Nitrate regulation of metabolism and growth

Enhancing quality traits in staple crops: current advances and future perspectives

Staple crops such as rice, wheat and maize are crucial for global food security; however, improving their quality remains a significant challenge. This review summarizes recent advances in enhancing crop quality, focusing on key areas such as the molecular mechanisms underlying endosperm filling initiation, starch granule synthesis, protein body formation, and the interactions between carbon and nitrogen metabolism. It also highlights ten unresolved questions related to starch-protein spatial distribution, epigenetic regulation, and the environmental impacts on quality traits. The integration of multi-omics approaches, and rational design strategies presents opportunities to develop high-yield "super-crop" varieties with enhanced nutritional value, better processing characteristics, and attributes preferred by consumers. Addressing these challenges is crucial to promote sustainable agriculture and achieve the dual objectives of food security and environmental conservation.

The root hairless mutant buzz in Brachypodium distachyon shows increased nitrate uptake and signaling but does not affect overall nitrogen use efficiency

Root systems are uniquely adapted to fluctuations in external nutrient availability. In response to suboptimal nitrogen conditions, plants adopt a root foraging strategy that favors a deeper and more branched root architecture, enabling them to explore and acquire soil resources. This response is gradually suppressed as nitrogen conditions improve. However, the root hairless mutant buzz in Brachypodium distachyon shows a constitutive nitrogen-foraging phenotype with increased root growth and root branching under nitrate-rich conditions. To investigate how this unique root structure and root hair morphology in the buzz mutant affects nitrate metabolism, we measured the expression of nitrate-responsive genes, nitrate uptake and accumulation, nitrate reductase activity, and nitrogen use efficiency. We found that nitrate responses were upregulated by low nitrate conditions in buzz relative to wild type and correlated with increased expression of nitrate transport genes. In addition, buzz mutants showed increased nitrate uptake and a higher accumulation of nitrate in shoots. The buzz mutant also showed increased nitrate reductase activity in the shoots under low nitrate conditions. However, developmentally mature wild-type and buzz plants grown under low nitrate had similar nitrogen use efficiencies. These findings suggest that BUZZ influences nitrate signaling and that enhanced responsiveness to nitrate is required in buzz seedlings to compensate for the lack of root hairs. These data question the importance of root hairs in enhancing nitrate uptake and expand our understanding of how root hairs in grasses affect physiological responses to low nitrate availability.

Cenococcum geophilum impedes cadmium toxicity in Pinus massoniana by modulating nitrogen metabolism

Nitrogen (N) is of great significance to the absorption, distribution and detoxification of cadmium (Cd). Ectomycorrhizal fungi (EMF) are able to affect the key processes of plant N uptake to resist Cd stress, while the mechanism is still unclear. Therefore, we explored potential strategies of Cenococcum geophilum (C. geophilum) symbiosis to alleviate Cd stress in Pinus massoniana (P. massoniana) from the perspective of plant N metabolism and soil N transformation. The results showed that inoculation of C. geophilum significantly increased the activities of NR, NiR and GS in the shoots and roots of P. massoniana, thereby promoting the assimilation of NO3- and NH4+ into amino acids. Moreover, C. geophilum promoted soil urease and protease activities, but decreased soil NH4+ content, indicating that C. geophilum might increase plant uptake of soil inorganic N. qRT-PCR results showed that C3 symbiosis significantly up-regulated the expression of genes encoding functions involved in NH4+ uptake (AMT3;1), NO3- uptake (NRT2.1, NRT2.4, NRT2.9), as well as Cd resistance (ABCC1 and ABCC2), meanwhile down-regulated the expression of NRT7.3, Cd transporter genes (HMA2 and NRAMP3) in the roots of P. massoniana seedlings. These results demonstrated that C. geophilum was able to alleviate Cd stress by increasing the absorption and assimilation of inorganic N in plants and inhibiting the transport of Cd from roots to shoots, which provided new insights into how EMF improved host resistance to abiotic stress.

Influence of Water and Fertilizer Reduction on Respiratory Metabolism in Sugar Beet Taproot (Beta vulgaris L.)

Inner Mongolia, a major region in China for growing sugar beet, faces challenges caused by unscientific water and fertilizer management. This mismanagement restricts the improvement of sugar beet yield and quality and exacerbates water waste and environmental pollution. This study aims to evaluate the effects of reduced water and fertilizer on the growth and physiological metabolism of sugar beet taproot. Field experiments were conducted in Ulanqab, Inner Mongolia, in 2022 and 2023, using a split-plot design with three levels each of fertilization and irrigation. The study analyzed the effects of reduced water and fertilizer treatments on fresh taproot weight, respiration rate, energy metabolism, respiratory enzyme activity, and gene expression in sugar beet taproot. It was found that a 10% reduction in fertilizer significantly increased the beet taproot fresh weight. Further research revealed that during the rapid leaf growth phase and the taproot and sugar growth period, a 10% reduction in fertilizer upregulated HK and IDH gene expression and downregulated G6PDH gene expression in the beet taproot. This increased HK and IDH activities, decreased G6PDH activity, enhanced the activity of the EMP-TCA pathway, and inhibited the PPP. Taproot weight was positively correlated with the respiration rate, ATP content, EC, and ATPase, HK, and IDH activities, thereby increasing the taproot growth rate and taproot fresh weight, with an average increase of 4.0% over two years. These findings introduce a novel method for optimizing fertilizer use, particularly beneficial in water-scarce regions. Implementing this strategy could help farmers in western Inner Mongolia and similar areas improve crop yield and sustainability. This study offers new insights into resource-efficient agricultural practices, highlighting the importance of customized fertilization strategies tailored to local environmental conditions.

Arabidopsis WRKY1 promotes monocarpic senescence by integrative regulation of flowering, leaf senescence, and nitrogen remobilization

Monocarpic senescence, characterized by whole-plant senescence following a single flowering phase, is widespread in seed plants, particularly in crops, determining seed harvest time and quality. However, how external and internal signals are systemically integrated into monocarpic senescence remains largely unknown. Here, we report that the Arabidopsis thaliana transcription factor WRKY1 plays essential roles in multiple key steps of monocarpic senescence. WRKY1 expression is induced by age, salicylic acid (SA), and nitrogen (N) deficiency. Flowering and leaf senescence are accelerated in the WRKY1 overexpression lines but are delayed in the wrky1 mutants. The combined DNA affinity purification sequencing and RNA sequencing analyses uncover the direct target genes of WRKY1. Further studies show that WRKY1 coordinately regulates three processes in monocarpic senescence: (1) suppressing FLOWERING LOCUS C gene expression to initiate flowering, (2) inducing SA biosynthesis genes to promote leaf senescence, and (3) activating the N assimilation and transport genes to trigger N remobilization. In summary, our study reveals how one stress-responsive transcription factor, WRKY1, integrates flowering, leaf senescence, and N remobilization processes into monocarpic senescence, providing important insights into plant lifetime regulation.

Peculiarity of the early metabolomic response in tomato after urea, ammonium or nitrate supply

Nitrogen (N) is the nutrient most applied in agriculture as fertilizer (as nitrate, Nit; ammonium, A; and/or urea, U, forms) and its availability strongly constrains the crop growth and yield. To investigate the early response (24 h) of N-deficient tomato plants to these three N forms, a physiological and molecular study was performed. In comparison to N-deficient plants, significant changes in the transcriptional, metabolomic and ionomic profiles were observed. As a probable consequence of N mobility in plants, a wide metabolic modulation occurred in old leaves rather than in young leaves. The metabolic profile of U and A-treated plants was more similar than Nit-treated plant profile, which in turn presented the lowest metabolic modulation with respect to N-deficient condition. Urea and A forms induced some changes at the biosynthesis of secondary metabolites, amino acids and phytohormones. Interestingly, a specific up-regulation by U and down-regulation by A of carbon synthesis occurred in roots. Along with the gene expression, data suggest that the specific N form influences the activation of metabolic pathways for its assimilation (cytosolic GS/AS and/or plastidial GS/GOGAT cycle). Urea induced an up-concentration of Cu and Mn in leaves and Zn in whole plant. This study highlights a metabolic reprogramming depending on the N form applied, and it also provide evidence of a direct relationship between urea nutrition and Zn concentration. The understanding of the metabolic pathways activated by the different N forms represents a milestone in improving the efficiency of urea fertilization in crops.

