The increasing importance of distinguishing among plant nitrogen sources

Regulation of nitrogen metabolism by COE2 under low sulfur stress in Arabidopsis

The interplay between nitrogen and sulfur assimilation synergistically supports and sustains plant growth and development, operating in tandem to ensure coordinated and optimal outcomes. Previously, we characterized Arabidopsis CHLOROPHYLL A/B-BINDING (CAB) overexpression 2 (COE2) mutant, which has a mutation in the NITRIC OXIDE-ASSOCIATED (NOA1) gene and exhibits deficiency in root growth under low nitrogen (LN) stress. This study found that the growth suppression in roots and shoots in coe2 correlates with decreased sensitivity to low sulfur stress treatment compared to the wild-type. Therefore, we examined the regulatory role of COE2 in nitrogen and sulfur interaction by assessing the expression of nitrogen metabolism-related genes in coe2 seedlings under low sulfur stress. Despite the notable upregulation of nitrate reductase genes (NIA1 and NIA2), there was a considerable reduction in nitrogen uptake and utilization, resulting in a substantial growth penalty. Moreover, the elevated expression of miR396 perhaps complemented growth stunting by selectively targeting and curtailing the expression levels of GROWTH REGULATING FACTOR 2 (GRF2), GRF4, and GRF9. This study underscores the vital role of COE2-mediated nitrogen signaling in facilitating seedling growth under sulfur deficiency stress.

Elevated CO2 and ammonium nitrogen promoted the plasticity of two maple in great lakes region by adjusting photosynthetic adaptation

Introduction

Climate change-related CO2 increases and different forms of nitrogen deposition are thought to affect the performance of plants, but their interactions have been poorly studied.

Methods

This study investigated the responses of photosynthesis and growth in two invasive maple species, amur maple (Acer ginnala Maxim.) and boxelder maple (Acer negundo L.), to elevated CO2 (400 µmol mol-1 (aCO2) vs. 800 µmol mol-1 (eCO2) and different forms of nitrogen fertilization (100% nitrate, 100% ammonium, and an equal mix of the two) with pot experiment under controlled conditions.

Results and discussion

The results showed that eCO2 significantly promoted photosynthesis, biomass, and stomatal conductance in both species. The biochemical limitation of photosynthesis was switched to RuBP regeneration (related to Jmax) under eCO2 from the Rubisco carboxylation limitation (related to Vcmax) under aCO2. Both species maximized carbon gain by lower specific leaf area and higher N concentration than control treatment, indicating robust morphological plasticity. Ammonium was not conducive to growth under aCO2, but it significantly promoted biomass and photosynthesis under eCO2. When nitrate was the sole nitrogen source, eCO2 significantly reduced N assimilation and growth. The total leaf N per tree was significantly higher in boxelder maple than in amur maple, while the carbon and nitrogen ratio was significantly lower in boxelder maple than in amur maple, suggesting that boxelder maple leaf litter may be more favorable for faster nutrient cycling. The results suggest that increases in ammonium under future elevated CO2 will enhance the plasticity and adaptation of the two maple species.

Moderate salinity and high ammonium/nitrate ratio enhance early growth in "summer wonder" lettuce cultivar

Because its impact in plant development and growth and its interaction with Na+ and Cl-, the supply of different N-forms to crops can be an easy-to-use tool with effective results on salinity tolerance. Here the effect of four N-NO3-/N-NH4+ ratios (mM; 2/0, 1.6/0.4, 0.4/1.6, 0/2) on adaptation to salt conditions (15 mM NaCl in a first experiment and 40 mM NaCl in a second experiment) was studied in young lettuce (cv "Summer wonder") plants. The experiments were carried out in greenhouse and under hydroponics conditions. The results show that this cultivar tolerates and adapts to moderate salinity by deploying several structural and physiological mechanisms; (i) increasing allocation of biomass to the root, (ii) increasing root Na+ uptake and storing it in the shoot and root tissues, (iii) increasing intrinsic water use efficiency and (iv) increasing root N and P uptake. The beneficial effect of salt exposure on growth was greater when the predominant N-form was N-NO3-. These plants with higher tissue N-NO3- concentration, decreased Cl- uptake and shoot and root Cl- concentration. Regardless of salt conditions, plants with a high proportion of N-NH4+ (1.6 mM) and a low proportion of N-NO3- (0.4 mM) had a greater growth and nitrogen use efficiency, that was associated with the improved uptake of nutrients, and the maintenance of water status.

Effect of humic substances on nitrogen cycling in soil-plant ecosystems: Advances, issues, and future perspectives

Nitrogen (N) cycle is one of the most significant biogeochemical cycles driven by soil microorganisms on the earth. Exogenous humic substances (HS), which include composted-HS and artificial-HS, as a new soil additive, can improve the water retention capacity, cation exchange capacity and soil nutrient utilization, compensating for the decrease of soil HS content caused by soil overutilization. This paper systematically reviewed the contribution of three different sources of HS in the soil-plant system and explained the mechanisms of N transformation through physiological and biochemical pathways. HS convert the living space and living environment of microorganisms by changing the structure and condition of soil. Generally, HS can fix atmospheric and soil N through biotic and abiotic mechanisms, which improved the availability of N. Besides, HS transform the root structure of plants through physiological and biochemical pathways to promote the absorption of inorganic N by plants. The redox properties of HS participate in soil N transformation by altering the electron gain and loss of microorganisms. Moreover, to alleviate the energy crisis and environmental problems caused by N pollution, we also illustrated the mechanisms reducing soil N2O emissions by HS and the application prospects of artificial-HS. Eventually, a combination of indoor simulation and field test, molecular biology and stable isotope techniques are needed to systematically analyze the potential mechanisms of soil N transformation, representing an important step forward for understanding the relevance between remediation of environmental pollution and improvement of the N utilization in soil-plant system.

Organ-specific characteristics govern the relationship between histone code dynamics and transcriptional reprogramming during nitrogen response in tomato

Environmental stimuli trigger rapid transcriptional reprogramming of gene networks. These responses occur in the context of the local chromatin landscape, but the contribution of organ-specific dynamic chromatin modifications in responses to external signals remains largely unexplored. We treated tomato seedlings with a supply of nitrate and measured the genome-wide changes of four histone marks, the permissive marks H3K27ac, H3K4me3, and H3K36me3 and repressive mark H3K27me3, in shoots and roots separately, as well as H3K9me2 in shoots. Dynamic and organ-specific histone acetylation and methylation were observed at functionally relevant gene loci. Integration of transcriptomic and epigenomic datasets generated from the same organ revealed largely syngenetic relations between changes in transcript levels and histone modifications, with the exception of H3K27me3 in shoots, where an increased level of this repressive mark is observed at genes activated by nitrate. Application of a machine learning approach revealed organ-specific rules regarding the importance of individual histone marks, as H3K36me3 is the most successful mark in predicting gene regulation events in shoots, while H3K4me3 is the strongest individual predictor in roots. Our integrated study substantiates a view that during plant environmental responses, the relationships between histone code dynamics and gene regulation are highly dependent on organ-specific contexts.

Nitrate-responsive transcriptome analysis of rice RGA1 mutant reveals the role of G-protein alpha subunit in negative regulation of nitrogen-sensitivity and use efficiency

KEY MESSAGE

Nitrate-responsive transcriptomic, phenotypic and physiological analyses of rice RGA1 mutant revealed many novel RGA1-regulated genes/processes/traits related to nitrogen use efficiency, and provided robust genetic evidence of RGA1-regulation of NUE. Nitrogen (N) use efficiency (NUE) is important for sustainable agriculture. G-protein signalling was implicated in N-response/NUE in rice, but needed firm genetic characterization of the role of alpha subunit (RGA1). The knock-out mutant of RGA1 in japonica rice exhibited lesser nitrate-dose sensitivity than the wild type (WT), in yield and NUE. We, therefore, investigated its genomewide nitrate-response relative to WT. It revealed 3416 differentially expressed genes (DEGs), including 719 associated with development, grain yield and phenotypic traits for NUE. The upregulated DEGs were related to photosynthesis, chlorophyll, tetrapyrrole and porphyrin biosynthesis, while the downregulated DEGs belonged to cellular protein metabolism and transport, small GTPase signalling, cell redox homeostasis, etc. We validated 26 nitrate-responsive DEGs across functional categories by RT-qPCR. Physiological validation of nitrate-response in the mutant and the WT at 1.5 and 15 mM doses revealed higher chlorophyll and stomatal length but decreased stomatal density, conductance and transpiration. The consequent increase in photosynthesis and water use efficiency may have contributed to better yield and NUE in the mutant, whereas the WT was N-dose sensitive. The mutant was not as N-dose-responsive as the WT in shoot/root growth, productive tillers and heading date, but equally responsive as WT in total N and protein content. The RGA1 mutant was less impacted by higher N-dose or salt stress in terms of yield, protein content, photosynthetic performance, relative water content, water use efficiency and catalase activity. PPI network analyses revealed known NUE-related proteins as RGA1 interactors. Therefore, RGA1 negatively regulates N-dose sensitivity and NUE in rice.

