Nitrogen-phosphorus interplay: old story with molecular tale

Identification of a small secreted protein, PlSSP, that contributes to the symbiotic association of Phomopsis liquidambaris with rice under nitrogen starvation

Endophytic fungi are crucial for enhancing plant growth and stress tolerance. Phomopsis liquidambaris B3, a broad-spectrum endophytic fungus, significantly improves plant nitrogen uptake and growth under nitrogen-limited conditions. In this study, we identified a small secreted protein, PlSSP, which localizes to the cytoplasmic matrix of host cells and modulates plant immune responses. Using proteomic and transcriptomic approaches, we found that PlSSP upregulates key defense-related genes, including members of the PR and WRKY families, as well as genes involved in reactive oxygen species scavenging and nitrogen assimilation. Structural analysis revealed PlSSP's secondary and thermal stability features, which likely contribute to its functional interaction with host cellular components. Functional analyses demonstrated that PlSSP expression correlates with increased fungal colonization and rice biomass accumulation under nitrogen-starved conditions. These results advance our understanding of how P. liquidambaris promotes plant resilience and nutrient uptake, providing insights with potential applications in sustainable agriculture.

Imbalance between boron and phosphorus supply influences boron deficiency symptoms in Brassica napus L

BACKGROUND

The occurrence of boron (B) deficiency in Brassicaceae crops has increased in recent years. Inappropriate application of B with other nutrients often exacerbates symptoms of B deficiency. The aim of this study was to explore the interactive effects of B and phosphorus (P) on the B deficiency symptoms of rapeseed (Brassica napus L.). Two rapeseed cultivars ('W10' and 'ZS11') were treated with two B application rates (low and high B) and three P application rates (low, medium, and high P), and the growth parameters (root morphology, B absorption and distribution, and the P/B ratio) were examined in pot and hydroponic experiments.

RESULTS

Under low B conditions, plants showed severely reduced root and shoot growth but it was greatly improved when supplemented with medium P supply. Further analysis revealed that high P combined with low B decreased the B concentration of newly initiated leaves and seeds, and increased the P/B ratio in plants compared with the medium P and low B combination, resulting in the aggravation of B deficiency of rapeseed. In comparison with the B-inefficient cultivar 'W10', the B-efficient cultivar 'ZS11' had superior growth and seed yield under low B conditions. Furthermore, 'W10' and 'ZS11' displayed significant differences in the response of the interaction between B and P to plant P/B ratio and root morphological parameters, which may reflect distinct genotype characteristics.

CONCLUSION

The findings emphasize the importance of interactions between B and P in the growth and yield formation of rapeseed in B-deficient soils, as imbalanced B and P supply can exacerbate B deficiency symptoms in rapeseed. © 2025 Society of Chemical Industry.

Nutrient limitations on photosynthesis: from individual to combinational stresses

Liebig's law of the minimum states that increasing photosynthetic productivity on nutrient-impoverished soils depends on addressing the most limiting nutrient. Research has identified the roles of different mineral nutrients in photosynthetic processes. However, diffusional and biochemical regulation of photosynthesis both feature patterns of cumulative effects that jointly determine photosynthetic capacity. More importantly, responses to multiple nutrient stresses are not simply additive and require a comprehensive understanding of how these stresses interact and impact photosynthetic performance. In this review we highlight key macroelements for photosynthesis - nitrogen, phosphorus, potassium, and magnesium - focusing on their unique functions and interactions in regulating carbon fixation under multiple nutrient deficiencies, with the goal of enhancing crop productivity through balanced nutrient applications.

Decoding PHR-Orchestrated Stress Adaptation: A Genome-Wide Integrative Analysis of Transcriptional Regulation Under Abiotic Stress in Eucalyptus grandis

The phosphate starvation response (PHR) transcription factor family play central regulatory roles in nutrient signaling, but its relationship with other abiotic stress remains elusive. In the woody plant Eucalyptus grandis, we characterized 12 EgPHRs, which were phylogenetically divided into three groups, with group I exhibiting conserved structural features (e.g., unique motif composition and exon number). Notably, a protein-protein interaction network analysis revealed that EgPHR had a species-specific protein-protein interaction network: EgPHR6 interacted with SPX proteins of multiple species, while Eucalyptus and poplar PHR uniquely bound to TRARAC-kinesin ATPase, suggesting functional differences between woody and herbaceous plants. A promoter sequence analysis revealed a regulatory network of 59 transcription factors (TFs, e.g., BPC, MYBs, ERFs and WUS), mainly associated with tissue differentiation, abiotic stress, and hormonal responses that regulated EgPHRs' expression. Transcriptomics and RT-qPCR gene expression analyses showed that all EgPHRs dynamically responded to phosphate (Pi) starvation, with the expression of EgPHR2 and EgPHR6 exhibiting sustained induction, and were also regulated by salt, cold, jasmonic acid, and boron deficiency. Strikingly, nitrogen starvation suppressed most EgPHRs, highlighting crosstalk between nutrient signaling pathways. These findings revealed the multifaceted regulatory role of EgPHRs in adaptation to abiotic stresses and provided insights into their unique evolutionary and functional characteristics in woody plants.

Harnessing plant growth-promoting bacteria (Herbaspirillum seropedicae) from an optimal mineral nitrogen supply: A study on improving nitrogen use efficiency in marandu palisadegrass

Increasing nitrogen use efficiency (NUE) remains a crucial topic in contemporary agriculture. Inoculation with endophytic diazotrophic bacteria offers a potential solution, but the results vary with the N-fertilization regime. Here, we examined the efficacy of inoculation with Herbaspirillum seropedicae strain HRC54 in enhancing NUE and promoting the growth of Marandu palisadegrass with varying levels of N-urea (0, 25, 50, and 100 mg N kg soil⁻1). We evaluated NUE indicators and conducted complementary analyses covering biochemical, physiological, nutritional and growth-related parameters after cultivating the plants within a greenhouse environment and maintaining controlled conditions of temperature and humidity. Growth promotion was evident in inoculated plants receiving up to 50 mg N kg soil-1, with enhanced root growth orchestrating the improvement in NUE. Inoculation also improved the nutritional status of the plants (increased N and P accumulation and N balance index) and increased photosynthesis-related parameters, resulting in increased biomass yield. Insufficient N supply led to oxidative stress (overproduction of H₂O₂ and MDA), which was associated with a reduction in photosystem II efficiency, chlorophyll concentration, and soluble proteins, but only in plants that did not receive microbial inoculation. Conversely, a high N supply (100 mg N kg soil-1) combined with H. seropedicae had no synergistic effect, as NUE and the associated benefits did not improve. Therefore, inoculation with H. seropedicae is effective at increasing NUE when combined with moderate N rates. These findings support a more rational use of N fertilizers to optimize inoculation benefits and enhance NUE in tropical forage crops.

Impact of NPK fertilization on the metabolomic profile and nutritional quality of Portulaca oleracea L. using nuclear magnetic resonance analysis

Purslane is a plant with high nutritional content that is mainly produced in the central part of Mexico. The nutritional content of purslane depends on various factors such as climatic and soil conditions, phenology, and fertilization. This article describes the 1H NMR metabolomics profiling of purslane in relation to fertilization at two harvest stages: C1 and C2 (27 and 42 days after emergence). During the first stage, 30 metabolites were identified including free amino acids and organic acids. In the second stage, 35 metabolites were identified, with higher concentrations of carbohydrates and nucleosides being observed. Multivariate analysis revealed differences in the metabolome between harvests C1 and C2. Notably, higher abundances of fructose, galactose, α-glucose, β-glucose, myo-inositol, sucrose, and nucleosides such as adenosine and uridine were observed in C2. Discriminant analysis further demonstrated variations in metabolites among plants treated with different doses of nitrogen, phosphorus, and potassium at the two harvest stages studied. Plants treated with the highest dose of nitrogen (300 kg N ha-1) exhibited maximum levels of metabolites, while low nitrogen-treated plants (0 kg N ha-1) displayed an inverse trend. Amino acids such as alanine, asparagine, GABA, glutamine, histidine, isoleucine, leucine, phenylalanine, proline, threonine, tyrosine, and valine were found to be the most abundant in plants treated with N300. In contrast, untreated plants showed higher levels of citric acid and malic acid. Our results highlight the effectiveness of 1H NMR as a methodology for understanding the role of fertilization and nutrient content in optimizing the crop production of purslane.

