Endophytes isolated from Panax notoginseng converted ginsenosides

Progress on metabolites of Astragalus medicinal plants and a new factor affecting their formation: Biotransformation of endophytic fungi

It is generally believed that the main influencing factors of plant metabolism are genetic and environmental factors. However, the transformation and catalysis of metabolic intermediates by endophytic fungi have become a new factor and resource attracting attention in recent years. There are over 2000 precious plant species in the Astragalus genus. In the past decade, at least 303 high-value metabolites have been isolated from the Astragalus medicinal plants, including 124 saponins, 150 flavonoids, two alkaloids, six sterols, and over 20 other types of compounds. These medicinal plants contain abundant endophytic fungi with unique functions, and nearly 600 endophytic fungi with known identity have been detected, but only about 35 strains belonging to 13 genera have been isolated. Among them, at least four strains affiliated to Penicillium roseopurpureum, Alternaria eureka, Neosartorya hiratsukae, and Camarosporium laburnicola have demonstrated the ability to biotransform four saponin compounds from the Astragalus genus, resulting in the production of 66 new compounds, which have significantly enhanced our understanding of the formation of metabolites in plants of the Astragalus genus. They provide a scientific basis for improving the cultivation quality of Astragalus plants through the modification of dominant fungal endophytes or reshaping the endophytic fungal community. Additionally, they open up new avenues for the discovery of specialized, green, efficient, and sustainable biotransformation pathways for complex pharmaceutical intermediates.

Temporal patterns of endophytic microbial heterogeneity across distinct ecological compartments within the Panax ginseng root system following deforestation for cultivation

Alterations in the microbial community significantly impact the yield and quality of ginseng. Yet, the dynamics of microbial community shifts within the root endophytes of ginseng across varying cultivation periods remain inadequately understood. This study zeroes in on the microbial community variations within the xylem (M), phloem (R), and fibrous roots (X) of ginseng during the fourth (F4) and fifth (F5) years of cultivation, aiming to bridge this research gap. We assessed soil physicochemical properties, enzyme activities, and nine individual saponins, complemented by high-throughput sequencing techniques (16S rDNA and ITS) to determine their profiles. The results showed that cultivation years mainly affected the microbial diversity of endophytic bacteria in ginseng fibrous roots compartment: the ASVs number and α-diversity Chao1 index of bacteria and fungi in F5X compartment with higher cultivation years were significantly higher than those in F4X compartment with lower cultivation years. It is speculated that the changes of fibrous roots bacterial groups may be related to the regulation of amino acid metabolic pathway. Such as D-glutamine and D-glutamate metabolism D-glutamine, cysteine and methionine metabolism regulation. The dominant bacteria in ginseng root are Proteobacteria (relative abundance 52.07-80.35%), Cyanobacteria (1.97-42.52%) and Bacteroidota (1.11-5.08%). Firmicutes (1.28-3.76%). There were two dominant phyla: Ascomycota (60.10-93.71%) and Basidiomycota (2.25-30.57%). Endophytic fungi were more closely related to soil physicochemical properties and enzyme activities. AN, TK, OP, SWC and EC were the main driving factors of endophytic flora of ginseng root. Tetracladium decreased with the increase of cultivation years, and the decrease was more significant in phloem (F4R: 33.36%, F5R: 16.48%). The relative abundance of Bradyrhizobium, Agrobacterium and Bacillus in each ecological niche increased with the increase of cultivation years. The relative abundance of Bradyrhizobium and Agrobacterium in F5X increased by 8.35 and 9.29 times, respectively, and Bacillus in F5M increased by 5.57 times. We found a variety of potential beneficial bacteria and pathogen antagonists related to ginseng biomass and saponins, such as Bradyrhizobium, Agrobacterium, Bacillus and Exophiala, which have good potential for practical application and development.

Endophytic fungi of Panax sokpayensis produce bioactive ginsenoside Compound K in flask fermentation

Endophytes of Panax have the potential to produce their host plant secondary metabolites, ginsenosides. Panax sokpayensis, an endemic traditional medicinal plant of the Sikkim Himalayas was explored for the isolation of endophytic fungi. In the present study, we have isolated 35 endophytic fungal cultures from the rhizome of P. sokpayensis and screened for ginsenosides production by HPLC by comparing the peak retention time with that of standard ginsenosides. The HPLC analysis revealed that out of 35 isolates, the mycelial extracts of four fungal endophytes (PSRF52, PSRF53, PSRF49 and PSRF58) exhibited peaks with a similar retention time of the standard ginsenoside, Compound K (CK). LC-ESI-MS/MS analysis led to the confirmation of ginsenoside CK production by the four fungal endophytes which showed a compound with m/z 639.6278, similar to that of standard ginsenoside CK with yield in potato dextrose broth flask fermentation ranging from 0.0019 to 0.0386 mg/g of mycelial mass in dry weight basis. The four prospective fungal endophyte isolates were identified as Thermothielavioides terrestris PSRF52, Aspergillus sp. PSRF49, Rutstroemiaceae sp. strain PSRF53, and Phaeosphaeriaceae sp. strain PSRF58 based on ITS sequencing. The present finding highlights the need for further study on growth optimization and other culture parameters to exploit the endophytes as an alternative source for ginsenoside CK production.

