Search Results (1,008)

The actinobacterial strain DEC002 was isolated recently from volcanic soils of Deception Island. Its taxonomic identity was resolved through a polyphasic strategy integrating morphology, physiological profiling, multilocus phylogeny, and genome-wide comparisons to resolve its identity. Concatenated core gene trees together with average nucleotide identity and digital DNA–DNA hybridization values place DEC002 within Actinacidiphila fildesensis with robust support. This is the first molecular confirmation of the species beyond King George Island and secures a second verified locality within the South Shetland Archipelago. Growth at low temperature with tolerance to moderate salinity indicates a psychrotolerant lifestyle. Cell-free supernatants inhibited representatives of foodborne Gram-negative and Gram-positive bacteria, including representatives of Enterobacteriaceae, Vibrio, Staphylococcus and Streptococcus. Genome analysis revealed enrichment in multiple biosynthetic gene clusters for nonribosomal peptides, polyketides, terpenes, and ribosomally synthesized and post-translationally modified peptides (RiPPs), supporting the biosynthetic potential of the strain. Functional annotations emphasize replication and repair modules, mobile element-associated proteins, helix–turn–helix regulators, and versatile transport systems, features coherent with cold stress and oligotrophic soils. Antibiotic susceptibility assays indicate a broad resistance phenotype under the experimental conditions tested, together with extracellular antimicrobial activity. These data refine the biogeography of A. fildesensis and indicate DEC002 as a credible Antarctic source of specialized metabolites with antimicrobial promise. Full article

Background/Objectives: Dendrobium officinale (D. officinale), an endangered ornamental and medicinal orchid, displays significant variability in its bioactive compounds depending on geographical and environmental factors. To decipher these influences, we investigated metabolic divergence across three cultivars (GN, LS, DX) cultivated in greenhouse and outdoor conditions using untargeted metabolomics. Methods: Metabolites extracted from stem and leaf tissues were analyzed via UHPLC-Q Exactive Orbitrap MS, and the raw data were processed using XCMS for peak alignment and quantification. Differentially abundant metabolites (DAMs) were identified by multivariate statistical analyses including PCA and OPLS-DA. Metabolic pathways were annotated using KEGG, HMDB, and LIPID Maps databases, with enrichment analysis and visualization performed via TBtools II and Hiplot. Results: Metabolite profiling and multivariate analysis revealed distinct chemotypes. The DX cultivar exhibited anthocyanin enrichment in its stems, correlating with a red pigmentation, while GN accumulated specific amino acid derivatives. Tissue-specific metabolic specialization was evident, with leaves displaying greater flavonoid diversity and stems prioritizing lipid and amino acid metabolism. Outdoor cultivation enhanced flavonoid biosynthesis, whereas greenhouse conditions favored alkaloid accumulation. Functional analysis identified both conserved pathways, like phenylpropanoid biosynthesis, and varietal-specific adaptations in amino acid and secondary metabolism. Notably, alkaloid levels declined sharply during plant defoliation. Conclusions: Our findings demonstrate that environmental factors and geographical origin synergistically shape the metabolic profiles of D. officinale. This provides a scientific basis for optimizing cultivation strategies—through targeted environmental adjustments and varietal selection—to enhance the yield of desired bioactive compounds. Full article

