Improving coordination of plant growth and nitrogen metabolism for sustainable agriculture

Trehalose-6-phosphate synthase 8 increases photosynthesis and seed yield in Brassica napus

Trehalose-6-phosphate (T6P) functions as a vital proxy for assessing carbohydrate status in plants. While class II T6P synthases (TPS) do not exhibit TPS activity, they are believed to play pivotal regulatory roles in trehalose metabolism. However, their precise functions in carbon metabolism and crop yield have remained largely unknown. Here, BnaC02.TPS8, a class II TPS gene, is shown to be specifically expressed in mature leaves and the developing pod walls of Brassica napus. Overexpression of BnaC02.TPS8 increased photosynthesis and the accumulation of sugars, starch, and biomass compared to wild type. Metabolomic analysis of BnaC02.TPS8 overexpressing lines and CRISPR/Cas9 mutants indicated that BnaC02.TPS8 enhanced the partitioning of photoassimilate into starch and sucrose, as opposed to glycolytic intermediates and organic acids, which might be associated with TPS activity. Furthermore, the overexpression of BnaC02.TPS8 not only increased seed yield but also enhanced seed oil accumulation and improved the oil fatty acid composition in B. napus under both high nitrogen (N) and low N conditions in the field. These results highlight the role of class II TPS in impacting photosynthesis and seed yield of B. napus, and BnaC02.TPS8 emerges as a promising target for improving B. napus seed yield.

Mycorrhizosphere bacteria inhibit greenhouse gas emissions from microplastics contaminated soil by regulating soil enzyme activities and microbial community structure

Microplastics (MPs) accumulation in terrestrial ecosystems can affect greenhouse gases (GHGs) production by altering microbial and soil structure. Presently, research on the MPs effect on plants is not consistent, and underlying molecular mechanisms associated with GHGs are yet unknown. For the first time, we conducted a microcosm study to explore the impact of MPs addition (Raw vs. aged) and Trichoderma longibrachiatum and Bacillus subtilis inoculation (Sole vs. combination) on GHGs emission, soil community structure, physiochemical properties, and enzyme activities. Our results indicated that the addition of aged MPs considerably enhanced the GHGs emissions (N2O (+16%) and CO2 (+21%), respectively), C and N cycling gene expression, microbial biomass carbon, and soil physiochemical properties than raw MPs. However, the soil microbial community structure and enzyme activities were enhanced in raw MPs added treatments, irrespective of the MPs type added to soil. However, microbial inoculation significantly reduced GHGs emission by altering the expression of C and N cycling genes in both types of MPs added treatments. The soil microbial community structure, enzymes activities, physiochemical properties and microbial biomass carbon were enhanced in the presence of microbial inoculation in both type of MPs. Among sole and combined inoculation of Trichoderma and Bacillus subtilis, the co-applied Trichoderma and Bacillus subtilis considerably reduced the GHGs emission (N2O (-64%) and CO2 (-61%), respectively) by altering the expression of C and N cycling genes regardless of MPs type used. The combined inoculation also enhanced soil enzyme activities, microbial community structure, physiochemical properties and microbial biomass carbon in both types of MPs treatment. Our findings provide evidence that polyethylene MPs likely pose a high risk of GHGs emission while combined application of Trichoderma and Bacillus subtilis significantly reduced GHGs emission by altering C and N cycling gene expression, soil microbial community structure, and enzyme activities under MPs pollution in a terrestrial ecosystem.

Function of hormone signaling in regulating nitrogen-use efficiency in plants

Nitrogen (N) is one of the most important nutrients for crop plant performance, however, the excessive application of nitrogenous fertilizers in agriculture significantly increases production costs and causes severe environmental problems. Therefore, comprehensively understanding the molecular mechanisms of N-use efficiency (NUE) with the aim of developing new crop varieties that combine high yields with improved NUE is an urgent goal for achieving more sustainable agriculture. Plant NUE is a complex trait that is affected by multiple factors, of which hormones are known to play pivotal roles. In this review, we focus on the interaction between the biosynthesis and signaling pathways of plant hormones with N metabolism, and summarize recent studies on the interplay between hormones and N, including how N regulates multiple hormone biosynthesis, transport and signaling and how hormones modulate root system architecture (RSA) in response to external N sources. Finally, we explore potential strategies for promoting crop NUE by modulating hormone synthesis, transport and signaling. This provides insights for future breeding of N-efficient crop varieties and the advancement of sustainable agriculture.

