)-based biodegradable mulch film (BM) and polyethylene (PE) mulch film (PM) were investigated for plant growth, physio-biochemical processes, and gene expressions. Both types of microplastics significantly reduced the height and dry weight of rice plant. Oxidative stress was induced by microplastics in rice shoot and root, with levels of ROS relatively higher under treatment PM than that under treatment BM. Transcriptomic data showed that more genes were down-regulated by treatment PM than that by treatment BM. Genes encoding ammonium and nitrate transporters were down-regulated by both types of microplastics in rice roots at vegetative stage, whereas up-regulated at reproductive stage, as compared to their respective treatment with no microplastics (CK). Similar results regarding phenylpropanoid biosynthesis pathway and lignin content were also observed in rice roots. Net photosynthetic rate and SPAD value were significantly inhibited by treatments BM and PM in rice shoot, and the expression of genes involved in light reaction was reduced at vegetative stage, whereas there were no differences of them at reproductive stage, as compared to their respective treatment CK. Our study suggests that microplastics from BM and PM both affect the growth of rice plants via nitrogen metabolism and photosynthesis. The negative effects imposed by both types of microplastics on rice plant can be mitigated with the growth of plants, and the negative effects of microplastics from PE mulch film on rice plant are relatively stronger than that from the PBAT-based biodegradable film.

The rice transcription factor Nhd1 regulates root growth and nitrogen uptake by activating nitrogen transporters

Plants adjust root architecture and nitrogen (N) transporter activity to meet the variable N demand, but their integrated regulatory mechanism remains unclear. We have previously reported that a floral factor in rice (Oryza sativa), N-mediated heading date-1 (Nhd1), regulates flowering time. Here, we show that Nhd1 can directly activate the transcription of the high-affinity ammonium (NH4+) transporter 1;3 (OsAMT1;3) and the dual affinity nitrate (NO3-) transporter 2.4 (OsNRT2.4). Knockout of Nhd1 inhibited root growth in the presence of NO3- or a low concentration of NH4+. Compared to the wild-type (WT), nhd1 and osamt1;3 mutants showed a similar decrease in root growth and N uptake under low NH4+ supply, while nhd1 and osnrt2.4 mutants showed comparable root inhibition and altered NO3- translocation in shoots. The defects of nhd1 mutants in NH4+ uptake and root growth response to various N supplies were restored by overexpression of OsAMT1;3 or OsNRT2.4. However, when grown in a paddy field with low N availability, nhd1 mutants accumulated more N and achieved a higher N uptake efficiency (NUpE) due to the delayed flowering time and prolonged growth period. Our findings reveal a molecular mechanism underlying the growth duration-dependent NUpE.

Biochar-based fertiliser enhances nutrient uptake and transport in rice seedlings

Biochar-based compound fertilisers (BCF) are gaining increasing attention as they are cost-effectiveness and improve soil fertility and crop yield. However, little is known about the mechanisms by which micron-size BCF particles enhance crop growth. In the present study, Wuyunjing7 rice seedlings were exposed to micron-size particles of wheat straw-based BCF (mBCF) diffused through a 25-μm nylon mesh. The control was fertilised with urea, diammonium phosphate, and potassium chloride to ensure that both treatments received comparables level of N, P, and K. The effects of mBCF on rice seedling growth were evaluated by determining the changes in nitrogen uptake and utilisation via nitrogen content measurements, short-term ¹⁵N-NH₄⁺ influx assays, and analyses of transcript-level nutrient transporter gene expression. The shoot biomass of rice seedling treated with mBCF at the rate of 5 mg/ g soil was 33% greater than that for the control. Root and shoot ¹⁵N accumulation rates were 44% and 14% higher, respectively, in the mBCF-treated than the control. The mBCF-treated rice seedlings had higher phosphorus, potassium, and iron content than the control. Moreover, the treatments significantly differed in terms of their nutrient transporter gene expression levels. Spectroscopy and microscopy were used to visualise nutrient distributions across transverse root sections. There were relatively higher iron oxide nanoparticle and silicon-based compound concentrations in the roots of the mBCF-treated rice seedlings than in those of the control. The foregoing difference might account for the fact that the growth of the mBCF-treated rice was superior to that of the control. We demonstrated that the mBCF treatment created a more negative electrical potential at the root epidermal cell layer (~ - 160 mV) than the root surface. This potential difference may have been the driving force for mineral nutrient absorption.

