Flavonoid mediated selective cross-talk between plants and beneficial soil microbiome

Trichoderma sp. strain AM6 whole-genome guided untargeted metabolomics: Terpenoid backbone synthesis and modulation of VOCs in tea (Camellia sinensis L.)

Industrial cash crop tea is a cherished drink for its bioactive components like terpenoids and flavonoids shaping its flavor and health benefits. Trichoderma species are potent biocontrol agents and plant growth regulators, with unexplored potential in modulation of C. sinensis terpenoid biosynthesis. Genome sequencing of a tea root-associated Trichoderma sp. strain AM6 revealed a genome size of 39.91 Mbp, comprising 446 contigs organized into 406 scaffolds, with 98.8 % completeness. Single scaffold mitochondrial genome assembly of 34,430 bp in length with a GC content of 28.03 % encodes a total of 49 genes including 27 tRNA, 2 rRNA, and 20 protein-coding genes. Metabolic pathway analysis indicates exclusive reliance on the mevalonate pathway for terpenoid biosynthesis in Trichoderma, unlike C. sinensis, which utilizes both the mevalonate and non-mevalonate (MEP/DOXP) pathways. Untargeted LC-ESI-MS/MS analysis of Trichoderma identified 11,841 secondary metabolites, including 34 monoterpenoids, 72-diterpenoids, and 76-sesquiterpenoids, emphasizing its metabolic diversity. Comparative phylogenomic study positioned it as a phylogenetically distinct species with unique adaptive traits. Untargeted GC-MS shows high volatile abundance from microbial consortia (T5) followed by only Trichoderma treatment (T2) compared to control (T1). Terpenoid transcripts of C. sinensis from the plant-microbe consortium assembly sets illuminate upregulation of genes assigned to 3-hydroxy-3-methylglutaryl-Co-A reductase (HMGCR) and downregulation of genes assigned to 1-Deoxy-D-xylulose-5-phosphate (DXS), indicating metabolic shift towards more mevalonate pathway activity influenced by this novel Trichoderma strain itself and in combination with other tea root-associated microbes.

Integration of transcriptome, metabolome and high-throughput amplicon sequencing reveals potential mechanisms of antioxidant activity and environmental adaptation in the purple-leaf phenotype of Coffea cultivars

To understand its potential in meeting the increasing market demand for high-quality and resistant coffee varieties., the study focused on evaluating a leaf color mutation in Coffea arabica L. (purple coffee) and comparing it with the control (Catimor). Analysis of antioxidant indices revealed that purple coffee exhibited significantly higher levels of TAC (total anthocyanin content), DPPH (2,2-dyphenyl-1-picrylhydrazyl), POD (peroxidase), and PPO (polyphenol oxidase) compared to Catimor, indicating stronger antioxidant activities. Multi-omics analysis was conducted to create metabolic profiles, genetic maps, and phyllosphere microbial communities of the two Coffea genotypes. The metabolome and transcriptome results showed higher levels of flavonoids and phenolic acids in purple coffee, along with different gene expression patterns. The up-regulation of key genes in the phenylpropanoid pathway was identified to result in a notable alteration in the accumulation of flavonoids and phenolic acids. The co-occurrence network analysis of bacterial communities identified 10 keystone OTUs (operational taxonomic units), including Methylobacterium-Methylorubrum, 1174-901-12, Massilia, Comamonas, Klenkia, and Salinicola, all of which are Proteobacteria. The results of the co-analysis demonstrated a strong correlation between keystone OTUs and both phenylpropanoid metabolism and antioxidant activity. Taken together, we hypothesize that the up-regulation of key genes in the phenylpropanoid metabolite pathway in purple coffee facilitates the synthesis of flavonoids and phenolic acids, which suppresses the abundance of microbial taxa and thus enhances antioxidant activity and environment adaptability. These findings provide valuable insights for future research on the environmental adaptation of coffee and hold potential in breeding high flavonoid content coffee leaf tea.

Exogenous melatonin enhances drought tolerance and germination in common buckwheat seeds through the coordinated effects of antioxidant and osmotic regulation

BACKGROUND

Drought stress is a major constraint on seed germination and crop productivity, particularly for drought-sensitive crops like common buckwheat (Fagopyrum esculentum). Exogenous melatonin has emerged as a promising strategy to mitigate drought stress by enhancing plant physiological and biochemical responses. However, its specific roles in regulating antioxidant defenses, osmotic adjustment, and plant compounds biosynthesis during buckwheat seed germination under drought stress remain poorly understood.

RESULTS

This study investigated the effects of 200 µM exogenous melatonin on common buckwheat germination under polyethylene glycol (PEG-6000)-induced drought stress. Melatonin significantly improved germination rates and radicle growth, reduced membrane damage, and enhanced osmotic regulation by increasing proline, soluble sugars, and proteins. Antioxidant enzyme activities (catalase, peroxidase, and superoxide dismutase) and associated gene expression (FtCAT, FtPOD, FtSOD) were markedly upregulated. Molecular docking and dynamics simulations revealed a stable interaction between rutin, a secondary metabolite, and catalase, suggesting enhanced enzyme stabilization. Additionally, melatonin increased rutin and methyl jasmonate synthesis, which contributed to antioxidant defenses and reduced oxidative damage. The coordinated effects of melatonin improved drought tolerance in buckwheat seeds by optimizing osmotic balance, strengthening antioxidant capacity, and stabilizing cellular structures.

CONCLUSIONS

Exogenous melatonin enhances drought tolerance in common buckwheat seeds through the coordinated regulation of antioxidant defenses, osmotic adjustment, and plant compounds production, including methyl jasmonate and rutin, during germination. These findings offer valuable insights for developing practical strategies to improve drought resilience and crop establishment in sensitive agricultural species under water-limited conditions.

Enriched Flavonoid Compounds Confer Enhanced Resistance to Fusarium-Induced Root Rot in Oil Tea Plants

Root rot in Camellia oleifera complicates the development of targeted control measures owing to its complex aetiology. Although breeding resistant varieties of C. oleifera presents a promising solution, research into cultivation strategies and potential resistance mechanisms against root rot remains limited. In this study, we investigated six cultivars of C. oleifera that exhibit varying levels of resistance to root rot. We conducted transcriptome analysis, measurements of soil physicochemical properties and an analysis of the fungal microbiome to explore the relationship between Fusarium-induced root rot and flavonoid compounds in the rhizosphere. The resistant cultivar CL18 demonstrated superior performance concerning root rot incidence, root health status and the expression levels of genes associated with flavonoid biosynthesis in this study. Significant differences were observed in the composition and diversity of rhizosphere fungal communities among the various cultivars of C. oleifera. The abundance of Fusarium in the rhizosphere soil of CL18 was low, and a negative correlation was identified between the flavonoid content in the soil and the abundance of Fusarium. Our study uncovers the role of flavonoids in the resistance of C. oleifera to root rot, thereby offering new strategies for disease management and the breeding of resistant cultivars.

Exogenous nano-silicon enhances the ability of intercropped faba bean to alleviate cadmium toxicity and resist Fusarium wilt

Excessive soil cadmium (Cd) and the accumulation of pathogens pose serious threats to legume growth. However, it remains unclear whether intercropping (IFcd) and its combined treatment with silicon nanoparticles (Si-NPs) (IFcd + Si) can alleviate these challenges under Cd stress, as well as the underlying mechanisms involved. This study systematically elucidated the mechanism of faba bean-wheat intercropping and Si-NPs regulating faba bean growth under Cd stress using rhizosphere metabolomics and 16 S rRNA microbiome analysis. The results showed that IFcd and IFcd + Si treatments significantly reduced Cd accumulation by 17.3% and 56.2%, and Fusarium wilt incidence by 11.1% and 33.3%, respectively, compared with monoculture faba bean (MFcd) while promoting root and plant growth. These treatments reduced oxidative stress markers, including H2O2, MDA, and O2-, and increased the activity of defense enzymes, such as SOD, APX, and POD in plants. Furthermore, they increased NH4+-N and available potassium levels in rhizosphere soils. Interestingly, the NH4+-N content increased and was significantly positively correlated with urease (URE) activity and negatively correlated with Cd. Beneficial bacteria and functional metabolites were enriched in the rhizosphere of faba bean. Joint analysis revealed increased relative abundances of Sphingomonas, Intrasporangium, and Streptomyces, which were positively correlated with antibacterial metabolites, such as sordarin, lactucin, and 15-methylpalmate. This explains the reduced Cd accumulation and Fusarium wilt in plants. These findings provide mechanistic insights into how intercropping with Si-NPs mitigates Cd stress and controls soil-borne diseases by regulating rhizosphere metabolites, bacterial communities, and plant resistance.