Generally, forest trees with medicinal value present diverse chemotypes considered key determinants of efficacy, safety, and commercial valuation. Such heterogeneity varies among tissues, genotypes, and seasons, and stress exposure. This review summarizes how regulatory controls and genome architecture affect the stability and synthesis of secondary metabolites in woody medicinally important taxa. Detailed haplotypic and chromosomal analyses have recently identified diverse and repeatable architectural drivers. Among these, LTR/transposon-mediated revamping, neofunctionalization, biosynthetic gene clusters, and tandem duplication play a special role in reshaping pathway capacity. The enzymatic regulation of these drivers translates this “capacity” into harvest-pertinent chemistry by employing conserved TF modules, hormone crosstalk, and emergent chromatin/epigenetic layers. Nevertheless, major parameters pertaining to the tissue-specific storage, transport, and compartmentalization of these chemotypes are contextualized with certain limitations. In this review, the integration of GWAS/eQTL/TWAS with multi-tissue is explained in addition to the replacement of a single reference with pangenome/haplotype frameworks, and explicit modeling of G × E further strengthen genotype-to-chemotype mapping. Therefore, in this review we summarize practical workflows for chemotype discovery utilizing staged validation models of heterologous reconstitution, isotope/spatial evidence, and chemistry. These findings were supported by data on saponins, alkaloids, iridoids, and defense response. Such an integration links mechanistic understanding to authentication, standardization, and sustainable utilization strategies in woody medicinal trees. Full article

Salicylic acid (SA) is involved in plant defense responses to environmental stressors by modulating gene expression and specialized metabolites production, enhancing plant adaptive resilience through systemic signaling pathways. This study investigates the impact of exogenous application of SA on the metabolism of iridoids and phenolic compounds—characteristic specialized metabolites of the Nepeta species, associated with diverse biological activities. Nepetalactone (NL) is a characteristic monoterpene iridoid, while rosmarinic acid (RA) represents the most abundant phenolic compound within the genus. We explored the effects of varying SA concentrations (2 µM, 5 µM, 10 µM, and 20 µM) on iridoid and phenolic metabolism in in vitro-grown Nepeta nuda, following 7 days and 28 days of elicitation. A significant increase in trans,trans-NL content was observed after 7-day exposure to 2 µM SA, while prolonged exposure led to a decrease in its levels, particularly at higher SA concentrations. Gene expression analysis revealed that 7 days of exposure to lower concentrations of SA upregulated genes coding for NAD-dependent nepetalactol-related short-chain dehydrogenase/reductases (NEPSs), key regulatory enzymes catalyzing the final steps of NL biosynthesis. In contrast, prolonged exposure to 20 µM SA downregulated genes coding for geraniol 8-hydroxylase (NnG8H) and 8-hydroxygeraniol oxidoreductase (Nn8HGO), which resulted in reduced iridoid content. Conversely, SA treatment notably increased RA content after prolonged exposure to 20 µM SA, which is a result of the enhanced expression of all analyzed RA biosynthesis-related genes. These findings demonstrate that both concentration and duration of SA treatment are critical determinants of elicitation outcomes in N. nuda. Strategic manipulation of these parameters can redirect metabolic flux toward either iridoid or phenolic compounds production, and enhance biotechnological production of specialized metabolites in N. nuda. Full article

Leaves of Actinidia chinensis Planch. var. deliciosa (A.Chev.) A.Chev. (A. deliciosa) represent agro-industrial byproducts with potential for valorization. The present study evaluated the metabolomics profiling, cytotoxicity, genotoxicity, and antigenotoxicity of the methanolic extract of A. deliciosa leaves. The metabolomics profiling was determined using an untargeted metabolomic approach employing UPLC-HRMS. Cytotoxicity, genotoxicity, and antigenotoxicity were assessed in Chinese hamster ovary K1 (CHO-K1) cells using the in vitro cytokinesis-block micronucleus (CBMN) assay. The metabolic profile of A. deliciosa leaf extracts revealed the presence of three major classes of secondary/specialized metabolites: proanthocyanidins, flavonols, and triterpenoid saponins. Medium-polar metabolites were monomeric fla-van-3-ols, such as (+)-catechin and (−)-epicatechin, oligomeric procyanidins and prodelphinidins, and flavonols. Certain glycosylated flavonols and their derivatives, such as myricetin, quercetin, and kaempferol. Low-polarity metabolites were characterized by low-polarity triterpenoids such as maslinic, corosolic, oleanolic, and ursolic acids. At concentrations of 37.5, 75, and 150 µg/mL, the extract did not significantly increase micronuclei frequency compared to untreated control cells, indicating an absence of genotoxic potential. Moreover, co-treatment of CHO-K1 cells with the extract and mitomycin C (MMC) at 0.025 µg/mL resulted in a significant reduction in micronuclei formation induced by MMC at concentrations of 75 and 150 µg/mL, suggesting antigenotoxic activity likely associated with the phytochemical constituents presented in the extract. Full article

