Search Results (757)

The ecological rice–eel co-culture system is not only beneficial for enhancing productivity and sustainability in agriculture but also plays a crucial role in promoting environmental health. In the present study, based on the long-term positioning trial of the rice–eel co-culture system that began in 2016 and was sampled in 2023, the effects of reduced nitrogen fertilizer application on soil physico-chemical properties and the bacterial community were investigated. Treatments included a conventional regular fertilization treatment (RT), rice–eel co-culture system regular fertilization (IT), and nitrogen-reduction 10%, 30%, and 50% fertilization treatments (IT90, IT70, and IT50). Our research demonstrated the following: (1) Compared to RT, IT significantly increased soil water-stable macroaggregates (R0.25), mean weight diameter (MWD), geometric mean diameter (GMD), and available phosphorus content, with the increases of 15.66%, 25.49%, 36.00%, and 18.42%, respectively. Among the nitrogen-reduction fertilization treatments, IT90 showed the most significant effect. Compared to IT, IT90 significantly increased R0.25, MWD, GMD, and available nitrogen content, with increases of 4.4%, 7.81%, 8.82%, and 28.89%, respectively. (2) Compared to RT, at the phylum level, the diversity of Chloroflexi was significantly increased under IT and IT50, and the diversity of Gemmatimonadota was significantly increased under IT90, IT70, and IT50. The diversity of Acidobacteriota was significantly higher in IT90 and IT70 compared to IT. It was shown that the rice–eel co-culture system and nitrogen fertilizer reduction could effectively improve the degradation capacity of organic matter and promote soil nitrogen cycling. In addition, redundancy analysis (RDA) identified total phosphorus, total nitrogen, and available nitrogen (p = 0.007) as the three most important environmental factors driving changes in the bacterial community. (3) The functional prediction analysis of soil microbiota showed that, compared to RT, the diversity of pathways related to biosynthesis (carbohydrate biosynthesis and cell structure biosynthesis) and metabolism (L-glutamate and L-glutamine biosynthesis) was significantly higher under IT70, IT90, IT, and IT50 (in descending order). However, the diversity of pathways associated with degradation/utilization/assimilation (secondary metabolite degradation and amine and polyamine degradation) was significantly lower under all the rice–eel co-culture treatments. In conclusion, the rice–eel co-culture system improved soil physicochemical properties and the soil microbial environment compared with conventional planting, and the best soil improvement was achieved with 10% less N fertilizer application. Full article

Background/Objectives: Nitrogen (N) is an essential macronutrient that strongly influences maize growth and metabolism. While many studies have focused on nitrogen responses during later developmental stages, early-stage physiological and metabolic responses remain less explored. This study investigated the effect of different nitrogen-deficient levels on maize seedling growth and primary metabolite profiles. Methods: Seedlings were treated with N-modified nutrient solution, which contained 0% to 120% of the standard nitrogen level (8.5 mM). Results: Nitrogen starvation (N0) significantly reduced plant height (by 11–14%), shoot fresh weight (over 30%) compared to the optimal N supply (N100). Total leaf nitrogen content under N0–N20 was less than half of that in N100, whereas moderate N deficiency resulted in moderate reductions in growth and nitrogen content. Metabolite analysis revealed that N deficiency induced the accumulation of soluble sugars and organic acids (up to threefold), while sufficient N promoted the synthesis of amino acids related to nitrogen assimilation and protein biosynthesis. Statistical analyses (PCA and ANOVA) showed that both genotypes (MB and TYC) and tissue type (upper vs. lower leaves) influenced the metabolic response to nitrogen, with MB displaying more consistent shifts and TYC exhibiting greater variability under moderate stress. Conclusions: These findings highlight the sensitivity of maize seedlings to early nitrogen deficiency, with severity influenced by nitrogen level, tissue-specific position, and genotype; thus underscore the close coordination between physiological growth and primary metabolic pathways in response to nitrogen availability. These findings expand current knowledge of nitrogen response mechanisms and offer practical insights for improving nitrogen use efficiency in maize cultivation. Full article