Physiological mechanisms of heavy metal detoxification in tomato plants mediated by endophytic fungi under nickel and cadmium stress

Heavy metal (HM) pollution in agricultural soils threatens plant growth and food security, underscoring the urgency for sustainable and eco-friendly solutions. This study investigates the potential of endophytic fungi, Fusarium proliferatum SL3 and Aspergillus terreus MGRF2, in mitigating nickel (Ni) and cadmium (Cd) stress in Solanum lycopersicum (tomato). These fungi were evaluated for their plant growth-promoting traits, including the production of indole-3-acetic acid (IAA) and siderophores, offering a sustainable strategy for alleviating HM toxicity. Inoculation with SL3 and MGRF2 significantly reduced metal accumulation in plant tissues by enhancing metal immobilization and modifying root architecture. Microscopic analysis revealed that fungi protected root epidermal cells from Ni- and Cd-induced damage, preserving cellular integrity and preventing plasmolysis. Fungal-treated plants exhibited improved growth and biomass, with SL3 demonstrating superior Cd stress mitigation and MGRF2 excelling under Ni stress. Photosynthetic pigment levels, including chlorophyll-a and carotenoids, were restored, highlighting the role of fungi in maintaining photosynthetic efficiency. Antioxidant activity was also modulated, as reduced glutathione (GSH) levels and increased flavonoid production were observed, contributing to enhanced oxidative stress management. Hormonal profiling revealed that fungal inoculation balanced stress-induced hormonal disruptions, with lower abscisic acid (ABA) levels and improved salicylic acid (SA) and gibberellic acid (GA) pathways. These changes facilitated better stress adaptation, enhanced nutrient uptake, and improved physiological performance. qRT-PCR analysis further revealed differential gene expression patterns, while antioxidant enzyme activity strengthened the plants' defense against HM-induced oxidative damage. Multivariate analyses highlighted shoot and root traits as critical indicators of resilience, with fungal inoculation driving substantial improvements. These findings demonstrate the potential of SL3 and MGRF2 as eco-friendly bioinoculants, offering a sustainable and cost-effective approach to reducing HMs toxicity in contaminated soils while enhancing crop productivity. This work highlights the promising role of plant-microbe interactions in advancing sustainable agriculture and addressing the challenges posed by heavy metal pollution.

Co-inoculation of Trichoderma and tea root-associated bacteria enhance flavonoid production and abundance of mycorrhizal colonization in tea (Camellia sinensis)

Tea is one of the most popular nonalcoholic beverages, that contains several medicinally important flavonoids. Due to seasonal variation and various environmental stresses, the overall consistency of tea flavonoids affects the tea quality. To combat stress, plants stimulate symbiotic relationships with root-associated beneficial microbiomes that sustain nutrient allocation. Therefore, a study has been designed to understand the role of the tea root microbiome in sustaining tea leaf flavonoid production. To enumerate the microbiome, tea root and rhizoplane soil were collected from 3 years of healthy plants from Jalpaiguri district, West Bengal, India. A culture-independent approach was adopted to identify root and rhizosphere microbial diversity (BioSample: SAMN31404869; SRA: SRS15503027 [rhizosphere soil metagenome] BioSample: SAMN31404868;SRA:SRS15503030 [root metagenome]. In addition to diverse microbes, four mycorrhiza fungi, i.e., Glomus intraradices, Glomus irregulare, Paraglomus occultum and Scutellospora heterogama were predominant in collected root samples. A culture-dependent approach was also adopted to isolate several plant growth-promoting bacteria [Bacillus sp. D56, Bacillus sp. D42, Bacillus sp. DR15, Rhizobium sp. DR23 (NCBI Accession: OR821747-OR821750)] and one fungal [Trichoderma sp. AM6 (NCBI Accession:OM915414)] strain. A pot experiment was designed to assess the impact of that isolated microbiome on tea seedlings. After six months of microbiome inoculation, tea plants' physicochemical and transcriptional parameters were evaluated. The results confer that the microbiome-treated treatments [(T1-without any microbial inoculation; NCBI Accession: SAMN33591153), Trichoderma sp. AM6 (T2; NCBI Accession: SAMN33591155) and Trichoderma sp. AM6 +VAM containing tea root+synthetic microbial consortia (T5; NCBI Accession: SAMN33591154)] could enhance the total flavonoid content in tea seedlings by upregulating certain transcripts associated with the flavonoid biosynthesis pathway of tea.

Metabolite-driven mechanisms reveal chemical ecology of Lehmann Lovegrass (Eragrostis lehmanniana) invasion in North American semi-arid ecosystems

Invasive plants threaten global ecosystems, yet traditional analyses of functional traits cannot fully explain their dominance over co-occurring natives. Metabolomics offers insights into plant invasions, but single-technique studies often miss critical biochemical mechanisms. We employ a multimodal metabolomics approach (¹H NMR, LC MS/MS, FT-ICR-MS, and MALDI-MSI) to investigate the biochemical basis of Lehmann lovegrass (Eragrostis lehmanniana) invasion in semi-arid North America, comparing it with a co-occurring native grass, Arizona cottontop (Digitaria californica). Our analysis reveals three metabolomic traits of Lehmann lovegrass compared to Arizona cottontop: Enhanced nitrogen allocation in shoots, reduced defensive metabolites in root layers; and increased root exudate modulation under stress conditions. These traits suggest Lehmann lovegrass succeeds through adaptation to increasing aridity rather than direct competition, demonstrating adaptation to nutrient-poor environments and high phenotypic plasticity in response to increasing aridity. This integrated metabolomic approach provides new mechanistic insights into invasion ecology and plant adaptation under environmental change.

Diurnal Rhythmicity in the Rhizosphere Microbiome-Mechanistic Insights and Significance for Rhizosphere Function

The rhizosphere is a key interface between plants, microbes and the soil which influences plant health and nutrition and modulates terrestrial biogeochemical cycling. Recent research has shown that the rhizosphere environment is far more dynamic than previously recognised, with evidence emerging for diurnal rhythmicity in rhizosphere chemistry and microbial community composition. This rhythmicity is in part linked to the host plant's circadian rhythm, although some heterotrophic rhizosphere bacteria and fungi may also possess intrinsic rhythmicity. We review the evidence for diurnal rhythmicity in rhizosphere microbial communities and its link to the plant circadian clock. Factors which may drive microbial rhythmicity are discussed, including diurnal change in root exudate flux and composition, rhizosphere physico-chemical properties and plant immunity. Microbial processes which could contribute to community rhythmicity are considered, including self-sustained microbial rhythms, bacterial movement into and out of the rhizosphere, and microbe-microbe interactions. We also consider evidence that changes in microbial composition mediated by the plant circadian clock may affect microbial function and its significance for plant health and broader soil biogeochemical cycling processes. We identify key knowledge gaps and approaches which could help to resolve the spatial and temporal variation and functional significance of rhizosphere microbial rhythmicity. This includes unravelling the factors which determine the oscillation of microbial activity, growth and death, and cross-talk with the host over diurnal time frames. We conclude that diurnal rhythmicity is an inherent characteristic of the rhizosphere and that temporal factors should be considered and reported in rhizosphere studies.

Integrated transcriptome and metabolome analyses reveals the mechanisms of function loss of Lr29 leaf rust resistance gene at high temperatures in wheat

Leaf rust (LR) is one of the most common diseases of wheat. The resistance gene Lr29 provides wide resistance to LR, but loses its function under high temperatures. Despite the importance of this gene, the mechanism of resistance is unclear. In this study we investigated the resistance mechanism of the Lr29 gene to LR at the seedling stage, as well as the reasons behind the loss of gene function at high temperatures by using integrated transcriptome and metabolome analyses. Results suggests that the pathways of reactive oxygen species (ROS), which could be due to expression of genes including LOX (lipoxygenase), APX (ascorbate peroxidase) and GST (glutathione S-transferase), play a key role in the resistance of Lr29 to LR, furthermore flavonoids, such as epicatechin, cosmosiin, apiin, vitexin and rutin, were identified as the key metabolites linked to Lr29 resistance. We also found that, at high temperatures, Lr29 downregulated the genes and metabolites associated with glycolysis and the tricarboxylic acid (TCA) cycle, while genes and metabolites related to the shikimic acid pathway were upregulated. This study might provide a valuable theoretical foundation for the cloning of the Lr29 gene, the analysis of its disease resistance mechanism, and the understanding of how temperature affects gene function.

