Recent Advances in Carbon and Nitrogen Metabolism in C3 Plants

Proline Tagging for Stress Tolerance in Plants

In environments with high levels of stress conditions, plants accumulate various metabolic products under stress conditions. Among these products, amino acids have a cardinal role in supporting and maintaining plant developmental processes. The increase in proline content and stress tolerance in plants has been found optimistic, suggesting the importance of proline in mitigating stress through osmotic adjustments. Exogenous application and pretreatment of plants with proline increase growth and development under various stressful conditions, but excessive proline has negative influence on growth. Proline has two biosynthetic routes: glutamate or the ornithine pathway, and whether plants synthesize proline by glutamate or ornithine precursors is still debatable as relatively little is known about it. Plants have the innate machinery to synthesize proline from both pathways, but the switch of a particular pathway under which it can be activated and deactivated depends upon various factors. Therefore, in this review, we elucidate the importance of proline in stress mitigation; the optimal amount of proline required for maximum benefit; levels at which it inhibits the growth, conditions, and factors that regulate proline biosynthesis; and lastly, how we can benefit from all these answers to obtain better stress tolerance in plants.

Nanotechnology in Plant Nanobionics: Mechanisms, Applications, and Future Perspectives

Plants are vital to ecosystems and human survival, possessing intricate internal and inter-plant signaling networks that allow them to adapt quickly to changing environments and maintain ecological balance. The integration of engineered nanomaterials (ENMs) with plant systems has led to the emergence of plant nanobionics, a field that holds the potential to enhance plant capabilities significantly. This integration may result in improved photosynthesis, increased nutrient uptake, and accelerated growth and development. Plants treated with ENMs can be stress mitigators, pollutant detectors, environmental sensors, and even light emitters. This review explores recent advancements in plant nanobionics, focusing on nanoparticle (NP) synthesis, adhesion, uptake, transport, fate, and application in enhancing plant physiological functioning, stress mitigation, plant health monitoring, energy production, environmental sensing, and overall plant growth and productivity. Potential research directions and challenges in plant nanobionics are highlighted, and how material optimization and innovation are propelling the growth in the field of smart agriculture, pollution remediation, and energy/biomass production are discussed.

Exploring Plant Resilience Through Secondary Metabolite Profiling: Advances in Stress Response and Crop Improvement

The metabolome, encompassing small molecules within organisms, provides critical insights into physiology, environmental influences, and stress responses. Metabolomics enables comprehensive analysis of plant metabolites, uncovering biomarkers and mechanisms underlying stress adaptation. Regulatory genes such as MYB and WRKY are central to secondary metabolite synthesis and environmental resilience. By integrating metabolomics with genomics, researchers can explore stress-related pathways and advance crop improvement efforts. This review examines metabolomic profiling under stress conditions, emphasizing drought tolerance mechanisms mediated by amino acids and organic acids. Additionally, it highlights the shikimate pathway's pivotal role in synthesizing amino acids and secondary metabolites essential for plant defense. These insights contribute to understanding metabolic networks that drive plant resilience, informing strategies for agricultural sustainability.

Dynamic proteome and acetylome profiling reveals key regulators of sucrose accumulation in sugarcane

KEY MESSAGE

Lysine acetylation and protein abundance both play crucial roles in regulating sucrose accumulation in sugarcane, with 73 dual-function proteins identified as potential targets for molecular breeding to enhance sucrose levels. Lysine acetylation plays a crucial role in regulating various biological processes in plants, but its role in sucrose accumulation in sugarcane remains unexplored In this study, we conducted a comprehensive quantitative proteome and acetylated proteome analysis on the leaves of two sugarcane genotypes with high and low sucrose levels at early, middle, and late stages of sucrose accumulation. Quantitative proteome analysis identified 2363 differentially abundant proteins (DAPs), of which 165 were associated with sugar metabolism pathways, providing more targets for improving sucrose content in sugarcane. The acetylated proteome analysis identified 1397 differentially acetylated proteins (DAcPs) with 2377 acetylation sites. Many DAcPs were also involved in sugar metabolism, demonstrating that lysine acetylation is associated with sucrose accumulation. A comparison of the DAPs and DAcPs identified 650 overlapping proteins, with 73 of them related to sugar metabolism, confirming dual regulatory roles of protein abundance and acetylation in sucrose accumulation in sugarcane. These 73 proteins serve as targets for sucrose improvement with dual regulatory effects. Our data also suggest that histone acetylation and nitrogen metabolism may be related to sucrose accumulation. This work enhances our understanding of the mechanisms regulating sucrose accumulation and proposes targets for improving sucrose content in sugarcane through molecular breeding.

Multi-Omics and Physiological Analysis Reveal Crosstalk Between Aphid Resistance and Nitrogen Fertilization in Wheat

The availability of nitrogen (N) can dramatically influence crops resistance to herbivorous insects. However, the interaction between N fertilization and crop resistance to insects is not well understood. In this study, the effects of N fertilization on the grain aphid (Sitobion miscanthi) were investigated using three wheat (Triticum aestivum) cultivars with different aphid resistances. We measured aphid life cycle parameters, fecundity, survival rate, weight and feeding behavior, in conjunction with wheat metabolomics, transcriptomics and alien introgression analysis. Our results demonstrated that higher N application benefits aphid feeding across all three wheat cultivars. We also reveal that the highly resistant cultivar (ZM9) can only exert its resistance-advantage under low N fertilization, losing its advantage compared to moderately resistant cultivar YN19 and susceptible cultivar YN23 under higher N fertilization. The effects of N fertilization on wheat-aphid interactions were due to changes in the regulation of carbon and nitrogen metabolism. Integration of multi-omics highlighted specific aphid-induced differentially expressed genes (DEGs, e.g., TUB6, Tubulin 6; ENODL20, Early nodulin-like protein 20; ACT7 Actin 7; Prx47, Peroxidase 47) and significantly different metabolites (SDMs, e.g., crotonoside, guanine, 2'-O-methyladenosine, ferulic acid) in ZM9. Additionally, we report the unique SDMs-DEGs interactions, associated with introgression during wheat domestication, may help infer aphid resistance. In summary, this study provides new insights into the relationships between N fertilization practices, defense responses and integrated pest management for sustainable wheat production.

Genome-wide analysis of Q binding reveals a regulatory network that coordinates wheat grain yield and grain protein content

Wheat is an important cereal crop used to produce diverse and popular food worldwide because of its high grain yield (GY) and grain protein content (GPC). However, GY and GPC are usually negatively correlated. We previously reported that favorable alleles of the wheat domestication gene Q can synchronously increase GY and GPC, but the underlying mechanisms remain largely unknown. In this study, we investigated the regulatory network involving Q associated with GY and GPC in young grains through DNA affinity purification sequencing and transcriptome sequencing analyses, electrophoretic mobility shift and dual-luciferase assays, and transgenic approaches. Three Q-binding motifs, namely TTAAGG, AAACA[A/T]A, and GTAC[T/G]A, were identified. Notably, genes related to photosynthesis or carbon and nitrogen metabolism were enriched and regulated by Q. Moreover, Q was revealed to bind directly to its own gene and the glutamine synthetase gene TaGSr-4D to increase expression, thereby influencing nitrogen assimilation during the grain filling stage and increasing GPC. Considered together, our study findings provide molecular evidence of the positive regulatory effects of Q on wheat GY and GPC.

Mitigating low-temperature stress in alfalfa by postponing phosphorus application and remodeling of antioxidant activities and carbon-nitrogen metabolism

Low-temperature stress has become a major limiting factor for the sustainable production of forage crops and animal husbandry. This experimental study evaluated the effects of optimizing phosphorus application on the antioxidant properties and carbon-nitrogen metabolism physiology of alfalfa (Medicago sativa L.) under LT stress, aiming to provide a reference for efficient stress-resistant alfalfa production. In this study, the LT tolerant cultivar 'Caoyuan' (CY) and LT sensitive cultivar 'Xinmu' (XM) were used as plant materials, and the physiological changes of alfalfa plants under natural temperature (NT) and LT were compared under traditional phosphorus application (R1) and postponing phosphorus application (R2) treatments. The results showed that LT stress increased the accumulation of malondialdehyde (MDA) in alfalfa plants and inhibited root activity, carbon metabolism, and photosynthesis in both cultivars. The negative impacts of LT are more prevalent in XM than in CY. The postponing phosphorus application treatments enhanced root vitality as compared to the traditional phosphorus application treatments and accumulated more soluble sugar (5.6-11.2%), sucrose (8.5-14.0%), proline (7.5-11.7%), and soluble protein (8.3-11.7%) by increasing the enzyme activities related to carbon-nitrogen metabolism. Under postponing phosphorus application treatments, the enzymatic activities of antioxidants and regulation of osmotic sub-stances significantly increased in the leaves, MDA contents were decreased by 4.6-7.6%, and chlorophyll contents were increased by 4.8-8.6%, the net photosynthetic rate in alfalfa leaves increased by 5.1-7.5%. Besides, plant dry weight, root dry weight, and plant phosphorus concentration increased by 5.8-16.9%, 7.8-21.0%, and 5.1-9.9% under postponing phosphorus application treatments. In summary, split-phosphorus fertilization improved the nutrient absorption capacity of alfalfa roots compared to traditional phosphorus application treatments under LT stress. Moreover, it improved the carbon-nitrogen metabolism physiology and photosynthetic production capacity of the alfalfa plants, thus reducing the adverse effects of LT stress on the growth and development of alfalfa.