TaTCP6 is required for efficient and balanced utilization of nitrate and phosphorus in wheat

High crop yields require adequate nutrients, particularly nitrate (N) and phosphorus (P). Identifying regulators for efficient N-P utilization is critical in wheat. To explore N-P interactions, we analyze root transcriptomes under varying N-P supplies and identify TaTCP6 as a potential regulator. Nitrate-stimulated TaTCP6 directly triggers the expression of genes related to nitrogen utilization. TaTCP6 competes with TaSPX1/4 for the release of TaPHR2, and also interacts with TaPHR2 to enhance the transactivation capacity of downstream genes. Thus, through the dual roles of TaTCP6, the TCP6-SPX-PHR2 module activates the expression of phosphorus starvation response (PSR) genes. Inhibiting TaTCP6 reduces N and P absorption, negatively impacting yield, while overexpressing TaTCP6 increases grain yield. Notably, overexpression of TaSPX1 suppresses nitrogen utilization genes, especially under low phosphorus conditions. In conclusion, our findings highlight the role of TaTCP6 in coordinating N and P utilization and propose a strategy to reduce fertilizer inputs for sustainable agriculture.

The phosphate starvation response regulator PHR2 antagonizes arbuscule maintenance in Medicago

Phosphate starvation response (PHR) transcription factors play essential roles in regulating phosphate uptake in plants through binding to the P1BS cis-element in the promoter of phosphate starvation response genes. Recently, PHRs were also shown to positively regulate arbuscular mycorrhizal colonization in rice and lotus by controlling the expression of many symbiotic genes. However, their role in arbuscule development has remained unclear. In Medicago, we previously showed that arbuscule degradation is controlled by two SPX proteins that are highly expressed in arbuscule-containing cells. Since SPX proteins bind to PHRs and repress their activity in a phosphate-dependent manner, we investigated whether arbuscule maintenance is also regulated by PHR. Here, we show that PHR2 is a major regulator of the phosphate starvation response in Medicago. Knockout of phr2 showed reduced phosphate starvation response, symbiotic gene expression, and fungal colonization levels. However, the arbuscules that formed showed less degradation, suggesting a negative role for PHR2 in arbuscule maintenance. This was supported by the observation that overexpression of PHR2 led to enhanced degradation of arbuscules. Although many arbuscule-induced genes contain P1BS elements in their promoters, we found that the P1BS cis-elements in the promoter of the symbiotic phosphate transporter PT4 are not required for arbuscule-containing cell expression. Since both PHR2 and SPX1/3 negatively affect arbuscule maintenance, our results indicate that they control arbuscule maintenance partly via different mechanisms. While PHR2 potentiates symbiotic gene expression and colonization, its activity in arbuscule-containing cells needs to be tightly controlled to maintain a successful symbiosis in Medicago.

Physiological and Transcriptional Responses to Phosphorus Deficiency and Glucose-6-Phosphate Supplementation in Neopyropia yezoensis

Neopyropia yezoensis, a marine red algae species, has significant economic and ecological value. However, phosphorus (P) deficiency has emerged as a growing concern in many cultivation regions, negatively impacting its growth. To adapt to P deficiency, algae have evolved various strategies, including using dissolved organic phosphorus (DOP) sources to sustain growth. Despite its prevalence as a form of DOP, the utilization mechanism of glucose-6-phosphate (G6P) by N. yezoensis remains unclear. In this study, the physiological and transcriptional responses of N. yezoensis to P deficiency and G6P supplementation were examined. The results demonstrated that prolonged P deficiency significantly inhibited the growth of N. yezoensis and had a negative impact on physiological indicators such as photosynthetic pigments and antioxidant enzyme activity. However, G6P treatment gradually alleviated these adverse effects over time. Both P deficiency and G6P treatment were associated with increased expression of genes involved in signal transduction and P starvation responses while concurrently downregulating genes related to photosynthesis and antioxidant defenses. In contrast, the suppression of gene expression was less significant under G6P treatment. This study elucidates the adaptive strategies of N. yezoensis in response to P deficiency and clarifies the regulatory pathways involved in G6P utilization, providing novel insights into its P nutrient acquisition and metabolic regulation.

Genome-wide identification and expression analysis of phosphate-sensing SPX proteins in oats

Phosphorus is indispensable to plant growth and development. Soil phosphorus deficiency poses a substantial constraint on crop yield. SPXs play pivotal roles in phosphate transport and absorption in plants. Yet, the functions of SPXs of oat (Avena sativa L.) under abiotic stresses remain unclear. In this study, we conducted a genome-wide analysis of 169 SPXs from hexaploid oat and five closely related plant species. All homologous AsSPXs were found to arise from duplication events and depict a strong purifying selection. Subcellular localization prediction revealed that AsSPXs were mainly located on the plasma membrane. Seventeen cis-acting elements, predominantly comprising light-, low temperature-, abscisic acid-, and drought-responsive elements, were dispersed in the promoter regions of AsSPXs. Analysis of cis-regulatory elements, protein-protein interaction networks, and qRT-PCR showed that AsSPXs are not solely involved in phosphorus starvation response but also in various stress responses. Notably, AsSPX18-5D (AVESA.00001b.r3.5Dg0002895) exerted pivotal roles in conferring resistance against low phosphorus, salt, and ABA treatments. Our study aimed to explore important stress-resistant genes in oat. Our results could provide a basis for future studies on the evolution and functions of the AsSPX gene family and a crucial foundation for comprehending how oat responds to environmental stresses.

PHR1 negatively regulates nitrate reductase activity by directly inhibiting the transcription of NIA1 in Arabidopsis

Nitrogen (N) and phosphorus (P), as indispensable mineral elements, both play pivotal roles in plant growth and development. Despite the intimate association between nitrate signaling and inorganic phosphate (Pi) signaling, the regulatory function of Pi in N metabolism remains poorly understood. In this study, we observed that Pi deficiency leads to a reduction in the activity of nitrate reductase (NR), an essential enzyme involved in N metabolism. Furthermore, PHOSPHATE STARVATION RESPONSE 1 (PHR1), a key regulator of Pi signaling, exerts a negative impact on both NR activity and the expression of its coding gene NIA1. Importantly, our analysis utilizing yeast one-hybrid (Y1H) and electrophoretic mobility shift assay (EMSA) techniques reveals the direct binding of PHR1 to the NIA1 promoter via the P1BS motifs. Subsequent transient transcription expression assay (TTEA) demonstrates PHR1 as a transcriptional suppressor of NIA1. In addition, it was also observed that the SPX (SYG1/Pho81/XPR1) proteins SPX1 and SPX4 can attenuate the transcriptional inhibition of NIA1 by PHR1. Collectively, these findings reveal a mechanism through which PHR1-mediated Pi signal governs N metabolism, thus offering evidence for the precise modulation of plant growth and development via N-P interaction.

CsSPX3-CsPHL7-CsGS1/CsTS1 module mediated Pi-regulated negatively theanine biosynthesis in tea (Camellia sinensis)

Phosphorus (P) is the macronutrients essential for the development and growth of plants, but how external inorganic phosphate (Pi) level and signaling affect tea plant growth and characteristic secondary metabolite biosynthesis are not understood. Theanine is major secondary metabolites, and its contents largely determine tea favor and nutrition qualities. Here, we found theanine contents in tea leaves and roots declined as Pi concentration increased in tea plants after Pi feeding. The transcriptome analysis of global gene expression in tea leaves under Pi feeding suggested a wide range of genes involved in Pi/N transport and responses were altered. Among them, CsSPX3 and CsPHL7 transcript levels in response to Pi feeding to tea plants, their expression patterns were generally opposite to these of major theanine biosynthesis genes, indicating possible regulatory correlations. Biochemical analyses showed that CsSPX3 interacted with CsPHL7, and CsPHL7 negatively regulated theanine biosynthesis genes CsGS1 and CsTS1. Meanwhile, VIGS and transient overexpression systems in tea plants verified the functions of CsSPX3 and CsPHL7 in mediating Pi-feeding-repressed theanine biosynthesis. This study offers fresh insights into the regulatory mechanism underlying Pi repression of theanine biosynthesis, and the CsSPX3-CsPHL7-CsGS1/CsTS1 module plays a role in high Pi inhibition of theanine production in tea leaves. It has an instructional significance for guiding the high-quality tea production in tea garden fertilization.

