Multifaceted roles of flavonoids mediating plant-microbe interactions

Biofortification of flavonoids in nuts along the agro-food chain for improved nutritional and health benefits, a comprehensive review and future prespectives

Flavonoids are found ubiquitous in dietary sources with potential antioxidant properties, and have received widespread attention for their health benefits. Nuts, rich in flavonoids, are popular among consumers for their crunchy flavor and nutritious content. The review summarizes studies pertaining to the diverse types and distribution of flavonoids in nuts, their potential health benefits, as well as management strategies for flavonoids accumulation and enhancement across the whole agro-food chain, including the selection of nut varieties, the suitable growing conditions, the optimal harvesting period of nuts, and appropriate post-harvest measures, such as chemical conditioning, ideal storage conditions, and post-harvest processing methods. Furthermore, associated metabolic pathways, and applied metabolic engineering to improve flavonoids´ levels in nuts are described. This review examines the application of flavonoids biofortification in nuts across the agro-food chain, exploring its potential for sustainable development in the nut flavonoids industry, and emphasizing its importance for people's diet and health.

Harnessing microbes as sun cream against high light stress

Plants rely on solar energy for growth through photosynthesis, yet excessive light intensity can induce physiological damage. Despite the considerable harm, inadequate attention has been directed toward understanding how plant-associated microorganisms mitigate this stress, and the impact of high light intensity on plant microbial communities remains underexplored. Through this Viewpoint, we aim to highlight the potential of microbial communities to enhance plant resilience and understand how light stress can shape plant microbiome. A full understanding of these dynamics is essential to design strategies that take advantage of microbial assistance to plants under light stress and to effectively manage the impact of changing light conditions on plant-microbe interactions.

Plant Coumarin Metabolism-Microbe Interactions: An Effective Strategy for Reducing Imidacloprid Residues and Enhancing the Nutritional Quality of Pepper

Imidacloprid (IMI) stress positively correlates with the potential of coumarins to alleviate abiotic stress. However, little is known about the pathways and mechanisms by which coumarin reduces the IMI residue by regulating plant secondary metabolism and plant-microbe interactions. This study examined the impact of coumarin on the uptake, translocation, and metabolism of IMI in pepper plants by modulating the signal molecule levels and microbial communities in the rhizosphere and phyllosphere. Analysis of 2 h─28 d pesticide residue dynamics revealed that coumarin dramatically reduced IMI concentration in pepper fruits. Coumarin upregulated the phenylpropane pathway genes, which increased the levels of flavonoids, phenolic acids, phytohormones, and capsaicinoids. Importantly, phyllosphere and rhizosphere microbial diversity results showed that coumarin improved the abundance of beneficial microorganisms and positively correlated with secondary metabolite secretion. Therefore, coumarin exploited the interaction between the phenylpropane and coumarin synthesis pathways and beneficial microbes to enhance the nutritional quality and IMI degradation.

Integrated Transcriptome and Metabolome Analysis Reveals Insights into Flavone and Flavonol Biosynthesis in Salicylic Acid-Induced Citrus Huanglongbing Tolerance

Salicylic acid (SA) exhibits positive effects against Citrus Huanglongbing (HLB), but how SA affects citrus resistance to HLB is currently unknown. This study conducted integrated transcriptome and metabolome analyses on SA-treated Citrus sinensis (HLB-sensitive) and Poncirus trifoliata (HLB-tolerant). The results indicated that the syntheses of flavones and flavonols were induced by SA, while the expression levels of associated genes and the contents of corresponding metabolites varied significantly between the two species after SA treatment or HLB infection. These differences may underpin the enhanced HLB management through SA treatment and the inherent HLB tolerance of P. trifoliata. Furthermore, two insertions of miniature inverted-repeat transposable element (MITE) were identified within the promoter of PtrF3'H in P. trifoliata, whereas none were found in the promoter of CsF3'H in C. sinensis. These MITE insertions notably enhanced the promoter activity of PtrF3'H in an SA-dependent manner. Our findings deepen the understanding of the correlation between SA response and HLB tolerance in Citrus.

Beneficial microorganisms: Regulating growth and defense for plant welfare

Beneficial microorganisms (BMs) promote plant growth and enhance stress resistance. This review summarizes how BMs induce growth promotion by improving nutrient uptake, producing growth-promoting hormones and stimulating root development. How BMs enhance disease resistance and help protect plants from abiotic stresses has also been explored. Growth-defense trade-offs are known to affect the ability of plants to survive under unfavourable conditions. This review discusses studies demonstrating that BMs regulate growth-defense trade-offs through microbe-associated molecular patterns and multiple pathways, including the leucine-rich repeat receptor-like kinase pathway, abscisic acid signalling pathway and specific transcriptional factor regulation. This multifaceted relationship underscores the significance of BMs in sustainable agriculture. Finally, the need for integration of artificial intelligence to revolutionize biofertilizer research has been highlighted. This review also elucidates the cutting-edge advancements and potential of plant-microbe synergistic microbial agents.

Priming grapevines with oregano essential oil vapour results in a metabolomic shift eliciting resistance against downy mildew

BACKGROUND

Priming plants with natural products is extensively studied in the agricultural field to reduce the use of synthetic and copper-based pesticides. Previous studies have shown that Oregano essential oil vapour (OEOV) is an effective priming agent against downy mildew (DM) in grapevine (Vitis vinifera L. cv. Chasselas), activating different transcriptomic regulated defence mechanisms.

RESULTS

In the present study, we complement transcriptomic data with metabolomic insights, confirming some previous regulating patterns and highlighting new mechanisms underlying OEOV-induced resistance. A significant modulation of the phenylpropanoid pathway was noted. The data also confirmed the induction of an oxidative stress response indicated by an up-regulation of reactive oxygen species (ROS)-related genes and a congruent depletion of putative L-glutathione. Interestingly, OEOV promoted the accumulation of organic metabolites such as terpenes and other potential phytoalexins, which could potentially contribute to grapevine innate immune response to Plasmopara viticola.

CONCLUSION

Overall, this study uncovered a diverse influence of OEOV on V. vinifera defence mechanisms against DM, enhancing our comprehension of the mode of action of essential oils. This insight offers various prospects for crafting innovative biocontrol products, fostering a more dynamic and sustainable approach to agriculture.

Root exudate-mediated assemblage of rhizo-microbiome enhances Fusarium wilt suppression in chrysanthemum

Intercropping is emerging as a sustainable strategy to manage soil-borne diseases, yet the underlying mechanisms remain largely elusive. Here, we investigated how intercropping chrysanthemum (Chrysanthemum morifolium) with ginger (Zingiber officinale) suppressed Fusarium wilt and influenced the associated rhizo-microbiome. Chrysanthemum plants in intercropping systems exhibited a marked reduction in wilt severity and greater biomass compared to those grown in monoculture. In contrast, soil sterilization intensified wilt severity and abrogated the benefits of intercropping, highlighting the critical role of soil microbiota. 16S rRNA gene amplicon analysis revealed that intercropping significantly changed the composition and structure of rhizo-bacterial communities, particularly enriching Burkholderia species, which were closely associated with plant growth and disease resistance. Further investigation demonstrated that ginger root exudates, including sinapyl alcohol and 6-gingerol, greatly promoted the proliferation and colonization of Burkholderia sp. in chrysanthemum rhizosphere, conferring the enhanced disease suppression. Metabolomic profiling revealed that ginger root exudates stimulated the release of specific metabolites by chrysanthemum roots, which promoted the growth and biofilm formation of Burkholderia sp. Our findings uncovered the mechanism by which intercropping chrysanthemum with ginger plants modulated the rhizo-microbiome and thereby resulted in the enhanced disease suppression, offering insights into optimizing plant-microbe interactions for improving crop health and productivity.

Integrated Transcriptomic and Metabolomic Analysis Revealed Regulatory Mechanisms on Flavonoids Biosynthesis in the Skin of Passion Fruit (Passiflora spp.)