Association between host nitrogen absorption and root-associated microbial community in field-grown wheat

Plant roots and rhizosphere soils assemble diverse microbial communities, and these root-associated microbiomes profoundly influence host development. Modern wheat has given rise to numerous cultivars for its wide range of ecological adaptations and commercial uses. Variations in nitrogen uptake by different wheat cultivars are widely observed in production practices. However, little is known about the composition and structure of the root-associated microbiota in different wheat cultivars, and it is not sure whether root-associated microbial communities are relevant in host nitrogen absorption. Therefore, there is an urgent need for systematic assessment of root-associated microbial communities and their association with host nitrogen absorption in field-grown wheat. Here, we investigated the root-associated microbial community composition, structure, and keystone taxa in wheat cultivars with different nitrogen absorption characteristics at different stages and their relationships with edaphic variables and host nitrogen uptake. Our results indicated that cultivar nitrogen absorption characteristics strongly interacted with bacterial and archaeal communities in the roots and edaphic physicochemical factors. The impact of host cultivar identity, developmental stage, and spatial niche on bacterial and archaeal community structure and network complexity increased progressively from rhizosphere soils to roots. The root microbial community had a significant direct effect on plant nitrogen absorption, while plant nitrogen absorption and soil temperature also significantly influenced root microbial community structure. The cultivar with higher nitrogen absorption at the jointing stage tended to cooperate with root microbial community to facilitate their own nitrogen absorption. Our work provides important information for further wheat microbiome manipulation to influence host nitrogen absorption. KEY POINTS: • Wheat cultivar and developmental stage affected microbiome structure and network. • The root microbial community strongly interacted with plant nitrogen absorption. • High nitrogen absorption cultivar tended to cooperate with root microbiome.

Identification and functional characterization of the sugarcane (Saccharum spp.) AMT2-type ammonium transporter ScAMT3;3 revealed a presumed role in shoot ammonium remobilization

Sugarcane (Saccharum spp.) is an important crop for sugar and bioethanol production worldwide. To maintain and increase sugarcane yields in marginal areas, the use of nitrogen (N) fertilizers is essential, but N overuse may result in the leaching of reactive N to the natural environment. Despite the importance of N in sugarcane production, little is known about the molecular mechanisms involved in N homeostasis in this crop, particularly regarding ammonium (NH4 +), the sugarcane's preferred source of N. Here, using a sugarcane bacterial artificial chromosome (BAC) library and a series of in silico analyses, we identified an AMMONIUM TRANSPORTER (AMT) from the AMT2 subfamily, sugarcane AMMONIUM TRANSPORTER 3;3 (ScAMT3;3), which is constitutively and highly expressed in young and mature leaves. To characterize its biochemical function, we ectopically expressed ScAMT3;3 in heterologous systems (Saccharomyces cerevisiae and Arabidopsis thaliana). The complementation of triple mep mutant yeast demonstrated that ScAMT3;3 is functional for NH3/H+ cotransport at high availability of NH4 + and under physiological pH conditions. The ectopic expression of ScAMT3;3 in the Arabidopsis quadruple AMT knockout mutant restored the transport capacity of 15N-NH4 + in roots and plant growth under specific N availability conditions, confirming the role of ScAMT3;3 in NH4 + transport in planta. Our results indicate that ScAMT3;3 belongs to the low-affinity transport system (Km 270.9 µM; Vmax 209.3 µmol g-1 root DW h-1). We were able to infer that ScAMT3;3 plays a presumed role in NH4 + source-sink remobilization in the shoots via phloem loading. These findings help to shed light on the functionality of a novel AMT2-type protein and provide bases for future research focusing on the improvement of sugarcane yield and N use efficiency.

Involvement of plant signaling network and cell metabolic homeostasis in nitrogen deficiency-induced early leaf senescence

Nitrogen (N) is a basic building block that plays an essential role in the maintenance of normal plant growth and its metabolic functions through complex regulatory networks. Such the N metabolic network comprises a series of transcription factors (TFs), with the coordinated actions of phytohormone and sugar signaling to sustain cell homeostasis. The fluctuating N concentration in plant tissues alters the sensitivity of several signaling pathways to stressful environments and regulates the senescent-associated changes in cellular structure and metabolic process. Here, we review recent advances in the interaction between N assimilation and carbon metabolism in response to N deficiency and its regulation to the nutrient remobilization from source to sink during leaf senescence. The regulatory networks of N and sugar signaling for N deficiency-induced leaf senescence is further discussed to explain the effects of N deficiency on chloroplast disassembly, reactive oxygen species (ROS) burst, asparagine metabolism, sugar transport, autophagy process, Ca2+ signaling, circadian clock response, brassinazole-resistant 1 (BZRI), and other stress cell signaling. A comprehensive understanding for the metabolic mechanism and regulatory network underlying N deficiency-induced leaf senescence may provide a theoretical guide to optimize the source-sink relationship during grain filling for the achievement of high yield by a selection of crop cultivars with the properly prolonged lifespan of functional leaves and/or by appropriate agronomic managements.

Hyphosphere microorganisms facilitate hyphal spreading and root colonization of plant symbiotic fungus in ammonium-enriched soil

Anthropogenic nitrogen inputs lead to a high ammonium (NH4+)/nitrate (NO3-) ratio in the soil, which restricts hyphal spreading of soil fungi. Access of symbiotic fungi to roots is a prerequisite for plant-fungal interactions. Hyphosphere bacteria protect fungi from environmental stress, yet the impact of hyphosphere bacteria on adaptation of host fungi to NH4+-enriched conditions remains unclear. By developing soil microcosm assays, we report that a plant-symbiotic fungus, Phomopsis liquidambaris, harbors specific hyphosphere bacteria that facilitate hyphal spreading and assist in the root colonization in NH4+-enriched soil. Genetic manipulation, 16S rRNA gene analysis and coinoculation assays revealed that the genus Enterobacter was enriched in the hyphosphere of NH4+-sensitive wild-type compared to NH4+-preferring nitrite reductase-deficient strain. The representative Enterobacter sp. SZ2-promoted hyphal spreading is only evident in nonsterilized soil. We further identified an increased abundance and diversity of ammonia-oxidizing archaea (AOA) and a synchronously decreased NH4+:NO3- ratio following SZ2 inoculation. Microbial supplementation and inhibitor assays showed that AOA-mediated reduction in NH4+:NO3- ratio is responsible for SZ2-enhanced fungal adaptation to NH4+-enriched conditions. The Ph. liquidambaris-Enterobacter-AOA triple interaction promoted rice growth in NH4+-enriched soil. Our study reveals the essential role of hyphosphere microorganism-based hyphal spreading in plant-fungal symbiosis establishment within nitrogen-affected agroecosystems.