Dynamic changes of endophytic bacteria in the bark and leaves of medicinal plant Eucommia ulmoides in different seasons

The bark and leaves of the Eucommia ulmoides Oliv. (E. ulmoides) have good medicinal value. Studies show endophytes play important roles in host medicinal plant secondary metabolite synthesis, with season being a key influencing factor. Therefore, we used 16 S rRNA to detect endophytic bacteria (EB) in E. ulmoides bark and leaves collected in winter, spring, summer, and autumn, and analyzed the contents of major active components respectively. The results showed that the species diversity and richness of EB of the E. ulmoides bark were higher than those of leaves in all seasons except fall. Among them, the higher species diversity and richness were found in the E. ulmoides bark in winter and spring. EB community structure differed significantly between medicinal tissues and seasons. Concurrently, the bark and leaves of E. ulmoides showed abundant characteristic EB across seasons. For active components, geniposidic acid showed a significant positive correlation with EB diversity and richness, while the opposite was true for aucubin. Additionally, some dominant EB exhibited close correlations with the accumulation of active components. Delftia, enriched in autumn, correlated significantly positively with aucubin. Notably, the impact of the same EB genera on active components differed across medicinal tissues. For example, Sphingomonas, enriched in summer, correlated significantly positively with pinoresinol diglucoside (PDG) in the bark, but with aucubin in the leaves. In summary, EB of E. ulmoides was demonstrated high seasonal dynamics and tissue specificity, with seasonal characteristic EB like Delftia and Sphingomonas correlating with the accumulation of active components in medicinal tissues.

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.

Influence of sampling location and processing on the assembly and network of Polygoni Multiflori Radix surface microbiome

The raw and processed roots of Polygonum multiflorum Thunb is a popular traditional Chinese medicine. However, Polygoni Multiflori Radix is easily contaminated by toxigenic fungi and mycotoxins during harvesting, processing, and transportation, thereby posing a health risk for consumers. This study aims to investigate the presence of fungi on the surface of raw and processed Polygoni Multiflori Radix collected from four producing areas using high-throughput sequencing. Results showed that the phyla Ascomycota and Basidiomycota, the genera Xeromyces, Cystofilobasidium, Eurotium, and Aspergillus were the dominant fungus, and significant differences are presented in four areas and two processed products. Three potential mycotoxin-producing fungi were detected, namely Trichosporon cutaneum, Aspergillus restrictus, and Fusarium oxysporum. The α-diversity and network complexity showed significant differences in four areas. Chao 1 and Shannon were highest in Yunnan (YN), then incrementally decreased from SC (Sichuan) to AH (Anhui) and GD (Guangdong) areas. Meanwhile, α-diversity was also strongly influenced by processing. Chao 1 and Shannon indices were higher in the raw group, however, the network complexity and connectivity were higher in the processed group. In conclusion, the assembly and network of the surface microbiome on Polygoni Multiflori Radix were influenced by sampling location and processing. This work provides details on the surface microbiome of Polygoni Multiflori Radix samples, which could ensure the drug and consumers' safety.

Biotransformation of American Ginseng Stems and Leaves by an Endophytic Fungus Umbelopsis sp. and Its Effect on Alzheimer's Disease Control

BACKGROUND

Common ginsenosides can be transformed into rare ginsenosides through microbial fermentation, and some rare ginsenosides can prevent Alzheimer's disease (AD). This study aimed to transform common ginsenosides into rare ginsenosides through solid-state fermentation of American ginseng stems and leaves (AGSL) by an endophytic fungus and to explore whether fermented saponin extracts prevent AD.

METHODS

The powders of AGSL were fermented in a solid state by endophytic fungus. Total saponins were extracted from fermentation products using the methanol extraction method. The types of saponins were analyzed by liquid chromatography mass spectrometry (LC/MS). The Aβ42 concentration and β-secretase activity were measured by ELISA for the prevention of AD.

RESULTS

After AGSL was fermented by an endophytic fungus NSJG, the total saponin concentration of the fermented extract G-SL was higher than the unfermented CK-SL. Rare ginsenoside Rh1 was newly produced and the yield of compound K (561.79%), Rh2 (77.48%), and F2 (40.89%) was increased in G-SL. G-SL had a higher inhibition rate on Aβ42 concentration (42.75%) and β-secretase activity (42.22%) than CK-SL, possibly because the rare ginsenoside Rh1, Rh2, F2, and compound K included in it have a strong inhibitory effect on AD.