Mung bean (Vigna radiate) sprouts are a popular choice among sprouted vegetables in Asia. Currently, the impact of nitrogen sources on the growth of mung bean sprouts remains poorly understood, and the underlying biological mechanisms responsible for the observed nonlinear growth patterns at different nitrogen levels have yet to be elucidated. In this research, in addition to conventional growth monitoring and quality evaluation, a comparative proteomics method was applied to investigate the molecular mechanisms of mung bean in response to 0, 0.025, 0.05, 0.075, and 0.1% urea concentrations. Our results indicated that mung bean sprout height and yield increased with rising urea concentrations but were suppressed beyond the L3 level (0.075% urea). Nitrate nitrogen and free amino acid content rose steadily with urea levels, whereas protein content, nitrate reductase activity, and nitrite levels followed a peak-then-decline trend, peaking at intermediate concentrations. Differential expression protein analysis was conducted on mung bean sprouts treated with different concentrations of urea, and more differentially expressed proteins participated in the L3 urea concentration. Analysis of common differential proteins among comparison groups showed that the mung bean sprouts enhanced their adaptability to urea stress environments by upregulating chlorophyll a-b binding protein and cationic amino acid transporter and downregulating the levels of glycosyltransferase, L-ascorbic acid, and cytochrome P450. The proteomic analysis uncovered the regulatory mechanisms governing these metabolic pathways, identifying 47 differentially expressed proteins (DEPs) involved in the biosynthesis of proteins, free amino acids, and nitrogen-related metabolites. Full article

Seed germination and early seedling growth are pivotal stages that define crop establishment and yield potential. Conventional agrochemicals used to improve these processes often raise environmental concerns, highlighting the need for sustainable alternatives. In this study, we demonstrated that water treated with cylindrical dielectric barrier discharge (c-DBD) plasma, enriched with nitric oxide (NO) and reactive nitrogen species (RNS), markedly enhanced onion (Allium cepa) seed germination and seedling vigor. The plasma-treated water (PTW) promoted rapid imbibition, broke dormancy, and accelerated germination rates beyond 98%. Seedlings irrigated with PTW exhibited significantly increased biomass, root and shoot length, chlorophyll content, and antioxidant enzyme activities, accompanied by reduced lipid peroxidation. Transcriptomic profiling revealed that PTW orchestrated a multifaceted regulatory network by upregulating gibberellin biosynthesis genes (GA3OX1/2), suppressing abscisic acid signaling components (ABI5), and activating phenylpropanoid metabolic pathways (PAL, 4CL) and antioxidant defense genes (RBOH1, SOD). These molecular changes coincided with elevated NO₂⁻ and NO₃⁻ levels and finely tuned hydrogen peroxide dynamics, underpinning redox signaling crucial for seed activation and stress resilience. Our findings establish plasma-generated NO-enriched water as an innovative, eco-friendly technology that leverages redox and hormone crosstalk to stimulate germination and early growth, offering promising applications in sustainable agriculture. Full article

Olive Mill Solid Waste (OMSW) presents an environmental challenge due to its toxicity and difficulties in its recycling. Prior studies suggest its potential as a substrate ingredient for cultivating edible mushrooms. Here, we investigate how varying OMSW concentrations in the substrate affect the synthesis pathways of α-glucan and β-glucan polysaccharides, alongside transcriptional and metabolic changes in Pleurotus eryngii. We also assessed the mushroom’s protein and nitrogen content. Our results highlight the critical role of substrate composition, demonstrating that the OMSW concentration significantly influences mushroom growth, yield, protein content, gene expression, and metabolite profiles. These findings establish OMSW not only as a viable recycling resource but also as a modulator of health-promoting compound synthesis in P. eryngii. Full article