Significant Enrichment of Potential Pathogenic Fungi in Soil Mediated by Flavonoids, Phenolic Acids, and Organic Acids

It is well established that root exudates play a crucial role in shaping the assembly of plant rhizosphere microbial communities. Nonetheless, our understanding of how different types of exudates influence the abundance of potential pathogens in soil remains insufficient. Investigating the effects of root exudates on soil-dwelling pathogenic fungi is imperative for a comprehensive understanding of plant-fungal interactions within soil ecosystems and for maintaining soil health. This study aimed to elucidate the effects of the principal components of root exudates-flavonoids (FLA), phenolic acids (PA), and organic acids (OA)-on soil microbial communities and soil properties, as well as to investigate their mechanisms of action on soil potential pathogenic fungi. The results demonstrated that the addition of these components significantly modified the composition and diversity of soil microbial communities, with OA treatment notably altering the composition of dominant microbial taxa. Furthermore, the introduction of these substances facilitated the proliferation of saprophytic fungi. Additionally, the incorporation of flavonoids, phenolic acids, and organic acids led to an increased abundance of potential pathogenic fungi in the soil, particularly in the FLA and PA treatments. It was observed that the addition of these substances enhanced soil fertility, pH, and antioxidant enzyme activity. Specifically, FLA and PA treatments reduced the abundance of dominant microbial taxa, whereas OA treatment altered the composition of these taxa. These findings suggest that the inclusion of flavonoids, phenolic acids, and organic acids could potentially augment the enrichment of soil potential pathogenic fungi by modulating soil properties and enzymatic activities. These results offer valuable insights into the interactions between plants and fungal communities in soil ecosystems and provide a scientific foundation for the management and maintenance of soil health.

A Mycorrhiza-Induced UDP-Glucosyl Transferase Negatively Regulates the Arbuscular Mycorrhizal Symbiosis

Most terrestrial plants can establish a reciprocal symbiosis with arbuscular mycorrhizal (AM) fungi to cope with adverse environmental stresses. The development of AM symbiosis is energetically costly and needs to be dynamically controlled by plants to maintain the association at mutual beneficial levels. Multiple components involved in the autoregulation of mycorrhiza (AOM) have been recently identified from several plant species; however, the mechanisms underlying the feedback regulation of AM symbiosis remain largely unknown. Here, we report that AM colonization promotes the flavonol biosynthesis pathway in tomato (Solanum lycopersicum), and an AM-specific UDP-glucosyltransferase SlUGT132, which probably has the flavonol glycosylation activity, negatively regulates AM development. SlUGT132 was predominantly expressed in the arbuscule-containing cells, and its knockout or knockdown mutants showed increased soluble sugar content, root colonization level and arbuscule formation. Conversely, overexpression of SlUGT132 resulted in declined soluble sugar content and mycorrhization degree. Metabolomic assay revealed decreased contents of astragalin, tiliroside and cynaroside in slugt132 mycorrhizal roots, but increased accumulation of these flavonoid glycosides in SlUGT132-overexpressing plant roots. Our results highlight the presence of a novel, SlUGT132-mediated AOM mechanism, which enable plants to flexibly control the accumulation of soluble sugars and flavonoid glycosides in mycorrhizal roots and modulate colonization levels.

The flavonoid metabolic pathway genes Ac4CL1, Ac4CL3 and AcHCT1 positively regulate the kiwifruit immune response to Pseudomonas syringae pv. actinidiae

Psa primarily utilises the type III secretion system (T3SS) to deliver effector proteins (T3Es) into host cells, thereby regulating host immune responses. However, the mechanism by which kiwifruit responds to T3SS remains unclear. To elucidate the molecular reaction of kiwifruit plants to Psa infection, M228 and mutant M228△hrcS strains were employed to inoculate Actinidia chinensis var. chinensis for performing comparative transcriptional and metabolomic analyses. Transcriptome analysis identified 973 differentially expressed genes (DEGs) related to flavonoid synthesis, pathogen interaction, and hormone signaling pathways during the critical period of Psa infection at 48 h post-inoculation. In the subsequent metabolomic analysis, flavonoid-related differential metabolites were significantly enriched after the loss of T3SS.Through multi-omics analysis, 22 differentially expressed genes related to flavonoid biosynthesis were identified. Finally, it was discovered that the transient overexpression of 3 genes significantly enhanced kiwifruit resistance to Psa. qRT-PCR analysis indicated that Ac4CL1, Ac4CL3 and AcHCT1 promote host resistance to disease, while Ac4CL3 negatively regulates host resistance to Psa. These findings enrich the plant immune regulation network involved in the interaction between kiwifruit and Psa, providing functional genes and directions with potential application for breeding kiwifruit resistance to canker disease.

Legume-specific recruitment of rhizobia by hyphae of arbuscular mycorrhizal fungi

The legume-rhizobia symbiosis possesses great potential for sustainable agriculture because of its ability to fix atmospheric nitrogen, reducing crop dependence on nitrogen fertilizers. Rhizobia recognize the host legume through flavonoids released by the roots. These signals are detected by bacteria typically over a few millimeters. Recent research has shown that arbuscular mycorrhizal fungi extend this recognition beyond 15 cm by transporting flavonoids along their hyphae. In soil, common mycorrhizal networks (CMNs) linking plants are formed by arbuscular mycorrhizal fungi. We hypothesized that such networks linking different legumes can transmit host-specific signals, guiding rhizobia to their appropriate hosts. Using in vitro and greenhouse microcosms, we linked Medicago truncatula and Glycine max via a CMN of Rhizophagus irregularis and inoculated GFP-labeled Sinorhizobium meliloti and mCherry-labeled Bradyrhizobium diazoefficiens on the hyphae. S. meliloti preferentially migrated towards M. truncatula, whereas B. diazoefficiens preferentially migrated towards G. max (155 ± 8 and 13 ± 3 nodules, respectively). This was confirmed in the greenhouse with a higher concentration of S. meliloti (2.1-2.5 × 105 CFU·g-1) near M. truncatula and a higher concentration of B. diazoefficiens (1.5-1.6 × 105 CFU·g-1) near G. max (71-82 and 15-18 nodules, respectively). Metabolomics revealed host-specific flavonoids in hyphal exudates: M. truncatula-connected hyphae released DL-liquiritigenin, naringenin, sakuranetin, and 3,7-dimethylquercetin, whereas G. max-connected hyphae released daidzin, 6"-O-malonyldaidzin, irilone, and erylatissin A. These findings establish that common mycorrhizal networks constitute a "navigation system", using chemical signals to orient rhizobia towards their specific hosts, thereby improving nodulation with potential applications in agriculture.

Root hair developmental regulators orchestrate drought triggered microbiome changes and the interaction with beneficial Rhizobiaceae

Drought is one of the most serious abiotic stresses, and emerging evidence suggest plant microbiome affects plant drought tolerance. However, there is a lack of genetic evidence regarding whether and how plants orchestrate the dynamic assembly of the microbiome upon drought. By utilizing mutants with enhanced or decreased root hair densities, we find that root hair regulators also affect drought induced root microbiome changes. Rhizobiaceae is a key biomarker taxa affected by root hair related mutants. We isolated and sequenced 1479 root associated microbes, and confirmed that several Rhizobium strains presented stress-alleviating activities. Metagenome, root transcriptome and root metabolome studies further reveal the multi-omic changes upon drought stress. We knocked out an ornithine cyclodeaminase (ocd) gene in Rhizobium sp. 4F10, which significantly dampens its stress alleviating ability. Our genetic and integrated multi-omics studies confirm the involvement of host genetic effects in reshaping a stress-alleviating root microbiome during drought, and provide mechanistic insights into Rhizobiaceae mediated abiotic stress protection.

A mass spectrometry-based peptidomic dataset of the spermosphere in common bean (Phaseolus vulgaris L.) seeds

The spermosphere, a dynamic microenvironment surrounding germinating seeds, is shaped by the complex interactions between natural compounds exuded by seeds and seed-associated microbial communities. While peptides exuded by plants are known to influence microbiota diversity, little is known about those specifically exuded by seeds. In this study, we characterised the peptidome profile of the spermosphere for the first time using seeds from eight genotypes of common bean (Phaseolus vulgaris) grown in two contrasting production regions. An untargeted LC-MS/MS peptidomic analysis revealed 3,258 peptides derived from 414 precursor proteins of common bean in the spermosphere. This comprehensive peptidomic dataset provides valuable insights into the characteristics of peptides exuded by common bean seeds in the spermosphere. It can be used to identify peptides with potential antimicrobial or other biological activities, advancing our understanding of the functional roles of seed-exuded peptides in the spermosphere.