Passion fruit is one of the most famous fruit crops in tropical and subtropical regions due to its high edible, medicinal, and ornamental value. Flavonoids, a class of plant secondary metabolites, have important health-related roles. In this study, a total of 151 flavonoid metabolites were identified, of which 25 key metabolites may be the main contributors to the purple phenotype. Using RNA sequencing, 11,180 differentially expressed genes (DEGs) were identified. Among these, 48 flavonoid biosynthesis genes (PAL, 4CL, C4H, CHS, CHI, F3H, DFR, ANS, and UFGT) and 123 transcription factors were identified. Furthermore, 12 distinct modules were identified through weighted gene coexpression network analysis, of which the brown module displays a robust positive correlation with numerous flavonoid metabolites. Overexpression of PeMYB114 significantly promoted flavonoids accumulation in tobacco leaves. Our study provided a key candidate gene for molecular breeding to improve color traits in passion fruit.

Ralstonia solanacearum infection induces tobacco root to secrete chemoattractants to recruit antagonistic bacteria and defensive compounds to inhibit pathogen

BACKGROUND

Plant root exudates play crucial roles in maintaining the structure and function of the whole belowground ecosystem and regulating the interactions between roots and soil microorganisms. Ralstonia solanacearum causes bacterial wilt disease in many plants, while root exudate-mediated inhibition of pathogen infection is poorly understood. Here, we characterize the chemical divergence between root exudates of healthy and diseased tobacco plants and the effects of that variability on the rhizosphere microbial community and the occurrence of bacterial wilt.

RESULTS

Compared with the healthy plants, root exudates in diseased plants showed distinct exudation patterns and metabolite profiles including increased amounts of flavonoids, phenylpropanoids, terpenoids and defense-related hormones, as well as distinct bacterial community composition, as illustrated by an increased abundance of Ralstonia and decreased abundances of Bacillus and Streptomyces in diseased plants rhizosphere. Pathogen infection stimulated roots to secrete more defensive compounds to inhibit pathogen growth. Change of root exudates modulated rhizosphere microbial community. Specific root exudates could benefit plants by attracting antagonistic Bacillus amyloliquefaciens and inhibiting pathogens. Bacillus amyloliquefaciens could utilize specific root exudates as carbon sources. Benzyl cinnamatel promoted the biofilm formation and colonization of B. amyloliquefaciens on roots.

CONCLUSION

To defend against pathogen invasion, tobacco plants recruited antagonistic and plant growth-promoting rhizobacteria to the rhizosphere by modifying root exudate profiles. Specific signal molecules are recommended to recruit beneficial microorganisms for controlling bacterial wilt. The results provide insights concerning the metabolic divergence of root exudates integral to understanding root-microorganism interaction. © 2024 Society of Chemical Industry.

Harnessing biosynthesized selenium nanoparticles for recruitment of beneficial soil microbes to plant roots

Root exudates can benefit plant growth and health by reshaping the rhizosphere microbiome. Whether nanoparticles biosynthesized by rhizosphere microbes play a similar role in plant microbiome manipulation remains enigmatic. Herein, we collect elemental selenium nanoparticles (SeNPs) from selenobacteria associated with maize roots. In vitro and soil assays show that the SeNPs enhanced plant performance by recruiting plant growth-promoting bacteria (e.g., Bacillus) in a dose-dependent manner. Multiomic profilings unravel a cross-kingdom-signaling cascade that mediates efficient biosynthesis of SeNPs by selenobacteria. Specifically, maize roots perceive histamine signaling from Bacillus spp., which stimulates the plant to produce p-coumarate via root exudation. The rpoS gene in selenobacteria (e.g., Pseudomonas sp. ZY71) responds to p-coumarate signaling and positively regulates the biosynthesis of SeNPs. This study demonstrates a novel mechanism for recruiting host-beneficial soil microbes by microbially synthesized nanoparticles and unlocks promising possibilities for plant microbiome manipulation.

Mitigating risks from atrazine drift to soybeans through foliar pre-spraying with a degrading bacterium

Herbicides play a crucial role in managing weeds in agriculture, ensuring the productivity and quality of crops. However, herbicide drift poses a significant threat to sensitive plants, necessitating the consideration of ecosystem-based solutions to address this issue. In this study, foliar pre-spraying of atrazine-degrading Paenarthrobacter sp. AT5 was proposed as a new approach to mitigate the risks associated with atrazine drift on soybeans. Exposure to atrazine reduced chlorophyll levels and disturbed the antioxidant system and metabolic processes in soybean leaves, ultimately causing leaves to turn yellow. However, by pre-spraying, strain AT5 successfully colonized the surface of soybean leaves and mitigated the harmful effects of atrazine. This was achieved by slowing down atrazine absorption, expediting its reduction (half-life decreased from 2.22 d to 0.86 d), altering its degradation pathway (enhancing hydroxylation while weakening alkylation), and enhancing the interaction within phyllosphere bacteria communities. This study introduces a new approach that is both eco-friendly and user-friendly for reducing the risks of herbicide drift to sensitive crops, hence promoting the development of mixed cropping.

Regulation of drought stress on nutrient cycle and metabolism of rhizosphere microorganisms in desert riparian forest

Microbial communities in desert riparian forest ecosystems have developed unique adaptive strategies to thrive in harsh habitats shaped by prolonged exposure to abiotic stressors. However, the influence of drought stress on the functional and metabolic characteristics of soil rhizosphere microorganisms remains unknown. Therefore, this study aimed to investigate the effects of drought stress on soil biogeochemistry and metabolism and analyze the relationship between the biogeochemical cycle processes and network of differentially-expressed metabolites. Using metagenomics and metabolomics, this study explored the microbial functional cycle and differential metabolic pathways within desert riparian forests. The predominant biogeochemical cycles in the study area were the Carbon and Nitrogen cycles, comprising 78.90 % of C, N, Phosphorus, Sulfur and Iron cycles. Drought led to increased soil C fixation, reduced C degradation and methane metabolism, weakened denitrification, and decreased N fixation. Furthermore, drought can disrupt iron homeostasis and reduce its absorption. The differential metabolic pathways of drought stress include flavonoid biosynthesis, arachidonic acid metabolism, steroid hormone biosynthesis, and starch and sucrose degradation. Network analysis of functional genes and metabolism revealed a pronounced competitive relationship between the C cycle and metabolic network, whereas the Fe cycle and metabolic network promoted each other, optimizing resource utilization. Partial least squares analysis revealed that drought hindered the expression and metabolic processes and functional genes, whereas the rhizosphere environment facilitated metabolic expression and the functional genes. The rhizosphere effect primarily promoted metabolic processes indirectly through soil enzyme activities. The integrated multi-omics analysis further revealed that the effects of drought and the rhizosphere play a predominant role in shaping soil functional potential and the accumulation of metabolites. These insights deepen our comprehension of desert riparian forest ecosystems and offer strong support for the functionality of nutrient cycling and metabolite dynamics.

Rhizospheric soil chemical properties and microbial response to a gradient of Chromolaena odorata(L) invasion in the Mount Cameroon Region

Chromolaena odorata is a noxious alien invasive weed species with an enormous impact on the terrestrial ecosystem. The allelopathic potentials of this weed have had little attention, leading to changes in soil properties and microbial communities. This study investigates the impacts of Chromolaena odorata invasion gradients on rhizospheric soil chemical properties and microbial response in the Mount Cameroon Region. Forty-eight soil samples at four different degrees of invasion (uninvaded, low degree invasion, moderate degree invasion and high degree invasion) based on species coverage within subplots in four study areas were collected and rhizospheric soil chemical properties, microbial load, phosphatases activities and secondary metabolites were evaluated. At medium-degree invasion, rhizospheric soil concentrations of P, K and Fe increased with arbuscular mycorrhizal fungi (AMF) colonization and phosphatases enzyme activities. Soil C, N and organic matter were significantly increased at high-degree invasion, supporting the use of the plant as a fallow crop. Acid phosphatase activity ranged from 0.69 to 0.90 mmol h-1 kg-1 and was significantly different at different degrees of invasion. AMF colonization ranged from 23.33 to 50.00%, with a strong positive correlation between AMF colonization and phosphatase activity. Soil bacterial load was high (46 × 105 CFU/g- 67 × 105 CFU/g), with mostly Staphylococcus having health concerns about its spread. The invasion situation had no significant effect on soil bacterial load, but high-degree invasion significantly increased fungal load. Low-degree invaded soils had high saponin (24.55±0.00 mg/g), flavonoid (47.7 mg/g) and tannin (28.68 mg/g) concentrations. The investigation reveals that Chromolaena odorata invasion altered rhizospheric soil properties and microbial communities significantly, thereby influencing ecosystem dynamics and soil nutrient availability. However, further studies elucidating kinds of secondary metabolites, identifying microbial communities, and monitoring soil changes influenced by C. odorata are essential for effective ecosystem management.