Improving Crop Nitrogen Use Efficiency Toward Sustainable Green Revolution

The Green Revolution of the 1960s improved crop yields in part through the widespread cultivation of semidwarf plant varieties, which resist lodging but require a high-nitrogen (N) fertilizer input. Because environmentally degrading synthetic fertilizer use underlies current worldwide cereal yields, future agricultural sustainability demands enhanced N use efficiency (NUE). Here, we summarize the current understanding of how plants sense, uptake, and respond to N availability in the model plants that can be used to improve sustainable productivity in agriculture. Recent progress in unlocking the genetic basis of NUE within the broader context of plant systems biology has provided insights into the coordination of plant growth and nutrient assimilation and inspired the implementation of a new breeding strategy to cut fertilizer use in high-yield cereal crops. We conclude that identifying fresh targets for N sensing and response in crops would simultaneously enable improved grain productivity and NUE to launch a new Green Revolution and promote future food security.

CBL-Interacting Protein Kinase OsCIPK18 Regulates the Response of Ammonium Toxicity in Rice Roots

Ammonium ( NH 4 + ) is one of the major nitrogen sources for plants. However, excessive ammonium can cause serious harm to the growth and development of plants, i.e., ammonium toxicity. The primary regulatory mechanisms behind ammonium toxicity are still poorly characterized. In this study, we showed that OsCIPK18, a CBL-interacting protein kinase, plays an important role in response to ammonium toxicity by comparative analysis of the physiological and whole transcriptome of the T-DNA insertion mutant (cipk18) and the wild-type (WT). Root biomass and length of cipk18 are less inhibited by excess NH 4 + compared with WT, indicating increased resistance to ammonium toxicity. Transcriptome analysis reveals that OsCIPK18 affects the NH 4 + uptake by regulating the expression of OsAMT1;2 and other NH 4 + transporters, but does not affect ammonium assimilation. Differentially expressed genes induced by excess NH 4 + in WT and cipk18 were associated with functions, such as ion transport, metabolism, cell wall formation, and phytohormones signaling, suggesting a fundamental role for OsCIPK18 in ammonium toxicity. We further identified a transcriptional regulatory network downstream of OsCIPK18 under NH 4 + stress that is centered on several core transcription factors. Moreover, OsCIPK18 might function as a transmitter in the auxin and abscisic acid (ABA) signaling pathways affected by excess ammonium. These data allowed us to define an OsCIPK18-regulated/dependent transcriptomic network for the response of ammonium toxicity and provide new insights into the mechanisms underlying ammonium toxicity.

Insights to improve the plant nutrient transport by CRISPR/Cas system

We need to improve food production to feed the ever growing world population especially in a changing climate. Nutrient deficiency in soils is one of the primary bottlenecks affecting the crop production both in developed and developing countries. Farmers are forced to apply synthetic fertilizers to improve the crop production to meet the demand. Understanding the mechanism of nutrient transport is helpful to improve the nutrient-use efficiency of crops and promote the sustainable agriculture. Many transporters involved in the acquisition, export and redistribution of nutrients in plants are characterized. In these studies, heterologous systems like yeast and Xenopus were most frequently used to study the transport function of plant nutrient transporters. CRIPSR/Cas system introduced recently has taken central stage for efficient genome editing in diverse organisms including plants. In this review, we discuss the key nutrient transporters involved in the acquisition and redistribution of nutrients from soil. We draw insights on the possible application CRISPR/Cas system for improving the nutrient transport in plants by engineering key residues of nutrient transporters, transcriptional regulation of nutrient transport signals, engineering motifs in promoters and transcription factors. CRISPR-based engineering of plant nutrient transport not only helps to study the process in native plants with conserved regulatory system but also aid to develop non-transgenic crops with better nutrient use-efficiency. This will reduce the application of synthetic fertilizers and promote the sustainable agriculture strengthening the food and nutrient security.

