Journal of Agricultural and Food Chemistry

Potato (Solanum tuberosum L.), the worlds fourth most cultivated crop, suffers yield losses of up to 40-50% from early blight caused by the necrotrophic fungal pathogen Alternaria solani. In this study we performed gas chromatography-mass spectrometry (GC-MS)-based untargeted metabolomics to characterize temporal alterations in metabolite composition, metabolic pathway regulation, and discriminatory biomarker metabolites in the susceptible Indian potato variety Kufri Jyoti, analyzing infected leaves, non-infected leaves, and lesion-associated necrotic tissues across four days post-inoculation (DPI).Metabolite annotation identified 58 compounds, including sugars, organic acids, amino acids, and secondary metabolites.. Multivariate analyses resolved distinct, largely non-overlapping metabolic clusters for control, infected leaves (1-4 DPI), and lesion tissue (Bs1-Bs3). A biphasic metabolic response was observed: early infection (1-2 DPI) was characterized by general suppression of primary metabolism, while late infection (3-4 DPI) showed pronounced upregulation of glycolysis, the TCA cycle, GS/GOGAT, and the shikimate pathway. Key discriminatory metabolites included asparagine, oxoproline, GABA, phenylalanine, and aromatic amino acids. Lesion tissues exhibited distinct metabolic fingerprints, with early disruption of amino acid recycling followed by a late rebound of defense-associated metabolites. Notably, defence-associated phenolics were detected exclusively within lesion tissue and were absent from whole-leaf profiles, demonstrating that spatially resolved lesion sampling captures defence chemistry that whole-leaf analysis alone would miss. The identified biomarker metabolites, particularly those linked to the shikimate and GS/GOGAT pathways, represent promising candidates for metabolite-assisted breeding and targeted crop protection strategies against early blight in potato. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=115 SRC="FIGDIR/small/745268v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@18131edorg.highwire.dtl.DTLVardef@f4fbe6org.highwire.dtl.DTLVardef@1c5db61org.highwire.dtl.DTLVardef@c5ef6d_HPS_FORMAT_FIGEXP M_FIG C_FIG

Traditional Mongolian fermented foods have been extensively utilized for dietary regulation and the promotion of gastrointestinal health. However, spontaneous fermentation remains inherently unpredictable, leading to significant variations in microbial community dynamics, metabolite accumulation, and the consistency and quality of the final product. Drawing on the traditional preparation of Mongolian acidic foods, this study established a controlled production strategy for whole-wheat probiotic fermented soup (WWPFS) by combining enzymatic pretreatment with probiotic-directed fermentation. Physicochemical characterization, 16S rRNA gene-based microbial community profiling, LC-MS/MS-based untargeted metabolomics, safety evaluation, and an Escherichia coli-induced gut microbiota dysbiosis model were employed to optimize and comprehensively characterize the fermentation process of WWPFS. The optimized process established a reproducible fermentation system consistently dominated by Lactobacillus and Bacillus across independent fermentation batches. Compared with traditional spontaneous fermentation, probiotic-directed fermentation remodeled the physicochemical properties of the whole-wheat matrix, including carbon, nitrogen, phosphorus, sulfur, and mineral composition, and facilitated the accumulation of putatively annotated LC-MS/MS features, including DL-lactate, 1,4-D-xylobiose, diacetyl, and phenyllactic-acid-related features derivatives. Acute oral and 28-day repeated-dose toxicity evaluations showed no treatment-related adverse effects within the tested dose range and study duration. In the Escherichia coli-induced gut microbiota dysbiosis mouse model, microbial richness, diversity, and community structure differed among the experimental groups, and both low- and high-dose WWPFS groups showed significant shifts in overall gut microbial community composition relative to the model group after multiple-testing correction, together with directional recovery of selected model-responsive bacterial genera. Cross-system integration identified coordinated response patterns between fermentation-derived metabolite features and model-responsive gut bacterial taxa, supporting a potential metabolite-microbiota link in WWPFS-mediated gut microbiota modulation. In summary, probiotic-directed fermentation improved the controllability of the traditional Mongolian fermented food production process, reshaped its metabolic profile, and enhanced its potential to modulate the gut microbiota. These findings provide experimental evidence supporting the modernization of traditional Mongolian fermented foods and the development of probiotic-based functional foods.