CONCLUSION

The fermented saponin extracts of AGSL show more inhibition effects on AD and may be promising therapeutic drugs or nutrients for AD.

Plants and endophytes interaction: a "secret wedlock" for sustainable biosynthesis of pharmaceutically important secondary metabolites

Many plants possess immense pharmacological properties because of the presence of various therapeutic bioactive secondary metabolites that are of great importance in many pharmaceutical industries. Therefore, to strike a balance between meeting industry demands and conserving natural habitats, medicinal plants are being cultivated on a large scale. However, to enhance the yield and simultaneously manage the various pest infestations, agrochemicals are being routinely used that have a detrimental impact on the whole ecosystem, ranging from biodiversity loss to water pollution, soil degradation, nutrient imbalance and enormous health hazards to both consumers and agricultural workers. To address the challenges, biological eco-friendly alternatives are being looked upon with high hopes where endophytes pitch in as key players due to their tight association with the host plants. The intricate interplay between plants and endophytic microorganisms has emerged as a captivating subject of scientific investigation, with profound implications for the sustainable biosynthesis of pharmaceutically important secondary metabolites. This review delves into the hidden world of the "secret wedlock" between plants and endophytes, elucidating their multifaceted interactions that underpin the synthesis of bioactive compounds with medicinal significance in their plant hosts. Here, we briefly review endophytic diversity association with medicinal plants and highlight the potential role of core endomicrobiome. We also propose that successful implementation of in situ microbiome manipulation through high-end techniques can pave the way towards a more sustainable and pharmaceutically enriched future.

Tomato root-associated Sphingobium harbors genes for catabolizing toxic steroidal glycoalkaloids

IMPORTANCE

Saponins are a group of plant specialized metabolites with various bioactive properties, both for human health and soil microorganisms. Our previous works demonstrated that Sphingobium is enriched in both soils treated with a steroid-type saponin, such as tomatine, and in the tomato rhizosphere. Despite the importance of saponins in plant-microbe interactions in the rhizosphere, the genes involved in the catabolism of saponins and their aglycones (sapogenins) remain largely unknown. Here we identified several enzymes that catalyzed the degradation of steroid-type saponins in a Sphingobium isolate from tomato roots, RC1. A comparative genomic analysis of Sphingobium revealed the limited distribution of genes for saponin degradation in our saponin-degrading isolates and several other isolates, suggesting the possible involvement of the saponin degradation pathway in the root colonization of Sphingobium spp. The genes that participate in the catabolism of sapogenins could be applied to the development of new industrially valuable sapogenin molecules.

Panax notoginseng-microbiota interactions: From plant cultivation to medicinal application

BACKGROUND

Microbiomes and their host plants are closely linked with each other; for example, the microbiome affects plant growth, fitness, nutrient uptake, stress tolerance and pathogen resistance, whereas the host plant supports the photosynthetically carbon-rich nutrition of the microbiome. The importance of the microbiome in plant‒soil ecosystems is unquestioned and has expanded to influence the medicinal application of some herbal plants via the gut microbiota.

PURPOSE

Herbal plant-microbiome interactions may provide novel knowledge to enhance the robustness of herbal plant crop performance and medicinal applications, which requires a systematic review and preceding discussion.

STUDY DESIGN AND METHODS

The interactions between Panax notoginseng and microorganisms (from soil to host) were reviewed from the literature. The terms "Panax notoginseng" and "microbiota" were used in combination with the keywords "microbiota/microbes", "bacteria/bacterium" or "fungi/fungus" or "endophyte", as well as our targeted bioactive phytochemicals, including saponins and ginsenosides.

RESULT

Our study focuses on the famous medicinal herb Panax notoginseng F. H. Chen and proposes that the microbiota is a crucial participant not only in the cultivation of this herbal plant but also in its medicinal application. We also summarize and discuss how these plant‒microbe co-associations shape the assembly of plant-related microbiomes and produce bioactive phytochemicals, as well as influence beneficial herbal traits, such as herbal plant health and pharmacology. In addition, we also highlight future directions.

CONCLUSION

The rhizosphere and endophytic microbiome of Panax notoginseng are indirectly or directly involved in plant health, biomass production, and the synthesis/biotransformation of plant secondary metabolites. Harnessing the microbiome to improve the quality of traditional Chinese medicine and improve the value of medicinal plants for human health is highly promising.