Unveiling Metabolic Crosstalk: Bacillus-Mediated Defense Priming in Pine Needles Against Pathogen Infection

Background/Objectives: Plant growth-promoting rhizobacteria (PGPR), particularly Bacillus spp., are pivotal in enhancing plant defense mechanisms against pathogens. This study aims to investigate the metabolic reprogramming of pine needles induced by Bacillus csuftcsp75 in response to the pathogen Diplodia pinea P9, evaluating its potential as a sustainable biocontrol agent. Methods: Using liquid chromatography-mass spectrometry (LC-MS/MS), we performed a principal component analysis and a cluster analysis to assess the metabolic alterations in treated versus control groups. This study focused on specific metabolites associated with plant defense. Results: Our findings indicate that treatment with Bacillus csuftcsp75 significantly modifies the metabolic profiles of pine needles, leading to notable increases in metabolites associated with flavonoid biosynthesis, particularly phenylpropanoid metabolism, as well as amino acid metabolism pathways. These metabolic changes indicate enhanced systemic acquired resistance (SAR) and induced systemic resistance (ISR), with treated plants exhibiting elevated levels of defense-related compounds such as 5-hydroxytryptophol and oleanolic acid. Conclusions: This study reveals that Bacillus csuftcsp75 enhances defense against pathogen P9 by modulating pine needle metabolism and activating key immune pathways, inducing systemic acquired resistance and induced systemic resistance, offering a natural alternative to chemical pesticides in sustainable agriculture.

Development of an HPPD-Inhibitor Resistant Wheat and Multiomics Integrative Analysis of Herbicide Toxicity and OsHIS1 Detoxification in Wheat

Weed infestation in agricultural fields significantly diminishes crop yields. Herbicides are widely used as a primary method of weed control. Developing herbicide-resistant crops through the expression of resistant genes represents a sustainable approach. This study generated wheat germplasms highly resistant to 4-hydroxyphenylpyruvate dioxygenase (HPPD)-inhibiting herbicides by transforming the rice HPPD INHIBITOR SENSITIVE 1 (OsHIS1) gene into Xinong 511, conferring resistance to mesotrione at levels up to nine times the typical field application rate (1350 g ai ha-1). Agronomic trait evaluations under greenhouse and field conditions showed no additional effects on wheat. Herbicide susceptibility assays confirmed the specific resistance to different HPPD inhibitors. Transcriptome and metabolome analyses revealed regulation of flavonoid and photosynthesis-antenna protein pathways in the herbicide functional. Collectively, OsHIS1 could be applied in the production of herbicide-resistant wheat.

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.

Arsenic-induced enhancement of diazotrophic recruitment and nitrogen fixation in Pteris vittata rhizosphere

Heavy metal contamination poses an escalating global challenge to soil ecosystems, with hyperaccumulators playing a crucial role in environmental remediation and resource recovery. The enrichment of diazotrophs and resulting nitrogen accumulation promoted hyperaccumulator growth and facilitated phytoremediation. Nonetheless, the regulatory mechanism of hyperaccumulator biological nitrogen fixation has remained elusive. Here, we report the mechanism by which arsenic regulates biological nitrogen fixation in the arsenic-hyperaccumulator Pteris vittata. Field investigations and greenhouse experiments, based on multi-omics approaches, reveal that elevated arsenic stress induces an enrichment of key diazotrophs, enhances plant nitrogen acquisition, and thus improves plant growth. Metabolomic analysis and microfluidic experiments further demonstrate that the upregulation of specific root metabolites plays a crucial role in recruiting key diazotrophic bacteria. These findings highlight the pivotal role of nitrogen-acquisition mechanisms in the arsenic hyperaccumulation of Pteris vittata, and provide valuable insights into the plant stress resistance.

Exploring the Nonlinear Relationship Between Dietary Flavonoid Intake and Periodontitis

INTRODUCTION AND AIMS

Flavonoids are non-nutrient bioactive substances widely found in plants, possessing antioxidant and anti-inflammatory properties. Periodontitis is a long-term inflammatory disease that impacts the tissues supporting the teeth, poses a substantial burden on public health and individuals alike. This study aims to explore the association between dietary flavonoid intake and periodontitis.

METHODS

This study included 3005 participants from the 2009 to 2010 National Health and Nutrition Examination Survey. We compared the weighted prevalence of periodontitis across different participant groups. Binary logistic regression analysis was conducted to evaluate the relationship between dietary flavonoid intake and periodontitis. The restricted cubic spline plot was used to explore nonlinear relationships.

RESULTS

The prevalence of periodontitis among participants with total flavonoid intake in quartiles Q1 to Q4 was 54.95%, 44.11%, 40.62%, and 48.28%, respectively. When compared to the Q1 group of total flavonoid intake, the OR values for Q2 to Q4 groups were 0.58 (95% CI: 0.39-0.86, P = .01), 0.50 (95% CI: 0.35-0.73, P = .001), and 0.68 (95% CI: 0.50-0.91, P = .01), respectively. A significant nonlinear association was observed between ln-transformed total flavonoid intake and the likelihood of developing periodontitis (nonlinearity P < .001). The inflection point was identified at an ln-transformed total flavonoid intake of 4.05, corresponding to a total flavonoid intake of 57.54 mg. Beyond this inflection point, as the total flavonoid intake value continues to rise, there was a diminishing protective effect against periodontitis.

CONCLUSIONS

Higher dietary flavonoid intake is associated with a reduced risk of periodontitis, with the greatest protective effect observed at moderate intake levels.

CLINICAL RELEVANCE

Understanding the association between flavonoid intake and periodontitis can guide dietary recommendations and interventions aimed at preventing periodontitis. This study supports the potential role of a flavonoid-rich diet in promoting periodontal health, suggesting that dietary modifications could be a viable strategy in periodontal disease prevention and management.

Rhizosphere bacterial community is mainly determined by soil environmental factors, but the active bacterial diversity is mainly shaped by plant selection

BACKGROUND

The assembly of the rhizosphere community, even the diazotroph community, is mainly shaped by soil environmental factors (including soil climate and physiochemical characteristics) and plant selection. To better understand the driving forces on the active overall and nitrogen-fixing bacterial community compositions, we characterized the communities of tobacco rhizosphere soil collected from three sampling sites with a large geographic scale (> 600 km).

RESULTS

The results indicate that the diversity and community composition of the overall bacterial and diazotroph communities are obviously differed according to the sampling sites. Still, no significant difference is found between the communities in rootzone and rhizosphere samples. Climate variables including mean annual precipitation (MAP) and mean annual temperature (MAT), soil physiochemical characteristics including available nitrogen (AN), available potassium (AK) and pH are main factors that affect the bacterial and diazotroph community structures in the three sampling sites. Furthermore, MAP and MAT, AN and available phosphorus (AP), total nitrogen (TN) and organic carbon (OC), AK and electrical conductivity (EC) showed similar effects, but pH showed independent effect on the composition of the overall bacteria and diazotroph communities. However, the alpha diversity indices of active overall and nitrogen-fixing bacteria in the rhizosphere are obviously higher than in the rootzone samples, and no significant differences are observed among different sampling sites. Proteobacteria is the predominant active phylum of all samples for overall and nitrogen-fixing bacteria. Escherichia-Shigella, Achromobacter, Streptomyces and Sphingomonas are the dominant active bacterial genera, and Bradyrhizobium, Skermanella and Extensimonas are dominant active nitrogen-fixing bacteria genera in rhizosphere. Furthermore, the high active abundance of Escherichia-Shigella but low abundance of Ralstonia in all three sampling sites indicate high root-knot nematode infection and low wilt disease endemic risk.