Temperature is a major determinant of plant metabolic plasticity, yet its role in directing volatile and semi-volatile specialized metabolism in Ginkgo biloba remains poorly understood. In this study, we investigated how contrasting low- and high-temperature treatments reshape secondary metabolite contents in G. biloba microclones cultivated in vitro. Plants were exposed to cold (+3 °C) and heat (+30 °C) conditions, and their responses were analyzed using GC–MS profiling, anatomical measurements, chlorophyll fluorescence, and multivariate statistics. Cold treatment selectively increased the abundances of monoterpenes (13.22%) and sesquiterpenes (13.83%), with the strongest accumulation of caryophyllene, eucalyptol, and (1S)-camphor. In contrast, heat treatment reduced ester content to 3.73% and strongly enriched oxy-sesquiterpenes (46.50%) and lactone/ketone/spiroketone (29.54%) contents. The enhanced accumulation of isocalamendiol, isoshyobunone, cyclohexanone derivative, dehydroxy-isocalamendiol, and (+)-2-bornanone was observed under heat. According to the multivariate analysis, control plants were associated with traits reflecting optimal physiological performance, including greater parenchyma, phloem, and xylem thickness, larger vascular bundles, longer stomata, and higher NPQ, qN, Y(NPQ), and F_v/F_m. Cold-treated plants showed thicker epidermis and sclerenchyma, higher stomatal density and width, elevated Y(NO), and an enrichment of esters and terpenoids, whereas heat-treated plants were characterized by thicker adaxial and abaxial epidermis, increased mesophyll thickness, and higher levels of oxygenated metabolites. These findings expand current knowledge beyond terpene trilactones and flavonoids and identify Ginkgo microclones as a useful in vitro model for temperature-guided metabolic reprogramming and targeted metabolite enrichment. Full article

Glandular trichomes (GTs) are epidermal outgrowths that function as “natural cell factories” for the synthesis of specialized metabolites. Beyond their traditional understanding, GTs on cucumber fruits can form an undesirable trait known as bloom, which negatively affects market value. However, the secretory process, metabolite profiles, and genetic regulation underlying GT development in cucumber remain largely unclear. In this study, we employed scanning electron microscopy (SEM), transmission electron microscopy (TEM), histochemical staining, multi-omics analyses, and liquid chromatography–mass spectrometry (LC-MS) to systematically investigate GT development. The secretory process was classified into four distinct stages via SEM observations: morphogenesis, active metabolism, head sunken, and metabolite release. TEM revealed progressive ultrastructural changes, including increased organelle abundance and expansion of the periplasmic space, which facilitate metabolite transport and release. This process occurs through an autonomous mechanism involving osmiophilic substances and eventual cell rupture. LC-MS analysis identified 744 metabolites belonging to 11 classes, with phenylpropanoids/polyketides—particularly flavonoids—being the most abundant. While metabolite classes are conserved between European greenhouse and North China ecotypes, specific metabolite contents vary significantly. Multi-transcriptome analysis identified 60 candidate genes associated with GT development. Among these, CsaV4_3G003418 was functionally validated through virus-induced gene silencing (VIGS) to be involved in early GT development. Collectively, this work elucidates the secretory mechanism and metabolic characteristics of cucumber GTs, providing a foundation for future functional studies and biotechnological applications of secondary metabolites. Full article