Temperature is the most critical factor in fish preservation. Superchilled storage represents a novel technology that effectively retards quality deterioration in aquatic products. This study investigated the flavor variation patterns and deterioration mechanisms in 16 northern pike (Esox lucius) samples during superchilled storage (−3 °C) based on analysis using gas chromatography-ion mobility spectrometry (GC-IMS) and ultra-performance liquid chromatography–quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF/MS). The results indicate that GC-MS analysis identified 25 key volatile flavor compounds. These comprised seven ketones, thirteen alcohols, aldehydes including 2-methylbutanal, esters such as 2-heptyl acetate and methyl butyrate, as well as nitrogen-containing compounds, exemplified by pyrazines and indole. Non-targeted metabolomics further revealed four pivotal metabolic pathways, glycerophospholipid metabolism, purine metabolism, the pentose phosphate pathway, and arginine biosynthesis. These metabolic pathways were found to regulate flavor changes through modulation of lipid oxidation, nucleotide degradation, and amino acid metabolism. Notably, the arginine biosynthesis pathway exhibited significant correlations with the development of characteristic cold-storage off-flavors, mediated by glutamate accumulation and fumarate depletion. This investigation provided a theoretical foundation for optimizing preservation strategies in cold-water fish species at the molecular level. Full article

(1) Background: The escalating issue of soil degradation caused by excessive chemical fertilizer application poses significant threats to the sustainable development of Chinese flowering cabbage (Brassica campestris L. ssp. chinensis (L.) var. utilis Tsen et Lee) production. This research aimed to identify the impacts of reduced chemical fertilizer application integrated with organic amendments on cabbage yield and rhizosphere soil microenvironment characteristics. (2) Methods: A biennial field experiment was conducted during the 2022–2023 growing seasons at Lijun Town, Yinchuan City, Ningxia Hui Autonomous Region. Five treatments were tested: (i) Control (CK, no fertilizer); (ii) Conventional chemical fertilization (CF1, chemical fertilizer only); (iii) Reduced chemical fertilization (CF2, 30% less chemical fertilizer); (iv) CF2 + Well-decomposed chicken manure (FCM, 30% less chemical fertilizer + rotted chicken manure); and (v) CF2 + Vermicompost (FEM, 30% less chemical fertilizer + vermicompost). (3) Results: In 2023, the FCM treatment reduced electrical conductivity (EC) by 24.80% and pH by 2.16%, while the FEM treatment decreased EC by 31.13% and pH by 3.84% compared to controls. The FEM treatment significantly enhanced total nitrogen content by 12.71% and 8.85% relative to CF1 and FCM treatments, respectively. Compared to CF1, FEM increased soil organic matter content by 10.49% in 2022 and 11.24% in 2023. Organic fertilizer amendments elevated available nitrogen, phosphorus, and potassium levels while enhancing sucrase activity: FCM and FEM treatments increased sucrase activity by 23.62% and 32.00%, respectively, in 2022. Organic fertilization improved bacterial diversity and richness, optimized microbial community structure, and increased the relative abundance of Bacillus. It also upregulated microbial metabolic pathways related to carbohydrate and amino acid metabolism. Soil nutrients and bacterial community structure showed positive correlations with yield, whereas soil enzyme activities exhibited negative correlations. Key factors influencing yield were identified as Proteobacteria, Chloroflexi, available potassium, organic matter, available nitrogen, Actinobacteria, Firmicutes, total nitrogen, pH, and sucrase activity. (4) Conclusions: Integrated analysis of yield and soil microenvironmental parameters demonstrates that the fertilization regimen combining 30% chemical fertilizer reduction with vermicompost amendment (FEM) constitutes a more efficient fertilization strategy for Chinese flowering cabbage, making it suitable for regional promotion in the Ningxia area. Full article