CONCLUSION

These results indicate that soil environmental factors contribute more to the tobacco rhizosphere bacterial community assemblage, but the rhizosphere contributes more to the diversity of active overall bacteria and nitrogen-fixing bacteria in the community. Our study provides novel knowledge for the assemble of rhizosphere bacterial and active bacteria communities across a large geographical scale.

C4 cereal and biofuel crop microbiomes

Microbiomes provide multiple life-support functions for plants, including nutrient acquisition and tolerance to abiotic and biotic stresses. Considering the importance of C4 cereal and biofuel crops for food security under climate change conditions, more attention has been given recently to C4 plant microbiome assembly and functions. Here, we review the current status of C4 cereal and biofuel crop microbiome research with a focus on beneficial microbial traits for crop growth and health. We highlight the importance of environmental factors and plant genetics in C4 crop microbiome assembly and pinpoint current knowledge gaps. Finally, we discuss the potential of foxtail millet as a C4 model species and outline future perspectives of C4 plant microbiome research.

Distinct metabolites affect the phloem fungal communities in ash trees (Fraxinus spp.) native and nonnative to the highly invasive emerald ash borer (AGRILUS PLANIPENNIS)

Emerald ash borer (EAB, Agrilus planipennis) is an invasive killer of ash trees (Fraxinus spp.) in North America and Europe. Ash species co-evolved with EAB in their native range in Asia are mostly resistant, although the precise mechanism(s) remain unclear. Very little is also known about EAB or ash tree microbiomes. We performed the first joint comparison of phloem mycobiome and metabolites between a native and a nonnative ash species, infested and uninfested with EAB, in conjunction with investigation of larval mycobiome. Phloem mycobiome communities differed between the tree species, but both were unaffected by EAB infestation. Several indicator taxa in the larval gut shared a similarly high relative abundance only with the native host trees. Widely targeted metabolomics revealed 24 distinct metabolites in native trees and 53 metabolites in nonnative trees, respectively, that differed in relative content between infested and uninfested trees only in one species. Interestingly, four metabolites shared a strong relationship with the phloem mycobiomes, majority of which affected only the native trees. Collectively, our results demonstrate a complex interplay between host tree chemistry and mycobiome, and suggest the shared relationships between the mycobiomes of the native host tree and EAB may reflect their shared co-evolution.

Biosynthesis and differential spatial distribution of the 3-deoxyanthocyanidins apigenidin and luteolinidin at the interface of a plant-cyanobacteria symbiosis exposed to cold

Aquatic ferns of the genus Azolla (Azolla) form highly productive symbioses with filamentous cyanobacteria fixing N2 in their leaf cavities, Nostoc azollae. Stressed symbioses characteristically turn red due to 3-deoxyanthocyanidin (DA) accumulation, rare in angiosperms and of unknown function. To understand DA accumulation upon cold acclimation and recovery, we integrated laser-desorption-ionization mass-spectrometry-imaging (LDI-MSI), a new Azolla filiculoides genome-assembly and annotation, and dual RNA-sequencing into phenotypic analyses of the symbioses. Azolla sp. Anzali recovered even when cold-induced DA-accumulation was inhibited by abscisic acid. Cyanobacterial filaments generally disappeared upon cold acclimation and Nostoc azollae transcript profiles were unlike those of resting stages formed in cold-resistant sporocarps, yet filaments re-appeared in leaf cavities of newly formed green fronds upon cold-recovery. The high transcript accumulation upon cold acclimation of AfDFR1 encoding a flavanone 4-reductase active in vitro suggested that the enzyme of the first step in the DA-pathway may regulate accumulation of DAs in different tissues. However, LDI-MSI highlighted the necessity to describe metabolite accumulation beyond class assignments as individual DA and caffeoylquinic acid metabolites accumulated differentially. For example, luteolinidin accumulated in epithelial cells, including those lining the leaf cavity, supporting a role for the former in the symbiotic interaction during cold acclimation.

Community metagenomics reveals the processes of cadmium resistance regulated by microbial functions in soils with Oryza sativa root exudate input

Plants exert a profound influence on their rhizosphere microbiome through the secretion of root exudates, thereby imparting critical effects on their growth and overall health. The results unveil that japonica rice showcases a remarkable augmentation in its antioxidative stress mechanisms under Cd stress. This augmentation is characterized by the sequestration of heavy metal ions within the root system and the prodigious secretion of a spectrum of flavonoids, including Quercetin, Luteolin, Apigenin, Kaempferide, and Sakuranetin. These flavonoids operate as formidable guardians, shielding the plant from oxidative damage instigated by Cd-induced stress. Furthermore, the metagenomic analyses divulge the transformative potential of flavonoids, as they induce profound alterations in the composition and structural dynamics of plant rhizosphere microbial communities. These alterations manifest through the recruitment of plant growth-promoting bacteria, effectively engineering a conducive milieu for japonica rice. In addition, our symbiotic network analysis discerns that flavonoid compounds significantly improved the positive correlations among dominant species within the rhizosphere of japonica rice. This, in turn, bolsters the stability and intricacy of the microenvironmental ecological network. KEGG functional analyses reveal a notable upregulation in the expression of flavonoid functional genes, specifically cadA, cznA, nccC, and czrB, alongside an array of transporters, encompassing RND, ABC, MIT, and P-ATPase. These molecular orchestrations distinctly demarcated the rhizosphere microbiome of japonica rice, markedly enhancing its tolerance to Cd-induced stress. These findings not only shed light on the establishment of Cd-resistant bacterial consortia in rice but also herald a promising avenue for the precise modulation of plant rhizosphere microbiomes, thereby fortifying the safety and efficiency of crop production.

Integrated Analysis of Metabolites and Microorganisms Reveals the Anthracnose Resistance Benefits from Cyanidin Mediated by Proteobacteria in Tea Plants

Anthocyanins, key quality components of tea, act as an important bridge between plants and the environment due to their function on protecting plants from biotic and abiotic irritants. This study aimed to assess the interactions between anthocyanins metabolism and the environment. Purple (P) and green (G) leaves with different anthocyanin contents were inoculated with tea plant anthracnose. High-throughput metabolomics and 16S microbial diversity sequencing methods were used to screen the anthocyanin fractions of tea plant leaves responsive to anthracnose. The interconnections between metabolites and the resistance of phyllosphere microorganisms to fungal pathogens were then analyzed. The results showed that leaves with high anthocyanin content (0.14% of diseased area ratio) were less impacted by anthracnose infestation than leaves with low anthocyanin (3.12%). The cyanidin content decreased after infection in purple leaves (PR) and increased in green leaves (GR). The relative abundance of Cyanobacteria was suppressed by the significant enrichment of Proteobacteria after anthracnose infection in green leaves. However, there were no significant differences between these two groups of microorganisms in purple leaves. Collinear network analysis revealed a strong correlation between Cyanobacteria and Dihydrosorbinol and between Proteobacteria and cyanidin metabolites. Among them, OTU456 (Bosea) was identified as the key taxonomic group of bacterial communities in the green-infected leaf network. In summary, the anthracnose resistance benefits from cyanidin mediated by proteobacteria in tea plants. These results deepen our understanding of the regulation of secondary metabolism in tea plants and the formation of plant resistance.

