Stable Isotope-Assisted Evaluation of Different Extraction Solvents for Untargeted Metabolomics of Plants

Metabolic profiling and antibacterial activity of tree wood extracts obtained under variable extraction conditions

INTRODUCTION

Tree bacterial diseases are a threat in forestry due to their increasing incidence and severity. Understanding tree defence mechanisms requires evaluating metabolic changes arising during infection. Metabolite extraction affects the chemical diversity of the samples and, therefore, the biological relevance of the data. Metabolite extraction has been standardized for several biological models. However, little information is available regarding how it influences wood extract's chemical diversity.

OBJECTIVES

This study aimed to develop a methodological approach to obtain extracts from different tree species with the highest reproducibility and chemical diversity possible, to ensure proper coverage of the trees' metabolome.

METHODS

A full factorial design was used to evaluate the effect of solvent type, extraction temperature and number of extraction cycles on the metabolic profile, chemical diversity and antibacterial activity of four tree species.

RESULTS

Solvent, temperature and their interaction significantly affected the extracts' chemical diversity, while the number of extraction cycles positively correlated with yield and antibacterial activity. Although 60% of the features were recovered in all the tested conditions, differences in the presence and abundance of specific chemical classes per tree were observed, including organooxygen compounds, prenol lipids, carboxylic acids, and flavonoids.

CONCLUSIONS

Each tree species has a unique metabolic profile, which means that no single protocol is universally effective. Extraction at 50 °C for three cycles using 80% methanol or chloroform/methanol/water showed the best results and is suggested for studying wood metabolome. These observations highlight the need to tailor extraction protocols to each tree species to ensure comprehensive metabolome coverage for metabolic profiling.

Widely Targeted Metabolomics Revealed the Metabolic Basis of Physiological Function and Flavor of Natto

Background: Natto is a fermented product derived from soybeans through the action of Bacillus subtilis natto, possessing various pharmacological and health-promoting properties. However, due to the absence of large-scale and systematic investigations into its metabolite profile, the mechanisms governing the biological functions and flavor characteristics of natto remain incompletely elucidated. Methods: In this study, a comprehensive, widely targeted metabolome analysis was conducted using UHPLC-MS/MS to compare soybeans and natto. Results: A total of 569 metabolites were identified, of which 160 exhibited differential expression between natto and soybeans, including 28 amino acids and their derivatives, 19 flavonoids, 18 alkaloids, and 10 nucleotides and their derivatives. Pathway enrichment analysis further demonstrated significant differences in the metabolic pathways between natto and soybeans, with these 160 differentially expressed metabolites primarily distributed across 40 metabolic pathways. KEGG pathway enrichment analysis of natto metabolites revealed that the majority of these mapped to three key metabolic pathways. Variations in the content of flavonoids and alkaloids, as well as changes in amino acid and saccharide composition and abundance, were found to collectively contribute to the distinctive flavor and biological functionality of natto. Conclusions: This study lays the foundation for future efforts to enhance the quality of natto.

Effects of transgenic modification on the bacterial communities in different niches of maize under glyphosate toxicity

Transgenic glyphosate-resistant maize has emerged as a way to expand the use of glyphosate for weed control. Studying the microbiome in the tissues and rhizosphere soil of transgenic plants is vital for understanding the glyphosate-resistant mechanism and optimizing the transgenic design of crops. In our study, the expression of a mutant cp4epsps gene in transgenic maize, which confers tolerance to glyphosate, was performed using the maize variety Xianyu 335 as the genetically modified acceptor line. This transgenic modification did not affect the initial bacterial community in the leaf, stem, or root of maize, but promoted a differential bacterial community in the rhizosphere soil. Under glyphosate application, the abundance of beneficial bacteria involved in N fixation and P solubilization in plant tissues and the rhizosphere soil of glyphosate-resistance maize were higher than those in the glyphosate-sensitive maize. In contrast, the abundance of pathogens had the opposite trend, suggesting that the enhanced health of transgenic maize prevented microbiome deterioration under glyphosate. The re-inoculation of bacterial strains isolated from glyphosate-resistance maize into the leaf and rhizosphere soil of glyphosate-sensitive maize resulted in an enhanced photosynthetic capacity in response to glyphosate, demonstrating the vital role of specific bacteria for glyphosate resistance. Our study provides important evidence of how transgenic maize tolerance to herbicides affects the bacterial communities across the maize niches under glyphosate toxicity.

An ideal leaf spraying strategy of brown sugar for edible medicinal plants of Viola inconspicua

The typical edible medicinal plants of Viola inconspicua were compared with leaf-green, biomass, metabolomes, and bacterial communities, after leaf-spraying water (A), brown sugar water (B), brown sugar, urea, and KH2PO4 water (C), or KH2PO4 and urea water (D). The plants sprayed with C solution presented relatively normal leaf-green and the highest biomass. In contrast of A group, B, C, and D groups were found with 72, 94, and 104 leaf differently accumulated metabolites (DAMs) and 105, 88, and 92 root DAMs, respectively. Typically, relative abundances of amino acids were elevated in C and D groups, while those of leaf flavonoids were increased in B group. Noticeably, leaf DAMs of C group versus A group had strong correlations with one to more phylum- or/and genus-dominant bacteria of C group. Taken together, leaf-spraying brown sugar, urea, and KH2PO4 water are ideal for holding leaf-green and biomass in V. inconspicua plants.

Untargeted Metabolomics and Soil Community Metagenomics Analyses Combined with Machine Learning Evaluation Uncover Geographic Differences in Ginseng from Different Locations

Panax ginseng C.A. Meyer, known as the "King of Herbs," has been used as a nutritional supplement for both food and medicine with the functions of relieving fatigue and improving immunity for thousands of years in China. In agricultural planting, soil environments of different geographical origins lead to obvious differences in the quality of ginseng, but the potential mechanism of the differences remains unclear. In this study, 20 key differential metabolites, including ginsenoside Rb1, glucose 6-phosphate, etc., were found in ginseng from 10 locations in China using an ultra-high performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UHPLC-QTOF-MS)-untargeted metabolomics approach. The soil properties were analyzed and combined with metagenomics technology to explore the possible relationships among microbial elements in planting soil. Through Spearman correlation analysis, it was found that the top 10 microbial colonies with the highest abundance in the soil were significantly correlated with key metabolites. In addition, the relationship model established by the random forest algorithm and the quantitative relationship between soil microbial abundance and ginseng metabolites were successfully predicted. The XGboost model was used to determine 20(R)-ginseng Rg2 and 2'(R)-ginseng Rg3 as feature labeled metabolites, and the optimal ginseng production area was discovered. These results prove that the accumulation of metabolites in ginseng was influenced by microorganisms in the planting soil, which led to geographical differences in ginseng quality.

Muti-omics revealed the mechanisms of MT-conferred tolerance of Elymus nutans Griseb. to low temperature at XiZang

BACKGROUND

Low temperature seriously limited the development of grass and crops in plateau. Thus, it is urgent to develop an effective strategy for improving the plant cold tolerance and elucidate the underlying mechanisms.

RESULTS

We found that MT alleviated the effects of cold stress on suppressing ENG growth, then improved cold tolerance of ENG. Integration of transcriptome and metabolome profiles showed that both cold exposure (TW) and MT reprogrammed the transcription pattern of galactose and flavonoids biosynthesis, leading to changes in compositions of soluble sugar and flavonoids in ENG. Additionally, TW inhibited the photosynthesis, and destroyed the antioxidant system of ENG, leading to accumulation of oxidant radicals represented by MDA. By contrast, MT promoted activities of antioxidant enzymes and flavonoid accumulation in ENG under cold condition, then reduced the MDA content and maintained normal expression of photosynthesis-related genes in ENG even under TW. Importantly, MT mainly enhanced cold tolerance of ENG via activating zeatin synthesis to regulate flavonoid biosynthesis in vivo. Typically, WRKY11 was identified to regulate MT-associated zeatin synthesis in ENG via directly binding on zeatin3 promoter.

CONCLUSIONS

MT could enhance ENG tolerance to cold stress via strengthening antioxidant system and especially zeatin synthesis to promote accumulation of flavonoids in ENG. Thus, our research gain insight into the global mechanisms of MT in promoting cold tolerance of ENG, then provided guidance for protecting plant from cold stress in plateau.