Volatile organic compounds (VOCs) define the distinctive aroma of cannabis and critically influence consumer preference, cultivar authentication, and breeding programs. However, systematic characterization of VOC diversity across commercial drug-type cultivars remains limited. This study presents a comprehensive volatilomics-based phenotypic characterization of 165 commercial drug-type cannabis accessions using gas chromatography with flame ionization detection and mass spectrometry (GC-FID/MS). We identified 61 high-confidence VOCs assigned to three biosynthetic classes: terpenoids (n = 45), fatty acid-derived volatiles (n = 12) and amino acid-derived volatiles (n = 4), resolved into 12 subclasses. Analysis of variance revealed highly significant among-accession differences for all compounds (p < 0.001; 2 = 0.67-0.97), with repeatability estimates averaging 0.81 (range 0.50-0.95). Unsupervised clustering partitioned accessions into three distinct chemotypes (n = 90, 53, and 22), supported by principal component and t-SNE analyses. Machine learning-based feature selection identified a consensus panel of 12 discriminative compounds (camphene, -fenchene, sabinene, -terpinene, ({+/-})-limonene, -humulene, linalool, endo-fenchol, {Delta}3-carene, -thujene, {gamma}-terpinene and -phellandrene) that recovered the chemotype assignment of 32 of 33 held-out accessions. Estimated odor-activity screening ranked prenylthiol, -pinene, ({+/-})-limonene, linalool and myrcene highest among the odor-active compounds. All three chemotypes shared a prenylthiol-dominated core (67-77% of summed OAV) and were distinguished by the extent and nature of terpenoid modulation of that core: minimally modulated (Cluster ZERO), citrus-floral modulated (Cluster ONE) and pine-terpenic modulated (Cluster TWO). These findings indicate that volatile diversity in this panel can be summarized by three reproducible chemotypes, providing a quantitative basis for accession characterization and a foundation for future breeding and quality-assessment studies.

Background and aims Plant volatile organic compounds (VOCs) change dynamically with plant development and in response to environmental conditions. However, their potential as non-invasive indicators of phenological progression remains poorly explored. In this study, we developed a framework integrating automated VOC sampling, time-resolved VOC profiling, and machine-learning analysis for the non-invasive assessment of plant phenology. Using soybean (Glycine max (L.) Merr.), we investigated whether development-associated temporal variation in VOC emissions could delineate and predict developmental phases. Methods We collected VOCs daily under controlled environmental conditions from 16 to 43 days after sowing, spanning the transition from vegetative to reproductive stages, using an automated sampling system coupled with thermal desorption-gas chromatograph-mass spectrometer (TD-GC-MS). To characterise temporal changes in VOC profiles associated with phenological progression, we analysed the daily VOC data using a multi-step pipeline combining statistical filtering and similarity-based network analysis. We defined VOC-derived developmental phases from similarity patterns in the VOC profiles, then developed and evaluated machine-learning models to predict these phases. Key results Seven VOCs exhibited distinct phase-dependent dynamics, including green leaf volatiles and monoterpenes showing characteristic temporal changes during phenological progression. Network-based clustering of VOC profiles resolved five developmental phases closely aligned with conventional developmental stages. A machine-learning model predicted these phases from the VOC profiles with high predictive accuracy on independent test data, demonstrating that phenological progression could be quantitatively inferred from VOC emission patterns. Conclusions Our findings support VOC profiling as a reliable and non-invasive approach for assessing phenological progression in soybean. By extracting temporally structured VOC signals, this framework captures developmental information that may be difficult to obtain through visual observation alone, particularly after canopy closure. VOC profiling offers a practical tool for monitoring crop developmental dynamics and has broader potential for plant phenotyping and precision crop management.