Castanopsis hystrix (C. hystrix) is one of the most dominant and ecologically important species in subtropical evergreen broad-leaved forests of China. Interactions between its root and rhizosphere microorganisms play a pivotal role in nutrient acquisition and in mediating plant response s to environmental stresses. In this study, high-throughput 16S ribosomal RNA (16S rRNA) sequencing combined with untargeted metabolomics was employed to systematically characterize the rhizosphere microbial community and root exudates in C. hystrix. The results showed that, compared with non-rhizosphere soil, bacterial diversity in the rhizosphere of C. hystrix was significantly reduced, while several specialized and potentially efficient taxa were selectively enriched, particularly Candidatus_Solibacter, Candidatus_Xiphinematobacter, and Candidatus_Koribacter, thereby reshaping a distinct rhizosphere-specific community structure. Metabolomic analyses further revealed that 129 metabolites were significantly enriched in the rhizosphere, including four major classes of compounds associated with plant stress resistance: lipids and lipid-like molecules, organoheterocyclic compounds, organic acids and derivatives, and phenylpropanoids and polyketides. The enrichment of these metabolites likely contributes substantially to stress tolerance in C. hystrix. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis identified six defense-related metabolic pathways, including pyrimidine metabolism, steroid biosynthesis, nucleotide metabolism, plant hormone signal transduction, ATP-binding cassette transporter (ABC transporters), and the biosynthesis of various plant secondary metabolites. Further correlation analysis and co-occurrence network analysis suggested that C. hystrix may potentially influence the enrichment of beneficial microorganisms through rhizosphere metabolites selectively, which could reduce the reliance on external nutrient acquisition and enhance the stress resilience of C. hystrix. Our study provides a comprehensive perspective for elucidating rhizosphere interaction networks and their ecological functions in C. hystrix, thereby enhancing our understanding of the environmental adaptability of dominant tree species in subtropical forests. Full article

Diet is a key modulator of the gut microbiota, thereby influencing host physiology. Microbial colonization begins early in life, influenced by maternal sources, mode of birth, diet, and environmental exposures, and stabilizes into an adult-like microbiome during early childhood. This maturation yields a microbial ecosystem dominated by Firmicutes and Bacteroidetes that contributes to host physiological homeostasis. Gut microorganisms function as an integrated metabolic system that transforms dietary substrates into bioactive metabolites, including short-chain fatty acids (SCFAs), amino acid-derived compounds, and microbial lipids. These metabolites regulate glucose and lipid metabolism, intestinal barrier integrity, and immune modulation. Although many metabolic functions are conserved, their activity is shaped by diet, microbial cross-feeding, and local intestinal conditions, enabling functional specialization within the gut. Disruption of this system, known as dysbiosis, is associated with alterations in microbial diversity and metabolic output that have been linked to metabolic diseases, including obesity and related disorders. Evidence from experimental models and observational studies suggests that these associations may involve interconnected inflammatory and metabolic mechanisms, such as impaired intestinal barrier function, low-grade inflammation, and altered dietary energy harvest; however, causal relationships in humans remain incompletely understood. Beyond peripheral effects, the gut microbiome influences host metabolism via the gut–brain axis, a bidirectional network that integrates neural, endocrine, immune, and metabolic signaling. Microbiota-derived metabolites and gut hormone modulation contribute to appetite regulation, energy balance, and glucose homeostasis, while central neuroendocrine signaling can reciprocally shape the intestinal microbial niche. Collectively, these findings highlight the gut microbiome as a central regulator of host metabolism, whose disruption may contribute to the development of metabolic disease. Full article

