Integration of transcriptome and metabolome reveals the accumulation of related metabolites and gene regulation networks during quinoa seed development.

Quinoa seeds are gluten- and cholesterol-free, contain all amino acids required by the human body, have a high protein content, provide endocrine regulation, protein supplementation, and cardiovascular protection effects. However, metabolite accumulation and transcriptional regulatory networks in quinoa seed development are not well understood. Four key stages of seed development in Dianli-3260 and Dianli-557 were thus analyzed and 849 metabolites were identified, among which sugars, amino acids, and lipids were key for developmental processes, and their accumulation showed a gradual decrease. Transcriptome analysis identified 40,345 genes, of which 20,917 were differential between the M and F phases, including 8279 and 12,638 up- and down-regulated genes, respectively. Grain development processes were mainly enriched in galactose metabolism, pentose and glucuronate interconversions, the biosynthesis of amino acids, and carbon metabolism pathways, in which raffinose, phosphoenolpyruvate, series and other metabolites are significantly enriched, gene-LOC110689372, Gene-LOC110710556 and gene-LOC110714584 are significantly expressed, and these metabolites and genes play an important role in carbohydrate metabolism, lipid and Amino acid synthesis of quinoa. This study provides a theoretical basis to expand our understanding of the molecular and metabolic development of quinoa grains.

Effects of Arbuscular Mycorrhizal Fungi on Alleviating Cadmium Stress in Medicago truncatula Gaertn.

Heavy metal contamination is a global problem for ecosystems and human health. Remediation of contaminated soils has received much attention in the last decade. Aided mitigation of heavy metal phytotoxicity by arbuscular mycorrhizal fungi (AMF) is a cost-effective and environmentally friendly strategy. This study was carried out to investigate the mitigation effect of AMF inoculation on heavy metal toxicity in Medicago truncatula under soil cadmium stress. Therefore, a pot experiment was designed to evaluate the growth, chlorophyll fluorescence, Cd uptake and distribution, malondialdehyde (MDA) content, root soil physicochemical properties, and metabolite profile analysis of M. truncatula with/without AMF inoculation in Cd (20 mg/Kg)-contaminated soil. The results showed that inoculating AMF under Cd stress might enhance photosynthetic efficiency, increase plant biomass, decrease Cd and MDA content, and improve soil physicochemical properties in M. truncatula. Non-targeted metabolite analysis revealed that inoculation with AMF under Cd stress significantly upregulated the production of various amino acids in inter-root metabolism and increase organic acid and phytohormone synthesis. This study provides information on the physiological responses of mycorrhizal plants to heavy metal stress, which could help provide deeper insight into the mechanisms of heavy metal remediation by AMF.

The role of estrogen in circular RNA and metabonomics in a Neisseria gonorrhoeae infection model.

Background: Previous study shows that estrogen exerts both immunosuppressive and immunostimulative effects. Methods: In this study, estrogen was added to a Neisseria gonorrhoeae infection model, and transcriptome sequencing and metabolomics studies were performed to clarify the changes in circular RNA (circRNA) and metabolic pathways regulated by the addition of estrogen. Results: The results showed that following the addition of estrogen to the gonococcal infection model, the expression of circRNAs was up-regulated and the expression of circRNAs was down-regulated. In the metabolic group, it was found that after the addition of estrogen, the expression of nine metabolites was down-regulated and 61 metabolites were up-regulated. Furthermore, through network interaction analysis of differentially-expressed circRNAs and differentially-expressed metabolites, we found that the top 10 significantly related metabolites and circRNA were 2-Epoxybutane/novel_circ_0024520; 1,2-Epoxybutane/novel_circ_0061793; 2-Imino-4-methylpiperidine/novel_circ_0012178; 2-Imino-4-methylpiperidine/novel_circ_0056959; Acetone oxime/novel_circ_0012178; Adifoline/novel_circ_0012178; CARBETAPENTANE/novel_circ_0054387; CARBETAPENTANE/novel_circ_0056959; deoxy-PF1140/mmu_circ_0000397; and Methyl (2E,6Z)-dodecadienoate/novel_circ_0012178. Among these, CARBETAPENTANE/novel_circ_0054387 and CARBETAPENTANE/novel_circ_0056959 were positively correlated, while the remaining metabolites were negatively correlated. Conclusions: In this study, high-throughput sequencing and metabolomics mass spectrum were applied to screen the differentially-expressed circRNAs and metabolites regulated by estrogen, which will help to provide new research ideas and indicators for asymptomatic infections in women, and can be meaningful for the relevant study in the future.

Effects of polystyrene nanoplastics (PSNPs) on the physiology and molecular metabolism of corn (Zea mays L.) seedlings.

The effects of polystyrene nanoplastics (PSNPs) on the physiological and molecular metabolism of corn seedlings were examined by treating corn (Zea mays L.) seedlings with 100, 300, and 500 nm diameter PSNPs and examining plant photosynthetic characteristics, antioxidant enzyme systems, and molecular metabolism. After 15 days of exposure to PSNPs with different particle sizes (50 mg·L-1), the photosynthetic characteristics of the plant remained stable, and the maximum photochemical quantum yield (Fv/Fm) and non-photochemical quenching coefficient (NPQ) had no significant effects. The root microstructure was damaged and the antioxidant enzyme system was activated, and the content of malondialdehyde (MDA) was significantly increased by 2.25-4.50-fold. In addition, 100 nm and 300 nm PSNPs exposure caused root superoxide dismutase (SOD) activity to increase 1.28-fold and 1.53-fold, and glutathione-peroxidase (GSH-PX) activity increased 1.30-fold and 1.58-fold. Non-targeted metabolomics analysis identified a total of 304 metabolites. Exposure to 100, 300, and 500 nm PSNPs led to the production of 85 (upregulated: 85, downregulated: 0), 73 (upregulated: 73, downregulated: 0), and 86 (upregulated: 84, downregulated: 2) differentially expressed metabolites, respectively, in the plant roots. Co-expressed differential metabolites accounted for 38.2% of the metabolites and indicated a metabolic imbalance primarily in organic acids and derivatives in the root system. The most significant enrichment pathways were those of alanine, aspartate, and glutamate metabolism. Overall, exposure to PSNPs of different particle sizes activated the root antioxidant enzyme system and interfered with plant basic metabolism. The alanine, aspartate, and glutamate metabolic pathways appear to be closely related to plant mechanisms for tolerance/detoxification of PSNPs.