Green synthesis of zinc oxide nanoparticles (ZnO NPs) offers a sustainable strategy for developing multifunctional antimicrobial nanomaterials. In this study, ZnO NPs were synthesized using Azadirachta indica leaf extract and characterized by UV-vis spectroscopy, FTIR, XRD, SEM, and GC-MS. The nanoparticles exhibited a characteristic absorption peak at 352 nm, a direct band gap of 3.07 eV, and hexagonal wurtzite crystallinity with an average crystallite size of approximately 32 nm. The biosynthesized ZnO NPs showed concentration-dependent antibacterial activity against Erwinia carotovora, producing inhibition zones of up to 25.9 mm. Mechanistic studies revealed significant membrane damage, evidenced by 4.77-fold and 5.62-fold increases in extracellular protein and amino acid leakage, respectively, with marked alterations in bacterial protein profiles detected by SDS-PAGE. The nanoparticles also exhibited strong antioxidant activity, achieving 89.4% DPPH radical scavenging, and induced dose-dependent cytotoxicity in HepG2 cells with an estimated IC50 of 124.8 g/mL. These findings demonstrate that neem-mediated ZnO nanoparticles possess potent antibacterial activity through membrane disruption while exhibiting promising antioxidant properties, highlighting their potential as eco-friendly nanomaterials for the management of bacterial soft rot and other phytopathogenic diseases.

Type 2 diabetes (T2D) is a prevalent metabolic disorder affecting millions worldwide, characterized by insulin resistance and impaired glucose homeostasis. While mammalian models are widely used, Drosophila melanogaster provides a powerful alternative due to its conserved insulin signaling pathways, genetic tractability, and suitability for high throughput studies. In addition to glucose dysregulation, lipid metabolism plays a crucial role in T2D pathophysiology, as alterations in lipid composition contribute to insulin resistance and metabolic dysfunction. Lipidomic studies have emerged as an essential approach to identify metabolic signatures and potential biomarkers for disease progression and therapeutic targeting. In this study, T2D like model was established by inducing insulin resistance through knockdown of the insulin receptor in brain insulin-producing cells using the dilp2-Gal4>UAS-InRRNAi system. This genetic manipulation resulted in significant metabolic dysregulation, including elevated glucose, trehalose, and triacylglyceride levels, along with increased oxidative stress indicators. Additionally, mRNA expression analysis of key insulin signaling components, including insulin receptor substrate 1, dilp2, dilp3, dilp5, and phosphorylated Akt, further validated the model. To further investigate metabolic alterations, Lipid profiling was performed using ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UPLC-QTOF-MS) in non targeted LC-MS-based metabolomics approach to identify lipid biomarkers associated with T2D. Multivariate statistical analyses, including PCA and PLS-DA, revealed distinct lipid signatures between wild-type and T2D flies. Notably, specific phosphatidylglycerol species PG 34:0, PG 34:4, PA 38:3, PIP 38:1, PIP2 38:6, and LPS 24:0 demonstrated an area under the curve (AUC) of 1, indicating their strong reliability as lipid biomarkers for T2D diagnosis.

Although the biosynthetic pathways of benzylisoquinoline alkaloids (BIAs) have been extensively investigated in several plant species, their transcriptional regulatory mechanisms remain only partially understood. Jasmonate (JA)-responsive group IX APETALA2/Ethylene Responsive Factor (AP2/ERF) transcription factors (TFs) are well-known regulators of specialized plant metabolism, including the biosynthesis of various alkaloids. However, their specific roles in BIA biosynthesis remain largely elusive. Here, we isolated five novel group IX AP2/ERF TFs, designated Benzylisoquinoline alkaloid Jasmonate-responsive AP2/ERF (BJE1-5), from Coptis japonica. Phylogenetic analysis revealed that Benzylisoquinoline alkaloid Jasmonate-responsive AP2/ERF (BJE) proteins belong to subclades distinct from group IXa, which contains well-known AP2/ERF TFs involved in alkaloid biosynthesis. Transient expression analyses in C. japonica protoplasts demonstrated that certain BJEs, particularly CjBJE3 and CjBJE5, positively regulated BIA biosynthetic genes through a mutual regulatory network among BJE members. Moreover, CjBJE3 expression was regulated by CjbHLH1, a unique-type basic helix-loop-helix (bHLH) TF specific to BIA-producing plants. Furthermore, heterologous expression of CjBJE3 and CjBJE5 in cultured Eschscholzia californica cells significantly enhanced the overall BIA production, particularly by increasing end-product benzophenanthridine BIAs, highlighting several uncharacterized biosynthetic genes clustered in the genome. Our findings suggest that BIA-producing species have developed a specific regulatory network comprised of CjbHLH1 and BJE TFs, providing valuable clues for identifying novel biosynthetic enzymes.