Integrating vermicompost, black soldier fly, and inorganic fertilizers enhances corn growth and yield

To achieve good agricultural practices and maximize the economic yield of corn, farmers should reduce the use of inorganic fertilizers. A field experiment was conducted in the Chonnabot district, Khon Kaen province, Thailand, during the 2022 and 2023 growing seasons. The aim was to assess the impact of different organic fertilizers and their combinations on the growth and yield of commercial sweet corn (Zea mays L. saccharata) and waxy corn (Zea mays L. var. ceratina) hybrids. The results showed that sweet corn had significantly higher ear fresh weight, protein, fat, and fiber content compared to waxy corn, with values of 7,529.20 kg ha-1, 14.48 %, 4.74 %, and 1.30 %, respectively. Two treatments, F4 (190.63 kg N ha-1 + 46.88 kg P ha-1 + 46.88 kg K ha-1) and F3 (6,250 kg ha-1 of black soldier fly (BSF) + 95.31 kg N ha-1 + 23.44 kg P ha-1 + 23.44 kg K ha-1) resulted in the highest ear fresh weight, with 6,569.90 and 6,275.40 kg ha-1, respectively. In contrast, F4 showed higher protein (12.04 %), fat (4.62 %), and fiber content (0.91 %) than F3. Significant improvements were observed in SPAD value, biomass, and yield parameters. Corn plants treated with a combination of vermicompost, BSF, and inorganic fertilizer showed higher ear length, ear diameter, ear fresh weight, and dry biomass than control plants (no fertilizer management, F1). The F1 treatment led to higher carbohydrate content in both corn cultivars tested, with a notable impact on pink waxy corn (82.06 %). Our findings suggest that using a combination of BSF and inorganic fertilizers is promising for reducing the use of inorganic fertilizers and providing the highest net income among the three fresh corn cultivars. Pink waxy corn showed greater adaptability under low soil fertility conditions owing to better yield components than purple waxy corn when evaluated without fertilizers.

Combined Transcriptomics and Metabolomics Uncover the Potential Mechanism of Plant Growth-Promoting Rhizobacteria on the Regrowth of Leymus chinensis After Mowing

Mowing significantly influences nutrient cycling and stimulates metabolic adjustments in plants to promote regrowth. Plant growth-promoting rhizobacteria (PGPR) are crucial for enhancing plant growth, nutrient absorption, and stress resilience; however, whether inoculation with PGPR after mowing can enhance plant regrowth capacity further, as well as its specific regulatory mechanisms, remains unexplored. In this study, PGPR Pantoea eucalyptus (B13) was inoculated into mowed Leymus chinensis to evaluate its effects on phenotypic traits, root nutrient contents, and hormone levels during the regrowth process and to further explore its role in the regrowth of L. chinensis after mowing. The results showed that after mowing, root nutrient and sugar contents decreased significantly, while the signal pathways related to stress hormones were activated. This indicates that after mowing, root resources tend to sacrifice a part of growth and prioritize defense. After mowing, B13 inoculation regulated the plant's internal hormone balance by reducing the levels and signal of JA, SA, and ABA and upregulated the signal transduction of growth hormones in the root, thus optimizing growth and defense in a mowing environment. Transcriptomic and metabolomic analyses indicated that B13 promoted nutrient uptake and transport in L. chinensis root, maintained hormone homeostasis, enhanced metabolic pathways related to carbohydrates, energy, and amino acid metabolism to cope with mowing stress, and promoted root growth and regeneration of shoot. This study reveals the regenerative strategy regulated by B13 in perennial forage grasses, helping optimize resource utilization, increase yield, and enhance grassland stability and resilience.

Biodegradable and conventional mulches inhibit nitrogen fixation by peanut root nodules - potentially related to microplastics in the soil

Mulching has been demonstrated to improve the soil environment and promote plant growth. However, the effects of mulching and mulch-derived microplastics (MPs) on nitrogen fixation by root nodules remain unclear. In this study, we investigated the effects of polyethylene (PE) and polylactic acid-polybutylene adipate-co-terephthalate (PLA-PBAT) film mulching on nitrogen fixation by root nodules after 4 years of continuous mulching using 15N tracer technology. Additionally, we examined the relationship between nitrogen fixation and MPs. We found a reduction in the proportion of nitrogen fixation by nodules (54.3 %-58.7 %) due to mulching. This decrease may be attributed to reduced dinitrogenase activity and flavonoid content at the seedling stage caused by mulching, and mulching with PLA-PBAT films significantly decreased the abundance of Bradyrhizobium at maturity. Furthermore, combined analysis of nitrogen-fixing bacteria (nifH) and metabolomes indicated that N-lauroylethanolamine may act as a regulatory signal influencing the root nodule nitrogen fixation process and that mulching resulted in significant changes in its content. The mantel test and PLS-PM suggest that microplastic from mulching may harm root nodule nitrogen fixation. This study reveals the influence of mulching on plant nitrogen uptake and the potential threat of mulch-derived microplastics, with a special focus on root nodule nitrogen fixation.

Chitosan nanoparticles alleviate chromium toxicity by modulating metabolic homeostasis and promoting chromium sequestration in Zea mays L

Chitosan nanoparticles (CSNPs) have been proposed as a potential alternative in alleviating chromium (Cr) toxicity. However, the mechanisms underlying remains poorly understood. This study investigates the effects of CSNPs on carbon/nitrogen metabolism, cell wall Cr binding capacity, and antioxidant activity in Zea mays L. under Cr stress. Cr stress decreased the total dry weight (DW) by 48.5 %. By contrast, the total DW was reduced by only 26.2 % in CSNPs-treated plants. Analysis of transcriptomic, enzyme activity, and metabolite content data, CSNPs-treated plants exhibited a higher level of relatively stable Carbon and Nitrogen metabolism than untreated plants. CSNPs application resulted in a substantial increase in the levels of sucrose and soluble protein by 78.0 % and 19.4 % in the leaves, and 60.0 % and 59.7 % in the roots, respectively. Meanwhile, CSNPs increased the contents of glutathione, phytochelatin, and cell wall polysaccharide. This increase resulted in a higher retention of Cr in vacuole and cell wall. Additionally, CSNPs alleviated the oxidative damage by improving antioxidant activity. Overall, our results suggest that CSNPs alleviates Cr toxicity by modulating metabolic homeostasis and promoting Cr sequestration in maize plants. This study provides new insights into the mechanisms underlying CSNPs-mediated Cr stress response with potential implications for crop production.

Characterization of Arabidopsis eskimo1 reveals a metabolic link between xylan O-acetylation and aliphatic glucosinolate metabolism

Glucuronoxylan is present mainly in the dicot of the secondary cell walls, often O-acetylated, which stabilizes cell structure by maintaining interaction with cellulose and other cell wall components. Some members of the Golgi localized Trichome Birefringence-Like (TBL) family function as xylan O-acetyl transferase (XOAT). The primary XOAT in the stem of Arabidopsis is ESKIMO1/TBL29, and its disruption results in decreased xylan acetylation, stunted plant growth, and collapsed xylem vessels. To elucidate the effect on metabolic reprogramming and identify the underlying cause of the stunted growth in eskimo1, we performed transcriptomic, targeted, and untargeted metabolome analysis, mainly in the inflorescence stem tissue. RNA sequencing analysis revealed that the genes involved in the biosynthesis, regulation, and transport of aliphatic glucosinolates (GSLs) were upregulated, whereas those responsible for indolic GSL metabolism were unaffected in the eskimo1 inflorescence stem. Consistently, aliphatic GSLs, such as 4-methylsulfinylbutyl (4MSOB), were increased in stem tissues and seeds. This shift in the profile of aliphatic GSLs in eskimo1 was further supported by the quantification of the soluble acetate, decrease in accumulation of GSL precursor, i.e., methionine, and increase in the level of jasmonic acid.

Effects of Different LED Spectra on the Antioxidant Capacity and Nitrogen Metabolism of Chinese Cabbage (Brassica rapa L. ssp. Pekinensis)

Light quality optimization is a cost-effective method for increasing leafy vegetable quality in plant factories. Light-emitting diodes (LEDs) that enable the precise modulation of light quality were used in this study to examine the effects of red-blue (RB), red-blue-green (RBG), red-blue-purple (RBP), and red-blue-far-red (RBF) lights on the growth, antioxidant capacity, and nitrogen metabolism of Chinese cabbage leaves, while white light served as the control (CK). Results showed that the chlorophyll, carotenoid, vitamin C, amino acid, total flavonoid, and antioxidant levels of Chinese cabbage were all significantly increased under RBP combined light treatment. Meanwhile, RBG combined light treatment significantly increased the levels of amino acids but decreased the nitrite content of Chinese cabbage. In addition, RBF combined light treatment remarkably increased the amino acid levels but decreased the antioxidant capacity of Chinese cabbage. In conclusion, the addition of purple light to red-blue light was effective in improving the nutritional value and antioxidant capacity of Chinese cabbage. This light condition can be used as a model for a supplemental lighting strategy for leafy vegetables in plant factory production.