Tissue ontogeny and chemical composition influence bacterial biodiversity in the wood and shoot tip of Populus nigra

Plant-microbe interactions significantly influence plant growth dynamics and adaptability. This study explores the impact of metabolites on microbial biodiversity in shoot tips and wood of Populus nigra under greenhouse conditions, using high-throughput sequencing and metabolite profiling. Branches from P. nigra were harvested, rooted, and transplanted into pots for growth. After 3 months, tissue samples from shoot tips and wood were collected, and metabolites extracted and analysed using GC-MS and LC-MS. Genomic DNA was extracted and subjected to high-throughput sequencing for bacterial biodiversity profiling. Both datasets were analysed using bioinformatic and statistical pipelines. Metabolite profiling indicated that shoot tips had a higher relative abundance of primary and secondary metabolites, including sugars, fatty acids, organic acids, phenolic acid derivatives and salicinoids, while wood was enriched in flavonoids. Bacterial biodiversity also differed significantly between these tissues, with Clostridiales, Bacteroidales and Bacillales dominating in shoot tips, associated with rapid growth and anaerobic fermentation, while wood tissues were characterized by diazotrophs from Rhizobiales, Sphingomonadales and Frankiales. PCoA clustering confirmed tissue-specific microbial differences. Functional analysis revealed an enrichment of fundamental cellular processes in shoot tips, while wood exhibited pathways related to degradation and mortality. Metabolite profiling revealed significant variations in primary and secondary metabolites, highlighting their influence on microbial biodiversity across plant tissues. The dominance of specific bacterial orders and distinct functional pathways in each tissue suggests a tailored microbial response to the unique environments of shoot tips and wood.

The drought-induced plasticity of mineral nutrients contributes to drought tolerance discrimination in durum wheat

Drought is a major challenge for the cultivation of durum wheat, a crucial crop for global food security. Plants respond to drought by adjusting their mineral nutrient profiles to cope with water scarcity, showing the importance of nutrient plasticity for plant acclimation and adaptation to diverse environments. Therefore, it is essential to understand the genetic basis of mineral nutrient profile plasticity in durum wheat under drought stress to select drought-tolerant varieties. The research study investigated the responses of different durum wheat genotypes to severe drought stress at the seedling stage. The study employed an ionomic, molecular, biochemical and physiological approach to shed light on distinct behaviors among different genotypes. The drought tolerance of SVEMS16, SVEVO, and BULEL was related to their capacity of maintaining or increasing nutrient's accumulation, while the limited nutrient acquisition capability of CRESO and S.CAP likely resulted in their susceptibility to drought. The study highlighted the importance of macronutrients such as SO42-, NO3-, PO43-, and K+ in stress resilience and identified variant-containing genes potentially influencing nutritional variations under drought. These findings provide valuable insights for further field studies to assess the drought tolerance of durum wheat genotypes across various growth stages, ultimately ensuring food security and sustainable production in the face of changing environmental conditions.

Light stress elicits soilborne disease suppression mediated by root-secreted flavonoids in Panax notoginseng

Developing disease-suppressive soils is an effective approach for managing soilborne diseases, which can be achieved through crop metabolism and root secretion modification to recruit beneficial soil microbiota. Many factors, such as light, can elicit and modify plant metabolomic activities, resulting in disease suppression. To investigate the impact of light, Panax notoginseng was planted in a greenhouse and forest, conditioned with three levels of light intensities, including the optimal (15% light transmittance of full light), suboptimal low (5% light transmittance of full light) and suboptimal high (30% light transmittance of full light) intensities. We assessed the rhizosphere microbiota of P. notoginseng and root rot disease caused by soilborne pathogen Ilyonectria destructans, and elucidated the mechanism. Results showed that suboptimal light conditions alleviated root rot disease of P. notoginseng by enriching beneficial microbiota in the rhizosphere. Both low and high light stresses enhanced the secondary metabolism profile in favor of plant defense, particularly the flavonoid pathway. Notably, high light stress demonstrated a robust ability to promote flavonoid metabolism and secretion, resulting in the enrichment of more beneficial microorganisms that suppressed the soilborne pathogen I. destructans. These findings highlight the potential for adjusting canopy light intensities to improve soil health and promote sustainable agriculture.

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.

The Genome-Wide Identification of the Dihydroflavonol 4-Reductase (DFR) Gene Family and Its Expression Analysis in Different Fruit Coloring Stages of Strawberry

Dihydroflavonol 4-reductase (DFR) significantly influences the modification of flower color. To explore the role of DFR in the synthesis of strawberry anthocyanins, in this study, we downloaded the CDS sequences of the DFR gene family from the Arabidopsis genome database TAIR; the DFR family of forest strawberry was compared; then, a functional domain screen was performed using NCBI; the selected strawberry DFR genes were analyzed; and the expression characteristics of the family members were studied by qRT-PCR. The results showed that there are 57 members of the DFR gene family in strawberry, which are mainly expressed in the cytoplasm and chloroplast; most of them are hydrophilic proteins; and the secondary structure of the protein is mainly composed of α-helices and random coils. The analysis revealed that FvDFR genes mostly contain light, hormone, abiotic stress, and meristem response elements. From the results of the qRT-PCR analysis, the relative expression of each member of the FvDFR gene was significantly different, which was expressed throughout the process of fruit coloring. Most genes had the highest expression levels in the full coloring stage (S4). The expression of FvDFR30, FvDFR54, and FvDFR56 during the S4 period was 8, 2.4, and 2.4 times higher than during the S1 period, indicating that the DFR gene plays a key role in regulating the fruit coloration of strawberry. In the strawberry genome, 57 members of the strawberry DFR gene family were identified. The higher the DFR gene expression, the higher the anthocyanin content, and the DFR gene may be the key gene in anthocyanin synthesis. Collectively, the DFR gene is closely related to fruit coloring, which lays a foundation for further exploring the function of the DFR gene family.

Phenoxyacetic acid enhances nodulation symbiosis during the rapid growth stage of soybean

Root exudates are known signaling agents that influence legume root nodulation, but the molecular mechanisms for nonflavonoid molecules remain largely unexplored. The number of soybean root nodules during the initial growth phase shows substantial discrepancies at distinct developmental junctures. Using a combination of metabolomics analyses on root exudates and nodulation experiments, we identify a pivotal role for certain root exudates during the rapid growth phase in promoting nodulation. Phenoxyacetic acid (POA) was found to activate the expression of GmGA2ox10 and thereby facilitate rhizobial infection and the formation of infection threads. Furthermore, POA exerts regulatory control on the miR172c-NNC1 module to foster nodule primordia development and consequently increase nodule numbers. These findings collectively highlight the important role of POA in enhancing nodulation during the accelerated growth phase of soybeans.

Metabolites-induced co-evolutionary warfare between plants, viruses, and their associated vectors: So close yet so far away

Agriculture and global food security encounter significant challenges due to viral threats. In the following decades, several molecular studies have focused on discovering biosynthetic pathways of numerous defensive and signaling compounds, as key regulators of plant interactions, either with viruses or their associated vectors. Nevertheless, the complexities of specialized metabolites mediated plant-virus-vector tripartite viewpoint and the identification of their co-evolutionary crossroads toward antiviral defense system, remain elusive. The current study reviews the various roles of plant-specialized metabolites (PSMs) and how plants use these metabolites to defend against viruses. It discusses recent examples of specialized metabolites that have broad-spectrum antiviral properties. Additionally, the study presents the co-evolutionary basis of metabolite-mediated plant-virus-insect interactions as a potential bioinspired approach to combat viral threats. The prospects also show promising metabolic engineering strategies aimed at discovering a wide range of PSMs that are effective in fending off viruses and their related vectors. These advances in understanding the potential role of PSMs in plant-virus interactions not only serve as a cornerstone for developing plant antiviral systems, but also highlight essential principles of biological control.

Transcriptomic insights into the potential impacts of flavonoids and nodule-specific cysteine-rich peptides on nitrogen fixation in Vicia villosa and Vicia sativa

Vicia villosa (VV) and Vicia sativa (VS) are legume forages highly valued for their excellent nitrogen fixation. However, no research has addressed the mechanisms underlying their differences in nitrogen fixation. This study employed physiological, cytological, and comparative transcriptomic approaches to elucidate the disparities in nitrogen fixation between them. Our results showed that the total amount of nitrogen fixed was 60.45% greater in VV than in VS, and the comprehensive nitrogen response performance was 94.19% greater, while the nitrogen fixation efficiency was the same. The infection zone and differentiated bacteroid proportion in mature VV root nodules were 33.76% and 19.35% greater, respectively, than those in VS. The size of the VV genome was 15.16% larger than that of the VS genome, consistent with its greater biomass. A significant enrichment of the flavonoid biosynthetic pathway was found only for VV-specific genes, among which chalcone-flavonone isomerase, caffeoyl-CoA-O-methyltransferase and stilbene synthase were extremely highly expressed. The VV-specific genes also exhibited significant enrichment in symbiotic nodulation; genes related to nodule-specific cysteine-rich peptides (NCRs) comprised 61.11% of the highly expressed genes. qRT‒PCR demonstrated that greater enrichment and expression of the dominant NCR (Unigene0004451) were associated with greater nodule bacteroid differentiation and greater nitrogen fixation in VV. Our findings suggest that the greater total nitrogen fixation of VV was attributed to its larger biomass, leading to a greater nitrogen demand and enhanced fixation physiology. This process is likely achieved by the synergistic effects of high bacteroid differentiation along with high expression of flavonoid and NCR genes.