Investigating the Impact of Flavonoids on Aspergillus flavus: Insights into Cell Wall Damage and Biofilms

Aspergillus flavus, a fungus known for producing aflatoxins, poses significant threats to agriculture and global health. Flavonoids, plant-derived compounds, inhibit A. flavus proliferation and mitigate aflatoxin production, although the precise molecular and physical mechanisms underlying these effects remain poorly understood. In this study, we investigated three flavonoids-apigenin, luteolin, and quercetin-applied to A. flavus NRRL 3357. We determined the following: (1) glycosylated luteolin led to a 10% reduction in maximum fungal growth capacity; (2) quercetin affected cell wall integrity by triggering extreme mycelial collapse, while apigenin and luteolin caused peeling of the outer layer of cell wall; (3) luteolin exhibited the highest antioxidant capacity in the environment compared to apigenin and quercetin; (4) osmotic stress assays did not reveal morphological defects; (5) flavonoids promoted cell adherence, a precursor for biofilm formation; and (6) RNA sequencing analysis revealed that flavonoids impact expression of putative cell wall and plasma membrane biosynthesis genes. Our findings suggest that the differential effects of quercetin, luteolin, and apigenin on membrane integrity and biofilm formation may be driven by their interactions with fungal cell walls. These insights may inform the development of novel antifungal additives or plant breeding strategies focusing on plant-derived compounds in crop protection.

Nanostructures for Delivery of Flavonoids with Antibacterial Potential against Klebsiella pneumoniae

Flavonoids are secondary metabolites that exhibit remarkable biological activities, including antimicrobial properties against Klebsiella pneumoniae, a pathogen responsible for several serious nosocomial infections. However, oral administration of these compounds faces considerable challenges, such as low bioavailability and chemical instability. Thus, the encapsulation of flavonoids in nanosystems emerges as a promising strategy to mitigate these limitations, offering protection against degradation; greater solubility; and, in some cases, controlled and targeted release. Different types of nanocarriers, such as polymeric nanoparticles, liposomes, and polymeric micelles, among others, have shown potential to increase the antimicrobial efficacy of flavonoids by reducing the therapeutic dose required and minimizing side effects. In addition, advances in nanotechnology enable co-encapsulation with other therapeutic agents and the development of systems responsive to more specific stimuli, optimizing treatment. In this context, the present article provides an updated review of the literature on flavonoids and the main nanocarriers used for delivering flavonoids with antibacterial properties against Klebsiella pneumoniae.

Flavonoids Biotransformation by Human Gut Bacterium Dorea sp. MRG-IFC3 Cell-Free Extract

Human gut bacterium Dorea sp. MRG-IFC3 is unique in that it is capable of metabolizing puerarin, an isoflavone C-glycoside, whereas it shows broad substrate glycosidase activity for the various flavonoid O-glycosides. To address the question on the substrate specificity, as well as biochemical characteristics, cell-free biotransformation of flavonoid glycosides was performed under various conditions. The results showed that there are two different enzyme systems responsible for the metabolism of flavonoid C-glycosides and O-glycosides in the MRG-IFC3 strain. The system responsible for the conversion of puerarin was inducible and comprised of two enzymes. One enzyme oxidizes puerarin to 3"-oxo-puerarin and the other enzyme converts 3"-oxo-puearin to daidzein. The second enzyme was only active toward 3"-oxo-puerarin. The activity of puerarin conversion to daidzein was enhanced in the presence of Mn2+ and NAD+. It was concluded that the puerarin C-deglycosylation by Dorea sp. MRG-IFC3 possibly adopts the same biochemical mechanism as the strain PUE, a species of Dorea longicatena.

Alleviation of cotton growth suppression caused by salinity through biochar is strongly linked to the microbial metabolic potential in saline-alkali soil

Biochar is a typical soil organic amendment; however, there is limited understanding of its impact on the metabolic characteristics of microorganisms in saline-alkaline soil microenvironment, as well as the advantages and disadvantages of plant-microorganism interactions. To elucidate the mechanisms underlying the impact of saline-alkali stress on cotton, a 6-month pot experiment was conducted, involving the sowing of cotton seedlings in saline-alkali soil. Three different biochar application levels were established: 0 % (C0), 1 % (C1), and 2 % (C2). Results indicated that biochar addition improved the biomass of cotton plants, especially under C2 treatment; the dry weight of cotton bolls were 8.15 times that of C0. Biochar application led to a rise in the accumulation of photosynthetic pigments by 8.30-51.89 % and carbohydrates by 7.4-10.7 times, respectively. Moreover, peroxidase (POD) activity, the content of glutathione (GSH), and ascorbic acid (ASA) were elevated by 23.97 %, 118.39 %, and 48.30 % under C2 treatment, respectively. Biochar caused a reduction in Na+ uptake by 8.21-39.47 %, relative electrical conductivity (REC) of plants, and improved K+/Na+ and Ca2+/Na+ ratio indicating that biochar alleviated salinity-caused growth reduction. Additionally, the application of biochar enhanced the absorption intensity of polysaccharide fingerprints in cotton leaves and roots. Two-factor co-occurrence analysis indicated that the key differential metabolites connected to several metabolic pathways were L-phenylalanine, piperidine, L-tryptophan, and allysine. Interestingly, biochar altered the metabolic characteristics of saline-alkali soil, especially related to the biosynthesis and metabolism of amino acids and purine metabolism. In conclusion, this study demonstrates that biochar may be advantageous in saline soil microenvironment; it has a favorable impact on how plants and soil microbial metabolism interact.

Exploring the interplay between the core microbiota, physicochemical factors, agrobiochemical cycles in the soil of the historic tokaj mád wine region

A Hungarian survey of Tokaj-Mád vineyards was conducted. Shotgun metabarcoding was applied to decipher the microbial-terroir. The results of 60 soil samples showed that there were three dominant fungal phyla, Ascomycota 66.36% ± 15.26%, Basidiomycota 18.78% ± 14.90%, Mucoromycota 11.89% ± 8.99%, representing 97% of operational taxonomic units (OTUs). Mutual interactions between microbiota diversity and soil physicochemical parameters were revealed. Principal component analysis showed descriptive clustering patterns of microbial taxonomy and resistance gene profiles in the case of the four historic vineyards (Szent Tamás, Király, Betsek, Nyúlászó). Linear discriminant analysis effect size was performed, revealing pronounced shifts in community taxonomy based on soil physicochemical properties. Twelve clades exhibited the most significant shifts (LDA > 4.0), including the phyla Verrucomicrobia, Bacteroidetes, Chloroflexi, and Rokubacteria, the classes Acidobacteria, Deltaproteobacteria, Gemmatimonadetes, and Betaproteobacteria, the order Sphingomonadales, Hypomicrobiales, as well as the family Sphingomonadaceae and the genus Sphingomonas. Three out of the four historic vineyards exhibited the highest occurrences of the bacterial genus Bradyrhizobium, known for its positive influence on plant development and physiology through the secretion of steroid phytohormones. During ripening, the taxonomical composition of the soil fungal microbiota clustered into distinct groups depending on altitude, differences that were not reflected in bacteriomes. Network analyses were performed to unravel changes in fungal interactiomes when comparing postveraison and preharvest samples. In addition to the arbuscular mycorrhiza Glomeraceae, the families Mycosphaerellacae and Rhyzopodaceae and the class Agaricomycetes were found to have important roles in maintaining soil microbial community resilience. Functional metagenomics showed that the soil Na content stimulated several of the microbiota-related agrobiogeochemical cycles, such as nitrogen and sulphur metabolism; steroid, bisphenol, toluene, dioxin and atrazine degradation and the synthesis of folate.