Calcium regulates primary nitrate response associated gene transcription in a time- and dose-dependent manner

Nitrate (NO3-) is the primary source of nitrogen preferred by most arable crops, including wheat. The pioneering experiment on primary nitrate response (PNR) was carried out three decades ago. Since then, much research has been carried out to understand the NO3- signaling. Nitrate is sensed by the dual affinity NO3- transceptor NPF6.3, which further relays the information to a master regulator NIN-like protein 7 (NLP7) through calcium-dependent protein kinases (CPK10, CPK30, CPK32), highlighting the importance of calcium ion (Ca2+) as one of the important secondary messengers in relaying the NO3- signaling in Arabidopsis. In a previous study, we found that Ca2+ regulates nitrogen starvation response in wheat. In this study, 10 days old NO3--starved wheat seedlings were exposed to various treatments. Our study on time course changes in expression of PNR sentinel genes; NPF6.1, NPF6.2, NRT2.1, NRT2.3, NR, and NIR in wheat manifest the highest level of expression at 30 min after NO3- exposure. The use of Ca2+ chelator EGTA confirmed the involvement of Ca2+ in the regulation of transcription of NPFs and NRTs as well the NO3- uptake. We also observed the NO3- dose-dependent and tissue-specific regulation of nitrate reductase activity involving Ca2+ as a mediator. The participation of Ca2+ in the PNR and NO3- signaling in wheat is confirmed by pharmacological analysis, physiological evidences, and protoplast-based Ca2+ localization.

Imbalanced metabolism induced NH4+ accumulation and its effect on the central metabolism of Methylomonas sp. ZR1

Nitrogen and carbon are the two most essential nutrient elements, and their metabolism is tightly coupled in single carbon metabolic microorganisms. However, the nitrogen metabolism and the nitrogen/carbon (N/C) metabolic balance in single-carbon metabolism is poorly studied. In this study, the nitrogen metabolism pattern of the fast growing methanotrophs Methylomonas sp. ZR1 grown in methane and methanol was studied. Effect study of different nitrogen sources on the cell growth of ZR1 indicates that nitrate salts are the best nitrogen source supporting the growth of ZR1 using methane and methanol as carbon source. However, its metabolic intermediate ammonium was found to accumulate with high N/C ratio in the medium and consequently inhibit the growth of ZR1. Studies of carbon and nitrogen metabolic kinetic under different N/C ratio conditions indicate that the accumulation of NH4+ is caused by the imbalanced nitrogen and carbon metabolism in ZR1. Feeding carbon skeleton α-ketoglutaric acid could effectively relieve the inhibition effect of NH4+ on the growth of ZR1, which further confirms this assumption. qPCR analysis of the expression level of the central metabolic key enzyme gene indicates that the nitrogen metabolic intermediate ammonium has strong regulation effect on the central nitrogen and carbon metabolism in ZR1. qPCR-combined genomic analysis confirms that a third ammonium assimilation pathway glycine synthesis system is operated in ZR1 to balance the nitrogen and carbon metabolism. Based on the qPCR result, it was also found that ZR1 employs two strategies to relieve ammonium stress in the presence of ammonium: assimilating excess ammonium or cutting off the nitrogen reduction reactions according to the available C1 substrate. Validating the connections between single-carbon and nitrogen metabolism and studying the accumulation and assimilation mechanism of ammonium will contribute to understand how nitrogen regulates cellular growth in single-carbon metabolic microorganisms.

Network Analysis of Metabolome and Transcriptome Revealed Regulation of Different Nitrogen Concentrations on Hybrid Poplar Cambium Development

Secondary development is a key biological characteristic of woody plants and the basis of wood formation. Exogenous nitrogen can affect the secondary growth of poplar, and some regulatory mechanisms have been found in the secondary xylem. However, the effect of nitrogen on cambium has not been reported. Herein, we investigated the effects of different nitrogen concentrations on cambium development using combined transcriptome and metabolome analysis. The results show that, compared with 1 mM NH4NO3 (M), the layers of hybrid poplar cambium cells decreased under the 0.15 mM NH4NO3 (L) and 0.3 mM NH4NO3 (LM) treatments. However, there was no difference in the layers of hybrid poplar cambium cells under the 3 mM NH4NO3 (HM) and 5 mM NH4NO3 (H) treatments. Totals of 2365, 824, 649 and 398 DEGs were identified in the M versus (vs.) L, M vs. LM, M vs. HM and M vs. H groups, respectively. Expression profile analysis of the DEGs showed that exogenous nitrogen affected the gene expression involved in plant hormone signal transduction, phenylpropanoid biosynthesis, the starch and sucrose metabolism pathway and the ubiquitin-mediated proteolysis pathway. In M vs. L, M vs. LM, M vs. HM and M vs. H, differential metabolites were enriched in flavonoids, lignans, coumarins and saccharides. The combined analysis of the transcriptome and metabolome showed that some genes and metabolites in plant hormone signal transduction, phenylpropanoid biosynthesis and starch and sucrose metabolism pathways may be involved in nitrogen regulation in cambium development, whose functions need to be verified. In this study, from the point of view that nitrogen influences cambium development to regulate wood formation, the network analysis of the transcriptome and metabolomics of cambium under different nitrogen supply levels was studied for the first time, revealing the potential regulatory and metabolic mechanisms involved in this process and providing new insights into the effects of nitrogen on wood development.

A biostimulant prepared from red seaweed Kappaphycus alvarezii induces flowering and improves the growth of Pisum sativum grown under optimum and nitrogen-limited conditions

Nitrogen (N) is one of the critical elements required by plants and is therefore one of the important limiting factors for growth and yield. To increase agricultural productivity, farmers are using excessive N fertilizers to the soil, which poses a threat to the ecosystem, as most of the applied nitrogen fertilizer is not taken up by crops, and runoff to aquatic bodies and the environment causes eutrophication, pollution, and greenhouse gas emissions. In this study, we used LBS6, a Kappaphycus alvarezii-based biostimulant as a sustainable alternative to improve the growth of plants under different NO3 - fertigation. A root drench treatment of 1 ml/L LBS6 significantly improved the growth of Pisum sativum plants grown under optimum and deficient N conditions. No significant difference was observed in the growth of LBS6-treated plants grown with excessive N. The application of LBS6 induced flowering under optimum and deficient N conditions. The total nitrogen, nitrate and ammonia contents of tissues were found to be higher in treated plants grown under N deficient conditions. The LBS6 treatments had significantly higher chlorophyll content in those plants grown under N-deficient conditions. The root drench application of LBS6 also regulated photosynthetic efficiency by modulating electron and proton transport-related processes of leaves in the light-adapted state. The rate of linear electron flux, proton conductivity and steady-state proton flux across the thylakoid membrane were found to be higher in LBS6-treated plants. Additionally, LBS6 also reduced nitrogen starvation-induced, reactive oxygen species accumulation by reduction in lipid peroxidation in treated plants. Gene expression analysis showed differential regulation of expression of those genes involved in N uptake, transport, assimilation, and remobilization in LBS6-treated plants. Taken together, LBS6 improved growth of those treated plants under optimum and nitrogen-limited condition by positively modulating their biochemical, molecular, and physiological processes.

Integrated comparative transcriptome and physiological analysis reveals the metabolic responses underlying genotype variations in NH4+ tolerance

Several mechanisms have been proposed to explain NH4 + toxicity. However, the core information about the biochemical regulation of plants in response to NH4 + toxicity is still lacking. In this study, the tissue NH4 + concentration is an important factor contributing to variations in plant growth even under nitrate nutrition and NH4 + tolerance under ammonium nutrition. Furthermore, NH4 + led to the reprogramming of the transcriptional profile, as genes related to trehalose-6-phosphate and zeatin biosynthesis were downregulated, whereas genes related to nitrogen metabolism, camalexin, stilbenoid and phenylpropanoid biosynthesis were upregulated. Further analysis revealed that a large number of genes, which enriched in phenylpropanoid and stilbenoid biosynthesis, were uniquely upregulated in the NH4 +- tolerant ecotype Or-1. These results suggested that the NH4 +-tolerant ecotype showed a more intense response to NH4 + by activating defense processes and pathways. Importantly, the tolerant ecotype had a higher 15NH4 + uptake and nitrogen utilization efficiency, but lower NH4 +, indicating the tolerant ecotype maintained a low NH4 + level, mainly by promoting NH4 + assimilation rather than inhibiting NH4 + uptake. The carbon and nitrogen metabolism analysis revealed that the tolerant ecotype had a stronger carbon skeleton production capacity with higher levels of hexokinase, pyruvate kinase, and glutamate dehydrogenase activity to assimilate free NH4 +, Taken together, the results revealed the core mechanisms utilized by plants in response to NH4 +, which are consequently of ecological and agricultural importance.

Mechanisms of metabolic adaptation in the duckweed Lemna gibba: an integrated metabolic, transcriptomic and flux analysis

BACKGROUND

Duckweeds are small, rapidly growing aquatic flowering plants. Due to their ability for biomass production at high rates they represent promising candidates for biofuel feedstocks. Duckweeds are also excellent model organisms because they can be maintained in well-defined liquid media, usually reproduce asexually, and because genomic resources are becoming increasingly available. To demonstrate the utility of duckweed for integrated metabolic studies, we examined the metabolic adaptation of growing Lemna gibba cultures to different nutritional conditions.

