Autotoxic Ginsenoside Stress Induces Changes in Root Exudates to Recruit the Beneficial Burkholderia Strain B36 as Revealed by Transcriptomic and Metabolomic Approaches

Early inoculation and bacterial community assembly in plants: A review

The relationship between plants and early colonizing microbes is crucial for regulating agricultural ecosystems. Recent evidence strongly suggests that by introducing beneficial microbes during the seed or seedling stages, the diversity and assembly structure of the plant-related microbial community during later plant development can be altered, recruiting beneficial bacteria to enhance plant protection. However, the mechanisms of community assembly and their effects on plant growth are still not fully understood. To deepen our understanding of the importance of early inoculation for improving plant performance, this review comprehensively summarizes recent research advancements on the effects of early introduction on plant growth and adaptability. The mechanisms and ecological significance of early inoculation in the assembly of plant-related bacterial communities are discussed, with particular emphasis on the importance of seed endophytes, plant growth-promoting rhizobacteria (PGPR), and synthetic microbial consortia as microbial inoculants in enhancing plant health and productivity. Additionally, this review proposes a new strategy: sequential inoculation during the seed and seedling stages, aiming to maximize the effects of microbes.

Synergistic effect of grassland plants and beneficial rhizosphere bacteria helps plants cope with overgrazing stress

BACKGROUND

Overgrazing (OG) is an important driver of grassland degradation and productivity decline. Highly effective synergy between plants and rhizosphere growth-promoting rhizobacteria (PGPR) may be a major way for grassland plants to effectively cope with OG stress. There have been few reports providing solid evidence on how this synergy occurs.

RESULT

This study combined with multi-omics analysis and the interaction effect of specific root exudate with PGPR B68, aiming to reveal the synergistic effect and regulatory mechanism of L. chinensis and PGPR under overgrazing stress. The results showed that Leymus chinensis plants with OG history can recruit the beneficial Phyllobacterium sp. B68 by regulating specific root exudate compounds(such as amino acid L-leucyl-L-alanine and alkaloid cordycepin). These compounds enhanced B68 rhizosphere colonization by promoting B68 chemotaxis and biofilm formation. The pot study experiments indicated that the bacterial isolates used as bio inoculants increased L. chinensis growth (mainly including plant height and biomass) by significantly increasing the chlorophyll content, RuBisCO activity, soluble sugar, plant hormones and nutrient content. Metagenomics results show that B68 inoculation significantly altered rhizosphere soil bacterial community composition and function. Additionally, B68 systemically upregulated the expression level of genes involved in plant hormone signaling, nutrient and sugar transporters, nitrogen metabolism, cell division, cell wall modification and photosynthesis to promote plant growth. The above results indicate that the PGPR B68 recruited by the root exudates of L. chinensis under OG helps the plant adapt to stress by promoting nutrient uptake and transport, maintaining hormone homeostasis, and enhancing the expression of genes related to plant growth and nutrient metabolism.

CONCLUSION

This study provides new insights into the positive interactions between grassland plants and rhizosphere bacteria under OG stress, offering valuable knowledge for developing new fertilizers and better management practices for degraded rangeland restoration and sustainable agriculture development.

CLINICAL TRIAL NUMBER

Not applicable.

Impact of Ectropis grisescens Warren (Lepidoptera: Geometridae) Infestation on the Tea Plant Rhizosphere Microbiome and Its Potential for Enhanced Biocontrol and Plant Health Management