Mycosporine-like amino acids (MAAs) are among nature's most effective sunscreen compounds, capable of converting harmful ultraviolet radiation into harmless heat, and are widely distributed in marine organisms such as red macroalgae. Although decades of research have led to numerous discoveries, the rate of new MAA identifications has declined. To address this, we considerably expanded our previously developed combinatorial MAA database, increasing the number of covered structures tenfold. Following a comprehensive literature search for plausible but undescribed building blocks, the database now incorporates an extensive set of proteinogenic and non-proteinogenic amino acids, as well as other marine organic osmolytes, in combination with all (currently) known MAA scaffolds. This expanded resource was integrated into our identification platform, which combines UHPLC-VWD-HRMS2 analysis, feature-based molecular networking, and bioinformatics-driven annotation. Application of this updated workflow enabled the isolation and structural elucidation of a novel MAA, mycosporine-cysteinolic acid, from the red marine macroalga Vertebrata lanosa. Altogether, this study provides a valuable extension of the bioinformatics-based MAA screening pipeline, enhancing the annotation and discovery of novel MAAs in natural matrices.

Cannabis is well known for its pungent, skunk-like aroma. Recent chemical studies have identified prenylated and C6 volatile sulfur compounds as contributors to its skunky and citrus-like aromas, but the pathways that produce these compounds remain unknown. This gap limits efforts to explain variation in sulfur-aroma traits and to selectively enhance or reduce those traits. To address this gap, we used the known chemistry of sulfur-containing volatiles in Cannabis and characterized sulfur and volatile biosynthetic pathways in other plant species to select candidate enzyme groups. Because the GMO cultivar is anecdotally associated with a pronounced sulfurous aroma, reference protein sequences and profile hidden Markov models were used to search its version 1 (v1) primary high-confidence protein set of 55,790 sequences. These searches recovered 975 unique proteins. Sequence screening retained 941 candidates across 20 reporting categories; 939 contained all expected domains, while the two candidates assigned to the methionine gamma-lyase (MGL)-nearest category had no category-specific expected-domain rule. The largest reporting category comprised 359 proteins containing a cytochrome P450 domain, recovered through a search motivated by cytochrome P450 family 74 (CYP74) enzymes involved in oxylipin and plant volatile formation. Thirteen of these proteins were also recovered by at least one full-length CYP74 reference search. Other large reporting categories included 218 sugar-transferase, 83 glutathione-transferase, and 61 alcohol dehydrogenase candidates. Comparison with the Cannabis Expression Atlas linked 168 candidates to 128 annotated genes through 100%-identity amino-acid matches spanning at least 80% of each GMO v1 candidate protein. Twenty-nine genes were tissue-specific, including 13 root-specific and 6 trichome-specific genes. These results define candidates for biochemical testing and direct searches for additional enzymes acting upstream and downstream in Cannabis sulfur-volatile pathways.

1. Since plants interact with their environment through complex combinations of phytochemicals rather than metabolites in isolation, quantifying plant chemodiversity is of increasing interest. Although functionally relevant, structural disparity is mostly neglected in measures of chemodiversity because its integration relies on known compound identity, limiting broad application. 2. We established an approach deriving compound dissimilarity from UV-Vis spectra in HPLC-DAD datasets, evaluated how it relates to structure- or biosynthesis-based approaches, and examined whether it provides meaningful contributions to chemodiversity measures. For this, we applied it in an experiment full-factorially testing the effects of drought and herbivory on Solanum dulcamara leaf chemodiversity. 3. UV-Vis spectral dissimilarity aligned well with fMCS-based structural dissimilarity and reflected structural relationships within a set of standards. Incorporating it into chemodiversity analysis improved separation of the effects of drought and herbivory. Especially in the combination of both stresses, their distinct effects on different leaf metabolites were only fully reflected when accounting for compound disparity. 4. Hence, UV-Vis spectral dissimilarity captures chemically meaningful compound relatedness without requiring compound identity. Using it as a proxy for compound disparity adds a biologically relevant dimension to measures of chemodiversity with broader implications when assessing functional consequences of phytochemical diversity.