Optimization of Fermentation Conditions and Product Identification of a Saponin-Producing Endophytic Fungus

BACKGROUND

Some fungal endophytes isolated from P. ginseng may present a new method of obtaining saponins. This experiment aimed to optimize the total saponin yield produced through in vitro fermentation by an endophytic fungus and analyze its saponin species in the fermented extract.

METHODS

Fermentation protocols were optimized with a uniform design and verified through regression analysis to maximize the total saponin yield. The saponin types under optimal fermentation conditions were then identified and analyzed using Liquid Chromatography-Mass Spectrometry.

RESULTS

The Trametes versicolor strain NSJ105 (gene accession number: OR144428) isolated from wild ginseng could produce total saponins. The total saponin yield could be increased more than two-fold through the optimization of fermentation conditions. The concentration of the total saponins achieved by the verified protocol 105-DP was close to the predicted value. The fermentation conditions of the 105-DP protocol were as follows: potato concentration 97.3 mg/mL, glucose concentration 20.6 mg/mL, inoculum volume 2.1%, fermentation broth pH 2.1, fermentation temperature 29.2 °C, and fermentation time 6 d. It was detected and analyzed that the fermented extract of 105-DP contained the ginsenosides Rf and Rb3.

CONCLUSION

The endophytic fungus Trametes versicolor strain NSJ105 has potential application value in saponin production.

Phytotherapy of abnormality of fear memory: A narrative review of mechanisms

It is generally believed that in post-traumatic stress disorder (PTSD), the high expression of fear memory is mainly determined by amygdala hyperactivity and hippocampus hypoactivity. In this review, we firstly updated the mechanisms of fear memory, and then searched the experimental evidence of phytotherapy for fear memory in the past five years. Based on the summary of those experimental studies, we further discussed the future research strategies of plant medicines, including the study of the mechanism of specific brain regions, the optimal time for the prevention and treatment of fear memory-related diseases such as PTSD, and the development of new drugs with active components of plant medicines. Accordingly, plant medicines play a clear role in improving fear memory abnormalities and have the drug development potential in the treatment of fear-related disorders.

Genetic diversity, plant growth promotion potential, and antimicrobial activity of culturable endophytic actinobacteria isolated from Aconitum carmichaelii Debeaux

AIM

This study evaluated the phylogenetic diversity, plant growth promotion capacity, antifungal activity, and biocontrol potential of culturable actinobacterial endophytes isolated from the medicinal plant Aconitum carmichaelii Debeaux.

METHODS AND RESULTS

Isolation of actinobacteria from healthy A. carmichaelii plants was carried out on six different media. Full-length 16S rRNA gene was amplified by PCR from the genomic DNA of each strain. Indole-3-acetic acid and siderophore production were quantitatively assessed by the Salkowski and Chrome Azurol S methods, respectively. Rice seeds germination and seedling growth were employed to evaluate plant growth promotion capacities of candidate strains. Dual-culture assay and pot experiments were performed to investigate the antifungal and biocontrol potential of isolates. We obtained 129 actinobacterial isolates from A. carmichaelii, and they belonged to 49 species in 7 genera. These strains exhibited diverse plant growth promotion ability, among which one strain significantly enhanced rice seeds germination, while 31 strains significantly facilitated rice seedling growth. SWUST-123 showed strong antifungal activity against four pathogens in vitro and was most compatible with Qingchuan cultivar. SWUST-123 reduced around 40% of southern blight disease occurrence compared to blank control treatment. .

CONCLUSION

Aconitum carmichaelii harbored genetically diverse actinobacterial endophytes exhibiting diverse plant growth promotion and antifungal potential, some of which can be served as good candidates for biofertilizers and biocontrol agents.

Compound K Production: Achievements and Perspectives

Compound K (CK) is one of the major metabolites found in mammalian blood and organs following oral administration of Panax plants. CK, also known as minor ginsenoside, can be absorbed in the systemic circulation. It has garnered significant attention in healthcare and medical products due to its pharmacological activities, such as antioxidation, anticancer, antiproliferation, antidiabetics, neuroprotection, and anti-atherogenic activities. However, CK is not found in natural ginseng plants but in traditional chemical synthesis, which uses toxic solvents and leads to environmental pollution during the harvest process. Moreover, enzymatic reactions are impractical for industrial CK production due to low yield and high costs. Although CK could be generated from major ginsenosides, most ginsenosides, including protopanaxatriol-oleanane and ocotillol-type, are not converted into CK by catalyzing β-glucosidase. Therefore, microbial cell systems have been used as a promising solution, providing a safe and efficient approach to CK production. This review provides a summary of various approaches for the production of CK, including chemical and enzymatic reactions, biotransformation by the human intestinal bacteria and endophytes as well as engineered microbes. Moreover, the approaches for CK production have been discussed to improve the productivity of target compounds.