Mining for QTL controlling maize low-phosphorus response genes combined with deep resequencing of RIL parental genomes and in silico GWAS analysis

KEY MESSAGE

Extensive and comprehensive phenotypic data from a maize RIL population under both low- and normal-Pi treatments were used to conduct QTL mapping. Additionally, we integrated parental resequencing data from the RIL population, GWAS results, and transcriptome data to identify candidate genes associated with low-Pi stress in maize. Phosphorus (Pi) is one of the essential nutrients that greatly affect the maize yield. However, the genes underlying the QTL controlling maize low-Pi response remain largely unknown. In this study, a total of 38 traits at both seedling and maturity stages were evaluated under low- and normal-Pi conditions using a RIL population constructed from X178 (tolerant) and 9782 (sensitive), and most traits varied significantly between low- and normal-Pi treatments. Twenty-nine QTLs specific to low-Pi conditions were identified after excluding those with common intervals under both low- and normal-Pi conditions. Furthermore, 45 additional QTLs were identified based on the index value ((Trait_under_LowPi-Trait_under_NormalPi)/Trait_under_NormalPi) of each trait. These 74 QTLs collectively were classified as Pi-dependent QTLs. Additionally, 39 Pi-dependent QTLs were clustered in nine HotspotQTLs. The Pi-dependent QTL interval contained 19,613 unique genes, 6,999 of which exhibited sequence differences with non-synonymous mutation sites between X178 and 9782. Combined with in silico GWAS results, 277 consistent candidate genes were identified, with 124 genes located within the HotspotQTL intervals. The transcriptome analysis revealed that 21 genes, including the Pi transporter ZmPT7 and the strigolactones pathway-related gene ZmPDR1, exhibited consistent low-Pi stress response patterns across various maize inbred lines or tissues. It is noteworthy that ZmPDR1 in maize roots can be sharply up-regulated by low-Pi stress, suggesting its potential importance as a candidate gene for responding to low-Pi stress through the strigolactones pathway.

Genome-wide association studies dissect low-phosphorus stress response genes underling field and seedling traits in maize

Phosphorus (P) is an essential element for plant growth, and its deficiency can cause decreased crop yield. This study systematically evaluated the low-phosphate (Pi) response traits in a large population at maturity and seedling stages, and explored candidate genes and their interrelationships with specific traits. The results revealed a greater sensitivity of seedling maize to low-Pi stress compared to that at maturity stage. The phenotypic response patterns to low-Pi stress at different stages were independent. Chlorophyll content was found to be a potential indicator for screening low-Pi-tolerant materials in the field. A total of 2900 and 1446 significantly associated genes at the maturity and seedling stages were identified, respectively. Among these genes, 972 were uniquely associated with maturity traits, while 330 were specifically detected at the seedling stage under low-Pi stress. Moreover, 768 and 733 genes were specifically associated with index values (low-Pi trait/normal-Pi trait) at maturity and seedling stage, respectively. Genetic network diagrams showed that the low-Pi response gene Zm00001d022226 was specifically associated with multiple primary P-related traits under low-Pi conditions. A total of 963 out of 2966 genes specifically associated with traits under low-Pi conditions or index values were found to be induced by low-Pi stress. Notably, ZmSPX4.1 and ZmSPX2 were sharply up-regulated in response to low-Pi stress across different lines or tissues. These findings advance our understanding of maize's response to low-Pi stress at different developmental stages, shedding light on the genes and pathways implicated in this response.

Exploring the phosphorus-starch content balance mechanisms in maize grains using GWAS population and transcriptome data

Examining the connection between P and starch-related signals can help elucidate the balance between nutrients and yield. This study utilized 307 diverse maize inbred lines to conduct multi-year and multi-plot trials, aiming to explore the relationship among P content, starch content, and 100-kernel weight (HKW) of mature grains. A significant negative correlation was found between P content and both starch content and HKW, while starch content showed a positive correlation with HKW. The starch granules in grains with high-P and low-starch content (HPLS) were significantly smaller compared to grains with low-P high-starch content (LPHS). Additionally, mian04185-4 (HPLS) exhibited irregular and loosely packed starch granules. A significant decrease in ZmPHOs genes expression was detected in the HPLS line ZNC442 as compared to the LPHS line SCML0849, while no expression difference was observed in AGPase encoding genes between these two lines. The down-regulated genes in ZNC442 grains were enriched in nucleotide sugar and fatty acid anabolic pathways, while up-regulated genes were enriched in the ABC transporters pathway. An accelerated breakdown of fat as the P content increased was also observed. This implied that HPLS was resulted from elevated lipid decomposition and inadequate carbon sources. The GWAS analysis identified 514 significantly associated genes, out of which 248 were differentially expressed. Zm00001d052392 was found to be significantly associated with P content/HKW, exhibiting high expression in SCML0849 but almost no expression in ZNC442. Overall, these findings suggested new approaches for achieving a P-yield balance through the manipulation of lipid metabolic pathways in grains.

Soil chemical fumigation alters soil phosphorus cycling: effects and potential mechanisms

Soil chemical fumigation is an effective and popular method to increase agricultural productivity. However, the broad-spectrum bioactivity of fumigants causes harm to soil beneficial microorganisms involved in the soil phosphorous cycle, such as soil phosphorus solubilizing microorganisms (PSMs). We review the effects of soil chemical fumigation on soil phosphorus cycling, and the potential underlying mechanisms that ultimately lead to altered phosphorus availability for crops. These complex processes involve the highly diverse PSM community and a plethora of soil phosphorus forms. We discuss phosphatizing amendments aimed at counteracting the possible negative effects of fumigation on phosphorus availability, phosphorus use efficiency, and crop yields. We also emphasize distinguishing between the effects on soil phosphorus cycling caused by the chemical fumigants, and those caused by the fumigation process (e.g. plastic mulching). These are typically conflated in the literature; distinguishing them is critical for identifying appropriate amendments to remediate possible post-fumigation soil phosphorus deficiencies.

Phosphorus uptake, transport, and signaling in woody and model plants

Phosphorus (P), a critical macronutrient for plant growth and reproduction, is primarily acquired and translocated in the form of inorganic phosphate (Pi) by roots. Pi deficiency is widespread in many natural ecosystems, including forest plantations, due to its slow movement and easy fixation in soils. Plants have evolved complex and delicate regulation mechanisms on molecular and physiological levels to cope with Pi deficiency. Over the past two decades, extensive research has been performed to decipher the underlying molecular mechanisms that regulate the Pi starvation responses (PSR) in plants. This review highlights the prospects of Pi uptake, transport, and signaling in woody plants based on the backbone of model and crop plants. In addition, this review also highlights the interactions between phosphorus and other mineral nutrients such as Nitrogen (N) and Iron (Fe). Finally, this review discusses the challenges and potential future directions of Pi research in woody plants, including characterizing the woody-specific regulatory mechanisms of Pi signaling and evaluating the regulatory roles of Pi on woody-specific traits such as wood formation and ultimately generating high Phosphorus Use Efficiency (PUE) woody plants.

