Maize source leaf adaptation to nitrogen deficiency affects not only nitrogen and carbon metabolism but also control of phosphate homeostasis

Comparative transcriptome analysis reveals major genes, transcription factors and biosynthetic pathways associated with leaf senescence in rice under different nitrogen application

BACKGROUND

Rice (Oryza sativa L.) is one of the most important food crops in the world and the application of nitrogen fertilizer is an effective means of ensuring stable and high rice yields. However, excessive application of nitrogen fertilizer not only causes a decline in the quality of rice, but also leads to a series of environmental costs. Nitrogen reutilization is closely related to leaf senescence, and nitrogen deficiency will lead to early functional leaf senescence, whereas moderate nitrogen application will help to delay leaf senescence and promote the production of photosynthetic assimilation products in leaves to achieve yield increase. Therefore, it is important to explore the mechanism by which nitrogen affects rice senescence, to search for genes that are tolerant to low nitrogen, and to delay the premature senescence of rice functional leaves.

RESULTS

The present study was investigated the transcriptional changes in flag leaves between full heading and mature grain stages of rice (O. sativa) sp. japonica 'NanGeng 5718' under varying nitrogen (N) application: 0 kg/ha (no nitrogen; 0N), 240 kg/ha (moderate nitrogen; MN), and 300 kg/ha (high nitrogen; HN). Compared to MN condition, a total of 10427 and 8177 differentially expressed genes (DEGs) were detected in 0N and HN, respectively. We selected DEGs with opposite expression trends under 0N and HN conditions for GO and KEGG analyses to reveal the molecular mechanisms of nitrogen response involving DEGs. We confirmed that different N applications caused reprogramming of plant hormone signal transduction, glycolysis/gluconeogenesis, ascorbate and aldarate metabolism and photosynthesis pathways in regulating leaf senescence. Most DEGs of the jasmonic acid, ethylene, abscisic acid and salicylic acid metabolic pathways were up-regulated under 0N condition, whereas DEGs related to cytokinin and ascorbate metabolic pathways were induced in HN. Major transcription factors include ERF, WRKY, NAC and bZIP TF families have similar expression patterns which were induced under N starvation condition.

CONCLUSION

Our results revealed that different nitrogen levels regulate rice leaf senescence mainly by affecting hormone levels and ascorbic acid biosynthesis. Jasmonic acid, ethylene, abscisic acid and salicylic acid promote early leaf senescence under low nitrogen condition, ethylene and ascorbate delay senescence under high nitrogen condition. In addition, ERF, WRKY, NAC and bZIP TF families promote early leaf senescence. The relevant genes can be used as candidate genes for the regulation of senescence. The results will provide gene reference for further genomic studies and new insights into the gene functions, pathways and transcription factors of N level regulates leaf senescence in rice, thereby improving NUE and reducing the adverse effects of over-application of N.

Tryptophan regulates sorghum root growth and enhances low nitrogen tolerance

Over evolutionary time, plants have developed sophisticated regulatory mechanisms to adapt to fluctuating nitrogen (N) environments, ensuring that their growth is balanced with their responses to N stress. This study explored the potential of L-tryptophan (Trp) in regulating sorghum root growth under conditions of N limitation. Here, two distinct sorghum genotypes (low-N tolerance 398B and low-N sensitive CS3541) were utilized for investigating effect of low-N stress on root morphology and conducting a comparative transcriptomics analysis. Our foundings indicated that 398B exhibited longer roots, greater root dry weights, and a higher Trp content compared to CS3541 under low-N conditions. Furthermore, transcriptome analysis revealed substantial differences in gene expression profiles related to Trp pathway and carbon (C) and N metabolism pathways between the two genotypes. Additional experiments were conducted to assess the effects of exogenous Trp treatment on the interplay between sorghum root growth and low-N tolerance. Our observations showed that Trp-treated plants developed longer root and had elevated levels of Trp and IAA under low-N conditons. Concurrently, these plants demonstrated stronger physiological activities in C and N metabolism when subjected to low-N stress. These results underscored the pivotal role of Trp on root growth and low-N stress responses by balancing IAA levels and C and N metabolism. This study not only deepens our understanding of how plants maintain growth plasticity during environmental stress but also provides valuable insights into the availability of amino acid in crops, which could be instrumental in developing strategies for promoting crop resilience to N deficiency.

Testing the trade-balance model: resource stoichiometry does not sufficiently explain AM effects

Variations in arbuscular mycorrhizae (AM) effects on plant growth (MGR) are commonly assumed to result from cost : benefit balances, with C as the cost and, most frequently, P as the benefit. The trade-balance model (TBM) adopts these assumptions and hypothesizes that mycorrhizal benefit depends on C : N : P stoichiometry. Although widely accepted, the TBM has not been experimentally tested. We isolated the parameters included in the TBM and tested these assumptions using it as framework. Oryza sativa plants were supplied with different N : P ratios at low light level, establishing different C : P and C : N exchange rates, and C, N or P limitation. MGR and effects on nutrient uptake, %M, ERM, photosynthesis and shoot starch were measured. C distribution to AM fungi played no role in MGR, and N was essential for all AM effects, including on P nutrition. C distribution to AM and MGR varied with the limiting nutrient (N or P), and evidence of extensive interplay between N and P was observed. The TBM was not confirmed. The results agreed with the exchange of surplus resources and source-sink regulation of resource distribution among plants and AMF. Rather than depending on exchange rates, resource exchange may simply obey both symbiont needs, not requiring further regulation.

C4 Phosphoenolpyruvate Carboxylase: Evolution and transcriptional regulation

Photosynthetic phosphoenolpyruvate carboxylase (PEPC) catalyses the irreversible carboxylation of phosphoenolpyruvate (PEP), producing oxaloacetate (OAA). This enzyme catalyses the first step of carbon fixation in C4 photosynthesis, contributing to the high photosynthetic efficiency of C4 plants. PEPC is also involved in replenishing tricarboxylic acid cycle intermediates, such as OAA, being involved in the C/N balance. In plants, PEPCs are classified in two types: bacterial type (BTPC) and plant-type (PTPC), which includes photosynthetic and non-photosynthetic PEPCs. During C4 evolution, photosynthetic PEPCs evolved independently. C4 PEPCs evolved to be highly expressed and active in a spatial-specific manner. Their gene expression pattern is also regulated by developmental cues, light, circadian clock as well as adverse environmental conditions. However, the gene regulatory networks controlling C4 PEPC gene expression, namely its cell-specificity, are largely unknown. Therefore, after an introduction to the evolution of PEPCs, this review aims to discuss the current knowledge regarding the transcriptional regulation of C4 PEPCs, focusing on cell-specific and developmental expression dynamics, light and circadian regulation, as well as response to abiotic stress. In conclusion, this review aims to highlight the evolution, transcriptional regulation by different signals and importance of PEPC in C4 photosynthesis and its potential as tool for crop improvement.

Recent advances in unraveling the mystery of combined nutrient stress in plants

Efficiently regulating growth to adapt to varying resource availability is crucial for organisms, including plants. In particular, the acquisition of essential nutrients is vital for plant development, as a shortage of just one nutrient can significantly decrease crop yield. However, plants constantly experience fluctuations in the presence of multiple essential mineral nutrients, leading to combined nutrient stress conditions. Unfortunately, our understanding of how plants perceive and respond to these multiple stresses remains limited. Unlocking this mystery could provide valuable insights and help enhance plant nutrition strategies. This review focuses specifically on the regulation of phosphorous homeostasis in plants, with a primary emphasis on recent studies that have shed light on the intricate interactions between phosphorous and other essential elements, such as nitrogen, iron, and zinc, as well as non-essential elements like aluminum and sodium. By summarizing and consolidating these findings, this review aims to contribute to a better understanding of how plants respond to and cope with combined nutrient stress.

Mining genic resources regulating nitrogen-use efficiency based on integrative biological analyses and their breeding applications in maize and other crops

Nitrogen (N) is an essential factor for limiting crop yields, and cultivation of crops with low nitrogen-use efficiency (NUE) exhibits increasing environmental and ecological risks. Hence, it is crucial to mine valuable NUE improvement genes, which is very important to develop and breed new crop varieties with high NUE in sustainable agriculture system. Quantitative trait locus (QTL) and genome-wide association study (GWAS) analysis are the most common methods for dissecting genetic variations underlying complex traits. In addition, with the advancement of biotechnology, multi-omics technologies can be used to accelerate the process of exploring genetic variations. In this study, we integrate the substantial data of QTLs, quantitative trait nucleotides (QTNs) from GWAS, and multi-omics data including transcriptome, proteome, and metabolome and further analyze their interactions to predict some NUE-related candidate genes. We also provide the genic resources for NUE improvement among maize, rice, wheat, and sorghum by homologous alignment and collinearity analysis. Furthermore, we propose to utilize the knowledge gained from classical cases to provide the frameworks for improving NUE and breeding N-efficient varieties through integrated genomics, systems biology, and modern breeding technologies.