Diversity and correlation analysis of endophytes and metabolites of Panax quinquefolius L. in various tissues

BACKGROUND

Panax quinquefolius L. (American ginseng) is widely used in medicine due to its wealth of diverse pharmacological effects. Endophytes colonize within P. quinquefolius in multiple tissue types. However, the relationship between endophytes and the production of their active ingredients in different parts of the plant is not clear.

RESULTS

In this study, the relationship of endophytic diversity and the metabolites produced in different plant tissues of P. quinquefolius were analyzed using metagenomic and metabolomic approaches. The results showed relatively similar endophyte composition in roots and fibrils, but obvious differences between endophyte populations in stems and leaves. Species abundance analysis showed that at the phylum level, the dominant bacterial phylum was Cyanobacteria for roots, fibrils, stems and leaves, Ascomycota forroots and fibrils roots, and Basidiomycota for stems and leaves. LC-MS/MS technology was used to quantitatively analyze the metabolites in different tissues of P. quinquefolius. A total of 398 metabolites and 294 differential metaboliteswere identified, mainly organic acids, sugars, amino acids, polyphenols, and saponins. Most of the differential metabolites were enriched in metabolic pathways such as phenylpropane biosynthesis, flavonoid biosynthesis, citric acid cycle, and amino acid biosynthesis. Correlation analysis showed a positive and negative correlation between the endophytes and the differential metabolites. Conexibacter significantly enriched in root and fibril was significantly positively correlated with saponin differential metabolites, while cyberlindnera significantly enriched in stem and leaf was significantly negatively correlated with differential metabolites (p < 0.05).

CONCLUSION

The endophytic communities diversity were relatively similar in the roots and fibrils of P. quinquefolius, while there were greater differences between the stems and leaves. There was significant difference in metabolite content between different tissues of P. quinquefolius. Correlation analysis methods demonstrated a correlation between endophytes and differential metabolism.

Culturable endophytic fungi community structure isolated from Codonopsis pilosula roots and effect of season and geographic location on their structures

BACKGROUND

Rhizosphere soil physicochemical, endophytic fungi have an important role in plant growth. A large number of endophytic fungi play an indispensable role in promoting plant growth and development, and they can provide protection for host plants by producing a variety of secondary metabolites to resist and inhibit plant pathogens. Due to the terrain of Gansu province is north-south and longitudinal, different climatic conditions, altitude, terrain and growth environment will affect the growth of Codonopsis pilosula, and the changes in these environmental factors directly affect the quality and yield of C. pilosula in different production areas. However, In C. pilosula, the connection between soil nutrients, spatiotemporal variation and the community structure of endophytic fungi isolated from C. pilosula roots has not been well studied.

RESULTS

Seven hundred six strains of endophytic fungi were obtained using tissue isolation and the hyphaend-purification method from C. pilosula roots that picked at all seasons and six districts (Huichuan, HC; Longxi, LX; Zhangxian, ZX; Minxian, MX; Weiyuan, WY; and Lintao, LT) in Gansu Province, China. Fusarium sp. (205 strains, 29.04%), Aspergillus sp. (196 strains, 27.76%), Alternaria sp. (73 strains, 10.34%), Penicillium sp. (58 strains, 8.22%) and Plectosphaerella sp. (56 strains, 7.93%) were the dominant genus. The species composition differed from temporal and spatial distribution (Autumn and Winter were higher than Spring and Summer, MX and LT had the highest similarity, HC and LT had the lowest). physical and chemical of soil like Electroconductibility (EC), Total nitrogen (TN), Catalase (CAT), Urease (URE) and Sucrase (SUC) had significant effects on agronomic traits of C. pilosula (P < 0.05). AK (Spring and Summer), TN (Autumn) and altitude (Winter) are the main driving factors for the change of endophytic fungal community. Moreover, geographic location (such as altitude, latitude and longitude) also has effects on the diversity of endophytic fungi.

CONCLUSIONS

These results suggested that soil nutrients and enzyme, seasonal variation and geographical locations have an impact on shaping the community structure of culturable endophytic fungi in the roots of C. pilosula and its root traits. This suggests that climatic conditions may play a driving role in the growth and development of C. pilosula.