Bacillus licheniformisYB06: A Rhizosphere-Genome-Wide Analysis and Plant Growth-Promoting Analysis of a Plant Growth-Promoting Rhizobacterium Isolated from Codonopsis pilosula

Codonopsis pilosula, commonly known as Dangshen, is a valuable medicinal plant, but its slow growth and susceptibility to environmental stress pose challenges for its cultivation. In pursuit of sustainable agricultural practices to enhance the yield and quality of Dangshen, the present study isolated a bacterial strain exhibiting plant growth-promoting potential from the rhizosphere of C. pilosula. This strain was subsequently identified as Bacillus licheniformisYB06. Assessment of its plant growth-promoting attributes revealed the potential of B. licheniformis YB06 as a biofertilizer. Whole-genome sequencing of B. licheniformis YB06 revealed a genome size of 4,226,888 bp with a GC content of 46.22%, harboring 4325 predicted protein-coding sequences. Genomic analysis of B. licheniformis YB06 revealed a diverse array of genes linked to induced systemic resistance (ISR) and plant growth-promoting (PGP) traits, encompassing phytohormone production, nitrogen assimilation and reduction, siderophore biosynthesis, phosphate solubilization, biofilm formation, synthesis of PGP-related amino acids, and flagellar motility. Seed germination assays demonstrated the positive effects of B. licheniformis YB06 on the germination and growth of C. pilosula seedlings. Furthermore, we explored various fertilization regimes, particularly the B. licheniformis YB06-based biofertilizer, were investigated for their impact on the structure and diversity of the C. pilosula rhizosphere soil bacterial community. Our findings revealed that fertilization significantly impacted soil bacterial composition and diversity, with the combined application of B. licheniformis YB06-based biofertilizer and organic fertilizer exhibiting a particularly pronounced enhancement of rhizosphere bacterial community structure and diversity. This study represents the first report on the beneficial effects of B. licheniformis YB06 on both the growth of C. pilosula and the composition of its rhizosphere soil microbial community. These findings provide a theoretical foundation and practical guidance for the development of novel bio-organic compound fertilizers, thereby contributing to the sustainable cultivation of C. pilosula.

24-epibrassinolide enhances drought tolerance in grapevine (Vitis vinifera L.) by regulating carbon and nitrogen metabolism

KEY MESSAGE

Exogenous application of 24-epibrassinolide can alleviate oxidative damage, improve photosynthetic capacity, and regulate carbon and nitrogen assimilation, thus improving the tolerance of grapevine (Vitis vinifera L.) to drought stress. Brassinosteroids (BRs) are a group of plant steroid hormones in plants and are involved in regulating plant tolerance to drought stress. This study aimed to investigate the regulation effects of BRs on the carbon and nitrogen metabolism in grapevine under drought stress. The results indicated that drought stress led to the accumulation of superoxide radicals and hydrogen peroxide and an increase in lipid peroxidation. A reduction in oxidative damage was observed in EBR-pretreated plants, which was probably due to the improved antioxidant concentration. Moreover, exogenous EBR improved the photosynthetic capacity and sucrose phosphate synthase activity, and decreased the sucrose synthase, acid invertase, and neutral invertase, resulting in improved sucrose (190%) and starch (17%) concentrations. Furthermore, EBR pretreatment strengthened nitrate reduction and ammonium assimilation. A 57% increase in nitrate reductase activity and a 13% increase in glutamine synthetase activity were observed in EBR pretreated grapevines. Meanwhile, EBR pretreated plants accumulated a greater amount of proline, which contributed to osmotic adjustment and ROS scavenging. In summary, exogenous EBR enhanced drought tolerance in grapevines by alleviating oxidative damage and regulating carbon and nitrogen metabolism.

Stratified Effects of Tillage and Crop Rotations on Soil Microbes in Carbon and Nitrogen Cycles at Different Soil Depths in Long-Term Corn, Soybean, and Wheat Cultivation

Understanding the soil bacterial communities involved in carbon (C) and nitrogen (N) cycling can inform beneficial tillage and crop rotation practices for sustainability and crop production. This study evaluated soil bacterial diversity, compositional structure, and functions associated with C-N cycling at two soil depths (0-15 cm and 15-30 cm) under long-term tillage (conventional tillage [CT] and no-till [NT]) and crop rotation (monocultures of corn, soybean, and wheat and corn-soybean-wheat rotation) systems. The soil microbial communities were characterized by metabarcoding the 16S rRNA gene V4-V5 regions using Illumina MiSeq. The results showed that long-term NT reduced the soil bacterial diversity at 15-30 cm compared to CT, while no significant differences were found at 0-15 cm. The bacterial communities differed significantly at the two soil depths under NT but not under CT. Notably, over 70% of the tillage-responding KEGG orthologs (KOs) associated with C fixation (primarily in the reductive citric acid cycle) were more abundant under NT than under CT at both depths. The tillage practices significantly affected bacteria involved in biological nitrogen (N2) fixation at the 0-15 cm soil depth, as well as bacteria involved in denitrification at both soil depths. The crop type and rotation regimes had limited effects on bacterial diversity and structure but significantly affected specific C-N-cycling genes. For instance, three KOs associated with the Calvin-Benson cycle for C fixation and four KOs related to various N-cycling processes were more abundant in the soil of wheat than in that of corn or soybean. These findings indicate that the long-term tillage practices had a greater influence than crop rotation on the soil bacterial communities, particularly in the C- and N-cycling processes. Integrated management practices that consider the combined effects of tillage, crop rotation, and crop types on soil bacterial functional groups are essential for sustainable agriculture.

Mineral and Organic Fertilizers' Effect on the Growth of Young Argane Trees (Argania spinosa L.) and Soil Properties under Vulnerable Conditions

Argania spinosa (L.) Skeels is an endemic species to Morocco that has multiple uses. It plays multiple important roles in terms of its botanical, ecological, and economic properties. However, the domestication of this species will open up considerable economic opportunities for Morocco. Here, for the first time, we assessed the effect of different doses of compost and NPK fertilizers on the vegetative growth parameters, biochemical and antioxidant potential of the Argania spinosa plant, and soil properties. Over a two-year period (2022-2023), eight different treatments were applied across two experimental sites. These treatments included the following: T0 (Control), T1 (F1-80.50.70 g NPK/plant), T2 (F1-125.75.100 g NPK/plant), T3 (F2-160.100.140 g NPK/plant), T4 (F2-250.150.200 g NPK/plant), T5 (F1-2.5 kg/plant compost), T6 (F1-5 kg/plant compost), T7 (F2-5 kg/plant compost), and T8 (F2-10 kg/plant compost), with F1 and F2 being the frequencies of application. We compared several doses of fertilizers with no fertilization as a control. The results showed a significant influence of the compost and NPK fertilizer on the vegetative growth parameters. For the Tamjlojt site, the first year is important because treatments T3 and T4 significantly increased height by 71.94 ± 21.15% and 74.31 ± 12.31%, respectively. For the circumference, the results showed a significant improvement by the treatments T4 and T3, and T1 demonstrated the highest gain. For the collar diameter, all treatments showed a significant difference. The most notable difference was observed with treatments T3 and T7 with 115.63 ± 33.88% and 101.09 ± 20.84%, respectively. For the Rasmouka site, the second year was the most important. The treatments with the most important height increase were T7 and T8, with a value of 43.14 ± 10.06% and 36.44 ± 9.95%; the same was observed for collar diameter as a significant increase was found in T8 and T7 with a value of 55.05 ± 15.7% and 54.08 ± 9.64%. For the circumference parameter, the treatments that increased significantly this parameter were T8 and T7 with a value of 53.36 ± 15.11% and 50.34 ± 11.29% in 2023. In addition, the highest content of carbohydrates was recorded for the treatment T3 with a value of 148.89 ± 8.11 (mg EG/g). For phenolic determination, the highest value was 2532 ± 457.13 (µg GAE/mL), shown for treatment T1. For flavonoids, the treatments that showed a significant effect were T1 and T6 with a value of 2261.98 ± 184.61 and 1237.70 ± 95.65 (µg QE/mL), respectively. For the impact on soil properties, the electrical conductivity, at the Tamjlojt site, treatment T1 showed a significant increase to 1139.00 ± 241.30 (ms/cm), while at the Rasmouka site, treatment T8 showed a significant increase to 303.33 ± 9.33 (ms/cm). Concerning organic carbon, all treatments resulted in increased percentages of this parameter in the soil. For the Tamjlojt site, the T7 treatment had a significant positive effect on this parameter with a value of 0.87 ± 0.12%. For the Rasmouka site, the T3 treatment increased the percentage of organic carbon with a value of 1.17 ± 0.07%. In addition, the organic matter content showed an improvement with a value of 2.02 ± 0.12%. As there are no previous studies in Argania spinosa fertilization, this study greatly contributes to our understanding of the benefits of using different fertilizers at different doses, in particular T8 and T7 as organic fertilizers and T3, T4 as chemical ones, on argan growth, the biochemical and antioxidant properties of leaves, and its soil properties.

