Linking Plant Secondary Metabolites and Plant Microbiomes: A Review

Structure and dynamics of microbial communities associated with the resurrection plant Boea hygrometrica in response to drought stress

MAIN CONCLUSION

The resurrection plant Boea hygrometrica selectively recruits and assembles drought-specific microbial communities across the plant-soil compartments, which may benefit plant growth and fitness under extreme drought conditions. Plant-associated microbes are essential for facilitating plant growth and fitness under drought stress. The resurrection plant Boea hygrometrica in natural habitats with seasonal rainfall can survive rapid desiccation, yet their interaction with microbiomes under drought conditions remains unexplored. This study examined the bacterial and fungal microbiome structure and drought response across plant-soil compartments of B. hygrometrica by high-throughput amplicon sequencing of 16S rRNA gene and internal transcribed spacer. Our results demonstrated that the diversity, composition, and functional profile of the microbial community varied considerably across the plant-soil compartments and were strongly affected by drought stress. Bacterial and fungal diversity was significantly reduced from soil to endosphere and belowground to aboveground compartments. The compartment-specific enrichment of the dominant bacteria phylum Cyanobacteriota and genus Methylorubrum in leaf endosphere, genera Pseudonocardia in rhizosphere soil and Actinoplanes in root endosphere, and fungal phylum Ascomycota in the aboveground compartments and genera Knufia in root endosphere and Cladosporium in leaf endosphere composed part of the core microbiota with corresponding enrichment of beneficial functions for plant growth and fitness. Moreover, the recruitment of dominant microbial genera Sphingosinicella and Plectosphaerella, Ceratobasidiaceae mycorrhizal fungi, and numerous plant growth-promoting bacteria involving nutrient supply and auxin regulation was observed in desiccated B. hygrometrica plants. Our results suggest that the stable assembled drought-specific microbial community of B. hygrometrica may contribute to plant survival under extreme environments and provide valuable microbial resources for the microbe-mediated drought tolerance enhancement in crops.

Comparative Analysis of Primary and Secondary Metabolites in Different In Vitro Tissues of Narcissus tazetta var. chinensis

Narcissus tazetta var. chinensis is a perennial monocot plant that is well known for its pharmaceutical and ornamental uses. This study aimed to understand the changes in the primary and secondary metabolites in different in vitro tissues of N. tazetta (callus, adventitious root, and shoot) using high-performance liquid chromatography and gas chromatography time-of-flight mass spectrometry. In addition, to optimize the most efficient in vitro culture methods for primary and secondary metabolite production, N. tazetta bulbs were used as explants and cultivated in Murashige and Skoog (MS) medium containing different hormones at various concentrations. In addition, the present study found suitable hormonal concentrations for callus, adventitious root, and shoot induction and analyzed the primary and secondary metabolites. The MS medium supplemented with 1.0 mg L-1 dicamba, 3.0 mg L-1 indole-3-butyric acid (IBA), and 3.0 mg L-1 6-benzylaminopurine (BAP) was the most efficient media for callus, adventitious root, and shoot induction in N. tazetta. The tissue induced in this medium was subjected to primary (amines, amino acids, organic acids, sugars, and sugar alcohols) and secondary metabolite (galantamine and phenolic acids) analysis. The shoots and roots showed the highest amounts of metabolites. This study showed that bulb in vitro culture can be an efficient micropropagation method for N. tazetta and the production of primary and secondary metabolites, offering implications for the mass production of primary and secondary metabolite compounds from N. tazetta tissues generated in vitro.

Microbial regulation of plant secondary metabolites: Impact, mechanisms and prospects

Plant secondary metabolites possess a wide range of pharmacological activities and play crucial biological roles. They serve as both a defense response during pathogen attack and a valuable drug resource. The role of microorganisms in the regulation of plant secondary metabolism has been widely recognized. The addition of specific microorganisms can increase the synthesis of secondary metabolites, and their beneficial effects depend on environmental factors and plant-related microorganisms. This article summarizes the impact and regulatory mechanisms of different microorganisms on the main secondary metabolic products of plants. We emphasize the mechanisms by which microorganisms regulate hormone levels, nutrient absorption, the supply of precursor substances, and enzyme and gene expression to promote the accumulation of plant secondary metabolites. In addition, the possible negative feedback regulation of microorganisms is discussed. The identification of additional unknown microbes and other driving factors affecting plant secondary metabolism is essential. The prospects for further analysis of medicinal plant genomes and the establishment of a genetic operation system for plant secondary metabolism research are proposed. This study provides new ideas for the use of microbial resources for biological synthesis research and the improvement of crop anti-inverse traits for the use of microbial resources.

Efficacy of DAP coated with bacterial strains and their metabolites for soil phosphorus availability and maize growth

Phosphorus (P) use efficiency in alkaline/calcareous soils is only 20% due to precipitation of P2O5 with calcium and magnesium. However, coating Diammonium Phosphate (DAP) with phosphorus solubilizing bacteria (PSB) is more appropriate to increase fertilizer use efficiency. Therefore, with the aim to use inorganic fertilizers more effectively present study was conducted to investigate comparative effect of coated DAP with PSB strains Bacillus subtilis ZE15 (MN003400), Bacillus subtilis ZR3 (MN007185), Bacillus megaterium ZE32 (MN003401) and Bacillus megaterium ZR19 (MN007186) and their extracted metabolites with uncoated DAP under axenic conditions. Gene sequencing was done against various sources of phosphorus to analyze genes responsible for phosphatase activity. Alkaline phosphatase (ALP) gene amplicon of 380bp from all tested strains was showed in 1% w/v gel. Release pattern of P was also improved with coated fertilizer. The results showed that coated phosphatic fertilizer enhanced shoot dry weight by 43 and 46% under bacterial and metabolites coating respectively. Shoot and root length up to 44 and 42% with metabolites coated DAP and 41% with bacterial coated DAP. Physiological attributes also showed significant improvement with coated DAP over conventional. The results supported the application of coated DAP as a useful medium to raise crop yield even at lower application rates i.e., 50 and 75% DAP than non-coated 100% DAP application which advocated this coating technique a promising approach for advancing circular economy and sustainable development in modern agriculture.

Soil microbiota and herbivory drive the assembly of tomato plant-associated microbial communities through different mechanisms

Plant-associated microbial communities are key to shaping many aspects of plant biology. In this study, we tested whether soil microbial communities and herbivory influence the bacterial community of tomato plants and whether their influence in different plant compartments is driven by microbial spillover between compartments or whether plants are involved in mediating this effect. We grew our plants in soils hosting three different microbial communities and covered (or not) the soil surface to prevent (or allow) passive microbial spillover between compartments, and we exposed them (or not) to herbivory by Manduca sexta. Here we show that the soil-driven effect on aboveground compartments is consistently detected regardless of soil coverage, whereas soil cover influences the herbivore-driven effect on belowground microbiota. Together, our results suggest that the soil microbiota influences aboveground plant and insect microbial communities via changes in plant metabolism and physiology or by sharing microorganisms via xylem sap. In contrast, herbivores influence the belowground plant microbiota via a combination of microbial spillover and changes in plant metabolism. These results demonstrate the important role of plants in linking aboveground and belowground microbiota, and can foster further research on soil microbiota manipulation for sustainable pest management.

Isolation and characterization of Paenibacillus peoriae JC-3jx from Dendrobium nobile

Dendrobium is a rich source of high-value natural components. Endophytic fungi are well studied, yet bacteria research is limited. In this study, endophytic bacteria from Dendrobium nobile were isolated using an improved method, showing inhibition of pathogens and growth promotion. JC-3jx, identified as Paenibacillus peoriae, exhibited significant inhibitory activity against tested fungi and bacteria, including Escherichia coli. JC-3jx also promoted corn seed rooting and Dendrobium growth, highlighting its excellent biocontrol and growth-promoting potential.

Bio-organic fertilizer facilitated phytoremediation of heavy metal(loid)s-contaminated saline soil by mediating the plant-soil-rhizomicrobiota interactions

Bio-organic fertilizer (BOF) was effective to promote the phytoremediation efficiency of heavy metal(loid)s-contaminated saline soil (HCSS) by improving rhizosphere soil properties, especially microbiome. However, there existed unclear impacts of BOF on plant metabolome and plant-driven manipulation on rhizosphere soil microbiota in HCSS, which were pivotal contributors to stress defense of plants trapped in adverse conditions. Here, a pot experiment was conducted to explore the mechanisms of BOF in improving alfalfa (Medicago sativa)-performing phytoremediation of HCSS. BOF application significantly increased the biomass (150.87-401.58 %) to support the augments of accumulation regarding heavy metal(loid)s (87.50 %-410.54 %) and salts (38.27 %-271.04 %) in alfalfa. BOF promoted nutrients and aggregates stability but declined pH of rhizosphere soil, accompanied by the boosts of rhizomicrobiota including increased activity, reshaped community structure, enriched plant growth promoting rhizobacteria (Blastococcus, Modestobacter, Actinophytocola, Bacillus, and Streptomyces), strengthened mycorrhizal symbiosis (Leohumicola, Funneliformis, and unclassified_f_Ceratobasidiaceae), optimized co-occurrence networks, and beneficial shift of keystones. The conjoint analysis of plant metabolome and physiological indices confirmed that BOF reprogrammed the metabolic processes (synthesis, catabolism, and long-distance transport of amino acid, lipid, carbohydrate, phytohormone, stress-resistant secondary metabolites, etc) and physiological functions (energy supply, photosynthesis, plant immunity, nutrients assimilation, etc) that are associated intimately. The consortium of root metabolome, soil metabolome, and soil microbiome revealed that BOF facilitated the exudation of metabolites correlated with rhizomicrobiota (structure, biomarker, and keystone) and rhizosphere oxidative status, e.g., fatty acyls, phenols, coumarins, phenylpropanoids, highlighting the plant-driven regulation on rhizosphere soil microbes and environment. By compiling various results and omics data, it was concluded that BOF favored the adaptation and phytoremediation efficiency of alfalfa by mediating the plant-soil-rhizomicrobiota interactions. The results would deepen understanding of the mechanisms by which BOF improved phytoremediation of HCSS, and provide theoretical guidance to soil amelioration and BOF application.

