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In this study, effects of continuous cropping on soil properties, enzyme activities, and relative abundance, community composition and diversity of fungal taxa were investigated. Rhizosphere soil from field continuously cropped for one-year, three-year and five-year by Coptis chinensis Franch. was collected and analyzed. Illumina high-throughput sequencing analysis showed that continuous cropping of C. chinensis resulted in a significant and continuous decline in the richness and diversity of soil fungal population. Ascomycota, Zygomycota, Basidiomycota, and Glomeromycota were the dominant phyla of fungi detected in rhizosphere soil. Fungal genera such as Phoma, Volutella, Pachycudonia, Heterodermia, Gibberella, Cladosporium, Trichocladium, and Sporothrix, were more dominant in continuously cropped samples for three-year and five-year compared to that for one-year. By contrast, genera, such as Zygosaccharomyces, Pseudotaeniolina, Hydnum, Umbelopsis, Humicola, Crustoderma, Psilocybe, Coralloidiomyces, Mortierella, Polyporus, Pyrenula, and Monographella showed higher relative abundance in one-year samples than that in three-year and five-year samples. Cluster analysis of the fungal communities from three samples of rhizosphere soil from C. chinensis field revealed that the fungal community composition, diversity, and structure were significantly affected by the continuous cropping. Continuous cropping of C. chinensis also led to significant declines in soil pH, urease, and catalase activities. Redundancy analysis showed that the soil pH had the most significant effect on soil fungal population under continuous cropping of C. chinensis.

Root rot disease poses a devastating threat to Coptis chinensis Franch , a medicinal plant prized for its bioactive alkaloids. To dissect its defense mechanisms, we conducted integrated transcriptomic and metabolomic analyses on resistant (R), early-stage infected (S-ES), and late-stage infected (S-LS) plants Our findings reveal a disease severity-dependent escalation in flavonoid metabolism. Key metabolites, such as kaempferol and quercetin derivatives, were significantly increased compared to R, paralleled by progressive upregulation of biosynthetic genes ( PAL , CHS , CHI , FLS ). Strikingly, salicylic acid (SA)-associated metabolites and pathway genes ( NPR1 , NPR3 / NPR4 ) showed no differential expression across groups, contrasting with typical SA-mediated defenses in other species. This study uncovers flavonoid biosynthesis as the primary defense strategy in C. chinensis during root rot progression, while SA signaling may not be the main defense mechanism. These results provide actionable targets for enhancing disease resistance in medicinal plants through metabolic engineering.

The medicinal plant Coptis chinensis is highly susceptible to root rot caused predominantly by Fusarium spp., threatening yield and medicinal quality. Biological control agents (BCAs) from the genus Bacillus are promising, yet their host mechanisms remain incompletely defined. We evaluated a four-strain Bacillus consortium as BCAs in field-grown C. chinensis and profiled host roots using transcriptomics and metabolomics. Pre-inoculation with the BCA mixture resulted in a modest, albeit statistically non-significant, reduction in disease index following Fusarium solani challenge. Multi-omics analyses showed that BCA treatment reprogrammed genes and metabolites associated with amino acid metabolism, accompanied by increased glutamine (Gln) accumulation. Supplementing culture medium with exogenous Gln inhibited F. solani growth in a concentration-dependent manner in vitro. Notably, F. solani or BCAs alone elicited modest regulation of canonical defense genes, whereas BCA pre-inoculation followed by F. solani robustly up-regulated defense modules across MAPK signaling, plant–pathogen interaction, and hormone signaling (JA, ET, SA), consistent with molecular immune priming. These results suggest that the BCA consortium induces resistance- and priming-related molecular markers in C. chinensis by modulating amino acid metabolism and host immunity. These findings provide a mechanistic basis for the potential application of BCAs in the sustainable management of C. chinensis root rot.