Regulation of ammonium acquisition and use in Oryza longistaminata ramets under nitrogen source heterogeneity

Oryza longistaminata, a wild rice, vegetatively reproduces and forms a networked clonal colony consisting of ramets connected by rhizomes. Although water, nutrients, and other molecules can be transferred between ramets via the rhizomes, inter-ramet communication in response to spatially heterogeneous nitrogen availability is not well understood. We studied the response of ramet pairs to heterogeneous nitrogen availability using a split hydroponic system that allowed each ramet root to be exposed to different conditions. Ammonium uptake was compensatively enhanced in the sufficient-side root when roots of the ramet pairs were exposed to ammonium-sufficient and ammonium-deficient conditions. Comparative transcriptome analysis revealed that a gene regulatory network for effective ammonium assimilation and amino acid biosynthesis was activated in the sufficient-side roots. Allocation of absorbed nitrogen from the nitrogen-sufficient to the nitrogen-deficient ramets was rather limited. Nitrogen was preferentially used for newly growing axillary buds on the sufficient-side ramets. Biosynthesis of trans-zeatin (tZ), a cytokinin, was upregulated in response to the nitrogen supply, but tZ appeared not to target the compensatory regulation. Our results also implied that the O. longistaminata putative ortholog of rice (Oryza sativa) C-terminally encoded peptide1 plays a role as a nitrogen-deficient signal in inter-ramet communication, providing compensatory upregulation of nitrogen assimilatory genes. These results provide insights into the molecular basis for efficient growth strategies of asexually proliferating plants growing in areas where the distribution of ammonium ions is spatially heterogeneous.

Cytosolic Glutamine Synthetase GS1;3 Is Involved in Rice Grain Ripening and Germination

Ammonium is combined with glutamate to form glutamine. This reaction is catalyzed by glutamine synthetase (GS or GLN). Plants harbor several isoforms of cytosolic GS (GS1). Rice GS1;3 is highly expressed in seeds during grain filling and germination, suggesting a unique role in these processes. This study aimed to investigate the role of GS1;3 for rice growth and yield. Tos17 insertion lines for GS1;3 were isolated, and the nitrogen (N), amino acid, and ammonium contents of GS1;3 mutant grains were compared to wild-type grains. The spatiotemporal expression of GS1;3 and the growth and yield of rice plants were evaluated in hydroponic culture and the paddy field. Additionally, the stable isotope of N was used to trace the foliar N flux during grain filling. Results showed that the loss of GS1;3 retarded seed germination. Seeds of GS1;3 mutants accumulated glutamate but did not show a marked change in the level of phytohormones. The expression of GS1;3 was detected at the beginning of germination, with limited promoter activity in seeds. GS1;3 mutants showed a considerably decreased ripening ratio and decreased N efflux in the 12th leaf blade under N deficient conditions. The β-glucuronidase gene expression under control of the GS1;3 promoter was detected in the vascular tissue and aleurone cell layer of developing grains. These data suggest unique physiological roles of GS1;3 in the early stage of seed germination and grain filling under N deficient conditions in rice.

Plant nitrogen nutrition: The roles of arbuscular mycorrhizal fungi

Nitrogen (N) is the most abundant mineral nutrient required by plants, and crop productivity depends heavily on N fertilization in many soils. Production and application of N fertilizers consume huge amounts of energy and substantially increase the costs of agricultural production. Excess N compounds released from agricultural systems are also detrimental to the environment. Thus, increasing plant N uptake efficiency is essential for the development of sustainable agriculture. Arbuscular mycorrhizal (AM) fungi are beneficial symbionts of most terrestrial plants that facilitate plant nutrient uptake and increase host resistance to diverse environmental stresses. AM association is an endosymbiotic process that relies on the differentiation of both host plant roots and AM fungi to create novel contact interfaces within the cells of plant roots. AM plants have two pathways for nutrient uptake: either direct uptake via the root hairs and root epidermis, or indirectly through AM fungal hyphae into root cortical cells. Over the last few years, great progress has been made in deciphering the molecular mechanisms underlying the AM-mediated modulation of nutrient uptake processes, and a growing number of fungal and plant genes responsible for the uptake of nutrients from soil or transfer across the fungi-root interface have been identified. Here, we mainly summarize the recent advances in N uptake, assimilation, and translocation in AM symbiosis, and also discuss how N interplays with C and P in modulating AM development, as well as the synergies between AM fungi and soil microbial communities in N uptake.