Changes in Quality Characteristics and Metabolite Composition of Low-Temperature and Nitrogen-Modified Atmosphere in Indica Rice during Storage

A low temperature (LT) is used to delay grain deterioration effectively. In practical applications, a nitrogen-modified atmosphere (N2) is also an effective way of preventing grain pests and delaying grain deterioration. However, there are few studies on grain quality changes using a combination treatment of an LT and N2 during storage. In this study, the storage quality, processing characteristics, and metabolites of rice under conventional storage (CS), LT (20 °C), N2 (95%), and LT+N2 treatments were analyzed for 180 days, under a controlled humidity of 65% ± 2%. The results showed that compared to the CS, LT, and N2 treatments, the LT+N2 treatment had the best effect in retarding the increase in MDA and electrical conductivity and deferring the decrease in CAT activity. In addition, the LT+N2 treatment maintained the color of the rice better and sustained a better processing quality. Non-targeted metabolomics analysis further confirmed that the LT+N2 treatment maintained the vigor of the rice and retarded its spoilage by activating the metabolisms of amino acids, carbohydrates, and flavonoids. These results suggest a favorable practice for preventing storage deterioration and increasing the processing quality for rice storage. They provided new insights into the mechanisms of rice quality changes using the combination treatment of an LT and N2.

Elucidating the mechanisms of Buyang Huanwu Decoction in treating chronic cerebral ischemia: A combined approach using network pharmacology, molecular docking, and in vivo validation

OBJECTIVE

This study aimed to explore the potential mechanisms of Buyang Huanwu Decoction (BHD) in regulating the AKT/TP53 pathway and reducing inflammatory responses for the treatment of chronic cerebral ischemia (CCI) using UHPLC-QE-MS combined with network pharmacology, molecular docking techniques, and animal experiment validation.

METHODS

Targets of seven herbal components in BHD, such as Astragalus membranaceus, Paeoniae Rubra Radix, and Ligusticum chuanxiong, were identified through TCMSP and HERB databases. CCI-related targets were obtained from DisGeNET and Genecards, with an intersection analysis conducted to determine shared targets between the disease and the herbal components. Functional enrichment analysis of these intersecting targets was performed. Networks of gene ontology and pathway associations with these targets were constructed and visualized. A pharmacological network involving intersecting genes and active components was delineated. A protein-protein interaction network was established for these intersecting targets and visualized using Cytoscape 3.9.1. The top five genes from the PPI network and their corresponding active components underwent molecular docking. Finally, the 2-vessel occlusion (2-VO) induced CCI rat model was treated with BHD, and the network pharmacology findings were validated using Western blot, RT-PCR, behavioral tests, laser speckle imaging, ELISA, HE staining, Nissl staining, LFB staining, and immunohistochemistry and immunofluorescence.

RESULTS

After filtration and deduplication, 150 intersecting genes were obtained, with the top five active components by Degree value identified as Quercetin, Beta-Sitosterol, Oleic Acid, Kaempferol, and Succinic Acid. KEGG pathway enrichment analysis linked key target genes significantly with Lipid and atherosclerosis, AGE-RAGE signaling pathway, IL-17 signaling pathway, and TNF signaling pathway. The PPI network highlighted ALB, IL-6, AKT1, TP53, and IL-1β as key protein targets. Molecular docking results showed the strongest binding affinity between ALB and Beta-Sitosterol. Behavioral tests using the Morris water maze indicated that both medium and high doses of BHD could enhance spatial memory in 2-VO model rats, with high-dose BHD being more effective. Laser speckle results showed that BHD at medium and high doses could facilitate CBF recovery in CCI rats, demonstrating a dose-response relationship. HE staining indicated that all doses of BHD could reduce neuronal damage in the cortex and hippocampal CA1 region to varying extents, with the highest dose being the most efficacious. Nissl staining showed that nimodipine and medium and high doses of BHD could alleviate Nissl body damage. LFB staining indicated that nimodipine and medium and high doses of BHD could reduce the pathological damage to fiber bundles and myelin sheaths in the internal capsule and corpus callosum of CCI rats. ELISA results showed that nimodipine and BHD at medium and high doses could decrease the levels of TNF-α, IL-6, IL-17, and IL-1β in the serum of CCI rats (p < 0.05). Immunohistochemistry and immunofluorescence demonstrated that BHD could activate the AKT signaling pathway and inhibit TP53 in treating CCI. Western blot and RT-PCR results indicated that nimodipine and all doses of BHD could upregulate Akt1 expression and downregulate Alb, Tp53, Il-1β, and Il-6 expression in the hippocampus of CCI rats to varying degrees (p < 0.05).

CONCLUSION

BHD exerts therapeutic effects in the treatment of CCI by regulating targets, such as AKT1, ALB, TP53, IL-1β, and IL-6, and reducing inflammatory responses.

Integrated metabolomics and transcriptomics reveal that HhERF9 positively regulates salt tolerance in Hibiscus hamabo Siebold & Zuccarini

Hibiscus hamabo Siebold & Zuccarini is one of the few semi-mangrove plants in the genus Hibiscus that can survive in saline-alkali soil and flooded land, but the mechanism underlying its adaptation to salt soil remains unknown. Here, to uncover this unsolved mystery, we characterized the changes in the accumulation of specific metabolites under salt stress in H. hamabo by integrating physiological, metabolic, and transcriptomic data, and found that osmotic adjustment and abscisic acid (ABA) is highly associated with the salt stress response. Further, a weighted gene co-expression network analysis was performed on the root transcriptome data, which identified three key candidate transcription factors responsive to salt stress. Among them, the expression HhERF9 was significantly upregulated under salt stress and ABA treatment and was involved in regulating the expression of genes related to the salt stress response. Further research indicated that HhERF9 enhances the accumulation of proline and soluble sugars by regulating the expression of genes such as NHX2 and P5CS. These findings provide a reference for improving H. hamabo through targeted genetic engineering and lay a theoretical foundation for its future promotion and cultivation in saline-alkali areas.

Metabolome and Its Mechanism Profiling in the Synergistic Toxic Effects Induced by Co-Exposure of Tenuazonic Acid and Patulin in Caco-2 Cells

Tenuazonic acid (TeA), usually found in cereals, fruits, vegetables, oil crops, and their products, was classified as one of the highest public health problems by EFSA as early as 2011, but it has still not been regulated by legislation due to the limited toxicological profile. Moreover, it has been reported that the coexistence of TeA and patulin (PAT) has been found in certain agricultural products; however, there are no available data about the combined toxicity. Considering that the gastrointestinal tract is the physiological barrier of the body, it would be the first target site at which exogenous substances interact with the body. Thus, we assessed the combined toxicity (cell viability, ROS, CAT, and ATP) in Caco-2 cells using mathematical modeling (Chou-Talalay) and explored mechanisms using non-targeted metabolomics and molecular biology methods. It revealed that the co-exposure of TeA + PAT (12.5 μg/mL + 0.5 μg/mL) can induce enhanced toxic effects and more severe oxidative stress. Mechanistically, the lipid and amino acid metabolisms and PI3K/AKT/FOXO signaling pathways were mainly involved in the TeA + PAT-induced synergistic toxic effects. Our study not only enriches the scientific basis for the development of regulatory policies but also provides potential targets and treatment options for alleviating toxicities.

Metabolomic profiling reveals biomarkers for diverse flesh colors in jelly fungi (Auricularia cornea)

Auricularia cornea has garnered attention due to its nutrition, culinary applications, and promising commercial prospects. However, there is little information available regarding the metabolic profiling of various colors strains. In this study, 642 metabolites across 64 classes were identified by LC-MS/MS to understand the metabolic variations between white, pink and dark brown strains. Notably, prenol lipids, carboxylic acids and fatty acyls accounted for 46.8 % of the total. Comparative analysis revealed 17 shared differential metabolites (DMs) among them. ACP vs ACW exhibited 17 unique metabolites, including d-arginine and maleic acid, etc. ACP vs ACB showed 5 unique metabolites, with only PS(18:1(9Z)/0:0) demonstrating up-regulation. ACB vs ACW showed 8 unique metabolites, including 4-hydroxymandelic acid and 5'-methylthioadenosine, etc. KEGG enrichment analysis highlighted pathway variations, and MetPA analysis identified key-pathways influencing DMs accumulation in A. cornea. This pioneering metabolomics study offers insights into A. cornea metabolic profiling, potential applications, and guides further research.