Unveiling Metal Tolerance Mechanisms in Leersia hexandra Swartz under Cr/Ni Co-Pollution by Studying Endophytes and Plant Metabolites

Heavy metal pollution poses significant environmental challenges, and understanding how plants and endophytic bacteria interact to mitigate these challenges is of utmost importance. In this study, we investigated the roles of endophytic bacteria, particularly Chryseobacterium and Comamonas, in Leersia hexandra Swartz (L. hexandra) in response to chromium and nickel co-pollution. Our results demonstrated the remarkable tolerance of Chryseobacterium and Comamonas to heavy metals, and their potential to become dominant species in the presence of co-pollution. We observed a close relationship between these endophytic bacteria and the significant differences in metabolites, particularly carbohydrates, flavonoids, and amino acids in L. hexandra. These findings shed light on the potential of endophytic bacteria to promote the production of aspartic acid and other metabolites in plants as a response to abiotic stressors. Furthermore, our study presents a new direction for plant and bioremediation strategies in heavy metal pollution and enhances our understanding of L. hexandra's mechanisms for heavy metal tolerance.

Analysis of Primary and Secondary Metabolites, Physical Properties, Antioxidant and Antidiabetic Activities, and Chemical Composition of Rosmarinus officinalis Essential Oils under Differential Water Stress Conditions

This study investigated the effects of varying water stress levels on Rosmarinus officinalis essential oils (EO). Three samples (S1, S2, and S3) were cultivated under different stress levels (40, 60, and 80%). Increased water stress led to changes in primary and secondary metabolites, EO contents, and physical properties. Antioxidant activity varied, with S2 exhibiting the highest IC50 value. In terms of antidiabetic activity, S2 showed robust α-amylase inhibition, while S3 displayed a commendable influence. For α-galactosidase inhibition, S3 had a moderate effect, and S2 stood out with increased efficacy. Gas chromatography-mass spectrometry analysis revealed stress-induced changes in major compounds. The study enhances the understanding of plant responses to water stress, with potential applications in antioxidant therapy and diabetes management. The findings emphasize the importance of sustainable water management for optimizing the EO quality in its various uses.

Deep eutectic solvent-based shaking-assisted extraction for determination of bioactive compounds from Norway spruce roots

Polyphenolic compounds play an essential role in plant growth, reproduction, and defense mechanisms against pathogens and environmental stresses. Extracting these compounds is the initial step in assessing phytochemical changes, where the choice of extraction method significantly influences the extracted analytes. However, due to environmental factors, analyzing numerous samples is necessary for statistically significant results, often leading to the use of harmful organic solvents for extraction. Therefore, in this study, a novel DES-based shaking-assisted extraction procedure for the separation of polyphenolic compounds from plant samples followed by LC-ESI-QTOF-MS analysis was developed. The DES was prepared from choline chloride (ChCl) as the hydrogen bond acceptor (HBA) and fructose (Fru) as the hydrogen bond donor (HBD) at various molar ratios with the addition of 30% water to reduce viscosity. Several experimental variables affecting extraction efficiency were studied and optimized using one-variable-at-a-time (OVAT) and confirmed by response surface design (RS). Nearly the same experimental conditions were obtained using both optimization methods and were set as follows: 30 mg of sample, 300 mg of ChCl:Fru 1:2 DES containing 30% w/w of water, 500 rpm shaking speed, 30 min extraction time, 10°C extraction temperature. The results were compared with those obtained using conventional solvents, such as ethanol, methanol and water, whereby the DES-based shaking-assisted extraction method showed a higher efficiency than the classical procedures. The greenness of the developed method was compared with the greenness of existing procedures for the extraction of polyphenolic substances from solid plant samples using the complementary green analytical procedure index (ComplexGAPI) approach, while the results for the developed method were better or comparable to the existing ones. In addition, the practicability of the developed procedure was evaluated by application of the blue applicability grade index (BAGI) metric. The developed procedure was applied to the determination of spruce root samples with satisfactory results and has the potential for use in the analysis of similar plant samples.

Essentials in the acquisition, interpretation, and reporting of plant metabolite profiles

Plant metabolite profiling reveals the diversity of secondary or specialized metabolites in the plant kingdom with its hundreds of thousands of species. Specialized plant metabolites constitute a vast class of chemicals posing significant challenges in analytical chemistry. In order to be of maximum scientific relevance, reports dealing with these compounds and their source species must be transparent, make use of standards and reference materials, and be based on correctly and traceably identified plant material. Essential aspects in qualitative plant metabolite profiling include: (i) critical review of previous literature and a reasoned sampling strategy; (ii) transparent plant sampling with wild material documented by vouchers in public herbaria and, optimally, seed banks; (iii) if possible, inclusion of generally available reference plant material; (iv) transparent, documented state-of-the art chemical analysis, ideally including chemical reference standards; (v) testing for artefacts during preparative extraction and isolation, using gentle analytical methods; (vi) careful chemical data interpretation, avoiding over- and misinterpretation and taking into account phytochemical complexity when assigning identification confidence levels, and (vii) taking all previous scientific knowledge into account in reporting the scientific data. From the current stage of the phytochemical literature, selected comments and suggestions are given. In the past, proposed revisions of botanical taxonomy were sometimes based on metabolite profiles, but this approach ("chemosystematics" or "chemotaxonomy") is outdated due to the advent of DNA sequence-based phylogenies. In contrast, systematic comparisons of plant metabolite profiles in a known phylogenetic framework remain relevant. This approach, known as chemophenetics, allows characterizing species and clades based on their array of specialized metabolites, aids in deducing the evolution of biosynthetic pathways and coevolution, and can serve in identifying new sources of rare and economically interesting natural products.

Genome-Wide Identification and Expression Profiling of Velvet Complex Transcription Factors in Populus alba × Populus glandulosa

The discovery of new genes with novel functions is a major driver of adaptive evolutionary innovation in plants. Especially in woody plants, due to genome expansion, new genes evolve to regulate the processes of growth and development. In this study, we characterized the unique VeA transcription factor family in Populus alba × Populus glandulosa, which is associated with secondary metabolism. Twenty VeA genes were characterized systematically on their phylogeny, genomic distribution, gene structure and conserved motif, promoter binding site, and expression profiling. Furthermore, through ChIP-qPCR, Y1H, and effector-reporter assays, it was demonstrated that PagMYB128 directly regulated PagVeA3 to influence the biosynthesis of secondary metabolites. These results provide a basis for further elucidating the function of VeAs gene in poplar and its genetic regulation mechanism.

Morphoanatomical study of the species Zanthoxylum kleinii (R.S. Cowan) P.G. Waterman (Rutaceae)

The order Sapindales is comprised of nine families and in Brazil it is represented by six, including Rutaceae Juss., which constitutes the largest group of this order. A variety of species of Zanthoxylum L. are distributed throughout the country, and among them is the species Zanthoxylum kleinii (R.S. Cowan) P.G. Waterman, which is found in the states of Brazil. This study aimed to characterize the morphoanatomy of the leaf, petiole, rachis, and stem of the species Z. kleinii. Histochemical tests were performed, and the sections were visualized under optical and scanning electron microscopy. The analysis showed that the morphoanatomical characteristics of the species are: hypoestomatic leaflets; stomata classified as anomocytic, tetracytic, and anisocytic; dorsiventral mesophyll; cavities that produce a secretion of lipid nature, present in the leaflet, rachis, and petiole; colleters distributed in the leaf; presence of simple non-glandular trichomes in all structures; and prismatic crystals in the petiole. Histochemical tests indicated the presence of phenolic and lipophilic compounds, mucilage, and lignin. With the result of this research, it was possible to identify the nature of the compounds secreted by the secretory structures of the leaves; in addition, the morphoanatomical characterization of Z. kleinii can provide relevant data for future studies for other organs of the species not yet described. Furthermore, contributing concomitantly with data for the genus, in this way, supporting to differentiate them. RESEARCH HIGHLIGHTS: Ultrastructural features observed by microscopic techniques. Calcium oxalate crystals present in the rachis. Microchemical tests confirmed the presence of colleters in the leaflet.