RESULTS

To establish a framework for quantitative metabolic research in duckweeds we derived a central carbon metabolism network model of Lemna gibba based on its draft genome. Lemna gibba fronds were grown with nitrate or glutamine as nitrogen source. The two conditions were compared by quantification of growth kinetics, metabolite levels, transcript abundance, as well as by 13C-metabolic flux analysis. While growing with glutamine, the fronds grew 1.4 times faster and accumulated more protein and less cell wall components compared to plants grown on nitrate. Characterization of photomixotrophic growth by 13C-metabolic flux analysis showed that, under both metabolic growth conditions, the Calvin-Benson-Bassham cycle and the oxidative pentose-phosphate pathway are highly active, creating a futile cycle with net ATP consumption. Depending on the nitrogen source, substantial reorganization of fluxes around the tricarboxylic acid cycle took place, leading to differential formation of the biosynthetic precursors of the Asp and Gln families of proteinogenic amino acids. Despite the substantial reorganization of fluxes around the tricarboxylic acid cycle, flux changes could largely not be associated with changes in transcripts.

CONCLUSIONS

Through integrated analysis of growth rate, biomass composition, metabolite levels, and metabolic flux, we show that Lemna gibba is an excellent system for quantitative metabolic studies in plants. Our study showed that Lemna gibba adjusts to different nitrogen sources by reorganizing central metabolism. The observed disconnect between gene expression regulation and metabolism underscores the importance of metabolic flux analysis as a tool in such studies.

OsMADS5 interacts with OsSPL14/17 to inhibit rice root elongation by restricting cell proliferation of root meristem under ammonium supply

Nitrogen (N) is a vital major nutrient for rice (Oryza sativa). Rice responds to different applications of N by altering its root morphology, including root elongation. Although ammonium (NH 4 + ) is the primary source of N for rice,NH 4 + is toxic to rice roots and inhibits root elongation. However, the precise molecular mechanism thatNH 4 + -inhibited root elongation of rice is not well understood. Here, we identified a rice T-DNA insert mutant of OsMADS5 with a longer seminal root (SR) under sufficient N conditions. Reverse-transcription quantitative PCR analysis revealed that the expression level of OsMADS5 was increased underNH 4 + compared withNO 3 - supply. UnderNH 4 + conditions, knocking out OsMADS5 (cas9) produced a longer SR, phenocopying osmads5, while there was no significant difference in SR length between wild-type and cas9 underNO 3 - supply. Moreover, OsMADS5-overexpression plants displayed the opposite SR phenotype. Further study demonstrated that enhancement of OsMADS5 byNH 4 + supply inhibited rice SR elongation, likely by reducing root meristem activity of root tip, with the involvement of OsCYCB1;1. We also found that OsMADS5 interacted with OsSPL14 and OsSPL17 (OsSPL14/17) to repress their transcriptional activation by attenuating DNA binding ability. Moreover, loss of OsSPL14/17 function in osmads5 eliminated its stimulative effect on SR elongation underNH 4 + conditions, implying OsSPL14/17 may function downstream of OsMADS5 to mediate rice SR elongation underNH 4 + supply. Overall, our results indicate the existence of a novel modulatory pathway in which enhancement of OsMADS5 byNH 4 + supply represses the transcriptional activities of OsSPL14/17 to restrict SR elongation of rice.

In vivo visualization of nitrate dynamics using a genetically encoded fluorescent biosensor

Nitrate (NO₃^-) uptake and distribution are critical to plant life. Although the upstream regulation of NO₃^- uptake and downstream responses to NO₃^- in a variety of cells have been well studied, it is still not possible to directly visualize the spatial and temporal distribution of NO₃^- with high resolution at the cellular level. Here, we report a nuclear-localized, genetically encoded fluorescent biosensor, which we named NitraMeter3.0, for the quantitative visualization of NO₃^- distribution in Arabidopsis thaliana. This biosensor tracked the spatiotemporal distribution of NO₃^- along the primary root axis and disruptions by genetic mutation of transport (low NO₃^- uptake) and assimilation (high NO₃^- accumulation). The developed biosensor effectively monitors NO₃^- concentrations at the cellular level in real time and spatiotemporal changes during the plant life cycle.

NIN-like protein 7 transcription factor is a plant nitrate sensor

Nitrate is an essential nutrient and signaling molecule for plant growth. Plants sense intracellular nitrate to adjust their metabolic and growth responses. Here we identify the primary nitrate sensor in plants. We found that mutation of all seven Arabidopsis NIN-like protein (NLP) transcription factors abolished plants' primary nitrate responses and developmental programs. Analyses of NIN-NLP7 chimeras and nitrate binding revealed that NLP7 is derepressed upon nitrate perception via its amino terminus. A genetically encoded fluorescent split biosensor, mCitrine-NLP7, enabled visualization of single-cell nitrate dynamics in planta. The nitrate sensor domain of NLP7 resembles the bacterial nitrate sensor NreA. Substitutions of conserved residues in the ligand-binding pocket impaired the ability of nitrate-triggered NLP7 to control transcription, transport, metabolism, development, and biomass. We propose that NLP7 represents a nitrate sensor in land plants.

OsTBP2.1, a TATA-Binding Protein, Alters the Ratio of OsNRT2.3b to OsNRT2.3a and Improves Rice Grain Yield

The OsNRT2.3a and OsNRT2.3b isoforms play important roles in the uptake and transport of nitrate during rice growth. However, it is unclear which cis-acting element controls the transcription of OsNRT2.3 into these specific isoforms. In this study, we used a yeast one-hybrid assay to obtain the TATA-box binding protein OsTBP2.1, which binds to the TATA-box of OsNRT2.3, and verified its important role through transient expression and RNA-seq. We found that the TATA-box of OsNRT2.3 mutants and binding protein OsTBP2.1 together increased the transcription ratio of OsNRT2.3b to OsNRT2.3a. The overexpression of OsTBP2.1 promoted nitrogen uptake and increased rice yield compared with the wild-type; however, the OsTBP2.1 T-DNA mutant lines exhibited the opposite trend. Detailed analyses demonstrated that the TATA-box was the key cis-regulatory element for OsNRT2.3 to be transcribed into OsNRT2.3a and OsNRT2.3b. Additionally, this key cis-regulatory element, together with the binding protein OsTBP2.1, promoted the development of rice and increased grain yield.

Nitrate signaling and use efficiency in crops

Nitrate (NO₃^-) is not only an essential nutrient but also an important signaling molecule for plant growth. Low nitrogen use efficiency (NUE) of crops is causing increasingly serious environmental and ecological problems. Understanding the molecular mechanisms of NO₃^- regulation in crops is crucial for NUE improvement in agriculture. During the last several years, significant progress has been made in understanding the regulation of NO₃^- signaling in crops, and some key NO₃^- signaling factors have been shown to play important roles in NO₃^- utilization. However, no detailed reviews have yet summarized these advances. Here, we focus mainly on recent advances in crop NO₃^- signaling, including short-term signaling, long-term signaling, and the impact of environmental factors. We also review the regulation of crop NUE by crucial genes involved in NO₃^- signaling. This review provides useful information for further research on NO₃^- signaling in crops and a theoretical basis for breeding new crop varieties with high NUE, which has great significance for sustainable agriculture.

Ammonium and nitric oxide condition the establishment of Arabidopsis Ler/Kas-2 immune-related hybrid incompatibility

High ammonium suppresses hybrid incompatibility between Ler and Kas-2 accessions through lowering nitric oxide levels and nitrate reductase activity required for autoimmunity. The immune-related hybrid incompatibility (HI) between Landsberg erecta (Ler) and Kashmir-2 (Kas-2) accessions is due to a deleterious genetic interaction between the RPP1 (RECOGNITION OF PERONOSPORA PARASITICA1)-like Ler locus and Kas-2 alleles of the receptor-like kinase SRF3 (STRUBBELIG RECEPTOR FAMILY 3). The genetic incompatibility is temperature-dependent and leads to constitutive activation of the salicylic acid (SA) pathway, dwarfism and cell death at 14-16 °C. Here we investigated the effect of nutrition on the occurrence of Ler/Kas-2 HI and found that high ammonium suppresses Ler/Kas-2 incompatible phenotypes independently of the ammonium/nitrate ratio. Ammonium feeding leads to compromised disease resistance to Pseudomonas syringae pv. tomato DC3000, lower total SA, nitric oxide and nitrate reductase activity in Ler/Kas-2 incompatible hybrids. In addition, we find that Ler/Kas-2 incompatibility is dependent on NPR1 (NONEXPRESSER OF PR GENES 1) and nitric oxide production. Overall, this work highlights the effect of nutrition on the expression of incompatible phenotypes independently of temperature.