Effect of Subsoiling on the Nutritional Quality of Grains of Maize Hybrids of Different Eras

To achieve high maize (Zea mays L.) yields and quality grain, it is necessary to develop stress-resistant cultivars and related cultivation practices, aiming to maximize efficiency. Thus, our objectives were (i) to investigate the impact of tillage practices and maize hybrids (which have improved over time) on yield and its components, and (ii) to characterize the response pattern of maize hybrid grain nutrient quality components to subsoiling. To achieve this, we conducted field trials with five maize hybrids from different eras under two tillage practices: rotary tillage and subsoiling. We compared grain yield, nutritional quality, and other indicators across different tillage conditions from the 1970s to the 2010s. The main results of this study are as follows: under rotary tillage conditions, the 2010s hybrid (DH618) significantly increased yields (9.37-55.89%) compared to hybrids from the 1970s-2000s. After subsoiling, the physiologically mature grains of all hybrids exhibited minimal changes in crude protein and fat content, while there was a significant reduction in the total soluble sugar content of the grains. After subsoiling, there was a substantial 8.14 to 12.79 percent increase in total starch accumulation in the grain for all hybrids during the period of 47-75 days post-anthesis. Furthermore, during the period of 47-75 days after anthesis, the consumption of grain crude protein significantly contributed to the accumulation of total starch in the grains. Ultimately, subsoiling significantly increased the yield of each hybrid and enhanced the total grain starch content at physiological maturity of all hybrids, with the 2010s hybrid (DH618) performing exceptionally well.

Evaluation of Decay Kinetics of Black Elderberry Antioxidants from Fruits and Flowers

The health-promoting properties of black elderberry are related to its high content of polyphenols (natural antioxidants), which eliminate free radicals and prevent the formation of oxidative stress responsible for many diseases. The aim of this work was to determine, the anti-radical effect of Sambucus nigra infusions based on the reaction with 2,2-diphenyl-1-picrylhydrazyl (DPPH) and galvinoxyl (Glv) radicals and to determine the function describing the disappearance curves of these radicals. The antioxidant properties of infusions obtained from the flowers and fruits of this plant were tested using the modified Brand-Williams method using DPPH and Glv radicals. Higher antioxidant activity towards both the DPPH and Glv radicals was found in flowers compared to fruits. In addition, it was found that the process of quenching radicals in the reaction with Sambucus nigra infusions proceeds in accordance with the assumptions of second-order reaction kinetics. The infusion obtained from flowers quenched radicals faster than fruit infusions. The applied second-order kinetics equation may enable estimation of antioxidants levels in natural sources of radicals.

Slight drought during flowering period can improve Tartary buckwheat yield by regulating carbon and nitrogen metabolism

This study aimed to clarify the effects of drought during flowering period on the carbon and nitrogen metabolism, growth, and yield of Tartary buckwheat. Tartary buckwheat cultivar Jinqiao 2 was treated with well-watered (CK), slight soil-drought stress (LD), moderate soil-drought stress (MD), and severe soil-drought stress (SD), with the soil water potential maintained at - 0.02 to - 0.03, - 0.04 to - 0.05, - 0.05 to - 0.06, and - 0.06 to - 0.07 MPa, respectively. With prolonged growth period and an increase in drought stress, the antioxidant enzyme activities and the contents of substances and activities of enzymes related to carbon and nitrogen metabolism in Tartary buckwheat leaves initially increased and then decreased. Meanwhile, the contents of malondialdehyde and superoxide anion showed a continuous. LD treatment induced the highest antioxidant enzyme activities and the contents of substances and activities of enzymes related to carbon and nitrogen metabolism but the lowest contents of malondialdehyde and superoxide anion in Tartary buckwheat leaves. Compared with CK, LD treatment increased the grain number, 1000-grain weight (MTS), and yield per plant by 6.52%, 17.37%, and 12.35%, respectively. In summary, LD treatment can increase the antioxidant enzyme activities and the contents of substances and activities of enzymes related to carbon and nitrogen metabolism, thus enhancing the adaptability of Tartary buckwheat to drought stress and increasing the yield per plant.

Response mechanism of carbon metabolism of Pinus massoniana to gradient high temperature and drought stress

BACKGROUND

The carbon metabolism pathway is of paramount importance for the growth and development of plants, exerting a pivotal regulatory role in stress responses. The exacerbation of drought impacts on the plant carbon cycle due to global warming necessitates comprehensive investigation into the response mechanisms of Masson Pine (Pinus massoniana Lamb.), an exemplary pioneer drought-tolerant tree, thereby establishing a foundation for predicting future forest ecosystem responses to climate change.

RESULTS

The seedlings of Masson Pine were utilized as experimental materials in this study, and the transcriptome, metabolome, and photosynthesis were assessed under varying temperatures and drought intensities. The findings demonstrated that the impact of high temperature and drought on the photosynthetic rate and transpiration rate of Masson Pine seedlings was more pronounced compared to individual stressors. The analysis of transcriptome data revealed that the carbon metabolic pathways of Masson Pine seedlings were significantly influenced by high temperature and drought co-stress, with a particular impact on genes involved in starch and sucrose metabolism. The metabolome analysis revealed that only trehalose and Galactose 1-phosphate were specifically associated with the starch and sucrose metabolic pathways. Furthermore, the trehalose metabolic heat map was constructed by integrating metabolome and transcriptome data, revealing a significant increase in trehalose levels across all three comparison groups. Additionally, the PmTPS1, PmTPS5, and PmTPPD genes were identified as key regulatory genes governing trehalose accumulation.

CONCLUSIONS

The combined effects of high temperature and drought on photosynthetic rate, transpiration rate, transcriptome, and metabolome were more pronounced than those induced by either high temperature or drought alone. Starch and sucrose metabolism emerged as the pivotal carbon metabolic pathways in response to high temperature and drought stress in Masson pine. Trehalose along with PmTPS1, PmTPS5, and PmTPPD genes played crucial roles as metabolites and key regulators within the starch and sucrose metabolism.

Enhancement of soybean tolerance to water stress through regulation of nitrogen and antioxidant defence mechanisms mediated by the synergistic role of salicylic acid and thiourea

Water stress (WS) poses a significant threat to global food and energy security by adversely affecting soybean growth and nitrogen metabolism. This study explores the synergistic effects of exogenous salicylic acid (SA, 0.5 mM) and thiourea (TU, 400 mg L-1), potent plant growth regulators, on soybean responses under WS conditions. The treatments involved foliar spraying for 3 days before inducing WS by reducing soil moisture to 50% of field capacity, followed by 2 weeks of cultivation under normal or WS conditions. WS significantly reduced plant biomass, chlorophyll content, photosynthetic efficiency, water status, protein content, and total nitrogen content in roots and leaves. Concurrently, it elevated levels of leaf malondialdehyde, H2O2, proline, nitrate, and ammonium. WS also triggered an increase in antioxidant enzyme activity and osmolyte accumulation in soybean plants. Application of SA and TU enhanced the activities of key enzymes crucial for nitrogen assimilation and amino acid synthesis. Moreover, SA and TU improved plant growth, water status, chlorophyll content, photosynthetic efficiency, protein content, and total nitrogen content, while reducing oxidative stress and leaf proline levels. Indeed, the simultaneous application of SA and TU demonstrated a heightened impact compared to their separate use, suggesting a synergistic interaction. This study underscores the potential of SA and TU to enhance WS tolerance in soybean plants by modulating nitrogen metabolism and mitigating oxidative damage. These findings hold significant promise for improving crop productivity and quality in the face of escalating water limitations due to climate change.

Enhanced Rice Resistance to Sheath Blight through Nitrate Transporter 1.1B Mutation without Yield Loss under NH4+ Fertilization

Nitrogen fertilization can promote rice yield but decrease resistance to sheath blight (ShB). In this study, the nitrate transporter 1.1b (nrt1.1b) mutant that exhibited less susceptibility to ShB but without compromising yield under NH4+ fertilization was screened. NRT1.1B's regulation of ShB resistance was independent of the total nitrogen concentration in rice under NH4+ conditions. In nrt1.1b mutant plants, the NH4+ application modulated auxin signaling, chlorophyll content, and phosphate signaling to promote ShB resistance. Furthermore, the findings indicated that NRT1.1B negatively regulated ShB resistance by positively modulating the expression of H+-ATPase gene OSA3 and phosphate transport gene PT8. The mutation of OSA3 and PT8 promoted ShB resistance by increasing the apoplastic pH in rice. Our study identified the ShB resistance mutant nrt1.1b, which maintained normal nitrogen use efficiency without compromising yield.