Common mycorrhizal network: the predominant socialist and capitalist responses of possible plant-plant and plant-microbe interactions for sustainable agriculture

Plants engage in a variety of interactions, including sharing nutrients through common mycorrhizal networks (CMNs), which are facilitated by arbuscular mycorrhizal fungi (AMF). These networks can promote the establishment, growth, and distribution of limited nutrients that are important for plant growth, which in turn benefits the entire network of plants. Interactions between plants and microbes in the rhizosphere are complex and can either be socialist or capitalist in nature, and the knowledge of these interactions is equally important for the progress of sustainable agricultural practice. In the socialist network, resources are distributed more evenly, providing benefits for all connected plants, such as symbiosis. For example, direct or indirect transfer of nutrients to plants, direct stimulation of growth through phytohormones, antagonism toward pathogenic microorganisms, and mitigation of stresses. For the capitalist network, AMF would be privately controlled for the profit of certain groups of plants, hence increasing competition between connected plants. Such plant interactions invading by microbes act as saprophytic and cause necrotrophy in the colonizing plants. In the first case, an excess of the nutritional resources may be donated to the receiver plants by direct transfer. In the second case, an unequal distribution of resources occurs, which certainly favor individual groups and increases competition between interactions. This largely depends on which of these responses is predominant ("socialist" or "capitalist") at the moment plants are connected. Therefore, some plant species might benefit from CMNs more than others, depending on the fungal species and plant species involved in the association. Nevertheless, benefits and disadvantages from the interactions between the connected plants are hard to distinguish in nature once most of the plants are colonized simultaneously by multiple fungal species, each with its own cost-benefits. Classifying plant-microbe interactions based on their habitat specificity, such as their presence on leaf surfaces (phyllospheric), within plant tissues (endophytic), on root surfaces (rhizospheric), or as surface-dwelling organisms (epiphytic), helps to highlight the dense and intricate connections between plants and microbes that occur both above and below ground. In these complex relationships, microbes often engage in mutualistic interactions where both parties derive mutual benefits, exemplifying the socialistic or capitalistic nature of these interactions. This review discusses the ubiquity, functioning, and management interventions of different types of plant-plant and plant-microbe interactions in CMNs, and how they promote plant growth and address environmental challenges for sustainable agriculture.

Discussion: Harnessing microbiome-mediated adaptations in insect pollinators to mitigate climate change impact on crop pollination

Insect pollinators, vital for agriculture and biodiversity, face escalating threats from climate change. We argue and explore the pivotal role of the microbiomes in shaping adaptations of insect pollinator resilience amid climate-induced challenges (climate change and habitat alteration). Examining diverse taxonomic groups, we unravel the interplay between insect physiology, microbiomes, and adaptive mechanisms. Climate-driven alterations in microbiomes impact insect health, behavior, and plant interactions, posing significant effects on agricultural ecosystems. We propose harnessing microbiome-mediated adaptations as a strategic approach to mitigate climate change impacts on crop pollination. Insights into insect-pollinator microbiomes offer transformative avenues for sustainable agriculture, including probiotic interventions (use of EM PROBIOTIC) and microbiome engineering (such as engineering gut bacteria) to induce immune responses and enhanced pollination services. Integrating microbiome insights into conservation practices elucidates strategies for preserving pollinator habitats, optimizing agricultural landscapes, and developing policies to safeguard pollinator health in the face of environmental changes. Finally, we stress interdisciplinary collaboration and the urgency of understanding pollinator microbiome dynamics under climate change in future research.

Terricoxanthones A-E, unprecedented dihydropyran-containing dimeric xanthones from the endophytic fungus Neurospora terricola HDF-Br-2 associated with the vulnerable conifer Pseudotsuga gaussenii

An investigation on the secondary metabolites from a rice culture broth of the endophytic fungus Neurospora terricola HDF-Br-2 derived from the vulnerable conifer Pseudotsuga gaussenii led to the isolation and characterization of 34 structurally diverse polyketides (1-34). Seven of them are previously undescribed, including five unprecedented dihydropyran-containing (terricoxanthones A-E, 1-5, resp.) and one rare tetrahydrofuran-containing (terricoxanthone F, 6) dimeric xanthones. The structures were elucidated by spectroscopic methods and single-crystal X-ray diffraction analyses. Terricoxanthones each were obtained as a racemic mixture. Their plausible biosynthetic relationships were briefly proposed. Compounds 6, aspergillusone A (8), and alatinone (27) displayed considerable inhibition against Candida albicans with MIC values of 8-16 μg/mL. 4-Hydroxyvertixanthone (12) and 27 exhibited significant inhibitory activities against Staphylococcus aureus, with MIC values of 4-8 μg/mL. Furthermore, compounds 8 and 27 could disrupt biofilm of S. aureus and C. albicans at 128 μg/mL. The findings not only extend the skeletons of xanthone dimers and contribute to the diversity of metabolites of endophytes associated with the endangered Chinese conifer P. gaussenii, but could further reveal the important role of protecting plant species diversity in support of chemical diversity and potential sources of new therapeutics.

Minimum Concentrations of Slow Pyrolysis Paper and Walnut Hull Cyclone Biochars Needed to Inactivate Escherichia coli O157:H7 in Soil

Antimicrobial properties of biochar have been attributed to its ability to inactivate foodborne pathogens in soil, to varying degrees. High concentrations of biochar have reduced E. coli O157:H7 in soil and dairy manure compost, based on alkaline pH. Preliminary studies evaluating 31 different biochars determined that two slow pyrolysis biochars (paper biochar and walnut hull cyclone biochar) were the most effective at inactivating E. coli in soil. A study was conducted to determine the lowest percentages of paper and walnut hull cyclone biochars needed to reduce E. coli O157:H7 in soil. A model soil was adjusted to 17.75% moisture, and the two types of biochar were added at concentrations of 1.0, 1.5, 2.0, 2.5, 3.5, 4.5, 5.5, and 6.5%. Nontoxigenic E. coli O157:H7 were inoculated into soil at 6.84 log CFU/g and stored for up to 6 weeks at 21°C. Mean E. coli O157:H7 counts were 6.01-6.86 log CFU/g at all weeks between 1 and 6 in soil-only positive control samples. Populations in all soil amended with 1.0 and 1.5% of either type of biochar (as well as 2.0% of the walnut hull biochar) resulted in ≤0.68 log reductions at week 6, when compared with positive controls. All other concentrations (i.e., ≥2.0% paper and ≥2.5% walnut hull) inactivated ≥2.7 log at all weeks between 1 and 6 (p < 0.05). At the end of 6 weeks, E. coli O157:H7 declined by 2.84 log in 2.0% paper biochar samples, while concentrations of between 2.5 and 6.5% paper biochar completely inactivated E. coli O157:H7, as determined by spiral plating, at weeks 5 and 6. In contrast, 2.0% walnut hull biochar lowered populations by only 0.38 log at week 6, although 2.5-6.5% concentrations of walnut hull biochar resulted in complete inactivation at all weeks between 3 and 6, as assessed by spiral plating. In summary, ≥2.5% paper or walnut hull biochar reduced ≥5.0 log of E. coli O157:H7 during the 6-week storage period, which we attribute to high soil alkalinity. Amended at a 2.5% concentration, the pH of soil with paper or walnut hull biochar was 10.67 and 10.06, respectively. Results from this study may assist growers in the use of alkaline biochar for inactivating E. coli O157:H7 in soil.

Interplay between Amaryllidaceae alkaloids, the bacteriome and phytopathogens in Lycoris radiata

Alkaloids are a large group of plant secondary metabolites with various structures and activities. It is important to understand their functions in the interplay between plants and the beneficial and pathogenic microbiota. Amaryllidaceae alkaloids (AAs) are unique secondary metabolites in Amaryllidaceae plants. Here, we studied the interplay between AAs and the bacteriome in Lycoris radiata, a traditional Chinese medicinal plant containing high amounts of AAs. The relationship between AAs and bacterial composition in different tissues of L. radiata was studied. In vitro experiments revealed that AAs have varying levels of antimicrobial activity against endophytic bacteria and pathogenic fungi, indicating the importance of AA synthesis in maintaining a balance between plants and beneficial/pathogenic microbiota. Using bacterial synthetic communities with different compositions, we observed a positive feedback loop between bacteria insensitive to AAs and their ability to increase accumulation of AAs in L. radiata, especially in leaves. This may allow insensitive bacteria to outcompete sensitive ones for plant resources. Moreover, the accumulation of AAs enhanced by insensitive bacteria could benefit plants when challenged with fungal pathogens. This study highlights the functions of alkaloids in plant-microbe interactions, opening new avenues for designing plant microbiomes that could contribute to sustainable agriculture.

The endophytic fungal community plays a crucial role in the resistance of host plants to necrotic bacterial pathogens

Konjac species (Amorphophallus spp.) are the only plant species in the world that are rich in a large amount of konjac glucomannan (KGM). These plants are widely cultivated as cash crops in tropical and subtropical countries in Asia, including China. Pectobacterium carotovorum subsp. carotovorum (Pcc) is one of the most destructive bacterial pathogens of konjac. Here, we analyzed the interactions between Pcc and susceptible and resistant konjac species from multiple perspectives. At the transcriptional and metabolic levels, the susceptible species A. konjac and resistant species A. muelleri exhibit similar molecular responses, activating plant hormone signaling pathways and metabolizing defense compounds such as phenylpropanoids and flavonoids to resist infection. Interestingly, we found that Pcc stress can lead to rapid recombination of endophytic microbial communities within a very short period (96 h). Under conditions of bacterial pathogen infection, the relative abundance of most bacterial communities in konjac tissue decreased sharply compared with that in healthy plants, while the relative abundance of some beneficial fungal communities increased significantly. The relative abundance of Cladosporium increased significantly in both kinds of infected konjac compared to that in healthy plants, and the relative abundance in resistant A. muelleri plants was greater than that in susceptible A. konjac plants. Among the isolated cultivable microorganisms, all three strains of Cladosporium strongly inhibited Pcc growth. Our results further elucidate the potential mechanism underlying konjac resistance to Pcc infection, highlighting the important role of endophytic microbial communities in resisting bacterial pathogen infections, especially the more direct role of fungal communities in inhibiting pathogen growth.