Influence of microorganisms on flavor substances and functional components of sojae semen praeparatum during fermentation: A study integrating comparative metabolomics and high-throughput sequencing

Sojae semen praeparatum (SSP), a fermented product known for its distinctive flavor and medicinal properties, undergoes a complex fermentation process due to the action of various microorganisms. Despite its widespread use, the effect of these microorganisms on the flavor compounds and functional components of SSP remains poorly understood. This study aimed to shed light on this aspect by identifying 20 metabolites as potential key flavor substances in SSP. Moreover, glycine and lysine were identified as crucial flavor substances. Additionally, 24 metabolites were identified as key functional components. The dominant microorganisms involved in the fermentation process were examined, revealing six genera of fungi and 12 genera of bacteria. At the species level, 16 microorganisms were identified as dominant through metagenome sequencing. Spearman correlation analysis demonstrated a strong association between dominant microorganisms and both flavor substances and functional components. Furthermore, the study validated the significance of four core functional microorganisms in improving the flavor and quality of SSP. This comprehensive exploration of functional microorganisms of SSP on key flavor substances/functional components during SSP fermentation. The study findings serve as a valuable reference for enhancing the overall flavor and quality of SSP.

Advances of Ion Mobility Platform for Plant Metabolomics

Metabolomics aims to profile the extensive array of metabolites that exists in different types of matrices using modern analytical techniques. These techniques help to separate, identify, and quantify the plethora of chemical compounds at various analytical platforms. Hence, ion mobility spectrometry (IMS) has emerged as an advanced analytical approach, exclusively owing to the 3D separation of metabolites and their isomers. Furthermore, separated metabolites are identified based on their mass fragmentation pattern and CCS (collision cross-section) values. The IMS provides an advanced alternative dimension to separate the isomeric metabolites with enhanced throughput with lesser chemical noise. Thus, the present review highlights the types, factors affecting the resolution, and applications of IMMS (Ion mobility mass spectrometry) for isomeric separations, and ionic contaminants in the plant samples. Furthermore, an overview of IMS-based applications for the identification of plant metabolites (volatile and non-volatile) over the last few decades has been discussed, followed by future assumptions for creating IM-based databases. Such approaches could be significant to accelerate and improve our knowledge of the vast chemical diversity found in plants.

Dynamic changes of microbiota and metabolite of traditional Hainan dregs vinegar during fermentation based on metagenomics and metabolomics

Hainan dregs vinegar (HNDV) is a traditional fermented food in China that is renowned for its unique flavor. HNDV is one of the most popular vinegars in Southeast Asia. However, research on the microorganisms and characteristic metabolites specific to HNDV is lacking. This study investigated the changes in microbial succession, volatile flavor compounds and characteristic non-volatile flavor compounds during HNDV fermentation based on metagenomics and metabolomics. The predominant microbial genera were Lactococcus, Limosilactobacillus, Lactiplantibacillus, and Saccharomyces. Unlike traditional vinegar, l-lactic acid was identified as the primary organic acid in HNDV. Noteworthy flavor compounds specific to HNDV included 3-methylthiopropanol and dl-phenylalanine. Significant associations were observed between six predominant microorganisms and six characteristic volatile flavor compounds, as well as seven characteristic non-volatile flavor compounds. The present results contribute to the development of starter cultures and the enhancement of HNDV quality.

Identification of characteristic flavor compounds and small molecule metabolites during the ripening process of Nuodeng ham by GC-IMS, GC-MS combined with metabolomics

To investigate effects of metabolites and volatile compounds on the quality of Nuodeng ham, gas chromatography-mass spectrometry (GC-MS), ultra-high performance liquid chromatography-Q exactive orbitrap-mass spectrometry (UHPLC-QE-MS), and gas chromatography-ion transfer spectroscopy (GC-IMS) were used to analyze the differences of free fatty acids, small molecule metabolites and volatile compounds of Nuodeng ham at different ripening stages (the first, second and third year sample). 40 free fatty acids were detected. 757 and 300 metabolites were detected in positive and negative ion modes, respectively. 48 differential metabolites (VIP ≥ 1.5, P < 0.05) might important components affecting flavor differences of Nuodeng ham. Metabolic pathways revealed that fermenting-ripening of ham was associated with 31 metabolic pathways, among, 19 pathways were significant (Impact > 0.01, P < 0.05). 58 volatile compounds were identified, combined with PCA and PLS-DA, 15 flavor markers were screened out. These findings provide a scientific basis for further research on the flavor formation mechanism of Nuodeng ham.

Analysis of the mechanism of curcumin against osteoarthritis using metabolomics and transcriptomics

Curcumin, a polyphenolic compound derived from the turmeric plant (Curcuma longa), has been extensively studied for its anti-inflammatory and anti-proliferative properties. The safety and efficacy of curcumin have been thoroughly validated. Nevertheless, the underlying mechanism for treating osteoarthritis remains ambiguous. This study aims to reveal the potential mechanism of curcumin in treating osteoarthritis by using metabolomics and transcriptomics. Firstly, we validated the effect of curcumin on inflammatory factors in human articular chondrocytes. Secondly, we explored the cellular metabolism mechanism of curcumin against osteoarthritis using cell metabolomics. Thirdly, we assessed the differences in gene expression of human articular chondrocytes through transcriptomics. Lastly, to evaluate the essential targets and elucidate the potential mechanism underlying the therapeutic effects of curcumin in osteoarthritis, we conducted a screening of the proteins within the shared pathway of metabolomics and transcriptomics. Our results demonstrated that curcumin significantly decreased the levels of inflammatory markers, such as IL-β, IL-6, and TNF-α, in human articular chondrocytes. Cell metabolomics identified 106 differential metabolites, including beta-aminopropionitrile, 3-amino-2-piperidone, pyrrole-2-carboxaldehyde, and various other components. The transcriptomic analysis yielded 1050 differential mRNAs. Enrichment analysis showed that the differential metabolites and mRNAs were significantly enriched in seven pathways, including glycine, serine, and threonine metabolism; pentose and glucuronate interconversions; glycerolipid metabolism; histidine metabolism; mucin-type o-glycan biosynthesis; inositol phosphate metabolism; and cysteine and methionine metabolism. A total of 23 key targets were identified to be involved in these pathways. We speculate that curcumin may alleviate osteoarthritis by targeting key proteins involved in glycine, serine, and threonine metabolism; inhibiting pyruvate production; and modulating glycolysis.

Effect of L. Plantarum Y279 and W. Cibaria Y113 on microorganism, lipid oxidation and fatty acid metabolites in Yu jiaosuan, A Chinese tradition fermented snack

Fatty acids are one of the main sources of flavour in fermented Yu jiaosuan (YJS) in southwest China. Bacilli (50.18 %) and Oxyphotobacteria (32.70 %) were the dominant class. Lactiplantibacillus (40.51 %) and Weissella (20.43 %) were the dominant species in the inoculated fermented group (HY). The peroxide value (ZY: 0.025 g/100 g, HY: 0.016 g/100 g) and lipoxygenase (LOX) (ZY: 5.7654 U/min·g, HY: 3.3856 U/min·g) in the HY group were significantly lower compared with the natural fermentation group (ZY), while acid lipase activity (ZY: 0.3184 U/h·g, HY: 0.7075 U/h·g) and neutral lipase activity (ZY: 12.65443 U/h·g, HY: 20.25142 U/h·g) were significantly higher than the control sample. Totally 40 differential fatty acid metabolites were screened. Arachidonic acid metabolism, unsaturated fatty acid biosynthesis and linoleic acid metabolism were potential metabolic pathways. Seven major bacterial species were closely associated with 15 differential fatty acid. This study contributes to the targeted production of fatty acid functional active substances of YJS.