Molecular hydrogen positively regulates nitrate uptake and seed size by targeting nitrate reductase

Although the sources of molecular hydrogen (H2) synthesis in plants remain to be fully elucidated, ample evidence shows that plant-based H2 can regulate development and stress responses. Here, we present genetic and molecular evidence indicating that nitrate reductase (NR) might be a target of H2 sensing that positively regulates nitrogen use efficiency (NUE) and seed size in Arabidopsis (Arabidopsis thaliana). The expression level of NR and changes of NUE under control and, in particular, low nitrogen supply were positively associated with H2 addition supplied exogenously or through genetic manipulation. The improvement in nitrate assimilation achieved by H2 was also mediated via NR dephosphorylation. H2 control of seed size was impaired by NR mutation. Further genetic evidence revealed that H2, NR, and nitric oxide can synergistically regulate nitrate assimilation in response to N starvation conditions. Collectively, our data indicate that NR might be a target for H2 sensing, ultimately positively regulating nitrate uptake and seed size. These results provide insights into H2 signaling and its functions in plant metabolism.

Allelic variations of ClACO gene improve nitrogen uptake via ethylene-mediated root architecture in watermelon

KEY MESSAGE

The ClACO gene encoding 1-aminocyclopropane-1-carboxylate oxidase enabled highly efficient 15N uptake in watermelon. Nitrogen is one of the most essential nutrient elements that play a pivotal role in regulating plant growth and development for crop productivity. Elucidating the genetic basis of high nitrogen uptake is the key to improve nitrogen use efficiency for sustainable agricultural productivity. Whereas previous researches on nitrogen absorption process are mainly focused on a few model plants or crops. To date, the causal genes that determine the efficient nitrogen uptake of watermelon have not been mapped and remains largely unknown. Here, we fine-mapped the 1-aminocyclopropane-1-carboxylate oxidase (ClACO) gene associated with nitrogen uptake efficiency in watermelon via bulked segregant analysis (BSA). The variations in the ClACO gene led to the changes of gene expression levels between two watermelon accessions with different nitrogen uptake efficiencies. Intriguingly, in terms of the transcript abundance of ClACO, it was concomitant with significant differences in ethylene evolutions in roots and root architectures between the two accessions and among the different genotypic offsprings of the recombinant BC2F1(ZJU132)-18. These findings suggest that ethylene as a negative regulator altered nitrogen uptake efficiency in watermelon by controlling root development. In conclusion, our current study will provide valuable target gene for precise breeding of 'green' watermelon varieties with high-nitrogen uptake efficiencies.

Epigenetic Regulation of Nitrogen Signaling and Adaptation in Plants

Nitrogen (N) is a crucial nutrient that plays a significant role in enhancing crop yield. Its availability, including both supply and deficiency, serves as a crucial signal for plant development. However, excessive N use in agriculture leads to environmental and economic issues. Enhancing nitrogen use efficiency (NUE) is, therefore, essential to minimize negative impacts. Prior studies have investigated the genetic factors involved in N responses and the process of low-nitrogen (LN) adaptation. In this review, we discuss recent advances in understanding how epigenetic modifications, including DNA methylation, histone modification, and small RNA, participate in the regulation of N response and LN adaptation. We highlight the importance of decoding the epigenome at various levels to accelerate the functional study of how plants respond to N availability. Understanding the epigenetic control of N signaling and adaptation can lead to new strategies to improve NUE and enhance crop productivity sustainably.