Melatonin confers tolerance to nitrogen deficiency through regulating MdHY5 in apple plants

Nitrogen (N) is an essential nutrient for crop growth and development, significantly influencing both yield and quality. Melatonin (MT), a known enhancer of abiotic stress tolerance, has been extensively studied. However, its relationship with nutrient stress, particularly N deficiency, and the underlying regulatory mechanisms of MT on N absorption remain unclear. In this study, exogenous MT treatment was found to improve the tolerance of apple plants to N deficiency. Apple plants overexpressing the MT biosynthetic gene N-acetylserotonin methyltransferase 9 (MdASMT9) were used to further investigate the effects of endogenous MT on low-N stress. Overexpression of MdASMT9 improved the light harvesting and heat transfer capability of apple plants, thereby mitigating the detrimental effects of N deficiency on the photosynthetic system. Proteomic and physiological data analyses indicated that MdASMT9 overexpression enhanced the trichloroacetic acid cycle and positively modulated amino acid metabolism to counteract N-deficiency stress. Additionally, both exogenous and endogenous MT promoted the transcription of MdHY5, which in turn bound to the MdNRT2.1 and MdNRT2.4 promoters and activated their expression. Notably, MT-mediated promotion of MdNRT2.1 and MdNRT2.4 expression through regulating MdHY5, ultimately enhancing N absorption. Taken together, these findings shed light on the association between MdASMT9-mediated MT biosynthesis and N absorption in apple plants under N-deficiency conditions.

Transcriptome Profiling Reveals the Gene Network Responding to Low Nitrogen Stress in Wheat

As one of the essential nutrients for plants, nitrogen (N) has a major impact on the yield and quality of wheat worldwide. Due to chemical fertilizer pollution, it has become increasingly important to improve crop yield by increasing N use efficiency (NUE). Therefore, understanding the response mechanisms to low N (LN) stress is essential for the regulation of NUE in wheat. In this study, LN stress significantly accelerated wheat root growth, but inhibited shoot growth. Further transcriptome analysis showed that 8468 differentially expressed genes (DEGs) responded to LN stress. The roots and shoots displayed opposite response patterns, of which the majority of DEGs in roots were up-regulated (66.15%; 2955/4467), but the majority of DEGs in shoots were down-regulated (71.62%; 3274/4565). GO and KEGG analyses showed that nitrate reductase activity, nitrate assimilation, and N metabolism were significantly enriched in both the roots and shoots. Transcription factor (TF) and protein kinase analysis showed that genes such as MYB-related (38/38 genes) may function in a tissue-specific manner to respond to LN stress. Moreover, 20 out of 107 N signaling homologous genes were differentially expressed in wheat. A total of 47 transcriptome datasets were used for weighted gene co-expression network analysis (17,840 genes), and five TFs were identified as the potential hub regulatory genes involved in the response to LN stress in wheat. Our findings provide insight into the functional mechanisms in response to LN stress and five candidate regulatory genes in wheat. These results will provide a basis for further research on promoting NUE in wheat.

Exploring membrane vesicles in citrus fruits: a comparative analysis of conventional and organic farming approaches

BACKGROUND

Recently, vesicles derived from plant cell membranes have received attention for their potential use as active biomolecules and nanocarriers, and obtaining them from organic crops may be an interesting option because different farming systems can affect production, plant secondary metabolism and biochemistry of cell membranes. The present study aimed to determine how organic and conventional farming affects the mineral nutrition, gas exchange, CO2 fixation and biochemical composition of lemon fruits, which could have an impact on the different fractions of cell membranes in pulp and juice.

RESULTS

Organic trees had higher intrinsic water use efficiency (WUEi) but conventional trees had higher stomatal conductance (gs) and nitrogen use efficiency (NUtE). Also, organic lemons had significantly higher levels of some micronutrients (Ca, Cu, Fe and Zn). Second, the main differences in the membrane vesicles showed that organic pulp vesicles had a higher antioxidant activity and more oleic acid, whereas both types of vesicles from conventional lemons had more linoleic acid.

CONCLUSION

In conclusion, organic farming did not alter carbon fixation parameters but impacted nitrogen fixation and water uptake, and resulted in higher micronutrient levels in lemons. These mineral nutritional changes could be related to the higher production of membranes that showed suitable morphological traits and a high antioxidant activity, positively correlated with a high amount of oleic acid, which could have stronger cell protection characteristics. © 2023 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

1-nonene plays an important role in the response of maize-aphid-ladybird tritrophic interactions to nitrogen

Plant volatile organic compounds (VOCs) are the key distress signals involved in tritrophic interactions, by which plants recruit predators to protect themselves from herbivores. However, the effect of nitrogen fertilization on VOCs that mediate tritrophic interactions remains largely unidentified. In this study, a maize (Zea mays)-aphid (Rhopalosiphum padi)-ladybird (Harmonia axyridis) tritrophic interaction model was constructed under high-nitrogen (HN) and low-nitrogen (LN) regimens. H. axyridis had a stronger tendency to be attracted by aphid-infested maize under HN conditions. Then, volatiles were collected and identified from maize leaves on which aphids had fed. All of the HN-induced volatiles (HNIVs) elicited an electroantennogram (EAG) response from H. axyridis. Of these HNIVs, 1-nonene was attractive to H. axyridis under simulated natural volatilization. Furthermore, our regression showed that the release of 1-nonene was positively correlated with H. axyridis visitation rates. Supplying 1-nonene to maize on which aphids had fed under LN enhanced attractiveness to H. axyridis. These results supported the conclusion that 1-nonene was the active compound that mediated the response to nitrogen in the tritrophic interaction. In addition, the 1-nonene synthesis pathway was hypothesized, and we found that the release of 1-nonene might be related to the presence of salicylic acid (SA) and abscisic acid (ABA). This research contributes to the development of novel environmentally friendly strategies to optimize nitrogen fertilizer application and to improve pest control in maize crops.

P. Reddy G, Li Z, Chen F, Sun Y, Zhao Z. The nitrogen-dependent GABA pathway of tomato provides resistance to a globally invasive fruit fly

Introduction

The primary metabolism of plants, which is mediated by nitrogen, is closely related to the defense response to insect herbivores.

Methods

An experimental system was established to examine how nitrogen mediated tomato resistance to an insect herbivore, the oriental fruit fly (Bactrocera dorsalis). All tomatoes were randomly assigned to the suitable nitrogen (control, CK) treatment, nitrogen excess (NE) treatment and nitrogen deficiency (ND) treatment.

Results

We found that nitrogen excess significantly increased the aboveground biomass of tomato and increased the pupal biomass of B. dorsalis. Metabolome analysis showed that nitrogen excess promoted the biosynthesis of amino acids in healthy fruits, including γ-aminobutyric acid (GABA), arginine and asparagine. GABA was not a differential metabolite induced by injury by B. dorsalis under nitrogen excess, but it was significantly induced in infested fruits at appropriate nitrogen levels. GABA supplementation not only increased the aboveground biomass of plants but also improved the defensive response of tomato.

Discussion

The biosynthesis of GABA in tomato is a resistance response to feeding by B. dorsalis in appropriate nitrogen, whereas nitrogen excess facilitates the pupal weight of B. dorsalis by inhibiting synthesis of the GABA pathway. This study concluded that excess nitrogen inhibits tomato defenses in plant-insect interactions by inhibiting GABA synthesis, answering some unresolved questions about the nitrogen-dependent GABA resistance pathway to herbivores.

Plant growth-promoting rhizobacteria: A good companion for heavy metal phytoremediation

Phytoremediation is an environment-friendly approach regarded as a potential candidate for remediating heavy metal (HM)-contaminated soils. However, the low efficacy of phytoremediation is a major limitation that hampers its large-scale application. Therefore, developing strategies to enhance phytoremediation efficacy for contaminated soils is crucial. Plant growth-promoting rhizobacteria (PGPR) considerably contribute to phytoremediation intensification. To improve the efficiency of plant-microbe symbiosis for remediation, the mechanisms underlying PGPR-stimulated HM accumulation and tolerance in plants should be comprehensively understood. This review focuses on hyperaccumulators, PGPR, and the mechanisms by which PGPR enhance phytoremediation from four aspects: providing nutrients to plants, secreting plant hormones and specific enzymes, inducing systemic resistance, and altering the bioavailability of HMs in soils. It also provides a theoretical and technical basis for future research on PGPR synergism in promoting the phytoextraction efficiency in HM-contaminated soils.

An Integrated Analysis of Metabolome, Transcriptome, and Physiology Revealed the Molecular and Physiological Response of Citrus sinensis Roots to Prolonged Nitrogen Deficiency

Citrus sinensis seedlings were supplied with a nutrient solution containing 15 (control) or 0 (nitrogen (N) deficiency) mM N for 10 weeks. Extensive metabolic and gene reprogramming occurred in 0 mM N-treated roots (RN0) to cope with N deficiency, including: (a) enhancing the ability to keep phosphate homeostasis by elevating the abundances of metabolites containing phosphorus and the compartmentation of phosphate in plastids, and/or downregulating low-phosphate-inducible genes; (b) improving the ability to keep N homeostasis by lowering the levels of metabolites containing N but not phosphorus, upregulating N compound degradation, the root/shoot ratio, and the expression of genes involved in N uptake, and resulting in transitions from N-rich alkaloids to carbon (C)-rich phenylpropanoids and phenolic compounds (excluding indole alkaloids) and from N-rich amino acids to C-rich carbohydrates and organic acids; (c) upregulating the ability to maintain energy homeostasis by increasing energy production (tricarboxylic acid cycle, glycolysis/gluconeogenesis, oxidative phosphorylation, and ATP biosynthetic process) and decreasing energy utilization for amino acid and protein biosynthesis and new root building; (d) elevating the transmembrane transport of metabolites, thus enhancing the remobilization and recycling of useful compounds; and (e) activating protein processing in the endoplasmic reticulum. RN0 had a higher ability to detoxify reactive oxygen species and aldehydes, thus protecting RN0 against oxidative injury and delaying root senescence.