Ginsenosides and Biotic Stress Responses of Ginseng

Ginsenosides are saponins that possess a sugar moiety attached to a hydrophobic aglycone triterpenoid. They have been widely studied for their various medicinal benefits, such as their neuroprotective and anti-cancer activities, but their role in the biology of ginseng plants has been much less widely documented. In the wild, ginsengs are slow-growing perennials with roots that can survive for approximately 30 years; thus, they need to defend themselves against many potential biotic stresses over many decades. Biotic stresses would be a major natural selection pressure and may at least partially explain why ginseng roots expend considerable resources in order to accumulate relatively large amounts of ginsenosides. Ginsenosides may provide ginseng with antimicrobial activity against pathogens, antifeedant activity against insects and other herbivores, and allelopathic activity against other plants. In addition, the interaction of ginseng with pathogenic and non-pathogenic microorganisms and their elicitors may trigger increases in different root ginsenosides and associated gene expression, although some pathogens may be able to suppress this behavior. While not covered in this review, ginsenosides also have roles in ginseng development and abiotic stress tolerance. This review shows that there is considerable evidence supporting ginsenosides as important elements of ginseng's defense against a variety of biotic stresses.

Root endophytic bacterial community composition of Aconitum carmichaelii debx. from three main producing areas in China

Aconitum carmichaelii Debx. is famous for the bioactive aconitum alkaloids as traditional Chinese medicine. Endophytic bacteria play vital roles in plant growth, health, and the production of secondary metabolites such as alkaloids. In this study, we employed 16 S rRNA amplicon high-throughput sequencing to determine the root endophytic bacterial community of A. carmichaelii Debx. collected from three main producing areas including the geo-authentic area in China, high performance liquid chromatography to measure the contents of six bioactive alkaloids and correlation analysis to explore the relationship among environmental factors, alkaloids contents, and endophytic bacterial community. The results indicated that the root core microbiota of A. carmichaelii Debx. was dominated by Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria. Root endophytic bacterial community in the geo-authentic area was distinct from the other two regions. Soil nitrogen contents, organic matter, and temperature were the main factors contributing to the endophytic bacterial community structure. Significant correlation was found between alkaloids contents and some bacterial genera. Particularly, the abundance of Lactobacillus was positively correlated with the contents of benzoyl-mesaconitine and benzoyl-aconine. This study provided the first insight into the root endophytic bacterial community composition of A. carmichaelii Debx., and can direct further isolation of functional bacterial strains.

Microorganisms for Ginsenosides Biosynthesis: Recent Progress, Challenges, and Perspectives

Ginsenosides are major bioactive compounds present in the Panax species. Ginsenosides exhibit various pharmaceutical properties, including anticancer, anti-inflammatory, antimetastatic, hypertension, and neurodegenerative disorder activities. Although several commercial products have been presented on the market, most of the current chemical processes have an unfriendly environment and a high cost of downstream processing. Compared to plant extraction, microbial production exhibits high efficiency, high selectivity, and saves time for the manufacturing of industrial products. To reach the full potential of the pharmaceutical resource of ginsenoside, a suitable microorganism has been developed as a novel approach. In this review, cell biological mechanisms in anticancer activities and the present state of research on the production of ginsenosides are summarized. Microbial hosts, including native endophytes and engineered microbes, have been used as novel and promising approaches. Furthermore, the present challenges and perspectives of using microbial hosts to produce ginsenosides have been discussed.

Specific Enriched Acinetobacter in Camellia Weevil Gut Facilitate the Degradation of Tea Saponin: Inferred from Bacterial Genomic and Transcriptomic Analyses

Beneficial gut bacteria can enhance herbivorous arthropod adaptation to plant secondary compounds (PSMs), and specialist herbivores provide excellent examples of this. Tea saponin (TS) of Camellia oleifera is triterpenoids toxic to seed-feeding weevil pest, Curculio chinensis (CW). Previous studies disclosed that Acinetobacter, which was specific enriched in the CW's gut, was involved in helping CW evade TS toxicity of C. oleifera. However, it is still not clear whether Acinetobacter is associated with other anti-insect compounds, and the molecular mechanism of Acinetobacter degradation of TS has not been clarified. To address these questions, we explored the relationship between host plant toxin content and Acinetobacter of CW gut bacteria. Results demonstrated that TS content significantly affected the CW gut microbiome structure and enriched bacteria functional for TS degradation. We further isolated Acinetobacter strain and conducted its genome and transcriptome analyses for bacterial characterization and investigation on its role in TS degradation. Biological tests were carried out to verify the ability of the functional bacterium within CW larvae to detoxify TS. Our results showed that TS-degrading bacteria strain (Acinetobacter sp. AS23) genome contains 47 genes relating to triterpenoids degradation. The AS23 strain improved the survival rate of CW larvae, and the steroid degradation pathway could be the key one for AS23 to degrade TS. This study provides the direct evidence that gut bacteria mediate adaptation of herbivorous insects to phytochemical resistance. IMPORTANCE Microorganism is directly exposed to the plant toxin environment and play a crucial third party in herbivores gut. Although previous studies have proved the existence of gut bacteria that help CWs degrade TS, the specific core flora and its function have not been explored. In this study, we investigated the correlation between the larva gut microbiome and plant secondary metabolites. Acinetobacter genus was the target flora related to TS degradation. There were many terpenoids genes in Acinetobacter sp. AS23 genome. Results of transcriptome analysis and biological tests suggested that steroid degradation pathway be the key pathway of AS23 to degrade TS. This study not only provides direct evidence that gut microbes mediate the rapid adaptation of herbivorous insects to phytochemical resistance, but also provides a theoretical basis for further research on the molecular mechanism of intestinal bacteria cooperating with pests to adapt to plant toxins.