Plants recruit insecticidal bacteria to defend against herbivore attacks

Pest feeding affects the rhizobacteria community. The rhizomicrobiota activates salicylic acid and jasmonic acid signaling pathways to help plants deal with pest infestation. However, whether plants can recruit special pesticidal microorganisms to deal with attack from herbivores is unclear. A system composed of peanuts and first-instar larvae of Holotrichia parallela were used to analyze whether peanuts truly enrich the insecticidal bacteria after feeding by larvae, and whether inoculation of the enriched bacteria promotes the resistance of plants to herbivore. In this study, high-throughput sequencing of 16 S rRNA gene amplicons was used to demonstrate that infestation of the subterranean pest H. parallela quickly changed the rhizosphere bacterial community structure within 24 h, and the abundance of Enterobacteriaceae, especially Enterobacter, was manifestly enriched. Root feeding induced rhizobacteria to form a more complex co-occurrence network than the control. Rhizosphere bacteria were isolated, and 4 isolates with high toxicity against H. parallela larvae were obtained by random forest analysis. In a back-inoculation experiment using a split-root system, green fluorescent protein (GFP)-labeled Enterobacter sp. IPPBiotE33 was observed to be enriched in uneaten peanut roots. Additionally, supplementation with IPPBiotE33 alleviated the adverse effects of H. parallela on peanuts. Our findings indicated that herbivore infestation could induce plants to assemble bacteria with specific larvicidal activity to address threats.

Responses of plant immune system and rhizosphere soil microbiome to the elicitor BAR11 in Arabidopsis thaliana

Microbial elicitors have been shown to boost plant immunity by inducing defense responses to reduce plant disease. However, little is known about the changes in plant microbiome and metabolism in the process of enhancing plant immunity with elicitors. The protein elicitor BAR11, from Saccharothrix yanglingensis Hhs.015, induces defense responses in Arabidopsis thaliana that enhances resistance to pathogens. In this study, bar11 was inserted into Col-0 A. thaliana to obtain BAR11-Trans plant by Agrobacterium-mediated immersion transformation. BAR11-Trans exhibited an elevated defense level against Pseudomonas syringae pv. tomato DC3000 while experiencing a decline in biomass production of above-ground parts. In the process, BAR11-Trans increased the activity of phenylalanine ammonia lyase (PAL) and catalase (CAT), and up-regulated genes related to plant defense pathways. Furthermore, BAR11-Trans decreased root tip reactive oxygen species (ROS) levels while increasing ROS burst in the leaves. Soil transplantation experiments showed that soil planted with BAR11-Trans could enhance the resistance of Col-0 A. thaliana to DC3000. Analysis of A. thaliana rhizosphere soil through 16S rRNA amplified sequencing revealed that BAR11-Trans increased the relative abundance and diversity of the rhizosphere microbial community, leading to the recruitment of more plant probiotics. Additionally, the accumulation of kaempferitrin and robinin in BAR11-Trans influenced the physicochemical properties of rhizosphere soil and the composition of the bacterial community. In summary, BAR11-Trans exhibited heightened defense levels compared to Col-0, leading to increased secretion of secondary metabolites and the recruitment of a greater number of microorganisms to adapt to the environment. These findings offer novel insights for the potential application of elicitors in agricultural disease control.

Integrated transcriptomic and metabolomic analyses elucidate the mechanism of flavonoid biosynthesis in the regulation of mulberry seed germination under salt stress

Seed propagation is the main method of mulberry expansion in China, an important economic forest species. However, seed germination is the most sensitive stage to various abiotic stresses, especially salinity stress. To reveal the molecular regulatory mechanism of mulberry seed germination under salt stress, flavonoid metabolomics and transcriptomics analyses were performed on mulberry seeds germinated under 50 and 100 mmol/L NaCl stress. Analysis of the flavonoid metabolome revealed that a total of 145 differential flavonoid metabolites (DFMs) were classified into 9 groups, 40 flavonols, 32 flavones, 16 chalcones and 14 flavanones. Among them, 61.4% (89) of the DFMs accumulated continuously with increasing salt concentration, reaching the highest level at a 100 mmol/L salt concentration; these DFMs included quercetin-3-O-glucoside (isoquercitrin), kaempferol (3,5,7,4'-tetrahydroxyflavone), quercetin-7-O-glucoside, taxifolin (dihydroquercetin) and apigenin (4',5,7-trihydroxyflavone), indicating that these flavonoids may be key metabolites involved in the response to salt stress. Transcriptional analysis identified a total of 3055 differentially expressed genes (DEGs), most of which were enriched in flavonoid biosynthesis (ko00941), phenylpropanoid biosynthesis (ko00940) and biosynthesis of secondary metabolites (ko01110). Combined analysis of flavonoid metabolomic and transcriptomic data indicated that phenylalanine ammonia-lyase (PAL), 4-coumarate-CoA ligase (4CL), chalcone synthase (CHS), flavonol synthase (FLS), bifunctional dihydroflavonol 4-reductase/flavanone 4-reductase (DFR) and anthocyanidin reductase (ANR) were the key genes involved in flavonoid accumulation during mulberry seed germination under 50 and 100 mmol/L NaCl stress. In addition, three transcription factors, MYB, bHLH and NAC, were involved in the regulation of flavonoid accumulation under salt stress. The results of quantitative real-time PCR (qRT‒PCR) validation showed that the expression levels of 11 DEGs, including 7 genes involved in flavonoid biosynthesis, under different salt concentrations were consistent with the transcriptomic data, and parallel reaction monitoring (PRM) results showed that the expression levels of 6 key enzymes (proteins) involved in flavonoid synthesis were consistent with the accumulation of flavonoids. This study provides a new perspective for investigating the regulatory role of flavonoid biosynthesis in the regulation of mulberry seed germination under salt stress at different concentrations.

Recent advancements in multifaceted roles of flavonoids in plant-rhizomicrobiome interactions

The rhizosphere consists of a plethora of microbes, interacting with each other as well as with the plants present in proximity. The root exudates consist of a variety of secondary metabolites such as strigolactones and other phenolic compounds such as coumarin that helps in facilitating communication and forming associations with beneficial microbes in the rhizosphere. Among different secondary metabolites flavonoids (natural polyphenolic compounds) continuously increasing attention in scientific fields for showing several slews of biological activities. Flavonoids possess a benzo-γ-pyrone skeleton and several classes of flavonoids have been reported on the basis of their basic structure such as flavanones, flavonols, anthocyanins, etc. The mutualistic association between plant growth-promoting rhizobacteria (PGPR) and plants have been reported to help the host plants in surviving various biotic and abiotic stresses such as low nitrogen and phosphorus, drought and salinity stress, pathogen attack, and herbivory. This review sheds light upon one such component of root exudate known as flavonoids, which is well known for nodulation in legume plants. Apart from the well-known role in inducing nodulation in legumes, this group of compounds has anti-microbial and antifungal properties helping in establishing defensive mechanisms and playing a major role in forming mycorrhizal associations for the enhanced acquisition of nutrients such as iron and phosphorus. Further, this review highlights the role of flavonoids in plants for recruiting non-mutualistic microbes under stress and other important aspects regarding recent findings on the functions of this secondary metabolite in guiding the plant-microbe interaction and how organic matter affects its functionality in soil.

Two transcription factors, AcREM14 and AcC3H1, enhance the resistance of kiwifruit Actinidiachinensis var. chinensis to Pseudomonas syringae pv. actinidiae

Kiwifruit bacterial canker is a global disease caused by Pseudomonas syringae pv. actinidiae (Psa), which poses a major threat to kiwifruit production worldwide. Despite the economic importance of Actinidia chinensis var. chinensis, only a few resistant varieties have been identified to date. In this study, we screened 44 kiwifruit F1 hybrid lines derived from a cross between two A. chinensis var. chinensis lines and identified two offspring with distinct resistance to Psa: resistant offspring RH12 and susceptible offspring SH14. To identify traits associated with resistance, we performed a comparative transcriptomic analysis of these two lines. We identified several highly differentially expressed genes (DEGs) associated with flavonoid synthesis, pathogen interactions, and hormone signaling pathways, which play essential roles in disease resistance. Additionally, using weighted gene co-expression network analysis, we identified six core transcription factors. Moreover, qRT-PCR results demonstrated the high expression of AcC3H1 and AcREM14 in Psa-induced highly resistant hybrid lines. Ultimately, Overexpression of AcC3H1 and AcREM14 in kiwifruit enhanced disease resistance, and this was associated with upregulation of enzymatic activity and gene expression in the salicylic acid (SA) signaling pathway. Our study elucidates a molecular mechanism underlying disease resistance in kiwifruit and contributes to the advancement of research on kiwifruit breeding.