Ancient bayberry increased stress resistance by enriching tissue-specific microbiome and metabolites

The ancient bayberry demonstrates superior resistance to both biotic and abiotic stresses compared to cultivated bayberry, yet the underlying mechanisms remain largely unexplored. This study investigates whether long-term bayberry cultivation enhances stress resistance through modulation of tissue-specific microbes and metabolites. Employing microbiome amplicon sequencing alongside untargeted mass spectrometry analysis, we scrutinize the role of endosphere and rhizosphere microbial communities and metabolites in shaping the differential resistance observed between ancient and cultivated bayberry trees. Our findings highlight the presence of core microbiome and metabolites across various bayberry tissues, suggesting that the heightened resistance of ancient bayberry may stem from alterations in rhizosphere and endosphere microbial communities and secondary metabolites. Specifically, enrichment of Bacillus in roots and stems, Pseudomonas in leaves, and Mortierella in rhizosphere soil of ancient bayberry was noted. Furthermore, correlation analysis underscores the significance of enriched microbial species in enhancing ancient bayberry's resistance to stresses, with elevated levels of resistance-associated metabolites such as beta-myrcene, benzothiazole, L-glutamic acid, and gamma-aminobutyric acid identified through GC-MS metabolomics analysis. The beneficial role of these resistance-associated metabolites was further elucidated through assessment of their promotive and allelopathic effects, as well as their phytostatic and antioxidant functions in lettuce plants. Ultimately, our study delves into the intrinsic reasons behind the greater resistance of ancient bayberry to biotic and abiotic stresses by evaluating the impact of long-term planting on the microbial community and metabolites in the bayberry endosphere and rhizosphere, shedding light on the complex dynamics of host-microbial interactions.

Root-exuded benzoxazinoids can alleviate negative plant-soil feedbacks

Plants can suppress the growth of other plants by modifying soil properties. These negative plant-soil feedbacks are often species-specific, suggesting that some plants possess resistance strategies. However, the underlying mechanisms remain largely unknown. Here, we investigated whether benzoxazinoids, a class of dominant secondary metabolites that are exuded into the soil by maize and other cereals, allow maize plants to cope with plant-soil feedbacks. We find that three out of five tested crop species reduce maize (Zea mays L.) performance via negative plant-soil feedbacks relative to the mean across species. This effect is partially alleviated by the capacity of maize plants to produce benzoxazinoids. Soil complementation with purified benzoxazinoids restores the protective effect for benzoxazinoid-deficient mutants. Sterilization and reinoculation experiments suggest that benzoxazinoid-mediated protection acts via changes in soil biota. Substantial variation of the protective effect between experiments and soil types illustrates context dependency. In conclusion, exuded plant secondary metabolites allow plants to cope with plant-soil feedbacks. These findings expand the functional repertoire of plant secondary metabolites and reveal a mechanism by which plants can resist negative effects of soil feedbacks. The uncovered phenomenon may represent a promising avenue to stabilize plant performance in crop rotations.

Integrated microbiome and metabolomics analysis reveal the relationship between plant-specialized metabolites and microbial community in Phellodendron amurense

Phellodendron amurense is the essential source of bisbenzylisoquinoline alkaloids (BIAs), making it a highly valued raw material in traditional Chinese medicine. The plant's root secondary metabolism is intricately linked to the microbial communities that surround it. However, the root-associated microbiomes of P. amurense, as well as the potential correlation between its bioactive compounds and these microbiomes, remain poorly understood. Here, the metabolic profiles of root, rhizosphere, and bulk soils of P. amurense revealed the dramatic differences in the relative content of plant-specialized metabolites. A total of 31, 21, and 0 specialized metabolites in P. amurense were identified in the root, rhizosphere soil, and bulk soil, respectively, with higher content of the seven major BIAs observed in the rhizosphere compared with that in the bulk soils. The composition of the bulk and rhizosphere microbiomes was noticeably distinct from that of the endospheric microbiome. The phylum Cyanobacteria accounted for over 60% of the root endosphere communities, and the α-diversity in root was the lowest. Targeted seven BIAs, namely, berberine, palmatine, magnocurarine, phellodendrine, jatrorrhizine, tetrahydropalmatine, and magnoflorine, were significantly positively correlated with Nectriaceae and Sphingobacteriaceae. This study has illuminated the intricate interaction networks between P. amurense root-associated microorganisms and their key chemical compounds, providing the theoretical foundation for discovering biological fertilizers and laying the groundwork for cultivating high-quality medicinal plants.

Effect of micro-nano bubbles on the remediation of saline-alkali soil with microbial agent

The widespread distribution of saline-alkali soil around the world affects the health of ecological systems and the development of the national economy by limiting the growth of plants. However, the commonly used remediation technologies have the drawbacks of low efficiency, high cost, and secondary pollution. This study investigated the feasibility and efficacy of novel combined micro-nanobubbles (MNBs) and microbial agent (MA) technology for the remediation of saline-alkali soil. The results demonstrated that the combined MA-MNBs method greatly renovated the properties of saline-alkali soil compared with the technologies of single utilization of MA or MNBs process in the laboratory. The method resulted in a reduction of soil electrical conductivity and pH levels, an improvement in soil fertility, and the formation of soil aggregates. Moreover, the method significantly impacted the growth of plants, particularly in plant length, dry weight, and rhizome elongation. Further high-throughput sequencing and gene expression analysis revealed that the MA-MNBs method enhanced the abundance of soil microbial community compared with single MA and MNBs treatment. Gene enrichment analysis revealed that the MA-MNBs method could compensate for the shortcomings of single MA treatment and enhance the expression of energy metabolism and salt stress-related genes attributed to MNBs treatment, thereby significantly improving the growth and development of plants. Consistently, 6115 kg/ha of rice was yielded in the field for the saline-alkali soils using this MA-MNBs method, with zero crops before remediation. This study provided a novel, efficient, and green strategy for the remediation of saline-alkali soil without adding any chemicals.

Fungal-Bacterial Combinations in Plant Health under Stress: Physiological and Biochemical Characteristics of the Filamentous Fungus Serendipita indica and the Actinobacterium Zhihengliuella sp. ISTPL4 under In Vitro Arsenic Stress

Fungal-bacterial combinations have a significant role in increasing and improving plant health under various stress conditions. Metabolites secreted by fungi and bacteria play an important role in this process. Our study emphasizes the significance of secondary metabolites secreted by the fungus Serendipita indica alone and by an actinobacterium Zhihengliuella sp. ISTPL4 under normal growth conditions and arsenic (As) stress condition. Here, we evaluated the arsenic tolerance ability of S. indica alone and in combination with Z. sp. ISTPL4 under in vitro conditions. The growth of S. indica and Z. sp. ISTPL4 was measured in varying concentrations of arsenic and the effect of arsenic on spore size and morphology of S. indica was determined using confocal microscopy and scanning electron microscopy. The metabolomics study indicated that S. indica alone in normal growth conditions and under As stress released pentadecanoic acid, glycerol tricaprylate, L-proline and cyclo(L-prolyl-L-valine). Similarly, d-Ribose, 2-deoxy-bis(thioheptyl)-dithioacetal were secreted by a combination of S. indica and Z. sp. ISTPL4. Confocal studies revealed that spore size of S. indica decreased by 18% at 1.9 mM and by 15% when in combination with Z. sp. ISTPL4 at a 2.4 mM concentration of As. Arsenic above this concentration resulted in spore degeneration and hyphae fragmentation. Scanning electron microscopy (SEM) results indicated an increased spore size of S. indica in the presence of Z. sp. ISTPL4 (18 ± 0.75 µm) compared to S. indica alone (14 ± 0.24 µm) under normal growth conditions. Our study concluded that the suggested combination of microbial consortium can be used to increase sustainable agriculture by combating biotic as well as abiotic stress. This is because the metabolites released by the microbial combination display antifungal and antibacterial properties. The metabolites, besides evading stress, also confer other survival strategies. Therefore, the choice of consortia and combination partners is important and can help in developing strategies for coping with As stress.

