Genomic and Transcriptomic Analysis Provide Insights Into Root Rot Resistance in Panax notoginseng

Genomic and metabolomic insights into the antimicrobial compounds and plant growth-promoting potential of Bacillus velezensis B115

The B115 strain, isolated from the inter-root soil of healthy plants in a continuous cropping site of Panax notoginseng, was identified as Bacillus velezensis B115 by 16S rDNA sequence comparison and comparative genomic analysis. B115 is a strain of beneficial microorganisms present in the inter-root zone of plants, with favorable plant growth-promoting properties and antagonistic effects against the plant pathogen Fusarium oxysporum. However, the whole genome of B115 remains unclear, thus restricting its potential applications. To address this gap, the whole genome of B115 has been sequenced and annotated to elucidate the molecular mechanisms underlying its plant growth-promoting and antimicrobial activities. The genome analysis revealed that B115 comprises a single circular chromosome of 4,200,774 bp and a plasmid region 16,878 bp long, possessing a GC content of 45.95%. Moreover, 4349 protein-coding genes were predicted. Notably, the B115 genome contains a substantial number of genes (103) involved in the biosynthesis, transport, and catabolism of secondary metabolites. Through genome mining, 13 BGCs and 540 genes encoding secondary metabolites with predicted roles were identified, including members of the surfactin and fengycin families. Utilizing LC-MS/MS technologies, 2318 metabolites were detected in the fermentation broth of B. velezensis B115, encompassing compounds such as Corynebactin, Gamabufotalin, Pracinostat, Indoleacetic acid, (8)-Gingerol, Luteolin, Liquiritigenin, and other metabolites with antimicrobial, growth-promoting, antioxidant, and antitumor properties. By exploring secondary metabolite-related genes and predicting potential secondary metabolites from the B115 genome based on the whole-genome sequence results, we further elucidate the genomic basis for its ability to promote plant growth and inhibit pathogen activity.

Root rot in medicinal plants: a review of extensive research progress

Root rot is a general term for soil-borne diseases that cause the necrosis and decay of underground plant parts. It has a wide host range and occurs in various types of plants, including crops, horticultural crops and medicinal plants. Due to the fact that medicinal plants generally have a long growth cycle and are primarily the root and rhizome herbs. This results in root rot causing more serious damage in medicinal plant cultivation than in other plants. Infected medicinal plants have shrivel or yellowed leaves, rotting rhizomes, and even death of the entire plant, resulting in a sharp decline in yield or even total crop failure, but also seriously reduce the commercial specifications and effective ingredient content of medicinal plants. The pathogens of root rot are complex and diverse, and Fusarium fungi have been reported as the most widespread pathogen. With the expansion of medicinal plant cultivation, root rot has occurred frequently in many medicinal plants such as Araliaceae, Fabaceae, Ranunculaceae, and Solanaceae and other medicinal plants. This article reviews recent research progress on root rot in medicinal plants, covering various aspects such as disease characteristics, occurrence, pathogen species, damage to medicinal plants, disease mechanisms, control measures, and genetic factors. The aim is to provide reference for better control of root rot of medicinal plants.

Recent advances in functional assays of WRKY transcription factors in plant immunity against pathogens

WRKY transcription factors (TFs) are one of the largest transcription factor families in plants and play important roles in plant processes, most notably in responding to diverse biotic and abiotic stresses. This article reviews the recent research progresses on WRKY TFs in regulating plant immunity, which includes both positive and negative regulation. WRKY TFs were shown to regulate plant defense against pathogens including fungi, bacteria, oomycetes, and viruses by modulating downstream pathogen resistance genes or interacting with other regulators. Plant signaling pathways or components involved in the regulatory network of WRKY-mediated plant immunity mainly involve the action of phytohormones, MAPKs (Mitogen-activated protein kinases), and other transcription factors. The interaction of WRKY TFs with these factors during pathogen resistance was discussed in this article, which may contribute to understanding the mechanisms of WRKY transcription factors in plant immunity.

Menthone lowers H3K27ac levels to inhibit Fusarium proliferatum growth

Background

The antifungal properties of essential oils (EOs) and their active constituents have been well documented. Histone acetylation is pivotal in modulating gene expression and influences biological processes in living organisms.