Signaling in Legume-Rhizobia Symbiosis

Legumes represent an important source of food protein for human nutrition and animal feed. Therefore, sustainable production of legume crops is an issue of global importance. It is well-known that legume-rhizobia symbiosis allows an increase in the productivity and resilience of legume crops. The efficiency of this mutualistic association strongly depends on precise regulation of the complex interactions between plant and rhizobia. Their molecular dialogue represents a complex multi-staged process, each step of which is critically important for the overall success of the symbiosis. In particular, understanding the details of the molecular mechanisms behind the nodule formation and functioning might give access to new legume cultivars with improved crop productivity. Therefore, here we provide a comprehensive literature overview on the dynamics of the signaling network underlying the development of the legume-rhizobia symbiosis. Thereby, we pay special attention to the new findings in the field, as well as the principal directions of the current and prospective research. For this, here we comprehensively address the principal signaling events involved in the nodule inception, development, functioning, and senescence.

The Complex Interplay between Arbuscular Mycorrhizal Fungi and Strigolactone: Mechanisms, Sinergies, Applications and Future Directions

Plants, the cornerstone of life on Earth, are constantly struggling with a number of challenges arising from both biotic and abiotic stressors. To overcome these adverse factors, plants have evolved complex defense mechanisms involving both a number of cell signaling pathways and a complex network of interactions with microorganisms. Among these interactions, the relationship between symbiotic arbuscular mycorrhizal fungi (AMF) and strigolactones (SLs) stands as an important interplay that has a significant impact on increased resistance to environmental stresses and improved nutrient uptake and the subsequent enhanced plant growth. AMF establishes mutualistic partnerships with plants by colonizing root systems, and offers a range of benefits, such as increased nutrient absorption, improved water uptake and increased resistance to both biotic and abiotic stresses. SLs play a fundamental role in shaping root architecture, promoting the growth of lateral roots and regulating plant defense responses. AMF can promote the production and release of SLs by plants, which in turn promote symbiotic interactions due to their role as signaling molecules with the ability to attract beneficial microbes. The complete knowledge of this synergy has the potential to develop applications to optimize agricultural practices, improve nutrient use efficiency and ultimately increase crop yields. This review explores the roles played by AMF and SLs in plant development and stress tolerance, highlighting their individual contributions and the synergistic nature of their interaction.

The Rpf107 gene, a homolog of LOR, is required for the symbiotic nodulation of Robinia pseudoacacia

MAIN CONCLUSION

Rpf107 is involved in the infection process of rhizobia and the maintenance of symbiotic nitrogen fixation in black locust root nodules. The LURP-one related (LOR) protein family plays a pivotal role in mediating plant defense responses against both biotic and abiotic stresses. However, our understanding of its function in the symbiotic interaction between legumes and rhizobia remains limited. Here, Rpf107, a homolog of LOR, was identified in Robinia pseudoacacia (black locust). The subcellular localization of Rpf107 was analyzed, and its function was investigated using RNA interference (RNAi) and overexpression techniques. The subcellular localization assay revealed that Rpf107 was mainly distributed in the plasma membrane and nucleus. Rpf107 silencing prevented rhizobial infection and hampered plant growth. The number of infected cells in the nitrogen fixation zone of the Rpf107-RNAi nodules was also noticeably lower than that in the control nodules. Notably, Rpf107 silencing resulted in bacteroid degradation and the premature aging of nodules. In contrast, the overexpression of Rpf107 delayed the senescence of nodules and prolonged the nitrogen-fixing ability of nodules. These results demonstrate that Rpf107 was involved in the infection of rhizobia and the maintenance of symbiotic nitrogen fixation in black locust root nodules. The findings reveal that a member of the LOR protein family plays a role in leguminous root nodule symbiosis, which is helpful to clarify the functions of plant LOR protein family and fully understand the molecular mechanisms underlying legume-rhizobium symbiosis.

Dynamic metabolites: A bridge between plants and microbes

Plant metabolites have a great influence on soil microbiomes. Although few studies provided insights into plant-microbe interactions, we still know very little about how plants recruit their microbiome. Here, we discuss the dynamic progress that typical metabolites shape microbes by a variety of factors, such as physiographic factors, cultivar factors, phylogeny factors, and environmental stress. Several kinds of metabolites have been reviewed, including plant primary metabolites (PPMs), phytohormones, and plant secondary metabolites (PSMs). The microbes assembled by plant metabolites in return exert beneficial effects on plants, which have been widely applied in agriculture. What's more, we point out existing problems and future research directions, such as unclear mechanisms, few species, simple parts, and ignorance of absolute abundance. This review may inspire readers to study plant-metabolite-microbe interactions in the future.

Strategies to fortify the nutritional values of polished rice by implanting selective traits from brown rice: A nutrigenomics-based approach

Whole-grain cereals are important components of a healthy diet. It reduces the risk of many deadly diseases like cardiovascular diseases, diabetes, cancer, etc. Brown rice is an example of whole grain food, which is highly nutritious due to the presence of various bioactive compounds (flavonoids, phenolics, vitamins, phytosterols, oils, etc.) associated with the rice bran layer of brown rice. White rice is devoid of the nutritious rice bran layer and thus lacks the bioactive compounds which are the major attractants of brown rice. Therefore, to confer health benefits to the public at large, the nutrigenomic potential of white rice may be improved by integrating the phytochemicals associated with the rice bran layer of brown rice into it via biofortification processes like conventional breeding, agronomic practices, metabolic engineering, CRISPR/Cas9 technology, and RNAi techniques. Thus, this review article focuses on improving the nutritional qualities of white/polished rice through biofortification processes, utilizing new breeding technologies (NBTs).

An emerging role of heterotrimeric G-proteins in nodulation and nitrogen sensing

MAIN CONCLUSION

A comprehensive understanding of nitrogen signaling cascades involving heterotrimeric G-proteins and their putative receptors can assist in the production of nitrogen-efficient plants. Plants are immobile in nature, so they must endure abiotic stresses including nutrient stress. Plant development and agricultural productivity are frequently constrained by the restricted availability of nitrogen in the soil. Non-legume plants acquire nitrogen from the soil through root membrane-bound transporters. In depleted soil nitrogen conditions, legumes are naturally conditioned to fix atmospheric nitrogen with the aid of nodulation elicited by nitrogen-fixing bacteria. Moreover, apart from the symbiotic nitrogen fixation process, nitrogen uptake from the soil can also be a significant secondary source to satisfy the nitrogen requirements of legumes. Heterotrimeric G-proteins function as molecular switches to help plant cells relay diverse stimuli emanating from external stress conditions. They are comprised of Gα, Gβ and Gγ subunits, which cooperate with several downstream effectors to regulate multiple plant signaling events. In the present review, we concentrate on signaling mechanisms that regulate plant nitrogen nutrition. Our review highlights the potential of heterotrimeric G-proteins, together with their putative receptors, to assist the legume root nodule symbiosis (RNS) cascade, particularly during calcium spiking and nodulation. Additionally, the functions of heterotrimeric G-proteins in nitrogen acquisition by plant roots as well as in improving nitrogen use efficiency (NUE) have also been discussed. Future research oriented towards heterotrimeric G-proteins through genome editing tools can be a game changer in the enhancement of the nitrogen fixation process. This will foster the precise manipulation and production of plants to ensure global food security in an era of climate change by enhancing crop productivity and minimizing reliance on external inputs.

Metabolomic Reconfiguration in Primed Barley (Hordeum vulgare) Plants in Response to Pyrenophora teres f. teres Infection

Necrotrophic fungi affect a wide range of plants and cause significant crop losses. For the activation of multi-layered innate immune defences, plants can be primed or pre-conditioned to rapidly and more efficiently counteract this pathogen. Untargeted and targeted metabolomics analyses were applied to elucidate the biochemical processes involved in the response of 3,5-dichloroanthranilic acid (3,5-DCAA) primed barley plants to Pyrenophora teres f. teres (Ptt). A susceptible barley cultivar ('Hessekwa') at the third leaf growth stage was treated with 3,5-DCAA 24 h prior to infection using a Ptt conidia suspension. The infection was monitored over 2, 4, and 6 days post-inoculation. For untargeted studies, ultra-high performance liquid chromatography coupled with high-resolution mass spectrometry (UHPLC-MS) was used to analyse methanolic plant extracts. Acquired data were processed to generate the data matrices utilised in chemometric modelling and multi-dimensional data mining. For targeted studies, selected metabolites from the amino acids, phenolic acids, and alkaloids classes were quantified using multiple reaction monitoring (MRM) mass spectrometry. 3,5-DCAA was effective as a priming agent in delaying the onset and intensity of symptoms but could not prevent the progression of the disease. Unsupervised learning methods revealed clear differences between the sample extracts from the control plants and the infected plants. Both orthogonal projection to latent structure-discriminant analysis (OPLS-DA) and 'shared and unique structures' (SUS) plots allowed for the extraction of potential markers of the primed and naïve plant responses to Ptt. These include classes of organic acids, fatty acids, amino acids, phenolic acids, and derivatives and flavonoids. Among these, 5-oxo-proline and citric acid were notable as priming response-related metabolites. Metabolites from the tricarboxylic acid pathway were only discriminant in the primed plant infected with Ptt. Furthermore, the quantification of targeted metabolites revealed that hydroxycinnamic acids were significantly more prominent in the primed infected plants, especially at 2 d.p.i. Our research advances efforts to better understand regulated and reprogrammed metabolic responses that constitute defence priming in barley against Ptt.