Comparative functional analyses of PHR1, PHL1, and PHL4 transcription factors in regulating Arabidopsis responses to phosphate starvation

To cope with phosphate (Pi) starvation, plants trigger an array of adaptive responses to sustain their growth and development. These responses are largely controlled at transcriptional levels. In Arabidopsis (Arabidopsis thaliana), PHOSPHATE RESPONSE 1 (PHR1) is a key regulator of plant physiological and transcriptional responses to Pi starvation. PHR1 belongs to a MYB-CC-type transcription factor family which contains 15 members. In this PHR1 family, PHR1/PHR1-like 1(PHL1) and PHL2/PHL3 form two distinct modules in regulating plant development and transcriptional responses to Pi starvation. PHL4 is the most closely related member to PHR1. Previously, using the phr1phl4 mutant, we showed that PHL4 is also involved in regulating plant Pi responses. However, the precise roles of PHL1 and PHL4 in regulating plant Pi responses and their functional relationships with PHR1 have not been clearly defined. In this work, we further used the phl1phl4 and phr1phl1phl4 mutants to perform comparative phenotypic and transcriptomic analyses with phr1, phr1phl1, and phr1phl4. The results showed that both PHL1 and PHL4 act redundantly and equally with PHR1 to regulate leaf senescence, Pi starvation induced-inhibition of primary root growth, and accumulation of anthocyanins in shoots. Unlike PHR1 and PHL1, however, the role of PHL4 in maintaining Pi homeostasis is negligible. In regulating transcriptional responses to Pi starvation at genomic levels, both PHL1 and PHL4 play minor roles when acts alone, however, they act synergistically with PHR1. In regulating Pi starvation-responsive genes, PHL4 also function less than PHL1 in terms of the number of the genes it regulates and the magnitude of gene transcription it affects. Furthermore, no synergistic interaction was found between PHL1 and PHL4 in regulating plant response to Pi starvation. Therefore, our results clarified the roles of PHL1 and PHL4 in regulating plant responses to Pi starvation. In addition, this work revealed a new function of these three transcription factors in regulating flowering time.

Adaptation Strategies of Seedling Root Response to Nitrogen and Phosphorus Addition

The escalation of global nitrogen deposition levels has heightened the inhibitory impact of phosphorus limitation on plant growth in subtropical forests. Plant roots area particularly sensitive tissue to nitrogen and phosphorus elements. Changes in the morphological characteristics of plant roots signify alterations in adaptive strategies. However, our understanding of resource-use strategies of roots in this environment remains limited. In this study, we conducted a 10-month experiment at the Castanopsis kawakamii Nature Reserve to evaluate the response of traits of seedling roots (such as specific root length, average diameter, nitrogen content, and phosphorus content) to nitrogen and phosphorus addition. The aim was to reveal the adaptation strategies of roots in different nitrogen and phosphorus addition concentrations. The results showed that: (1) The single phosphorus and nitrogen-phosphorus interaction addition increased the specific root length, surface area, and root phosphorus content. In addition, single nitrogen addition promotes an increase in the average root diameter. (2) Non-nitrogen phosphorus addition and single nitrogen addition tended to adopt a conservative resource-use strategy to maintain growth under low phosphorus conditions. (3) Under the single phosphorus addition and interactive addition of phosphorus and nitrogen, the roots adopted an acquisitive resource-use strategy to obtain more available phosphorus resources. Accordingly, the adaptation strategy of seedling roots can be regulated by adding appropriate concentrations of nitrogen or phosphorus, thereby promoting the natural regeneration of subtropical forests.

Phosphorus/nitrogen sensing and signaling in diverse root-fungus symbioses

Establishing mutualistic relationships between plants and fungi is crucial for overcoming nutrient deficiencies in plants. This review highlights the intricate nutrient sensing and uptake mechanisms used by plants in response to phosphate and nitrogen starvation, as well as their interactions with plant immunity. The coordination of transport systems in both host plants and fungal partners ensures efficient nutrient uptake and assimilation, contributing to the long-term maintenance of these mutualistic associations. It is also essential to understand the distinct responses of fungal partners to external nutrient levels and forms, as they significantly impact the outcomes of symbiotic interactions. Our review also highlights the importance of evolutionarily younger and newly discovered root-fungus associations, such as endophytic associations, which offer potential benefits for improving plant nutrition. Mechanistic insights into the complex dynamics of phosphorus and nitrogen sensing within diverse root-fungus associations can facilitate the identification of molecular targets for engineering symbiotic systems and developing plant phenotypes with enhanced nutrient use efficiency. Ultimately, this knowledge can inform tailored fertilizer management practices to optimize plant nutrition.

Phosphate Transporter OsPT4, Ubiquitinated by E3 Ligase OsAIRP2, Plays a Crucial Role in Phosphorus and Nitrogen Translocation and Consumption in Germinating Seed

Phosphorus (P) and nitrogen (N) are essential macronutrients necessary for plant growth and development. OsPT4 is a high-affinity phosphate (Pi) transporter that has a positive impact on nutrient uptake and seed development. In this study, the expression patterns of different Pi transporter genes in germinating seeds were determined, and the relative expression of OsPT4 was induced in Pi-deficient seeds and gradually increased with the passage of germination time. The analysis of P, N, Pi, and amino acid concentrations in germinating seeds of OsPT4 mutants showed that the OsPT4 mutation caused P and N retention and a continuous reduction in multiple amino acid concentrations in germinating seeds. Transcriptome analysis and qRT-PCR results also indicated that the OsPT4 mutation inhibits the expression of genes related to P and N transportation and amino acid synthesis in germinating seeds. In addition, the paraffin section and TUNEL assay of OsPT4 mutant germinating seeds suggests that OsPT4 mutation causes programmed cell death (PCD) delayed in the aleurone layer and inhibition of leaf outgrowth. Moreover, we also found that OsPT4 was ubiquitinated by OsAIRP2, which is a C3HC4-type RING E3 Ub ligase. Our studies illustrate that OsPT4 plays a crucial role in P and N collaborative translocation and consumption in germinating seeds. It also provides a theoretical basis for the molecules and physiological mechanisms of P and N cross-talk under suppressed Pi uptake conditions.

Sailing in complex nutrient signaling networks: Where I am, where to go, and how to go?

To ensure survival and promote growth, sessile plants have developed intricate internal signaling networks tailored in diverse cells and organs with both shared and specialized functions that respond to various internal and external cues. A fascinating question arises: how can a plant cell or organ diagnose the spatial and temporal information it is experiencing to know "where I am," and then is able to make the accurate specific responses to decide "where to go" and "how to go," despite the absence of neuronal systems found in mammals. Drawing inspiration from recent comprehensive investigations into diverse nutrient signaling pathways in plants, this review focuses on the interactive nutrient signaling networks mediated by various nutrient sensors and transducers. We assess and illustrate examples of how cells and organs exhibit specific responses to changing spatial and temporal information within these interactive plant nutrient networks. In addition, we elucidate the underlying mechanisms by which plants employ posttranslational modification codes to integrate different upstream nutrient signals, thereby conferring response specificities to the signaling hub proteins. Furthermore, we discuss recent breakthrough studies that demonstrate the potential of modulating nutrient sensing and signaling as promising strategies to enhance crop yield, even with reduced fertilizer application.

Balanced nitrogen-iron sufficiency boosts grain yield and nitrogen use efficiency by promoting tillering

Crop yield plays a critical role in global food security. For optimal plant growth and maximal crop yields, nutrients must be balanced. However, the potential significance of balanced nitrogen-iron (N-Fe) for improving crop yield and nitrogen use efficiency (NUE) has not previously been addressed. Here, we show that balanced N-Fe sufficiency significantly increases tiller number and boosts yield and NUE in rice and wheat. NIN-like protein 4 (OsNLP4) plays a pivotal role in maintaining the N-Fe balance by coordinately regulating the expression of multiple genes involved in N and Fe metabolism and signaling. OsNLP4 also suppresses OsD3 expression and strigolactone (SL) signaling, thereby promoting tillering. Balanced N-Fe sufficiency promotes the nuclear localization of OsNLP4 by reducing H2O2 levels, reinforcing the functions of OsNLP4. Interestingly, we found that OsNLP4 upregulates the expression of a set of H2O2-scavenging genes to promote its own accumulation in the nucleus. Furthermore, we demonstrated that foliar spraying of balanced N-Fe fertilizer at the tillering stage can effectively increase tiller number, yield, and NUE of both rice and wheat in the field. Collectively, these findings reveal the previously unrecognized effects of N-Fe balance on grain yield and NUE as well as the molecular mechanism by which the OsNLP4-OsD3 module integrates N-Fe nutrient signals to downregulate SL signaling and thereby promote rice tillering. Our study sheds light on how N-Fe nutrient signals modulate rice tillering and provide potential innovative approaches that improve crop yield with reduced N fertilizer input for benefitting sustainable agriculture worldwide.