Zinc and nitrogen synergistic act on root-to-shoot translocation and preferential distribution in rice

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Zn promoted translocation and distribution of N into leaves and brown rice.

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Zn induced the expression levels of N transporter genes in both root and shoot.

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Zn increased the N assimilation level in leaves.

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N promoted translocation and distribution of Zn into leaves and brown rice.

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N up-regulated the expression levels of Zn transporter genes in both root and shoot.

Introduction

Multiple studies have shown strong relationships between different nutrients in plants, and the important role of N in Zn acquisition and translocation has been recognized.

Objectives

The aim of this study was to estimate the effect of Zn on N uptake, translocation, and distribution in rice as well as the corresponding molecular mechanisms. We also aimed to evaluate the impact of N on the Zn content in rice grains which is closely related to the Zn nutrition in humans with rice-based diets.

Methods

We conducted both field trials and hydroponic cultures of two rice cultivars to analyze the growth and yield, the uptake, translocation, and distribution of N and Zn, as well as the expression of N transport and assimilation genes, and the Zn transporter genes under different combined applications of N and Zn.

Results

Zn supply promoted the root-to-shoot translocation (12–70% increasing) and distribution of N into the leaves (19–49% increasing) and brown rice (6–9% increasing) and increased the rice biomass (by 14–35%) and yield (by 13–63%). Zn supply induced the expression of OsNRTs and OsAMTs in both roots and shoots, but repressed the expression of OsNiR2, OsGS1;2, and OsFd-GOGAT in roots, whereas it activated the expression of OsNiR2, OsGS1;1, OsGS2, and OsFd-GOGAT in the shoots. Moreover, the enzyme activities of nitrite reductase, nitrate reductase, and glutamine synthetase increased and the free NO₃^– concentration decreased, but the soluble protein concentration increased significantly in the shoots after Zn supply. Synergistically, N significantly facilitated the root-to-shoot translocation (1.68–11.66 fold) and distribution of Zn into the leaves (1.68–6.37 fold) and brown rice (7–12% increasing) and upregulated the expression levels of Zn transporter genes in both the roots and shoots.

Conclusions

We propose a working model of the cross-talk between Zn and N in rice plants, which will aid in the appropriate combined application of Zn and N fertilizers in the field to improve both N utilization in plants and Zn nutrition in humans with rice-based diets.

Transcripts related with ammonium use and effects of gibberellin on expressions of the transcripts responding to ammonium in two invasive and native Xanthium species

Soil nitrogen forms are important for exotic plant invasions. However, little effort has been made to study the molecular mechanisms underlying the utilization of different N forms in co-occurring invasive and native plants. The invasive plant Xanthium strumarium prefers nitrate relative to ammonium, and mainly invades nitrate-dominated environments, while it co-occurring native congener X. sibiricum prefers ammonium. Here, we addressed the genetic bases for the interspecific difference in ammonium use and the effects of gibberellin (GA). Twenty-six transcripts related with GA biosynthesis and ammonium utilization were induced by ammonium in X. sibiricum, while only ten in X. strumarium and none for ammonium uptake. XsiAMT1.1a, XsiGLN1.1 and XsiGLT1b may be crucial for the strong ability to absorb and assimilate ammonium in X. sibiricum. All tested transcripts were significantly up-regulated by GA1 and GA4 in X. sibiricum. XsiGA3OX1a, which was also induced by ammonium, may be involved in this regulation. Consistently, glutamine synthetase activity increased significantly with increasing ammonium-N/nitrate-N ratio for X. sibiricum, while decreased for X. strumarium. Our study is the first to determine the molecular mechanisms with which invasive and native plants use ammonium differently, contributing to understanding the invasion mechanisms of X. strumarium and its invasion habitat selection.