Core rhizosphere microbiome of Panax notoginseng and its associations with belowground biomass and saponin contents

The core rhizosphere microbiome is critical for plant fitness. However, its contribution to the belowground biomass and saponin contents of Panax notoginseng remains unclear. High-throughput sequencing of amplicon and metagenome was performed to obtain the microbiome profiles and functional traits in P. notoginseng rhizosphere across a large spatial scale. We obtained 639 bacterial and 310 fungal core OTUs, which were mainly affected by soil pH and organic matter (OM). The core taxa were grouped into four ecological clusters (i.e. high pH, low pH, high OM and low OM) for sharing similar habitat preferences. Furthermore, structural equation modelling (SEM) and correlation analyses revealed that the diversity and composition of core microbiomes, as well as the metagenome-derived microbial functions, were related to belowground biomass and saponin contents. Key microbial genera related to the two plant indicators were also identified. In short, this study explored the main driving environmental factors of core microbiomes in the P. notoginseng rhizosphere and revealed that the core microbiomes and microbial functions potentially contributed to the belowground biomass and saponin contents of the plant. This work may enhance our understanding of interactions between microbes and perennial plants and improve our ability to manage root microbiota for the sustainable production of herbal medicine.

Wild Panax plants adapt to their thermal environment by harboring abundant beneficial seed endophytic bacteria

The seed microbiome of crop wild relatives is a potential reservoir of beneficial traits that potentially improve their host plant resilience to fluctuating environments and pathogenic threats. Herein, we studied the seed microbiome of three species of the medicinal genus Panax (P. vietnamensis, P. japonicas, and P. stipuleanatus) collected from seven locations in Southwest China. We used qPCR and metabarcoding high-throughput sequencing to target both endophytic bacteria and fungi. Seed bacterial absolute abundance (1.1 × 109∼1.0 × 107 gene copy numbers per gram seed) was substantially higher than that of fungi (7.6 × 105∼3.7 × 102). Host plant genotype was the main driver of seed microbiome composition for both bacteria and fungi. Panax growing hypothermal environments significantly shaped their seed endophytic bacterial but not fungal microbiota. The three Panax species’ seeds harbored unique microbes [averaged ∼150 amplicon sequence variants (ASVs)], sharing only 12 bacterial ASVs (half affiliated to Halomonas) and four fungal ASVs. Network analysis showed that the Panax seed endophytic bacteria tend to form inter-weaved functional modules that are majorly connected by core members from the genus Halomonas, Pseudomonas, and Pantoea. These genera have been associated with nutrient cycling, plant, disease suppression, and tolerance to environmental fluctuation. Together, these novel insights may shade light on the ecological strategies of wild Panax plants adaptation to their thermal environment by possessing abundant beneficial seed endophytic bacteria.

Evidence for saponin diversity-mycobiome links and conservatism of plant-fungi interaction patterns across Holarctic disjunct Panax species

Although interplays between plant and coevolved microorganisms are believed to drive landscape formation and ecosystem services, the relationships between the mycobiome and phytochemical evolution and the evolutionary characteristics of plant-mycobiome interaction patterns are still unclear. The present study explored fungal communities from 405 multiniche samples of three Holarctic disjunct Panax species. The overall mycobiomes showed compartment-dominated variations and dynamic universality. Neutral models were fitted for each compartment at the Panax genus (I) and species (II) levels to infer the community assembly mechanism and identify fungal subgroups potentially representing different plant-fungi interaction results, i.e., the potentially selected, opposed, and neutral taxa. Selection contributed more to the endosphere than to external compartments. The nonneutral taxa showed significant phylogenetic clustering. In Model I, the opposed subgroups could best reflect Panax saponin diversities (r = 0.69), and genera with highly positive correlations to specific saponins were identified using machine learning. Although mycobiomes in the three species differed significantly, subgroups in Model II were phylogenetically clustered based on potential interaction type rather than plant species, indicating potentially conservative plant-fungi interactions. In summary, the finding of strong links between invaders and saponin diversity can help explore the underlying mechanisms of saponin biosynthesis evolution from microbial insights, which is important to understanding the formation of the current landscape. The potential conservatism of plant-fungi interaction patterns suggests that the related genetic modules and selection pressures were convergent across Panax species, advancing our understanding of plant interplay with biotic environments.