High-quality chromosome-level genome assembly and multi-omics analysis of rosemary (Salvia rosmarinus) reveals new insights into the environmental and genome adaptation

High-quality genome of rosemary (Salvia rosmarinus) represents a valuable resource and tool for understanding genome evolution and environmental adaptation as well as its genetic improvement. However, the existing rosemary genome did not provide insights into the relationship between antioxidant components and environmental adaptability. In this study, by employing Nanopore sequencing and Hi-C technologies, a total of 1.17 Gb (97.96%) genome sequences were mapped to 12 chromosomes with 46 121 protein-coding genes and 1265 non-coding RNA genes. Comparative genome analysis reveals that rosemary had a closely genetic relationship with Salvia splendens and Salvia miltiorrhiza, and it diverged from them approximately 33.7 million years ago (MYA), and one whole-genome duplication occurred around 28.3 MYA in rosemary genome. Among all identified rosemary genes, 1918 gene families were expanded, 35 of which are involved in the biosynthesis of antioxidant components. These expanded gene families enhance the ability of rosemary adaptation to adverse environments. Multi-omics (integrated transcriptome and metabolome) analysis showed the tissue-specific distribution of antioxidant components related to environmental adaptation. During the drought, heat and salt stress treatments, 36 genes in the biosynthesis pathways of carnosic acid, rosmarinic acid and flavonoids were up-regulated, illustrating the important role of these antioxidant components in responding to abiotic stresses by adjusting ROS homeostasis. Moreover, cooperating with the photosynthesis, substance and energy metabolism, protein and ion balance, the collaborative system maintained cell stability and improved the ability of rosemary against harsh environment. This study provides a genomic data platform for gene discovery and precision breeding in rosemary. Our results also provide new insights into the adaptive evolution of rosemary and the contribution of antioxidant components in resistance to harsh environments.

Revealing Medicinal Constituents of Bistorta vivipara Based on Non-Targeted Metabolomics and 16S rDNA Gene Sequencing Technology

Bistorta vivipara is a medicinal plant with a long history, but there are few studies on the effects of its medicinal components and endophytic bacteria on the accumulation of secondary metabolites. Therefore, in this study, non-targeted metabolomics techniques and 16s rDNA techniques were used to study B. vivipara from different regions. A total of 1290 metabolites and 437 differential metabolites were identified from all samples. Among them, flavonoids, isoflavonoids, and benzopyrans are the main medicinal components of B. vivipara; these have potential anticancer, antiviral, and antioxidant properties, as well as potential applications for the treatment of atrial fibrillation. In addition, irigenin, an important medicinal component, was identified for the first time. The endophytic bacterial communities in the root tissues of B. vivipara from different regions were also different in composition and richness. Hierarchical clustering heat map analysis showed that Proteobacteria and Actinobacteriota bacteria significantly affected the accumulation of many medicinal components in the roots of B. vivipara.

Community ecological succession of endophytic fungi associates with medicinal compound accumulation in Sophora alopecuroides

Endophytic fungi of medicinal plants are symbiotic with the host and play an important role in determining metabolites. To understand the relationship between the accumulation of Sophora alopecuroides' medicinal bioactive compounds and the ecological succession of endophytic fungi, here we collected samples from S. alopecuroides at four developmental stages (adult, flowering, podding, and mature) and different organs (roots, stems, leaves, and seeds) at the mature stage. We then used high-performance liquid chromatography-mass spectrometry and high-throughput sequencing on the internal transcribed spacer region to identify the medicinal compounds and endophytic fungal communities in each sample. The endophytic fungal community characteristics and accumulation of medicinally bioactive compounds of S. alopecuroides varied with the host's developmental stages and organs, with the highest total alkaloids content of 111.9 mg/g at the mature stage. Membership analysis and network connection analysis showed a total of 15 core endophytic fungi in different developmental stages and 16 core endophytic fungi in different organs at the mature stage. The unclassified Ascomycota, Aspergillus, and Alternaria were significantly and positively correlated with the medicinal compounds of S. alopecuroides at the mature stage (r > 0.6 or r < -0.6; P < 0.05). In this study, we identified key endophytic fungal resources that affect the content of medicinally bioactive compounds in S. alopecuroides. This discovery could lay the foundation for enhancing the yield of medicinally bioactive compounds in S. alopecuroides and the development and application of functional endophytic fungi.IMPORTANCESophora alopecuroides is a traditional Chinese herbal medicine. The major medicinal chemicals are considered to be quinolizidine alkaloids. Quinolizidine alkaloids have been widely used for the treatment of tumors, dysentery, and enteritis. Previous studies have found that endophytic fungi in S. alopecuroides can promote the accumulation of host quinolizidine alkaloids. However, the relationship between the accumulation of S. alopecuroides' medicinal bioactive compounds and the ecological succession of endophytic fungi remains unclear. In this study, we screened the key endophytic fungal resources affecting the content of medicinally bioactive compounds and laid the foundation for subsequent research on the mechanism by which endophytic fungi promote the accumulation of medicinally bioactive compounds in S. alopecuroides.

Interactions of rhizosphere microbiota-environmental factors-pharmacological active ingredients of Eucommia ulmoides

MAIN CONCLUSION

The composition, diversity and co-occurrence patterns of the rhizosphere microbiota of E. ulmoides were significantly influenced by environmental factors, and which were potentially associated with the contents of pharmacological active ingredients. Eucommia ulmoides is an important perennial medicinal plant. However, little is known about the interactions among microbiota, environmental factors (EFs), and pharmacological active ingredients (PAIs) of E. ulmoides. Herein, we analyzed the interactions among rhizosphere microbiota-EFs-PAIs of E. ulmoides by amplicon sequencing and multi-analytical approach. Our results revealed variations in the dominant genera, diversity, and co-occurrence networks of the rhizosphere microbiota of E. ulmoides across different geographical locations. Notably, available nitrogen exerted the strongest influence on fungal dominant genera, while pH significantly impacted bacterial dominant genera. Rainfall and relative humidity exhibited pronounced effects on the α-diversity of fungal groups, whereas available phosphorus influenced the number of nodes in fungal co-occurrence networks. Altitude and total phosphorus had substantial effects on the average degree and nodes in bacterial co-occurrence networks. Furthermore, the dominant genera, diversity and co-occurrence network of rhizosphere microbiota of E. ulmoides were significantly correlated with the content of PAIs. Specifically, the abundance of rhizosphere dominant genera Filobasidium, Hannaella and Nitrospira were significantly correlated with the content of pinoresinol diglucoside (PD). Similarly, the abundance of Vishniacozyma and Bradyrhizobium correlated significantly with the content of geniposidic acid (GC), while the abundance of Gemmatimonas was significantly correlated with the content of aucubin. Moreover, the bacterial co-occurrence network parameters including average degree, density, and edge, were significantly correlated with the content of GC and aucubin. The α-diversity index Chao1 also displayed a significant correlation with the content of PD. These findings contribute to a more comprehensive understanding of the interactions between medicinal plants and microbes.

Flavonoids influence key rhizocompetence traits for early root colonization and PCB degradation potential of Paraburkholderia xenovorans LB400

Introduction

Flavonoids are among the main plant root exudation components, and, in addition to their role in symbiosis, they can broadly affect the functionality of plant-associated microbes: in polluted environments, for instance, flavonoids can induce the expression of the enzymatic degradative machinery to clean-up soils from xenobiotics like polychlorinated biphenyls (PCBs). However, their involvement in root community recruitment and assembly involving non-symbiotic beneficial interactions remains understudied and may be crucial to sustain the holobiont fitness under PCB stress.

Methods

By using a set of model pure flavonoid molecules and a natural blend of root exudates (REs) with altered flavonoid composition produced by Arabidopsis mutant lines affected in flavonoid biosynthesis and abundance (null mutant tt4, flavonoid aglycones hyperproducer tt8, and flavonoid conjugates hyperaccumulator ttg), we investigated flavonoid contribution in stimulating rhizocompetence traits and the catabolic potential of the model bacterial strain for PCB degradation Paraburkholderia xenovorans LB400.

Results

Flavonoids influenced the traits involved in bacterial recruitment in the rhizoplane by improving chemotaxis and motility responses, by increasing biofilm formation and by promoting the growth and activation of the PCB-degradative pathway of strain LB400, being thus potentially exploited as carbon sources, stimulating factors and chemoattractant molecules. Indeed, early rhizoplane colonization was favored in plantlets of the tt8 Arabidopsis mutant and reduced in the ttg line. Bacterial growth was promoted by the REs of mutant lines tt4 and tt8 under control conditions and reduced upon PCB-18 stress, showing no significant differences compared with the WT and ttg, indicating that unidentified plant metabolites could be involved. PCB stress presumably altered the Arabidopsis root exudation profile, although a sudden "cry-for-help" response to recruit strain LB400 was excluded and flavonoids appeared not to be the main determinants. In the in vitro plant-microbe interaction assays, plant growth promotion and PCB resistance promoted by strain LB400 seemed to act through flavonoid-independent mechanisms without altering bacterial colonization efficiency and root adhesion pattern.

Discussions

This study further contributes to elucidate the vast array of functions provided by flavonoids in orchestrating the early events of PCB-degrading strain LB400 recruitment in the rhizosphere and to support the holobiont fitness by stimulating the catabolic machinery involved in xenobiotics decomposition and removal.