Uptake of glucose from the rhizosphere, mediated by apple MdHT1.2, regulates carbohydrate allocation

Plant roots can absorb sugars from the rhizosphere, which reduces the consumption of carbon derived from photosynthesis. However, the underlying mechanisms that roots use to control sugar absorption from soil are poorly understood. Here, we identified an apple (Malus × domestica Borkh.) hexose transporter, MdHT1.2, that functions on the root epidermis to absorb glucose (Glc) from the rhizosphere. Based on RNA-seq data, MdHT1.2 showed the highest expression level among 29 MdHT genes in apple roots. Biochemical analyses demonstrated that MdHT1.2 was mainly expressed in the epidermal cells of fine roots, and its protein was located on the plasma membrane. The roots of transgenic apple and Solanum lycopersicum lines overexpressing MdHT1.2 had an increased capability to absorb Glc when fed with [13C]-labeled Glc or 2-NBDG, whereas silencing MdHT1.2 in apple showed the opposite results. Further studies established that MdHT1.2-mediated Glc absorption from the rhizosphere changed the carbon assimilate allocation between apple shoot and root, which regulated plant growth. Additionally, a grafting experiment in tomato confirmed that increasing the Glc uptake capacity in the root overexpressing MdHT1.2 could facilitate carbohydrate partitioning to the fruit. Collectively, our study demonstrated that MdHT1.2 functions on the root epidermis to absorb rhizospheric Glc, which regulates the carbohydrate allocation for plant growth and fruit sugar accumulation.

Effects of drought and salt stress on seed germination and seedling growth of Elymus nutans

Drought and soil salinization are global environmental issues, and Elymus nutans play an important role in vegetation restoration in arid and saline environments due to their excellent stress resistance. In the process of vegetation restoration, the stage from germination to seedling growth of forage is crucial. This experiment studied the effects of PEG-6000 simulated drought stress and NaCl simulated salinization stress on the germination of E. nutans seeds, and explored the growth of forage seedlings from sowing to 28 days under drought and salinization stress conditions. The results showed that under the same environmental water potential, there were significant differences in responses of seed germination, seedling growth, organic carbon, total nitrogen and total phosphorus of above-ground and underground parts of E. nutans to drought stress and salinization stress. Using the membership function method to comprehensively evaluate the seed germination and seedling indicators of E. nutans, it was found that under the same environmental water potential, E. nutans was more severely affected by drought stress during both the seed germination and seedling growth stages. E. nutans showed better salt tolerance than drought resistance.

Identification and expression characteristics of NLP (NIN-like protein) gene family in pepper (Capsicum annuum L.)

BACKGROUND

Pepper (Capsicum annum L.) is the main crop in the vegetable industry. The growth and development of peppers are regulated by nitrate, but there is limited research on the molecular mechanisms of nitrate absorption and assimilation in peppers. A plant specific transcription factor NLP plays an important role in nitrate signal transduction.

METHODS AND RESULTS

In this study, a total of 7 NLP members were identified based on pepper genome data. Two nitrogen transport elements (GCN4) were found in the CaNLP5 promoter. In the phylogenetic tree, CaNLP members are divided into three branches, with pepper NLP and tomato NLP having the closest genetic relationship. The expression levels of CaNLP1, CaNLP3, and CaNLP4 are relatively high in the roots, stems, and leaves. The expression level of CaNLP7 gene is relatively high during the 5-7 days of pepper fruit color transformation. After various non-Biotic stress and hormone treatments, the expression of CaNLP1 was at a high level. The expression of CaNLP3 and CaNLP4 was down regulated in leaves, but up regulated in roots. Under conditions of nitrogen deficiency and sufficient nitrate, the expression patterns of NLP genes in pepper leaves and roots were determined.

CONCLUSION

These results provide important insights into the multiple functions of CaNLPs in regulating nitrate absorption and transport.

Schizotrophic Sclerotinia sclerotiorum-Mediated Root and Rhizosphere Microbiome Alterations Activate Growth and Disease Resistance in Wheat

Sclerotinia sclerotiorum, a widespread pathogen of dicotyledons, can grow endophytically in wheat, providing protection against Fusarium head blight and stripe rust and enhancing wheat yield. In this study, we found that wheat seed treatment with strain DT-8, infected with S. sclerotiorum hypovirulence-associated DNA virus 1 (SsHADV-1) and used as a "plant vaccine" for brassica protection, could significantly increase the diversity of the fungal and bacterial community in rhizosphere soil, while the diversity of the fungal community was obviously decreased in the wheat root. Interestingly, the relative abundance of potential plant growth-promoting rhizobacteria (PGPR) and biocontrol agents increased significantly in the DT-8-treated wheat rhizosphere soil. These data might be responsible for wheat growth promotion and disease resistance. These results may provide novel insights for understanding the interaction between the schizotrophic microorganism and the microbiota of plant roots and rhizosphere, screening and utilizing beneficial microorganisms, and further reducing chemical pesticide utilization and increasing crop productivity. IMPORTANCE Fungal pathogens are seriously threatening food security and natural ecosystems; efficient and environmentally friendly control methods are essential to increase world crop production. S. sclerotiorum, a widespread pathogen of dicotyledons, can grow endophytically in wheat, providing protection against Fusarium head blight and stripe rust and enhancing wheat yield. In this study, we discovered that S. sclerotiorum treatment increased the diversity of the soil fungal and bacterial community in rhizosphere soil, while the diversity of the fungal community was obviously decreased in the wheat root. More importantly, the relative abundance of potential PGPR and bio-control agents increased significantly in the S. sclerotiorum-treated wheat rhizosphere soil. The importance of this work is that schizotrophic S. sclerotiorum promotes wheat growth and enhances resistance against fungal diseases via changes in the structure of the root and rhizosphere microbiome.

Genetic regulation of nitrogen use efficiency in Gossypium spp

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

Potentiating Biosynthesis of Alkaloids and Polyphenolic Substances in Catharanthus roseus Plant Using ĸ-Carrageenan

Catharanthus roseus is a medicinal plant that produces indole alkaloids, which are utilized in anticancer therapy. Vinblastine and vincristine, two commercially important antineoplastic alkaloids, are mostly found in the leaves of Catharanthus roseus. ĸ-carrageenan has been proven as plant growth promoting substance for a number of medicinal and agricultural plants. Considering the importance of ĸ-carrageenan as a promoter of plant growth and phytochemical constituents, especially alkaloids production in Catharanthus roseus, an experiment was carried out to explore the effect of ĸ-carrageenan on the plant growth, phytochemicals content, pigments content, and production of antitumor alkaloids in Catharanthus roseus after planting. Foliar application of ĸ-carrageenan (at 0, 400, 600 and 800 ppm) significantly improved the performance of Catharanthus roseus. Phytochemical analysis involved determining the amount of total phenolics (TP), flavonoids (F), free amino acids (FAA), alkaloids (TAC) and pigments contents by spectrophotometer, minerals by ICP, amino acids, phenolic compounds and alkaloids (Vincamine, Catharanthine, Vincracine (Vincristine), and vinblastine) analysis uses HPLC. The results indicated that all examined ĸ-carrageenan treatments led to a significant (p ≤ 0.05) increase in growth parameters compared to the untreated plants. Phytochemical examination indicates that the spray of ĸ-carrageenan at 800 mg L^-1 increased the yield of alkaloids (Vincamine, Catharanthine and Vincracine (Vincristine)) by 41.85 μg/g DW, total phenolic compounds by 3948.6 μg gallic/g FW, the content of flavonoids 951.3 μg quercetin /g FW and carotenoids content 32.97 mg/g FW as compared to the control. An amount of 400 ppm ĸ-carrageenan treatment gave the best contents of FAA, Chl a, Chl b and anthocyanin. The element content of K, Ca, Cu, Zn and Se increased by treatments. Amino acids constituents and phenolics compounds contents were altered by ĸ-carrageenan.

Identification of Fungal and Bacterial Denitrification Inhibitors Targeting Copper Nitrite Reductase

The usage of nitrification inhibitors is one of the strategies that reduce or slow down the denitrification process to prevent nitrogen loss to the atmosphere in the form of N₂O. Directly targeting microbial denitrification could be one of the mitigation strategies; however, until now little efforts have been devoted toward the development of denitrification inhibitors. Here, we have identified small-molecule inhibitors of one of the proteins involved in the fungal denitrification pathway. Specifically, virtual screening was employed to identify the inhibitors of copper-containing nitrite reductase (FoNirK) of the filamentous fungus Fusarium oxysporum. Three series of chemical compounds were identified, out of which compounds belonging to two chemical scaffolds inhibited FoNirK enzymatic activity in low micromolar ranges. Several compounds also displayed moderate inhibition of fungal denitrification activity in vivo. Evaluation of in vitro activity against NirK from denitrifying bacterium Achromobacter xylosoxidans (AxNirK) and in vivo bacterial denitrification revealed a similar inhibitory profile.