Genome-wide identification, characterization, and expression analysis of the ammonium transporter gene family in tea plants (Camellia sinensis L.)

As a preferred nitrogen form, ammonium (NH₄ ⁺ ) transport via specific transporters is particularly important for the growth and development of tea plants (Camellia sinensis L.). However, our understanding of the functions of the AMT family in tea plants is limited. We identified and named 16 putative AMT genes according to phylogenetic analysis. All CsAMT genes were divided into three groups, distributed on 12 chromosomes with only one segmental duplication repetition. The CsAMT genes showed different expression levels in different organs, and most of them were expressed mainly in the apical buds and roots. Complementation analysis of yeast mutants showed that CsAMTs restored the uptake of NH₄ ⁺ . This study provides insights into the genome-wide distribution and spatial expression of AMT genes in tea plants.

Three polarly localized ammonium transporter 1 members are cooperatively responsible for ammonium uptake in rice under low ammonium condition

Ammonium is a preferential nitrogen form for rice (Oryza sativa) grown in paddy field, but the molecular mechanisms for ammonium uptake have not been well understood. We functionally characterized three members belonging to ammonium transporter 1 (AMT1) and investigated their contributions to ammonium uptake. Spatial expression analysis showed that the upregulated expression of OsAMT1;1 and OsAMT1;2 and downregulated expression of OsAMT1;3 by ammonium were higher in the root mature region than in the root tips. All OsAMT1 members were polarly localized at the distal side of exodermis in the mature region of crown roots and lateral roots. Upon exposure to ammonium, localization of OsAMT1;1 and OsAMT1;2 was also observed in the endoplasmic reticulum, but their abundance in the plasma membrane was not changed. Single knockout of either gene did not affect ammonium uptake, but knockout of all three genes resulted in 95% reduction of ammonium uptake. However, the nitrogen uptake did not differ between the wild-type rice and triple mutants at high ammonium and nitrate supply. Our results indicate that three OsAMT1 members are cooperatively required for uptake of low ammonium in rice roots and that they undergo a distinct regulatory mechanism in response to ammonium.

Transporters and transcription factors gene families involved in improving nitrogen use efficiency (NUE) and assimilation in rice (Oryza sativa L.)

Nitrogen (N) as a macronutrient is an important determinant of plant growth. The excessive usage of chemical fertilizers is increasing environmental pollution; hence, the improvement of crop's nitrogen use efficiency (NUE) is imperative for sustainable agriculture. N uptake, transportation, assimilation, and remobilization are four important determinants of plant NUE. Oryza sativa L. (rice) is a staple food for approximately half of the human population, around the globe and improvement in rice yield is pivotal for rice breeders. The N transporters, enzymes indulged in N assimilation, and several transcription factors affect the rice NUE and subsequent yield. Although, a couple of improvements have been made regarding rice NUE, the knowledge about regulatory mechanisms operating NUE is scarce. The current review provides a precise knowledge of how rice plants detect soil N and how this detection is translated into the language of responses that regulate the growth. Additionally, the transcription factors that control N-associated genes in rice are discussed in detail. This mechanistic insight will help the researchers to improve rice yield with minimized use of chemical fertilizers.

Rice amino acid transporter-like 6 (OsATL6) is involved in amino acid homeostasis by modulating the vacuolar storage of glutamine in roots