The effects of core microorganism community on flavor compounds and active substances during the aging process of Citri Reticulatae Pericarpium

Citri Reticulatae Pericarpium (CRP) is a traditional herbal and food spice, the flavor and active compounds content of Xinhui CRP improves with aging. To investigate the pattern of microbial community succession during the aging of Xinhui CRP and its correlation with changes in flavor compounds, the high-throughput sequencing, HPLC, and GC-IMS were used to analyze the microbial community, flavonoids, and flavor compounds of five different aging years in this study. The results revealed different dominant microbial communities in Xinhui CRP at different aging time, and unclassified Bacteria were the predominant bacterial genus during 10-15 years of aging. As the aging time increases, the abundance of microbial community decreases and gradually stabilizes. At the fungal genus level, Xeromyces (>99 %) were the dominant genus during the 10-15 years aging time and had a significant correlation with polymethoxyflavones (PMFs), and the concentrations of PMFs increased with the progression of aging years. The GC-IMS results revealed distinctive flavor profiles in Xinhui CRP across different aging years, floral and fruity aromas, such as heptanal, 3-methyl-3-butenol, and 1-butanol, among others, with increasing aging years. A comprehensive correlation analysis further elucidates the close relationship between the core microorganism community and flavor formation in Xinhui CRP (p < 0.05). Notably, Pseudomonas and Escherichia Shigella exhibited significant correlations with beta-pinene and alpha-pinene, whereas Aureobasidium and Sarcopodium were associated with nerol and α-phellandrene (p < 0.05). This study provides new ideas for accelerating the good quality and flavor of Xinhui CRP during the aging process from the perspective of key microorganisms.

GmAMT2.1/2.2-dependent ammonium nitrogen and metabolites shape rhizosphere microbiome assembly to mitigate cadmium toxicity

Cadmium (Cd), a heavy metal, is negatively associated with plant growth. AMT (ammonium transporter) genes can confer Cd resistance and enhance nitrogen (N) uptake in soybeans. The potential of AMT genes to alleviate Cd toxicity by modulating rhizosphere microbiota remains unkonwn. Here, the rhizosphere microbial taxonomic and metabolic differences in three genotypes, i.e., double knockout and overexpression lines and wild type, were identified. The results showed that GmAMT2.1/2.2 genes could induce soybean to recruit beneficial microorganisms, such as Tumebacillus, Alicyclobacillus, and Penicillium, by altering metabolites. The bacterial, fungal, and cross-kingdom synthetic microbial communities (SynComs) formed by these microorganisms can help soybean resist Cd toxicity. The mechanisms by which SynComs help soybeans resist Cd stress include reducing Cd content, increasing ammonium (NH4+-N) uptake and regulating specific functional genes in soybeans. Overall, this study provides valuable insights for the developing microbial formulations that enhance Cd resistance in sustainable agriculture.

Integrated Transcriptome and Metabolome Analysis Reveals Molecular Mechanisms Underlying Resistance to Phytophthora Root Rot

Soybean production is significantly impacted by Phytophthora root rot (PRR), which is caused by Phytophthora sojae. The nucleotide-binding leucine-rich repeat (NLR) gene family plays a crucial role in plant disease resistance. However, current understanding of the function of soybean NLR genes in resistance to PRR is limited. To address this knowledge gap, transgenic soybean plants overexpressing the NLR gene (Glyma.18g283200) were generated to elucidate the molecular mechanism of resistance. Here, transcript changes and metabolic differences were investigated at three time points (12, 24, and 36 h) after P. sojae infection in hypocotyls of two soybean lines, Dongnong 50 (susceptible line, WT) and Glyma.18g283200 overexpression line (resistant line, OE). Based on the changes in differentially expressed genes (DEGs) in response to P. sojae infection in different lines and at different time points, it was speculated that HOPZ-ACTIVATED RESISTANCE 1 (ZAR1), valine, leucine, and isoleucine degradation, and phytohormone signaling may be involved in the defense response of soybean to P. sojae at the transcriptome level by GO term and KEGG pathway enrichment analysis. Differentially accumulated metabolites (DAMs) analysis revealed that a total of 223 and 210 differential metabolites were identified in the positive ion (POS) and negative ion (NEG) modes, respectively. An integrated pathway-level analysis of transcriptomics (obtained by RNA-seq) and metabolomics data revealed that isoflavone biosynthesis was associated with disease resistance. This work provides valuable insights that can be used in breeding programs aiming to enhance soybean resistance against PRR.

Metabolomic and transcriptomic analyses highlight metabolic regulatory networks of Salvia miltiorrhiza in response to replant disease

BACKGROUND

Salvia miltiorrhiza, a well-known traditional Chinese medicine, frequently suffers from replant diseases that adversely affect its quality and yield. To elucidate S. miltiorrhiza's metabolic adaptations to replant disease, we analyzed its metabolome and transcriptome, comparing normal and replant diseased plants for the first time.

RESULTS

We identified 1,269 metabolites, 257 of which were differentially accumulated metabolites, and identified 217 differentially expressed genes. Integrated transcriptomic and metabolomic analyses revealed a significant up-regulation and co-expression of metabolites and genes associated with plant hormone signal transduction and flavonoid biosynthesis pathways in replant diseases. Within plant hormone signal transduction pathway, plants afflicted with replant disease markedly accumulated indole-3-acetic acid and abscisic acid, correlating with high expression of their biosynthesis-related genes (SmAmidase, SmALDH, SmNCED, and SmAAOX3). Simultaneously, changes in hormone concentrations activated plant hormone signal transduction pathways. Moreover, under replant disease, metabolites in the local flavonoid metabolite biosynthetic pathway were significantly accumulated, consistent with the up-regulated gene (SmHTC1 and SmHTC2). The qRT-PCR analysis largely aligned with the transcriptomic results, confirming the trends in gene expression. Moreover, we identified 10 transcription factors co-expressed with differentially accumulated metabolites.

CONCLUSIONS

Overall, we revealed the key genes and metabolites of S. miltiorrhiza under replant disease, establishing a robust foundation for future inquiries into the molecular responses to combat replant stress.

Integrated full-length transcriptome and metabolome analysis reveals the defence response of melon to gummy stem blight

Gummy stem blight (GSB), a widespread disease causing great loss to cucurbit production, has become a major threat to melon cultivation. However, the melon-GSB interaction remains largely unknown. Here, full-length transcriptome and widely targeted metabolome were used to investigate the defence responses of resistant (PI511089) and susceptible (Payzawat) melon accessions to GSB pathogen infection at 24 h. The biosynthesis of secondary metabolites and MAPK signalling pathway were specifically enriched for differentially expressed genes in PI511890, while carbohydrate metabolism and amino acid metabolism were specifically enriched in Payzawat. More than 1000 novel genes were identified and MAPK signalling pathway was specifically enriched for them in PI511890. There were 11 793 alternative splicing events involving in the defence response to GSB. Totally, 910 metabolites were identified in Payzawat and PI511890, and flavonoids were the dominant metabolites. Integrated full-length transcriptome and metabolome analysis showed eriodictyol and oxalic acid were the potential marker metabolites for GSB resistance in melon. Moreover, posttranscription regulation was widely involved in the defence response of melon to GSB pathogen infection. These results not only improve our understanding on the interaction between melon and GSB, but also facilitate the genetic improvement of melon with GSB resistance.