Genome-wide identification of BcGRF genes in flowering Chinese cabbage and preliminary functional analysis of BcGRF8 in nitrogen metabolism

Growth-regulating factors (GRFs) are a unique family of transcription factors with well-characterized functions in plant growth and development. However, few studies have evaluated their roles in the absorption and assimilation of nitrate. In this study, we characterized the GRF family genes of flowering Chinese cabbage (Brassica campestris), an important vegetable crop in South China. Using bioinformatics methods, we identified BcGRF genes and analyzed their evolutionary relationships, conserved motifs, and sequence characteristics. Through genome-wide analysis, we identified 17 BcGRF genes distributed on seven chromosomes. A phylogenetic analysis revealed that the BcGRF genes could be categorized into five subfamilies. RT-qPCR analysis showed that BcGRF1, 8, 10, and 17 expression clearly increased in response to nitrogen (N) deficiency, particularly at 8 h after treatment. BcGRF8 expression was the most sensitive to N deficiency and was significantly correlated with the expression patterns of most key genes related to N metabolism. Using yeast one-hybrid and dual-luciferase assays, we discovered that BcGRF8 strongly enhances the driving activity of the BcNRT1.1 gene promoter. Next, we investigated the molecular mechanism by which BcGRF8 participates in nitrate assimilation and N signaling pathways by expressing it in Arabidopsis. BcGRF8 was localized in the cell nucleus and BcGRF8 overexpression significantly increased the shoot and root fresh weights, seedling root length, and lateral root number in Arabidopsis. In addition, BcGRF8 overexpression considerably reduced the nitrate contents under both nitrate-poor and -rich conditions in Arabidopsis. Finally, we found that BcGRF8 broadly regulates genes related to N uptake, utilization, and signaling. Our results demonstrate that BcGRF8 substantially accelerates plant growth and nitrate assimilation under both nitrate-poor and -rich conditions by increasing the number of lateral roots and the expression of genes involved in N uptake and assimilation, providing a basis for crop improvement.

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

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

Nitrogen-Fixing Symbiotic Paraburkholderia Species: Current Knowledge and Future Perspectives

A century after the discovery of rhizobia, the first Beta-proteobacteria species (beta-rhizobia) were isolated from legume nodules in South Africa and South America. Since then, numerous species belonging to the Burkholderiaceae family have been isolated. The presence of a highly branching lineage of nodulation genes in beta-rhizobia suggests a long symbiotic history. In this review, we focus on the beta-rhizobial genus Paraburkholderia, which includes two main groups: the South American mimosoid-nodulating Paraburkholderia and the South African predominantly papilionoid-nodulating Paraburkholderia. Here, we discuss the latest knowledge on Paraburkholderia nitrogen-fixing symbionts in each step of the symbiosis, from their survival in the soil, through the first contact with the legumes until the formation of an efficient nitrogen-fixing symbiosis in root nodules. Special attention is given to the strain P. phymatum STM815T that exhibits extraordinary features, such as the ability to: (i) enter into symbiosis with more than 50 legume species, including the agriculturally important common bean, (ii) outcompete other rhizobial species for nodulation of several legumes, and (iii) endure stressful soil conditions (e.g., high salt concentration and low pH) and high temperatures.

1The harm of residual plastic film and its accumulation driving factors in northwest China

The background to this research is stark and rather troubling: the ongoing accumulation of residual plastic film (RPF) in farmland ultimately threatens the sustainable development of agriculture and food security. In this study, we selected 15 counties in northern China to analyze the effect of RPF content on soil properties and crop yield and the driving factors through sampling and survey questionnaire. The linear mixed-effects model revealed the four main factors affecting RPF content, ranked as follows: plastic film mulching years > government recycling policy > spacing between rows > recycling methods (0.47493 > 0.25635 > 0.23380 > 0.17001). The contribution value of plastic film thickness was very low (R²(M) = 0.099). The plastic film width and spacing within rows did not significantly affect RPF content. The structural equation model showed that the RPF had both direct (-0.111) and indirect (-0.010) effects on maize yield. A 1 kg ha^-1 increase in RPF content decreased maize yield by 27.67 kg ha^-1. RPF did not directly affect soil organic carbon (SOC), pH, or ammonium nitrogen. RPF mainly aggravated soil salinization by increasing soil nitrate-nitrogen, available phosphorus, and available potassium, increasing SOC and decreasing pH, thus reducing crop yield. To the best of our knowledge, this is the first study to combine the driving factors of RPF accumulation and the effects of RPF on soil properties and crop yield in a large-scale sampling and survey questionnaire. RPF accumulation in the study area has aggravated soil salinization and reduced crop yields. Hence, measures are needed to alleviate the current situation. Local governments should formulate RPF recovery policies based on their actual situation. At the national level, more research is needed to develop RPF recovery machinery to improve efficiency.

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

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

Breeding for Higher Yields of Wheat and Rice through Modifying Nitrogen Metabolism

Wheat and rice produce nutritious grains that provide 32% of the protein in the human diet globally. Here, we examine how genetic modifications to improve assimilation of the inorganic nitrogen forms ammonium and nitrate into protein influence grain yield of these crops. Successful breeding for modified nitrogen metabolism has focused on genes that coordinate nitrogen and carbon metabolism, including those that regulate tillering, heading date, and ammonium assimilation. Gaps in our current understanding include (1) species differences among candidate genes in nitrogen metabolism pathways, (2) the extent to which relative abundance of these nitrogen forms across natural soil environments shape crop responses, and (3) natural variation and genetic architecture of nitrogen-mediated yield improvement. Despite extensive research on the genetics of nitrogen metabolism since the rise of synthetic fertilizers, only a few projects targeting nitrogen pathways have resulted in development of cultivars with higher yields. To continue improving grain yield and quality, breeding strategies need to focus concurrently on both carbon and nitrogen assimilation and consider manipulating genes with smaller effects or that underlie regulatory networks as well as genes directly associated with nitrogen metabolism.

Acclimation of sugar beet in morphological, physiological and BvAMT1.2 expression under low and high nitrogen supply

Understanding the response and tolerance mechanisms of nitrogen (N) stress is essential for the taproot plant of sugar beet. Hence, in this study, low (0.5 and 3 mmol/L; N0.5 and N3), moderate (5 mmol/L; N5; control) and high (10 and 12 mmol/L; N10 and N12) N were imposed to sugar beet to comparatively investigate the growth and physiological changes, and expression pattern of the gene involving ammonia transporting at different seedling stages. The results showed that, different from N5 which could induce maximum biomass of beet seedlings, low N was more likely to inhibit the growth of beet seedlings than high N treatments. Morphological differences and adverse factors increased significantly with extension of stress time, but sugar beet seedlings displayed a variety of physical responses to different N concentrations to adapt to N abnormal. At 14 d, the chlorophyll content, leaf and root surface area, total dry weight and nitrogen content of seedlings treated with N0.5 decreased 15.83%, 53.65%, 73.94%, 78.08% and 24.88% respectively, compared with N12; however, the root shoot ratio increased significantly as well as superoxide dismutase (SOD), peroxidase (POD), glutamine synthetase (GS) activity and malondialdehyde (MDA) and proline content, especially in root. The expression of BvAMT1.2 was also regulated in an N concentration-dependent manner, and was mainly involved in the tolerance of beet leaves to N stress, which significantly positively correlated to GS activity on the basis of its high affinity to N. It can be deduced that the stored nutrients under low N could only maintain relatively stable root growth, and faced difficulty in being transported to the shoots. Sugar beet was relatively resilient to N0.5 stress according to the mean affiliation function analysis. These results provide a theoretical basis for the extensive cultivation of sugar beet in N-stressed soil.