Nitrogen Journey in Plants: From Uptake to Metabolism, Stress Response, and Microbe Interaction

Plants uptake and assimilate nitrogen from the soil in the form of nitrate, ammonium ions, and available amino acids from organic sources. Plant nitrate and ammonium transporters are responsible for nitrate and ammonium translocation from the soil into the roots. The unique structure of these transporters determines the specificity of each transporter, and structural analyses reveal the mechanisms by which these transporters function. Following absorption, the nitrogen metabolism pathway incorporates the nitrogen into organic compounds via glutamine synthetase and glutamate synthase that convert ammonium ions into glutamine and glutamate. Different isoforms of glutamine synthetase and glutamate synthase exist, enabling plants to fine-tune nitrogen metabolism based on environmental cues. Under stressful conditions, nitric oxide has been found to enhance plant survival under drought stress. Furthermore, the interaction between salinity stress and nitrogen availability in plants has been studied, with nitric oxide identified as a potential mediator of responses to salt stress. Conversely, excessive use of nitrate fertilizers can lead to health and environmental issues. Therefore, alternative strategies, such as establishing nitrogen fixation in plants through diazotrophic microbiota, have been explored to reduce reliance on synthetic fertilizers. Ultimately, genomics can identify new genes related to nitrogen fixation, which could be harnessed to improve plant productivity.

Finding Balance in Adversity: Nitrate Signaling as the Key to Plant Growth, Resilience, and Stress Response

To effectively adapt to changing environments, plants must maintain a delicate balance between growth and resistance or tolerance to various stresses. Nitrate, a significant inorganic nitrogen source in soils, not only acts as an essential nutrient but also functions as a critical signaling molecule that regulates multiple aspects of plant growth and development. In recent years, substantial advancements have been made in understanding nitrate sensing, calcium-dependent nitrate signal transmission, and nitrate-induced transcriptional cascades. Mounting evidence suggests that the primary response to nitrate is influenced by environmental conditions, while nitrate availability plays a pivotal role in stress tolerance responses. Therefore, this review aims to provide an overview of the transcriptional and post-transcriptional regulation of key components in the nitrate signaling pathway, namely, NRT1.1, NLP7, and CIPK23, under abiotic stresses. Additionally, we discuss the specificity of nitrate sensing and signaling as well as the involvement of epigenetic regulators. A comprehensive understanding of the integration between nitrate signaling transduction and abiotic stress responses is crucial for developing future crops with enhanced nitrogen-use efficiency and heightened resilience.

Multi-omics strategies uncover the molecular mechanisms of nitrogen, phosphorus and potassium deficiency responses in Brassica napus

BACKGROUND

Nitrogen (N), phosphorus (P) and potassium (K) are critical macronutrients in crops, such that deficiency in any of N, P or K has substantial effects on crop growth. However, the specific commonalities of plant responses to different macronutrient deficiencies remain largely unknown.

METHODS

Here, we assessed the phenotypic and physiological performances along with whole transcriptome and metabolomic profiles of rapeseed seedlings exposed to N, P and K deficiency stresses.

RESULTS

Quantities of reactive oxygen species were significantly increased by all macronutrient deficiencies. N and K deficiencies resulted in more severe root development responses than P deficiency, as well as greater chlorophyll content reduction in leaves (associated with disrupted chloroplast structure). Transcriptome and metabolome analyses validated the macronutrient-specific responses, with more pronounced effects of N and P deficiencies on mRNAs, microRNAs (miRNAs), circular RNAs (circRNAs) and metabolites relative to K deficiency. Tissue-specific responses also occurred, with greater effects of macronutrient deficiencies on roots compared with shoots. We further uncovered a set of common responders with simultaneous roles in all three macronutrient deficiencies, including 112 mRNAs and 10 miRNAs involved in hormonal signaling, ion transport and oxidative stress in the root, and 33 mRNAs and 6 miRNAs with roles in abiotic stress response and photosynthesis in the shoot. 27 and seven common miRNA-mRNA pairs with role in miRNA-mediated regulation of oxidoreduction processes and ion transmembrane transport were identified in all three macronutrient deficiencies. No circRNA was responsive to three macronutrient deficiency stresses, but two common circRNAs were identified for two macronutrient deficiencies. Combined analysis of circRNAs, miRNAs and mRNAs suggested that two circRNAs act as decoys for miR156 and participate in oxidoreduction processes and transmembrane transport in both N- and P-deprived roots. Simultaneously, dramatic alterations of metabolites also occurred. Associations of RNAs with metabolites were observed, and suggested potential positive regulatory roles for tricarboxylic acids, azoles, carbohydrates, sterols and auxins, and negative regulatory roles for aromatic and aspartate amino acids, glucosamine-containing compounds, cinnamic acid, and nicotianamine in plant adaptation to macronutrient deficiency.

CONCLUSIONS

Our findings revealed strategies to rescue rapeseed from macronutrient deficiency stress, including reducing the expression of non-essential genes and activating or enhancing the expression of anti-stress genes, aided by plant hormones, ion transporters and stress responders. The common responders to different macronutrient deficiencies identified could be targeted to enhance nutrient use efficiency in rapeseed.

PHOSPHATE STARVATION RESPONSE1 (PHR1) interacts with JASMONATE ZIM-DOMAIN (JAZ) and MYC2 to modulate phosphate deficiency-induced jasmonate signaling in Arabidopsis

Phosphorus (P) is a macronutrient necessary for plant growth and development. Inorganic phosphate (Pi) deficiency modulates the signaling pathway of the phytohormone jasmonate in Arabidopsis thaliana, but the underlying molecular mechanism currently remains elusive. Here, we confirmed that jasmonate signaling was enhanced under low Pi conditions, and the CORONATINE INSENSITIVE1 (COI1)-mediated pathway is critical for this process. A mechanistic investigation revealed that several JASMONATE ZIM-DOMAIN (JAZ) repressors physically interacted with the Pi signaling-related core transcription factors PHOSPHATE STARVATION RESPONSE1 (PHR1), PHR1-LIKE2 (PHL2), and PHL3. Phenotypic analyses showed that PHR1 and its homologs positively regulated jasmonate-induced anthocyanin accumulation and root growth inhibition. PHR1 stimulated the expression of several jasmonate-responsive genes, whereas JAZ proteins interfered with its transcriptional function. Furthermore, PHR1 physically associated with the basic helix-loop-helix (bHLH) transcription factors MYC2, MYC3, and MYC4. Genetic analyses and biochemical assays indicated that PHR1 and MYC2 synergistically increased the transcription of downstream jasmonate-responsive genes and enhanced the responses to jasmonate. Collectively, our study reveals the crucial regulatory roles of PHR1 in modulating jasmonate responses and provides a mechanistic understanding of how PHR1 functions together with JAZ and MYC2 to maintain the appropriate level of jasmonate signaling under conditions of Pi deficiency.

Genome-Wide Identification and Analysis of OsSPXs Revealed Its Genetic Influence on Cold Tolerance of Dongxiang Wild Rice (DXWR)

SPX-domain proteins (small proteins with only the SPX domain) have been proven to be involved in phosphate-related signal transduction and regulation pathways. Except for OsSPX1 research showing that it plays a role in the process of rice adaptation to cold stress, the potential functions of other SPX genes in cold stress are unknown. Therefore, in this study, we identified six OsSPXs from the whole genome of DXWR. The phylogeny of OsSPXs has a strong correlation with its motif. Transcriptome data analysis showed that OsSPXs were highly sensitive to cold stress, and real-time PCR verified that the levels of OsSPX1, OsSPX2, OsSPX4, and OsSPX6 in cold-tolerant materials (DXWR) during cold treatment were higher than that of cold-sensitive rice (GZX49). The promoter region of DXWR OsSPXs contains a large number of cis-acting elements related to abiotic stress tolerance and plant hormone response. At the same time, these genes have expression patterns that are highly similar to cold-tolerance genes. This study provides useful information about OsSPXs, which is helpful for the gene-function research of DXWR and genetic improvements during breeding.