The Role of Glutamine Synthetase (GS) and Glutamate Synthase (GOGAT) in the Improvement of Nitrogen Use Efficiency in Cereals

Cereals are the most broadly produced crops and represent the primary source of food worldwide. Nitrogen (N) is a critical mineral nutrient for plant growth and high yield, and the quality of cereal crops greatly depends on a suitable N supply. In the last decades, a massive use of N fertilizers has been achieved in the desire to have high yields of cereal crops, leading to damaging effects for the environment, ecosystems, and human health. To ensure agricultural sustainability and the required food source, many attempts have been made towards developing cereal crops with a more effective nitrogen use efficiency (NUE). NUE depends on N uptake, utilization, and lastly, combining the capability to assimilate N into carbon skeletons and remobilize the N assimilated. The glutamine synthetase (GS)/glutamate synthase (GOGAT) cycle represents a crucial metabolic step of N assimilation, regulating crop yield. In this review, the physiological and genetic studies on GS and GOGAT of the main cereal crops will be examined, giving emphasis on their implications in NUE.

Effects of Low Light after Heading on the Yield of Direct Seeding Rice and Its Physiological Response Mechanism

As a photophilous plant, rice is susceptible to low-light stress during its growth. The Sichuan Basin is a typical low-light rice-producing area. In this study, eight rice varieties with different shade tolerances were studied from 2021 to 2022. The physiological adaptability and yield formation characteristics of rice were studied with respect to photosynthetic physiological characteristics and dry matter accumulation characteristics, and the response mechanism of rice to low light stress was revealed. The results showed that the shading treatment significantly increased the chlorophyll a, chlorophyll b, and total chlorophyll contents in the leaves of direct-seeded rice after heading, and the total chlorophyll content increased by 1.68-29.70%. Nitrate reductase (NR) activity first increased and then decreased under each treatment, and the shading treatment reduced the NR activity of direct-seeded rice. Compared to the control treatment, the peroxidase (POD) activity of each variety increased from 7 to 24 d after the shading treatment. The transketolase (TK) activity in direct-seeded hybrid rice increased under low light stress. Compared with the control, shading treatment significantly reduced the aboveground dry matter, grain number per panicle, and seed setting rate of direct-seeded rice at the full heading stage and maturity stage, thus reducing the yield of direct-seeded rice by 26.10-34.11%. However, under the shading treatment, Zhenliangyou 2018 and Jingliangyou 534 maintained higher chlorophyll content and related enzyme activities, accumulated more photosynthetic products, and reduced yield. In general, Zhenliangyou 2018 and Jingliangyou 534 still had a yield of 7.06-8.33 t·hm-2 under low light. It indicated that Zhenliangyou 2018 and Jingliangyou 534 had better stability and stronger tolerance to weak light stress and had a higher yield potential in weak light areas such as Sichuan.

Avicennia germinans leaf traits in degraded, restored, and natural mangrove ecosystems of Guyana

Mangrove leaves have unique features that enable them to cope with shifting environmental conditions while preserving their general functionality and efficiency. We examined the morphological characteristics and chlorophyll content (spectroscopically) of 600 mature Avicennia germinans leaves selected from 30 trees located in one degraded, one restored, and one natural mangrove ecosystem along Guyana's coastline. Systematic sampling was carried out using the closest individual sampling method in the wet and dry seasons. We hypothesized that both habitat type and seasonality influence the leaf traits and chlorophyll content of A. germinans. Our findings showed that A. germinans leaves are mesophyllous, and traits such as leaf perimeter, area, length, width, dry mass, wet mass, turgid mass, leaf-specific area, and relative water content showed fluctuations in ecosystems (one-way ANOVA, p < .05) as well as seasonally (paired t-test, p < .05). Substantial, positive correlations (p < .05, R > .75) were also established for over 10 leaf parameters in both seasons while PCA and multiple regression analyses further confirmed the strong relationships between leaf morphological features and their respective locations. Changes in chlorophyll concentration were most noticeable in the degraded ecosystem while variations in leaf traits were more pronounced in the restored mangrove area. This may be due to the various disturbances found in each ecosystem coupled with fluctuations in the seasons. Our results demonstrate that mangroves, to some extent, alter their plant structures to cope with environmental stressors present in the various ecosystems they thrive in to maintain their survival.

Physiological and Transcriptomic Analysis Provides Insights into Low Nitrogen Stress in Foxtail Millet (Setaria italica L.)

Foxtail millet (Setaria italica (L.) P. Beauv) is an important food and forage crop that is well adapted to nutrient-poor soils. However, our understanding of how different LN-tolerant foxtail millet varieties adapt to long-term low nitrogen (LN) stress at the physiological and molecular levels remains limited. In this study, two foxtail millet varieties with contrasting LN tolerance properties were investigated through analyses of physiological parameters and transcriptomics. The physiological results indicate that JG20 (high tolerance to LN) exhibited superior biomass accumulation both in its shoots and roots, and higher nitrogen content, soluble sugar concentration, soluble protein concentration, zeatin concentration in shoot, and lower soluble sugar and soluble protein concentration in its roots compared to JG22 (sensitive to LN) under LN, this indicated that the LN-tolerant foxtail millet variety can allocate more functional substance to its shoots to sustain aboveground growth and maintain high root activity by utilizing low soluble sugar and protein under LN conditions. In the transcriptomics analysis, JG20 exhibited a greater number of differentially expressed genes (DEGs) compared to JG22 in both its shoots and roots in response to LN stress. These LN-responsive genes were enriched in glycolysis metabolism, photosynthesis, hormone metabolism, and nitrogen metabolism. Furthermore, in the shoots, the glutamine synthetase gene SiGS5, chlorophyll apoprotein of photosystem II gene SiPsbQ, ATP synthase subunit gene Sib, zeatin synthesis genes SiAHP1, and aldose 1-epimerase gene SiAEP, and, in the roots, the high-affinity nitrate transporter genes SiNRT2.3, SiNRT2.4, glutamate synthase gene SiGOGAT2, fructose-bisphosphate aldolase gene SiFBA5, were important genes involved in the LN tolerance of the foxtail millet variety. Hence, our study implies that the identified genes and metabolic pathways contribute valuable insights into the mechanisms underlying LN tolerance in foxtail millet.

Effect of Mowing on Wheat Growth at Seeding Stage

Winter wheat is used as forage at the tillering stage in many countries; however, the regrowth pattern of wheat after mowing remains unclear. In this study, the growth patterns of wheat were revealed through cytological and physiological assessments as well as transcriptome sequencing. The results of agronomic traits and paraffin sections showed that the shoot growth rate increased, but root growth was inhibited after mowing. The submicroscopic structure revealed a decrease in heterochromatin in the tillering node cell and a change in mitochondrial shape in the tillering node and secondary root. Analysis of the transcriptome showed the number of differentially expressed genes (DEGs) involved in biological processes, cellular components, and molecular functions; 2492 upregulated DEGs and 1534 downregulated DEGs were identified. The results of the experimental study showed that mowing induced expression of DEGs in the phenylpropanoid biosynthesis pathway and increased the activity of PAL and 4CL. The upregulated DEGs in the starch and sucrose metabolism pathways and related enzyme activity alterations indicated that the sugar degradation rate increased. The DEGs in the nitrogen metabolism pathway biosynthesis of the amino acids, phenylpropanoid biosynthesis metabolism, and in the TCA pathway also changed after mowing. Hormone content and related gene expression was also altered in the tillering and secondary roots after mowing. When jasmonic acid and ethylene were used to treat the wheat after mowing, the regeneration rate increased, whereas abscisic acid inhibited regrowth. This study revealed the wheat growth patterns after mowing, which could lead to a better understanding of the development of dual-purpose wheat.

Meta-learning approach for bacteria classification and identification of informative genes of the Bacillus megaterium: tomato roots tissue interaction

Plant growth-promoting rhizobacteria (PGPRs) are bacteria that colonize the plant roots. These beneficial bacteria have an influence on plant development through multiple mechanisms, such as nutrient availability, alleviating biotic and abiotic stress, and secrete phytohormones. Therefore, their inoculation constitutes a powerful tool towards sustainable agriculture and crop production. To understand plant-PGPRs interaction we present the classification of PGPR using machine learning and meta-learning classifiers namely Support Vector Machine (SVM), Kernel Logistic Regression (KLR), meta-SVM and meta-KLR to predict the presence of Bacillus megaterium inoculated in tomato root tissues using publicly available transcriptomic data. The original dataset presents 36 significantly differentially expressed genes. As the meta-KLR achieved near-optimal performance considering all the relevant metrics, this meta learner was afterwards used to identify the informative genes (IGs). The outcomes showed 157 IGs, being present all significantly differentially expressed genes previously identified. Among the IGs, 113 were identified as tomato genes, 5 as Bacillus subtilis proteins, 1 as Escherichia coli protein and 6 were unidentified. Then, a functional enrichment analysis of the tomato IGs showed 175 biological processes, 22 molecular functions and 20 KEGG pathways involved in B. megaterium-tomato interaction. Furthermore, the biological networks study of their Arabidopsis thaliana orthologous genes identified the co-expression, predicted interaction, shared protein domains and co-localization networks.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03690-0.