Plant-derived small molecules possess highly diverse physicochemical properties, and the computational design of their protein recognition elements depends not only on the global structural quality of candidate backbones, but also on whether the local binding pocket, ligand-contact pattern, and predefined recognition conformation can be consistently retained after sequence design and structural back-prediction. To explore pocket-design strategies for different types of natural-product small molecules, this study selected capsaicin, (4R)-limonene, and quercetin as model ligands, representing a flexible amphipathic molecule, a compact hydrophobic monoterpene, and a rigid polyphenolic flavonoid scaffold, respectively, and covering the dimensions of pungent sensory flavor, volatile aroma, and flavonoid functional constituents. A ligand- physicochemical-property-guided computational design and multi-stage prioritization framework was established for candidate protein binders. The results showed that candidates with favorable initial global structural scores did not necessarily form reasonable local small-molecule binding pockets, indicating that evaluation of the local ligand environment is essential for candidate prioritization. After screening, 31 partial- pocket candidate backbones for capsaicin, 75 buried hydrophobic-pocket candidate backbones for (4R)-limonene, and 56 pocket-qualified candidate backbones for quercetin were obtained. Further sequence design and structural back-prediction analyses indicated that a subset of candidates could maintain the original pocket geometry and major ligand-contact patterns after sequence realization. Overall, these results suggest that the physicochemical properties of different plant-derived small molecules substantially influence the efficiency of de novo protein pocket formation, with compact hydrophobic ligands being more compatible with buried hydrophobic- pocket strategies, whereas flexible or multipolar ligands require a more refined balance between hydrophobic burial and polar exposure. This study provides a pre- experimental computational prioritization framework for natural-product small- molecule-recognizing proteins and offers candidate resources for subsequent protein expression, in vitro binding validation, active-constituent enrichment, and development of small-molecule biorecognition tools. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=107 SRC="FIGDIR/small/743643v1_ufig1.gif" ALT="Figure 1"> View larger version (50K): org.highwire.dtl.DTLVardef@8fe6c2org.highwire.dtl.DTLVardef@176cef2org.highwire.dtl.DTLVardef@10c8201org.highwire.dtl.DTLVardef@2b28cf_HPS_FORMAT_FIGEXP M_FIG C_FIG

Tomato production, yield and fruit quality face major challenges due to several factors, including the complex polygenic inheritance of agronomically relevant traits, biotic and abiotic stresses, and increasingly stringent regulations limiting the use of phytosanitary products. In this context, bioinoculants have emerged as a sustainable strategy capable of enhancing yield without compromising fruit quality, conferring protection against different stresses and exerting a minimal or no impact on environment and human health. In this study, we evaluated the effects and the underlying mechanisms by which Streptomyces sp. N2A, an actinobacteria isolated from soybean rhizosphere, promotes seed germination, vegetative growth and yield in tomato, without modifying fruit quality. The obtained results demonstrated that the bacterial treatment significantly improved seedlin[g]s emergence and growth and development in vegetative stage. At harvest, yield was also significantly enhanced, mainly driven by increased individual fruit weight, which was positively correlated with a thicker pericarp in fruits from N2A-treated plants. Transcriptional analysis during fruit development revealed a coordinated induction of auxin and cytokinin signaling pathways before and after anthesis, providing a hormonal framework that underlies the promotion of pericarp growth. This study provides evidence of the beneficial effect of inoculation with Streptomyces sp. N2A on tomato yield and constitutes the first report describing the modification of fruit morphology and expression of genes involved in phytohormonal modulation during early growth and development, induced by a plant growth-promoting Streptomyces.