Assessing the impact of Chlorantraniliprole (CAP) pesticide stress on oilseed rape (Brassia campestris L.): Residue dynamics, enzyme activities, and metabolite profiling

This study investigates the effects of chlorantraniliprole (CAP) pesticide stress on oilseed rape through comprehensive pot experiments. Assessing CAP residue variations in soil and oilseed rape (Brassia campestris L.), enzyme activities (POD, CPR, GST), and differential metabolites, we unveil significant findings. The average CAP residue levels were 18.38-13.70 mg/kg in unplanted soil, 9.94-6.30 mg/kg in planted soil, and 0-4.18 mg/kg in oilseed rape samples, respectively. Soil microbial influences and systemic pesticide translocation into oilseed rape contribute to CAP residue variations. Under the influence of CAP stress, oilseed rape displays escalated enzyme activities (POD, CPR, GST) and manifests 57 differential metabolites. Among these, 32 demonstrate considerable downregulation, mainly impacting amino acids and phenolic compounds, while 25 exhibit noteworthy overexpression, primarily affecting flavonoid compounds. This impact extends to 24 metabolic pathways, notably influencing amide biosynthesis, as well as arginine and proline metabolism. These findings underscore the discernible effects of CAP pesticide stress on oilseed rape.

A green-footprint approach for parallel multiclass analysis of contaminants in roasted coffee via LC-HRMS

The development and validation of a simple, comprehensive, and environment-friendly procedure to determine pesticide residues, naturally occurring and processing contaminants in roasted coffee is presented. A solid-liquid extraction of pesticides and mycotoxins with ethyl acetate and the concurrent partition of acrylamide to an aqueous phase follows a parallel analytical strategy that requires a single analytical portion to determine contaminants that are typically analyzed by dedicated single residue methods. The partition rules the lipids out of the aqueous extract before an "in-tube" dispersive solid phase microextraction (dSPME) for acrylamide retention. This is followed by the elution with buffer prior to injection. This extract is independently introduced into the system front end followed by the injection of the compounds from the organic phase, yet all spotted in the same run. A novel liquid chromatography high-resolution mass spectrometry (LC-HRMS) method setup enables the quantification of 186 compounds at 10 µg/kg, 226 at 5 µg/kg, and the acrylamide at 200 µg/kg for a total of 414 molecules, with acceptable recoveries (70-120%) and precision (RSD < 20%) making this strategy significantly faster and cost-effective than the dedicated single residue methods. Even though the presence of chlorpyrifos, acrylamide, and ochratoxin A was confirmed on samples of different origins, the findings were below the limit of quantification. During the storage of raw coffee, no proof of masking of OTA was found; however, condensation with glucose was evidenced during thermal processing experiments with sucrose by using stable isotope labeling (SIL). No detected conjugates were found in roasted nor in commercial sugar-added torrefacto samples, an industrial processing usually carried out above the decomposition temperature of the disaccharide.

Agricultural tillage practice and rhizosphere selection interactively drive the improvement of soybean plant biomass

Rhizosphere microbes play key roles in plant growth and productivity in agricultural systems. One of the critical issues is revealing the interaction of agricultural management (M) and rhizosphere selection effects (R) on soil microbial communities, root exudates and plant productivity. Through a field management experiment, we found that bacteria were more sensitive to the M × R interaction effect than fungi, and the positive effect of rhizosphere bacterial diversity on plant biomass existed in the bacterial three two-tillage system. In addition, inoculation experiments demonstrated that the nitrogen cycle-related isolate Stenotrophomonas could promote plant growth and alter the activities of extracellular enzymes N-acetyl- d-glucosaminidase and leucine aminopeptidase in rhizosphere soil. Microbe-metabolites network analysis revealed that hubnodes Burkholderia-Caballeronia-Paraburkholderia and Pseudomonas were recruited by specific root metabolites under the M × R interaction effect, and the inoculation of 10 rhizosphere-matched isolates further proved that these microbes could promote the growth of soybean seedlings. Kyoto Encyclopaedia of Genes and Genomes pathway analysis indicated that the growth-promoting mechanisms of these beneficial genera were closely related to metabolic pathways such as amino acid metabolism, melatonin biosynthesis, aerobactin biosynthesis and so on. This study provides field observation and experimental evidence to reveal the close relationship between beneficial rhizosphere microbes and plant productivity under the M × R interaction effect.

Integrated Transcriptome and Metabolome Analysis Reveals the Molecular Mechanism of Rust Resistance in Resistant (Youkang) and Susceptive (Tengjiao) Zanthoxylum armatum Cultivars

Chinese pepper rust is a live parasitic fungal disease caused by Coleosporium zanthoxyli, which seriously affects the cultivation and industrial development of Z. armatum. Cultivating and planting resistant cultivars is considered the most economical and environmentally friendly strategy to control this disease. Therefore, the mining of excellent genes for rust resistance and the analysis of the mechanism of rust resistance are the key strategies to achieve the targeted breeding of rust resistance. However, there is no relevant report on pepper rust resistance at present. The aim of the present study was to further explore the resistance mechanism of pepper by screening the rust-resistant germplasm resources in the early stage. Combined with the analysis of plant pathology, transcriptomics, and metabolomics, we found that compared with susceptible cultivar TJ, resistant cultivar YK had 2752 differentially expressed genes (DEGs, 1253 up-, and 1499 downregulated) and 321 differentially accumulated metabolites (DAMs, 133 up- and 188 down-accumulated) after pathogen infection. And the genes and metabolites related to phenylpropanoid metabolism were highly enriched in resistant varieties, which indicated that phenylpropanoid metabolism might mediate the resistance of Z. armatum. This finding was further confirmed by a real-time quantitative polymerase chain reaction analysis, which revealed that the expression levels of core genes involved in phenylpropane metabolism in disease-resistant varieties were high. In addition, the difference in flavonoid and MeJA contents in the leaves between resistant and susceptible varieties further supported the conclusion that the flavonoid pathway and methyl jasmonate may be involved in the formation of Chinese pepper resistance. Our research results not only help to better understand the resistance mechanism of Z. armatum rust but also contribute to the breeding and utilization of resistant varieties.

Peroxisomal compartmentalization of amino acid biosynthesis reactions imposes an upper limit on compartment size

Cellular metabolism relies on just a few redox cofactors. Selective compartmentalization may prevent competition between metabolic reactions requiring the same cofactor. Is such compartmentalization necessary for optimal cell function? Is there an optimal compartment size? Here we probe these fundamental questions using peroxisomal compartmentalization of the last steps of lysine and histidine biosynthesis in the fission yeast Schizosaccharomyces japonicus. We show that compartmentalization of these NAD+ dependent reactions together with a dedicated NADH/NAD+ recycling enzyme supports optimal growth when an increased demand for anabolic reactions taxes cellular redox balance. In turn, compartmentalization constrains the size of individual organelles, with larger peroxisomes accumulating all the required enzymes but unable to support both biosynthetic reactions at the same time. Our reengineering and physiological experiments indicate that compartmentalized biosynthetic reactions are sensitive to the size of the compartment, likely due to scaling-dependent changes within the system, such as enzyme packing density.

Mass Spectrometry-Based Multi-omics Integration with a Single Set of C. elegans Samples

Mass spectrometry-based large-scale multi-omics research has proven to be powerful in answering biological questions; nonetheless, it faces many challenges from sample preparation to downstream data integration. To efficiently extract biomolecules of different physicochemical properties, preparation of various sample type needs specific tailoring, especially of difficult ones, such as Caenorhabditis elegans. In this study, we sought to develop a multi-omics sample preparation method starting with a single set ofC. elegans samples to save time, minimize variability, expand biomolecule coverage, and promote multi-omics integration. We investigated tissue disruption methods to effectively release biomolecules and optimized extraction strategies to achieve broader and more reproducible biomolecule coverage in proteomics, lipidomics, and metabolomics workflows. In our assessment, we also considered speediness and usability of the approaches. The developed method was validated through a study of 16C. elegans samples designed to shine light on mitochondrial unfolded protein response (UPRmt), induced by three unique stressors─knocking down electron transfer chain element cco-1, mitochondrial ribosome protein S5 mrps-5, and antibiotic treatment Doxycycline. Our findings suggested that the method achieved great coverage of proteome, lipidome, and metabolome with high reproducibility and validated that all stressors triggered UPRmt in C. elegans, although generating unique molecular signatures. Innate immune response was activated, and triglycerides were decreased under all three stressor conditions. Additionally, Doxycycline treatment elicited more distinct proteomic, lipidomic, and metabolomic response than the other two treatments. This method has been successfully used to process Saccharomyces cerevisiae (data not shown) and can likely be applied to other organisms for multi-omics research.