Molecular mechanisms and genetic improvement of low-phosphorus tolerance in rice

Phosphorus (P) is a macronutrient required for plant growth and reproduction. Orthophosphate (Pi), the preferred P form for plant uptake, is easily fixed in the soil, making it unavailable to plants. Limited phosphate rock resources, low phosphate fertilizer use efficiency and high demands for green agriculture production make it important to clarify the molecular mechanisms underlying plant responses to P deficiency and to improve plant phosphate efficiency in crops. Over the past 20 years, tremendous progress has been made in understanding the regulatory mechanisms of the plant P starvation response. Here, we systematically review current research on the mechanisms of Pi acquisition, transport and distribution from the rhizosphere to the shoot; Pi redistribution and reuse during reproductive growth; and the molecular mechanisms of arbuscular mycorrhizal symbiosis in rice (Oryza sativa L.) under Pi deficiency. Furthermore, we discuss several strategies for boosting P utilization efficiency and yield in rice.

Emerging trends in nitrogen and phosphorus signalling in photosynthetic eukaryotes

Phosphorus (P) and nitrogen (N) are the major nutrients that constrain plant and algal growth in nature. Recent advances in understanding nutrient signalling mechanisms of these organisms have revealed molecular attributes to optimise N and P acquisition. This has illuminated the importance of interplay between N and P regulatory networks, highlighting a need to study synergistic interactions rather than single-nutrient effects. Emerging insights of nutrient signalling in polyphyletic model plants and algae hint that, although core P-starvation signalling components are conserved, distinct mechanisms for P (and N) sensing have arisen. Here, the N and P signalling mechanisms of diverse photosynthetic eukaryotes are examined, drawing parallels and differences between taxa. Future directions to understand their molecular basis, evolution, and ecology are proposed.

Cooperative interactions between nitrogen fixation and phosphorus nutrition in legumes

Legumes such as soybean are considered important crops as they provide proteins and oils for humans and livestock around the world. Different from other crops, leguminous crops accumulate nitrogen (N) for plant growth through symbiotic nitrogen fixation (SNF) in coordination with rhizobia. A number of studies have shown that efficient SNF requires the cooperation of other nutrients, especially phosphorus (P), a nutrient deficient in most soils. During the last decades, great progress has been made in understanding the molecular mechanisms underlying the interactions between SNF and P nutrition, specifically through the identification of transporters involved in P transport to nodules and bacteroids, signal transduction, and regulation of P homeostasis in nodules. These studies revealed a distinct N-P interaction in leguminous crops, which is characterized by specific signaling cross talk between P and SNF. This review aimed to present an updated picture of the cross talk between N fixation and P nutrition in legumes, focusing on soybean as a model crop, and Medicago truncatula and Lotus japonicus as model plants. We also discuss the possibilities for enhancing SNF through improving P nutrition, which are important for high and sustainable production of leguminous crops.

The fine-tuning of mycorrhizal pathway in sorghum depends on both nitrogen-phosphorus availability and the identity of the fungal partner

Sorghum is an important worldwide source of food, feed and fibres. Like most plants, it forms mutualistic symbioses with arbuscular mycorrhizal fungi (AMF), but the nutritional basis of mycorrhiza-responsiveness is largely unknown. Here, we investigated the transcriptional and physiological responses of sorghum to two different AMF species, Rhizophagus irregularis and Funneliformis mosseae, under 16 different conditions of nitrogen (N) and phosphorus (P) supply. Our experiment reveals fine-scale differences between two AMF species in the nutritional interactions with sorghum plants. Physiological and gene expression patterns (ammonium transporters: AMT; phosphate transporters: PHT) indicate the existence of generalist or specialist mycorrhizal pathway. While R. irregularis switched on the mycorrhizal pathway independently of the plant nutritional status, F. mosseae influenced the mycorrhizal pathway depending on the N-to-P plant ratio and soil supply. The differences between both AMF species suggest some AMT and PHT as ideal candidates to develop markers for improving efficiency of nutrient acquisition in sorghum under P and N limitation, and for the selection of plant genotypes.

Trypsin is a coordinate regulator of N and P nutrients in marine phytoplankton

Trypsin is best known as a digestive enzyme in animals, but remains unexplored in phytoplankton, the major primary producers in the ocean. Here we report the prevalence of trypsin genes in global ocean phytoplankton and significant influences of environmental nitrogen (N) and phosphorus (P) on their expression. Using CRISPR/Cas9 mediated-knockout and overexpression analyses, we further reveal that a trypsin in Phaeodactylum tricornutum (PtTryp2) functions to repress N acquisition, but its expression decreases under N-deficiency to promote N acquisition. On the contrary, PtTryp2 promotes phosphate uptake per se, and its expression increases under P-deficiency to further reinforce P acquisition. Furthermore, PtTryp2 knockout led to amplitude magnification of the nitrate and phosphate uptake 'seesaw', whereas PtTryp2 overexpression dampened it, linking PtTryp2 to stabilizing N:P stoichiometry. Our data demonstrate that PtTryp2 is a coordinate regulator of N:P stoichiometric homeostasis. The study opens a window for deciphering how phytoplankton adapt to nutrient-variable marine environments.

Plant Foraging Strategies Driven by Distinct Genetic Modules: Cross-Ecosystem Transcriptomics Approach

Plants have evolved diverse strategies for foraging, e.g., mycorrhizae, modification of root system architecture, and secretion of phosphatase. Despite extensive molecular/physiological studies on individual strategies under laboratory/greenhouse conditions, there is little information about how plants orchestrate these strategies in the field. We hypothesized that individual strategies are independently driven by corresponding genetic modules in response to deficiency/unbalance in nutrients. Roots colonized by mycorrhizal fungi, leaves, and root-zone soils were collected from 251 maize plants grown across the United States Corn Belt and Japan, which provided a large gradient of soil characteristics/agricultural practice and thus gene expression for foraging. RNA was extracted from the roots, sequenced, and subjected to gene coexpression network analysis. Nineteen genetic modules were defined and functionally characterized, from which three genetic modules, mycorrhiza formation, phosphate starvation response (PSR), and root development, were selected as those directly involved in foraging. The mycorrhizal module consists of genes responsible for mycorrhiza formation and was upregulated by both phosphorus and nitrogen deficiencies. The PSR module that consists of genes encoding phosphate transporter, secreted acid phosphatase, and enzymes involved in internal-phosphate recycling was regulated independent of the mycorrhizal module and strongly upregulated by phosphorus deficiency relative to nitrogen. The root development module that consists of regulatory genes for root development and cellulose biogenesis was upregulated by phosphorus and nitrogen enrichment. The expression of this module was negatively correlated with that of the mycorrhizal module, suggesting that root development is intrinsically an opposite strategy of mycorrhizae. Our approach provides new insights into understanding plant foraging strategies in complex environments at the molecular level.

Arbuscular Mycorrhizal Fungi Compete Asymmetrically for Amino Acids with Native and Invasive Solidago

Arbuscular mycorrhizal fungi (AMF) and soil amino acids both affect plant performance. However, little is known about how AMF compete for amino acids with native and invasive congeners. We conducted a factorial experiment (inoculation, native and invasive species, and amino acids) to examine the competition for amino acids between soil microbes and both native and invasive congeners. The competition for amino acids between AMF and invasive Solidago canadensis was weaker than that observed between AMF and native S. decurrens. This asymmetric competition increased the growth advantage of S. canadensis over S. decurrens. The efficacy (biomass production per unit of nitrogen supply) of amino acids compared to ammonium was smaller in S. canadensis than in S. decurrens when both species were grown without inoculation, but the opposite was the case when both species were grown with AMF. AMF and all microbes differentially altered four phenotypic traits (plant height, leaf chlorophyll content, leaf number, and root biomass allocation) and the pathways determining the effects of amino acids on growth advantages. These findings suggest that AMF could enhance plant invasiveness through asymmetric competition for amino acids and that amino acid-driven invasiveness might be differentially regulated by different microbial guilds.