An integrated nitrogen utilization gene network and transcriptome analysis reveal candidate genes in response to nitrogen deficiency in Brassica napus

Nitrogen (N) is an essential factor for crop yield. Here, we characterized 605 genes from 25 gene families that form the complex gene networks of N utilization pathway in Brassica napus. We found unequal gene distribution between the A_n- and C_n-sub-genomes, and that genes derived from Brassica rapa were more retained. Transcriptome analysis indicated that N utilization pathway gene activity shifted in a spatio-temporal manner in B. napus. A low N (LN) stress RNA-seq of B. napus seedling leaves and roots was generated, which proved that most N utilization related genes were sensitive to LN stress, thereby forming co-expression network modules. Nine candidate genes in N utilization pathway were confirmed to be significantly induced under N deficiency conditions in B. napus roots, indicating their potential roles in LN stress response process. Analyses of 22 representative species confirmed that the N utilization gene networks were widely present in plants ranging from Chlorophyta to angiosperms with a rapid expansion trend. Consistent with B. napus, the genes in this pathway commonly showed a wide and conserved expression profile in response to N stress in other plants. The network, genes, and gene-regulatory modules identified here represent resources that may enhance the N utilization efficiency or the LN tolerance of B. napus.

Soil physicochemical properties associated with the yield and phytochemical composition of the edible halophyte Crithmum maritimum

There is growing interest in the consumption of halophytes due to their excellent nutritional profile and antioxidant properties, and their cultivation offers viable alternatives in the face of irreversible global salinization of soils. Nevertheless, abiotic factors strongly influence their phytochemical composition, and little is known about how growing conditions can produce plants with the best nutritional and functional properties. Crithmum maritimum is an edible halophyte with antioxidant properties and considerable potential for sustainable agriculture in marginal environments. However, it is found naturally in contrasting habitats with variable soil physicochemical properties and the extent to which edaphic factors can influence plant performance, accumulation of phytochemicals and their quality remains unknown. We investigated the influence of soil physicochemical properties (texture, pH, electrical conductivity, organic matter content and mineral element concentrations) on growth and reproductive performance, nutritional traits, and the accumulation of specific metabolites in C. maritimum. Soil, leaf and seed samples were taken from eight C. maritimum populations located on the southern coasts of Spain and Portugal. We found greater vegetative growth and seed production in coarser, sandier soils with lower microelement concentrations. The nutritional traits of leaves varied, with soil organic matter and macronutrient content associated with reduced leaf Na, protein and phenolic (mainly flavonoid) concentrations, whereas soils with lower pH and Fe concentrations, and higher clay content yielded plants with lower leaf Zn concentration and greater accumulation of hydroxycinnamic acids. The nutritional value of the seed oil composition appeared to be enhanced in soils with coarser texture and lower microelement concentrations. The accumulation of specific phenolic compounds in the seed was influenced by a wide range of soil properties including texture, pH and some microelements. These findings will inform the commercial cultivation of C. maritimum, particularly in the economic exploitation of poorly utilized, saline soils.

Transcriptome and Co-Expression Network Analysis Reveals the Molecular Mechanism of Rice Root Systems in Response to Low-Nitrogen Conditions

Nitrogen is an important nutrient for plant growth and essential metabolic processes. Roots integrally obtain nutrients from soil and are closely related to the growth and development of plants. In this study, the morphological analysis of rice root tissues collected at different time points under low-nitrogen and normal nitrogen conditions demonstrated that, compared with normal nitrogen treatment, the root growth and nitrogen use efficiency (NUE) of rice under low-nitrogen treatment were significantly improved. To better understand the molecular mechanisms of the rice root system’s response to low-nitrogen conditions, a comprehensive transcriptome analysis of rice seedling roots under low-nitrogen and control conditions was conducted in this study. As a result, 3171 differentially expressed genes (DEGs) were identified. Rice seedling roots enhance NUE and promote root development by regulating the genes related to nitrogen absorption and utilization, carbon metabolism, root growth and development, and phytohormones, thereby adapting to low-nitrogen conditions. A total of 25,377 genes were divided into 14 modules using weighted gene co-expression network analysis (WGCNA). Two modules were significantly associated with nitrogen absorption and utilization. A total of 8 core genes and 43 co-expression candidates related to nitrogen absorption and utilization were obtained in these two modules. Further studies on these genes will contribute to the understanding of low-nitrogen adaptation and nitrogen utilization mechanisms in rice.

Transcriptome and Metabolome Reveal the Molecular Mechanism of Barley Genotypes Underlying the Response to Low Nitrogen and Resupply

Nitrogen is one of the most important mineral elements for plant growth and development. Excessive nitrogen application not only pollutes the environment, but also reduces the quality of crops. However, are few studies on the mechanism of barley tolerance to low nitrogen at both the transcriptome and metabolomics levels. In this study, the nitrogen-efficient genotype (W26) and the nitrogen-sensitive genotype (W20) of barley were treated with low nitrogen (LN) for 3 days and 18 days, then treated with resupplied nitrogen (RN) from 18 to 21 days. Later, the biomass and the nitrogen content were measured, and RNA-seq and metabolites were analyzed. The nitrogen use efficiency (NUE) of W26 and W20 treated with LN for 21 days was estimated by nitrogen content and dry weight, and the values were 87.54% and 61.74%, respectively. It turned out to have a significant difference in the two genotypes under the LN condition. According to the transcriptome analysis, 7926 differentially expressed genes (DEGs) and 7537 DEGs were identified in the leaves of W26 and W20, respectively, and 6579 DEGs and 7128 DEGs were found in the roots of W26 and W20, respectively. After analysis of the metabolites, 458 differentially expressed metabolites (DAMs) and 425 DAMs were found in the leaves of W26 and W20, respectively, and 486 DAMs and 368 DAMs were found in the roots of W26 and W20, respectively. According to the KEGG joint analysis of DEGs and DAMs, it was discovered that glutathione (GSH) metabolism was the pathway of significant enrichment in the leaves of both W26 and W20. In this study, the metabolic pathways of nitrogen metabolism and GSH metabolism of barley under nitrogen were constructed based on the related DAMs and DEGs. In leaves, GSH, amino acids, and amides were the main identified DAMs, while in roots, GSH, amino acids, and phenylpropanes were mainly found DAMs. Finally, some nitrogen-efficient candidate genes and metabolites were selected based on the results of this study. The responses of W26 and W20 to low nitrogen stress were significantly different at the transcriptional and metabolic levels. The candidate genes that have been screened will be verified in future. These data not only provide new insights into how barley responds to LN, but also provide new directions for studying the molecular mechanisms of barley under abiotic stress.

Comparative transcriptomic and metabolomic analysis revealed molecular mechanism of two wheat near-isogenic lines response to nitrogen application

Nitrogen (N) is an essential nutrient element required for plant growth, and the development of wheat varieties with high nitrogen use efficiency (NUE) is an urgent need for sustainable crop production. However, the molecular mechanism of NUE between diverse wheat varieties in response to N application remains unclear. To reveal the possible molecular mechanisms underlying this complex phenomenon, we investigated the transcriptional and metabolic changes of flag leaves of two wheat near-isogenic lines (NILs) differing in NUE under two N fertilizer treatments. Comparative transcriptome analysis indicated that the expression levels of the genes responsible for carbon and nitrogen metabolism were significantly higher in high-NUE wheat. The metabolome comparison revealed that the activity of the tricarboxylic acid (TCA) cycle was enhanced in high-NUE wheat, while reduced in low-NUE wheat after the N fertilizer application. Additionally, amino acid metabolism increased in both wheat NILs but more increased in high-NUE wheat. In summary, more upregulated transcripts and metabolites were identified in high-NUE wheat, and this study provides valuable new insights for improving NUE in wheat.

Analysis of metabolic differences in maize in different growth stages under nitrogen stress based on UPLC-QTOF-MS

Introduction

Maize has a high demand for nitrogen during the growth period. The study of metabolic changes in maize can provide a theoretical basis for rational nitrogen nutrition regulation.

Methods

In order to investigate the changes of different metabolites and their metabolic pathways in maize leaves under nitrogen stress, we used ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UPLC-QTOF-MS) for metabolomic analysis of maize leaves under different nitrogen treatments at three critical growth stages (V4, V12 and R1) in a pot experiment under natural conditions.

Results and discussion

The results showed that nitrogen stress significantly affected sugar metabolism and nitrogen metabolism, and affected carbon and nitrogen balance, and the effects of stress on maize leaves metabolism increased with the growth process. Metabolic pathways such as the TCA cycle and starch and sucrose metabolism were mainly affected at the seeding stage (V4). The stress response to nitrogen deficiency also showed significant upregulation of flavonoids such as luteolin and astragalin during the booting stage (V12) and anthesis-silking stage (R1). During R1 stage, the synthesis of tryptophan and phenylalanine and the degradation of lysine were significantly affected. Compared with nitrogen stress, the metabolic synthesis of key amino acids and jasmonic acid were intensified and the TCA cycle was promoted under nitrogen sufficiency conditions. This study initially revealed that the response mechanism of maize to nitrogen stress at the metabolic level.