Sugar Starvation Disrupts Lipid Breakdown by Inducing Autophagy in Embryonic Axes of Lupin (Lupinus spp.) Germinating Seeds

Under nutrient deficiency or starvation conditions, the mobilization of storage compounds during seed germination is enhanced to primarily supply respiratory substrates and hence increase the potential of cell survival. Nevertheless, we found that, under sugar starvation conditions in isolated embryonic axes of white lupin (Lupinus albus L.) and Andean lupin (Lupinus mutabilis Sweet) cultured in vitro for 96 h, the disruption of lipid breakdown occurs, as was reflected in the higher lipid content in the sugar-starved (-S) than in the sucrose-fed (+S) axes. We postulate that pexophagy (autophagic degradation of the peroxisome-a key organelle in lipid catabolism) is one of the reasons for the disruption in lipid breakdown under starvation conditions. Evidence of pexophagy can be: (i) the higher transcript level of genes encoding proteins of pexophagy machinery, and (ii) the lower content of the peroxisome marker Pex14p and its increase caused by an autophagy inhibitor (concanamycin A) in -S axes in comparison to the +S axes. Additionally, based on ultrastructure observation, we documented that, under sugar starvation conditions lipophagy (autophagic degradation of whole lipid droplets) may also occur but this type of selective autophagy seems to be restricted under starvation conditions. Our results also show that autophagy occurs at the very early stages of plant growth and development, including the cells of embryonic seed organs, and allows cell survival under starvation conditions.

Proteome Landscape during Ripening of Solid Endosperm from Two Different Coconut Cultivars Reveals Contrasting Carbohydrate and Fatty Acid Metabolic Pathway Modulation

Cocos nucifera L. is a crop grown in the humid tropics. It is grouped into two classes of varieties: dwarf and tall; regardless of the variety, the endosperm of the coconut accumulates carbohydrates in the early stages of maturation and fatty acids in the later stages, although the biochemical factors that determine such behavior remain unknown. We used tandem mass tagging with synchronous precursor selection (TMT-SPS-MS3) to analyze the proteomes of solid endosperms from Yucatan green dwarf (YGD) and Mexican pacific tall (MPT) coconut cultivars. The analysis was conducted at immature, intermediate, and mature development stages to better understand the regulation of carbohydrate and lipid metabolisms. Proteomic analyses showed 244 proteins in YGD and 347 in MPT; from these, 155 proteins were shared between both cultivars. Furthermore, the proteomes related to glycolysis, photosynthesis, and gluconeogenesis, and those associated with the biosynthesis and elongation of fatty acids, were up-accumulated in the solid endosperm of MPT, while in YGD, they were down-accumulated. These results support that carbohydrate and fatty acid metabolisms differ among the developmental stages of the solid endosperm and between the dwarf and tall cultivars. This is the first proteomics study comparing different stages of maturity in two contrasting coconut cultivars and may help in understanding the maturity process in other palms.

Moderate organic fertilizer substitution for partial chemical fertilizer improved soil microbial carbon source utilization and bacterial community composition in rain-fed wheat fields: current year

Organic fertilizers can partially replace chemical fertilizers to improve agricultural production and reduce negative environmental impacts. To study the effect of organic fertilizer on soil microbial carbon source utilization and bacterial community composition in the field of rain-fed wheat, we conducted a field experiment from 2016 to 2017 in a completely randomized block design with four treatments: the control with 100% NPK compound fertilizer (N: P2O5: K2O = 20:10:10) of 750 kg/ha (CK), a combination of 60% NPK compound fertilizer with organic fertilizer of 150 kg/ha (FO1), 300 kg/ha (FO2), and 450 kg/ha (FO3), respectively. We investigated the yield, soil property, the utilization of 31 carbon sources by soil microbes, soil bacterial community composition, and function prediction at the maturation stage. The results showed that (1) compared with CK, organic fertilizer substitution treatments improved ear number per hectare (13%-26%), grain numbers per spike (8%-14%), 1000-grain weight (7%-9%), and yield (3%-7%). Organic fertilizer substitution treatments increased the total nitrogen, available nitrogen, available phosphorus, and soil organic matter contents by 26%, 102%, 12%, and 26%, respectively, compared with CK treatments. Organic fertilizer substitution treatments significantly advanced the partial productivity of fertilizers. (2) Carbohydrates and amino acids were found to be the most sensitive carbon sources for soil microorganisms in different treatments. Particularly for FO3 treatment, the utilization of β-Methyl D-Glucoside, L-Asparagine acid, and glycogen by soil microorganisms was higher than other treatments and positively correlated with soil nutrients and wheat yield. (3) Compared with CK, organic fertilizer substitution treatments increased the relative abundance of Proteobacteria, Acidobacteria, and Gemmatimonadetes and decreased the relative abundance of Actinobacteria and Firmicutes. Interestingly, FO3 treatment improved the relative abundance of Nitrosovibrio, Kaistobacter, Balneimonas, Skermanella, Pseudomonas, and Burkholderia belonging to Proteobacteria and significantly boosted the relative abundance of function gene K02433 [the aspartyl-tRNA (Asn)/glutamyl-tRNA (Gln)]. Based on the abovementioned findings, we suggest FO3 as the most appropriate organic substitution method in rain-fed wheat fields.

H2 S works synergistically with rhizobia to modify photosynthetic carbon assimilation and metabolism in nitrogen-deficient soybeans

Hydrogen sulfide (H₂ S) performs a crucial role in plant development and abiotic stress responses by interacting with other signalling molecules. However, the synergistic involvement of H₂ S and rhizobia in photosynthetic carbon (C) metabolism in soybean (Glycine max) under nitrogen (N) deficiency has been largely overlooked. Therefore, we scrutinised how H₂ S drives photosynthetic C fixation, utilisation, and accumulation in soybean-rhizobia symbiotic systems. When soybeans encountered N deficiency, organ growth, grain output, and nodule N-fixation performance were considerably improved owing to H₂ S and rhizobia. Furthermore, H₂ S collaborated with rhizobia to actively govern assimilation product generation and transport, modulating C allocation, utilisation, and accumulation. Additionally, H₂ S and rhizobia profoundly affected critical enzyme activities and coding gene expressions implicated in C fixation, transport, and metabolism. Furthermore, we observed substantial effects of H₂ S and rhizobia on primary metabolism and C-N coupled metabolic networks in essential organs via C metabolic regulation. Consequently, H₂ S synergy with rhizobia inspired complex primary metabolism and C-N coupled metabolic pathways by directing the expression of key enzymes and related coding genes involved in C metabolism, stimulating effective C fixation, transport, and distribution, and ultimately improving N fixation, growth, and grain yield in soybeans.

Mass spectrometry-based metabolite profiling reveals functional seasonal shifts in the metabolome of Zygophyllum dumosum Boiss and its relation to environmental conditions

MAIN CONCLUSION

A multi-year study of perennial Z. dumosum shows a consistent seasonal pattern in the changes of petiole metabolism, involving mainly organic acids, polyols, phenylpropanoids, sulfate conjugates, and piperazines. GC-MS and UPLC-QTOF-MS-based metabolite profiling was performed on the petioles of the perennial desert shrub Zygophyllum dumosum Boiss (Zygophyllaceae). The petioles, which are physiologically functional throughout the year and, thus, exposed to seasonal rhythms, were collected every month for 3 years from their natural ecosystem on a southeast-facing slope. Results showed a clear multi-year pattern following seasonal successions, despite different climate conditions, i.e., rainy and drought years, throughout the research period. The metabolic pattern of change encompassed an increase in the central metabolites, including most polyols, e.g., stress-related D-pinitol, organic and sugar acids, and in the dominant specialized metabolites, which were tentatively identified as sulfate, flavonoid, and piperazine conjugates during the summer-autumn period, while significantly high levels of free amino acids were detected during the winter-spring period. In parallel, the levels of most sugars (including glucose and fructose) increased in the petioles at the flowering stage at the beginning of the spring, while most of the di- and tri-saccharides accumulated at the beginning of seed development (May-June). Analysis of the conserved seasonal metabolite pattern of change shows that metabolic events are mostly related to the stage of plant development and its interaction with the environment and less to environmental conditions per se.

CO2 recycling by phosphoenolpyruvate carboxylase enables cassava leaf metabolism to tolerate low water availability

Cassava is a staple crop that acclimatizes well to dry weather and limited water availability. The drought response mechanism of quick stomatal closure observed in cassava has no explicit link to the metabolism connecting its physiological response and yield. Here, a genome-scale metabolic model of cassava photosynthetic leaves (leaf-MeCBM) was constructed to study on the metabolic response to drought and stomatal closure. As demonstrated by leaf-MeCBM, leaf metabolism reinforced the physiological response by increasing the internal CO₂ and then maintaining the normal operation of photosynthetic carbon fixation. We found that phosphoenolpyruvate carboxylase (PEPC) played a crucial role in the accumulation of the internal CO₂ pool when the CO₂ uptake rate was limited during stomatal closure. Based on the model simulation, PEPC mechanistically enhanced drought tolerance in cassava by providing sufficient CO₂ for carbon fixation by RuBisCO, resulting in high production of sucrose in cassava leaves. The metabolic reprogramming decreased leaf biomass production, which may lead to maintaining intracellular water balance by reducing the overall leaf area. This study indicates the association of metabolic and physiological responses to enhance tolerance, growth, and production of cassava in drought conditions.