Narrowing down molecular targets for improving phosphorus-use efficiency in maize (Zea mays L.)

Conventional agricultural practices rely heavily on chemical fertilizers to boost production. Among the fertilizers, phosphatic fertilizers are copiously used to ameliorate low-phosphate availability in the soil. However, phosphorus-use efficiency (PUE) for major cereals, including maize, is less than 30%; resulting in more than half of the applied phosphate being lost to the environment. Rock phosphate reserves are finite and predicted to exhaust in near future with the current rate of consumption. Thus, the dependence of modern agriculture on phosphatic fertilizers poses major food security and sustainability challenges. Strategies to optimize and improve PUE, like genetic interventions to develop high PUE cultivars, could have a major impact in this area. Here, we present the current understanding and recent advances in the biological phenomenon of phosphate uptake, translocation, and adaptive responses of plants under phosphate deficiency, with special reference to maize. Maize is one of the most important cereal crops that is cultivated globally under diverse agro-climatic conditions. It is an industrial, feed and food crop with multifarious uses and a fast-rising global demand and consumption. The interesting aspects of diversity in the root system architecture traits, the interplay between signaling pathways contributing to PUE, and an in-depth discussion on promising candidate genes for improving PUE in maize are elaborated.

Effects of Fertilizer Reduction and Straw Application on Dynamic Changes of Phosphorus in Overlying and Leaching Water in Rice Fields

In the process of rice cultivation, fertilizer reduction can effectively reduce the concentration of phosphorus (P) in overlying water and leaching water. In this study, the variation characteristics of P in overlying and leaching water under the conditions of fertilizer reduction and straw application and its impact on the environment were studied through a two-season rice field experiment. Four treatments were set, including no fertilizer without straw (CK), conventional fertilization (CF), 20% reduction in nitrogen (N) and P fertilization (RF), and 20% reduction in N and P fertilization with the wheat straw (RFWS). The results showed that RF could effectively reduce the risk of P loss due to its ability to decrease the concentration of P in overlying and leaching water. RFWS increased P concentrations in overlying and leaching water of rice fields. Total dissolved phosphorus (TDP) was the main form of total phosphorus (TP), and soluble reactive phosphorus (SRP) was the main form of TDP. The concentration of TP, TDP, and SRP in the overlying and leaching water peaked on the first day after fertilization, and then gradually decreased. The high-risk period of P loss was 0 to 10 days after fertilization. This study could provide appropriate strategies to reduce the risk of P loss during local rice cultivation and protect local water resources from eutrophication.

Twenty years of rice genomics research: From sequencing and functional genomics to quantitative genomics

Since the completion of the rice genome sequencing project in 2005, we have entered the era of rice genomics, which is still in its ascendancy. Rice genomics studies can be classified into three stages: structural genomics, functional genomics, and quantitative genomics. Structural genomics refers primarily to genome sequencing for the construction of a complete map of rice genome sequence. This is fundamental for rice genetics and molecular biology research. Functional genomics aims to decode the functions of rice genes. Quantitative genomics is large-scale sequence- and statistics-based research to define the quantitative traits and genetic features of rice populations. Rice genomics has been a transformative influence on rice biological research and contributes significantly to rice breeding, making rice a good model plant for studying crop sciences.

Impacts of corn stover management and fertilizer application on soil nutrient availability and enzymatic activity

Corn stover is a global resource used in many industrial sectors including bioenergy, fuel, and livestock operations. However, stover removal can negatively impact soil nutrient availability, especially nitrogen (N) and phosphorus (P), biological activity, and soil health. We evaluated the effects of corn stover management combined with N and P fertilization on soil quality, using soil chemical (nitrate, ammonium and Bray-1 P) and biological parameters (β-glucosidase, alkaline phosphatase, arylsulfatase activities and fluorescein diacetate hydrolysis—FDA). The experiment was performed on a Mollisol (Typic Endoaquoll) in a continuous corn system from 2013 to 2015 in Minnesota, USA. The treatments tested included six N rates (0 to 200 kg N ha⁻¹), five P rates (0 to 100 kg P₂O₅ ha⁻¹), and two residue management strategies (residue removed or incorporated) totalling 60 treatments. Corn stover management significantly impacted soil mineral-N forms and enzyme activity. In general, plots where residue was incorporated were found to have high NH₄⁺ and enzyme activity compared to plots where residue was removed. In contrast, fields where residue was removed showed higher NO₃⁻ than plots where residue was incorporated. Residue management had little effect on soil available P. Soil enzyme activity was affected by both nutrient and residue management. In most cases, activity of the enzymes measured in plots where residue was removed frequently showed a positive response to added N and P. In contrast, soil enzyme responses to applied N and P in plots where residue was incorporated were less evident. Soil available nutrients tended to decrease in plots where residue was removed compared with plots where residue was incorporated. In conclusion, stover removal was found to have significant potential to change soil chemical and biological properties and caution should be taken when significant amounts of stover are removed from continuous corn fields. The residue removal could decrease different enzymes related to C-cycle (β-glucosidase) and soil microbial activity (FDA) over continuous cropping seasons, impairing soil health.

Strigolactones: New players in the nitrogen-phosphorus signalling interplay

Nitrogen (N) and phosphorus (P) are among the most important macronutrients for plant growth and development, and the most widely used as fertilizers. Understanding how plants sense and respond to N and P deficiency is essential to optimize and reduce the use of chemical fertilizers. Strigolactones (SLs) are phytohormones acting as modulators and sensors of plant responses to P deficiency. In the present work, we assess the potential role of SLs in N starvation and in the N-P signalling interplay. Physiological, transcriptional and metabolic responses were analysed in wild-type and SL-deficient tomato plants grown under different P and N regimes, and in plants treated with a short-term pulse of the synthetic SL analogue 2'-epi-GR24. The results evidence that plants prioritize N over P status by affecting SL biosynthesis. We also show that SLs modulate the expression of key regulatory genes of phosphate and nitrate signalling pathways, including the N-P integrators PHO2 and NIGT1/HHO. The results support a key role for SLs as sensors during early plant responses to both N and phosphate starvation and mediating the N-P signalling interplay, indicating that SLs are involved in more physiological processes than so far proposed.

Nitrogen in plants: from nutrition to the modulation of abiotic stress adaptation

Nitrogen is one of the most important nutrient for plant growth and development; it is strongly associated with a variety of abiotic stress responses. As sessile organisms, plants have evolved to develop efficient strategies to manage N to support growth when exposed to a diverse range of stressors. This review summarizes the recent progress in the field of plant nitrate (NO3-) and ammonium (NH4+) uptake, which are the two major forms of N that are absorbed by plants. We explore the intricate relationship between NO3-/NH4+ and abiotic stress responses in plants, focusing on stresses from nutrient deficiencies, unfavorable pH, ions, and drought. Although many molecular details remain unclear, research has revealed a number of core signaling regulators that are associated with N-mediated abiotic stress responses. An in-depth understanding and exploration of the molecular processes that underpin the interactions between N and abiotic stresses is useful in the design of effective strategies to improve crop growth, development, and productivity.

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.

Intracellular phosphate sensing and regulation of phosphate transport systems in plants

Recent research on the regulation of cellular phosphate (Pi) homeostasis in eukaryotes has collectively made substantial advances in elucidating inositol pyrophosphates (PP-InsP) as Pi signaling molecules that are perceived by the SPX (Syg1, Pho81, and Xpr1) domains residing in multiple proteins involved in Pi transport and signaling. The PP-InsP-SPX signaling module is evolutionarily conserved across eukaryotes and has been elaborately adopted in plant Pi transport and signaling systems. In this review, we have integrated these advances with prior established knowledge of Pi and PP-InsP metabolism, intracellular Pi sensing, and transcriptional responses according to the dynamics of cellular Pi status in plants. Anticipated challenges and pending questions as well as prospects are also discussed.