Flavonoid synthesis in Lamiophlomis rotata from Qinghai-Tibet Plateau is influenced by soil properties, microbial community, and gene expression

Lamiophlomis rotata is a medicinal plant in Qinghai-Tibet Plateau, in which flavonoid compounds are the major medicinal components. However, it remains unclear how flavonoid metabolism of L. rotata is influenced by soil properties and microbial community. In this study, we collected L. rotata seedlings and rhizosphere soils from five habitats ranging from 3750 to 4270 m of altitude and analyzed the effects of habitat conditions on flavonoid metabolism. The activities of peroxidase, cellulase, and urease were increased with altitude, while those of alkaline phosphatase, alkaline protease, and sucrase were decreased with altitude. Analysis of OTUs showed that the total number of bacterial genera was higher than that of fungal genera. The highest number of fungal genera was 132, and that of bacterial genera was 33 in Batang (BT) town in Yushu County at an altitude of 3880 m, suggesting that the fungal communities may play a critical role in L. rotata rhizosphere soils. Flavonoids in leaves and roots of L. rotata shared a similar pattern, with a trend of increasing levels with altitude. The highest flavonoid content measured, 12.94 mg/g in leaves and 11.43 mg/g in roots, was from Zaduo (ZD) County at an altitude of 4208 m. Soil peroxidases affected quercetin content in leaves of L. rotata, while the fungus Sebacina affected flavonoid content in leaves and roots of L. rotata. The expression of PAL, F3'H, FLS, and FNS genes showed a declining trend in leaves with altitude, while F3H showed an increasing trend in both leaves and roots. Overall, soil physicochemical properties and microbial community affect flavonoid metabolism in L. rotata in Qinghai-Tibet Plateau. The variations in flavonoid content and gene expression as well as their associations with soil factors revealed the complexity of the growth conditions and genetic makeup in L. rotata habitats of Qinghai-Tibet Plateau.

Optimizing Crop Production with Bacterial Inputs: Insights into Chemical Dialogue between Sphingomonas sediminicola and Pisum sativum

The use of biological inputs is an interesting approach to optimize crop production and reduce the use of chemical inputs. Understanding the chemical communication between bacteria and plants is critical to optimizing this approach. Recently, we have shown that Sphingomonas (S.) sediminicola can improve both nitrogen supply and yield in pea. Here, we used biochemical methods and untargeted metabolomics to investigate the chemical dialog between S. sediminicola and pea. We also evaluated the metabolic capacities of S. sediminicola by metabolic profiling. Our results showed that peas release a wide range of hexoses, organic acids, and amino acids during their development, which can generally recruit and select fast-growing organisms. In the presence of S. sediminicola, a more specific pattern of these molecules took place, gradually adapting to the metabolic capabilities of the bacterium, especially for pentoses and flavonoids. In turn, S. sediminicola is able to produce several compounds involved in cell differentiation, biofilm formation, and quorum sensing to shape its environment, as well as several molecules that stimulate pea growth and plant defense mechanisms.

Elnosary M, L. Ashour M, M. Abd El-Moneam N, A. Shreadah M. Flavonoids Biosynthesis in Plants as a Defense Mechanism: Role and Function Concerning Pharmacodynamics and Pharmacokinetic Properties

Flavonoids are a major class of secondary metabolites that comprises more than 6000 compounds that have been identified. They are biosynthesized via the phenylpropanoid metabolic pathway that involves groups of enzymes such as isomerases, hydroxylases, and reductases that greatly affect the determination of the flavonoid skeleton. For example, transferase enzymes responsible for the modification of sugar result in changes in the physiological activity of the flavonoids and changes in their physical properties, such as solubility, reactivity, and interaction with cellular target molecules, which affect their pharmacodynamics and pharmacokinetic properties. In addition, flavonoids have diverse biological activities such as antioxidants, anticancer, and antiviral in managing Alzheimer’s disease. However, most marine flavonoids are still incompletely discovered because marine flavonoid biosynthesis is produced and possesses unique substitutions that are not commonly found in terrestrial bioactive compounds. The current chapter will illustrate the importance of flavonoids’ role in metabolism and the main difference between marine and terrestrial flavonoids.

Advances in the study of the function and mechanism of the action of flavonoids in plants under environmental stresses

MAIN CONCLUSION

This review summarizes the anti-stress effects of flavonoids in plants and highlights its role in the regulation of polar auxin transport and free radical scavenging mechanism. As secondary metabolites widely present in plants, flavonoids play a vital function in plant growth, but also in resistance to stresses. This review introduces the classification, structure and synthetic pathways of flavonoids. The effects of flavonoids in plant stress resistance were enumerated, and the mechanism of flavonoids in plant stress resistance was discussed in detail. It is clarified that plants under stress accumulate flavonoids by regulating the expression of flavonoid synthase genes. It was also determined that the synthesized flavonoids are transported in plants through three pathways: membrane transport proteins, vesicles, and bound to glutathione S-transferase (GST). At the same time, the paper explores that flavonoids regulate polar auxin transport (PAT) by acting on the auxin export carrier PIN-FORMED (PIN) in the form of ATP-binding cassette subfamily B/P-glycoprotein (ABCB/PGP) transporter, which can help plants to respond in a more dominant form to stress. We have demonstrated that the number and location of hydroxyl groups in the structure of flavonoids can determine their free radical scavenging ability and also elucidated the mechanism by which flavonoids exert free radical removal in cells. We also identified flavonoids as signaling molecules to promote rhizobial nodulation and colonization of arbuscular mycorrhizal fungi (AMF) to enhance plant-microbial symbiosis in defense to stresses. Given all this knowledge, we can foresee that the in-depth study of flavonoids will be an essential way to reveal plant tolerance and enhance plant stress resistance.

The Classification, Molecular Structure and Biological Biosynthesis of Flavonoids, and Their Roles in Biotic and Abiotic Stresses

With the climate constantly changing, plants suffer more frequently from various abiotic and biotic stresses. However, they have evolved biosynthetic machinery to survive in stressful environmental conditions. Flavonoids are involved in a variety of biological activities in plants, which can protect plants from different biotic (plant-parasitic nematodes, fungi and bacteria) and abiotic stresses (salt stress, drought stress, UV, higher and lower temperatures). Flavonoids contain several subgroups, including anthocyanidins, flavonols, flavones, flavanols, flavanones, chalcones, dihydrochalcones and dihydroflavonols, which are widely distributed in various plants. As the pathway of flavonoid biosynthesis has been well studied, many researchers have applied transgenic technologies in order to explore the molecular mechanism of genes associated with flavonoid biosynthesis; as such, many transgenic plants have shown a higher stress tolerance through the regulation of flavonoid content. In the present review, the classification, molecular structure and biological biosynthesis of flavonoids were summarized, and the roles of flavonoids under various forms of biotic and abiotic stress in plants were also included. In addition, the effect of applying genes associated with flavonoid biosynthesis on the enhancement of plant tolerance under various biotic and abiotic stresses was also discussed.

Integrated Transcriptomic and Metabolomic Analyses Reveal the Molecular and Metabolic Basis of Flavonoids in Areca catechu L

Areca catechu L., of the Arecaceae family, is widely distributed in tropical Asia. In A. catechu, the extracts and compounds, including flavonoids, have various pharmacological activities. Although there are many studies of flavonoids, the molecular mechanism of their biosynthesis and regulation remains unclear in A. catechu. In this study, 331 metabolites were identified from the root, stem, and leaf of A. catechu using untargeted metabolomics, including 107 flavonoids, 71 lipids, 44 amino acids and derivatives, and 33 alkaloids. The transcriptome analysis identified 6119 differentially expressed genes, and some were enriched in the flavonoid pathway. To analyze the biosynthetic mechanism of the metabolic differences in A. catechu tissues, 36 genes were identified through combined transcriptomic and metabolomic analysis, in which glycosyltransferase genes Acat_15g017010 and Acat_16g013670 were annotated as being involved in the glycosylation of kaempferol and chrysin by their expression and in vitro activities. Flavonoid biosynthesis could be regulated by the transcription factors, AcMYB5 and AcMYB194. This study laid a foundation for further research on the flavonoid biosynthetic pathway of A. catechu.