Revealing ecotype influences on Cistanche sinensis: from the perspective of endophytes to metabolites characteristics

Introduction

Plant microorganism is critical to plant health, adaptability, and productive forces. Intriguingly, the metabolites and microorganisms can act upon each other in a plant. The union of metabolomics and microbiome may uncover the crucial connections of the plant to its microbiome. It has important benefits for the agricultural industry and human being health, particularly for Chinese medical science investigation.

Methods

In this last 2 years study, on the strength of the UPLC-MS/MS detection platform, we accurately qualitatively, and quantitatively measured the Cistanche sinensis fleshy stems of two ecotypes. Thereafter, through high-throughput amplicon sequencing 16S/ITS sequences were procured.

Results

PhGs metabolites including echinacoside, isoacteoside, and cistanoside A were significantly downregulated at two ecotypes of C. sinensis. Add up to 876 metabolites were monitored and 231 differential metabolites were analyzed. Further analysis of 34 core differential metabolites showed that 15 compounds with up-regulated belonged to phenolic acids, flavonoids, and organic acids, while 19 compounds with down-regulated belonged to phenolic acids, flavonoids, alkaloids, amino acids, lipids, and nucleotides. There was no noteworthy discrepancy in the endophytic bacteria's α and β diversity between sandy and loam ecotypes. By comparison, the α and β diversity of endophytic fungi was notably distinct. The fungal community of the loam ecotype is more abundant than the sandy ecotype. However, there were few such differences in bacteria. Most abundant genera included typical endophytes such as Phyllobacterium, Mycobacterium, Cistanche, Geosmithia, and Fusarium. LEfSe results revealed there were 11 and 20 biomarkers of endophytic bacteria and fungi in C. sinensis at two ecotypes, respectively. The combination parsing of microflora and metabolites indicated noteworthy relativity between the endophytic fungal communities and metabolite output. Key correlation results that Anseongella was positive relation with Syringin, Arsenicitalea is negative relation with 7-methylxanthine and Pseudogymnoascus is completely positively correlated with nepetin-7-O-alloside.

Discussion

The aim of this research is: (1) to explore firstly the influence of ecotype on C. sinensis from the perspective of endophytes and metabolites; (2) to investigate the relationship between endophytes and metabolites. This discovery advances our understanding of the interaction between endophytes and plants and provides a theoretical basis for cultivation of C. sinensis in future.

Optimization of energy production and central carbon metabolism in a non-respiring eukaryote

Most eukaryotes respire oxygen, using it to generate biomass and energy. However, a few organisms have lost the capacity to respire. Understanding how they manage biomass and energy production may illuminate the critical points at which respiration feeds into central carbon metabolism and explain possible routes to its optimization. Here, we use two related fission yeasts, Schizosaccharomyces pombe and Schizosaccharomyces japonicus, as a comparative model system. We show that although S. japonicus does not respire oxygen, unlike S. pombe, it is capable of efficient NADH oxidation, amino acid synthesis, and ATP generation. We probe possible optimization strategies through the use of stable isotope tracing metabolomics, mass isotopologue distribution analysis, genetics, and physiological experiments. S. japonicus appears to have optimized cytosolic NADH oxidation via glycerol-3-phosphate synthesis. It runs a fully bifurcated TCA pathway, sustaining amino acid production. Finally, we propose that it has optimized glycolysis to maintain high ATP/ADP ratio, in part by using the pentose phosphate pathway as a glycolytic shunt, reducing allosteric inhibition of glycolysis and supporting biomass generation. By comparing two related organisms with vastly different metabolic strategies, our work highlights the versatility and plasticity of central carbon metabolism in eukaryotes, illuminating critical adaptations supporting the preferential use of glycolysis over oxidative phosphorylation.

Untargeted Plant Metabolomics: Evaluation of Lyophilization as a Sample Preparation Technique

Lyophilization is a common method used for stabilizing biological samples prior to storage or to concentrate extracts. However, it is possible that this process may alter the metabolic composition or lead to the loss of metabolites. In this study, the performance of lyophilization is investigated in the example of wheat roots. To this end, native and ¹³C-labelled, fresh or already lyophilized root samples, and (diluted) extracts with dilution factors up to 32 and authentic reference standards were investigated. All samples were analyzed using RP-LC-HRMS. Results show that using lyophilization for the stabilization of plant material altered the metabolic sample composition. Overall, 7% of all wheat metabolites detected in non-lyophilized samples were not detected in dried samples anymore, and up to 43% of the remaining metabolites exhibited significantly increased or decreased abundances. With respect to extract concentration, less than 5% of the expected metabolites were completely lost by lyophilization and the recovery rates of the remaining metabolites were slightly reduced with increasing concentration factors to an average of 85% at an enrichment factor of 32. Compound annotation did not indicate specific classes of wheat metabolites to be affected.

Flavonoids in Amomum tsaoko Crevost et Lemarie Ameliorate Loperamide-Induced Constipation in Mice by Regulating Gut Microbiota and Related Metabolites

Amomum tsaoko (AT) is a dietary botanical with laxative properties; however, the active ingredients and mechanisms are still unclear. The active fraction of AT aqueous extract (ATAE) for promoting defecation in slow transit constipation mice is the ethanol-soluble part (ATES). The total flavonoids of ATES (ATTF) were the main active component. ATTF significantly increased the abundance of Lactobacillus and Bacillus and reduced the dominant commensals, such as Lachnospiraceae, thereby changing the gut microbiota structure and composition. Meanwhile, ATTF changed the gut metabolites mainly enriched in pathways such as the serotonergic synapse. In addition, ATTF increased the serum serotonin (5-HT) content and mRNA expression of 5-hydroxytryptamine receptor 2A (5-HT_2A), Phospholipase A2 (PLA2), and Cyclooxygenase-2 (COX2), which are involved in the serotonergic synaptic pathway. ATTF increased Transient receptor potential A1 (TRPA1), which promotes the release of 5-HT, and Myosin light chain 3(MLC3), which promotes smooth muscle motility. Notably, we established a network between gut microbiota, gut metabolites, and host parameters. The dominant gut microbiota Lactobacillus and Bacillus, prostaglandin J2 (PGJ2) and laxative phenotypes showed the most significant associations. The above results suggest that ATTF may relieve constipation by regulating the gut microbiota and serotonergic synaptic pathway and has great potential for laxative drug development in the future.

Metabolomic analysis and ecofriendly enrichment of sunflower meal extract

BACKGROUND

The presence of phenolic compounds in sunflower is well reported in the literature; however, knowledge is scarce when it comes to the composition of other secondary metabolites in this species and their by-products. This work evaluated, for the first time, the phytochemical composition of sunflower meal produced in Brazil. A combination of mixture design and central composite rotatable design 2³ models was then applied to maximize the recovery of bioactive compounds using ecologically friendly solvents and concentrating by applying activated carbon, a sustainable adsorbent. The product of this extraction-concentration was also evaluated by an untargeted metabolomic approach using ultra-performance liquid chromatography coupled to mass spectrometry.

RESULTS

A diverse and abundant profile of phenolic compounds was obtained from Brazilian sunflower meal: in total, 51 natural products were tentatively identified, 35 of which for the first time in sunflower. The sorption capacity of the activated charcoal, in the optimized process conditions, was effective in the separation and concentration of minority secondary metabolites. The ecofriendly extract proved to be enriched in plumberoside, p-coumaric acid, and alkaloids.

CONCLUSIONS

Investigation of the phytochemical profile of sunflower meal produced in Brazil pointed to several secondary metabolites reported for the first time in sunflower samples, including phenolic compounds, alkaloids, and terpenes. The use of activated charcoal in an alkaline medium as an adsorbent for the concentration of these phytochemicals, from an aqueous extract, generated a potentially cost-effective, ecofriendly extract, enriched in minor metabolites, indicating a possible innovative way to selectively obtain these compounds from sunflower meal. © 2022 Society of Chemical Industry.