Hydrogen peroxide (H₂O₂) regulates plant metabolism. This study examined its effect on the biosynthesis of specialized metabolites in Baccharis conferta, a medicinal plant rich in phenolics and terpenes. Plants were elicited with 25 µM and 250 µM H₂O₂. Phenolic changes were evaluated by total phenolic content (TPC), total flavonoid content (TFC), phenylalanine ammonia-lyase (PAL) activity, and LC-MS analysis of flavonoids and hydroxycinnamic acids. Meanwhile, terpene changes were evaluated by HPTLC, total terpene content (TTC), and expression of the 1-deoxy-D-xylulose-5-phosphate synthase (Bco-DXS1) gene. H₂O₂ markedly modulated both pathways. Phenolic metabolism was activated, particularly under 25 µM H₂O₂, with PAL activity increasing by 52%, TPC by 42%, and TFC by 50% relative to the control. Chemical analysis revealed that five compounds, including chlorogenic acid, differed significantly across treatments. Gene expression analysis showed that 25 µM H₂O₂ upregulated Bco-DXS1 and increased TTC, whereas 250 µM H₂O₂ repressed gene expression but still enhanced terpene accumulation. Overall, these results suggest that moderate H₂O₂ levels function as a signaling molecule in B. conferta, simultaneously boosting phenolic and terpene pathways. This highlights controlled H₂O₂ elicitation as an effective biotechnological approach to increase the production of valuable metabolites in medicinal plant cultures. Full article

Hyphae fungi of the Trichoderma genus are widely recognized as effective biological control factors (BCAs) due to their ability to inhibit the growth of plant pathogens through a variety of mechanisms such as mycoparasitism, antibiotics or competition for resources. Specialized secondary metabolites (SMs), including volatile organic compounds (VOCs), lytic enzymes and surfactants, play an important role in these interactions. The aim of this study was to evaluate the antagonistic activity and characterization of secondary metabolites from the aqueous phase or suspended in an organic solvent produced by three strains of Trichoderma citrinoviride. The study focused on their enzymatic properties, surfactant potential and effect on the growth kinetics of sixteen fungal species. Antagonistic activity against phytopathogens was tested using the turbidimetric method, analyzing various forms of preparations. Lytic enzyme activity and surface tension of fluids were also evaluated. The C1 strain showed the broadest spectrum of antagonistic activity. Analysis of growth kinetics revealed that the way metabolites are prepared is crucial for their efficacy. Studies have shown that the effectiveness of biocontrol depends not only on the Trichoderma strain, but also on the extraction method and form of the preparation (e.g., rehydration of lyophilizate vs. organic phase extraction). The presence of diverse metabolites, including lytic enzymes, biosurfactants and volatile organic compounds, indicates a complex mechanism of action of T. citrinoviride, making this species an ideal candidate for the production of plant protection biopreparations. Full article

Plants adapted to gypsum-rich habitats often display unique metabolic specializations. This study investigated the organ-specific chemical diversity and biofunctional potential of Ebenus laguroides subsp. laguroides, a gypsum-endemic legume from Central Anatolia. Methanolic extracts of flowers, leaves, stems, and roots were analyzed for phenolic composition by LC–ESI–MS/MS and evaluated for antioxidant and enzyme inhibitory activities. Twenty-one phenolics were identified, dominated by hesperidin, verbascoside, and (+)-catechin, particularly abundant in stems. Stems exhibited the highest total phenolic (82.60 mg GAEs/g) and flavonoid (45.79 mg QEs/g) contents, correlating strongly with antioxidant capacity across multiple assays (r > 0.95). Enzyme inhibition tests revealed moderate but consistent activities, with roots showing the strongest acetylcholinesterase inhibition and stems the highest tyrosinase inhibition. Correlation analyses confirmed strong links between phenolic content, antioxidant potential, and enzyme modulation. The results highlight distinct organ-dependent metabolite patterns and demonstrate that E. laguroides subsp. laguroides is a noteworthy source of multifunctional phenolics. These findings contribute to understanding the chemical biodiversity and bioactivity relationships within Fabaceae species adapted to gypsum soils and provide a foundation for further phytochemical and pharmacological exploration. Full article