Mechanism on the promotion of host growth and enhancement of salt tolerance by Bacillaceae isolated from the rhizosphere of Reaumuria soongorica

Salt stress is a major abiotic stress that affects the growth of Reaumuria soongorica and many psammophytes in the desert areas of Northwest China. However, various Plant Growth-Promoting Rhizobacteria (PGPR) have been known to play an important role in promoting plant growth and alleviating the damaging effects of salt stress. In this study, three PGPR strains belonging to Bacillaceae were isolated from the rhizosphere of Reaumuria soongorica by morphological and molecular identification. All isolated strains exhibited capabilities of producing IAA, solubilizing phosphate, and fixing nitrogen, and were able to tolerate high levels of NaCl stress, up to 8-12%. The results of the pot-based experiment showed that salt (400 mM NaCl) stress inhibited Reaumuria soongorica seedlings' growth performance as well as biomass production, but after inoculation with strains P2, S37, and S40, the plant's height significantly increased by 26.87, 17.59, and 13.36%, respectively (p < 0.05), and both aboveground and root fresh weight significantly increased by more than 2 times compared to NaCl treatment. Additionally, inoculation with P2, S37, and S40 strains increased the content of photosynthetic pigments, proline, and soluble protein in Reaumuria soongorica seedlings under NaCl stress, while reducing the content of malondialdehyde and soluble sugars. Metabolomic analysis showed that strain S40 induces Reaumuria soongorica seedling leaves metabolome reprogramming to regulate cell metabolism, including plant hormone signal transduction and phenylalanine, tyrosine, and tryptophan biosynthesis pathways. Under NaCl stress, inoculation with strain S40 upregulated differential metabolites in plant hormone signal transduction pathways including plant hormones such as auxins (IAA), cytokinins, and jasmonic acid. The results indicate that inoculation with Bacillaceae can promote the growth of Reaumuria soongorica seedlings under NaCl stress and enhance salt tolerance by increasing the content of photosynthetic pigments, accumulating osmoregulatory substances, regulating plant hormone levels This study contributes to the enrichment of PGPR strains capable of promoting the growth of desert plants and has significant implications for the psammophytes growth and development in desert regions, as well as the effective utilization and transformation of saline-alkali lands.

Evaluation of Tunisian wheat endophytes as plant growth promoting bacteria and biological control agents against Fusarium culmorum

Plant growth-promoting rhizobacteria (PGPR) applications have emerged as an ideal substitute for synthetic chemicals by their ability to improve plant nutrition and resistance against pathogens. In this study, we isolated fourteen root endophytes from healthy wheat roots cultivated in Tunisia. The isolates were identified based from their 16S rRNA gene sequences. They belonged to Bacillota and Pseudomonadota taxa. Fourteen strains were tested for their growth-promoting and defense-eliciting potentials on durum wheat under greenhouse conditions, and for their in vitro biocontrol power against Fusarium culmorum, an ascomycete responsible for seedling blight, foot and root rot, and head blight diseases of wheat. We found that all the strains improved shoot and/or root biomass accumulation, with Bacillus mojavensis, Paenibacillus peoriae and Variovorax paradoxus showing the strongest promoting effects. These physiological effects were correlated with the plant growth-promoting traits of the bacterial endophytes, which produced indole-related compounds, ammonia, and hydrogen cyanide (HCN), and solubilized phosphate and zinc. Likewise, plant defense accumulations were modulated lastingly and systematically in roots and leaves by all the strains. Testing in vitro antagonism against F. culmorum revealed an inhibition activity exceeding 40% for five strains: Bacillus cereus, Paenibacillus peoriae, Paenibacillus polymyxa, Pantoae agglomerans, and Pseudomonas aeruginosa. These strains exhibited significant inhibitory effects on F. culmorum mycelia growth, sporulation, and/or macroconidia germination. P. peoriae performed best, with total inhibition of sporulation and macroconidia germination. These finding highlight the effectiveness of root bacterial endophytes in promoting plant growth and resistance, and in controlling phytopathogens such as F. culmorum. This is the first report identifying 14 bacterial candidates as potential agents for the control of F. culmorum, of which Paenibacillus peoriae and/or its intracellular metabolites have potential for development as biopesticides.

miR164-MhNAC1 regulates apple root nitrogen uptake under low nitrogen stress

Nitrogen is an essential nutrient for plant growth and serves as a signaling molecule to regulate gene expression inducing physiological, growth and developmental responses. An excess or deficiency of nitrogen may have adverse effects on plants. Studying nitrogen uptake will help us understand the molecular mechanisms of utilization for targeted molecular breeding. Here, we identified and functionally validated an NAC (NAM-ATAF1/2-CUC2) transcription factor based on the transcriptomes of two apple rootstocks with different nitrogen uptake efficiency. NAC1, a target gene of miR164, directly regulates the expression of the high-affinity nitrate transporter (MhNRT2.4) and citric acid transporter (MhMATE), affecting root nitrogen uptake. To examine the role of MhNAC1 in nitrogen uptake, we produced transgenic lines that overexpressed or silenced MhNAC1. Silencing MhNAC1 promoted nitrogen uptake and citric acid secretion in roots, and enhanced plant tolerance to low nitrogen conditions, while overexpression of MhNAC1 or silencing miR164 had the opposite effect. This study not only revealed the role of the miR164-MhNAC1 module in nitrogen uptake in apple rootstocks but also confirmed that citric acid secretion in roots affected nitrogen uptake, which provides a research basis for efficient nitrogen utilization and molecular breeding in apple.

Rhizosphere metabolic cross-talk from plant-soil-microbe tapping into agricultural sustainability: Current advance and perspectives

Rhizosphere interactions from plant-soil-microbiome occur dynamically all the time in the "black microzone" underground, where we can't see intuitively. Rhizosphere metabolites including root exudates and microbial metabolites act as various chemical signalings involving in rhizosphere interactions, and play vital roles on plant growth, development, disease suppression and resistance to stress conditions as well as proper soil health. Although rhizosphere metabolites are a mixture from plant roots and soil microbes, they often are discussed alone. As a rapid appearance of various omics platforms and analytical methods, it offers possibilities and opportunities for exploring rhizosphere interactions in unprecedented breadth and depth. However, our comprehensive understanding about the fine-tuning mechanisms of rhizosphere interactions mediated by these chemical compounds still remain clear. Thus, this review summarizes recent advances systemically including the features of rhizosphere metabolites and their effects on rhizosphere ecosystem, and looks forward to the future research perspectives, which contributes to facilitating better understanding of biochemical communications belowground and helping identify novel rhizosphere metabolites. We also address challenges for promoting the understanding about the roles of rhizosphere metabolites in different environmental stresses.

Rational management of the plant microbiome for the Second Green Revolution

The Green Revolution of the mid-20th century transformed agriculture worldwide and has resulted in environmental challenges. A new approach, the Second Green Revolution, seeks to enhance agricultural productivity while minimizing negative environmental impacts. Plant microbiomes play critical roles in plant growth and stress responses, and understanding plant-microbiome interactions is essential for developing sustainable agricultural practices that meet food security and safety challenges, which are among the United Nations Sustainable Development Goals. This review provides a comprehensive exploration of key deterministic processes crucial for developing microbiome management strategies, including the host effect, the facilitator effect, and microbe-microbe interactions. A hierarchical framework for plant microbiome modulation is proposed to bridge the gap between basic research and agricultural applications. This framework emphasizes three levels of modulation: single-strain, synthetic community, and in situ microbiome modulation. Overall, rational management of plant microbiomes has wide-ranging applications in agriculture and can potentially be a core technology for the Second Green Revolution.

Legume rhizodeposition promotes nitrogen fixation by soil microbiota under crop diversification

Biological nitrogen fixation by free-living bacteria and rhizobial symbiosis with legumes plays a key role in sustainable crop production. Here, we study how different crop combinations influence the interaction between peanut plants and their rhizosphere microbiota via metabolite deposition and functional responses of free-living and symbiotic nitrogen-fixing bacteria. Based on a long-term (8 year) diversified cropping field experiment, we find that peanut co-cultured with maize and oilseed rape lead to specific changes in peanut rhizosphere metabolite profiles and bacterial functions and nodulation. Flavonoids and coumarins accumulate due to the activation of phenylpropanoid biosynthesis pathways in peanuts. These changes enhance the growth and nitrogen fixation activity of free-living bacterial isolates, and root nodulation by symbiotic Bradyrhizobium isolates. Peanut plant root metabolites interact with Bradyrhizobium isolates contributing to initiate nodulation. Our findings demonstrate that tailored intercropping could be used to improve soil nitrogen availability through changes in the rhizosphere microbiome and its functions.