Identification of a UDP-glucosyltransferase conferring deoxynivalenol resistance in Aegilops tauschii and wheat

Aegilops tauschii is the diploid progenitor of the wheat D subgenome and a valuable resource for wheat breeding, yet, genetic analysis of resistance against Fusarium head blight (FHB) and the major Fusarium mycotoxin deoxynivalenol (DON) is lacking. We treated a panel of 147 Ae. tauschii accessions with either Fusarium graminearum spores or DON solution and recorded the associated disease spread or toxin-induced bleaching. A k-mer-based association mapping pipeline dissected the genetic basis of resistance and identified candidate genes. After DON infiltration nine accessions revealed severe bleaching symptoms concomitant with lower conversion rates of DON into the non-toxic DON-3-O-glucoside. We identified the gene AET5Gv20385300 on chromosome 5D encoding a uridine diphosphate (UDP)-glucosyltransferase (UGT) as the causal variant and the mutant allele resulting in a truncated protein was only found in the nine susceptible accessions. This UGT is also polymorphic in hexaploid wheat and when expressed in Saccharomyces cerevisiae only the full-length gene conferred resistance against DON. Analysing the D subgenome helped to elucidate the genetic control of FHB resistance and identified a UGT involved in DON detoxification in Ae. tauschii and hexaploid wheat. This resistance mechanism is highly conserved since the UGT is orthologous to the barley UGT HvUGT13248 indicating descent from a common ancestor of wheat and barley.

Polyphosphate Kinase Is Required for the Processes of Virulence and Persistence in Acinetobacter baumannii

Acinetobacter baumannii, one of the most successful bacteria causing severe nosocomial infection, was identified as a top-priority pathogen by the WHO. Thus, genetic manipulations to clarify the potential targets for fighting A. baumannii resistance and virulence are vital. Polyphosphate (polyP) kinase (PPK) is conserved in nearly all bacteria and is responsible for polyP formation, which is associated with bacterial pathogenicity and antibiotic resistance. In this study, ppk1-deficient (Δppk1::Apr), ppk1-complemented (Δppk1::Apr/PJL02-ppk1), and wild-type strains of A. baumannii ATCC 17978 were used to determine the influence of PPK1 on A. baumannii virulence and persistence mainly by polyP quantification, surface motility, biofilm formation, and bacterial persistence assays. Our work found that PPK1 is indispensable for polyP formation in vivo and that the motility of the PPK1-deficient strain was significantly impaired due to the lack of a pilus-like structure typically present compared with the complemented and wild-type strains. The deficiency of PPK1 also inhibited the biofilm formation of A. baumannii and decreased bacterial persistence under stimuli of high-concentration ampicillin (Amp) treatment, H₂O₂ stress, heat shock, and starvation stress. Furthermore, ppk1-deficient bacterium-infected mice showed a significantly reduced bacterial load and a decreased inflammatory response. However, complementation with PPK1 effectively rescued the impaired virulence and persistence of ppk1-deficient A. baumannii. In addition, metabonomic analysis revealed that PPK1 was associated with glycerophospholipid metabolism and fatty acid biosynthesis. Taken together, our results suggest that targeting PPK1 to control A. baumannii pathogenicity and persistence is a feasible strategy to fight this pathogen.

IMPORTANCEA. baumannii was identified as a top-priority pathogen by the WHO due to its antibiotic resistance. Meanwhile, the pathogenicity of A. baumannii mediated by several vital virulence factors also cannot be ignored. Here, the role of PPK1 in A. baumannii was also explored. We found that the motility ability and biofilm formation of a PPK1-deficient strain were significantly impaired. Furthermore, PPK1 was essential for its persistence maintenance to resist stimuli of high-concentration Amp treatment, H₂O₂ stress, heat shock, and starvation stress. Metabonomic analysis revealed that PPK1 was associated with glycerophospholipid metabolism and fatty acid biosynthesis. In addition, ppk1-deficient bacterium-infected mice showed significantly reduced bacterial loads and a decreased inflammatory responses in vivo. Together, our results suggest that PPK1 is vital for A. baumannii pathogenicity and persistence.

Effects of Storage Temperature on Indica-Japonica Hybrid Rice Metabolites, Analyzed Using Liquid Chromatography and Mass Spectrometry

The Yongyou series of indica-japonica hybrid rice has excellent production potential and storage performance. However, little is known about the underlying mechanism of its storage resistance. In this study, Yongyou 1540 rice (Oryza sativa cv. yongyou 1540) was stored at different temperatures, and the storability was validated though measuring nutritional components and apparent change. In addition, a broad-targeted metabolomic approach coupled with liquid chromatography-mass spectrometry was applied to analyze the metabolite changes. The study found that under high temperature storage conditions (35 °C), Yongyou 1540 was not significantly worse in terms of fatty acid value, whiteness value, and changes in electron microscope profile. A total of 19 key differential metabolites were screened, and lipid metabolites related to palmitoleic acid were found to affect the aging of rice. At the same time, two substances, guanosine 3′,5′-cyclophosphate and pipecolic acid, were beneficial to enhance the resistance of rice under harsh storage conditions, thereby delaying the deterioration of its quality and maintaining its quality. Significant regulation of galactose metabolism, alanine, aspartate and glutamate metabolism, butyrate metabolism, and arginine and proline metabolism pathways were probably responsible for the good storage capacity of Yongyou 1540.

Towards a broader view of the metabolome: untargeted profiling of soluble and bound polyphenols in plants

Phenylalanine (Phe) is a central precursor for numerous secondary plant metabolites with a multitude of biological functions. Recent studies on the fungal disease Fusarium head blight in wheat showed numerous Phe-derived defence metabolites to be induced in the presence of the pathogen. These studies also suggest a partial incorporation of Phe-derived secondary metabolites into the cell wall. To broaden the view of the metabolome to bound Phe derivatives, an existing approach using ¹³C-labelled Phe as tracer was extended. The developed workflow consists of three successive extractions with an acidified acetonitrile-methanol-water mixture to remove the soluble plant metabolites, followed by cell wall hydrolysis with 4M aqueous NaOH, acidification with aqueous HCl, and liquid-liquid extraction of the hydrolysate with ethyl acetate. The untargeted screening of Phe-derived metabolites revealed 156 soluble compounds and 90 compounds in the hydrolysed samples including known cell wall constituents like ferulic acid, coumaric acid, and tricin. Forty-nine metabolites were found exclusively in the hydrolysate. The average cumulative extraction yield of the soluble metabolites was 99.6%, with a range of 91.8 to 100%. Repeatability coefficients of variation of the protocol ranged from 10.5 to 25.9%, with a median of 16.3%. To demonstrate the suitability of the proposed method for a typical metabolomics application, mock-treated and Fusarium graminearum-treated wheat samples were compared. The study revealed differences between the hydrolysates of the two sample types, confirming the differential incorporation of Phe-derived metabolites into the cell wall under infection conditions.

Transcriptomic and Metabolomic Analyses Reveal a Potential Mechanism to Improve Soybean Resistance to Anthracnose

Anthracnose, caused by Colletotrichum truncatum, leads to large-scale reduction in quality and yield in soybean production. Limited information is available regarding the molecular mechanisms of resistance to anthracnose in soybean. We conducted a transcriptomic and targeted metabolomic analysis of pods from two soybean lines, "Zhechun No. 3" (ZC3) and ZC-2, in response to C. truncatum infection. Factors contributing to the enhanced resistance of ZC-2 to anthracnose compared with that of ZC3, included signal transduction (jasmonic acid, auxin, mitogen-activated protein kinase, and Ca²⁺ signaling), transcription factors (WRKY and bHLH), resistance genes (PTI1, RPP13, RGA2, RPS6, and ULP2B), pathogenesis-related genes (chitinase and lipid transfer protein), and terpenoid metabolism. Targeted metabolomic analysis revealed that terpenoid metabolism responded more promptly and more intensely to C. truncatum infection in ZC-2 than in ZC3. In vitro antifungal activity and resistance induction test confirmed that jasmonic acid, auxin signaling and terpenoids played important roles in soybean resistance to anthracnose. This research is the first study to explore the molecular mechanisms of soybean resistance to anthracnose. The findings are important for in-depth analysis of molecular resistance mechanisms, discovery of resistance genes, and to expedite the breeding of anthracnose-resistant soybean cultivars.