The root-associated microbiome significantly influences plant health and pest resistance, yet the temporal dynamics of its compositional and functional change in response to Ectropis grisescens Warren (Lepidoptera: Geometridae) infestation remain largely unexplored. The study took samples of leaves, roots, and rhizosphere soil at different times after the plants were attacked by E. grisescens. These samples were analyzed using transcriptomic and high-throughput sequencing of 16S rRNA techniques. The goal was to understand how the plant's defense mechanisms and the microbial community around the roots changed after the attack. Additionally, bacterial feedback assays were conducted to evaluate the effects of selected microbial strains on plant growth and pest defense responses. By conducting 16S rRNA sequencing on the collected soil samples, we found significant shifts in bacterial communities by the seventh day, suggesting a lag in community adaptation. Transcriptomic analysis revealed that E. grisescens attack induced reprogramming of the tea root transcriptome, upregulating genes related to defensive pathways such as phenylpropanoid and flavonoid biosynthesis. Metagenomic data indicated functional changes in the rhizosphere microbiome, with enrichment in genes linked to metabolic pathways and nitrogen cycling. Network analysis showed a reorganization of core microbial members, favoring nitrogen-fixing bacteria like Burkholderia species. Bacterial feedback assays confirmed that selected strains, notably Burkholderia cepacia strain ABC4 (T1) and a nine-strain consortium (T5), enhanced plant growth and defense responses, including elevated levels of flavonoids, polyphenols, caffeine, jasmonic acid, and increased peroxidase (POD) and superoxide dismutase (SOD) activities. This study emphasizes the potential of utilizing root-associated microbial communities for sustainable pest management in tea cultivation, thereby enhancing resilience in tea crops while maintaining ecosystem balance.

Licorice endophytes activate glycyrrhizin synthesis metabolic flux through feedback of β-glucuronidase conversion activity

Terpenoids are widely distributed in plants and are often used as defense molecules in plant-microbe interactions. However, endophytic microorganisms usually establish a better symbiotic relationship with their hosts by secreting enzymes to avoid defense plant metabolites. This study evaluated the in vitro biotransformation activity of licorice endophytic fungi on glycyrrhizin and further explored the molecular regulation of their in vivo colonization on the licorice growth and metabolism. The results indicated that licorice endophytic fungi generally possessed the ability to bio-transform glycyrrhizin, with Z6 and Z15 exhibiting glycyrrhizin-induced β-glucuronidase activity. The Z6GH2 and Z15GH2 proteins were identified to hydrolyze glycyrrhizin in different ways by prokaryotic and eukaryotic experiments. In vivo re-infestation of licorice by Z6 and Z15 revealed significant promotion of glycyrrhizin biosynthesis and accumulation by regulating the expression levels of genes involved in glycolysis and glycyrrhizin biosynthesis pathway in licorice. These findings were further validated in J3, which has glycyrrhizin biotransformation properties. In summary, this study reveals the molecular mechanism by which endophytic fungi with glycyrrhizin β-glucuronidase activity promote glycyrrhizin biosynthesis and accumulation in licorice through feedback regulation of its metabolic flux. These finding highlight the importance of endophytic fungi in regulating the accumulation of active ingredients in medicinal plants.

Harnessing Jasmonate Pathways: PgJAR1's Impact on Ginsenoside Accumulation in Ginseng

Ginsenosides, the most active components in Panax ginseng, exhibit pharmacological and therapeutic properties but are limited by their low abundance. Jasmonates (JAs), a class of stress-induced phytohormones, are integral in modulating plant defense responses and the biosynthesis of secondary metabolites, including ginsenosides. Jasmonoyl-isoleucine (JA-Ile), the primary bioactive JA compound, is biosynthesized by JA-Ile synthase 1 (JAR1). In this study, we cloned the 1555 bp PgJAR1 gene from ginseng roots and analyzed its structure, enzyme activity, and expression pattern. The PgJAR1 protein encompasses all the hallmark elements characteristic of the GH3 family. It exhibits N/C-terminal domains analogous to ANL, three ATP/AMP-binding motifs, and distinct secondary structures: an N-terminal beta-barrel with beta-sheets and alpha-helices, and a C-terminal beta-sheet surrounded by alpha-helices, similarly to AtGH3.11/AtJAR1. The recombinant PgJAR1 enzyme expressed in Escherichia coli BL21 specifically catalyzed jasmonic acid (JA) to JA-Ile. PgJAR1 is predominantly expressed in leaves and is upregulated by MeJA treatment. Moderate transient overexpression of PgJAR1 promoted the biosynthesis of both JA-Ile and ginsenosides, highlighting the crucial role of PgJAR1 in JA-Ile biosynthesis and its positive impact on ginsenoside accumulation. Nevertheless, elevated JA-Ile levels can impede cellular growth, reducing ginsenoside production. Consequently, balancing JA-Ile biosynthesis through PgJAR1 expression is essential for optimizing ginseng cultivation and enhancing its medicinal properties. Modulating endogenous JA-Ile levels offers a strategy for increasing ginsenoside production in ginseng plants.