Glutamine is a product of ammonium (NH₄⁺ ) assimilation catalyzed by glutamine synthetase (GS) and glutamate synthase (GOGAT). The growth of NH₄⁺ -preferring paddy rice (Oryza sativa L.) depends on root NH₄⁺ assimilation and the subsequent root-to-shoot allocation of glutamine; however, little is known about the mechanism of glutamine storage in roots. Here, using transcriptome and reverse genetics analyses, we show that the rice amino acid transporter-like 6 (OsATL6) protein exports glutamine to the root vacuoles under NH₄⁺ -replete conditions. OsATL6 was expressed, along with OsGS1;2 and OsNADH-GOGAT1, in wild-type (WT) roots fed with sufficient NH₄ Cl, and was induced by glutamine treatment. We generated two independent Tos17 retrotransposon insertion mutants showing reduced OsATL6 expression to determine the function of OsATL6. Compared with segregants lacking the Tos17 insertion, the OsATL6 knock-down mutant seedlings exhibited lower root glutamine content but higher glutamine concentration in the xylem sap and greater shoot growth under NH₄⁺ -replete conditions. The transient expression of monomeric red fluorescent protein-fused OsATL6 in onion epidermal cells confirmed the tonoplast localization of OsATL6. When OsATL6 was expressed in Xenopus laevis oocytes, glutamine efflux from the cell into the acidic bath solution increased. Under sufficient NH₄⁺ supply, OsATL6 transiently accumulated in sclerenchyma and pericycle cells, which are located adjacent to the Casparian strip, thus obstructing the apoplastic solute path, and in vascular parenchyma cells of WT roots before the peak accumulation of GS1;2 and NADH-GOGAT1 occurred. These findings suggest that OsATL6 temporarily stores excess glutamine, produced by NH₄⁺ assimilation, in root vacuoles before it can be translocated to the shoot.

Molecular Regulatory Networks for Improving Nitrogen Use Efficiency in Rice

Nitrogen is an important factor limiting the growth and yield of rice. However, the excessive application of nitrogen will lead to water eutrophication and economic costs. To create rice varieties with high nitrogen use efficiency (NUE) has always been an arduous task in rice breeding. The processes for improving NUE include nitrogen uptake, nitrogen transport from root to shoot, nitrogen assimilation, and nitrogen redistribution, with each step being indispensable to the improvement of NUE. Here, we summarize the effects of absorption, transport, and metabolism of nitrate, ammonium, and amino acids on NUE, as well as the role of hormones in improving rice NUE. Our discussion provide insight for further research in the future.

Effects of arbuscular mycorrhizal fungi on the nitrogen distribution in endangered Torreya jackii under nitrogen limitation

Arbuscular mycorrhizal fungi regulated the distribution of nitrogen in the leaves, thereby facilitating the adaptation of the endangered plant Torreya jackii to a low-nitrogen environment. Rhizophagus irregularis was inoculated into sterilized soil to investigate its impact on the distribution ratio of leaf nitrogen in cell wall proteins, cell membrane proteins, water-soluble proteins, and photosynthetic systems which includes the carboxylation system (P_C), energy metabolism (P_B), and light-harvesting system in the endangered species Torreya jackii. The results showed that R. irregularis reduced the specific leaf weight and the distribution ratio of nitrogen in cell wall proteins in the leaves of T. jackii, whereas it enhanced the distribution ratio of nitrogen in cell membrane proteins and water-soluble proteins. R. irregularis enabled more nitrogen uptake for growth by decreasing the distribution of nitrogen to the structural substances. At low-nitrogen levels, inoculation with R. irregularis improved the plant height (18.78 ~ 36.04%), shoot dry weight (50.53 ~ 64.33%), total dry weight (42.86 ~ 52.82%), maximal net photosynthetic rate (P_max) (16.83 ~ 20.11%), photosynthetic nitrogen use efficiency (PNUE) (40.01 ~ 43.14%), P_C (33.56 ~ 38.59%) and P_B (29.08 ~ 34.02%). However, it did not substantially affect the leaf nitrogen content per unit area or the leaf nitrogen content per unit mass. Moreover, P_max exhibited a significant positive correlation with P_C and P_B, and all three parameters showed a significant positive correlation with the PNUE, thereby revealing that R. irregularis increased the photosynthetic capacity and PNUE of T. jackii through boosting P_C and P_B.