Isolation and Characterization of an LBD Transcription Factor CsLBD39 from Tea Plant (Camellia sinensis) and Its Roles in Modulating Nitrate Content by Regulating Nitrate-Metabolism-Related Genes

Nitrate nitrogen is an important nitrogen source for tea plants’ growth and development. LBD transcription factors play important roles in response to the presence of nitrate in plants. The functional study of LBD transcription factors in tea plants remains limited. In this study, the LBD family gene CsLBD39 was isolated and characterized from tea plants. Sequence analysis indicated that CsLBD39 contained a highly conserved CX₂CX₆CX₃CX domain. The phylogenetic tree assay showed that CsLBD39 belonged to class II subfamily of the LBD family. CsLBD39 was highly expressed in flowers and root; we determined that its expression could be induced by nitrate treatment. The CsLBD39 protein was located in the nucleus and has transcriptional activation activity in yeast. Compared with the wild type, overexpression of CsLBD39 gene in Arabidopsis resulted in smaller rosettes, shorter main roots, reduced lateral roots and lower plant weights. The nitrate content and the expression levels of genes related to nitrate transport and regulation were decreased in transgenic Arabidopsis hosting CsLBD39 gene. Compared with the wild type, CsLBD39 overexpression in transgenic Arabidopsis had smaller cell structure of leaves, shorter diameter of stem cross section, and slender and compact cell of stem longitudinal section. Under KNO₃ treatment, the contents of nitrate, anthocyanins, and chlorophyll in leaves, and the content of nitrate in roots of Arabidopsis overexpressing CsLBD39 were reduced, the expression levels of nitrate transport and regulation related genes were decreased. The results revealed that CsLBD39 may be involved in nitrate signal transduction in tea plants as a negative regulator and laid the groundwork for future studies into the mechanism of nitrate response.

N addition rebalances the carbon and nitrogen metabolisms of Leymus chinensis through leaf N investment

Intensifying nitrogen (N) deposition disturbs the growth of grassland plants due to an imbalance between their carbon (C) and N metabolism. However, it's unclear how plant physiological strategies restore balance. We investigated the effects of multiple N addition levels (0-25 g N m^-2 yr^-1) on the coordination of C and N metabolism in a dominant grass (Leymus chinensis) in a semiarid grassland in northern China. To do so, we evaluated photosynthetic parameters, leaf N allocation, C- and N-based metabolites, and metabolic enzymes. We found that a moderate N level (10 g N m^-2 yr^-1) promoted carboxylation and electron transport by allocating more N to the photosynthetic apparatus and increasing ribulose bisphosphate carboxylase/oxygenase activity, thereby increasing photosynthetic capacity. The highest N level (25 g N m^-2 yr^-1) promoted N investment in nonphotosynthetic pathways and increased the free amino acids in the leaves. N addition stimulated the accumulation of C and N compounds across organs by activating sucrose phosphate synthase, nitrate reductase, and glutamine synthetase. This enhancement triggered a transformation of primary metabolites (nonstructural carbohydrates, proteins, amino acids) to secondary metabolites (flavonoids, phenols, and alkaloids) for temporary storage or as defense compounds. Citric acid, as the C skeleton for enhanced N metabolism, decreased significantly, and malic acid increased by catalysis of phosphoenolpyruvate carboxylase. Our findings show the adaptability of L. chinensis to different N-addition levels by adjusting its allocations of C and N metabolic compounds and confirm the roles of C and N coordination by grassland plants in these adaptations.

Understanding the effect of GO on nitrogen assimilation in wheat through transcriptomics and metabolic process analysis

The extensive use of graphene oxide (GO) has resulted in its inevitable entry into the environment. It has been established that GO is detrimental to nitrogen accumulation in plants, as nitrogen is one of the most important nutrient for plant growth. However, its influence on nitrogen assimilation has not yet been investigated comprehensively. Based on the analysis of transcriptomics and nitrogen metabolites, this study showed that 400 mg L^-1 GO exposure downregulated most of the genes encoding nitrogen-assimilating enzymes, including nitrate reductase (NR), glutamine synthetase (GS), glutamate synthase (GOGAT), and glutamate dehydrogenase (GDH). The activities of the above enzymes in wheat roots were also reduced with GO addition, and the activities of NR and GS, the rate-limiting enzymes of nitrate and ammonium assimilation, were approximately 75% and 76% lower with 400 mg L^-1 GO supply, respectively, compared to those upon control treatment. Correspondingly, GO appears to exert a negative effect on multiple nitrogen assimilation products, including nitrous nitrogen, ammonium nitrogen, glutamine, glutamate, and soluble protein. In summary, this study showed that GO has adverse effects on the nitrogen assimilation of plants, and NR and GS are the most affected sites. Our findings would provide deeper insights into the physiological and molecular mechanisms underlying GO phytotoxicity.

Joint interactions of carbon and nitrogen metabolism dominated by bicarbonate and nitrogen in Orychophragmus violaceus and Brassica napus under simulated karst habitats

Karst habitats are uniquely characterized by high bicarbonate, high nitrate, and low ammonium, which are in-conducive to their growth and biodiversity. The occurrence of inorganic carbon and nitrogen in karst soil profoundly affects the carbon/nitrogen metabolism and adaptability of plants. However, there has been no final conclusion to the joint interactions of carbon and nitrogen metabolism in plants under karst habitats. In this study, we selected a karst-adaptable plant Orychophragmus violaceus (Ov), and a non-karst-adaptable plant Brassica napus (Bn) as experimental plants, and compared their joint effects of carbon and nitrogen metabolism under simulated karst habitats. It was found that the two species had different joint effects of carbon and nitrogen metabolisms. Bicarbonate and nitrate joint promoted photosynthetic activity and glucose metabolism, facilitating the carbon/nitrogen metabolism and growth of Ov, but their impacts on the carbon and nitrogen metabolism were insignificant in Bn. Bicarbonate and ammonium joint inhibited the photosynthesis and nitrogen metabolism, but promoted water use efficiency in Ov, leading to its enhance of growth reduction, ammonium toxicity alleviation, and drought resistance, while they inhibited the water use efficiency of Bn. In general, bicarbonate and nitrate/ammonium more significantly joint affected the carbon and nitrogen metabolism in Ov than Bn, which is vital for Ov to adapt to karst habitats.

A Review of Remote Sensing for Water Quality Retrieval: Progress and Challenges

Water pollution has become one of the most serious issues threatening water environments, water as a resource and human health. The most urgent and effective measures rely on dynamic and accurate water quality monitoring on a large scale. Due to their temporal and spatial advantages, remote sensing technologies have been widely used to retrieve water quality data. With the development of hyper-spectral sensors, unmanned aerial vehicles (UAV) and artificial intelligence, there has been significant advancement in remotely sensed water quality retrieval owing to various data availabilities and retrieval methodologies. This article presents the application of remote sensing for water quality retrieval, and mainly discusses the research progress in terms of data sources and retrieval modes. In particular, we summarize some retrieval algorithms for several specific water quality variables, including total suspended matter (TSM), chlorophyll-a (Chl–a), colored dissolved organic matter (CDOM), chemical oxygen demand (COD), total nitrogen (TN) and total phosphorus (TP). We also discuss the significant challenges to atmospheric correction, remotely sensed data resolution, and retrieval model applicability in the domains of spatial, temporal and water complexity. Finally, we propose possible solutions to these challenges. The review can provide detailed references for future development and research in water quality retrieval.

Effects of oxygen fertilization on damage reduction in flooded snap bean (Phaseolus vulgaris L.)

Flooding is one of the major abiotic stresses for vegetable production in Florida. Hydroponic and pot trials were conducted with snap bean to evaluate the effects of oxygen fertilization on the biochemical and physiological status of flooded snap bean plants. There were three treatments in the hydroponic trials were: (1) flooded (control), (2) bubble aeration with ambient air, and (3) hydrogen peroxide (H₂O₂) applied at the beginning of the trial. Plant health was evaluated by determining nitrogen (N) and phosphorus (P) uptake rates. The greenhouse pot trials were used to quantify the effects of three different application rates of solid oxygen fertilizers as calcium peroxide (CaO₂) and magnesium peroxide (MgO₂). The results showed that plant N and P uptake rates were significantly greater (p < 0.05) with H₂O₂ than without H₂O₂. The N uptake rates with H₂O₂ were like that of those with bubbling. The uptake rate of NH₄⁺ was significantly greater than that of NO₃^- with the bubbling and H₂O₂ conditions_, but the uptake rate of NO₃^- was significantly greater than that of NH₄⁺ in the flooding condition. The plant height, leaf greenness, shoot biomass, and yield were all significantly greater with CaO₂ or MgO₂ than without either solid oxygen fertilizer. The minimum damage of flooded snap bean was found with 2 g CaO₂ or 4 g MgO₂ per pot. These results indicated that oxygen fertilization may potentially improve yield of flooded snap bean plants.

Global gene expression profiling under nitrogen stress identifies key genes involved in nitrogen stress adaptation in maize (Zea mays L.)