In silico analysis to identify potential antitubercular molecules in Morus alba through virtual screening and molecular dynamics simulations

A major obstacle in the treatment of tuberculosis (TB) is to combat the emerging resistant strains of its causing agent i.e. Mycobacterium tuberculosis (MTb). The emergence of multidrug-resistant and extensively drug-resistant -TB strains raise a requirement of new potential anti-tubercular compounds. In this direction, different plant parts of Morus alba were tested against MTb and found to be active with a minimum inhibitory concentration ranging between 125 µg/ml to 31.5 µg/ml. Further to identify the phytochompounds having anti-mycobacterium activity, phytocompounds of the plant were docked against the five MTb proteins (PDB ID: 3HEM, 4OTK, 2QO0, 2AQ1 and 6MNA). Among twenty-two tested phytocompounds, four phytocompounds with effective binding energy (kcal/mol): Petunidin-3-rutinoside (3HEM: -8.2, 4OTK: -6.9, 2QO0: -9.0, 2AQ1: -8.3 and 6MNA:-7.8), Quercetin-3'-glucoside (3HEM:-6.7, 4OTK:-7.6, 2QO0:-7.6, 2AQ1:7.6 and 6MNA:-6.4), Rutin (3HEM:-7.8, 4OTK:-7.5, 2QO0:-9.1, 2AQ1:9.3 and 6MNA:-6.9) and Isoquercitrin (3HEM:-7.3, 4OTK:-6.6, 2QO0:-7.7, 2AQ1:8.3 and 6MNA:-6.6) shows promising activity against all the five target proteins. Further molecular dynamics studies of Petunidin-3-rutinoside with three target proteins 3HEM, 2AQ1 and 2QO0 resulted with low values of average RMSD (3.723 Å, 3.261 Å, and 2.497 Å, respectively) show that the complexes have better conformational stability. The wet lab validation of the current study will pave the new dimensions for the cure of TB patients.Communicated by Ramaswamy H. Sarma.

The Genus Cladosporium: A Prospective Producer of Natural Products

Cladosporium, a genus of ascomycete fungi in the Dematiaceae family, is primarily recognized as a widespread environmental saprotrophic fungus or plant endophyte. Further research has shown that the genus is distributed in various environments, particularly in marine ecosystems, such as coral reefs, mangroves and the polar region. Cladosporium, especially the marine-derived Cladosporium, is a highly resourceful group of fungi whose natural products have garnered attention due to their diverse chemical structures and biological activities, as well as their potential as sources of novel leads to compounds for drug production. This review covers the sources, distribution, bioactivities, biosynthesis and structural characteristics of compounds isolated from Cladosporium in the period between January 2000 and December 2022, and conducts a comparative analysis of the Cladosporium isolated compounds derived from marine and terrestrial sources. Our results reveal that 34% of Cladosporium-derived natural products are reported for the first time. And 71.79% of the first reported compounds were isolated from marine-derived Cladosporium. Cladosporium-derived compounds exhibit diverse skeletal chemical structures, concentrating in the categories of polyketides (48.47%), alkaloids (19.21%), steroids and terpenoids (17.03%). Over half of the natural products isolated from Cladosporium have been found to have various biological activities, including cytotoxic, antibacterial, antiviral, antifungal and enzyme-inhibitory activities. These findings testify to the tremendous potential of Cladosporium, especially the marine-derived Cladosporium, to yield novel bioactive natural products, providing a structural foundation for the development of new drugs.

Microbiome-Mediated Strategies to Manage Major Soil-Borne Diseases of Tomato

The tomato (Solanum lycopersicum L.) is consumed globally as a fresh vegetable due to its high nutritional value and antioxidant properties. However, soil-borne diseases can severely limit tomato production. These diseases, such as bacterial wilt (BW), Fusarium wilt (FW), Verticillium wilt (VW), and root-knot nematodes (RKN), can significantly reduce the yield and quality of tomatoes. Using agrochemicals to combat these diseases can lead to chemical residues, pesticide resistance, and environmental pollution. Unfortunately, resistant varieties are not yet available. Therefore, we must find alternative strategies to protect tomatoes from these soil-borne diseases. One of the most promising solutions is harnessing microbial communities that can suppress disease and promote plant growth and immunity. Recent omics technologies and next-generation sequencing advances can help us develop microbiome-based strategies to mitigate tomato soil-borne diseases. This review emphasizes the importance of interdisciplinary approaches to understanding the utilization of beneficial microbiomes to mitigate soil-borne diseases and improve crop productivity.

Effect of Silica Xerogel Functionalization on Intensification of Rindera graeca Transgenic Roots Proliferation and Boosting Naphthoquinone Production

Secondary metabolites derived from plants are recognized as valuable products with several successful applications in the pharmaceutical, cosmetic, and food industries. The major limitation to the broader implementation of these compounds is their low manufacturing efficiency. Current efforts to overcome unprofitability depend mainly on biotechnological methods, especially through the application of plant in vitro cultures. This concept allows unprecedented bioengineering opportunities for culture system modifications with in situ product removal. The silica-based xerogels can be used as a novel, porous biomaterial characterized by a large surface area and high affinity to lipophilic secondary metabolites produced by plant tissue. This study aimed to investigate the influence of xerogel-based biomaterials functionalized with methyl, hydroxyl, carboxylic, and amine groups on Rindera graeca transgenic root growth and the production of naphthoquinone derivatives. The application of xerogel-based scaffolds functionalized with the methyl group resulted in more than 1.5 times higher biomass proliferation than for reference untreated culture. The naphthoquinone derivatives' production was noted exclusively in culture systems supplemented with xerogel functionalized with methyl and hydroxyl groups. Applying chemically functionalized xerogels as in situ adsorbents allowed for the enhanced growth and productivity of in vitro cultured R. graeca transgenic roots, facilitating product isolation due to their selective and efficient accumulation.

Nematocidal Potential of Phenolic Acids: A Phytochemical Seed-Coating Approach to Soybean Cyst Nematode Management

Soybeans, one of the most valuable crops worldwide, are annually decimated by the soybean cyst nematode (SCN), Heterodera glycines, resulting in massive losses in soybean yields and economic revenue. Conventional agricultural pesticides are generally effective in the short term; however, they pose growing threats to human and environmental health; therefore, alternative SCN management strategies are urgently needed. Preliminary findings show that phenolic acids are significantly induced during SCN infection and exhibit effective nematocidal activities in vitro. However, it is unclear whether these effects occur in planta or elicit any negative effects on plant growth traits. Here, we employed a phytochemical-based seed coating application on soybean seeds using phenolic acid derivatives (4HBD; 2,3DHBA) at variable concentrations and examined SCN inhibition against two SCN types. Moreover, we also examined plant growth traits under non-infected or SCN infected conditions. Notably, 2,3DHBA significantly inhibited SCN abundance in Race 2-infected plants with increasingly higher chemical doses. Interestingly, neither compound negatively affected soybean growth traits in control or SCN-infected plants. Our findings suggest that a phytochemical-based approach could offer an effective, more environmentally friendly solution to facilitate current SCN management strategies and fast-track the development of biopesticides to sustainably manage devastating pests such as SCN.

Unveiling the crucial role of soil microorganisms in carbon cycling: A review

Soil microorganisms, by actively participating in the decomposition and transformation of organic matter through diverse metabolic pathways, play a pivotal role in carbon cycling within soil systems and contribute to the stabilization of organic carbon, thereby influencing soil carbon storage and turnover. Investigating the processes, mechanisms, and driving factors of soil microbial carbon cycling is crucial for understanding the functionality of terrestrial carbon sinks and effectively addressing climate change. This review comprehensively discusses the role of soil microorganisms in soil carbon cycling from three perspectives: metabolic pathways, microbial communities, and environmental influences. It elucidates the roles of different microbial species in carbon cycling and highlights the impact of microbial interactions and environmental factors on carbon cycling. Through the synthesis of 2171 relevant papers in the Web of Science Core database, we elucidated the ecological community structure, activity, and assembly mechanisms of soil microorganisms crucial to the soil carbon cycle that have been widely analyzed. The integration of soil microbial carbon cycle and its driving factors are vital for accurately predicting and modeling biogeochemical cycles and effectively addressing the challenges posed by global climate change. Such integration is vital for accurately predicting and modeling biogeochemical cycles and effectively addressing the challenges posed by global climate change.

Metabolomics Reveals the Response Mechanisms of Potato Tubers to Light Exposure and Wounding during Storage and Cooking Processes

Potato is susceptible to light exposure and wounding during harvesting and transportation. However, the metabolite profile changes in these potato tubers are unclear. The potato cultivars in this study included Hezuo88 (HZ88), Shida6 (SD6), and Jianchuanhong (JCH); the effects of light exposure (L), wounding (W), and the cooking process on potato metabolites were determined. In total, 973 metabolites were identified, with differential metabolites (mainly alkaloids, flavonoids, and phenolic acids) accumulated on days 0 and 2 (0 d and 2 d) in the 0dHZ88 vs. 0dJCH (189), 0dHZ88 vs. 0dSD6 (147), 0dSD6 vs. 0dJCH (91), 0dJCH vs. 2dIJCH (151), 0dJCH vs. 2dWDJCH (250), 0dJCH vs. 2dWLJCH (255), 2dIJCH vs. 2dWDJCH (234), and 2dIJCH vs. 2dWLJCH (292) groups. The flavonoid content in the light exposure group was higher than that in the dark group. The alkaloid content in the wounded group was higher than that in the uninjured potato tuber group, but the lipid content in the wounded group was lower. Importantly, only 5.54% of the metabolites changed after potato tuber steaming. These results provide valuable information for the breeding and consumption of potato tubers.