Xanthomonas campestris pv. campestris (Xcc), the causal agent of black rot, has a significant impact on cabbage production worldwide. The goal of this research was to evaluate the effect of preventive foliar treatments with Bacillus velezensis strain RD-FC 88 on the primary and secondary metabolism of Xcc-infected cabbage cv. Futoški plants. Special attention was given to measuring metabolites’ changes, aiming to determine the influence of the applied biocontrol treatment on the development of plant immune response and resistance to pathogen. This study reports the first comprehensive biochemical and physiological analysis of the interaction between host plant, biocontrol strain and pathogen, thus providing novel insight into black rot management. Pathogen inoculation caused a significant decrease in the majority of measured metabolites, including most free amino acids (Gln, Ala, BCAA), phenolics, and glucosinolates. Preventive application of B. velezensis strain in Xcc-infected plants restored the levels of aromatic amino acids, Asp, Glu, Leu, Val, and Ala to control values. A similar pattern was observed in aliphatic glucosinolates sinigrin and glucoiberin, as well as for the indolic glucosinolate 4-methoxy-glucobrassicin. Additionally, increased accumulation of hydroxybenzoic acids, hydroxycinnamic acids, and kaempferol derivatives was also observed in the plants treated with the biocontrol strain and subsequently infected with Xcc, compared to plants solely infected with Xcc. The obtained results imply that the RD-FC 88 strain holds potential as an efficient priming agent, capable of stimulating cabbage cv. Futoški defense responses and enhancing its resistance to Xcc. Full article

Usnic acid (UA) is one of the most extensively studied specialized metabolites of lichens, attracting considerable interest due to its antimicrobial, anti-inflammatory, and cytotoxic properties. The efficiency of UA extraction from lichens depends on multiple interrelated biological and technological factors. This systematic review aims to synthesize and critically evaluate reported strategies for UA extraction from wild-grown lichen biomass, with particular emphasis on extraction efficiency, practicality, and application potential. This systematic literature review, based on the Scopus database was conducted by including original research articles reporting UA extraction from wild-growing lichens. The analysis covered species selection, sample pre-treatment, solvent type, and extraction methodology. A total of 117 studies were included. Due to the predominantly non-polar nature of UA, higher extraction efficiencies were generally achieved using solvents, including acetone, supercritical CO₂, vegetable oils, and lipophilic green solvent systems. Pre-treatment strategies such as grinding or flaking significantly enhanced extraction performance by improving mass transfer. Alongside conventional methods (maceration, reflux, Soxhlet), non-conventional techniques such as Supercritical Fluid Extraction (SFE), Ultrasound- (UAE), and Microwave-Assisted Extraction (MAE) enabled faster and more selective UA extraction with reduced solvent use. Notably, SFE have been reported as particularly promising in terms of selectivity, process control, and potential suitability for scale-up, with commercially available supercritical CO₂ extracts of Usnea species supporting the feasibility of this approach. This review provides a consolidated and application-oriented overview of UA extraction, highlighting strategies that balance efficiency, selectivity, sustainability, and practical implementation. Full article

This study investigated the cellular and mitochondrial toxicities of the pentacyclic triterpenoid and plant-specialized metabolite ursolic acid (UA) in human breast adenocarcinoma cell lines. Cell viability and clonogenic assays showed that UA induced potent cytotoxic and antiproliferative effects in MDA-MB-231 and MCF7 cells. Confocal images of living cells showed that UA caused a depolarization of the mitochondrial membrane potential and spectrophotometric measurement of electron transport chain enzyme activity in isolated organelles showed that UA induced a dose-dependent decrease in mitochondrial succinate-cytochrome reductase activity. These results demonstrate a direct, site-specific inhibitory effect of UA on mitochondrial bioenergetic function. Furthermore, the efficacy of a drug combination aimed concurrently at both major pathways of ATP production in breast cancer cells was investigated. The data show that when MDA-MB-231 and MCF7 cells were treated with UA in combination with either 2-deoxy-D-glucose or 3-bromopyruvate, two inhibitors of glycolysis, the resulting cytotoxicity was greater than that induced by any of the compounds used independently. The results of this study are important in that they demonstrate direct mitochondrial targets of UA and suggest the possibility of using this natural, plant-derived metabolite in combination with glycolytic inhibitors as a novel and effective dual treatment strategy for breast cancer cell killing. Full article