Maize is a heavy consumer of fertilizer nitrogen (N) which not only results in the high cost of cultivation but may also lead to environmental pollution. Therefore, there is a need to develop N-use efficient genotypes, a prerequisite for which is a greater understanding of N-deficiency stress adaptation. In this study, comparative transcriptome analysis was performed using leaf and root tissues from contrasting inbred lines, viz., DMI 56 (tolerant to N stress) and DMI 81 (susceptible to N stress) to delineate the differentially expressed genes (DEGs) under low-N stress. The contrasting lines were grown hydroponically in modified Hoagland solution having either sufficient- or deficient-N, followed by high-throughput RNA-sequencing. A total of 8 sequencing libraries were prepared and 88–97% of the sequenced raw reads were mapped to the reference B73 maize genome. Genes with a p value ≤ 0.05 and fold change of ≥ 2.0 or ≤ − 2 were considered as DEGs in various combinations performed between susceptible and tolerant genotypes. DEGs were further classified into different functional categories and pathways according to their putative functions. Gene Ontology based annotation of these DEGs identified three different functional categories: biological processes, molecular function, and cellular component. The KEGG and Mapman based analysis revealed that most of the DEGs fall into various metabolic pathways, biosynthesis of secondary metabolites, signal transduction, amino acid metabolism, N-assimilation and metabolism, and starch metabolism. Some of the key genes involved in N uptake (high-affinity nitrate transporter 2.2 and 2.5), N assimilation and metabolism (glutamine synthetase, asparagine synthetase), redox homeostasis (SOD, POX), and transcription factors (MYB36, AP2-EREBP) were found to be highly expressed in the tolerant genotype compared to susceptible one. The candidate genes identified in the present study might be playing a pivotal role in low-N stress adaptation in maize and hence could be useful in augmenting further research on N metabolism and development of N-deficiency tolerant maize cultivars.

Identification and characterization of apple MdNLP7 transcription factor in the nitrate response

Nitrogen is an essential nutrient for plant growth and development. Low utilization of nitrogen fertilizer during agricultural production causes a series of environmental problems, such as water eutrophication, soil acidity, and air pollution. Investigating the patterns and mechanisms of crop NO₃^- absorption and utilization therefore key to fully improving crop nitrogen utilization rates and promoting sustainable agricultural development. Apple is one of the most important horticultural crops in the world. Its nitrogen demand by apple during the growth period is very high, but few studies have been performed on apple genes, that regulate the NO₃^- response. Here, we found that the apple transcription factor MdNLP7 promoted nitrogen absorption and assimilation by activating the expression of MdNIA2 and MdNRT1.1. MdNLP7 also regulated H₂O₂ content by increasing catalase activity, which may also influence nitrate utilization. Our findings provide insight into the mechanisms by which MdNLP7 controls nitrate utilization in apple.

New insights into the role of chrysanthemum calcineurin B-like interacting protein kinase CmCIPK23 in nitrate signaling in Arabidopsis roots

Nitrate is an important source of nitrogen and also acts as a signaling molecule to trigger numerous physiological, growth, and developmental processes throughout the life of the plant. Many nitrate transporters, transcription factors, and protein kinases participate in the regulation of nitrate signaling. Here, we identified a gene encoding the chrysanthemum calcineurin B-like interacting protein kinase CmCIPK23, which participates in nitrate signaling pathways. In Arabidopsis, overexpression of CmCIPK23 significantly decreased lateral root number and length and primary root length compared to the WT when grown on modified Murashige and Skoog medium with KNO₃ as the sole nitrogen source (modified MS). The expression of nitrate-responsive genes differed significantly between CmCIPK23-overexpressing Arabidopsis (CmCIPK23-OE) and the WT after nitrate treatment. Nitrate content was significantly lower in CmCIPK23-OE roots, which may have resulted from reduced nitrate uptake at high external nitrate concentrations (≥ 1 mM). Nitrate reductase activity and the expression of nitrate reductase and glutamine synthase genes were lower in CmCIPK23-OE roots. We also found that CmCIPK23 interacted with the transcription factor CmTGA1, whose Arabidopsis homolog regulates the nitrate response. We inferred that CmCIPK23 overexpression influences root development on modified MS medium, as well as root nitrate uptake and assimilation at high external nitrate supply. These findings offer new perspectives on the mechanisms by which the chrysanthemum CBL interacting protein kinase CmCIPK23 influences nitrate signaling.

UCP1 and AOX1a contribute to regulation of carbon and nitrogen metabolism and yield in Arabidopsis under low nitrogen stress

Nitrogen (N) availability is a critical factor for plant development and crop yield, and it closely correlates to carbon (C) metabolism. Uncoupling protein (UCP) and alternative oxidase (AOX) exhibit a strong correlation with N and C metabolism. Here, we investigated the functions of UCP1 and AOX1a using their mutants and complementation lines in Arabidopsis adaptation to low N. Low N markedly increased AOX1a and UCP1 expression, alternative pathway capacity and UCP activity. Eight-day-old aox1a/ucp1 seedlings were more sensitive to low N than Col-0 and single mutants, exhibiting lower primary root length and higher anthocyanin accumulation. The net photosynthetic rate, electron transport rate, PSII actual photochemical efficiency, stomatal conductance and carboxylation efficiency were markedly decreased in ucp1 and aox1a/ucp1 compared to those in Col-0 and aox1a under low N stress; comparatively, chlorophyll content and non-photochemical quenching coefficient were the lowest and highest in aox1a/ucp1, respectively. Nitrate acquisition rate was accelerated in aox1a/ucp1, but its transport activity was decreased, which resulted in low nitrate content and nitrate reductase activity under low N condition. The C/N ratio in seeds, but not in leaves, is higher in aox1a/ucp1 than that in Col-0, aox1a and ucp1 under low N condition. RNA-seq analysis revealed that many genes involved in photosynthesis and C/N metabolism were markedly down-regulated in aox1a/ucp1 under low N stress. These results highlight the key roles of UCP1 and AOX1a in modulating photosynthetic capacity, C/N assimilation and distribution under low N stress.

Nitrogen nutrition modifies the susceptibility of Arabidopsis thaliana to the necrotrophic fungus, Alternaria brassicicola

The impact of the form of nitrogen (N) source (nitrate versus ammonium) on the susceptibility to Alternaria brassicicola, a necrotrophic fungus, has been examined in Arabidopsis thaliana at the rosette stage. Nitrate nutrition was found to increase fungal lesions considerably. There was a similar induction of defence gene expression following infection under both N nutritions, except for the phytoalexin deficient 3 gene, which was overexpressed with nitrate. Nitrate also led to a greater nitric oxide production occurring in planta during the saprophytic growth and lower nitrate reductase (NIA1) expression 7 days after inoculation. This suggests that nitrate reductase-dependent nitric oxide production had a dual role, whereby, despite its known role in the generic response to pathogens, it affected plant metabolism, and this facilitated fungal infection. In ammonium-grown plants, infection with A. brassicicola induced a stronger gene expression of ammonium transporters and significantly reduced the initially high ammonium content in the leaves. There was a significant interaction between N source and inoculation (presence versus absence of the fungus) on the total amino acid content, while N nutrition reconfigured the spectrum of major amino acids. Typically, a higher content of total amino acid, mainly due to a stronger increase in asparagine and glutamine, is observed under ammonium nutrition while, in nitrate-fed plants, glutamate was the only amino acid which content increased significantly after fungal inoculation. N nutrition thus appears to control fungal infection via a complex set of signalling and nutritional events, shedding light on how nitrate availability can modulate disease susceptibility.

Nitrogen form-mediated ethylene signal regulates root-to-shoot K+ translocation via NRT1.5

Nitrogen-potassium synergistic and antagonistic interactions are the typical case of nutrient interactions. However, the underlying mechanism for the integration of the external N form into K⁺ homeostasis remains unclear. Here, we show that opposite effects of NO₃^- and NH₄⁺ on root-shoot K⁺ translocation were due to differential regulation of an ethylene signalling pathway targeting the NRT1.5 transporter. NH₄⁺ upregulated the transcriptional activity of EIN3, but repressed the expression of NRT1.5. However, the addition of NO₃^- strongly suppressed the activity of EIN3, whereas its addition upregulated the expression of AtNRT1.5 and shoot K⁺ concentration. The 35S:EIN3/ein3eil1 plants, nrt1.5 mutants and nrt1.5/skor double mutants displayed a low K⁺ chlorosis phenotype, especially under NH₄⁺ conditions with low K⁺ supply. Ion content analyses indicate that root-to-shoot K⁺ translocation was significantly reduced in these mutants. A Y1H assay, an EMSA and a transient expression assay confirmed that AtEIN3 protein could directly bind to the promoter of NRT1.5 to repress its expression. Furthermore, grafted plants with the roots of 35S:EIN3 and ein3eil1/nrt1.5 mutants displayed marked leaf chlorosis with a low K⁺ concentration. Collectively, our findings reveal that the interaction between N form and K⁺ was achieved by modulating root-derived ethylene signals to regulate root-to-shoot K⁺ translocation via NRT1.5.