Combining GS-assisted GWAS and transcriptome analysis to mine candidate genes for nitrogen utilization efficiency in Populus cathayana

BACKGROUND

Forest trees such as poplar, shrub willow, et al. are essential natural resources for sustainable and renewable energy production, and their wood can reduce dependence on fossil fuels and reduce environmental pollution. However, the productivity of forest trees is often limited by the availability of nitrogen (N), improving nitrogen use efficiency (NUE) is an important way to address it. Currently, NUE genetic resources are scarce in forest tree research, and more genetic resources are urgently needed.

RESULTS

Here, we performed genome-wide association studies (GWAS) using the mixed linear model (MLM) to identify genetic loci regulating growth traits in Populus cathayana at two N levels, and attempted to enhance the signal strength of single nucleotide polymorphism (SNP) detection by performing genome selection (GS) assistance GWAS. The results of the two GWAS analyses identified 55 and 40 SNPs that were respectively associated with plant height (PH) and ground diameter (GD), and 92 and 69 candidate genes, including 30 overlapping genes. The prediction accuracy of the GS model (rrBLUP) for phenotype exceeds 0.9. Transcriptome analysis of 13 genotypes under two N levels showed that genes related to carbon and N metabolism, amino acid metabolism, energy metabolism, and signal transduction were differentially expressed in the xylem of P. cathayana under N treatment. Furthermore, we observed strong regional patterns in gene expression levels of P. cathayana, with significant differences between different regions. Among them, P. cathayana in Longquan region exhibited the highest response to N. Finally, through weighted gene co-expression network analysis (WGCNA), we identified a module closely related to the N metabolic process and eight hub genes.

CONCLUSIONS

Integrating the GWAS, RNA-seq and WGCNA data, we ultimately identified four key regulatory genes (PtrNAC123, PtrNAC025, Potri.002G233100, and Potri.006G236200) involved in the wood formation process, and they may affect P. cathayana growth and wood formation by regulating nitrogen metabolism. This study will provide strong evidence for N regulation mechanisms, and reliable genetic resources for growth and NUE genetic improvement in poplar.

Effects of Nodulation on Metabolite Concentrations in Xylem Sap and in the Organs of Soybean Plants Supplied with Different N Forms

The effects of nodulation on N metabolism in soybean plants supplied with various forms of N are not fully understood. Ureides are the principal forms of N transported from nodules, but nitrate and asparagine are the primary N compounds transported from roots supplied with NO3−. In this research, the effects of 1-day treatments of NO3−, NH4+, urea, or NO3− + NH4+ on N metabolite concentrations in xylem sap and each organ were compared between nodulated and non-nodulated soybeans. Capillary electrophoresis and colorimetry were used for the analysis. In the xylem sap of the nodulated plants with an N-free solution, ureides were the major N metabolites, followed by asparagine and glutamine. Ureides concentrations were much lower in the xylem sap of the non-nodulated soybeans. In the NO3− treatment, the concentrations of ureides in the xylem sap of the nodulated plants decreased compared to the control plants. In the NH4+, urea, and NO3− + NH4+ treatments, the concentrations of asparagine and glutamine increased significantly compared with the control and NO3− treatments. Similar changes with the N treatments were observed between the nodulated and non-nodulated soybeans, suggesting that nodulation does not have significant effects on the metabolism of absorbed N in roots.

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.

Cytoplasmic regulation of chloroplast ROS accumulation during effector-triggered immunity

Accumulating evidence suggests that chloroplasts are an important battleground during various microbe-host interactions. Plants have evolved layered strategies to reprogram chloroplasts to promote de novo biosynthesis of defense-related phytohormones and the accumulation of reactive oxygen species (ROS). In this minireview, we will discuss how the host controls chloroplast ROS accumulation during effector-triggered immunity (ETI) at the level of selective mRNA decay, translational regulation, and autophagy-dependent formation of Rubisco-containing bodies (RCBs). We hypothesize that regulation at the level of cytoplasmic mRNA decay impairs the repair cycle of photosystem II (PSII) and thus facilitates ROS generation at PSII. Meanwhile, removing Rubisco from chloroplasts potentially reduces both O₂ and NADPH consumption. As a consequence, an over-reduced stroma would further exacerbate PSII excitation pressure and enhance ROS production at photosystem I.

Carbon dots promoted soybean photosynthesis and amino acid biosynthesis under drought stress: Reactive oxygen species scavenging and nitrogen metabolism

With global warming and water scarcity, improving the drought tolerance and quality of crops is critical for food security and human health. Here, foliar application of carbon dots (CDs, 5 mg·L^-1) could scavenge reactive oxygen species accumulation in soybean leaves under drought stress, thereby enhancing photosynthesis and carbohydrate transport. Moreover, CDs stimulated root secretion (e.g., amino acids, organic acids, and auxins) and recruited beneficial microorganisms (e.g., Actinobacteria, Ascomycota, Acidobacteria and Glomeromycota), which facilitate nitrogen (N) activation in the soil. Meanwhile, the expression of GmNRT, GmAMT, and GmAQP genes were up-regulated, indicating enhanced N and water uptake. The results demonstrated that CDs could promote nitrogen metabolism and enhance amino acid biosynthesis. Particularly, the N content in soybean shoots and roots increased significantly by 13.2 % and 30.5 %, respectively. The amino acids content in soybean shoots and roots increased by 257.5 % and 57.5 %, respectively. Consequently, soybean yields increased significantly by 21.5 %, and the protein content in soybean kernels improved by 3.7 %. Therefore, foliar application of CDs can support sustainable nano-enabled agriculture to combat climate change.

Nitrogen assimilation and photorespiration become more efficient under chloride nutrition as a beneficial macronutrient

Chloride (Cl^-) and nitrate ( NO 3 - ) are closely related anions involved in plant growth. Their similar physical and chemical properties make them to interact in cellular processes like electrical balance and osmoregulation. Since both anions share transport mechanisms, Cl^- has been considered to antagonize NO 3 - uptake and accumulation in plants. However, we have recently demonstrated that Cl^- provided at beneficial macronutrient levels improves nitrogen (N) use efficiency (NUE). Biochemical mechanisms by which beneficial Cl^- nutrition improves NUE in plants are poorly understood. First, we determined that Cl^- nutrition at beneficial macronutrient levels did not impair the NO 3 - uptake efficiency, maintaining similar NO 3 - content in the root and in the xylem sap. Second, leaf NO 3 - content was significantly reduced by the treatment of 6 mM Cl^- in parallel with an increase in NO 3 - utilization and NUE. To verify whether Cl^- nutrition reduces leaf NO 3 - accumulation by inducing its assimilation, we analysed the content of N forms and the activity of different enzymes and genes involved in N metabolism. Chloride supply increased transcript accumulation and activity of most enzymes involved in NO 3 - assimilation into amino acids, along with a greater accumulation of organic N (mostly proteins). A reduced glycine/serine ratio and a greater ammonium accumulation pointed to a higher activity of the photorespiration pathway in leaves of Cl^--treated plants. Chloride, in turn, promoted higher transcript levels of genes encoding enzymes of the photorespiration pathway. Accordingly, microscopy observations suggested strong interactions between different cellular organelles involved in photorespiration. Therefore, in this work we demonstrate for the first time that the greater NO 3 - utilization and NUE induced by beneficial Cl^- nutrition is mainly due to the stimulation of NO 3 - assimilation and photorespiration, possibly favouring the production of ammonia, reductants and intermediates that optimize C-N re-utilization and plant growth. This work demonstrates new Cl^- functions and remarks on its relevance as a potential tool to manipulate NUE in plants.

Millet-inspired systems metabolic engineering of NUE in crops

The use of nitrogen (N) fertilizers in agriculture has a great ability to increase crop productivity. However, their excessive use has detrimental effects on the environment. Therefore, it is necessary to develop crop varieties with improved nitrogen use efficiency (NUE) that require less N but have substantial yields. Orphan crops such as millets are cultivated in limited regions and are well adapted to lower input conditions. Therefore, they serve as a rich source of beneficial traits that can be transferred into major crops to improve their NUE. This review highlights the tremendous potential of systems biology to unravel the enzymes and pathways involved in the N metabolism of millets, which can open new possibilities to generate transgenic crops with improved NUE.