Stimulating carbon and nitrogen metabolism of Chlorella pyrenoidosa to treat aquaculture wastewater and produce high-quality protein in plate photobioreactors

Wastewater treatment by microalgae is the economical and environmentally friendly strategy, but is still challenged with the strict discharge standards and valuable biomass exploitations. The carbon and nitrogen metabolism of Chlorella pyrenoidosa was improved by the red LED light and starch addition to treat Tilapia aquaculture wastewater (T-AW) and produce protein simultaneously in a plate photobioreactor. The red LED light was applied to improve the nutrient removals at an outdoor temperature, but the concentrations except total nitrogen did not satisfy the discharge standards. After starch addition, the removal efficiencies of total phosphorus, total nitrogen, chemical oxygen demand, and total ammonia nitrogen were 85.15, 96.96, 88.53, and 98.01 % in a flat-plate photobioreactor, respectively, which met the discharge standards and the protein production reached 0.60 g/L. At a molecular level, the metabolic flux and transcriptome analyses showed that red light promoted carbon flux of the Embden-Meyerhof-Pranas pathway and tricarboxylic cycle, and upregulated the levels of genes encoding α-amylase, glutamine synthetase, glutamate dehydrogenase, nitrate transporter, and ammonium transporter, which facilitated nutrients removal and provided nitrogen sources for protein biosynthesis. The harvesting C. pyrenoidosa possessed the 62 % essential amino acids and great lipid composition for biofuels. This study provided a new orientation for outdoor wastewater treatment and protein production by collaboratively regulating the carbon and nitrogen metabolism of microalgae.

Microplastics reduce nitrogen uptake in peanut plants by damaging root cells and impairing soil nitrogen cycling

Microplastic (MP) pollution severely impairs the sustainable development of modern agriculture. However, the mechanisms underlying the effects of MP contaminants on nutrient cycles in agroecosystems are poorly understood. In this study, we examined the impacts of two types of MPs, polypropylene (PP) and rubber crumb (RC), on nitrogen (N) transformation and N cycling in soil-peanut system. High concentrations of PP (1% w/w) and RC (1% w/w) inhibited vegetative growth and N uptake in peanut plants by damaging root cells and disturbing soil N cycling. These MPs damaged the plasma membranes of root cells and caused oxidative stress, as evidenced by the decreased number of xylem vessels, which in turn inhibited N uptake by roots. Integrated metagenomic and metabolomic analyses revealed that the differential soil metabolite levels in response to MP treatment affected the microbial community structure in the rhizosphere and the expression of key N cycling-related genes, resulting in altered N transformation and the decreased availability of N in rhizosphere soil. These findings provide the first evidence of the effects of MPs on N uptake in peanut plants and shed light on the importance of rational management of MPs for crop growth and yield in agroecosystems.

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.

Improving yield and quality of rice under acid rain stress by regulating nitrogen assimilation with exogenous Ca2

Acid rain threatens crop yield and nutritional quality, and Ca²⁺ can regulate plant responses to abiotic stresses. To improve the yield and nutritional quality of crops under acid rain stress, we applied exogenous Ca²⁺ to regulate nitrogen assimilation in rice seedlings under simulated acid rain stress (pH 4.5 or 3.0), taking yield and nutritional quality of rice as evaluation criteria. We found that Ca²⁺ (5 mM) maintained the total nitrogen content of rice at the seedling and booting stages to alleviate the inhibitory effect of simulated acid rain on rice yield. Meanwhile, Ca²⁺ improved the activity of glutamate synthase to eliminate the disruption of glutamine synthetase/glutamate synthase balance under simulated acid rain. It decreased the efficiency of nitrogen assimilation, thereby reducing the inhibition of essential amino acid content in rice. The mitigation effect on simulated acid rain at pH 4.5 was better than that of simulated acid rain at pH 3.0. Overall, Ca²⁺ may reduce the negative effect of acid rain on the yield and nutritional quality of crops.