Interspecific allelopathic interaction primes direct and indirect resistance in neighboring plants within agroforestry systems

The agroforestry system with high biodiversity enhances ecosystem stability and reduces vulnerability to environmental disturbances and diseases. Investigating the mechanisms of interspecies allelopathic interactions for disease suppression in agroforestry offers a sustainable strategy for plant disease management. Here, we used Panax ginseng cultivated under Pinus koraiensis forests, which have low occurrences of Alternaria leaf spot, as a model to explore the role of allelochemicals in disease suppression. Our findings demonstrate that foliar application of P. koraiensis needle leachates effectively enhanced the resistance of P. ginseng against Alternaria leaf spot. Using gas chromatography-mass spectrometry, we identified and quantified endo-borneol as a key compound in P. koraiensis leachates and confirmed its ability to prime resistance in neighboring P. ginseng plants. We discovered that endo-borneol not only directly activates defense-related pathways in P. ginseng to confer resistance but also indirectly recruits its beneficial rhizospheric microbiota by promoting the secretion of ginsenosides, thereby triggering induced systemic resistance. Notably, higher concentrations of endo-borneol, ranging from 10 to 100 mg/l, have a greater capacity to induce plant resistance and enhance root secretion, thereby recruiting more microbiota compared to lower concentrations ranging from 0.01 to 1 mg/l. Additionally, endo-borneol exhibits antifungal activities against the growth of the pathogen Alternaria panax when concentrations exceeded 10 mg/l. These results reveal the multifaceted functions of allelochemical endo-borneol in disease suppression within agroforestry systems and highlight its potential as an environmentally friendly agent for sustainable agriculture.

Transcriptional and Metabolomic Analyses Reveal That GmESR1 Increases Soybean Seed Protein Content Through the Phenylpropanoid Biosynthesis Pathway

Soybeans are an economically vital food crop, which is employed as a key source of oil and plant protein globally. This study identified an EREBP-type transcription factor, GmESR1 (Enhance of Shot Regeneration). GmESR1 overexpression has been observed to significantly increase seed protein content. Furthermore, the molecular mechanism by which GmESR1 affects protein accumulation through transcriptome and metabolomics was also identified. The transcriptomic and metabolomic analyses identified 95 differentially expressed genes and 83 differentially abundant metabolites during the seed mid-maturity stage. Co-analysis strategies revealed that GmESR1 overexpression inhibited the biosynthesis of lignin, cellulose, hemicellulose, and pectin via the phenylpropane biosynthetic pathway, thereby redistributing biomass within cells. The key genes and metabolites impacted by this biochemical process included Gm4CL-like, GmCCR, Syringin, and Coniferin. Moreover, it was also found that GmESR1 binds to (AATATTATCATTAAGTACGGAC) during seed development and inhibits the transcription of GmCCR. GmESR1 overexpression also enhanced sucrose transporter gene expression during seed development and increased the sucrose transport rate. These results offer new insight into the molecular mechanisms whereby GmESR1 increases protein levels within soybean seeds, guiding future molecular-assisted breeding efforts aimed at establishing high-protein soybean varieties.