Genetic variation underlying differential ammonium and nitrate responses in Arabidopsis thaliana

Nitrogen is an essential element required for plant growth and productivity. Understanding the mechanisms and natural genetic variation underlying nitrogen use in plants will facilitate the engineering of plant nitrogen use to maximize crop productivity while minimizing environmental costs. To understand the scope of natural variation that may influence nitrogen use, we grew 1,135 Arabidopsis thaliana natural genotypes on two nitrogen sources, nitrate and ammonium, and measured both developmental and defense metabolite traits. By using different environments and focusing on multiple traits, we identified a wide array of different nitrogen responses. These responses are associated with numerous genes, most of which were not previously associated with nitrogen responses. Only a small portion of these genes appear to be shared between environments or traits, while most are predominantly specific to a developmental or defense trait under a specific nitrogen source. Finally, by using a large population, we were able to identify unique nitrogen responses, such as preferring ammonium or nitrate, which appear to be generated by combinations of loci rather than a few large-effect loci. This suggests that it may be possible to obtain novel phenotypes in complex nitrogen responses by manipulating sets of genes with small effects rather than solely focusing on large-effect single gene manipulations.

Cadmium promotes the absorption of ammonium in hyperaccumulator Solanum nigrum L. mediated by ammonium transporters and aquaporins

Cadmium (Cd) is a toxic heavy metal affecting the normal growth of plants. Nitrate (NO₃^-) and ammonium (NH₄⁺) are the primary forms of inorganic nitrogen (N) absorbed by plants. However, the mechanism of N absorption and regulation under Cd stress remains unclear. This study found that: (1) Cd treatment affected the biomass, root length, and Cd²⁺ flux in Solanum nigrum seedling roots. Specifically, 50 μM Cd significantly inhibited NO₃^- influx while increased NH₄⁺ influx compared with 0 and 5 μM Cd treatments measured by non-invasive micro-test technology. (2) qRT-PCR analysis showed that 50 μM Cd inhibited the expressions of nitrate transporter genes, SnNRT2;4 and SnNRT2;4-like, increased the expressions of ammonium transporter genes, SnAMT1;2 and SnAMT1;3, in the roots. (3) Under NH₄⁺ supply, 50 μM Cd significantly induced the expressions of the aquaporin genes, SnPIP1;5, SnPIP2;7, and SnTIP2;1. Our results showed that 50 μM Cd stress promoted NH₄⁺ absorption by up-regulating the gene expressions of NH₄⁺ transporter and aquaporins, suggesting that high Cd stress can affect the preference of N nutrition in S. nigrum.

Novel method for the quantification of rosette area from images of Arabidopsis seedlings grown on agar plates

PREMISE

The agar-based culture of Arabidopsis seedlings is widely used for quantifying root traits. Shoot traits are generally overlooked in these studies, probably because the rosettes are often askew. A technique to assess the shoot surface area of seedlings grown inside agar culture dishes would facilitate simultaneous root and shoot phenotyping.

METHODS

We developed an image processing workflow in Python that estimates rosette area of Arabidopsis seedlings on agar culture dishes. We validated this method by comparing its output with other metrics of seedling growth. As part of a larger study on genetic variation in plant responses to nitrogen form and concentration, we measured the rosette areas from more than 2000 plate images.

RESULTS

The rosette area measured from plate images was strongly correlated with the rosette area measured from directly overhead and moderately correlated with seedling mass. Rosette area in the large image set was significantly influenced by genotype and nitrogen treatment. The broad-sense heritability of leaf area measured using this method was 0.28.

DISCUSSION

These results indicated that this approach for estimating rosette area produces accurate shoot phenotype data. It can be used with image sets for which other methods of leaf area quantification prove unsuitable.

Phyto-Friendly Soil Bacteria and Fungi Provide Beneficial Outcomes in the Host Plant by Differently Modulating Its Responses through (In)Direct Mechanisms

Sustainable agricultural systems based on the application of phyto-friendly bacteria and fungi are increasingly needed to preserve soil fertility and microbial biodiversity, as well as to reduce the use of chemical fertilizers and pesticides. Although there is considerable attention on the potential applications of microbial consortia as biofertilizers and biocontrol agents for crop management, knowledge on the molecular responses modulated in host plants because of these beneficial associations is still incomplete. This review provides an up-to-date overview of the different mechanisms of action triggered by plant-growth-promoting microorganisms (PGPMs) to promote host-plant growth and improve its defense system. In addition, we combined available gene-expression profiling data from tomato roots sampled in the early stages of interaction with Pseudomonas or Trichoderma strains to develop an integrated model that describes the common processes activated by both PGPMs and highlights the host's different responses to the two microorganisms. All the information gathered will help define new strategies for the selection of crop varieties with a better ability to benefit from the elicitation of microbial inoculants.

Phytomelatonin and plant mineral nutrition

Plant mineral nutrition is critical for agricultural productivity and for human nutrition; however, the availability of mineral elements is spatially and temporally heterogeneous in many ecosystems and agricultural landscapes. Nutrient imbalances trigger intricate signalling networks that modulate plant acclimation responses. One signalling agent of particular importance in such networks is phytomelatonin, a pleiotropic molecule with multiple functions. Evidence indicates that deficiencies or excesses of nutrients generally increase phytomelatonin levels in certain tissues, and it is increasingly thought to participate in the regulation of plant mineral nutrition. Alterations in endogenous phytomelatonin levels can protect plants from oxidative stress, influence root architecture, and influence nutrient uptake and efficiency of use through transcriptional and post-transcriptional regulation; such changes optimize mineral nutrient acquisition and ion homeostasis inside plant cells and thereby help to promote growth. This review summarizes current knowledge on the regulation of plant mineral nutrition by melatonin and highlights how endogenous phytomelatonin alters plant responses to specific mineral elements. In addition, we comprehensively discuss how melatonin influences uptake and transport under conditions of nutrient shortage.

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

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

Ectopic Expression of Arabidopsis thaliana zDof1.3 in Tomato (Solanum lycopersicum L.) Is Associated with Improved Greenhouse Productivity and Enhanced Carbon and Nitrogen Use

A large collection of transgenic tomato lines, each ectopically expressing a different Arabidopsis thaliana transcription factor, was screened for variants with alterations in leaf starch. Such lines may be affected in carbon partitioning, and in allocation to the sinks. We focused on ‘L4080’, which harbored an A. thaliana zDof (DNA-binding one zinc finger) isoform 1.3 (AtzDof1.3) gene, and which had a 2−4-fold higher starch-to-sucrose ratio in source leaves over the diel (p < 0.05). Our aim was to determine whether there were associated effects on productivity. L4080 plants were altered in nitrogen (N) and carbon (C) metabolism. The N-to-C ratio was higher in six-week-old L4080, and when treated with 1/10 N, L4080 growth was less inhibited compared to the wild-type and this was accompanied by faster root elongation (p < 0.05). The six-week-old L4080 acquired 42% more dry matter at 720 ppm CO2, compared to ambient CO2 (p < 0.05), while the wild-type (WT) remained unchanged. GC-MS-TOF data showed that L4080 source leaves were enriched in amino acids compared to the WT, and at 49 DPA, fruit had 25% greater mass, higher sucrose, and increased yield (25%; p < 0.05) compared to the WT. An Affymetrix cDNA array analysis suggested that only 0.39% of the 9000 cDNAs were altered by 1.5-fold (p < 0.01) in L4080 source leaves. 14C-labeling of fruit disks identified potential differences in 14-DPA fruit metabolism suggesting that post-transcriptional regulation was important. We conclude that AtzDof1.3 and the germplasm derived therefrom, should be investigated for their ‘climate-change adaptive’ potential.