Proofing Direct-Seeded Rice with Better Root Plasticity and Architecture

The underground reserve (root) has been an uncharted research territory with its untapped genetic variation yet to be exploited. Identifying ideal traits and breeding new rice varieties with efficient root system architecture (RSA) has great potential to increase resource-use efficiency and grain yield, especially under direct-seeded rice, by adapting to aerobic soil conditions. In this review, we tried to mine the available research information on the direct-seeded rice (DSR) root system to highlight the requirements of different root traits such as root architecture, length, number, density, thickness, diameter, and angle that play a pivotal role in determining the uptake of nutrients and moisture at different stages of plant growth. RSA also faces several stresses, due to excess or deficiency of moisture and nutrients, low or high temperature, or saline conditions. To counteract these hindrances, adaptation in response to stress becomes essential. Candidate genes such as early root growth enhancer PSTOL1, surface rooting QTL qSOR1, deep rooting gene DRO1, and numerous transporters for their respective nutrients and stress-responsive factors have been identified and validated under different circumstances. Identifying the desired QTLs and transporters underlying these traits and then designing an ideal root architecture can help in developing a suitable DSR cultivar and aid in further advancement in this direction.

Novel plant breeding techniques to advance nitrogen use efficiency in rice: A review

Recently, there has been a remarkable increase in rice production owing to genetic improvement and increase in application of synthetic fertilizers. For sustainable agriculture, there is dire need to maintain a balance between profitability and input cost. To meet the steady growing demands of the farming community, researchers are utilizing all available resources to identify nutrient use efficient germplasm, but with very little success. Therefore, it is essential to understand the underlying genetic mechanism controlling nutrients efficiency, with the nitrogen use efficiency (NUE) being the most important trait. Information regarding genetic factors controlling nitrogen (N) transporters, assimilators, and remobilizers can help to identify candidate germplasms via high-throughput technologies. Large-scale field trials have provided morphological, physiological, and biochemical trait data for the detection of genomic regions controlling NUE. The functional aspects of these attributes are time-consuming, costly, labor-intensive, and less accurate. Therefore, the application of novel plant breeding techniques (NPBTs) with context to genome engineering has opened new avenues of research for crop improvement programs. Most recently, genome editing technologies (GETs) have undergone enormous development with various versions from Cas9, Cpf1, base, and prime editing. These GETs have been vigorously adapted in plant sciences for novel trait development to insure food quantity and quality. Base editing has been successfully applied to improve NUE in rice, demonstrating the potential of GETs to develop germplasms with improved resource use efficiency. NPBTs continue to face regulatory setbacks in some countries due to genome editing being categorized in the same category as genetically modified (GM) crops. Therefore, it is essential to involve all stakeholders in a detailed discussion on NPBTs and to formulate uniform policies tackling biosafety, social, ethical, and environmental concerns. In the current review, we have discussed the genetic mechanism of NUE and NPBTs for crop improvement programs with proof of concepts, transgenic and GET application for the development of NUE germplasms, and regulatory aspects of genome edited crops with future directions considering NUE.

Nitrogen Use Efficiency in Sorghum: Exploring Native Variability for Traits Under Variable N-Regimes

Exploring the natural genetic variability and its exploitation for improved Nitrogen Use Efficiency (NUE) in sorghum is one of the primary goals in the modern crop improvement programs. The integrated strategies include high-throughput phenotyping, next generation sequencing (NGS)-based genotyping technologies, and a priori selected candidate gene studies that help understand the detailed physiological and molecular mechanisms underpinning this complex trait. A set of sixty diverse sorghum genotypes was evaluated for different vegetative, reproductive, and yield traits related to NUE in the field (under three N regimes) for two seasons. Significant variations for different yield and related traits under 0 and 50% N confirmed the availability of native genetic variability in sorghum under low N regimes. Sorghum genotypes with distinct genetic background had interestingly similar NUE associated traits. The Genotyping-By-Sequencing based SNPs (>89 K) were used to study the population structure, and phylogenetic groupings identified three distinct groups. The information of grain N and stalk N content of the individuals covered on the phylogenetic groups indicated randomness in the distribution for adaptation under variable N regimes. This study identified promising sorghum genotypes with consistent performance under varying environments, with buffer capacity for yield under low N conditions. We also report better performing genotypes for varied production use-grain, stover, and dual-purpose sorghum having differential adaptation response to NUE traits. Expression profiling of NUE associated genes in shoot and root tissues of contrasting lines (PVK801 and HDW703) grown in varying N conditions revealed interesting outcomes. Root tissues of contrasting lines exhibited differential expression profiles for transporter genes [ammonium transporter (SbAMT), nitrate transporters (SbNRT)]; primary assimilatory (glutamine synthetase (SbGS), glutamate synthase (SbGOGAT[NADH], SbGOGAT[Fd]), assimilatory genes [nitrite reductase (SbNiR[NADH]3)]; and amino acid biosynthesis associated gene [glutamate dehydrogenase (SbGDH)]. Identification and expression profiling of contrasting sorghum genotypes in varying N dosages will provide new information to understand the response of NUE genes toward adaptation to the differential N regimes in sorghum. High NUE genotypes identified from this study could be potential candidates for in-depth molecular analysis and contribute toward the development of N efficient sorghum cultivars.