Improving Nitrogen Use Efficiency in Rice for Sustainable Agriculture: Strategies and Future Perspectives

Nitrogen (N) is an important nutrient for the growth and development of rice. The application of N fertilizer has become one of the inevitable ways to increase rice yield due to insufficient soil N content. However, in order to achieve stable and high yield, farmers usually increase N fertilizer input without hesitation, resulting in a series of problems such as environmental pollution, energy waste and low production efficiency. For sustainable agriculture, improving the nitrogen use efficiency (NUE) to decrease N fertilizer input is imperative. In the present review, we firstly demonstrate the role of N in mediating root architecture, photosynthesis, metabolic balance, and yield components in rice. Furthermore, we further summarize the current agronomic practices for enhancing rice NUE, including balanced fertilization, the use of nitrification inhibitors and slow-release N fertilizers, the split application of N fertilizer, root zone fertilization, and so on. Finally, we discuss the recent advances of N efficiency-related genes with potential breeding value. These genes will contribute to improving the N uptake, maintain the N metabolism balance, and enhance the NUE, thereby breeding new varieties against low N tolerance to improve the rice yield and quality. Moreover, N-efficient varieties also need combine with precise N fertilizer management and advanced cultivation techniques to realize the maximum exploitation of their biological potential.

Carbon Dots Improve Nitrogen Bioavailability to Promote the Growth and Nutritional Quality of Soybeans under Drought Stress

The inefficient utilization of nitrogen (N) in soil and drought stress seriously threatens agricultural and food production. Herein, soil application of carbon dots (CDs, 5 mg kg^-1) promoted the growth and nutritional quality of soybeans by improving N bioavailability, which was beneficial to alleviate the economic losses caused by drought stress. Soil application of CDs enhanced the N-fixing ability of nodules, regulated rhizosphere processes, and ultimately enhanced N and water uptake in soybeans under drought stress. Compared to control (drought stress), the application of CDs under drought stress enhanced soybean nitrogenase activity by 8.6% and increased N content in soybean shoots and roots by 18.5% and 14.8%, respectively. CDs in soil promoted the secretion of root exudates (e.g., organic acids, fatty acids, and polyketides) and regulated beneficial microbial communities (e.g., Proteobacteria, Acidobacteria, Gemmatimonadetes, and Actinobacteria), thus enhancing the N release from soil. Besides, compared to control, the expression of GmNRT, GmAMT, GmLB, and GmAQP genes in roots were upregulated by 1.2-, 1.8-, 2.7-, and 2.3-fold respectively, implying enhanced N transport and water uptake. Furthermore, the proteins, fatty acids, and amino acids in soybean grains were improved by 3.4%, 6.9%, and 17.3%, respectively, as a result of improved N bioavailability. Therefore, CD-enabled agriculture is promising for improving the drought tolerance and quality of soybeans, which is of significance for food security in facing the crisis of global climate change.

Improving Crop Nitrogen Use Efficiency Toward Sustainable Green Revolution

The Green Revolution of the 1960s improved crop yields in part through the widespread cultivation of semidwarf plant varieties, which resist lodging but require a high-nitrogen (N) fertilizer input. Because environmentally degrading synthetic fertilizer use underlies current worldwide cereal yields, future agricultural sustainability demands enhanced N use efficiency (NUE). Here, we summarize the current understanding of how plants sense, uptake, and respond to N availability in the model plants that can be used to improve sustainable productivity in agriculture. Recent progress in unlocking the genetic basis of NUE within the broader context of plant systems biology has provided insights into the coordination of plant growth and nutrient assimilation and inspired the implementation of a new breeding strategy to cut fertilizer use in high-yield cereal crops. We conclude that identifying fresh targets for N sensing and response in crops would simultaneously enable improved grain productivity and NUE to launch a new Green Revolution and promote future food security.

Rice seed storage proteins: Biosynthetic pathways and the effects of environmental factors

Rice (Oryza sativa L.) is the most important food crop for at least half of the world's population. Due to improved living standards, the cultivation of high-quality rice for different purposes and markets has become a major goal. Rice quality is determined by the presence of many nutritional components, including seed storage proteins (SSPs), which are the second most abundant nutrient components of rice grains after starch. Rice SSP biosynthesis requires the participation of multiple organelles and is influenced by the external environment, making it challenging to understand the molecular details of SSP biosynthesis and improve rice protein quality. In this review, we highlight the current knowledge of rice SSP biosynthesis, including a detailed description of the key molecules involved in rice SSP biosynthetic processes and the major environmental factors affecting SSP biosynthesis. The effects of these factors on SSP accumulation and their contribution to rice quality are also discussed based on recent findings. This recent knowledge suggests not only new research directions for exploring rice SSP biosynthesis but also innovative strategies for breeding high-quality rice varieties.