In recent years, gut microbiota has emerged as a critical regulator of gastrointestinal health and disease, with its role in inflammatory bowel disease (IBD)—including Crohn’s disease and ulcerative colitis—being particularly significant. Among the many factors influencing the gut microbiota, dietary components such as fibers, fats, and polyphenols have received substantial attention. However, nitrogen-containing compounds, such as amino acids, nitrates, urea, and even nucleic acids, such as purines, remain underexplored despite their integral role in shaping microbial ecology, host metabolism, and immune responses. Some of these compounds are metabolized by gut bacteria into bioactive molecules such as short-chain fatty acids, ammonia, and nitric oxide, which exert diverse effects on mucosal integrity and inflammation. IBD pathophysiology is characterized by chronic inflammation, microbial dysbiosis, and compromised epithelial barriers. Nitrogen metabolism contributes significantly to these processes by influencing microbial composition, metabolite production, and host immune pathways. The breakdown of various nitrogen-containing compounds in the body leads to the production of byproducts, such as ammonia and hydrogen sulfide, which have been implicated in mucosal damage and immune dysregulation. At the same time, nitrogen-derived molecules, such as short-chain fatty acids and nitric oxide, exhibit protective effects, underscoring the dual role of dietary nitrogen in health and disease. This narrative review highlights the complex interactions between dietary nitrogen sources, gut microbiota, and IBD pathogenesis. We summarize the mechanisms by which nitrogen compounds influence microbial dynamics, identify their contributions to inflammation and barrier dysfunction, and explore their therapeutic potential. Multidisciplinary approaches integrating clinical, metabolomic, and microbiome research are essential to unravel the full scope of nitrogen’s role in gut health and identify novel therapeutic targets. Full article

Soybean relies on symbiotic nitrogen fixation (SNF) to support sustainable agriculture. In this study, we conducted a comprehensive analysis of the GmMYB transcription factor subfamily 20, with a focus on GmMYB62a and GmMYB62b. Phylogenetic and structural analyses revealed that these genes are evolutionarily conserved among legumes and possess distinct domain architectures. Expression profiling and GUS staining showed that GmMYB62a and GmMYB62b are constitutively expressed in nodules. Functional analyses revealed that loss of GmMYB62s function significantly reduced nodule density, while overexpression promoted nodulation. Transcriptomic analysis (RNA-seq) further demonstrated that GmMYB62s regulate key pathways, including hormone signaling, immune responses, and cell wall metabolism, thereby coordinating symbiotic interactions. Collectively, our findings identify GmMYB62a and GmMYB62b as critical molecular regulators of nodulation in soybean, providing promising targets for improving symbiotic nitrogen fixation efficiency in legume crops. Full article

Quercus acutissima seeds exhibit high desiccation sensitivity, posing significant challenges for long-term preservation. This study investigates the physiological and metabolic responses of soluble osmoprotectants—particularly soluble proteins and proline—during the desiccation process. Seeds were sampled at three critical moisture content levels: 38.8%, 26.8%, and 14.8%, corresponding to approximately 99%, 52%, and 0% germination, respectively. We measured germination ability, soluble protein content, and proline accumulation, and we performed untargeted metabolomic profiling using LC-MS. Soluble protein levels increased early but declined later during desiccation, while proline levels continuously increased for sustained osmotic adjustment. Metabolomics analysis identified a total of 2802 metabolites, with phenylpropanoids and polyketides (31.12%) and lipids and lipid-like molecules (29.05%) being the most abundant. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis showed that differentially expressed metabolites were mainly enriched in key pathways such as amino acid metabolism, energy metabolism, and nitrogen metabolism. Notably, most amino acids decreased in content, except for proline, which showed an increasing trend. Tricarboxylic acid cycle intermediates, especially citric acid and isocitric acid, showed significantly decreased levels, indicating energy metabolism imbalance due to uncoordinated consumption without effective replenishment. The reductions in key amino acids such as glutamic acid and aspartic acid further reflected metabolic network disruption. In summary, Q. acutissima seeds fail to establish an effective desiccation tolerance mechanism. The loss of soluble protein-based protection, limited capacity for proline-mediated osmotic regulation, and widespread metabolic disruption collectively lead to irreversible cellular damage. These findings highlight the inherent metabolic vulnerabilities of recalcitrant seeds and suggest potential preservation strategies, such as supplementing critical metabolites (e.g., TCA intermediates) during storage to delay metabolic collapse and mitigate desiccation-induced damage. Full article