Insight into saffron associated microbiota from different origins and explore the endophytes for enhancement of bioactive compounds

Crocus sativus L. is a perennial crop for its valuable active compounds. Plant-associated microbes impact on the quality and efficacy of medicinal herbs by promoting bioactive components accumulation. However, how microbes influence the accumulation of bioactive components in saffron have not been well studied. Here, the microbiome in C. sativus derived from 3 core production areas were deciphered by 16S rDNA sequencing and the relationship between endophytes and bioactive ingredients were further investigated. The main results are as follows: (1) Both Comamonadaceae and Burkholderiaceae were positively correlated with the content of bioactive components in the stigmas. (2) The synthesis of crocin was positively correlated with Xanthomonadaceae, negatively correlated with Lachnospiraceae and Prevotellaceae. Therefore, further investigation is required to determine whether Xanthomonadaceae plays an unknown function in the synthesis of crocin. These findings provide guidelines for disentangling the function of endophytes in the production of bioactive ingredients and thus for microbe-mediated breeding.

Trifolium repens L. recruits root-associated Microbacterium species to adapt to heavy metal stress in an abandoned Pb-Zn mining area

Root-associated microbiota provide great fitness to hosts under environmental stress. However, the underlying microecological mechanisms controlling the interaction between heavy metal-stressed plants and the microbiota are poorly understood. In this study, we screened and isolated representative amplicon sequence variants (strain M4) from rhizosphere soil samples of Trifolium repens L. growing in areas with high concentrations of heavy metals. To investigate the microecological mechanisms by which T. repens adapts to heavy metal stress in abandoned mining areas, we conducted potting experiments, bacterial growth promotion experiments, biofilm formation experiments, and chemotaxis experiments. The results showed that high concentrations of heavy metals significantly altered the rhizosphere bacterial community structure of T. repens and significantly enriched Microbacterium sp. Strain M4 was demonstrated to significantly increased the biomass and root length of T. repens under heavy metal stress. Additionally, L-proline and stigmasterol could promote bacterial growth and biofilm formation and induce chemotaxis for strain M4, suggesting that they are key rhizosphere secretions of T. repens for Microbacterium sp. recruitment. Our results suggested that T. repens adapted the heavy metal stress by reshaping rhizosphere secretions to modify the rhizosphere microbiota.

Host genotype and age shape the microbial community in the rhizosphere soils of Camellia forests

Microbiota living in the rhizosphere influences plant growth and fitness, from the opposite perspective; whether host genotypes control its root microbiota is of great interest to forest breeders and microbiologists. To improve low-yield plantations and promote sustainable management of Camellia oleifera, high-throughput sequencing was used to study the chemical properties and microbiome in rhizosphere soil of Camellia forests under three genotypes (common C. oleifera, local C. gauchowensis, and C. chekiangoleosa) and three growth stages (sapling stage at 4-year-old, primary fruit stage at 7-year-old, and full fruiting stage at 11-year-old). The results showed that the rhizosphere soil organic matter (OM), nutrient concentrations, diversity, and community composition of the microbiome were significantly varied among different Camellia genotypes. The relative abundance of symbiotic and pathotrophic fungi in the rhizosphere soil of C. chekiangoleosa was significantly higher than that of C. gauchowensis. Concentrations of OM, available phosphorus (AP), and bacterial alpha diversity increased with tree age. Fungi of Saitozyma, Mortierella, and Glomeromycota and bacteria of Burkholderia-Caballeronia-Paraburkholderia and Vicinamibacterales had potential for fertilizer development for Camellia plantation. Camellia genotypes and growth stages were significantly correlated with the rhizosphere soil pH, OM, and available potassium (AK). Soil pH and OM were key factors that affected the microbiome in the Camellia rhizosphere soils. In conclusion, tree genotypes and growth stages shaped microbial communities in Camellia rhizosphere soils, and some plant growth-promoting rhizobacteria were identified as preliminary candidates for improving Camellia plantation growth.

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.