Results

This study demonstrated that menthone, the primary component of Mentha haplocalyx EO, exhibited notable antifungal activity against Fusarium proliferatum (EC50 = 6.099 mmol/L). The treatment significantly inhibited hyphal growth, reduced spore germination rates from 31.49 to 4.95%, decreased spore viability from 46.88 to 20.91%, and reduced spore production by a factor of 17.92 compared with the control group while simultaneously enhancing cell membrane permeability. However, the direct relationship between menthone and histone acetylation in inhibiting F. proliferatum remains nebulous. Our RNA sequencing (RNA-seq) analysis identified 7,332 differentially expressed genes (DEGs) between the control and menthone-treated groups, 3,442 upregulated and 3,880 downregulated, primarily enriched in pathways related to ribosome biogenesis and energy metabolism. Chromatin immunoprecipitation sequencing (ChIP-seq) analysis revealed that menthone inhibited the growth of F. proliferatum by decreasing H3K27ac levels and interfering with the transcription of energy metabolism-related genes. By integrating the RNA-seq data with the ChIP-seq results, we identified 110 DEGs associated with reduced H3K27ac modification primarily associated with ribosome biogenesis. Menthone affected the growth of F. proliferatum by reducing the expression of ribosome biogenesis-related genes (FPRO_06392, FPRO_01260, FPRO_10795, and FPRO_01372).

Conclusion

This study elucidated the mechanism by which menthone inhibits F. proliferatum growth from a histone acetylation modification perspective, providing insights into its application as an antifungal agent to prevent root rot in Panax notoginseng.

New insights into the roles of fungi and bacteria in the development of medicinal plant

BACKGROUND

The interaction between microorganisms and medicinal plants is a popular topic. Previous studies consistently reported that microorganisms were mainly considered pathogens or contaminants. However, with the development of microbial detection technology, it has been demonstrated that fungi and bacteria affect beneficially the medicinal plant production chain.

AIM OF REVIEW

Microorganisms greatly affect medicinal plants, with microbial biosynthesis a high regarded topic in medicinal plant-microbial interactions. However, it lacks a systematic review discussing this relationship. Current microbial detection technologies also have certain advantages and disadvantages, it is essential to compare the characteristics of various technologies.

KEY SCIENTIFIC CONCEPTS OF REVIEW

This review first illustrates the role of fungi and bacteria in various medicinal plant production procedures, discusses the development of microbial detection and identification technologies in recent years, and concludes with microbial biosynthesis of natural products. The relationship between fungi, bacteria, and medicinal plants is discussed comprehensively. We also propose a future research model and direction for further studies.

Mining of disease-resistance genes in Crocus sativus based on transcriptome sequencing

Introduction: Crocus sativus L. has an important medicinal and economic value in traditional perennial Chinese medicine. However, due to its unique growth characteristics, during cultivation it is highly susceptible to disease. The absence of effective resistance genes restricts us to breed new resistant varieties of C. sativus. Methods: In present study, comprehensive transcriptome sequencing was introduced to explore the disease resistance of the candidate gene in healthy and corm rot-infected C. sativus. Results and discussion: Totally, 43.72 Gb of clean data was obtained from the assembly to generate 65,337 unigenes. By comparing the gene expression levels, 7,575 differentially expressed genes (DEGs) were primarily screened. A majority of the DEGs were completely in charge of defense and metabolism, and 152 of them were annotated as pathogen recognition genes (PRGs) based on the PGRdb dataset. The expression of some transcription factors including NAC, MYB, and WRKY members, changed significantly based on the dataset of transcriptome sequencing. Therefore, this study provides us some valuable information for exploring candidate genes involved in the disease resistance in C. sativus.

The loss of microbial autotoxin degradation functions is associated with the decline of beneficial bacterial agents induced by phenolic acids

Continuous cultivation of medicinal plants can disrupt the rhizosphere's microbial community. There is still a need to know about the beneficial bacterial community, their putative drivers, and the potential functions they may have. This study used different growth years of Sanqi ginseng (Panax notoginseng) with root rot to look at the beneficial microbial community structure, the function of microbial carbon source utilization, and the function of rhizosphere soil metabolism. The beneficial bacterial community changed and the relative abundance of beneficial agents was suppressed significantly with the successive Sanqi ginseng plantings. The carbon source utilization capacity and diversity increased significantly, whereas three autotoxin degradation-related pathways (biosynthesis of other secondary metabolites, metabolism of terpenoids and polyketides, and xenobiotics biodegradation and metabolism) were downregulated considerably with planting year extended. The changes in the beneficial agents were driven by the shifts in phenolic acid profiles, and the decline of beneficial microbes led to the loss of microbial autotoxin degradation functions. Overall, these results provide insight into beneficial microbes, microbial functions, phenolic acids, and their interactions, and these findings are essential for maintaining healthy and sustainable cultivation of Sanqi ginseng. IMPORTANCE Sanqi ginseng is a valuable perennial Chinese herb with various benefits for human health. However, continuous cultivation causes a high incidence of root rot disease, which leads to decreased yield and serious economic losses and ultimately impedes the sustainable development of Chinese medicine production. The significance of this study is to reveal the pattern of changes in beneficial bacteria and their related functions in root rot diseased rhizosphere with the successive planting years of Sanqi ginseng. This study found that the decline of beneficial bacterial agents mediated by phenolic acid profiles appears to be associated with the loss of microbial autotoxin degradation functions. This result may have new implications for deciphering the causes of Sanqi ginseng's continuous cropping obstacles.