Microbial community structure and metabolome profiling characteristics of soil contaminated by TNT, RDX, and HMX.

This experiment was conducted to evaluate the ecotoxicity of typical explosives and their mechanisms in the soil microenvironment. Here, TNT (trinitrotoluene), RDX (cyclotrimethylene trinitramine), and HMX (cyclotetramethylene tetranitramine) were used to simulate the soil pollution of single explosives and their combination. The changes in soil enzyme activity and microbial community structure and function were analyzed in soil, and the effects of explosives exposure on the soil metabolic spectrum were revealed by non-targeted metabonomics. TNT, RDX, and HMX exposure significantly inhibited soil microbial respiration and urease and dehydrogenase activities. Explosives treatment reduced the diversity and richness of the soil microbial community structure, and the microorganisms able to degrade explosives began to occupy the soil niche, with the Sphingomonadaceae, Actinobacteria, and Gammaproteobacteria showing significantly increased relative abundances. Non-targeted metabonomics analysis showed that the main soil differential metabolites under explosives stress were lipids and lipid-like molecules, organic acids and derivatives, with the phosphotransferase system (PTS) pathway the most enriched pathway. The metabolic pathways for carbohydrates, lipids, and amino acids in soil were specifically inhibited. Therefore, residues of TNT, RDX, and HMX in the soil could inhibit soil metabolic processes and change the structure of the soil microbial community.

Biodegradation and physiological response mechanism of a bacterial strain to 2,4,6-trinitrotoluene contamination.

The aim of this study was to reveal the biodegradation characteristics and physiological response mechanism of a newly isolated bacterium to 2,4,6-trinitrotoluene (TNT) contamination. A Klebsiella variicola strain with high efficiency of TNT degradation was used as the test strain to analyze the changes in cell growth, morphology, and functional groups under different TNT concentrations (0, 100 mg⋅L-1) and the effects of TNT stress on the metabolic profile as revealed by non-targeted metabonomics. A TNT concentration of 100 mg L-1 caused a significant increase in the 5-day biochemical oxygen demand (BOD5) to 950 mg L-1, while the degradation rate of TNT reached 100% within 30 h after inoculation with Klebsiella variicola. Fourier transform infrared spectroscopy (FTIR) analysis showed changes in the characteristic peak of triamide by TNT treatment. Non-targeted metabonomics identified a total of 544 differentially produced metabolites under TNT treatment (252 upregulated and 292 downregulated), mainly lipids and lipid-like molecules. The metabolic pathways associated with amino acid biosynthesis and metabolism were the most significantly enriched pathways, and simultaneous detection showed that TNT was degraded to 4-amino-2,6-dinitrotoluene (DNT), 2-hydroxylamino-4,6-DNT, 2-amino-4,6-DNT, 2-amino-4-nitrotoluene, and 2,4-DNT. These results confirmed that Klebsiella variicola has a high tolerance to TNT and efficiently degrades it. The degradation mechanism involves TNT-induced accelerated amino acid biosynthesis, production of a protease to catalyze the TNT transformation, and the participation of the transformed TNT products in cell metabolism.

Glucolytic fingerprinting reveals metabolic groups within the genus Bifidobacterium: an exploratory study.

Microorganisms of the genus Bifidobacterium are inhabitants of diverse niches including the digestive tract of humans and animals. The species Bifidobacterium adolescentis, Bifidobacterium animalis, Bifidobacterium bifidum, Bifidobacterium breve and Bifidobacterium longum have qualified presumption of safety status granted by EFSA and several strains are considered probiotic, and are being included in functional dairy fermented products. In the present work we carried out a preliminary exploration of general metabolic characteristics and organic acid production profiles of a reduced number of strains selected from these and other species of the genus Bifidobacterium. The use of resting cells allowed obtaining metabolic fingerprints without interference of metabolites accumulated during growth in culture media. Acetic acid was the most abundant organic acid formed per mol of glucose consumed (from 1.07 ± 0.03 to 1.71 ± 0.22 mol) followed by lactic acid (from 0.34 ± 0.06 to 0.90 ± 0.12 mol), with moderate differences in production among strains; pyruvic, succinic and formic acids were also produced at considerably lower proportions, with variability among strains. The acetic to lactic acid ratio showed lower values in stationary phase as regard to the exponential phase for most, but not all, the microorganisms; this was due to a decrease in acetic acid molar proportions together with increases of lactic acid proportions in stationary phase. A linear discriminant analysis allowed to cluster strains into species with 51-100% probability, evidencing different metabolic profiles, according to the relative production of organic acids from glucose by resting cells, of microorganisms collected at the exponential phase of growth. Looking for a single metabolic marker that could adequately discriminate metabolic groups, we found that groups established by the acetic to lactic acid ratio fit well with differences previously evidenced by the discriminant analysis. The proper establishment of metabolic groups within the genus Bifidobacterium could help to select the best suited probiotic strains for specific applications.