Evidence that class I glutamine amidotransferase, GAT1_2.1, acts as a glutaminase in roots of Arabidopsis thaliana

The glutamine amidotransferase gene GAT1_2.1 is a marker of N status in Arabidopsis root, linked to a shoot branching phenotype. The protein has an N-terminal glutamine amidotransferase domain and a C-terminal extension with no recognizable protein domain. A purified, recombinant version of the glutamine amidotransferase domain was catalytically active as a glutaminase, with apparent K_m value of 0.66 mM and V_max value of 2.6 μkatal per mg. This form complemented an E. coli glutaminase mutant, ΔYneH. Spiking of root metabolite extracts with either the N-terminal or full length form purified from transformed tobacco leaves led to reciprocal changes in glutamine and ammonia concentration. No product derived from amido-¹⁵N-labeled glutamine was identified. Visualization of GAT1_2.1-YPF transiently expressed in tobacco leaves confirmed its mitochondrial localization. gat1_2.1 exhibited reduced growth as compared with wild-type seedlings on media with glutamine as sole nitrogen source. Results of targeted metabolite profiling pointed to a possible activation of the GABA shunt in the mutant following glutamine treatments, with reduced levels of glutamic acid, 2-oxoglutarate and γ-aminobutyric acid and increased levels of succinic acid. GAT1_2.1 may act as a glutaminase, in concert with Glutamate Dehydrogenase 2, to hydrolyze glutamine and channel 2-oxoglutarate to the TCA cycle under high nitrogen conditions.

Transcriptome analysis reveals the inhibitory nature of high nitrate during adventitious roots formation in the apple rootstock

In the process of vegetative propagation of apple rootstocks, the development of adventitious roots (ARs) has crucial importance. Nitrate is an essential nutrient necessary for plant growth; however, the inhibitory effect of high nitrate on ARs formation has not been explored. The physiological and molecular mechanisms underlying ARs inhibition were examined in this study. Stem cuttings of B9 apple rootstock were cultured on two nitrate treatments (T1 = 18.7 mM L^-1 and T2 = 37.5 mM L^-1 ), where T2 was identified as ARs inhibiting treatment. Morphological and anatomical observations advocating that high availability of nitrate inhibited AR formation by delaying the ARs initiation and emergence stages, where the root number was 287%, and the length was 604.6% lower than the T1 cuttings. Moreover, the contents of endogenous hormones were also elevated in response to T2 at most of the time points, which may cause a hormonal imbalance within the plant body and drive toward ARs inhibition. Furthermore, 3686 genes were differentially expressed by high-throughput sequencing. Out of these, 1797 genes were upregulated, and 1889 genes were downregulated. Approximately 238 genes related to nitrate, hormones, root development, and cell-cycle induction pathways were selected according to their potential to be involved in ARs regulation. This is the first study providing information regarding the inhibitory effect of high nitrate on ARs formation in apple rootstock.

Indicative bacterial communities and taxa of disease-suppressing and growth-promoting composts and their associations to the rhizoplane

Compost applications vary in their plant growth promotion and plant disease suppression, likely due to differences in physico-chemical and biological parameters. Our hypothesis was that bacteria are important for plant growth promotion and disease suppression of composts and, therefore, composts having these traits would contain similar sets of indicative bacterial taxa. Seventeen composts prepared from five different commercial providers and different starting materials were classified accordingly with bioassays using cress plants and the pathogen Pythium ultimum. Using a metabarcoding approach, bacterial communities were assessed in bulk composts and cress rhizoplanes. Six and nine composts showed significant disease suppression or growth promotion, respectively, but these traits did not correlate. Growth promotion correlated positively with nitrate content of composts, whereas disease suppression correlated negatively with factors representing compost age. Growth promotion and disease suppression explained significant portions of variation in bacterial community structures, i.e. 11.5% and 14.7%, respectively. Among the sequence variants (SVs) associated with growth promotion, Microvirga, Acinetobacter, Streptomyces, Bradyrhizobium and Bacillus were highly promising, while in suppressive composts, Ureibacillus,Thermogutta and Sphingopyxis were most promising. Associated SVs represent the basis for developing prediction tools for growth promotion and disease suppression, a highly desired goal for targeted compost production and application.

HBI transcription factor-mediated ROS homeostasis regulates nitrate signal transduction

Nitrate is both an important nutrient and a critical signaling molecule that regulates plant metabolism, growth, and development. Although several components of the nitrate signaling pathway have been identified, the molecular mechanism of nitrate signaling remains unclear. Here, we showed that the growth-related transcription factors HOMOLOG OF BRASSINOSTEROID ENHANCED EXPRESSION2 INTERACTING WITH IBH1 (HBI1) and its three closest homologs (HBIs) positively regulate nitrate signaling in Arabidopsis thaliana. HBI1 is rapidly induced by nitrate through NLP6 and NLP7, which are master regulators of nitrate signaling. Mutations in HBIs result in the reduced effects of nitrate on plant growth and ∼22% nitrate-responsive genes no longer to be regulated by nitrate. HBIs increase the expression levels of a set of antioxidant genes to reduce the accumulation of reactive oxygen species (ROS) in plants. Nitrate treatment induces the nuclear localization of NLP7, whereas such promoting effects of nitrate are significantly impaired in the hbi-q and cat2 cat3 mutants, which accumulate high levels of H2O2. These results demonstrate that HBI-mediated ROS homeostasis regulates nitrate signal transduction through modulating the nucleocytoplasmic shuttling of NLP7. Overall, our findings reveal that nitrate treatment reduces the accumulation of H2O2, and H2O2 inhibits nitrate signaling, thereby forming a feedback regulatory loop to regulate plant growth and development.

GCN4 Regulates Secondary Metabolism through Activation of Antioxidant Gene Expression under Nitrogen Limitation Conditions in Ganoderma lucidum

Nitrogen limitation has been widely reported to affect the growth and development of fungi, and the transcription factor GCN4 (general control nonderepressible 4) is involved in nitrogen restriction. Here, we found that nitrogen limitation highly induced the expression of GCN4 and promoted the synthesis of ganoderic acid (GA), an important secondary metabolite in Ganoderma lucidum. The activated GCN4 is involved in regulating GA biosynthesis. In addition, the accumulation of reactive oxygen species (ROS) also affects the synthesis of GA under nitrogen restrictions. The silencing of the gcn4 gene led to further accumulation of ROS and increased the content of GA. Further studies found that GCN4 activated the transcription of antioxidant enzyme biosynthesis genes gr, gst2, and cat3 (encoding glutathione reductase, glutathione S-transferase, and catalase, respectively) through direct binding to the promoter of these genes to reduce the ROS accumulation. In conclusion, our study found that GCN4 directly interacts with the ROS signaling pathway to negatively regulate GA biosynthesis under nitrogen-limiting conditions. This provides an essential insight into the understanding of GCN4 transcriptional regulation of the ROS signaling pathway and enriches the knowledge of nitrogen regulation mechanisms in fungal secondary metabolism of G. lucidum. IMPORTANCE Nitrogen has been widely reported to regulate secondary metabolism in fungi. Our study assessed the specific nitrogen regulatory mechanisms in Ganoderma lucidum. We found that GCN4 directly interacts with the ROS signaling pathway to negatively regulate GA biosynthesis under nitrogen-limiting conditions. Our research highlights a novel insight that GCN4, the nitrogen utilization regulator, participates in secondary metabolism through ROS signal regulation. In addition, this also provides a theoretical foundation for exploring the regulation of other physiological processes by GCN4 through ROS in fungi.

Low nitrate alleviates iron deficiency by regulating iron homeostasis in apple

Iron (Fe) is an essential element for plant growth, development and metabolism. Due to its lack of solubility and low bioavailability in soil, Fe levels are usually far below the optimum amount for most plants' growth and development. In apple production, excessive use of nitrogen fertilizer may cause iron chlorosis symptoms in the newly growing leaves, but the regulatory mechanisms underlying this phenomenon are unclear. In this study, low nitrate (NO₃^- , LN) application alleviated the symptoms of Fe deficiency and promoted lower rhizosphere pH, which was beneficial for root Fe acquisition. At the same time, LN treatment increased citrate and abscisic acid accumulation in roots, which promoted Fe transport from root to shoot and maintained Fe homeostasis. Moreover, qRT-PCR analysis showed that nitrate application caused differential expression of genes related to Fe uptake and transport, as well as transcriptional regulators. In summary, our data reveal that low nitrate alleviated Fe deficiency through multiple pathways, demonstrating a new option for minimizing Fe deficiency by regulating the balance between nutrients.