Identification of Genes Associated with Nitrogen Stress Responses in Apple Leaves

Nitrogen (N) is an essential macronutrient that regulates diverse physiological processes for plant survival and development. In apple orchards, inappropriate N conditions can cause imbalanced growth and subsequent physiological disorders in trees. In order to investigate the molecular basis underlying the physiological signals for N stress responses, we examined the metabolic signals responsive to contrasting N stress conditions (deficient/excessive) in apple leaves using transcriptome approaches. The clustering of differentially expressed genes (DEGs) showed the expression dynamics of genes associated with each N stress group. Functional analyses of gene ontology and pathway enrichments revealed the potential candidates of metabolic signals responsible for N-deficient/excessive stress responses. The functional interactions of DEGs in each cluster were further explored by protein-protein interaction network analysis. Our results provided a comprehensive insight into molecular signals responsive to N stress conditions, and will be useful in future research to enhance the nutrition tolerance of tree crops.

Soybean responds to phosphate starvation through reversible protein phosphorylation

Phosphorus (P) deficiency is considered as a major constraint on crop production. Although a set of adaptative strategies are extensively suggested in soybean (Glycine max) to phosphate (Pi) deprivation, molecular mechanisms underlying reversible protein phosphorylation in soybean responses to P deficiency remains largely unclear. In this study, isobaric tags for relative and absolute quantitation, combined with liquid chromatography and tandem mass spectrometry analysis was performed to identify differential phosphoproteins in soybean roots under Pi sufficient and deficient conditions. A total of 427 phosphoproteins were found to exhibit differential accumulations, with 213 up-regulated and 214 down-regulated. Among them, a nitrate reductase, GmNR4 exhibiting increased phosphorylation levels under low Pi conditions, was further selected to evaluate the effects of phosphorylation on its nitrate reductase activity and subcellular localization. Mutations of GmNR4 phosphorylation levels significantly influenced its activity in vitro, but not for its subcellular localization. Taken together, identification of differential phosphoproteins reveled the complex regulatory pathways for soybean adaptation to Pi starvation through reversible protein phosphorylation.

Making the 'Green Revolution' Truly Green: Improving Crop Nitrogen Use Efficiency

Traditional breeding for high-yielding crops has mainly relied on the widespread cultivation of gibberellin (GA)-deficient semi-dwarf varieties, as dwarfism increases lodging resistance and allows for high nitrogen use, resulting in high grain yield. Although the adoption of semi-dwarf varieties in rice and wheat breeding brought big success to the 'Green Revolution' in the 20th century, it consequently increased the demand for nitrogen-based fertilizer, which causes severe threat to ecosystems and sustainable agriculture. To make the 'Green Revolution' truly green, it is necessary to develop new varieties with high nitrogen use efficiency (NUE). Under this demand, research on NUE, mainly for rice, has made great strides in the last decade. This mini-review focuses on three aspects of recent epoch-making findings on rice breeding for high NUE. The first one on 'NUE genes related to GA signaling' shows how promising it is to improve NUE in semi-dwarf Green Revolution varieties. The second aspect centers around the nitrate transporter1.1B, NRT1.1B; studies have revealed a nutrient signaling pathway through the discovery of the nitrate-NRT1.1B-SPX4-NLP3 cascade. The last one is based on the recent finding that the teosinte branched1, cycloidea, proliferating cell factor (TCP)-domain protein 19 underlies the genomic basis of geographical adaptation to soil nitrogen; OsTCP19 regulates the expression of a key transacting factor, DLT/SMOS2, which participates in the signaling of four different phytohormones, GA, auxin, brassinosteroid and strigolactone. Collectively, these breakthrough findings represent a significant step toward breeding high-NUE rice in the future.

Identification, structure analysis, and transcript profiling of phosphate transporters under Pi deficiency in duckweeds

Phosphate transporters (PHTs) mediate the uptake and translocation of phosphate in plants. A comprehensive analysis of the PHT family in aquatic plant is still lacking. In this study, we identified 73 PHT members of six major PHT families from four duckweed species. The phylogenetic analysis, gene structure and protein characteristics analysis revealed that PHT genes are highly conserved among duckweeds. Interaction network and miRNA target prediction showed that SpPHTs could interact with the important components of the nitrate/phosphate signaling pathway, and spo-miR399 might be a central regulator that mediates phosphate signal network in giant duckweed (Spirodela polyrhiza). The modeled 3D structure of SpPHT proteins shared a high level of homology with template structures, which provide information to understand their functions at proteomic level. The expression profiles derived from transcriptome data and quantitative real-time PCR revealed that SpPHT genes are respond to exogenous stimuli and remarkably induced by phosphate starvation, phosphate is absorbed from aquatic environment by the whole duckweed plant. This study lays the foundation for further functional studies on PHT genes for genetic improvement and the promotion of phosphate uptake efficiency in duckweeds.

Expression dynamics indicate the role of Jasmonic acid biosynthesis pathway in regulating macronutrient (N, P and K+) deficiency tolerance in rice (Oryza sativa L.)

Expression pattern indicates that JA biosynthesis pathway via regulating JA levels might control root system architecture to improve nutrient use efficiency (NUE) and N, P, K⁺ deficiency tolerance in rice. Deficiencies of macronutrients (N, P and K⁺) and consequent excessive use of fertilizers have dramatically reduced soil fertility. It calls for development of nutrient use efficient plants. Plants combat nutrient deficiencies by altering their root system architecture (RSA) to enhance the acquisition of nutrients from the soil. Amongst various phytohormones, Jasmonic acid (JA) is known to regulate plant root growth and modulate RSA. Therefore, to understand the role of JA in macronutrient deficiency in rice, expression pattern of JA biosynthesis genes was analyzed under N, P and K⁺ deficiencies. Several members belonging to different families of JA biosynthesis genes (PLA1, LOX, AOS, AOC, OPR, ACX and JAR1) showed differential expression exclusively in one nutrient deficiency or in multiple nutrient deficiencies. Expression analysis during developmental stages showed that several genes expressed significantly in vegetative tissues, particularly in root. In addition, JA biosynthesis genes were found to have significant expression under the treatment of different phytohormones, including Auxin, cytokinin, gibberellic acid (GA), abscisic acid (ABA), JA and abiotic stresses, such as drought, salinity and cold. Analysis of promoters of these genes revealed various cis-regulatory elements associated with hormone response, plant development and abiotic stresses. These findings suggest that JA biosynthesis pathway by regulating the level of JA might control the RSA thus, it may help rice plant in combating macronutrient deficiency.

Plant phospholipase D: novel structure, regulatory mechanism, and multifaceted functions with biotechnological application

Phospholipases D (PLDs) are important membrane lipid-modifying enzymes in eukaryotes. Phosphatidic acid, the product of PLD activity, is a vital signaling molecule. PLD-mediated lipid signaling has been the subject of extensive research leading to discovery of its crystal structure. PLDs are involved in the pathophysiology of several human diseases, therefore, viewed as promising targets for drug design. The availability of a eukaryotic PLD crystal structure will encourage PLD targeted drug designing. PLDs have been implicated in plants response to biotic and abiotic stresses. However, the molecular mechanism of response is not clear. Recently, several novel findings have shown that PLD mediated modulation of structural and developmental processes, such as: stomata movement, root growth and microtubule organization are crucial for plants adaptation to environmental stresses. Involvement of PLDs in regulating membrane remodeling, auxin mediated alteration of root system architecture and nutrient uptake to combat nitrogen and phosphorus deficiencies and magnesium toxicity is established. PLDs via vesicle trafficking modulate cytoskeleton and exocytosis to regulate self-incompatibility (SI) signaling in flowering plants, thereby contributes to plants hybrid vigor and diversity. In addition, the important role of PLDs has been recognized in biotechnologically important functions, including oil/TAG synthesis and maintenance of seed quality. In this review, we describe the crystal structure of a plant PLD and discuss the molecular mechanism of catalysis and activity regulation. Further, the role of PLDs in regulating plant development under biotic and abiotic stresses, nitrogen and phosphorus deficiency, magnesium ion toxicity, SI signaling and pollen tube growth and in important biotechnological applications has been discussed.