Tracking the Biostimulatory Effect of Fractions from a Commercial Plant Protein Hydrolysate in Greenhouse-Grown Lettuce

Protein hydrolysate biostimulants are environmentally friendly options for the reduction of nitrogen input, but their plant growth-promoting mechanisms are still not completely unveiled. Here, to put the “signaling peptide theory” to the test, a greenhouse experiment was undertaken using low (1 mM) and optimal (8 mM) NO3-treated butterhead lettuce and three molecular fractions (PH1 (>10 kDa), PH2 (1−10 kDa) and PH3 (<10 kDa) fractions), in addition to the whole product Vegamin®: PH, in a randomized block design. PH1 and PH3 significantly increased fresh yield (+8%) under optimal (lighter leaves), but not under low (darker leaves) NO3 conditions. Total ascorbic acid, lutein and β-carotene increased with PH3, and disinapoylgentobiose and kaempferol-3-hydroxyferuloyl-sophorosie-7-glucoside content increased with PH (whole/fractions) treatments, particularly under low NO3 conditions. The complete hydrolysate and analyzed peptide fractions have differential biostimulatory effects, enhancing the growth and nutritional quality of lettuce.

Metabolome and transcriptome profiles in quinoa seedlings in response to potassium supply

BACKGROUND

Quinoa (Chenopodium quinoa Willd.) is a herb within the Quinoa subfamily of Amaranthaceae, with remarkable environmental adaptability. Its edible young leaves and grains are rich in protein, amino acids, microorganisms, and minerals. Although assessing the effects of fertilization on quinoa yield and quality has become an intensive area of research focus, the associated underlying mechanisms remain unclear. As one of the three macro nutrients in plants, potassium has an important impact on plant growth and development. In this study, extensive metabolome and transcriptome analyses were conducted in quinoa seedlings 30 days after fertilizer application to characterize the growth response mechanism to potassium.  RESULTS: The differential metabolites and genes present in the seedlings of white and red quinoa cultivars were significantly enriched in the photosynthetic pathway. Moreover, the PsbQ enzyme on photosystem II and delta enzyme on ATP synthase were significantly down regulated in quinoa seedlings under potassium deficiency. Additionally, the differential metabolites and genes of red quinoa seedlings were significantly enriched in the arginine biosynthetic pathway.

CONCLUSIONS

These findings provide a more thorough understanding of the molecular changes in quinoa seedlings that occur under deficient, relative to normal, potassium levels. Furthermore, this study provides a theoretical basis regarding the importance of potassium fertilizers, as well as their efficient utilization by growing quinoa seedlings.

Yield and quality of alfalfa (Medicago sativa L.) in response to fertilizer application in China: A meta-analysis

INTRODUCTION

In China, alfalfa (Medicago sativa L.) often grows in marginal land with poor soil fertility and suboptimal climate conditions. Alfalfa production cannot meet demands both in yield and quality. It is necessary to apply fertilizers to achieve high yields and produce high-quality alfalfa in China. However, there is no understanding on the impact of fertilizer application on alfalfa production and the possible optimal application rates across China.

METHODS

We conducted a meta-analysis to explore the contribution of fertilizer application to the yield and quality of alfalfa based on a dataset from 86 studies published between 2004 and 2022.

RESULTS AND DISCUSSION

The results showed that fertilizer application not only increased alfalfa yield by 19.2% but also improved alfalfa quality by increasing crude protein (CP) by 7.7% and decreasing acid detergent fibre by 2.9% and neutral detergent fibre by 1.8% overall compared to the non-fertilizer control levels. The combined nitrogen (N), phosphorus (P) and potassium (K) and combined NP fertilizer applications achieved the greatest yield and CP concentration increases of 27.0% and 13.5%, respectively. Considering both yield and quality, the optimal rate of fertilizer application ranged from 30 to 60 kg ha^-1 for N, 120 to 150 kg ha^-1 for P and less than 120 kg ha^-1 for K. Meta-analysis further showed that the effect of fertilizer application on yield was greater in low soil organic matter (SOM) soils than in high SOM soils. In conclusion, fertilizer application is an effective strategy to improve the yield and quality of alfalfa in China, especially that grown in low SOM soils. This study is helpful for optimizing fertilization schedules of alfalfa in China.

Elevated pH-mediated mitigation of aluminum-toxicity in sweet orange (Citrus sinensis) roots involved the regulation of energy-rich compounds and phytohormones

For the first time, we used targeted metabolome to investigate the effects of pH-aluminum (Al) interactions on energy-rich compounds and their metabolites (ECMs) and phytohormones in sweet orange (Citrus sinensis) roots. The concentration of total ECMs (TECMs) was reduced by Al-toxicity in 4.0-treated roots, but unaffected significantly in pH 3.0-treated roots. However, the concentrations of most ECMs and TECMs were not lower in pH 4.0 + 1.0 mM Al-treated roots (P4AR) than in pH 3.0 + 1.0 mM Al-treated roots (P3AR). Increased pH improved the adaptability of ECMs to Al-toxicity in roots. For example, increased pH improved the utilization efficiency of ECMs and the conversion of organic phosphorus (P) from P-containing ECMs into available phosphate in Al-treated roots. We identified upregulated cytokinins (CKs), downregulated jasmonic acid (JA), methyl jasmonate (MEJA) and jasmonates (JAs), and unaltered indole-3-acetic acid (IAA) and salicylic acid (SA) in P3AR vs pH 3.0 + 0 mM Al-treated roots (P3R); upregulated JA, JAs and IAA, downregulated total CKs, and unaltered MEJA and SA in P4AR vs pH 4.0 + 0 mM Al-treated roots (P4R); and upregulated CKs, downregulated JA, MEJA, JAs and SA, and unaltered IAA in P3AR vs P4AR. Generally viewed, raised pH-mediated increments of JA, MEJA, total JAs, SA and IAA concentrations and reduction of CKs concentration in Al-treated roots might help to maintain nutrient homeostasis, increase Al-toxicity-induced exudation of organic acid anions and the compartmentation of Al in vacuole, and reduce oxidative stress and Al uptake, thereby conferring root Al-tolerance. In short, elevated pH-mediated mitigation of root Al-stress involved the regulation of ECMs and phytohormones.

Differential metabolic rearrangements in the roots and leaves of Cicer arietinum caused by single or double nitrate and/or phosphate deficiencies

Nitrate (NO₃ ^- ) and phosphate (Pi) deficiencies are the major constraints for chickpea productivity, significantly impacting global food security. However, excessive fertilization is expensive and can also lead to environmental pollution. Therefore, there is an urgent need to develop chickpea cultivars that are able to grow on soils deficient in both NO₃ ^- and Pi. This study focused on the identification of key NO₃ ^- and/or Pi starvation-responsive metabolic pathways in the leaves and roots of chickpea grown under single and double nutrient deficiencies of NO₃ ^- and Pi, in comparison with nutrient-sufficient conditions. A global metabolite analysis revealed organ-specific differences in the metabolic adaptation to nutrient deficiencies. Moreover, we found stronger adaptive responses in the roots and leaves to any single than combined nutrient-deficient stresses. For example, chickpea enhanced the allocation of carbon among nitrogen-rich amino acids (AAs) and increased the production of organic acids in roots under NO₃ ^- deficiency, whereas this adaptive response was not found under double nutrient deficiency. Nitrogen remobilization through the transport of AAs from leaves to roots was greater under NO₃ ^- deficiency than double nutrient deficiency conditions. Glucose-6-phosphate and fructose-6-phosphate accumulated in the roots under single nutrient deficiencies, but not under double nutrient deficiency, and higher glycolytic pathway activities were observed in both roots and leaves under single nutrient deficiency than double nutrient deficiency. Hence, the simultaneous deficiency generated a unique profile of metabolic changes that could not be simply described as the result of the combined deficiencies of the two nutrients.

Dissection of Crop Metabolome Responses to Nitrogen, Phosphorus, Potassium, and Other Nutrient Deficiencies

Crop growth and yield often face sophisticated environmental stresses, especially the low availability of mineral nutrients in soils, such as deficiencies of nitrogen, phosphorus, potassium, and others. Thus, it is of great importance to understand the mechanisms of crop response to mineral nutrient deficiencies, as a basis to contribute to genetic improvement and breeding of crop varieties with high nutrient efficiency for sustainable agriculture. With the advent of large-scale omics approaches, the metabolome based on mass spectrometry has been employed as a powerful and useful technique to dissect the biochemical, molecular, and genetic bases of metabolisms in many crops. Numerous metabolites have been demonstrated to play essential roles in plant growth and cellular stress response to nutrient limitations. Therefore, the purpose of this review was to summarize the recent advances in the dissection of crop metabolism responses to deficiencies of mineral nutrients, as well as the underlying adaptive mechanisms. This review is intended to provide insights into and perspectives on developing crop varieties with high nutrient efficiency through metabolite-based crop improvement.