Metabolomics Reveals 5-Aminolevulinic Acid Improved the Ability of Tea Leaves (Camellia sinensis L.) against Cold Stress

Tea is an important woody crop whose cultivation is severely limited by cold stress. Although 5-aminolevulinic acid (ALA) is known to be effective in alleviating abiotic stresses in plants, knowledge of the detailed metabolic response of tea plants to exogenous ALA-induced cold resistance is still limited-a lack which restricts our ability to protect tea plants from cold stress. In the present study, we performed an in-depth metabolomics analysis to elucidate the metabolic responses of tea plants to cold stress and explore the role of ALA in improving tea plants' cold-resistance capability. Metabolic profiles showed that cold stress altered various metabolisms in tea plants, especially galactose composition and flavonoid contents. Furthermore, exogenous ALA application altered a series of metabolisms associated with cold stress. Importantly, increases in metabolites, including catechin, 3,4-dihydroxyphenylacetic acid and procyanidin B2, involved in the mechanisms of ALA improved tea plants' cold resistance. Overall, our study deciphered detailed metabolic responses of tea plants to cold stress and elucidated the mechanisms of ALA in enhancing cold resistance through rebuilding compositions of soluble carbohydrates and flavonoids. Therefore, we have provided a basis for exogenous usage of ALA to protect tea plants from cold stress.

Analysis of the Formation of Sauce-Flavored Daqu Using Non-targeted Metabolomics

Sauce-flavored Daqu exhibits different colors after being stacked and fermented at high temperatures. Heiqu (black Daqu, BQ) with outstanding functions is difficult to obtain because its formation mechanism is unclear. In this study, we compared the metabolites in different types of Daqu using ultra-high-performance liquid chromatography triple quadrupole mass spectrometry to explore the formation process of BQ. We found that 251 differential metabolites were upregulated in BQ. Metabolic pathway analysis showed that "tyrosine metabolism" was enriched, and most metabolites in this pathway were differential metabolites upregulated in BQ. The tyrosine metabolic pathway is related to enzymatic browning and melanin production. In addition, the high-temperature and high-humidity fermentation environment of sauce-flavored Daqu promoted an increase in the melanoidin content via a typical Maillard reaction; thus, the melanoidin content in BQ was much higher than that in Huangqu and Baiqu. By strengthening the Maillard reaction precursor substances, amino acids, and reducing sugars, the content of Daqu melanoidin increased significantly after simulated fermentation. Therefore, the enzymatic browning product melanin and Maillard reaction product melanoidin are responsible for BQ formation. This study revealed the difference between BQ and other types of Daqu and provides theoretical guidance for controlling the formation of BQ and improving the quality of liquor.

Impact of prolonged withering on phenolic compounds and antioxidant capability in white tea using LC-MS-based metabolomics and HPLC analysis: Comparison with green tea

Contents of 20 bioactive compounds in 12 teas produced in Xinyang Region were determined by high performance liquid chromatography. Ultra-high performance liquid chromatography-quadrupole time of flight-mass spectrometry was developed for untargeted metabolomics analysis. Antioxidant activities were measured by 4 various assays. Those teas could be completely divided into green and white tea through principal component analysis, hierarchical cluster analysis and orthonormal partial least squares-discriminant analysis (R²Y = 0.996 and Q² = 0.982, respectively). The prolonged withering generated 472 differentiated metabolites between white and green tea, prompted significant decreases (variable importance in the projection > 1.0, p-value < 0.05 and fold change > 1.50) of most catechins and 8 phenolic acids to form 4 theaflavins, and benefited for the accumulation of 17 flavonoids and flavonoid glycosides, 8 flavanone and their derivatives, 20 free amino acids, 12 sugars and 1 purine alkaloid. Additionally, kaempferol and taxifolin contributed to 1,1-diphenyl-2-picrylhydrazyl (DPPH) scavenging ability of white tea.

Non-targeted metabolomic profiling of filamentous cyanobacteria Aphanizomenon flos-aquae exposed to a concentrated culture filtrate of Microcystis aeruginosa

Microcystis and Aphanizomenon are two toxic cyanobacteria genera, which frequently cause blooms in freshwater lakes. In some cases, succession of these two genera was observed in natural water bodies. Among the diverse factors contributing to such succession of dominant cyanobacterial genera, an allelopathic effect was proposed to be involved after the growth inhibitory effect of several Microcystis species on A. flos-aquae was investigated. However, the response of target species exposed to Microcystis are poorly described. In the present study, we used two toxic cyanobacteria strains, Aphanizomenon flos-aquae (Aph1395) and Microcystis aeruginosa strain 905 (Ma905) as research subjects. Aph1395 was inhibited with a necessarily concentrated culture filtrate of Ma905 (MA905-SPE), and the response of the inhibited Aph1395 cells was explored via non-targeted metabolomic profiling. In total, 3735 features were significantly different in the Aph1395 treated with Ma905-SPE vs. those treated with BG11 medium. Among them, the annotations of 146 differential features were considered to be confident via MS/MS spectrum matching analysis. Based on the reported physiological functions of the annotated differential features, we proposed a putative model that in the growth-inhibited Aph1395, a suite of increased or decreased features with activities in apoptosis, growth inhibition, and stress response processes contributed to, or defended against, the allelopathic effect caused by Ma905. Our findings provide insights into the interaction between the bloom forming cyanobacterial species that share the same ecological environment.

Investigation of Chemical Constituents of Eranthis longistipitata (Ranunculaceae): Coumarins and Furochromones

Aqueous-ethanol extracts (70%) from the leaves of Eranthis longistipitata Regel. (Ranunculaceae Juss.)-collected from natural populations of Kyrgyzstan-were studied by liquid chromatography with high-resolution mass spectrometry (LC-HRMS). There was no variation of the metabolic profiles among plants that were collected from different populations. More than 160 compounds were found in the leaves, of which 72 were identified to the class level and 58 to the individual-compound level. The class of flavonoids proved to be the most widely represented (19 compounds), including six aglycones [quercetin, kaempferol, aromadendrin, 6-methoxytaxifolin, phloretin, and (+)-catechin] and mono- and diglycosides (the other 13 compounds). In the analyzed samples of E. longistipitata, 14 fatty acid-related compounds were identified, but coumarins and furochromones that were found in E. longistipitata were the most interesting result; furochromones khelloside, khellin, visnagin, and cimifugin were found in E. longistipitata for the first time. Coumarins 5,7-dihydroxy-4-methylcoumarin, scoparone, fraxetin, and luvangetin and furochromones methoxsalen, 5-O-methylvisammioside, and visamminol-3'-O-glucoside were detected for the first time in the genus Eranthis Salisb. For all the above compounds, the structural formulas are given. Furthermore, detailed information (with structural formulas) is provided on the diversity of chromones and furochromones in other representatives of Eranthis. The presence of chromones in plants of the genus Eranthis confirms its closeness to the genus Actaea L. because chromones are synthesized by normal physiological processes only in these members of the Ranunculaceae family.

Fermented and Germinated Processing Improved the Protective Effects of Foxtail Millet Whole Grain Against Dextran Sulfate Sodium-Induced Acute Ulcerative Colitis and Gut Microbiota Dysbiosis in C57BL/6 Mice

This study investigated the effects of foxtail millet whole grain flours obtained through different processing methods on alleviating symptoms and gut microbiota dysbiosis in a dextran sulfate sodium (DSS)-induced murine colitis model. Sixty C57BL/6 mice were divided into six groups (n = 10 in each group), including one control group (CTRL) without DSS treatment and five DSS-treated groups receiving one of the following diets: AIN-93M standard diet (93MD), whole grain foxtail millet flour (FM), fermented (F-FM), germinated (G-FM), and fermented-germinated foxtail millet flour (FG-FM). A comparison of the disease activity index (DAI) demonstrated that foxtail millet whole grain-based diets could alleviate the symptoms of enteritis to varying degrees. In addition, 16S rRNA gene sequencing revealed that FG-FM almost completely alleviated DSS-induced dysbiosis. Mice on the FG-FM diet also had the lowest plasma IL-6 levels and claudin2 expression levels in the colon, indicating reduced systemic inflammation and improved gut barrier function. This study suggested that foxtail millet whole grain is an attractive choice for the intervention of IBD and gut microbiota dysbiosis, and its prebiotic properties are highly affected by the processing methods.