Antimicrobial resistance has intensified the search for sustainable natural products with antimicrobial properties. Pleurotus ostreatus cultivated on lignocellulosic agro-wastes, including cassava peel, offers potential for bioactive-compound production and agricultural waste valorization. Conventional antimicrobial screening, however, can be labour-intensive when multiple extracts and pathogens are evaluated. This study evaluated whether extraction solvent, broad pathogen taxonomic category, and batch-level mycochemical composition could predict the antimicrobial response of P. ostreatus extracts cultivated on cassava peel and identified the variables contributing most strongly to prediction. Ethanolic and aqueous mushroom extracts were evaluated against seven microbial pathogens using agar well diffusion and broth microdilution assays. The dataset comprised 42 observations. A Random Forest model with leave-one-out cross-validation (LOOCV) was used to model zone of inhibition as a regression task and minimum inhibitory concentration (MIC) as a binary classification task. The Random Forest regression model showed moderate internal predictive performance for zone of inhibition (R2 = 0.68, MAE = 0.62 mm, RMSE = 0.75 mm). Extraction solvent was the strongest predictor, whereas batch-level mycochemical variables contributed minimally. In contrast, MIC classification performed poorly (accuracy = 0.43; F1-score = 0.33), indicating that the available predictors were insufficient to discriminate the two observed MIC groups. The findings support machine learning as an exploratory complement to antimicrobial screening of mushroom-derived natural products. Given the limited dataset and three cultivation batches, the results are preliminary. Larger, multi-substrate and multi-species datasets with replicate-resolved biochemical measurements will be required to develop robust predictive models.

Arsenic (As) poses a major threat to rice productivity and food safety due to its high bioaccumulation potential and subsequent entry into the human food chain. In rice, As impairs seed germination, disrupts morpho-anatomical development, and induces oxidative stress. This study evaluates seed priming with an aqueous extract of the agricultural weed Amaranthus viridis (AvE) as a sustainable strategy to alleviate As-induced phytotoxicity. AvE priming significantly improved germination (71-75%) and morpho-physiological performance under As stress. It reduced oxidative stress markers, including H2O2 (21-38%), malondialdehyde (13-26%), and proline (18.9-44.7%), while increasing antioxidant metabolites, polyphenols and glutathione by up to 2.34-fold and 41%, respectively. Microscopy confirmed restoration of cellular integrity and anatomical organisation in primed seedlings. ICP-OES analysis showed that AvE priming reduced root As uptake by up to 39%, root-to-shoot translocation by up to 58%, and grain As accumulation by up to 95% compared with unprimed plants. qRT-PCR revealed modulation of genes involved in As homeostasis, indicating coordinated physiological and transcriptional responses. Importantly, improved agronomic performance further demonstrated the translational potential of this approach. This study provides the first evidence that A. viridis extract is a cost-effective, sustainable biostimulant for producing low-As rice in contaminated regions.

Copper is an essential redox-active micronutrient, but agricultural soils are increasingly contaminated by copper from mining, industrial discharge, and intensive agrochemical use, pushing concentrations beyond levels plants can tolerate. Excess copper triggers Fenton-like reactive oxygen species (ROS) generation, mitochondrial dysfunction, and impaired growth. Existing mitigation strategies, such as soil amendments, phytoremediation, antioxidants, and different chelators, have been explored to reduce copper toxicity, but their effectiveness can be limited by immobilization, poor specificity, and environmental persistence. The present work introduces a nanoparticle-based strategy for the direct sequestration of excess copper coupled with protection against the oxidative damage caused by copper stress. Here, we report MPA-iron oxide nanoparticles (MIONPs), sequentially functionalized with chitosan, glutathione, and 3-mercaptopropionic acid, designed to simultaneously scavenge ROS, restore redox homeostasis, and chelate copper via surface thiol groups. MIONPs showed a significant increase in copper binding capacity over bare iron oxide nanoparticles (BIONPs) and, in copper-stressed Solanum lycopersicum seedlings, significantly improved germination and root/shoot growth, reduced intracellular ROS, restored mitochondrial membrane potential, and preserved nuclear integrity. This integrated design establishes MIONPs as a promising, dual-function nanoplatform for sustainable copper stress management in agriculture.