Multilayered regulation of secondary metabolism in medicinal plants

Medicinal plants represent a huge reservoir of secondary metabolites (SMs), substances with significant pharmaceutical and industrial potential. However, obtaining secondary metabolites remains a challenge due to their low-yield accumulation in medicinal plants; moreover, these secondary metabolites are produced through tightly coordinated pathways involving many spatiotemporally and environmentally regulated steps. The first regulatory layer involves a complex network of transcription factors; a second, more recently discovered layer of complexity in the regulation of SMs is epigenetic modification, such as DNA methylation, histone modification and small RNA-based mechanisms, which can jointly or separately influence secondary metabolites by regulating gene expression. Here, we summarize the findings in the fields of genetic and epigenetic regulation with a special emphasis on SMs in medicinal plants, providing a new perspective on the multiple layers of regulation of gene expression.

Soil differentiation and soil comprehensive evaluation of in wild and cultivated Fritillaria pallidiflora Schrenk

Few studies have focused on the growth, soil quality and sustainability of medicinal plants under different soil conditions. In this study, the spatial heterogeneity of soil physical and chemical properties, the diversity of rhizosphere soil microbial community structure, and the characteristics of growth of the wild and cultivated medicinal plant, Siberian fritillary (Fritillaria pallidiflora Schrek) were analyzed, and the soil quality and ecosystem sustainability were comprehensively evaluated. The results showed that there was significant spatial variability of soil nutrients in the different habitats. Nitrate nitrogen (NO₃-N) was strongly variable, while those of the soil organic carbon (SOC) and available phosphorus (AP) were moderately variable. There was little variability among the soil available potassium (AK), electrical conductivity (EC), pH and ammonium nitrogen (NH₄-N). Inverse Distance Weighting spatial interpolation showed that SOC, NO₃-N, NH₄-H and EC were highly distributed in the southeastern part of the wild area, and the soil was more acidic in the original habitat than in the planting habitat. There was little AK and AP in the native habitat, and there was a high content in the planting habitat. Simultaneously, the soil microbial communities of the two soils also differed. The wild-type soil showed a "fungal" type, while the planted soil showed a "bacterial" type. Pathogenic bacteria were among the primary microflora in the planting area. In general, it is difficult to maintain the sustainable development and geo-herbalism of F. pallidiflora in today's cultivation mode because of the significant differences in soil nature, spatial heterogeneity and microbial community structure for the growth of F. pallidiflora. Therefore, future planting should focus on transforming it from intensive to mountain forest planting. This is highly significant for improving the planting efficiency of F. pallidiflora, protecting their geo-herbalism and germplasm resources, and maintaining the stability and sustainable development of the ecosystem.

Effects of lime and oxalic acid on antioxidant enzymes and active components of Panax notoginseng under cadmium stress

Cadmium (Cd) pollution poses potential safety risks for Panax notoginseng cultivation, a medicinal plant in Yunnan. Under exogenous Cd stress, field experiments were conducted to understand the effects of lime (0, 750, 2250 and 3750 kg hm⁻²) applied and oxalic acid (0, 0.1 and 0.2 mol L⁻¹) leaves sprayed on Cd accumulation, antioxidant system and medicinal components of P. notoginseng. The results showed that Lime and foliar spray of oxalic acid were able to elevate Ca²⁺ and alleviate Cd²⁺ toxicity in P. notoginseng under Cd stress. The addition of lime and oxalic acid increased the activities of antioxidant enzymes and alters osmoregulator metabolism. The most significant increase in CAT activities increased by 2.77 folds. And the highest increase of SOD activities was 1.78 folds under the application of oxalic acid. While MDA content decreased by 58.38%. There were very significant correlation with soluble sugar, free amino acid, proline and soluble protein. Lime and oxalic acid were able to increase calcium ions (Ca²⁺), decrease Cd content and improve the stress resistance of P. notoginseng, while increasing the production of total saponins and flavonoids. Cd content were the lowest, 68.57% lower than controls, and met the standard value (Cd ≤ 0.5 mg kg⁻¹, GB/T 19086-2008). The proportion of SPN was 7.73%, which reached the highest level of all treatments, the flavonoids content increased significantly by 21.74%, which reached the medicinal standard value and optimal yield.