Adaptive responses of carbon and nitrogen metabolisms to nitrogen-deficiency in Citrus sinensis seedlings

BACKGROUND

In China, nitrogen (N)-deficiency often occurs in Citrus orchards, which is one of the main causes of yield loss and fruit quality decline. Little information is known about the adaptive responses of Citrus carbon (C) and N metabolisms to N-deficiency. Seedlings of 'Xuegan' (Citrus sinensis (L.) Osbeck) were supplied with nutrient solution at an N concentration of 0 (N-deficiency), 5, 10, 15 or 20 mM for 10 weeks. Thereafter, we examined the effects of N supply on the levels of C and N in roots, stems and leaves, and the levels of organic acids, nonstructural carbohydrates, NH₄⁺-N, NO₃^--N, total soluble proteins, free amino acids (FAAs) and derivatives (FAADs), and the activities of key enzymes related to N assimilation and organic acid metabolism in roots and leaves.

RESULTS

N-deficiency elevated sucrose export from leaves to roots, C and N distributions in roots and C/N ratio in roots, stems and leaves, thus enhancing root dry weight/shoot dry weight ratio and N use efficiency. N-deficient leaves displayed decreased accumulation of starch and total nonstructural carbohydrates (TNC) and increased sucrose/starch ratio as well as a partitioning trend of assimilated C toward to sucrose, but N-deficient roots displayed elevated accumulation of starch and TNC and reduced sucrose/starch ratio as well as a partitioning trend of assimilated C toward to starch. N-deficiency reduced the concentrations of most FAADs and the ratios of total FAADs (TFAADs)/N in leaves and roots. N-deficiency reduced the demand for C skeleton precursors for amino acid biosynthesis, thus lowering TFAADs/C ratio in leaves and roots. N-deficiency increased (decreased) the relative amounts of C-rich (N-rich) FAADs, thus increasing the molar ratio of C/N in TFAADs in leaves and roots.

CONCLUSIONS

Our findings corroborated our hypothesis that C and N metabolisms displayed adaptive responses to N-deficiency in C. sinensis seedlings, and that some differences existed between roots and leaves in N-deficiency-induced alterations of and C and N metabolisms.

Molecular and Physiological Responses of Citrus sinensis Leaves to Long-Term Low pH Revealed by RNA-Seq Integrated with Targeted Metabolomics

Low pH-induced alterations in gene expression profiles and organic acids (OA) and free amino acid (FAA) abundances were investigated in sweet orange [Citrus sinensis (L.) Osbeck cv. Xuegan] leaves. We identified 503 downregulated and 349 upregulated genes in low pH-treated leaves. Further analysis indicated that low pH impaired light reaction and carbon fixation in photosynthetic organisms, thereby lowering photosynthesis in leaves. Low pH reduced carbon and carbohydrate metabolisms, OA biosynthesis and ATP production in leaves. Low pH downregulated the biosynthesis of nitrogen compounds, proteins, and FAAs in leaves, which might be conducive to maintaining energy homeostasis during ATP deprivation. Low pH-treated leaves displayed some adaptive responses to phosphate starvation, including phosphate recycling, lipid remodeling, and phosphate transport, thus enhancing leaf acid-tolerance. Low pH upregulated the expression of some reactive oxygen species (ROS) and aldehyde detoxifying enzyme (peroxidase and superoxidase) genes and the concentrations of some antioxidants (L-tryptophan, L-proline, nicotinic acid, pantothenic acid, and pyroglutamic acid), but it impaired the pentose phosphate pathway and V_E and secondary metabolite biosynthesis and downregulated the expression of some ROS and aldehyde detoxifying enzyme (ascorbate peroxidase, aldo-keto reductase, and 2-alkenal reductase) genes and the concentrations of some antioxidants (pyridoxine and γ-aminobutyric acid), thus disturbing the balance between production and detoxification of ROS and aldehydes and causing oxidative damage to leaves.

Metabolic Profiles Reveal Changes in the Leaves and Roots of Rapeseed (Brassica napus L.) Seedlings under Nitrogen Deficiency

Rapeseed (Brassica napus L.) is an important oil crop species and plays a crucial role in supplying edible oil worldwide. However, rapeseed production in the field is often severely inhibited due to nitrogen (N) deficiency. Metabolites play key roles in plant growth and resistance to environmental stress, but little is known about the differential synthesis and accumulation of metabolites underlying rapeseed adaptation to N deficiency. Here, we studied the phenotypic response and used LC–electrospray ionization (ESI), ESI–MS/MS, and widely untargeted metabolomic approaches to detect differences in rapeseed under normal N (HN) and N-deficient (LN) conditions. The results showed that N deficiency severely inhibited rapeseed shoot growth and promoted rapeseed root architectural changes under LN conditions. In total, 574 metabolites were detected, and there were 175 and 166 differentially accumulated metabolites in the leaves and roots between the HN and LN conditions, respectively. The significantly differentially accumulated metabolites were involved in four primary metabolic pathways, namely, sucrose, phenylalanine, amino acid, and tricarboxylic acid cycle metabolism. Notably, we found that plant hormones have distinct accumulation patterns in rapeseed and coordinate to play crucial roles in both maintaining growth and protecting against damage from plant disease under HN and LN conditions. Moreover, our results indicated that flavonoid compounds, especially anthocyanins and rutin, may play important roles in increasing root cell resistance to oxidative damage and soil pathogen infections. Overall, this work provides valuable information for understanding the overall metabolite changes in rapeseed under N deficiency conditions, which may be beneficial for improving and producing new varieties of rapeseed capable of high yields under low N conditions.

Seasonal dynamics of marine protist communities in tidally mixed coastal waters

Major seasonal community reorganizations and associated biomass variations are landmarks of plankton ecology. However, the processes of plankton community turnover rates have not been fully elucidated so far. Here, we analyse patterns of planktonic protist community succession in temperate latitudes, based on quantitative taxonomic data from both microscopy counts (cells >10 μm) and ribosomal DNA metabarcoding (size fraction >3 μm, 18S rRNA gene) from plankton samples collected bimonthly over 8 years (2009–2016) at the SOMLIT‐Astan station (Roscoff, Western English Channel). Based on morphology, diatoms were clearly the dominating group all year round and over the study period. Metabarcoding uncovered a wider diversity spectrum and revealed the prevalence of Dinophyceae and diatoms but also of Cryptophyta, Chlorophyta, Cercozoa, Syndiniales and Ciliophora in terms of read counts and or richness. The use of morphological and molecular analyses in combination allowed improving the taxonomic resolution and to identify the sequence of the dominant species and OTUs (18S V4 rDNA‐derived taxa) that drive annual plankton successions. We detected that some of these dominant OTUs were benthic as a result of the intense tidal mixing typical of the French coasts in the English Channel. Our analysis of the temporal structure of community changes point to a strong seasonality and resilience. The temporal structure of environmental variables (especially Photosynthetic Active Radiation, temperature and macronutrients) and temporal structures generated by species life cycles and or species interactions, are key drivers of the observed cyclic annual plankton turnover.

Uncovering Pathways Highly Correlated to NUE through a Combined Metabolomics and Transcriptomics Approach in Eggplant

Nitrogen (N) fertilization is one of the main inputs to increase crop yield and food production. However, crops utilize only 30–40% of N applied; the remainder is leached into the soil, causing environmental and health damage. In this scenario, the improvement of nitrogen-use efficiency (NUE) will be an essential strategy for sustainable agriculture. Here, we compared two pairs of NUE-contrasting eggplant (Solanum melongena L.) genotypes, employing GC-MS and UPLC-qTOF-MS-based technologies to determine the differential profiles of primary and secondary metabolites in root and shoot tissues, under N starvation as well as at short- and long-term N-limiting resupply. Firstly, differences in the primary metabolism pathways of shoots related to alanine, aspartate and glutamate; starch, sucrose and glycine; serine and threonine; and in secondary metabolites biosynthesis were detected. An integrated analysis between differentially accumulated metabolites and expressed transcripts highlighted a key role of glycine accumulation and the related glyA transcript in the N-use-efficient genotypes to cope with N-limiting stress. Interestingly, a correlation between both sucrose synthase (SUS)- and fructokinase (scrK)-transcript abundances, as well as D-glucose and D-fructose accumulation, appeared useful to distinguish the N-use-efficient genotypes. Furthermore, increased levels of L-aspartate and L-asparagine in the N-use-efficient genotypes at short-term low-N exposure were detected. Granule-bound starch synthase (WAXY) and endoglucanase (E3.2.1.4) downregulation at long-term N stress was observed. Therefore, genes and metabolites related to these pathways could be exploited to improve NUE in eggplant.

Dissecting the metabolic reprogramming of maize root under nitrogen-deficient stress conditions

The growth and development of maize (Zea mays L.) largely depends on its nutrient uptake through the root. Hence, studying its growth, response, and associated metabolic reprogramming to stress conditions is becoming an important research direction. A genome-scale metabolic model (GSM) for the maize root was developed to study its metabolic reprogramming under nitrogen stress conditions. The model was reconstructed based on the available information from KEGG, UniProt, and MaizeCyc. Transcriptomics data derived from the roots of hydroponically grown maize plants were used to incorporate regulatory constraints in the model and simulate nitrogen-non-limiting (N+) and nitrogen-deficient (N-) condition. Model-predicted flux-sum variability analysis achieved 70% accuracy compared with the experimental change of metabolite levels. In addition to predicting important metabolic reprogramming in central carbon, fatty acid, amino acid, and other secondary metabolism, maize root GSM predicted several metabolites (l-methionine, l-asparagine, l-lysine, cholesterol, and l-pipecolate) playing a regulatory role in the root biomass growth. Furthermore, this study revealed eight phosphatidylcholine and phosphatidylglycerol metabolites which, even though not coupled with biomass production, played a key role in the increased biomass production under N-deficient conditions. Overall, the omics-integrated GSM provides a promising tool to facilitate stress condition analysis for maize root and engineer better stress-tolerant maize genotypes.