The nitrogen cycle (N-cycle) is a cornerstone of global biogeochemistry, regulating nitrogen availability and affecting atmospheric chemistry, agricultural productivity, and ecological balance. Central to this cycle is the reversible interplay between nitrate (NO₃⁻) and nitrite (NO₂⁻), mediated by molybdenum-dependent enzymes—Nitrate reductases (NARs) and Nitrite oxidoreductases (NXRs). Despite catalyzing opposite reactions, these enzymes exhibit remarkable structural and mechanistic similarities. This review aims to elucidate the molecular underpinnings of nitrate reduction and nitrite oxidation by dissecting their enzymatic architectures, redox mechanisms, and evolutionary relationships. By focusing on recent structural, spectroscopic, and thermodynamic data, we explore how these two enzyme families represent “two sides of the same coin” in microbial nitrogen metabolism. Special emphasis is placed on the role of oxygen atom transfer (OAT) as a unifying mechanistic principle, the influence of environmental redox conditions, and the emerging evidence of bidirectional catalytic potential. Understanding this dynamic enzymatic interconversion provides insight into the flexibility and resilience of nitrogen-transforming pathways, with implications for environmental management, biotechnology, and synthetic biology. Full article

Cordycepin, a bioactive adenosine analog, holds promise in pharmaceutical and health product development. However, large-scale production remains constrained by the limitations of natural producers, Cordyceps spp. Herein, we report the reconstruction of the first genome-scale metabolic model (GSMM) for a cordycepin-producing strain of recombinant Aspergillus oryzae. The model, iNR1684, incorporated 1684 genes and 1947 reactions with 93% gene-protein-reaction coverage, which was validated by the experimental biomass composition and growth rate. In silico analyses identified key gene amplification targets in the pentose phosphate and one-carbon metabolism pathways, indicating that folate metabolism is crucial for enhancing cordycepin production. Nutrient optimization simulations revealed that chitosan, D-glucosamine, and L-aspartate preferentially supported cordycepin biosynthesis. Additionally, a carbon-to-nitrogen ratio of 11.6:1 was identified and experimentally validated to maximize production, higher than that reported for Cordyceps militaris. These findings correspond to a faster growth rate, enhanced carbon assimilation, and broader substrate utilization by A. oryzae. This study demonstrates the significant role of GSMM in uncovering rational engineering strategies and provides a quantitative framework for precision fermentation, offering scalable and sustainable solutions for industrial cordycepin production. Full article

Background: Huang Qin Decoction (HQD) is a well-established Traditional Chinese Medicine (TCM) formulation recognized for its application in the treatment of colorectal cancer (CRC). However, the precise therapeutic mechanisms remain inadequately defined. Methods: This study integrates metabolomics from a mouse model and network pharmacology to screen potential targets and bio-active ingredients of HQD. The pharmacological activity of HQD for CRC was evidenced via single-cell RNA sequencing (scRNA-seq), molecular docking, and molecular dynamics simulations. Atomic force microscopy (AFM) assays and cellular experimental validation were used to confirm the relative mechanisms. Results: The metabolite profile undergoes significant alterations, with metabolic reprogramming evident during the malignant progression of CRC liver metastasis. Network pharmacology analysis identified that HQD regulates several metabolic pathways, including arginine biosynthesis, alanine, aspartate, and glutamate metabolism, nitrogen metabolism, phenylalanine metabolism, and linoleic acid metabolism, by targeting key proteins such as aspartate aminotransferase (GOT1), cytochrome P450 1A2 (CYP1A2), and carbonic anhydrase 2 (CA2). ScRNA-seq analysis indicated that HQD may enhance the functionality of cytotoxic T cells, thereby reversing the immunosuppressive microenvironment. Virtual verification revealed a strong binding affinity between the identified hub targets and active constituents of HQD, a finding subsequently corroborated by AFM assays. Cellular experiments confirmed that naringenin treatment inhibits the proliferation, migration, and invasion of CRC cells by downregulating GOT1 expression and disrupting glutamine metabolism. Conclusions: Computational prediction and in vitro validation reveal the active ingredients, potential targets, and molecular mechanisms of HQD against CRC liver metastasis, thereby providing a scientific foundation for the application of TCM in CRC treatment. Full article