Edible mushrooms have been reported to have antimicrobial properties and other health benefits. This study aims to test the antimicrobial activities of several edible mushrooms from markets and test if co-culturing them with bacteria could induce stronger anti-bacterial properties. Commercial mushrooms, Hericium erinaceus (lions mane), Pleurotus ostreatus (oyster mushroom), Lentinula edodes (Shiitake) and Agaricus bisporus (button mushroom), were grown from strictly controlled/sterile substrates. Ethanol and water extracts from the mushrooms were prepared and tested against the bacteria Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, and Bacillus subtilis, and the fungus Candida albicans for antimicrobial activities. Shiitake water extract (SWE) showed strong antibacterial effects against all tested bacterial species, inhibitory effects on their biofilms, and antifungal activity. The antimicrobials in SWE seem to damage the cell wall and cell membrane of the bacteria, prefer weak acidic conditions, and are heat labile. Some antimicrobials are likely proteins and polysaccharides. In contrast, 3 other mushrooms displayed only weak antimicrobial effects. The fast-growing lions mane and oyster mushroom were co-cultured with different bacteria. The co-cultivation promoted the fruiting body development of lions mane. Co-culturing with S. aureus increased the anti-bacterial effects of lions mane against S. aureus, E. coli and particularly B. subtilis. Co-culturing the oyster mushroom with bacteria, especially B. subtilis and P. aeruginosa, boosted the mushroom growth. All tested bacteria, especially S. aureus, increased oyster mushroom anti-bacterial effect against E. coli and B. subtilis. The findings indicate that mushroom-bacteria co-culturing could have benefits both agriculturally and medicinally.

Endophytic fungi associated with the Himalayan yew (Taxus wallichiana) represent an underexplored source of bioactive secondary metabolites. This study investigated the extracellular metabolites of Annulohypoxylon purpureonitens isolated from Nepalese T. wallichiana using bioactivity screening combined with LCMS/MS-based metabolomics. The fungal extract exhibited broad-spectrum antibacterial activity, showing the strongest inhibition against Staphylococcus aureusand Enterococcus faecalis (MIC = 500 ug/mL). It also displayed notable antioxidant capacity(DPPH, ABTS, TPC &TFC) and cytotoxicity against HeLa and MCF-7 cancer cell lines. Metabolite profiling via GNPS molecular networking, manual MS/MS validation, and MASST reverse metabolomics putatively identified diverse compounds, including hydroquinidine, chlorogenic acid, muramic acid, and cordycepin conjugates widely distributed across public microbial datasets. Overall, A. purpureonitens is a promising source of multifunctional metabolites, laying a foundation for future compound isolation and functional characterization.

This study aims to investigate changes in protein secondary structures (-helix, -sheet, random coils, and -turn) and macronutrient distribution in different cool-season oat varieties and steam-pressure toasting durations using synchrotron-based mid-infrared (Mid-IR) spectroscopy and Fourier Transform Infrared spectroscopy (FTIR) imaging. All oat samples, provided by the Crop Development Center at the University of Saskatchewan, were harvested over three consecutive years (2018, 2019, and 2020). The first experiment compared four oat varieties (CDC Arborg, CDC Nasser, CDC Haymaker, and Summit), while the second examined CDC Nasser oats subjected to steam-pressure toasting (SPT) at 121 for 0, 30, 60, 90, and 120 minutes. FTIR chemical imaging revealed that carbohydrates, proteins and lipids in the four oat varieties were mainly concentrated in the endosperm, aleurone layer and embryo, crease region, and remained unchanged after SPT. Peak-fitting deconvolution of the Amide I band (1700-1600 cm-1) and subsequent quantitative analysis revealed that the four oat varieties exhibited broadly similar protein secondary structure profiles, with statistically significant but subtle variety effects detected for -helix (P = 0.026), -turn (P = 0.047), and the -helix to -sheet ratio (P = 0.048), however, -sheet and random coil proportions did not differ significantly among varieties. In contrast, SPT induced pronounced structural rearrangements, with significant increase in -sheet proportion (P = 0.003) and significant decreases in random coil content (P = 0.026). Notably, 30 minutes of toasting was sufficient to significantly increase -sheet and decrease the random coil contents. These changes are consistent with heat-induced protein denaturation and intermolecular -sheet aggregation, where thermal energy breaks the hydrogen bonds that stabilize the disordered random coil conformation, causing the unfolded polypeptide chains to reassemble into highly ordered -sheet aggregates. After SPT, the peak centers of Amide I and II bands shifted to lower wavenumbers and both bands broadened while their intensities were maintained, reflecting the reorganization of the remaining protein into -sheet aggregates rather than any loss of amide-active protein. These findings suggest that, although genotype has a relatively minor effect on the protein secondary structure of oats, hydrothermal treatments fundamentally reorganize the protein matrix from a disordered to an ordered conformation, which may have implications for protein digestibility, solubility, and nutritional function.