Photosynthetic product allocations of Pinus massoniana seedlings inoculated with ectomycorrhizal fungi along a nitrogen addition gradient

Quantifying the allocation of photosynthetic products among different carbon (C) pools is critical for understanding and predicting plant C turnover response to climate change. A field experiment with ectomycorrhizal fungi (EMF) and nitrogen (N) was established to investigate the effects on allocation of photosynthetic products in Pinus massoniana (Lamb.) seedlings given increased N deposition. Seedlings were subjected to N addition and symbiosis with EMF, and the short-term allocation of a ¹³C photosynthetic pulse into leaves, branches, stems, roots, and soil was traced. Photosynthetic rate and root respiration were measured. It was found that N addition changed the allocation pattern of photosynthetic products in various organs of P. massoniana. Furthermore, N addition, mycorrhizal symbiosis, and interaction of N and EMF, all increased the amount of C produced by photosynthesis. N application less than 60 kg N hm^-1 a^-1 could promote the transfer and allocation of photosynthetic products in P. massoniana organs, which peaks at 60 kg N hm^-1 a^-1, and the highest N treatment began to decrease at 90 kg N hm^-1 a^-1. EMF inoculation could expand the absorption area of plant roots to obtain more nutrients and synthesize more C and N compounds for promoting the growth of itself and the host plant, improving the net photosynthetic rate and the distribution of C produced by photosynthesis in various organs. This forms a benign C and N cycle, thereby reducing the effect of high N addition on plants. The optimal N addition concentration was 60 kg N hm^-1 a^-1, and the optimal EMF was Pt, which provides a theoretical basis for inoculating EMF during increasing N deposition in the future climate change scenario. This enables plants to distribute more photosynthetic products to their roots, thus affecting their own C distribution for promoting growth.

Metabolomics and Transcriptomics Integration of Early Response of Populus tomentosa to Reduced Nitrogen Availability

Nitrogen (N) is one of the most crucial elements for plant growth and development. However, little is known about the metabolic regulation of trees under conditions of N deficiency. In this investigation, gas chromatography-mass spectrometry (GC-MS) was used to determine global changes in metabolites and regulatory pathways in Populus tomentosa. Thirty metabolites were found to be changed significantly under conditions of low-N stress. N deficiency resulted in increased levels of carbohydrates and decreases in amino acids and some alcohols, as well as some secondary metabolites. Furthermore, an RNA-sequencing (RNA-Seq) analysis was performed to characterize the transcriptomic profiles, and 1,662 differentially expressed genes were identified in P. tomentosa. Intriguingly, four pathways related to carbohydrate metabolism were enriched. Genes involved in the gibberellic acid and indole-3-acetic acid pathways were found to be responsive to low-N stress, and the contents of hormones were then validated by high-performance liquid chromatography/electrospray ionization tandem mass spectrometry (HPLC-ESI-MS/MS). Coordinated metabolomics and transcriptomics analysis revealed a pattern of co-expression of five pairs of metabolites and unigenes. Overall, our investigation showed that metabolism directly related to N deficiency was depressed, while some components of energy metabolism were increased. These observations provided insights into the metabolic and molecular mechanisms underlying the interactions of N and carbon in poplar.

Nitrogen deficiency results in changes to cell wall composition of sorghum seedlings

Sorghum [Sorghum bicolor (L.) Moench] has been gaining attention as a feedstock for biomass energy production. While it is obvious that nitrogen (N) supply significantly affects sorghum growth and biomass accumulation, our knowledge is still limited regarding the effect of N on the biomass quality of sorghum, such as the contents and structures of lignin and other cell wall components. Therefore, in this study, we investigated the effects of N supply on the structure and composition of sorghum cell walls. The cell walls of hydroponically cultured sorghum seedlings grown under sufficient or deficient N conditions were analyzed using chemical, two-dimensional nuclear magnetic resonance, gene expression, and immunohistochemical methods. We found that the level of N supply considerably affected the cell wall structure and composition of sorghum seedlings. Limitation of N led to a decrease in the syringyl/guaiacyl lignin unit ratio and an increase in the amount and alteration of tissue distribution of several hemicelluloses, including mixed linkage (1 → 3), (1 → 4)-β-d-glucan, and arabinoxylan. At least some of these cell wall alterations could be associated with changes in gene expression. Nitrogen status is thus one of the factors affecting the cell wall properties of sorghum seedlings.

Nitrogen use efficiency (NUE): elucidated mechanisms, mapped genes and gene networks in maize (Zea mays L.)

Nitrogen, the vital primary plant growth nutrient at deficit soil conditions, drastically affects the growth and yield of a crop. Over the years, excess use of inorganic nitrogenous fertilizers resulted in pollution, eutrophication and thereby demanding the reduction in the use of chemical fertilizers. Being a C₄ plant with fibrous root system and high NUE, maize can be deployed to be the best candidate for better N uptake and utilization in nitrogen deficient soils. The maize germplasm sources has enormous genetic variation for better nitrogen uptake contributing traits. Adoption of single cross maize hybrids as well as inherent property of high NUE has helped maize cultivars to achieve the highest growth rate among the cereals during last decade. Further, considering the high cost of nitrogenous fertilizers, adverse effects on soil health and environmental impact, maize improvement demands better utilization of existing genetic variation for NUE via introgression of novel allelic combinations in existing cultivars. Marker assisted breeding efforts need to be supplemented with introgression of genes/QTLs related to NUE in ruling varieties and thereby enhancing the overall productivity of maize in a sustainable manner. To achieve this, we need mapped genes and network of interacting genes and proteins to be elucidated. Identified genes may be used in screening ideal maize genotypes in terms of better physiological functionality exhibiting high NUE. Future genome editing may help in developing lines with increased productivity under low N conditions in an environment of optimum agronomic practices.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-021-01113-z.

Adaptive Agricultural Strategies for Facing Water Deficit in Sweet Maize Production: A Case Study of a Semi-Arid Mediterranean Region

Maize is a crucial global commodity, which is used not only for food, but also as an alternative crop in biogas production and as a major energy-supply ingredient in animal diets. However, climate change is jeopardizing current maize production due to its direct impact on weather instability and water availability or its indirect effects on regional climate suitability loss. Hence, new areas for sweet maize cultivation should be considered in the future. Therefore, this study focuses on the possibility of producing maize in a challenging environment in Southern Italy considering rainfed cultivation and two irrigation regimes (full and deficit). The experiment was conducted during two subsequent growing seasons under semi-arid Mediterranean climate conditions. The overall results indicated a significant difference in biomass and yield between irrigated and non-irrigated treatments, and between full and deficit irrigation. Sweet maize cultivated under deficit irrigation gained less biomass than under full irrigation and its development and fruit maturation were delayed. Under deficit irrigation, the plants gave lower yields and a higher percentage of the panicle weight consisted of kernels. Irrigation water productivity was higher for deficit than for full irrigated treatment. These findings indicate the feasibility of sweet maize production in semi-arid areas of Southern Italy using adaptive agricultural strategies including deficit irrigation and controlled water stress. Given the importance of maize production, understanding of maize growth and productivity in a challenging environment may support future agricultural programming and thereby contribute e to mitigation of the direct and indirect effects of climate change.

miRNAomic Approach to Plant Nitrogen Starvation

Nitrogen (N) is one of the indispensable nutrients required by plants for their growth, development, and survival. Being a limited nutrient, it is mostly supplied exogenously to the plants, to maintain quality and productivity. The increased use of N fertilizers is associated with high-cost inputs and negative environmental consequences, which necessitates the development of nitrogen-use-efficient plants for sustainable agriculture. Understanding the regulatory mechanisms underlying N metabolism in plants under low N is one of the prerequisites for the development of nitrogen-use-efficient plants. One of the important and recently discovered groups of regulatory molecules acting at the posttranscriptional and translational levels are microRNAs (miRNAs). miRNAs are known to play critical roles in the regulation of gene expression in plants under different stress conditions including N stress. Several classes of miRNAs associated with N metabolism have been identified so far. These nitrogen-responsive miRNAs may provide a platform for a better understanding of the regulation of N metabolism and pave a way for the development of genotypes for better N utilization. The current review presents a brief outline of miRNAs and their regulatory role in N metabolism.