Plant growth-promoting rhizobacteria (PGPR) are beneficial rhizosphere microorganisms for plants. They can promote plant absorption of nutrients, inhibit pathogenic microorganisms, enhance plant tolerance to abiotic and biotic stresses, and improve plant growth. Isolating new beneficial microbes and elucidating their promoting mechanisms can facilitate the development of microbial fertilizers. This study combined transcriptome sequencing and related experiments to analyze the mechanism by which the endophytic fungus ‘BF-F’ promotes the growth of Sesuvium portulacastrum. We inoculated the ‘BF-F’ fungus beside S. portulacastrum seedlings as the experimental group. Meanwhile, S. portulacastrum seedlings not inoculated with ‘BF-F’ were set as the control group. After inoculation for 0 d, 7 d, 14 d, 21 d, and 28 d, the plant height and the number of roots were measured. Furthermore, transcriptome sequencing on the roots and leaves of the S. portulacastrum was conducted. Differentially expressed genes were screened, and KEGG enrichment analysis was performed. Nitrogen metabolism-related genes were selected, and qRT-PCR was conducted on these genes. Furthermore, we analyzed the metabolomics of ‘BF-F’ and its hormone products. The results showed that inoculation of ‘BF-F’ significantly promoted the growth of S. portulacastrum. After ‘BF-F’ inoculation, a large number of genes in S. portulacastrum were differentially expressed. The KEGG pathway enrichment results indicated that the ‘BF-F’ treatment affected multiple metabolic pathways in S. portulacastrum, including hormone signal transduction and nitrogen metabolism. The auxin signaling pathway was enhanced because of a decrease in AUX expression and an increase in ARF expression. Contrary to the auxin signal transduction pathway, the zeatin (ZT) signaling pathway was suppressed after the ‘BF-F’ treatment. ‘BF-F’ increased the expression of genes related to nitrogen metabolism (NRT, AMT, NR, and GAGOT), thereby promoting the nitrogen content in S. portulacastrum. The metabolites of ‘BF-F’ were analyzed, and we found that ‘BF-F’ can synthesize IAA and ZT, which are important for plant growth. Overall, ‘BF-F’ can produce IAA and enhance the nitrogen use efficiency of plants, which could have the potential to be used for developing a microbial fertilizer. Full article

Nitrogen (N) critically regulates wheat growth and grain quality, yet the molecular mechanisms underlying foliar nitrogen application remain unclear. This study evaluated the effects of foliar nitrogen application (12.25 kg ha⁻¹) on the growth, grain yield, and quality of spring wheat, as well as its molecular mechanisms. The results indicated that N was absorbed within 3 h post-application, with leaf nitrogen concentration peaking at 12 h. The N treatment increased whole-plant dry matter accumulation and grain protein content by 11.34% and 6.8%, respectively. Amino acid content peaked 24 h post-application, increasing by 25.3% compared to the control. RNA-sequencing analysis identified 4559 and 3455 differentially expressed genes at 3 h and 24 h after urea treatment, respectively, these DEGs being primarily involved in nitrogen metabolism, photosynthetic carbon fixation, amino acid biosynthesis, antioxidant systems, and nucleotide biosynthesis. Notably, the plastidic glutamine synthetase gene (GS2) is crucial in the initial phase of urea application (3 h post-treatment). The pronounced downregulation of GS2 initiates a reconfiguration of nitrogen assimilation pathways. This downregulation impedes glutamine synthesis, resulting in a transient accumulation of free ammonia. In response to ammonia toxicity, the leaves promptly activate the GDH (glutamate dehydrogenase) pathway to facilitate the temporary translocation of ammonium. This compensatory mechanism suggests that GS2 downregulation may be a key switch that redirects nitrogen metabolism from the GS/GOGAT cycle to the GDH bypass. Additionally, the upregulation of the purine and pyrimidine metabolic routes channels nitrogen resources towards nucleic acid synthesis, and thereby supporting growth. Amino acids are then transported to the seeds, culminating in enhanced seed protein content. This research elucidates the molecular mechanisms underlying the foliar response to urea application, offering significant insights for further investigation. Full article