Target of rapamycin (TOR) regulates the response to low nitrogen stress via autophagy and hormone pathways in Malus hupehensis

Target of rapamycin (TOR) is a highly conserved master regulator in eukaryotes; it regulates cell proliferation and growth by integrating different signals. However, little is known about the function of TOR in perennial woody plants. Different concentrations of AZD8055 (an inhibitor of TOR) were used in this study to investigate the role of TOR in the response to low nitrogen (N) stress in the wild apple species Malus hupehensis. Low N stress inhibited the growth of M. hupehensis plants, and 1 μM AZD alleviated this effect. Plants supplied with 1 μM AZD had higher photosynthetic capacity, which promoted the accumulation of biomass, as well as higher contents of N and anthocyanins and lower content of starch. Exogenous application of 1 μM AZD also promoted the development of the root system. Plants supplied with at least 5 μM AZD displayed early leaf senescence. RNA-seq analysis indicated that TOR altered the expression of genes related to the low N stress response, such as genes involved in photosystem, starch metabolism, autophagy, and hormone metabolism. Further analysis revealed altered autophagy in plants supplied with AZD under low N stress; the metabolism of plant hormones also changed following AZD supplementation. In sum, our findings revealed that appropriate inhibition of TOR activated autophagy and jasmonic acid signaling in M. hupehensis, which allowed plants to cope with low N stress. Severe TOR inhibition resulted in the excessive accumulation of salicylic acid, which probably led to programmed cell death in M. hupehensis.

Root endophyte differentially regulates plant response to NO3- and NH4+ nutrition by modulating N fluxes at the plant-fungal interface

In the soil, plant roots associated with fungi often encounter uneven distribution of nitrate (NO₃^- )/ammonium (NH₄⁺ ) patches, but the mechanism underlying N form-influenced plant-fungal interactions remains limited. We inoculated Arabidopsis with a root endophyte Phomopsis liquidambaris, and evaluated the effects of P. liquidambaris on plant performance under NO₃^- or NH₄⁺ nutrition. Under NO₃^- nutrition, P. liquidambaris inoculation promoted seedling growth, whereas under NH₄⁺ nutrition, P. liquidambaris suppressed seedling growth. Under high NH₄⁺ conditions, fungus-colonized roots displayed increased NH₄⁺ accumulation and NH₄⁺ efflux, similar to the effect of ammonium stress caused by elevated NH₄⁺ levels. Notably, this fungus excluded NH₄⁺ during interactions with host roots, thereby leading to increased NH₄⁺ levels at the plant-fungal interface under high NH₄⁺ conditions. A nitrite reductase-deficient strain that excludes NO₃^- but absorbs NH₄⁺ , decreased NH₄⁺ levels in Arabidopsis shoots and rescued plant growth and nitrogen metabolism under high NH₄⁺ levels. Transcriptomic analysis highlighted that P. liquidambaris had altered transcriptional responses associated with plant response to inorganic N forms. Our results demonstrate that fungus-regulated NO₃^- /NH₄⁺ dynamics at the plant-fungal interface alters plant response to NO₃^- /NH₄⁺ nutrition. This study highlights the essential functions of root endophytes in plant adaptation to soil nitrogen nutrients.

Nitrogen Uptake, Use Efficiency, and Productivity of Nigella sativa L. in Response to Fertilization and Plant Density

Nigella sativa L. has been recognized as one of the most important medicinal plants in many parts of the world for centuries. The purpose of the current study was to evaluate the effects of fertilization and plant density on nitrogen uptake, utilization efficiency, and productivity of N. sativa under Mediterranean conditions. The three-year experiment was set up in a split-plot design with three replications. There were 2 plant densities; 200 and 300 plants m−2 with 4 fertilization levels: control, seaweed compost, farmyard manure and inorganic fertilizer. The highest seed yield (749–840 kg ha−1) was found in plants subjected to low-density and inorganic fertilization. The seed nitrogen (N) uptake as well as the nitrogen harvest index (NHI) were positively affected by the increase of available nitrogen and negatively by the increase of plant density, with their highest values recorded in the low-density and inorganic fertilization. In conclusion, plant densities greater than 200 plants m−2 result in higher crop growth but lower seed yield and decreased nitrogen uptake and use efficiency in N. sativa seeds, whereas the application of inorganic fertilizers increases crop yield, nitrogen uptake, and utilization efficiency because these fertilizers present higher nitrogen levels with higher solubility and thus faster availability for the crop in comparison with organic fertilizers.

Ammonium has stronger Cd detoxification ability than nitrate by reducing Cd influx and increasing Cd fixation in Solanum nigrum L

Cadmium (Cd) is a harmful heavy metal that affects the growth and development of plants. Nitrogen (N) is an essential nutrient for plants, and appropriate N management can improve Cd tolerance. The aim of our study was to explore the effects of different forms of N on the molecular and physiological responses of the hyperaccumulator Solanum nigrum to Cd toxicity. Measurement of biomass, photosynthetic parameters, and Cd²⁺ fluxes using non-invasive micro-test technique, Cd fluorescent dying, biochemical methods and quantitative real-time PCR analysis were performed in our study. Our results showed that ammonium (NH₄⁺) has stronger Cd detoxification ability than nitrate (NO₃^-), which are likely attributed to the following three reasons: (1) NH₄⁺ decreased the influx and accumulation of Cd²⁺ by regulating the transcription of Cd transport-related genes; (2) the ameliorative effects of NH₄⁺ were accompanied by the increased retention of Cd in the cell walls of roots; and (3) NH₄⁺ up-regulated SnExp expression.

Genome assembly of alfalfa cultivar zhongmu-4 and identification of SNPs associated with agronomic traits

Alfalfa (Medicago sativa L.) is the most important legume forage crop worldwide with high nutritional value and yield. For a long time, the breeding of alfalfa was hampered by lacking reliable information on the autotetraploid genome and molecular markers linked to important agronomic traits. We herein reported the de novo assembly of the allele-aware chromosome-level genome of Zhongmu-4, a cultivar widely cultivated in China, and a comprehensive database of genomic variations based on resequencing of 220 germplasms. Approximate 2.74 Gb contigs (N50 of 2.06 Mb), accounting for 88.39% of the estimated genome, were assembled, and 2.56 Gb contigs were anchored to 32 pseudo-chromosomes. A total of 34,922 allelic genes were identified from the allele-aware genome. We observed the expansion of gene families, especially those related to the nitrogen metabolism, and the increase of repetitive elements including transposable elements, which probably resulted in the increase of Zhongmu-4 genome compared with Medicago truncatula. Population structure analysis revealed that the accessions from Asia and South America had relatively lower genetic diversity than those from Europe, suggesting that geography may influence alfalfa genetic divergence during local adaption. Genome-wide association studies identified 101 single nucleotide polymorphisms (SNPs) associated with 27 agronomic traits. Two candidate genes were predicted to be correlated with fall dormancy and salt response. We believe that the allele-aware chromosome-level genome sequence of Zhongmu-4 combined with the resequencing data of the diverse alfalfa germplasms will facilitate genetic research and genomics-assisted breeding in variety improvement of alfalfa.

Knockdown of OsNRT2.4 modulates root morphology and alters nitrogen metabolism in response to low nitrate availability in rice

The expression patterns of the NRT2 genes have been well described; however, the role of OsNRT2.4 in root growth is not well known. In this study, we thus aimed at investigating the role of high-affinity NO3- transport OsNRT2.4 in root growth modulation. Through the amiRNA-mediated gene silencing technique, we successfully obtained osnrt2.4 knockdown lines to study the role of OsNRT2.4 on root growth under low nitrate conditions. We performed real-time PCR analysis to investigate the relative gene expression level in root and shoot, soluble metabolites, and measurement of root system. Knockdown of OsNRT2.4 decreased rice growth. The comparison with wild-type (WT) plants showed that (i) knockdown of OsNRT2.4 inhibited root formation under low NO3- supply; (ii) we demonstrated that the mutant lines had significantly increased NO3- uptake than WT plants when grown in different nitrate supplies; (iii) osnrt2.4 knockdown lines showed an alteration in nitrogen metabolism, and this affected the root growth; and (iv) the downregulation of OsNRT2.4 enhanced the expression of gene response of low external NO3- concentrations. Herein we provide new insights in OsNRT2.4 functions. Our data demonstrated that OsNRT2.4 plays a role in root growth, nitrogen metabolic pathway and probably have functions in nitrate transport from root to shoot under low nitrate availability in rice.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-021-01273-6.