Accumulation of Amino Acids and Flavonoids in Young Tea Shoots Is Highly Correlated With Carbon and Nitrogen Metabolism in Roots and Mature Leaves

The quality of tea product and the metabolism of quality-related compounds in young shoots are significantly affected by the nitrogen(N) supply. However, little is known of the metabolic changes that take place in tea roots and mature leaves under different supplies, which has a large effect on the accumulation of quality-related compounds in young shoots. In this study, young shoots, mature leaves, and roots under different N conditions were subjected to metabolite profiling using gas chromatography and ultraperformance liquid chromatography, coupled with quadrupole time-of-flight mass spectrometry. The contents of free amino acids (e.g., theanine and glutamate) involved in N metabolism were significantly greater under high N than under low N, while a high N supply reduced soluble sugars (e.g., glucose) in all three tissues. Organic acids (e.g., malate, fumarate, α-ketoglutatare, and succinate) involved in tricarboxylic acid cycle remarkably increased as the nitrogen supply increased, which confirms that carbon (C) allocation was restricted by increasing the nitrogen supply, especially in mature leaves. RT-PCR results indicated that gene expression related to nitrogen assimilation significantly increased in roots with increasing nitrogen supply, which had a significant positive relationship with the level of free amino acids in young shoots. In addition, the expression of most genes involved in flavonoid synthesis was significantly upregulated under conditions of low nitrogen supply relative to high nitrogen supply in young shoot and roots. These data suggest that enhanced assimilation of N in tea roots and the coordinated regulation of C (sugars, organic acids, and flavonoids) and N(amino acids) in mature leaves can lead to a high accumulation of amino acids in young shoots. Furthermore, as the N supply increased, more C was partitioned into compounds containing N in mature leaves and roots, resulting in a decrease in flavonoids in young shoots. In conclusion, the accumulation of amino acids and flavonoids in young tea shoots is highly correlated with carbon and nitrogen metabolism in roots and mature leaves.

Examination of the Productivity and Physiological Responses of Maize (Zea mays L.) to Nitrapyrin and Foliar Fertilizer Treatments

Nutrient stress has been known as the main limiting factor for maize growth and yield. Nitrapyrin, as a nitrification inhibitor-which reduces nitrogen loss-and foliar fertilizer treatments have been successfully used to enhance the efficiency of nutrient utilization, however, the impacts of these two technologies on physiological development, enzymatic responses, and productivity of maize are poorly studied. In this paper, the concentration of each stress indicator, such as contents of proline, malondialdehyde (MDA), relative chlorophyll, photosynthetic pigments, and the activity of superoxide dismutase (SOD) were measured in maize leaf tissues. In addition, biomass growth, as well as quantitative and qualitative parameters of yield production were examined. Results confirm the enhancing impact of nitrapyrin on the nitrogen use of maize. Furthermore, lower activity of proline, MDA, SOD, as well as higher photosynthetic activity were shown in maize with a more favorable nutrient supply due to nitrapyrin and foliar fertilizer treatments. The obtained findings draw attention to the future practical relevance of these technologies that can be implemented to enhance the physiological development and productivity of maize. However, this paper also highlights the importance of irrigation, as nutrient uptake from soil by the crops decreases during periods of drought.

Transcriptome Analysis Reveals Different Responsive Patterns to Nitrogen Deficiency in Two Wheat Near-Isogenic Lines Contrasting for Nitrogen Use Efficiency

Simple Summary

Nitrogen (N) limitation is the key factor for wheat production worldwide. Therefore, the development of genotypes with improved nitrogen use efficiency (NUE) is a prerequisite for sustainable and productive agriculture. Exploring the molecular mechanisms of low N stress tolerance is significant for breeding wheat cultivars with high NUE. To clarify the underlying molecular mechanisms of enhanced resilience to low N in high-NUE wheat, we performed an RNA sequencing (RNA-seq) analysis. In the current research, two wheat near-isogenic lines (NILs) differing dramatically in NUE were used to measure gene expression differences under different N treatments. There was a dramatic difference between two wheat NILs in response to N deficiency at the transcriptional level, and the classification of identified candidate genes may provide new valuable insights into the resilience mechanism of wheat.

Abstract

The development of crop cultivars with high nitrogen use efficiency (NUE) under low-N fertilizer inputs is imperative for sustainable agriculture. However, there has been little research on the molecular mechanisms underlying enhanced resilience to low N in high-NUE plants. The comparison of the transcriptional responses of genotypes contrasting for NUE will facilitate an understanding of the key molecular mechanism of wheat resilience to low-N stress. In the current study, the RNA sequencing (RNA-seq) technique was employed to investigate the genotypic difference in response to N deficiency between two wheat NILs (1Y, high-NUE, and 1W, low-NUE). In our research, high- and low-NUE wheat NILs showed different patterns of gene expression under N-deficient conditions, and these N-responsive genes were classified into two major classes, including “frontloaded genes” and “relatively upregulated genes”. In total, 103 and 45 genes were identified as frontloaded genes in high-NUE and low-NUE wheat, respectively. In summary, our study might provide potential directions for further understanding the molecular mechanism of high-NUE genotypes adapting to low-N stress.

Integration of the metabolome and transcriptome reveals the mechanism of resistance to low nitrogen supply in wild bermudagrass (Cynodon dactylon (L.) Pers.) roots

BACKGROUND

Nitrogen (N) is an essential macronutrient that significantly affects turf quality. Commercial cultivars of bermudagrass (Cynodon dactylon (L.) Pers.) require large amounts of nitrogenous fertilizer. Wild bermudagrass germplasm from natural habitats with poor nutrition and diverse N distributions is an important source for low-N-tolerant cultivated bermudagrass breeding. However, the mechanisms underlying the differences in N utilization among wild germplasm resources of bermudagrass are not clear.

RESULTS

To clarify the low N tolerance mechanism in wild bermudagrass germplasm, the growth, physiology, metabolome and transcriptome of two wild accessions, C291 (low-N-tolerant) and C716 (low-N-sensitive), were investigated. The results showed that root growth was less inhibited in low-N-tolerant C291 than in low-N-sensitive C716 under low N conditions; the root dry weight, soluble protein content and free amino acid content of C291 did not differ from those of the control, while those of C716 were significantly decreased. Down-regulation of N acquisition, primary N assimilation and amino acid biosynthesis was less pronounced in C291 than in C716 under low N conditions; glycolysis and the tricarboxylic acid (TCA) cycle pathway were also down-regulated, accompanied by a decrease in the biosynthesis of amino acids; strikingly, processes such as translation, biosynthesis of the structural constituent of ribosome, and the expression of individual aminoacyl-tRNA synthetase genes, most of genes associated with ribosomes related to protein synthesis were all up-regulated in C291, but down-regulated in C716.

CONCLUSIONS

Overall, low-N-tolerant wild bermudagrass tolerated low N nutrition by reducing N primary assimilation and amino acid biosynthesis, while promoting the root protein synthesis process and thereby maintaining root N status and normal growth.

The effect of NH4+ on phosphoenolpyruvate carboxykinase gene expression, metabolic flux and citrate content of citrus juice sacs

Citrate is one of the most important metabolites determining the flavour of citrus fruit. It has been reported that nitrogen supply may have an impact on acid level of fruit. Here, the relationship between nitrogen metabolism and citrate catabolism was studied in pumelo juice sacs. Differences in metabolites, gene expression and flux distributions were analyzed in juice sacs incubated in medium with and without NH₄⁺. Compared with those incubated with NH₄⁺, juice sacs under nitrogen deficiency exhibited enhanced flux through phosphoenolpyruvate carboxykinase (PEPCK) and accelerated consumption of citrate, while the other two TCA cycle efflux points, through malic enzyme (ME) and glutamate dehydrogenase (GDH), were both repressed. Consistent with the estimated fluxes, the expression of PEPCK1 was upregulated under nitrogen deficiency, while that of GDH1, GDH2, NAD-ME1 and NADP-ME2 were all repressed. Thus, we propose that PEPCK1 contributes to citrate degradation under nitrogen limitation.

Understanding Maize Response to Nitrogen Limitation in Different Light Conditions for the Improvement of Photosynthesis

The photosynthetic capacity of leaves is determined by their content of nitrogen (N). Nitrogen involved in photosynthesis is divided between soluble proteins and thylakoid membrane proteins. In C4 plants, the photosynthetic apparatus is partitioned between two cell types: mesophyll cells and bundle sheath. The enzymes involved in the C4 carbon cycle and assimilation of nitrogen are localized in a cell-specific manner. Although intracellular distribution of enzymes of N and carbon assimilation is variable, little is known about the physiological consequences of this distribution caused by light changes. Light intensity and nitrogen concentration influence content of nitrates in leaves and can induce activity of the main enzymes involved in N metabolism, and changes that reduce the photosynthesis rate also reduce photosynthetic N use efficiency. In this review, we wish to highlight and discuss how/whether light intensity can improve photosynthesis in maize during nitrogen limitation. We described the general regulation of changes in the main photosynthetic and nitrogen metabolism enzymes, their quantity and localization, thylakoid protein abundance, intracellular transport of organic acids as well as specific features connected with C4 photosynthesis, and addressed the major open questions related to N metabolism and effects of light on photosynthesis in C4 plants.