Accumulation patterns of tobacco root allelopathicals across different cropping durations and their correlation with continuous cropping challenges

Introduction

Continuous cropping challenges have gradually emerged as pivotal factors limiting the sustainable development of agricultural production. Allelopathicals are considered to be the primary obstacles. However, there is limited information on allelopathic accumulation across various continuous cropping years and its correlation with the associated challenges.

Methods

Tobacco was subjected to varying planting durations: 1 year (CR), 5 years (CC5), 10 years (CC10), and 15 years (CC15).

Results

Our findings unveiled discernible disparities in tobacco growth patterns across diverse continuous cropping periods. Notably, the most pronounced challenges were observed in the CC5 category, characterized by yield reduction, tobacco black shank outbreaks, and a decline in beneficial flora. Conversely, CC15 exhibited a substantial reduction in challenges as the continuous cropping persisted with no significant differences when compared to CR. Within the tobacco rhizosphere, we identified 14 distinct allelopathic compounds, with 10 of these compounds displaying noteworthy variations among the four treatments. Redundancy analysis (RDA) revealed that eight allelopathic compounds exhibited autotoxic effects on tobacco growth, with MA, heptadecanoic acid, and VA ranking as the most potent inhibitors. Interaction network highlighted the pivotal roles of VA and EA in promoting pathogen proliferation and impeding the enrichment of 13 beneficial bacterial genera. Furthermore, a structural equation model elucidated that MA and EA primarily exert direct toxic effects on tobacco, whereas VA fosters pathogen proliferation, inhibits the enrichment of beneficial bacteria, and synergistically exacerbates the challenges associated with continuous cropping alongside EA.

Discussion

These findings suggested discernible disparities in tobacco growth patterns across the various continuous cropping periods. The most pronounced challenges were observed in CC5, whereas CC15 exhibited a substantial reduction in challenges as continuous cropping persisted. VA may play a pivotal role in this phenomenon by interacting with pathogens, beneficial bacterial genera, and EA.

Mass spectrometry-based ginsenoside profiling: Recent applications, limitations, and perspectives

Ginseng, the roots of Panax species, is an important medicinal herb used as a tonic. As ginsenosides are key bioactive components of ginseng, holistic chemical profiling of them has provided many insights into understanding ginseng. Mass spectrometry has been a major methodology for profiling, which has been applied to realize numerous goals in ginseng research, such as the discrimination of different species, geographical origins, and ages, and the monitoring of processing and biotransformation. This review summarizes the various applications of ginsenoside profiling in ginseng research over the last three decades that have contributed to expanding our understanding of ginseng. However, we also note that most of the studies overlooked a crucial factor that influences the levels of ginsenosides: genetic variation. To highlight the effects of genetic variation on the chemical contents, we present our results of untargeted and targeted ginsenoside profiling of different genotypes cultivated under identical conditions, in addition to data regarding genome-level genetic diversity. Additionally, we analyze the other limitations of previous studies, such as imperfect variable control, deficient metadata, and lack of additional effort to validate causation. We conclude that the values of ginsenoside profiling studies can be enhanced by overcoming such limitations, as well as by integrating with other -omics techniques.

Exploiting root exudates to manage soil-borne disease complexes in a changing climate

Ongoing climate change will both profoundly impact land-use (e.g., changes in crop species or cultivar and cropping practices) and abiotic factors (e.g., moisture and temperature), which will in turn alter plant-microorganism interactions in soils, including soil-borne pathogens (i.e., plant pathogenic bacteria, fungi, oomycetes, viruses, and nematodes). These pathogens often cause soil-borne disease complexes, which, due to their complexity, frequently remain undiagnosed and unmanaged, leading to chronic yield and quality losses. Root exudates are a complex group of organic substances released in the rhizosphere with potential to recruit, repel, stimulate, inhibit, or kill other organisms, including the detrimental ones. An improved understanding of how root exudates affect interspecies and/or interkingdom interactions in the rhizosphere under ongoing climate change is a prerequisite to effectively manage plant-associated microbes, including those causing diseases.