The Dynamics of NO3- and NH4+ Uptake in Duckweed Are Coordinated with the Expression of Major Nitrogen Assimilation Genes

Duckweed plants play important roles in aquatic ecosystems worldwide. They rapidly accumulate biomass and have potential uses in bioremediation of water polluted by fertilizer runoff or other chemicals. Here we studied the assimilation of two major sources of inorganic nitrogen, nitrate (NO3- ) and ammonium (NH4+), in six duckweed species: Spirodela polyrhiza, Landoltia punctata, Lemna aequinoctialis, Lemna turionifera, Lemna minor, and Wolffia globosa. All six duckweed species preferred NH4+ over NO3- and started using NO3- only when NH4+ was depleted. Using the available genome sequence, we analyzed the molecular structure and expression of eight key nitrogen assimilation genes in S. polyrhiza. The expression of genes encoding nitrate reductase and nitrite reductase increased about 10-fold when NO3- was supplied and decreased when NH4+ was supplied. NO3- and NH4+ induced the glutamine synthetase (GS) genes GS1;2 and the GS2 by 2- to 5-fold, respectively, but repressed GS1;1 and GS1;3. NH4+ and NO3- upregulated the genes encoding ferredoxin- and NADH-dependent glutamate synthases (Fd-GOGAT and NADH-GOGAT). A survey of nitrogen assimilation gene promoters suggested complex regulation, with major roles for NRE-like and GAATC/GATTC cis-elements, TATA-based enhancers, GA/CTn repeats, and G-quadruplex structures. These results will inform efforts to improve bioremediation and nitrogen use efficiency.

Wheat grain yield decreased over the past 35 years, but protein content did not change

The extent to which rising atmospheric CO2 concentration has already influenced food production and quality is uncertain. Here, we analyzed annual field trials of autumn-planted common wheat in California from 1985 to 2019, a period during which the global atmospheric CO2 concentration increased 19%. Even after accounting for other major factors (cultivar, location, degree-days, soil temperature, total water applied, nitrogen fertilization, and pathogen infestation), wheat grain yield and protein yield declined 13% over this period, but grain protein content did not change. These results suggest that exposure to gradual CO2 enrichment over the past 35 years has adversely affected wheat grain and protein yield, but not grain protein content.

Nitrate Regulates Maize Root Transcriptome through Nitric Oxide Dependent and Independent Mechanisms

Maize root responds to nitrate by modulating its development through the coordinated action of many interacting players. Nitric oxide is produced in primary root early after the nitrate provision, thus inducing root elongation. In this study, RNA sequencing was applied to discover the main molecular signatures distinguishing the response of maize root to nitrate according to their dependency on, or independency of, nitric oxide, thus discriminating the signaling pathways regulated by nitrate through nitric oxide from those regulated by nitrate itself of by further downstream factors. A set of subsequent detailed functional annotation tools (Gene Ontology enrichment, MapMan, KEGG reconstruction pathway, transcription factors detection) were used to gain further information and the lateral root density was measured both in the presence of nitrate and in the presence of nitrate plus cPTIO, a specific NO scavenger, and compared to that observed for N-depleted roots. Our results led us to identify six clusters of transcripts according to their responsiveness to nitric oxide and to their regulation by nitrate provision. In general, shared and specific features for the six clusters were identified, allowing us to determine the overall root response to nitrate according to its dependency on nitric oxide.

The rapeseed genotypes with contrasting NUE response discrepantly to varied provision of ammonium and nitrate by regulating photosynthesis, root morphology, nutritional status, and oxidative stress response

Ammonium (NH₄⁺) and nitrate (NO₃^-) are the two predominant inorganic nitrogen (N) forms available to crops in agricultural soils. However, little is known about how the NH₄⁺:NO₃^- ratio affect the growth of Brassica napus. Here, we investigated the impact of five NH₄⁺:NO₃^- ratios (100:0, 75:25, 50:50, 25:75, 0:100) on plant growth, photosynthesis, root morphology, ammonium uptake, nutritional status, oxidative stress response, and relative expression of genes involved in these processes in two rapeseed genotypes with contrasting N use efficiency (NUE). Application of NO₃^- as a N source extremely improved rapeseed growth compare to NH₄⁺. However, the best growth of the N-inefficient genotype was observed under 75:25 NH₄⁺/NO₃^- ratio, while it happens for the N-efficient genotype only under the sole NO₃^- environment. The low-NUE genotype exhibited a more developed root system, higher photosynthetic capacity, higher nutrient accumulation, and better NH₄⁺ uptake ability under the 75:25 NH₄⁺/NO₃^- ratio, resulting in a decrease of malondialdehyde (MDA) in root. However, the high-NUE genotype performed better in the above aspects under the NO₃^--only condition. Nitrate decrease MDA by reducing the activities of superoxide dismutase, peroxidase, and catalase in root of the N-efficient genotype. Moreover, significant differences were detected for the expression levels of genes involved in N uptake and oxidative stress response between the two genotypes under two NH₄⁺/NO₃^- ratios. Taken together, our results indicate that the N-inefficient rapeseed genotype prefers mixed supply of ammonium and nitrate, whereas the genotype with high NUE prefers sole nitrate environment.

Cytokinin Regulation of Source-Sink Relationships in Plant-Pathogen Interactions

Cytokinins are plant hormones known for their role in mediating plant growth. First discovered for their ability to promote cell division, this class of hormones is now associated with many other cellular and physiological functions. One of these functions is the regulation of source-sink relationships, a tightly controlled process that is essential for proper plant growth and development. As discovered more recently, cytokinins are also important for the interaction of plants with pathogens, beneficial microbes and insects. Here, we review the importance of cytokinins in source-sink relationships in plants, with relation to both carbohydrates and amino acids, and highlight a possible function for this regulation in the context of plant biotic interactions.

Effects of the Denitrification Inhibitor "Procyanidins" on the Diversity, Interactions, and Potential Functions of Rhizosphere-Associated Microbiome

Some plant secondary metabolites, such as procyanidins, have been demonstrated to cause biological denitrification inhibition (BDI) of denitrifiers in soils concomitantly with a gain in plant biomass. The present work evaluated whether procyanidins had an impact on the diversity of nontarget microbial communities that are probably involved in soil fertility and ecosystem services. Lettuce plants were grown in two contrasting soils, namely Manziat (a loamy sand soil) and Serail (a sandy clay loam soil) with and without procyanidin amendment. Microbial diversity was assessed using Illumina sequencing of prokaryotic 16S rRNA gene and fungal ITS regions. We used a functional inference to evaluate the putative microbial functions present in both soils and reconstructed the microbial interaction network. The results showed a segregation of soil microbiomes present in Serail and Manziat that were dependent on specific soil edaphic variables. For example, Deltaproteobacteria was related to total nitrogen content in Manziat, while Leotiomycetes and Firmicutes were linked to Ca2+ in Serail. Procyanidin amendment did not affect the diversity and putative activity of microbial communities. In contrast, microbial interactions differed according to procyanidin amendment, with the results showing an enrichment of Entotheonellaeota and Mucoromycota in Serail soil and of Dependentiae and Rozellomycetes in Manziat soil.

Elevated atmospheric CO2 concentration triggers redistribution of nitrogen to promote tillering in rice

Elevated atmospheric CO₂ concentration (eCO₂) often reduces nitrogen (N) content in rice plants and stimulates tillering. However, there is a general consensus that reduced N would constrain rice tillering. To resolve this contradiction, we investigated N distribution and transcriptomic changes in different rice plant organs after subjecting them to eCO₂ and different N application rates. Our results showed that eCO₂ significantly promoted rice tillers (by 0.6, 1.1, 1.7, and 2.1 tillers/plant at 0, 75, 150, and 225 kg N ha^-1 N application rates, respectively) and more tillers were produced under higher N application rates, confirming that N availability constrained tillering in the early stages of growth. Although N content declined in the leaves (-11.0 to -20.7 mg g^-1) and sheaths (-9.8 to -28.8 mg g^-1) of rice plants exposed to eCO₂, the N content of newly emerged tillers on plants exposed to eCO₂ equaled or exceeded the N content of tillers produced under ambient CO₂ conditions. Apparently, the redistribution of N within the plant per se was a critical adaptation strategy to the eCO₂ condition. Transcriptomic analysis revealed that eCO₂ induced less extensive alteration of gene expression than did N application. Most importantly, the expression levels of multiple N-related transporters and receptors such as nitrate transporter NRT2.3a/b and NRT1.1a/b were differentially regulated in leaf and shoot apical meristem, suggesting that multiple genes were involved in sensing the N signal and transporting N metabolites to adapt to eCO₂. The redistribution of N in different organs could be a universal adaptation strategy of terrestrial plants to eCO₂.