Overexpression of OsPHR3 improves growth traits and facilitates nitrogen use efficiency under low phosphate condition

Phosphorus (P) and nitrogen (N) are both essential macronutrients for maintaining plant growth and development. In rice (Oryza sativa L.), OsPHR3 is one of the four paralogs of PHR1, which acts as a central regulator of phosphate (Pi) homeostasis, as well being involved in N homeostasis. However, the functions of OsPHR3 in N utilization under different Pi conditions have yet to be fully studied. In this study, we aimed to dissect the effect of OsPHR3-overexpression on N utilization under Pi deficient regimes. Biochemical, molecular and physiological assays were performed to determine the N-influx, translocation, and accumulation in OsPHR3-overexpressing rice lines, grown under Pi-sufficient and -deficient conditions, in both hydroponic and soil systems. Furthermore, important agronomic traits of these plants were also evaluated. The overexpression of OsPHR3 increased N uptake under Pi stress regimes. Increased N uptake also elevated total N concentrations in these plants by inducing N transporter genes expression. Furthermore, overexpression of OsPHR3 increased N use efficiency, 1000-grain weight and grain yield under different Pi conditions. We established new findings that OsPHR3-overexpression facilitates N utilization under Pi deficient conditions. This will help achieving higher yields by coordinating the utilization of N and P.

Comparative transcriptome analysis provides insights into steviol glycoside synthesis in stevia (Stevia rebaudiana Bertoni) leaves under nitrogen deficiency

Transcriptome analysis revealed the potential mechanism of nitrogen regulating steviol glycosides synthesis via shifting of leaf carbon metabolic flux or inducing certain transcription factors. Nitrogen (N) plays key regulatory roles in both stevia (Stevia rebaudiana) growth and the synthesis of its functional metabolite steviol glycosides (SGs), but the mechanism by which this nutrient regulates SGs synthesis remains to be elucidated. To address this question, a pot experiment was performed in a greenhouse where stevia plants fertilized with N (the control as CK plants) and compared with plants without the supply of N. Physiological and biochemical analyses were conducted to test the growth and metabolic responses of plants to N regimes. Our results showed that N deficiency significantly inhibited plant growth and leaf photosynthesis, while increased leaf SGs contents in stevia (49.97, 46.64 and 84.80% respectively for rebaudioside A, stevioside, and rebaudioside C), which may be partly due to "concentration effect". Then, transcriptome analysis was conducted to understand the underlying mechanisms. A total of 535 differentially expressed genes were identified, and carbon metabolism-related events were highlighted by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes. Many of these genes were significantly upregulated by N-deficiency, including those involved in "phenylpropanoid biosynthesis", "flavonoid biosynthesis" and "starch and sucrose metabolism". Our study also analyzed the expression patterns of SGs synthesis-related genes under two N regimes and the potential transcription factors linking N nutrition and SG metabolism. N-deficiency may promote SGs synthesis by changing the carbon metabolism flux or inducing certain transcription factors. Our results provide deeper insight into the relationship between N nutrition and SGs synthesis in stevia plants.

Agro-morphological and metabolomics analysis of low nitrogen stress response in Axonopus compressus

Axonopus compressus also known as carpet grass is a robust, stoloniferous grass that can grow in minimal fertilization and resists well to abiotic and biotic stresses including low nitrogen (LN) stress. This study aimed at characterizing the agro-morphological and metabolome responses to LN in carpet grass leaves. Under LN stress, carpet grass increased yellowness of leaves and root dry matter while reduced turf quality and shoot dry weight. The metabolome comparison between samples from optimum and LN conditions indicated 304 differentially accumulated metabolites (DAMs), which could be classified into 12 major and 31 subclasses. The results revealed that the leaf tissues accumulated more anthocyanins and other flavonoid metabolites under LN stress. Conversely, amino acids, nucleic acids and their derivatives were reduced in response to LN stress. The overall evaluation of individual metabolites and pathways, and previous studies on metabolomes indicated that carpet grass reduced its energy consumption in leaves and increased the level of organic acid metabolism and secondary metabolism in order to resist LN stress conditions.

Low nitrogen availability inhibits the phosphorus starvation response in maize (Zea mays ssp. mays L.)

BACKGROUND

Nitrogen (N) and phosphorus (P) are macronutrients essential for crop growth and productivity. In cultivated fields, N and P levels are rarely sufficient, contributing to the gap between realized and potential production. Fertilizer application increases nutrient availability, but is not available to all farmers, nor are current rates of application sustainable or environmentally desirable. Transcriptomic studies of cereal crops have revealed dramatic responses to either low N or low P single stress treatments. In the field, however, levels of both N and P may be suboptimal. The interaction between N and P starvation responses remains to be fully characterized.

RESULTS

We characterized growth and root and leaf transcriptomes of young maize plants under nutrient replete, low N, low P or combined low NP conditions. We identified 1555 genes to respond to our nutrient treatments, in one or both tissues. A large group of genes, including many classical P starvation response genes, were regulated antagonistically between low N and P conditions. An additional experiment over a range of N availability indicated that a mild reduction in N levels was sufficient to repress the low P induction of P starvation genes. Although expression of P transporter genes was repressed under low N or low NP, we confirmed earlier reports of P hyper accumulation under N limitation.

CONCLUSIONS

Transcriptional responses to low N or P were distinct, with few genes responding in a similar way to the two single stress treatments. In combined NP stress, the low N response dominated, and the P starvation response was largely suppressed. A mild reduction in N availability was sufficient to repress the induction of P starvation associated genes. We conclude that activation of the transcriptional response to P starvation in maize is contingent on N availability.

Nitrogen inputs influence vegetative metabolism in maize engineered with a seed-specific carotenoid pathway

Metabolomic profiling of a maize line engineered with an endosperm-specific carotenogenic pathway revealed unexpected metabolic readjustments of primary metabolism in leaves and roots. High-carotenoid (HC) maize was engineered to accumulate high levels of carotenoids in the endosperm. The metabolic interventions influenced the flux through non-target pathways in tissues that were not affected by the targeted intervention. HC maize at the vegetative stage also showed a reduced susceptibility to insect feeding. It is unknown, however, whether the metabolic history of the embryo has any impact on the metabolite composition in vegetative tissues. We, therefore, compared HC maize and its isogenic counterpart (M37W) to test the hypothesis that boosting the carotenoid content in the endosperm triggers compensatory effects in core metabolism in vegetative tissues. Specifically, we investigated whether the metabolite composition of leaves and roots at the V6 stage differs between HC and M37W, and whether N inputs further alter the core metabolism of HC compared to M37W. We found an increase in the abundance of organic acids from the tricarboxylic acid (TCA) cycle in HC even under restricted N conditions. In contrast, low levels of carotenoids and chlorophyll were measured regardless of N levels. Sugars were also significantly depleted in HC under low N. We propose a model explaining the observed genotype-dependent and input-dependent effects, in which organic acids derived from the TCA cycle accumulate during vegetative growth and contribute to the increased demand for pyruvate and/or acetyl-CoA in the endosperm and embryo. This response may in part reflect the transgenerational priming of vegetative tissues in the embryo induced by the increased demand for metabolic precursors during seed development in the previous generation.

Phosphate or nitrate imbalance induces stronger molecular responses than combined nutrient deprivation in roots and leaves of chickpea plants

The negative effects of phosphate (Pi) and/or nitrate (NO₃^- ) fertilizers on the environment have raised an urgent need to develop crop varieties with higher Pi and/or nitrogen use efficiencies for cultivation in low-fertility soils. Achieving this goal depends upon research that focuses on the identification of genes involved in plant responses to Pi and/or NO₃^- starvation. Although plant responses to individual deficiency in either Pi (-Pi/+NO₃^- ) or NO₃^- (+Pi/-NO₃^- ) have been separately studied, our understanding of plant responses to combined Pi and NO₃^- deficiency (-Pi/-NO₃^- ) is still very limited. Using RNA-sequencing approach, transcriptome changes in the roots and leaves of chickpea cultivated under -Pi/+NO₃^- , +Pi/-NO₃^- or -Pi/-NO₃^- conditions were investigated in a comparative manner. -Pi/-NO₃^- treatment displayed lesser effect on expression changes of genes related to Pi or NO₃^- transport, signalling networks, lipid remodelling, nitrogen and Pi scavenging/remobilization/recycling, carbon metabolism and hormone metabolism than -Pi/+NO₃^- or +Pi/-NO₃^- treatments. Therefore, the plant response to -Pi/-NO₃^- is not simply an additive result of plant responses to -Pi/+NO₃^- and +Pi/-NO₃^- treatments. Our results indicate that nutrient imbalance is a stronger stimulus for molecular reprogramming than an overall deficiency.

Social networks influence farming practices and agrarian sustainability

The social-ecological effects of agricultural intensification are complex. We explore farmers' perceptions about the impacts of their land management and the impact of social information flows on their management through a case study in a farming community in Navarra, Spain, that is undergoing agricultural intensification due to adoption of large scale irrigation. We found that modern technology adopters are aware that their management practices often have negative social-ecological implications; by contrast, more traditional farmers tend to recognize their positive impacts on non-material benefits such as those linked with traditions and traditional knowledge, and climate regulation. We found that farmers' awareness about nature contributions to people co-production and their land management decisions determine, in part, the structure of the social networks among the farming community. Since modern farmers are at the core of the social network, they are better able to control the information flow within the community. This has important implications, such as the fact that the traditional farmers, who are more aware of their impacts on the environment, rely on information controlled by more intensive modern farmers, potentially jeopardizing sustainable practices in this region. We suggest that this might be counteracted by helping traditional farmers obtain information tailored to their practices from outside the social network.