Low nitrogen conditions accelerate flowering by modulating the phosphorylation state of FLOWERING BHLH 4 in Arabidopsis

Nitrogen (N) is an essential nutrient that affects multiple plant developmental processes, including flowering. As flowering requires resources to develop sink tissues for reproduction, nutrient availability is tightly linked to this process. Low N levels accelerate floral transition; however, the molecular mechanisms underlying this response are not well understood. Here, we identify the FLOWERING BHLH 4 (FBH4) transcription factor as a key regulator of N-responsive flowering in Arabidopsis Low N-induced early flowering is compromised in fbh quadruple mutants. We found that FBH4 is a highly phosphorylated protein and that FBH4 phosphorylation levels decrease under low N conditions. In addition, decreased phosphorylation promotes FBH4 nuclear localization and transcriptional activation of the direct target CONSTANS (CO) and downstream florigen FLOWERING LOCUS T (FT) genes. Moreover, we demonstrate that the evolutionarily conserved cellular fuel sensor SNF1-RELATED KINASE 1 (SnRK1), whose kinase activity is down-regulated under low N conditions, directly phosphorylates FBH4. SnRK1 negatively regulates CO and FT transcript levels under high N conditions. Together, these results reveal a mechanism by which N levels may fine-tune FBH4 nuclear localization by adjusting the phosphorylation state to modulate flowering time. In addition to its role in flowering regulation, we also showed that FBH4 was involved in low N-induced up-regulation of nutrient recycling and remobilization-related gene expression. Thus, our findings provide insight into N-responsive growth phase transitions and optimization of plant fitness under nutrient-limited conditions.

GARP transcription factors repress Arabidopsis nitrogen starvation response via ROS-dependent and -independent pathways

Plants need to cope with strong variations of nitrogen availability in the soil. Although many molecular players are being discovered concerning how plants perceive NO3- provision, it is less clear how plants recognize a lack of nitrogen. Following nitrogen removal, plants activate their nitrogen starvation response (NSR), which is characterized by the activation of very high-affinity nitrate transport systems (NRT2.4 and NRT2.5) and other sentinel genes involved in N remobilization such as GDH3. Using a combination of functional genomics via transcription factor perturbation and molecular physiology studies, we show that the transcription factors belonging to the HHO subfamily are important regulators of NSR through two potential mechanisms. First, HHOs directly repress the high-affinity nitrate transporters, NRT2.4 and NRT2.5. hho mutants display increased high-affinity nitrate transport activity, opening up promising perspectives for biotechnological applications. Second, we show that reactive oxygen species (ROS) are important to control NSR in wild-type plants and that HRS1 and HHO1 overexpressors and mutants are affected in their ROS content, defining a potential feed-forward branch of the signaling pathway. Taken together, our results define the relationships of two types of molecular players controlling the NSR, namely ROS and the HHO transcription factors. This work (i) up opens perspectives on a poorly understood nutrient-related signaling pathway and (ii) defines targets for molecular breeding of plants with enhanced NO3- uptake.

SPL14/17 act downstream of strigolactone signalling to modulate rice root elongation in response to nitrate supply

Nitrogen (N) is an essential major nutrient for food crops. Although ammonium (NH₄⁺ ) is the primary N source of rice (Oryza sativa), nitrate (NO₃^- ) can also be absorbed and utilized. Rice responds to NO₃^- application by altering its root morphology, such as root elongation. Strigolactones (SLs) are important modulators of root length. However, the roles of SLs and their downstream genes in NO₃^- -induced root elongation remain unclear. Here, the levels of total N and SL (4-deoxyorobanchol) and the responses of seminal root (SR) lengths to NH₄⁺ and NO₃^- were investigated in rice plants. NO₃^- promoted SR elongation, possibly due to short-term signal perception and long-term nutrient function. Compared with NH₄⁺ conditions, higher SL signalling/levels and less D53 protein were recorded in roots of NO₃^- -treated rice plants. In contrast to wild-type plants, SR lengths of d mutants were less responsive to NO₃^- conditions, and application of rac-GR24 (SL analogue) restored SR length in d10 (SL biosynthesis mutant) but not in d3, d14, and d53 (SL-responsive mutants), suggesting that higher SL signalling/levels participate in NO₃^- -induced root elongation. D53 interacted with SPL17 and inhibited SPL17-mediated transactivation from the PIN1b promoter. Mutation of SPL14/17 and PIN1b caused insensitivity of the root elongation response to NO₃^- and rac-GR24 applications. Therefore, we conclude that perception of SLs by D14 leads to degradation of D53 via the proteasome system, which releases the suppression of SPL14/17-modulated transcription of PIN1b, resulting in root elongation under NO₃^- supply.

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.

Biochemical and Proteomic Changes in the Roots of M4 Grapevine Rootstock in Response to Nitrate Availability

In agricultural soils, nitrate (NO₃^-) is the major nitrogen (N) nutrient for plants, but few studies have analyzed molecular and biochemical responses involved in its acquisition by grapevine roots. In viticulture, considering grafting, NO₃^- acquisition is strictly dependent on rootstock. To improve the knowledge about N nutrition in grapevine, this study analyzed biochemical and proteomic changes induced by, NO₃^- availability, in a hydroponic system, in the roots of M4, a recently selected grapevine rootstock. The evaluation of biochemical parameters, such as NO₃^-, sugar and amino acid contents in roots, and the abundance of nitrate reductase, allowed us to define the time course of the metabolic adaptations to NO₃^- supply. On the basis of these results, the proteomic analysis was conducted by comparing the root profiles in N-starved plants and after 30 h of NO₃^- resupply. The analysis quantified 461 proteins, 26% of which differed in abundance between conditions. Overall, this approach highlighted, together with an increased N assimilatory metabolism, a concomitant rise in the oxidative pentose phosphate pathway and glycolysis, needed to fulfill the redox power and carbon skeleton demands, respectively. Moreover, a wide modulation of protein and amino acid metabolisms and changes of proteins involved in root development were observed. Finally, some results open new questions about the importance of redox-related post-translational modifications and of NO₃^- availability in modulating the dialog between root and rhizosphere.

Nitrogen Deficiency and Synergism between Continuous Light and Root Ammonium Supply Modulate Distinct but Overlapping Patterns of Phytohormone Composition in Xylem Sap of Tomato Plants

Continuous light (CL) or a predominant nitrogen supply as ammonium (NH4+) can induce leaf chlorosis and inhibit plant growth. The similarity in injuries caused by CL and NH4+ suggests involvement of overlapping mechanisms in plant responses to these conditions; however, these mechanisms are poorly understood. We addressed this topic by conducting full factorial experiments with tomato plants to investigate the effects of NO3- or NH4+ supply under diurnal light (DL) or CL. We used plants at ages of 26 and 15 days after sowing to initiate the treatments, and we modulated the intensity of the stress induced by CL and an exclusive NH4+ supply from mild to strong. Under DL, we also studied the effect of nitrogen (N) deficiency and mixed application of NO3- and NH4+. Under strong stress, CL and exclusive NH4+ supply synergistically inhibited plant growth and reduced chlorophyll content. Under mild stress, when no synergetic effect between CL and NH4+ was apparent on plant growth and chlorophyll content, we found a synergetic effect of CL and NH4+ on the accumulation of several plant stress hormones, with an especially strong effect for jasmonic acid (JA) and 1-aminocyclopropane-1-carboxylic acid (ACC), the immediate precursor of ethylene, in xylem sap. This modulation of the hormonal composition suggests a potential role for these plant hormones in plant growth responses to the combined application of CL and NH4+. No synergetic effect was observed between CL and NH4+ for the accumulation of soluble carbohydrates or of mineral ions, indicating that these plant traits are less sensitive than the modulation of hormonal composition in xylem sap to the combined CL and NH4+ application. Under diurnal light, NH4+ did not affect the hormonal composition of xylem sap; however, N deficiency strongly increased the concentrations of phaseic acid (PA), JA, and salicylic acid (SA), indicating that decreased N concentration rather than the presence of NO3- or NH4+ in the nutrient solution drives the hormone composition of the xylem sap. In conclusion, N deficiency or a combined application of CL and NH4+ induced the accumulation of JA in xylem sap. This accumulation, in combination with other plant hormones, defines the specific plant response to stress conditions.

The versatile GABA in plants

Gamma-aminobutyric acid (GABA) is a ubiquitous four-carbon, non-protein amino acid. GABA has been widely studied in animal central nervous systems, where it acts as an inhibitory neurotransmitter. In plants, it is metabolized through the GABA shunt pathway, a bypass of the tricarboxylic acid (TCA) cycle. Additionally, it can be synthesized through the polyamine metabolic pathway. GABA acts as a signal in Agrobacterium tumefaciens-mediated plant gene transformation and in plant development, especially in pollen tube elongation (to enter the ovule), root growth, fruit ripening, and seed germination. It is accumulated during plant responses to environmental stresses and pathogen and insect attacks. A high concentration of GABA elevates plant stress tolerance by improving photosynthesis, inhibiting reactive oxygen species (ROS) generation, activating antioxidant enzymes, and regulating stomatal opening in drought stress. The transporters of GABA in plants are reviewed in this work. We summarize the recent research on GABA function and transporters with the goal of providing a review of GABA in plants.