Photorespiration: The Futile Cycle?

Photorespiration, or C₂ photosynthesis, is generally considered a futile cycle that potentially decreases photosynthetic carbon fixation by more than 25%. Nonetheless, many essential processes, such as nitrogen assimilation, C₁ metabolism, and sulfur assimilation, depend on photorespiration. Most studies of photosynthetic and photorespiratory reactions are conducted with magnesium as the sole metal cofactor despite many of the enzymes involved in these reactions readily associating with manganese. Indeed, when manganese is present, the energy efficiency of these reactions may improve. This review summarizes some commonly used methods to quantify photorespiration, outlines the influence of metal cofactors on photorespiratory enzymes, and discusses why photorespiration may not be as wasteful as previously believed.

Nitrogen forms and metabolism affect plant defence to foliar and root pathogens in tomato

Nitrogen (N) influences a myriad of physiological processes while its effects on plant defences and the underlying mechanisms are largely unknown. Here, the interaction between tomato and pathogens was examined under four N regimes (sole NO₃^- or mixed NO₃^- /NH₄⁺ of total 1 and 7 mM N, denoting low and high N regimes, respectively) followed by inoculation with two bacterial pathogens, Pseudomonas syringae and Ralstonia solanacearum. Tomato immunity against both pathogens was generally higher under low N as well as NO₃^- as the sole N source. The disease susceptibility was reduced by silencing N metabolism genes such as NR, NiR and Fd-GOGAT, while increased in NiR1-overexpressed plants. Further studies demonstrated that the N-modulated defence was dependent on the salicylic acid (SA) defence pathway. Low N as well as the silencing of N metabolism genes increased the SA levels and transcripts of its maker genes, and low N-enhanced defence was blocked in NahG transgenic tomato plants that do not accumulate SA, while exogenous SA application attenuated the susceptibility of OE-NiR1. The study provides insights into the mechanisms of how nitrogen fertilization and metabolism affect plant immunity in tomato, which might be useful for designing effective agronomic strategies for the management of N supply.

Paraburkholderia phymatum Homocitrate Synthase NifV Plays a Key Role for Nitrogenase Activity during Symbiosis with Papilionoids and in Free-Living Growth Conditions

Homocitrate is an essential component of the iron-molybdenum cofactor of nitrogenase, the bacterial enzyme that catalyzes the reduction of dinitrogen (N₂) to ammonia. In nitrogen-fixing and nodulating alpha-rhizobia, homocitrate is usually provided to bacteroids in root nodules by their plant host. In contrast, non-nodulating free-living diazotrophs encode the homocitrate synthase (NifV) and reduce N₂ in nitrogen-limiting free-living conditions. Paraburkholderia phymatum STM815 is a beta-rhizobial strain, which can enter symbiosis with a broad range of legumes, including papilionoids and mimosoids. In contrast to most alpha-rhizobia, which lack nifV, P. phymatum harbors a copy of nifV on its symbiotic plasmid. We show here that P. phymatum nifV is essential for nitrogenase activity both in root nodules of papilionoid plants and in free-living growth conditions. Notably, nifV was dispensable in nodules of Mimosa pudica despite the fact that the gene was highly expressed during symbiosis with all tested papilionoid and mimosoid plants. A metabolome analysis of papilionoid and mimosoid root nodules infected with the P. phymatum wild-type strain revealed that among the approximately 400 measured metabolites, homocitrate and other metabolites involved in lysine biosynthesis and degradation have accumulated in all plant nodules compared to uninfected roots, suggesting an important role of these metabolites during symbiosis.

Nitrogen Uptake in Plants: The Plasma Membrane Root Transport Systems from a Physiological and Proteomic Perspective

Nitrogen nutrition in plants is a key determinant in crop productivity. The availability of nitrogen nutrients in the soil, both inorganic (nitrate and ammonium) and organic (urea and free amino acids), highly differs and influences plant physiology, growth, metabolism, and root morphology. Deciphering this multifaceted scenario is mandatory to improve the agricultural sustainability. In root cells, specific proteins located at the plasma membrane play key roles in the transport and sensing of nitrogen forms. This review outlines the current knowledge regarding the biochemical and physiological aspects behind the uptake of the individual nitrogen forms, their reciprocal interactions, the influences on root system architecture, and the relations with other proteins sustaining fundamental plasma membrane functionalities, such as aquaporins and H⁺-ATPase. This topic is explored starting from the information achieved in the model plant Arabidopsis and moving to crops in agricultural soils. Moreover, the main contributions provided by proteomics are described in order to highlight the goals and pitfalls of this approach and to get new hints for future studies.

Stable isotope analyses of nitrogen source and preference for ammonium versus nitrate of riparian plants during the plant growing season in Taihu Lake Basin

Plants are vital components of the nitrogen (N) cycling in the riparian zones. Understanding of N uptake strategies of riparian plants, including N sources and preference in N forms (ammonium (NH₄⁺) vs. nitrate (NO₃^-)), is essential to advance our knowledge on the role that plants play in regulating nutrient biogeochemical cyclings in the riparian areas. In this study, stable N isotopes (δ¹⁵N) of three riparian plants, including Acorus calamus, Canna indica and Phragmites australis, and the δ¹⁵N of NH₄⁺ and NO₃^- in different sources were measured during the plant growing season (June-September) in the Taihu Lake Basin. The dissolved inorganic N (DIN) from river water, groundwater, rainwater and soil were considered as the major N sources for plants in the riparian ecosystem. Our results indicated that soil was the largest source for plant N nutrition, with significantly different (P < 0.05) contributions from soil observed among plant species (80.5 ± 4.1, 73.9 ± 2.8 and 58.7 ± 6.1% for A. calamus, C. indica, and P. australis, respectively). Meanwhile, complex water networks, shallow water tables, and high DIN content in rainwater lead to nonignorable N contributions from river water, groundwater and rainwater to plants. Groundwater contributed more percentage of N to P. australis (12.8 ± 3.2%) than A. calamus (6.1 ± 1.9%) and C. indica (8.0 ± 1.5%), which is likely attributed to the deeper roots of P. australis. All plants showed similar N preference for NO₃^- during the growing season. External environmental conditions and plant characteristics and adaption to more abundant soil NO₃^- content are possible explanations. Our research could provide important information for vegetation selections during the process of riparian ecological restoration. Reasonable choice of vegetation is essential to plant growth and water quality management, especially in agricultural watersheds where N concentrations are relatively high in agricultural runoff due to the wide uses of N fertilizers.

Treated wastewater reuse for irrigation: Pros and cons

The appropriateness of using treated wastewater for crop or agricultural irrigation remains a bone of contention among experts and policymakers. Here, we outline and analyze not only the benefits but also the drawbacks of such a practice in order to suggest a way forward. To ensure that our review reflects the state-of-the-art in terms of technological advances and best practices, only literature published in the last decade is considered except for literature on the history of reuse. The review begins by highlighting growing water scarcity, the history of wastewater reuse in agriculture, and the limitations of existing studies. A short overview of the approach used in the write-up is outlined after the introduction. It then proceeds with an in-depth look at three broad areas: environmental impacts, public health impacts, and economic impacts. In terms of environmental impacts, effects on soil quality, water resources, plant growth, and soil microbial communities are analyzed. For each sub-area, the positive effects are described before the negative ones. The same approach is then applied to public health impacts, the focus of which is on human exposure to heavy metals and pathogens, and economic impacts, which are assessed with particular reference to investment cost, financial benefit to wastewater treatment plants (WWTPs), farm expenditure and income. Having weighed the advantages and disadvantages in each area, innovative measures are proposed for optimizing the benefits and mitigating the drawbacks of using treated wastewater for crop irrigation. Special consideration was given to contaminants of emerging concern and the known or perceived environmental and health risks associated with these contaminants.