N Absorption, Transport, and Recycling in Nodulated Soybean Plants by Split-Root Experiment Using 15N-Labeled Nitrate

Nitrate concentration is variable in soils, so the absorbed N from roots in a high-nitrate site is recycled from shoots to the root parts in N-poor niche. In this report, the absorption, transport, and recycling of N derived from 15N-labeled nitrate were investigated with split-root systems of nodulated soybean. The NO3− accumulated in the root in 5 mM NO3− solution; however, it was not detected in the roots and nodules in an N-free pot, indicating that NO3− itself is not recycled from leaves to underground parts. The total amount of 15NO3− absorption from 2 to 4 days of the plant with the N-free opposite half-root accelerated by 40% compared with both half-roots that received NO3−. This result might be due to the compensation for the N demand under one half-root could absorb NO3−. About 2–3% of the absorbed 15N was recycled to the opposite half-root, irrespective of N-free or NO3− solution, suggesting that N recycling from leaves to the roots was not affected by the presence or absence of NO3−. Concentrations of asparagine increased in the half-roots supplied with NO3− but not in N-free half-roots, suggesting that asparagine may not be a systemic signal for N status.

Geographical Origin Determination of Cigar at Different Spatial Scales Based on C and N Metabolites and Mineral Elements Combined with Chemometric Analysis

In this paper, five C and N metabolites and eighteen mineral elements were used to identify the cigar's geographical origin on a country scale (Dominica, Indonesia, and China) and on a prefecture scale (Yuxi, Puer, and Lincang in China). The results show that the best origin traceability method is the combination of C and N metabolites and mineral elements method. Its. Its accuracy of cross-validation can achieve 95% on a country scale and 94% on a prefecture scale. Determination accuracy is ranked as identification by combination > mineral elements > C and N metabolites. For geo-origin determination of cigars, mineral element identification is better than that metabolite identification. The algorithm and factors for origin determination are selected. The results can be used to guide cigar agricultural practices and monitor and regulate the cigar in production and circulation.

Physiological and Transcriptomic Analyses Reveal the Effects of Elevated Root-Zone CO2 on the Metabolism of Sugars and Starch in the Roots of Oriental Melon Seedlings

Root-zone CO2 is a major factor that affects crop growth, development, nutrient uptake, and metabolism. Oriental melon is affected by root-zone gases during growth, the microstructure, sugar and starch contents, enzymatic activities related to sugar and starch metabolism, and gene expression in the roots of oriental melon seedlings were investigated under three root-zone CO2 concentrations (CK: 0.2%, T1: 0.4%, T2: 1.1%). Elevated root-zone CO2 altered the cellular microstructure, accelerated the accumulation and release of starch grains, disrupted organelle formation, and accelerated root senescence. The sugar and starch contents and metabolic activity in the roots increased within a short duration following treatment. Compared to the control, 232 and 1492 differentially expressed genes (DEGs) were identified on the 6th day of treatment in T1 and T2 plants, respectively. The DEGs were enriched in three metabolic pathways. The majority of genes related to sucrose and starch hydrolysis were upregulated, while the genes related to sucrose metabolism were downregulated. The study revealed that oriental melon seedlings adapt to elevated root-zone CO2 stress by adjusting sugar and starch metabolism at the transcriptome level and provides new insights into the molecular mechanism underlying the response to elevated root-zone CO2 stress.

Enhancement of nitrogen use efficiency through agronomic and molecular based approaches in cotton

Cotton is a major fiber crop grown worldwide. Nitrogen (N) is an essential nutrient for cotton production and supports efficient crop production. It is a crucial nutrient that is required more than any other. Nitrogen management is a daunting task for plants; thus, various strategies, individually and collectively, have been adopted to improve its efficacy. The negative environmental impacts of excessive N application on cotton production have become harmful to consumers and growers. The 4R's of nutrient stewardship (right product, right rate, right time, and right place) is a newly developed agronomic practice that provides a solid foundation for achieving nitrogen use efficiency (NUE) in cotton production. Cropping systems are equally crucial for increasing production, profitability, environmental growth protection, and sustainability. This concept incorporates the right fertilizer source at the right rate, time, and place. In addition to agronomic practices, molecular approaches are equally important for improving cotton NUE. This could be achieved by increasing the efficacy of metabolic pathways at the cellular, organ, and structural levels and NUE-regulating enzymes and genes. This is a potential method to improve the role of N transporters in plants, resulting in better utilization and remobilization of N in cotton plants. Therefore, we suggest effective methods for accelerating NUE in cotton. This review aims to provide a detailed overview of agronomic and molecular approaches for improving NUE in cotton production, which benefits both the environment and growers.

Target of Rapamycin Regulates Photosynthesis and Cell Growth in Auxenochlorella pyrenoidosa

Auxenochlorella pyrenoidosa is an efficient photosynthetic microalga with autotrophic growth and reproduction, which has the advantages of rich nutrition and high protein content. Target of rapamycin (TOR) is a conserved protein kinase in eukaryotes both structurally and functionally, but little is known about the TOR signalling in Auxenochlorella pyrenoidosa. Here, we found a conserved ApTOR protein in Auxenochlorella pyrenoidosa, and the key components of TOR complex 1 (TORC1) were present, while the components RICTOR and SIN1 of the TORC2 were absent in Auxenochlorella pyrenoidosa. Drug sensitivity experiments showed that AZD8055 could effectively inhibit the growth of Auxenochlorella pyrenoidosa, whereas rapamycin, Torin1 and KU0063794 had no obvious effect on the growth of Auxenochlorella pyrenoidosaa. Transcriptome data results indicated that Auxenochlorella pyrenoidosa TOR (ApTOR) regulates various intracellular metabolism and signaling pathways in Auxenochlorella pyrenoidosa. Most genes related to chloroplast development and photosynthesis were significantly down-regulated under ApTOR inhibition by AZD8055. In addition, ApTOR was involved in regulating protein synthesis and catabolism by multiple metabolic pathways in Auxenochlorella pyrenoidosa. Importantly, the inhibition of ApTOR by AZD8055 disrupted the normal carbon and nitrogen metabolism, protein and fatty acid metabolism, and TCA cycle of Auxenochlorella pyrenoidosa cells, thus inhibiting the growth of Auxenochlorella pyrenoidosa. These RNA-seq results indicated that ApTOR plays important roles in photosynthesis, intracellular metabolism and cell growth, and provided some insights into the function of ApTOR in Auxenochlorella pyrenoidosa.

Identification and validation of a locus for wheat maximum root length independent of parental reproductive environment

Maximum root length (MRL) plays an important role in the uptake of nutrients and resisting abiotic stresses. Understanding the genetic mechanism of root development is of great significance for genetic improvement of wheat. Previous studies have confirmed that parental reproductive environment (PRE) has a significant impact on growth and development of the next generation in the whole life cycle of a given plant. In this study, a recombinant inbred line population genotyped using the Wheat55K SNP array, was used to map quantitative trait loci (QTL) for wheat seedling MRL based on the harvested seeds from five different PREs. A total of 5 QTL located on chromosomes 3D and 7A were identified. Among them, QMrl.sicau-2SY-3D.2 located in a 4.0 cM interval on chromosome 3D was likely independent of PREs. QMrl.sicau-2SY-7A.2 was detected in two tests and probably influenced by PREs. The effect of QMrl.sicau-2SY-3D.2 was further validated using the tightly linked kompetitive allele specific PCR (KASP) marker, KASP-AX-111589572, in populations with different genetic backgrounds. Lines with a combination of positive alleles from QMrl.sicau-2SY-3D.2 and QMrl.sicau-2SY-7A.2 have significantly longer MRL. Furthermore, four genes (TraesCS3D03G0612000, TraesCS3D03G0608400, TraesCS3D03G0613600, and TraesCS3D03G0602400) mainly expressed in wheat root were predicted to be associated with root growth. Taken together, this study reports on a major QTL independent of PREs and lays a foundation for understanding the regulation mechanism of wheat MRL at the seedling stage.

Transcriptome Analysis and Intraspecific Variation in Spanish Fir (Abies pinsapo Boiss.)

Spanish fir (Abies pinsapo Boiss.) is an endemic, endangered tree that has been scarcely investigated at the molecular level. In this work, the transcriptome of Spanish fir was assembled, providing a large catalog of expressed genes (22,769), within which a high proportion were full-length transcripts (12,545). This resource is valuable for functional genomics studies and genome annotation in this relict conifer species. Two intraspecific variations of A. pinsapo can be found within its largest population at the Sierra de las Nieves National Park: one with standard green needles and another with bluish-green needles. To elucidate the causes of both phenotypes, we studied different physiological and molecular markers and transcriptome profiles in the needles. "Green" trees showed higher electron transport efficiency and enhanced levels of chlorophyll, protein, and total nitrogen in the needles. In contrast, needles from "bluish" trees exhibited higher contents of carotenoids and cellulose. These results agreed with the differential transcriptomic profiles, suggesting an imbalance in the nitrogen status of "bluish" trees. Additionally, gene expression analyses suggested that these differences could be associated with different epigenomic profiles. Taken together, the reported data provide new transcriptome resources and a better understanding of the natural variation in this tree species, which can help improve guidelines for its conservation and the implementation of adaptive management strategies under climatic change.