Fostering plant growth performance under drought stress using rhizospheric microbes, their gene editing, and biochar

Stress due to drought lowers crop yield and frequently leads to a rise in food scarcity. Plants' intricate metabolic systems enable them to tolerate drought stress, but they are unable to handle it well. Adding some external, environmentally friendly supplements can boost plant growth and productivity when it comes to drought-stressed plants. In order to prevent the detrimental effects of drought in agricultural regions, environmentally friendly practices must be upheld. Plant growth-promoting rhizobacteria (PGPR) can exhibit beneficial phytostimulation, mineralization, and biocontrol activities under drought stress. The significant impact of the PGPR previously reported has not been accepted as an effective treatment to lessen drought stress. Recent studies have successfully shown that manipulating microbes can be a better option to reduce the severity of drought in plants. In this review, we demonstrate how modifying agents such as biochar, PGPR consortia, PGPR, and mycorrhizal fungi can help overcome drought stress responses in crop plants. This article also discusses CRISPR/Cas9-modifiable genes, increase plant's effectiveness in drought conditions, and increase plant resistance to drought stress. With an eco-friendly approach in mind, there is a need for practical management techniques having potential prospects based on an integrated strategy mediated by CRISPR-Cas9 editing, PGPR, which may alleviate the effects of drought stress in crops and aid in achieving the United Nation Sustainable Development Goals (UN-SDGs-2030).

Potato Microbiome: Relationship with Environmental Factors and Approaches for Microbiome Modulation

Every land plant exists in a close relationship with microbial communities of several niches: rhizosphere, endosphere, phyllosphere, etc. The growth and yield of potato-a critical food crop worldwide-highly depend on the diversity and structure of the bacterial and fungal communities with which the potato plant coexists. The potato plant has a specific part, tubers, and the soil near the tubers as a sub-compartment is usually called the "geocaulosphere", which is associated with the storage process and tare soil microbiome. Specific microbes can help the plant to adapt to particular environmental conditions and resist pathogens. There are a number of approaches to modulate the microbiome that provide organisms with desired features during inoculation. The mechanisms of plant-bacterial communication remain understudied, and for further engineering of microbiomes with particular features, the knowledge on the potato microbiome should be summarized. The most recent approaches to microbiome engineering include the construction of a synthetic microbial community or management of the plant microbiome using genome engineering. In this review, the various factors that determine the microbiome of potato and approaches that allow us to mitigate the negative impact of drought and pathogens are surveyed.

Unveiling terahertz wave stress effects and mechanisms in Pinellia ternata: Challenges, insights, and future directions

This review aims to elucidate the intricate effects and mechanisms of terahertz (THz) wave stress on Pinellia ternata, providing valuable insights into plant responses. The primary objective is to highlight the imperative for future research dedicated to comprehending THz wave impacts across plant structures, with a specific focus on the molecular intricacies governing root system structure and function, from shoots to roots. Notably, this review highlights the accelerated plant growth induced by THz waves, especially in conjunction with other environmental stressors, and the subsequent alterations in cellular homeostasis, resulting in the generation of reactive oxygen species (ROS) and an increase in brassinosteroids. Brassinosteroids are explored for their dual role as toxic by-products of stress metabolism and vital signal transduction molecules in plant responses to abiotic stresses. The paper further investigates the spatio-temporal regulation and long-distance transport of phytohormones, including growth hormone, cytokinin, and abscisic acid (ABA), which significantly influence the growth and development of P. ternata under THz wave stress. With a comprehensive review of Reactive oxygen species (ROS) and Brassinosteroid Insensitive (BRI) homeostasis and signalling under THz wave stress, the article elucidates the current understanding of BRI involvement in stress perception, stress signalling, and domestication response regulation. Additionally, it underscores the importance of spatio-temporal regulation and long-distance transport of key plant hormones, such as growth hormone, cytokinin, and ABA, in determining root growth and development under THz wave stress. The study of how plants perceive and respond to environmental stresses holds fundamental biological significance, and enhancing plant stress tolerance is crucial for promoting sustainable agricultural practices and mitigating the environmental burdens associated with low-tolerance crop cultivation.

Gene functions of the Ambystoma altamirani skin microbiome vary across space and time but potential antifungal genes are widespread and prevalent

Amphibian skin microbiomes can play a critical role in host survival against emerging diseases by protecting their host against pathogens. While a plethora of biotic and abiotic factors have been shown to influence the taxonomic diversity of amphibian skin microbiomes it remains unclear whether functional genomic diversity varies in response to temporal and environmental factors. Here we applied a metagenomic approach to evaluate whether seasonality, distinct elevations/sites, and pathogen presence influenced the functional genomic diversity of the A. altamirani skin microbiome. We obtained a gene catalogue of 92 107 nonredundant annotated genes and a set of 50 unique metagenome assembled genomes (MAGs). Our analysis showed that genes linked to general and potential antifungal traits significantly differed across seasons and sampling locations at different elevations. Moreover, we found that the functional genomic diversity of A. altamirani skin microbiome differed between B. dendrobatidis infected and not infected axolotls only during winter, suggesting an interaction between seasonality and pathogen infection. In addition, we identified the presence of genes and biosynthetic gene clusters (BGCs) linked to potential antifungal functions such as biofilm formation, quorum sensing, secretion systems, secondary metabolite biosynthesis, and chitin degradation. Interestingly genes linked to these potential antifungal traits were mainly identified in Burkholderiales and Chitinophagales MAGs. Overall, our results identified functional traits linked to potential antifungal functions in the A. altamirani skin microbiome regardless of variation in the functional diversity across seasons, elevations/sites, and pathogen presence. Our findings suggest that potential antifungal traits found in Burkholderiales and Chitinophagales taxa could be related to the capacity of A. altamirani to survive in the presence of Bd, although further experimental analyses are required to test this hypothesis.

Polyhydroxyalkanoate production by the plant beneficial rhizobacterium Pseudomonas chlororaphis PCL1606 influences survival and rhizospheric performance

Pseudomonas chlororaphis PCL1606 (PcPCL1606) is a model rhizobacterium used to study beneficial bacterial interactions with the plant rhizosphere. Many of its beneficial phenotypes depend on the production of the antifungal compound 2-hexyl, 5-propyl resorcinol (HPR). Transcriptomic analysis of PcPCL1606 and the deletional mutant in HPR production ΔdarB strain, assigned an additional regulatory role to HPR, and allowed the detection of differentially expressed genes during the bacterial interaction with the avocado rhizosphere. Interestingly, the putative genes phaG (PCL1606_46820) and phaI (PCL1606_56560), with a predicted role in polyhydroxyalkanoate biosynthesis, were detected to be under HPR control. Both putative genes were expressed in the HPR-producing wild-type strain, but strongly repressed in the derivative mutant ΔdarB, impaired in HPR production. Thus, a derivative mutant impaired in the phaG gene was constructed, characterized and compared with the wild-type strain PcPCL1606 and with the derivative mutant ΔdarB. The phaG mutant had strongly reduced PHA production by PcPCL1606, and displayed altered phenotypes involved in bacterial survival on the plant roots, such as tolerance to high temperature and hydrogen peroxide, and decreased root survival, in a similar way that the ΔdarB mutant. On the other hand, the phaG mutant does not have altered resistance to desiccation, motility, biofilm formation or adhesion phenotypes, as displayed by the HPR-defective ΔdarB mutant have. Interestingly, the mutant defective in PHA production also lacked a biocontrol phenotype against the soilborne pathogenic fungus Rosellinia necatrix, even when the derivative mutant still produced the antifungal HPR compound, demonstrating that the final biocontrol phenotype of PcPCL1606 first requires bacterial survival and adaptation traits to the soil and rhizosphere environment.

Changes in root metabolites and soil microbial community structures in rhizospheres of sugarcanes under different propagation methods

Root metabolites and soil microbial community structure in the rhizosphere play critical roles in crop growth. Here, we assessed the efficiency of conventional and tissue culture propagation methods in modulating the soil health and microbiota in the rhizosphere of sugarcane (Saccharum officinarum L.) plants. The seeding canes were obtained using newly planted and two-year ratooned canes propagated by conventional (CSN and CSR) or tissue culture (TCN and TCR) methods. Changes in soil fertility, root metabolites and soil microbial community structure in the rhizosphere of sugarcane plants obtained using these canes were assessed. The activities of soil β-glucosidase and aminopeptidase, soil microbial biomass nitrogen, and abundances of soil beneficial microbes, both at phyla and genera levels, were significantly higher in the rhizosphere of sugarcane plants in TCN and TCR treatments than those in that of plants in CSN and CSR treatments. Furthermore, flavonoid and flavonol biosynthesis and alanine, aspartate and glutamate metabolism were significantly upregulated in the roots of TCR and TCN plants compared with those in the roots of CSN and CSR plants. These results suggest that the tissue culture propagation method is a sustainable method for sugarcane cultivation to improve soil fertility and health in sugarcane rhizosphere.