Analysis of the molecular and biochemical mechanisms involved in the symbiotic relationship between Arbuscular mycorrhiza fungi and Manihot esculenta Crantz

INTRODUCTION

Plants and arbuscular mycorrhizal fungi (AMF) mutualistic interactions are essential for sustainable agriculture production. Although it is shown that AMF inoculation improves cassava physiological performances and yield traits, the molecular mechanisms involved in AM symbiosis remain largely unknown. Herein, we integrated metabolomics and transcriptomics analyses of symbiotic (Ri) and asymbiotic (CK) cassava roots and explored AM-induced biochemical and transcriptional changes.

RESULTS

Three weeks (3w) after AMF inoculations, proliferating fungal hyphae were observable, and plant height and root length were significantly increased. In total, we identified 1,016 metabolites, of which 25 were differentially accumulated (DAMs) at 3w. The most highly induced metabolites were 5-aminolevulinic acid, L-glutamic acid, and lysoPC 18:2. Transcriptome analysis identified 693 and 6,481 differentially expressed genes (DEGs) in the comparison between CK (3w) against Ri at 3w and 6w, respectively. Functional enrichment analyses of DAMs and DEGs unveiled transport, amino acids and sugar metabolisms, biosynthesis of secondary metabolites, plant hormone signal transduction, phenylpropanoid biosynthesis, and plant-pathogen interactions as the most differentially regulated pathways. Potential candidate genes, including nitrogen and phosphate transporters, transcription factors, phytohormone, sugar metabolism-related, and SYM (symbiosis) signaling pathway-related, were identified for future functional studies.

DISCUSSION

Our results provide molecular insights into AM symbiosis and valuable resources for improving cassava production.

Legumes Regulate Symbiosis with Rhizobia via Their Innate Immune System

Plant roots are constantly exposed to a diverse microbiota of pathogens and mutualistic partners. The host's immune system is an essential component for its survival, enabling it to monitor nearby microbes for potential threats and respond with a defence response when required. Current research suggests that the plant immune system has also been employed in the legume-rhizobia symbiosis as a means of monitoring different rhizobia strains and that successful rhizobia have evolved to overcome this system to infect the roots and initiate nodulation. With clear implications for host-specificity, the immune system has the potential to be an important target for engineering versatile crops for effective nodulation in the field. However, current knowledge of the interacting components governing this pathway is limited, and further research is required to build on what is currently known to improve our understanding. This review provides a general overview of the plant immune system's role in nodulation. With a focus on the cycles of microbe-associated molecular pattern-triggered immunity (MTI) and effector-triggered immunity (ETI), we highlight key molecular players and recent findings while addressing the current knowledge gaps in this area.

Fe-Based Nanomaterial-Induced Root Nodulation Is Modulated by Flavonoids to Improve Soybean (Glycine max) Growth and Quality

Innovative technology to increase efficient nitrogen (N) use while avoiding environmental damages is needed because of the increasing food demand of the rapidly growing global population. Soybean (Glycine max) has evolved a complex symbiosis with N-fixing bacteria that forms nodules to fix N. Herein, foliar application of 10 mg L^-1 Fe₇(PO₄)₆ and Fe₃O₄ nanomaterials (NMs) (Fe-based NMs) promoted soybean growth and root nodulation, thus improving the yield and quality over that of the unexposed control, EDTA-control, and 1 and 5 mg L^-1 NMs. Mechanistically, flavonoids, key signaling molecules at the initial signaling steps in nodulation, were increased by more than 20% upon exposure to 10 mg L^-1 Fe-based NMs, due to enhanced key enzyme (phenylalanine ammonia-lyase, PAL) activity and up-regulation of flavonoid biosynthetic genes (GmPAL, GmC4H, Gm4CL, and GmCHS). Accumulated flavonoids were secreted to the rhizosphere, recruiting rhizobia for colonization. Fe₇(PO₄)₆ NMs increased Allorhizobium by 87.3%, and Fe₃O₄ NMs increased Allorhizobium and Mesorhizobium by 142.2% and 34.9%, leading to increased root nodules by 50.0% and 35.4% over the unexposed control, respectively. Leghemoglobin content was also noticeably improved by 8.2-46.5% upon Fe-based NMs. The higher levels of nodule number and leghemoglobin content resulted in enhanced N content by 15.5-181.2% during the whole growth period. Finally, the yield (pod number and grain biomass) and quality (flavonoids, soluble protein, and elemental nutrients) were significantly increased more than 14% by Fe-based NMs. Our study provides an effective nanoenabled strategy for inducing root nodules to increase N use efficiency, and then both yield and quality of soybean.

Understanding plant-microbe interaction of rice and soybean with two contrasting diazotrophic bacteria through comparative transcriptome analysis

Understanding the beneficial plant-microbe interactions is becoming extremely critical for deploying microbes imparting plant fitness and achieving sustainability in agriculture. Diazotrophic bacteria have the unique ability to survive without external sources of nitrogen and simultaneously promote host plant growth, but the mechanisms of endophytic interaction in cereals and legumes have not been studied extensively. We have studied the early interaction of two diazotrophic bacteria, Gluconacetobacter diazotrophicus (GAB) and Bradyrhizobium japonicum (BRH), in 15-day-old seedlings of rice and soybean up to 120 h after inoculation (hai) under low-nitrogen medium. Root colonization of GAB in rice was higher than that of BRH, and BRH colonization was higher in soybean roots as observed from the scanning electron microscopy at 120 hai. Peroxidase enzyme was significantly higher at 24 hai but thereafter was reduced sharply in soybean and gradually in rice. The roots of rice and soybean inoculated with GAB and BRH harvested from five time points were pooled, and transcriptome analysis was executed along with control. Two pathways, "Plant pathogen interaction" and "MAPK signaling," were specific to Rice-Gluconacetobacter (RG), whereas the pathways related to nitrogen metabolism and plant hormone signaling were specific to Rice-Bradyrhizobium (RB) in rice. Comparative transcriptome analysis of the root tissues revealed that several plant-diazotroph-specific differentially expressed genes (DEGs) and metabolic pathways of plant-diazotroph-specific transcripts, viz., chitinase, brassinosteroid, auxin, Myeloblastosis (MYB), nodulin, and nitrate transporter (NRT), were common in all plant-diazotroph combinations; three transcripts, viz., nitrate transport accessory protein (NAR), thaumatin, and thionin, were exclusive in rice and another three transcripts, viz., NAC (NAM: no apical meristem, ATAF: Arabidopsis thaliana activating factor, and CUC: cup-shaped cotyledon), ABA (abscisic acid), and ammonium transporter, were exclusive in soybean. Differential expression of these transcripts and reduction in pathogenesis-related (PR) protein expression show the early interaction. Based on the interaction, it can be inferred that the compatibility of rice and soybean is more with GAB and BRH, respectively. We propose that rice is unable to identify the diazotroph as a beneficial microorganism or a pathogen from an early response. So, it expressed the hypersensitivity-related transcripts along with PR proteins. The molecular mechanism of diazotrophic associations of GAB and BRH with rice vis-à-vis soybean will shed light on the basic understanding of host responses to beneficial microorganisms.

Discerning Transcriptomic and Biochemical Responses of Arabidopsis thaliana Treated with the Biofertilizer Strain Priestia megaterium YC4-R4: Boosting Plant Central and Secondary Metabolism

As a response to the current challenges in agriculture, the application of alternatives to a more sustainable management is required. Thus, biofertilizers begin to emerge as a reliable alternative to improve crop development and resistance to stresses. Among other effects on the plant, the use of beneficial strains may cause changes in their metabolic regulation, as in cell wall biogenesis and in nutrient/ion transportation, improving their growth process. Previous works showed that inoculation with the strain Priestia megaterium YC4-R4 effectively promoted vegetative growth of Arabidopsis thaliana Col-0 plants. Hence, the present work recorded a strain-mediated induction of several pathways of the central and secondary metabolism of the plant, as the induction of lipid, cellulose, phenol, and flavonoid biosynthesis, by using transcriptomic and biochemical analyses.