Anti-browning effect of Rosa roxburghii on apple juice and identification of polyphenol oxidase inhibitors

Enzymatic browning control of cloudy fruit juice with natural substances has received much attention for improving its nutritional and commercial value. This study explored the anti-browning potential of Rosa roxburghii in apple juice. The anti-browning effects and mechanisms were evaluated by serial measurements of appearance, browning index, polyphenol oxidase (PPO) activity, UPLC-QE-Orbitrap-MS identification, inhibition kinetics and molecular docking. The results showed that Rosa roxburghii juice (0.25%-1.25% w/w) could effectively inhibit browning and PPO activity of apple juice. Ascorbic acid (1.67 g/100 g) as a reducing agent was a main anti-browning factor. Furthermore, seven phenolic compounds in Rosa roxburghii were screened as PPO inhibitors. Representative phenolic inhibitors induced mixed or competitive inhibition of PPO, mainly driven by hydrophobic forces and hydrogen bonds. This work demonstrates that Rosa roxburghii is a promising natural anti-browning ingredient to control the browning of cloudy apple juice due to abundant ascorbic acid and PPO inhibitors.

Global Metabolomics Reveals That Vibrio natriegens Enhances the Growth and Paramylon Synthesis of Euglena gracilis

The microalga Euglena gracilis is utilized in the food, medicinal, and supplement industries. However, its mass production is currently limited by its low production efficiency and high risk of microbial contamination. In this study, physiological and biochemical parameters of E. gracilis co-cultivated with the bacteria Vibrio natriegens were investigated. A previous study reports the benefits of E. gracilis and V. natriegens co-cultivation; however, no bacterium growth and molecular mechanisms were further investigated. Our results show that this co-cultivation positively increased total chlorophyll, microalgal growth, dry weight, and storage sugar paramylon content of E. gracilis compared to the pure culture without V. natriegens. This analysis represents the first comprehensive metabolomic study of microalgae-bacterial co-cultivation, with 339 metabolites identified. This co-cultivation system was shown to have synergistic metabolic interactions between microalgal and bacterial cells, with a significant increase in methyl carbamate, ectoine, choline, methyl N-methylanthranilate, gentiatibetine, 4R-aminopentanoic acid, and glu-val compared to the cultivation of E. gracilis alone. Taken together, these results fill significant gaps in the current understanding of microalgae-bacteria co-cultivation systems and provide novel insights into potential improvements for mass production and industrial applications of E. gracilis.

Endosphere Microbiome and Metabolic Differences Between the Spots and Green Parts of Tricyrtis macropoda Leaves

Background

Plant leaves are important organs for photosynthesis and biological energy production. The leaves of Tricyrtis macropoda have an unusual spotted pattern. However, whether the spots of T. macropoda affect the plant microbiome and metabolites is unclear. In this study, we compared differences in the endosphere microbiome and plant metabolites in green parts and spots and the effects of spots on the photosynthesis of leaves.

Methods

16S/ITS sequences and metabolite spectra were obtained by high-throughput amplicon sequencing and ultra-high-performance liquid chromatography–high-resolution mass spectrometry, respectively. Changes in the diversity of the endophytic microbial community and metabolites were studied, and the effect of T. macropoda leaf spots on photosynthesis was examined by chlorophyll fluorescence.

Results

The results showed that the relative abundance of Cercospora fungi in the leaf spots of T. macropoda was significantly higher than that in the green parts (P < 0.05) while Colletotrichum fungi showed low abundance in the spots. Alkaloid and ketone metabolites were decreased in the green parts compared with the spots, and amino acids, organic acids, lipids, and other compounds were increased in the green parts compared with the spots. A combined analysis of microbial communities and metabolites showed a significant correlation between the endophytic fungal communities and metabolite production. The changes in these metabolites may cause changes in local leaf color. In addition, we found that the spot areas of T. macropoda can be photosynthetically normal.

Conclusion

This research showed the relationship between endophytic microorganisms and metabolites, and the findings advance our understanding of endophyte–plant interactions and provide a new direction for investigating the relationship between endophytes and phenotypes.

Identification of a New Giant Emrbryo Allele, and Integrated Transcriptomics and Metabolomics Analysis of Giant Embryo Development in Rice

Rice embryos are rich in high-quality protein, lipid, vitamins and minerals, representing the most important nutritional part of brown rice. However, the molecular mechanism of rice embryo development is poorly understood. In this study, two rice cultivars with contrasting embryo size (the giant embryo cultivar Dapeimi and the normal embryo cultivar 187R) were used to explore excellent genes controlling embryo size, and the developed near-isogenic lines (NILs) (NIL-D, which has the giant embryo phenotype, and its matching line, NIL-X) were used to explore transcript and metabolic properties in the earlier maturation stage of giant embryo development under natural conditions. The map-based cloning results demonstrated that Dapeimi is a novel allelic mutant of the rice GIANT EMBRYO (GE) gene, and the functional mutation site is a single cytosine deletion in the exon1. A total of 285 differentially accumulated metabolites (DAMs) and 677 differentially expressed genes (DEGs) were identified between NIL-D and NIL-X. The analysis of DAMs indicated that plants lacking GE mainly promoted energy metabolism, amino acid metabolism, and lipid metabolism pathways in the rice embryo. Pearson correlation coefficient showed that 300 pairs of gene-metabolites were highly correlated. Among them, OsZS_02G0528500 and OsZS_12G0013700 were considered to be key genes regulating L-Aspartic acid and L-Tryptophan content during rice giant embryo development, which are promising to be good candidate genes to improve rice nutrition. By analyzing rice embryo development through a combination of strategies, this research contributes to a greater understanding of the molecular mechanism of rice embryo development, and provides a theoretical foundation for breeding high-nutrition varieties.

Enhanced Metabolome Coverage and Evaluation of Matrix Effects by the Use of Experimental-Condition-Matched 13C-Labeled Biological Samples in Isotope-Assisted LC-HRMS Metabolomics

Stable isotope-assisted approaches can improve untargeted liquid chromatography-high resolution mass spectrometry (LC-HRMS) metabolomics studies. Here, we demonstrate at the example of chemically stressed wheat that metabolome-wide internal standardization by globally ¹³C-labeled metabolite extract (GLMe-IS) of experimental-condition-matched biological samples can help to improve the detection of treatment-relevant metabolites and can aid in the post-acquisition assessment of putative matrix effects in samples obtained upon different treatments. For this, native extracts of toxin- and mock-treated (control) wheat ears were standardized by the addition of uniformly ¹³C-labeled wheat ear extracts that were cultivated under similar experimental conditions (toxin-treatment and control) and measured with LC-HRMS. The results show that 996 wheat-derived metabolites were detected with the non-condition-matched ¹³C-labeled metabolite extract, while another 68 were only covered by the experimental-condition-matched GLMe-IS. Additional testing is performed with the assumption that GLMe-IS enables compensation for matrix effects. Although on average no severe matrix differences between both experimental conditions were found, individual metabolites may be affected as is demonstrated by wrong decisions with respect to the classification of significantly altered metabolites. When GLMe-IS was applied to compensate for matrix effects, 272 metabolites showed significantly altered levels between treated and control samples, 42 of which would not have been classified as such without GLMe-IS.

Metabolomics reveals the "Invisible" detoxification mechanisms of Amaranthus hypochondriacus at three ages upon exposure to different levels of cadmium

To decipher the Cd hyperaccumulation and tolerance mechanisms of plants and increase phytoremediation efficiency, in this study, the physiological effects induced by environmentally relevant concentrations (0, 25 and 200 mg/kg) of Cd were characterized in Amaranthus hypochondriacus (K472) at three growth stages using LC/MS-based metabolomics. Metabolomic analysis identified 31, 29 and 30 significantly differential metabolites (SDMs) in K472 exposed to Cd at the early, intermediate and late stages of vegetative growth, respectively. These SDMs are involved in nine metabolic pathways responsible for antioxidation, osmotic balance regulation, energy supplementation and the promotion of metabolites that participate in phytochelatin (PC) synthesis. K472 at the intermediate stage of vegetative growth had the strongest tolerance to Cd with the combined action of Ala, Asp and Glu metabolism, purine metabolism, Gly, Ser and Thr metabolism and Pro and Arg metabolism. Among these crucial metabolic biomarkers, purine metabolism could be the primary regulatory target for increasing the Cd absorption of K472 for the restoration of Cd-contaminated soil.