Modulation of nitrate-induced phosphate response by the MYB transcription factor RLI1/HINGE1 in the nucleus

The coordinated utilization of nitrogen (N) and phosphorus (P) is vital for plants to maintain nutrient balance and achieve optimal growth. Previously, we revealed a mechanism by which nitrate induces genes for phosphate utilization; this mechanism depends on NRT1.1B-facilitated degradation of cytoplasmic SPX4, which in turn promotes cytoplasmic-nuclear shuttling of PHR2, the central transcription factor of phosphate signaling, and triggers the nitrate-induced phosphate response (NIPR) and N-P coordinated utilization in rice. In this study, we unveiled a fine-tuning mechanism of NIPR in the nucleus regulated by Highly Induced by Nitrate Gene 1 (HINGE1, also known as RLI1), a MYB-transcription factor closely related to PHR2. RLI1/HINGE1, which is transcriptionally activated by PHR2 under nitrate induction, can directly activate the expression of phosphate starvation-induced genes. More importantly, RLI1/HINGE1 competes with PHR2 for binding to its repressor proteins in the nucleus (SPX proteins), and consequently releases PHR2 to further enhance phosphate response. Therefore, RLI1/HINGE1 amplifies the phosphate response in the nucleus downstream of the cytoplasmic SPX4-PHR2 cascade, thereby enabling fine-tuning of N-P balance when nitrate supply is sufficient.

Accession-specific flowering time variation in response to nitrate fluctuation in Arabidopsis thalian a

Flowering time, a key transition point from vegetative to reproductive growth, is regulated by an intrinsic complex of endogenous and exogenous signals including nutrient status. For hundreds of years, nitrogen has been well known to modulate flowering time, but the molecular genetic basis on how plants adapt to ever-changing nitrogen availability remains not fully explored. Here we explore how Arabidopsis natural variation in flowering time responds to nitrate fluctuation. Upon nitrate availability change, we detect accession- and photoperiod-specific flowering responses, which also feature a accession-specific dependency on growth traits. The flowering time variation correlates well with the expression of floral integrators, SOC1 and FT, in an accession-specific manner. We find that gene expression variation of key hub genes in the photoperiod-circadian-clock (GI), aging (SPLs) and autonomous (FLC) pathways associates with the expression change of these integrators, hence flowering time variation. Our results thus shed light on the molecular genetic mechanisms on regulation of accession- and photoperiod-specific flowering time variation in response to nitrate availability.

Developmental stage-specific metabolite signatures in Arabidopsis thaliana under optimal and mild nitrogen limitation

Metabolites influence flowering time, and thus are among the major determinants of yield. Despite the reported role of trehalose 6-phosphate and nitrate signaling on the transition from the vegetative to the reproductive phase, little is known about other metabolites contributing and responding to developmental phase changes. To increase our understanding which metabolic traits change throughout development in Arabidopsis thaliana and to identify metabolic markers for the vegetative and reproductive phases, especially among individual amino acids (AA), we profiled metabolites of plants grown in optimal (ON) and limited nitrogen (N) (LN) conditions, the latter providing a mild but consistent limitation of N. We found that although LN plants adapt their growth to a decreased level of N, their metabolite profiles are strongly distinct from ON plant profiles, with N as the driving factor for the observed differences. We demonstrate that the vegetative and the reproductive phase are not only marked by growth parameters such as biomass and rosette area, but also by specific metabolite signatures including specific single AA. In summary, we identified N-dependent and -independent indicators manifesting developmental stages, indicating that the plant's metabolic status also reports on the developmental phases.

Specific leaf area is modulated by nitrogen via changes in primary metabolism and parenchymal thickness in pepper

Nitrogen promotes changes in SLA through metabolism and anatomical traits in Capsicum plants. Specific leaf area (SLA) is a key trait influencing light interception and light use efficiency that often impacts plant growth and production. SLA is a key trait explaining growth variations of plant species under different environments. Both light and nitrogen (N) supply are important determinants of SLA. To better understand the effect of irradiance level and N on SLA in Capsicum chinense, we evaluated primary metabolites and morphological traits of two commercial cultivars (Biquinho and Habanero) in response to changes in both parameters. Both genotypes showed increased SLA with shading, and a decrease in SLA in response to increased N supply, however, with Habanero showing a stable SLA in the range of N deficiency to sufficient N doses. Correlation analyses indicated that decreased SLA in response to higher N supply was mediated by altered amino acids, protein, and starch levels, influencing leaf density. Moreover, in the range of moderate N deficiency to N sufficiency, both genotypes exhibited differences in SLA response, with Biquinho and Habanero displaying alterations on palisade and spongy parenchyma, respectively. Altogether, the results suggest that SLA responses to N supply are modulated by the balance between certain metabolites content and genotype-dependent changes in the parenchyma cells influencing leaf thickness and density.

Potassium: A key modulator for cell homeostasis

Potassium (K) is the most vital and abundant macro element for the overall growth of plants and its deficiency or, excess concentration results in many diseases in plants. It is involved in regulation of many crucial roles in plant development. Depending on soil-root interactions, complex soil dynamics often results in unpredictable availability of the elements. Based on the importance index, K is considered to be the second only to nitrogen for the overall growth of plants. More than 60 enzymes within the plant system depend on K for its activation, in which K act as a key regulator. K helps plants to resist several abiotic and biotic stresses in the environment. We have reviewed the research progress about K's role in plants covering various important considerations of K highlighting the effects of microbes on soil K⁺; K and its contribution to adsorbed dose in plants; the importance of K⁺ deficiency; physiological functions of K⁺ transporters and channels; and interference of abiotic stressor in the regulatory role of K. This review further highlights the scope of future research regarding K.

Genome-wide identification and expression analyses of nitrate transporter family genes in wild soybean (Glycine soja)

Nitrate transporters (NRTs) are important channel proteins facilitating cross-membrane movement of small molecules like NO3- which is a critical nutrient for all life. However, the classification and evolution of nitrate transporters in the legume plants are still elusive. In this study, we surveyed the wild soybean (G. soja) genomic databases and identified 120 GsNRT1 and 5 GsNRT2 encoding genes. Phylogenetic analyses show that GsNRT1 subfamily is consisted of eight clades (NPF1 to NPF8), while GsNRT2 subfamily has only one clade. Gene chromosomal location and evolutionary historic analyses indicate that GsNRT genes are unevenly distributed on 19 out of 20 G. soja chromosomes and segmental duplications may take a major part in the expansion of GsNRT family. Investigations of gene structure and protein motif compositions suggest that GsNRT family members are highly conserved in structures of both gene and protein levels. In addition, we analyzed the spatial expression patterns of representative GsNRT genes and their responses to exogenous nitrogen and carbon supplies and different abiotic stresses. The qRT-PCR data indicated that 16 selected GsNRT genes showed various expression levels in the roots, stems, leaves, and pods of young G. soja plants, and these genes were regulated by not only nitrogen and carbohydrate nutrients but also NaCl, NaHCO3, abscisic acid (ABA), and salicylic acid (SA). These results suggest that GsNRT genes may be involved in the regulation of plant growth, development, and adaptation to environmental stresses, and the study will shed light on functional dissection of plant nitrate transporter proteins in the future.

The Arabidopsis Transcription Factor CDF3 Is Involved in Nitrogen Responses and Improves Nitrogen Use Efficiency in Tomato

Nitrate is an essential macronutrient and a signal molecule that regulates the expression of multiple genes involved in plant growth and development. Here, we describe the participation of Arabidopsis DNA binding with one finger (DOF) transcription factor CDF3 in nitrate responses and shows that CDF3 gene is induced under nitrate starvation. Moreover, knockout cdf3 mutant plants exhibit nitrate-dependent lateral and primary root modifications, whereas CDF3 overexpression plants show increased biomass and enhanced root development under both nitrogen poor and rich conditions. Expression analyses of 35S::CDF3 lines reveled that CDF3 regulates the expression of an important set of nitrate responsive genes including, glutamine synthetase-1, glutamate synthase-2, nitrate reductase-1, and nitrate transporters NRT2.1, NRT2.4, and NRT2.5 as well as carbon assimilation genes like PK1 and PEPC1 in response to N availability. Consistently, metabolite profiling disclosed that the total amount of key N metabolites like glutamate, glutamine, and asparagine were higher in CDF3-overexpressing plants, but lower in cdf3-1 in N limiting conditions. Moreover, overexpression of CDF3 in tomato increased N accumulation and yield efficiency under both optimum and limiting N supply. These results highlight CDF3 as an important regulatory factor for the nitrate response, and its potential for improving N use efficiency in crops.