Molecular Hydrogen Increases Quantitative and Qualitative Traits of Rice Grain in Field Trials

How to use environmentally friendly technology to enhance rice field and grain quality is a challenge for the scientific community. Here, we showed that the application of molecular hydrogen in the form of hydrogen nanobubble water could increase the length, width, and thickness of brown/rough rice and white rice, as well as 1000-grain weight, compared to the irrigation with ditch water. The above results were well matched with the transcriptional profiles of representative genes related to high yield, including up-regulation of heterotrimeric G protein β-subunit gene (RGB1) for cellular proliferation, Grain size 5 (GS5) for grain width, Small grain 1 (SMG1) for grain length and width, Grain weight 8 (GW8) for grain width and weight, and down-regulation of negatively correlated gene Grain size 3 (GS3) for grain length. Meanwhile, although total starch content in white rice is not altered by HNW, the content of amylose was decreased by 31.6%, which was parallel to the changes in the transcripts of the amylose metabolism genes. In particular, cadmium accumulation in white rice was significantly reduced, reaching 52% of the control group. This phenomenon was correlated well with the differential expression of transporter genes responsible for Cd entering plants, including down-regulated Natural resistance-associated macrophage protein (Nramp5), Heavy metal transporting ATPase (HMA2 and HMA3), and Iron-regulated transporters (IRT1), and for decreasing Cd accumulation in grain, including down-regulated Low cadmium (LCD). This study clearly showed that the application of molecular hydrogen might be used as an effective approach to increase field and grain quality of rice.

The regulatory module MdBT2-MdMYB88/MdMYB124-MdNRTs regulates nitrogen usage in apple

Less than 40% of the nitrogen (N) fertilizer applied to soil is absorbed by crops. Thus, improving the N use efficiency of crops is critical for agricultural development. However, the underlying regulation of these processes remains largely unknown, particularly in woody plants. By conducting yeast two-hybrid assays, we identified one interacting protein of MdMYB88 and MdMYB124 in apple (Malus × domestica), namely BTB and TAZ domain protein 2 (MdBT2). Ubiquitination and protein stabilization analysis revealed that MdBT2 ubiquitinates and degrades MdMYB88 and MdMYB124 via the 26S proteasome pathway. MdBT2 negatively regulates nitrogen usage as revealed by the reduced fresh weight, dry weight, N concentration, and N usage index of MdBT2 overexpression calli under low-N conditions. In contrast, MdMYB88 and MdMYB124 increase nitrate absorption, allocation, and remobilization by regulating expression of MdNRT2.4, MdNRT1.8, MdNRT1.7, and MdNRT1.5 under N limitation, thereby regulating N usage. The results obtained illustrate the mechanism of a regulatory module comprising MdBT2-MdMYB88/MdMYB124-MdNRTs, through which plants modulate N usage. These data contribute to a molecular approach to improve the N usage of fruit crops under limited N acquisition.

Targeting Nitrogen Metabolism and Transport Processes to Improve Plant Nitrogen Use Efficiency

In agricultural cropping systems, relatively large amounts of nitrogen (N) are applied for plant growth and development, and to achieve high yields. However, with increasing N application, plant N use efficiency generally decreases, which results in losses of N into the environment and subsequently detrimental consequences for both ecosystems and human health. A strategy for reducing N input and environmental losses while maintaining or increasing plant performance is the development of crops that effectively obtain, distribute, and utilize the available N. Generally, N is acquired from the soil in the inorganic forms of nitrate or ammonium and assimilated in roots or leaves as amino acids. The amino acids may be used within the source organs, but they are also the principal N compounds transported from source to sink in support of metabolism and growth. N uptake, synthesis of amino acids, and their partitioning within sources and toward sinks, as well as N utilization within sinks represent potential bottlenecks in the effective use of N for vegetative and reproductive growth. This review addresses recent discoveries in N metabolism and transport and their relevance for improving N use efficiency under high and low N conditions.