Plant root cellular architecture and cell wall composition influence plant productivity, stress resilience, biotic interactions, and potentially soil carbon accumulation. This study establishes comprehensive compositional parameters for roots of a lowland switchgrass genotype, DVR3. Root traits were analyzed in 12.5 cm depth segments, from Zone 1 near the surface to Zone 4 down to 50 cm. Mean abundance ({micro}g/mg) for major cell wall components included cellulose 470 {+/-} 20, xylose 250 {+/-} 20, lignin 170 {+/-} 15, and total suberin 35 {+/-} 5. Composition and cellular anatomy varied with depth, in a partially coordinated manner. Cross sections showed extensive aerenchyma in mature root regions despite greater root mass density, corresponding to abundant lignin and cellulose. Deep roots were enriched for pectin-associated traits, including arabinogalactan II, homogalacturonan, and arabinose-associated linkages. Suberin content did not vary significantly, though Casparian strip formation, endoderm and exoderm thickening, and suberin surface staining progressed with development. Similar trends in root lignin and specific root length were observed for another lowland switchgrass genotype, AP13. These results suggest that it may be possible to genetically enhance native switchgrass root chemistry to promote soil penetration and below-ground carbon accumulation by reducing variability with development, potentially via cell-type specific adjustments. HighlightOlder, shallower switchgrass crown roots are enriched in lignin and cellulose, and deeper, younger roots are pectin-rich with juvenile cellular anatomy. A more uniform compositional distribution might enhance below-ground traits. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=120 SRC="FIGDIR/small/744798v1_ufig1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@159de98org.highwire.dtl.DTLVardef@124d714org.highwire.dtl.DTLVardef@1a49c14org.highwire.dtl.DTLVardef@2fa67_HPS_FORMAT_FIGEXP M_FIG C_FIG Schematic summary of switchgrass root anatomy and composition across four 12.5-cm depth zones of a 50-cm root system. Zone 1 represents older, shallow roots and Zone 4 includes younger roots and root tips. Representative cross-sections show greater aerenchyma development in older roots than in young root tips. The compositional heatmap shows higher cellulose, lignin, and xylose in Zone 1, higher pectin and nitrogen in Zone 4, and relatively little variation in suberin across zones.

Romanian bors, a traditional fermented wheat bran beverage, is produced through spontaneous fermentation and represents a complex microbial ecosystem. Despite its cultural importance and presumed health benefits, its microbial ecology and functional potential remain poorly characterized. The present study aimed to elucidate the microbial community structure of bors and link it to functional traits relevant to fermentation performance and food functionality by integrating culture-independent sequencing with culture-dependent isolation and functional characterization. A total of 32 bors samples (12 commercial and 20 homemade) were analyzed. Amplicon-based sequencing revealed a microbiome dominated by lactic acid bacteria (LAB), with lactobacilli accounting for the majority of the bacterial communities and Lactobacillus amylolyticus being identified as the most prevalent and abundant species. The yeast communities were mainly composed of fermentative taxa, including Pichia kudriavzevii and Kluyveromyces marxianus. Lactobacillus amylolyticus and P. kudriavzevii were also the most frequently isolated species among bacteria and yeasts, respectively. These results highlighted a strong adaptation of the microbial isolates to starch-rich cereal substrates and underscored the central role of these microorganisms in wheat bran fermentation for bors production. Whereas the sequencing-based analyses showed no significant differences in overall diversity between the commercial and homemade bors samples, the cultivation-based results indicated a higher bacterial richness in the commercial products. Notably, the culture-dependent method captured substantially fewer taxa, highlighting the complementary nature of the two approaches. Of a total of 101 bacterial strains (88 LAB and 13 acetic acid bacteria) isolated, many exhibited rapid growth and strong acidification capacity, reaching pH values below 4.5 within 12 h. A functional screening revealed that 21 % of these strains displayed -amylase activity, 65 % phytase activity, and 50 % {beta}-glucosidase activity, highlighting their capacity to metabolize cereal substrates and enhance the nutrient availability of bors. All strains showed antibacterial activity against at least one indicator bacterium tested, with a universal inhibition of Listeria monocytogenes. Overall, Romanian bors harbored a lactic acid bacteria-dominated core microbiome with a significant functional diversity. These findings underscored its potential as a rich source of functional and technologically important strains for application in starter and protective culture development.