Rice PIN Auxin Efflux Carriers Modulate the Nitrogen Response in a Changing Nitrogen Growth Environment

Auxins play an essential role in regulating plant growth and adaptation to abiotic stresses, such as nutrient stress. Our current understanding of auxins is based almost entirely on the results of research on the eudicot Arabidopsis thaliana, however, the role of the rice PIN-FORMED (PIN) auxin efflux carriers in the regulation of the ammonium-dependent response remains elusive. Here, we analyzed the expression patterns in various organs/tissues and the ammonium-dependent response of rice PIN-family genes (OsPIN genes) via qRT-PCR, and attempted to elucidate the relationship between nitrogen (N) utilization and auxin transporters. To investigate auxin distribution under ammonium-dependent response after N deficiency in rice roots, we used DR5::VENUS reporter lines that retained a highly active synthetic auxin response. Subsequently, we confirmed that ammonium supplementation reduced the DR5::VENUS signal compared with that observed in the N-deficient condition. These results are consistent with the decreased expression patterns of almost all OsPIN genes in the presence of the ammonium-dependent response to N deficiency. Furthermore, the ospin1b mutant showed an insensitive phenotype in the ammonium-dependent response to N deficiency and disturbances in the regulation of several N-assimilation genes. These molecular and physiological findings suggest that auxin is involved in the ammonium assimilation process of rice, which is a model crop plant.

Thymol ameliorates ammonium toxicity via repressing polyamine oxidase-derived hydrogen peroxide and modulating ammonium transporters in rice root

Background

Ammonium is an indispensable nutrient for crop growth, but anoxic conditions or inappropriate fertilizer usage result in the increase in ammonium content in soil. Excessive ammonium causes phytotoxicity. Thymol is a kind of natural phenolic compound with anti-microbial properties. However, little is known about the role of thymol in modulating plant physiology. Here we find the novel role of thymol in protecting rice from ammonium toxicity.

Results

Thymol remarkably rescued rice seedlings growth from ammonium stress, which may resulted from the attenuation of reactive oxygen species (ROS) accumulation, oxidative injury, and cell death in both shoots and roots. Polyamine oxidase (PAO) metabolizes polyamines to produce ROS in plants in response to stress conditions. Thymol blocked ammonium-induced upregulation of a set of rice PAOs, which contributed to the decrease in ROS content. In rice seedlings upon ammonium stress, thymol downregulate the expression of ammonium transporters (AMT1;1 and AMT1;2); thymol upregulated the expression of calcineurin B-like interacting protein kinase 23 (CIPK23) and calcineurin B-like binding protein 1 (CBL1), two negative regulators of AMTs. This may help rice avoid ammonium overload in excessive ammonium environment. Correlation analysis indicated that PAOs, AMTs, and CBL1 were the targets of thymol in the detoxification of excessive ammonium.

Conclusion

Thymol facilitates rice tolerance against ammonium toxicity by decreasing PAO-derived ROS and modulating ammonium transporters. Such findings may be applicable in the modulation of nutrient acquisition during crop production.

Graphical abstract