Examining the Antioxidant and Superoxide Radical Scavenging Activity of Anise, (Pimpinella anisum L. Seeds), Esculetin, and 4-Methyl-Esculetin Using X-ray Diffraction, Hydrodynamic Voltammetry and DFT Methods

Pimpinella anisum L., or anise, is a plant that, besides its nutritional value, has been used in traditional medical practices and described in many cultures in the Mediterranean region. A possible reason for anise's therapeutic value is that it contains coumarins, which are known to have many biomedical and antioxidant properties. HPLC analysis in our laboratory of the anise extract shows the presence of the coumarin esculetin. We used a hydrodynamic voltammetry rotating ring-disk electrode (RRDE) method to measure the superoxide scavenging abilities of anise seeds and esculetin, which has marked scavenging activity. A related coumarin, 4-methyl-esculetin, also showed strong antioxidant activity as measured by RRDE. Moreover, this study includes the X-ray crystal structure of esculetin and 4-methyl-esculetin, which reveal the H-bond and the stacking intermolecular interactions of the two coumarins. Coordinates of esculetin crystal structure were used to perform a DFT study to arrive at the mechanism of superoxide scavenging. Besides performing a H(hydroxyl) abstraction in esculetin position 6 by superoxide, the scavenging also includes the presence of a second superoxide radical in a π-π approach. Both rings of esculetin were explored for this attack, but only the pyrone ring was effective. As a result, one product of esculetin scavenging is H2O2 formation, while the second superoxide remains π-π trapped within the pyrone ring to form an esculetin-η-O2 complex. Comparison with other coumarins shows that subtle structural differences in the coumarin framework can imply marked differences in scavenging. For instance, when the catechol moiety of esculetin (position 6,7) is shifted to position 7,8 in 4-methyl-7,8-dihydroxy coumarin, that coumarin shows a superoxide dismutase action, which, beside H2O2 formation, includes the formation and elimination of a molecule of O2. This is in contrast with the products formed through esculetin superoxide scavenging, where a second added superoxide remains trapped, and forms an esculetin-η-O2 complex.

Combined omics approaches expose metabolite-microbiota correlations in grape berries of three cultivars of Douro wine region

This study hypothesized the existence of cultivar-associated correlations between grape berry metabolites and its microbial residents, in Douro wine region. Integrated metabolomics with metabarcoding showed that the microbial biodiversity is not associated to berry sugar concentration, but closely connected to the profile of amino acids, flavonoids and wax compounds, which drove cultivar differentiation together with the prevalence of pathogenic fungi, yeasts and bacteria, mainly Dothideomycetes and Gammaproteobacteria. Over 7000 metabolite-microbiota correlations with ρ >|0.99| exposed a core of 15 metabolites linked to 11 microbial taxa. Serine, oxalate, cyanidin-3-O-glucoside, petunidin-3-O-glucoside, gallic acid, germanicol, sitosterol and erythrodiol correlated negatively to the abundance of most taxa, including Alternaria, Aureobasidium, Pseudopithomyces, Pseudomonas and Sphingomonas. In contrast, phenylalanine, asparagine, alanine, (epi)gallocatechin and procyanidin gallate mediated positive metabolite-OTU correlations. E. necator and A. carbonarius correlated negatively with stigmasterol and amyrin. Complex fungi-bacteria relationships ruled by Dothideomycetes and Alphaproteobacteria further suggest tight host-microbe interactions at the carposphere.

Genome editing for plant synthetic metabolic engineering and developmental regulation

Plant metabolism and development are a reflection of the orderly expression of genetic information intertwined with the environment interactions. Genome editing is the cornerstone for scientists to modify endogenous genes or introduce exogenous functional genes and metabolic pathways, holding immense potential applications in molecular breeding and biosynthesis. Over the course of nearly a decade of development, genome editing has advanced significantly beyond the simple cutting of double-stranded DNA, now enabling precise base and fragment replacements, regulation of gene expression and translation, as well as epigenetic modifications. However, the utilization of genome editing in plant synthetic metabolic engineering and developmental regulation remains exploratory. Here, we provide an introduction and a comprehensive overview of the editing attributes associated with various CRISPR/Cas tools, along with diverse strategies for the meticulous control of plant metabolic pathways and developments. Furthermore, we discuss the limitations of current approaches and future prospects for genome editing-driven plant breeding.

A Multi-Label Learning Framework for Predicting Chemical Classes and Biological Activities of Natural Products from Biosynthetic Gene Clusters

Natural products (NP) or secondary metabolites, as a class of small chemical molecules that are naturally synthesized by chromosomally clustered biosynthesis genes (also called biosynthetic gene clusters, BGCs) encoded enzymes or enzyme complexes, mediates the bioecological interactions between host and microbiota and provides a natural reservoir for screening drug-like therapeutic pharmaceuticals. In this work, we propose a multi-label learning framework to functionally annotate natural products or secondary metabolites solely from their catalytical biosynthetic gene clusters without experimentally conducting NP structural resolutions. All chemical classes and bioactivities constitute the label space, and the sequence domains of biosynthetic gene clusters that catalyse the biosynthesis of natural products constitute the feature space. In this multi-label learning framework, a joint representation of features (BGCs domains) and labels (natural products annotations) is efficiently learnt in an integral and low-dimensional space to accurately define the inter-class boundaries and scale to the learning problem of many imbalanced labels. Computational results on experimental data show that the proposed framework achieves satisfactory multi-label learning performance, and the learnt patterns of BGCs domains are transferrable across bacteria, or even across kingdom, for instance, from bacteria to Arabidopsis thaliana. Lastly, take Arabidopsis thaliana and its rhizosphere microbiome for example, we propose a pipeline combining existing BGCs identification tools and this proposed framework to find and functionally annotate novel natural products for downstream bioecological studies in terms of plant-microbiota-soil interactions and plant environmental adaption.

Pharmacological Activities of Rhododendron afghanicum; an Endemic Species of Khyber Pakhtunkhwa, Pakistan

Majority of different kinds of metabolites having therapeutic characteristics are thought to be stored in medicinal plants. So, the present study was aimed to explore the crude extract of leaves and stem of R. afghanicum for phytochemical screening and various pharmacological activities. Toxicological studies at 100 mg/kg showed 60 % mortality where its safe dose level was 90 mg/kg. Phytochemical screening revealed the presence of alkaloids, glycosides, flavonoids and tannins in both extracts. Bacterial strains were susceptible to (RLEt) and (RLM) crude extracts except Staphylococcus aureus. RSM showed maximum anti-inflammatory activity (20.16 %) followed by RSEt (20.14 %) where lowest activity was displayed by RLEt (18.46 %). Phytotoxic activity showed a substantial dose-dependent phyto-inhibition of Lemna minor. An outstanding cytotoxic potential was displayed with LD50 values of 9.46 and 13.03 μg/ml in both stem extracts. RLEt demonstrated a dose-dependent pain relief at 30, 60 and 90 mg/kg which was 31 %, 40 % and 52 % respectively. A considerable spasmolytic action was observed by the shrinkage of jejunum muscle in albino mice. RLEt at 1000 ppm showed (17 mm) and RLM at 1000 ppm showed (16 mm) zone of inhibition against Aspergillus niger. These findings support and corroborate the traditional applications of R. afghanicum for treating digestive, analgesic and inflammatory ailments.

NLRP3 inhibitors: Unleashing their therapeutic potential against inflammatory diseases

The NOD-like receptor pyrin domain-containing protein 3 (NLRP3) inflammasome has been linked to the release of pro-inflammatory cytokines and is essential for innate defence against infection and danger signals. These secreted cytokines improve the inflammatory response caused by tissue damage and associated inflammation. Consequently, the development of NLRP3 inflammasome inhibitors are viable option for the treatment of diverse inflammatory disorders. The significant anti-inflammatory effects of the NLRP3 inhibitors have severe side effects. Hence, the application of NLRP3 inhibitors against inflammatory disease has not yet been understood and most of the developed inhibitors are unsuccessful in clinical trials. The processes behind the NLRP3 complex, priming, and activation are the main emphasis of this review, which also covers therapeutical inhibitors of the NLRP3 inflammasome and potential therapeutic strategies for directing the NLRP3 inflammasome towards clinical development.

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.

Gut microbiomes of cycad-feeding insects tolerant to β-methylamino-L-alanine (BMAA) are rich in siderophore biosynthesis

Ingestion of the cycad toxins β-methylamino-L-alanine (BMAA) and azoxyglycosides is harmful to diverse organisms. However, some insects are specialized to feed on toxin-rich cycads with apparent immunity. Some cycad-feeding insects possess a common set of gut bacteria, which might play a role in detoxifying cycad toxins. Here, we investigated the composition of gut microbiota from a worldwide sample of cycadivorous insects and characterized the biosynthetic potential of selected bacteria. Cycadivorous insects shared a core gut microbiome consisting of six bacterial taxa, mainly belonging to the Proteobacteria, which we were able to isolate. To further investigate selected taxa from diverging lineages, we performed shotgun metagenomic sequencing of co-cultured bacterial sub-communities. We characterized the biosynthetic potential of four bacteria from Serratia, Pantoea, and two different Stenotrophomonas lineages, and discovered a suite of biosynthetic gene clusters notably rich in siderophores. Siderophore semi-untargeted metabolomics revealed a broad range of chemically related yet diverse iron-chelating metabolites, including desferrioxamine B, suggesting the occurrence of an unprecedented desferrioxamine-like biosynthetic pathway that remains to be identified. These results provide a foundation for future investigations into how cycadivorous insects tolerate diets rich in azoxyglycosides, BMAA, and other cycad toxins, including a possible role for bacterial siderophores.