The Endosphere Microbiome of Ginseng

The endosphere of ginseng contains a variety of fungal, bacterial, archaeal and viral endophytes. Bacterial endophytes are primarily members of the Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes, and fungal endophytes are primarily members of the Ascomycota, Zygomycota and Basidiomycota. Although archaea and viruses have been detected in symptomless ginseng plants, little is known about them. Many but not all studies have shown roots having the highest abundance and diversity of bacterial and fungal endophytes, with some endophytes showing specificity to above or belowground tissues. Abundance often increases with root age, although diversity can decrease, possibly related to increases in potential latent fungal pathogen infections. The descriptions of many endophytes that can metabolize ginsenosides indicate an adaptation of the microbes to the unique combination of secondary metabolites found in ginseng tissues. Most research on the benefits provided by bacterial and fungal endophytes has concentrated on improved plant nutrition, growth promotion and increased disease resistance, but little on their ability to increase abiotic stress resistance. Some other areas where more research is needed is field trials with endophyte-treated plants grown in various environments, genomic/metagenomic analysis of endophytes, and the effects of endophytes on induced disease resistance and abiotic stress tolerance.

Contents of lobetyolin, syringin, and atractylolide III in Codonopsis pilosula are related to dynamic changes of endophytes under drought stress

Background

Codonopsis pilosula, an important medicinal plant, can accumulate certain metabolites under moderate drought stress. Endophytes are involved in the metabolite accumulations within medicinal plants. It is still unknown that the endophytes of C. pilosula are associated with the accumulations of metabolites. This study aims to investigate the promoting effect of endophytes on the accumulations of active substances in C. pilosula under drought stress.

Methods

High–performance liquid chromatography and high–throughput sequencing technology were performed to investigate changes in the contents of secondary metabolite and endophyte abundances of C. pilosula under drought stress, respectively. Spearman’s correlation analysis was further conducted to identify the endophytic biomarkers related to accumulations of pharmacodynamic compounds. Culture-dependent experiments were performed to confirm the functions of endophytes in metabolite accumulations.

Results

The distribution of pharmacological components and diversity and composition of endophytes showed tissue specificity within C. pilosula. The contents of lobetyolin, syringin, and atractylolide III in C. pilosula under drought stress were increased by 8.47%‒86.47%, 28.78%‒230.98%, and 32.17%‒177.86%, respectively, in comparison with those in untreated groups. The Chao 1 and Shannon indices in different parts of drought–stressed C. pilosula increased compared with those in untreated parts. The composition of endophytic communities in drought treatment parts of C. pilosula was different from that in control parts. A total of 226 microbial taxa were identified as potential biomarkers, of which the abundances of 42 taxa were significantly and positively correlated to the pharmacodynamic contents. Culture-dependent experiments confirmed that the contents of lobetyolin and atractylolide III were increased by the application of Epicoccum thailandicum, Filobasidium magnum, and Paraphoma rhaphiolepidis at the rates of 11.12%‒46.02%, and that the content of syringin was increased by Pseudomonas nitroreducens at the rates of 118.61%‒119.36%.

Conclusions

Certain endophytes participated in the accumulations of bioactive metabolites, which provided a scientific evidence for the development and application of microorganisms to improve the quality of traditional Chinese medicine.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13020-021-00533-z.

Triterpenoid and Steroidal Saponins Differentially Influence Soil Bacterial Genera

Plant specialized metabolites (PSMs) are secreted into the rhizosphere, i.e., the soil zone surrounding the roots of plants. They are often involved in root-associated microbiome assembly, but the association between PSMs and microbiota is not well characterized. Saponins are a group of PSMs widely distributed in angiosperms. In this study, we compared the bacterial communities in field soils treated with the pure compounds of four different saponins. All saponin treatments decreased bacterial α-diversity and caused significant differences in β-diversity when compared with the control. The bacterial taxa depleted by saponin treatments were higher than the ones enriched; two families, Burkholderiaceae and Methylophilaceae, were enriched, while eighteen families were depleted with all saponin treatments. Sphingomonadaceae, which is abundant in the rhizosphere of saponin-producing plants (tomato and soybean), was enriched in soil treated with α-solanine, dioscin, and soyasaponins. α-Solanine and dioscin had a steroid-type aglycone that was found to specifically enrich Geobacteraceae, Lachnospiraceae, and Moraxellaceae, while soyasaponins and glycyrrhizin with an oleanane-type aglycone did not specifically enrich any of the bacterial families. At the bacterial genus level, the steroidal-type and oleanane-type saponins differentially influenced the soil bacterial taxa. Together, these results indicate that there is a relationship between the identities of saponins and their effects on soil bacterial communities.