Biocontrol potential of volatile organic compounds produced by Streptomyces corchorusii CG-G2 to strawberry anthracnose caused by Colletotrichum gloeosporioides

Colletotrichum gloeosporioides is a fungal disease of strawberry fruit. Biocontrol strategies holds tremendous promise in alleviating fruit decay. Here, 30 actinomycetes were isolated from rhizosphere soil of Calotropis gigantea. A strain labeled with CG-G2 exhibited the strongest antagonistic activity against C. gloeosporioides and was assigned as Streptomyces corchorusii. Compared to strain CG-G2 extracts, the volatile organic compounds (VOCs) had a high antifungal activity against anthracnose. These volatiles effectively inhibited mycelial growth and spore germination of C. gloeosporioides. The hyphal and conidial structure was severely destroyed. Metabolomics analysis revealed that VOCs inhibited C. gloeosporioides via inducing flavonoids metabolism contributing to antifungal activity. Three main antagonistic compounds in VOCs were identified as methyl 2-methyl butyrate, hexanenitrile and methyl 2-Ethyl hexanoate. Especially, methyl 2-methyl butyrate demonstrated a remarkable efficacy in inhibiting fruit decay and preserving fruit quality. Hence, S. corchorusii CG-G2 will be a potential biocontrol agent for controlling anthracnose on harvested fruits.

Biochar application alters soil metabolites and nitrogen cycle-related microorganisms in a soybean continuous cropping system

Biochar application is a promising practice to enhance soil fertility. However, it is unclear how field-aged biochar affects the soil metabolites and microbial communities in soybean fields. Here, the rhizosphere soil performance after amending with biochar addition rates at 0 (CK), 20 (B20), 40 (B40), and 60 t ha-1 (B60) was examined via a five-year in-situ field experiment based on a soybean continuous cropping system. Untargeted metabolomics and metagenomics analysis techniques were applied to study the regulatory mechanism of biochar on soybean growth from metabolomics and N cycle microbiology perspectives. We found that the contents of soil total N (TN), available N (Ava N), NH4+-N, and NO3--N were significantly increased with biochar addition amounts by 20.0-65.7 %, 3.6-10.7 %, 29.5-57.1 %, and 24.4-46.7 %, respectively. The B20, B40, and B60 triggered 259 (236 were up-regulated and 23 were down-regulated), 236 (220 were up-regulated and 16 were down-regulated), and 299 (264 were up-regulated and 35 were down-regulated) differential metabolites, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis and topology analysis demonstrated that differential metabolites were highly enriched in seven metabolic pathways such as Oxidative phosphorylation and Benzoxazinoid biosynthesis. Moreover, ten differential metabolites were up-regulated in all three treatments with biochar. Biochar treatments decreased the Nitrospira abundance in soybean rhizosphere soil while increasing Bradyrhizobium abundance significantly in B60. Mantel test revealed that as the biochar addition rate grows, the correlation between Nitrospira and soil properties other than NO3--N became stronger. In conclusion, the co-application of biochar with fertilizers is a feasible and effective way to improve soil N supply, even though biochar has undergone field aging. This work offers new insights into the variations in soil metabolites and microbial communities associated with N metabolism processes under biochar addition in soybean continuous cropping soils.

The salt-tolerance of perennial ryegrass is linked with root exudate profiles and microflora recruitment

Salinity poses a significant threat to plant growth and development. The root microbiota plays a key role in plant adaptation to saline environments. Nevertheless, it remains poorly understood whether and how perennial grass plants accumulate specific root-derived bacteria when exposed to salinity. Here, we systematically analyzed the composition and variation of rhizosphere and endophytic bacteria, as well as root exudates in perennial ryegrass differing in salt tolerance grown in unsterilized soils with and without salt. Both salt-sensitive (P1) and salt-tolerant (P2) perennial ryegrass genotypes grew better in unsterilized soils compared to sterilized soils under salt stress. The rhizosphere and endophytic bacteria of both P1 and P2 had lower alpha-diversity under salt treatment compared to control. The reduction of alpha-diversity was more pronounced for P1 than for P2. The specific root-derived bacteria, particularly the genus Pseudomonas, were enriched in rhizosphere and endophytic bacteria under salt stress. Changes in bacterial functionality induced by salt stress differed in P1 and P2. Additionally, more root exudates were altered under salt stress in P2 than in P1. The content of important root exudates, mainly including phenylpropanoids, benzenoids, organic acids, had a significantly positive correlation with the abundance of rhizosphere and endophytic bacteria under salt stress. The results indicate that the interactions between root-derived bacteria and root exudates are crucial for the salt tolerance of perennial ryegrass, which provides a potential strategy to manipulate root microbiome for improved stress tolerance of perennial grass species.

Multifunctional 5-hydroxyconiferaldehyde O-methyltransferases (CAldOMTs) in plant metabolism

Lignin, flavonoids, melatonin, and stilbenes are plant specialized metabolites with diverse physiological and biological functions, supporting plant growth and conferring stress resistance. Their biosynthesis requires O-methylations catalyzed by 5-hydroxyconiferaldehyde O-methyltransferase (CAldOMT; also called caffeic acid O-methyltransferase, COMT). CAldOMT was first known for its roles in syringyl (S) lignin biosynthesis in angiosperm cell walls and later found to be multifunctional. This enzyme also catalyzes O-methylations in flavonoid, melatonin, and stilbene biosynthetic pathways. Phylogenetic analysis indicated the convergent evolution of enzymes with OMT activities towards the monolignol biosynthetic pathway intermediates in some gymnosperm species that lack S-lignin and Selaginella moellendorffii, a lycophyte which produces S-lignin. Furthermore, neofunctionalization of CAldOMTs occurred repeatedly during evolution, generating unique O-methyltransferases (OMTs) with novel catalytic activities and/or accepting novel substrates, including lignans, 1,2,3-trihydroxybenzene, and phenylpropenes. This review summarizes multiple aspects of CAldOMTs and their related proteins in plant metabolism and discusses their evolution, molecular mechanism, and roles in biorefineries, agriculture, and synthetic biology.

Biofortified Rice Provides Rich Sakuranetin in Endosperm

Sakuranetin plays a key role as a phytoalexin in plant resistance to biotic and abiotic stresses, and possesses diverse health-promoting benefits. However, mature rice seeds do not contain detectable levels of sakuranetin. In the present study, a transgenic rice plant was developed in which the promoter of an endosperm-specific glutelin gene OsGluD-1 drives the expression of a specific enzyme naringenin 7-O-methyltransferase (NOMT) for sakuranetin biosynthesis. The presence of naringenin, which serves as the biosynthetic precursor of sakuranetin made this modification feasible in theory. Liquid chromatography tandem mass spectrometry (LC-MS/MS) validated that the seeds of transgenic rice accumulated remarkable sakuranetin at the mature stage, and higher at the filling stage. In addition, the panicle blast resistance of transgenic rice was significantly higher than that of the wild type. Specially, the matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) imaging was performed to detect the content and spatial distribution of sakuranetin and other nutritional metabolites in transgenic rice seeds. Notably, this genetic modification also did not change the nutritional and quality indicators such as soluble sugars, total amino acids, total flavonoids, amylose, total protein, and free amino acid content in rice. Meanwhile, the phenotypes of the transgenic plant during the whole growth and developmental periods and agricultural traits such as grain width, grain length, and 1000-grain weight exhibited no significant differences from the wild type. Collectively, the study provides a conceptual advance on cultivating sakuranetin-rich biofortified rice by metabolic engineering. This new breeding idea may not only enhance the disease resistance of cereal crop seeds but also improve the nutritional value of grains for human health benefits.