Background The sustained monoculture and irregular planting practices rendered the cultivated Coptis chinensis more prone to various diseases compared to its wild counterparts. Rewilding the rhizomicrobiome of cultivated plants has emerged as a promising strategy to promote plant growth, but ancestral microbiota suitable for C . chinensis remain largely uncharted. Results The amplicon data analyses revealed that habitat transition strongly influenced the rhizosphere microbial communities. The rhizomicrobiomes of wild C . chinensis encompassed a more diverse array of ecological groups and exhibited a greater functional diversity compared to their cultivated counterparts. A higher proportion of beneficial fungi was observed in the rhizosphere of wild C . chinensis , while the cultivated plants had a higher population of pathogenic fungi. Furthermore, a well-documented plant-growth-promoting rhizobacterium genus, Paraburkholderia , was found to play an essential role in the resistance of the wild C . chinensis to potential disease caused by Ilyonectria . Two strains of Paraburkholderia ( Paraburkholderia nemoris and Paraburkholderia phytofirmans ) were isolated, and in vitro experiments confirmed that these isolates possess various growth-promoting properties and antagonistic activities against known pathogens for C . chinensis root rot. Both of the Paraburkholderia isolates could markedly promote the plant immune response and enhance the overall health of the cultivated C . chinensis . Conclusions By a comprehensive comparison of the rhizosphere microbiome between wild and cultivated C . chinensis , the promising bacterial genus Paraburkholderia was identified as a beneficial microbe significantly promoting the growth of C . chinensis , providing pivotal insights for future endeavors aimed at engineering the rhizosphere microbiome of C . chinensis , as well as other medicinal herbs. 2yo9cdbZM8-eAP_KeBLbZB Video Abstract

Root rot reduces the yield and medical quality of C. chinensis (Cc). Previous studies of Coptis root rot focused on the identification of pathogens and the rhizosphere microbial community composition. The present study aimed to identify potential pathogenic and antagonistic microorganisms associated with root rot based on a high-throughput sequencing technique to prevent this disease. Healthy and diseased Cc in the endosphere and rhizosphere from the same field were collected to investigate the differences in microbiome composition and function. The results showed that the composition and function of microbes were different. The numbers of animal pathogens, soil saprotrophs, plant saprotrophs, and wood saprotrophs in the endosphere of diseased Cc were higher than those in the healthy endosphere and were dominated by Phaeosphaeriaceae, Cladorrhinum , Fusarium , Exophiala , and Melanommataceae. Fusarium , Volutella , Cladorrhinum , Cylindrocarpon , and Exophiala were significantly enriched in the endosphere of the diseased plants. Co-occurrence network analysis showed that Bacillus was negatively correlated with Fusarium , Volutella , and Cylindrocarpon , indicating that Bacillus may be antagonistic microorganisms. To verify the sequencing results, F. solani and F. avenaceum were isolated and verified as pathogens, and 14 Bacillus strains were isolated, which displayed an apparent suppression effect against the two pathogens on PDA medium and detached roots. The strategy of high-throughput sequencing has the potential for the comprehensive identification of pathogenic and antagonistic microorganisms for plant disease. These results provide research ideas and microbial resources for future studies on mitigating or preventing root rot damage to Cc.

Protoberberine alkaloids are a characteristic group of natural products in Coptis plants known for their notable pharmacological activities. However, the structural similarity and the substrate promiscuity of their biosynthetic enzymes have left the precise synthetic pathways remain unclarified, posing challenges to regulate product formation. In this study, we identified CcOMT8, a key enzyme responsible for C2‐methoxylation in the biosynthesis of epiberberine in C. chinensis, through methyl jasmonate elicitation analysis and comparative genomics‐based microsynteny analysis. Functional characterisation demonstrated that CcOMT8 specifically catalyses 2‐O‐methylation of (S)‐scoulerine, as verified by heterologous expression in both microbial and plant systems. Its lack of activity toward (S)‐cheilanthifoline further confirmed the specific route for epiberberine biosynthesis. Structural investigations of CcOMT8 and its complexes revealed key aspects of substrate recognition and a catalytic mechanism mediated by the His253‐Asp254‐Glu312 triad. Comparative structural analysis with 9‐O‐methyltransferases indicated that hydrophilic residues and reduced steric hindrance in the substrate binding pocket govern the regioselectivity of CcOMT8. Using focused rational iterative site‐specific mutagenesis (FRISM), we developed an optimised mutant, S109L/C250A/L300A, with 4.88‐fold enhanced catalytic efficiency. This study elucidates the biosynthetic pathway of epiberberine in Coptis, clarifies the molecular basis of enzyme‐directed metabolic flux, and provides efficient biocatalysts for the synthetic biosynthesis of protoberberine alkaloids.

Background The Plant-specific AP2/ERF gene family encodes proteins involved in various biological and physiological processes. Although the genome of Coptis chinensis Franch, a plant producing benzylisoquinoline alkaloids (BIAs), has been sequenced at the chromosome level, studies on the AP2/ERF gene family in C. chinensis are lacking. Thus, a genome-wide identification of AP2/ERF gene family in C. chinensis was conducted to explore its role in BIAs biosynthesis. Results A total of 96 CcAP2/ERF genes were identified and categorized into five subfamilies, including 43 ERFs, 32 DREBs, 17 AP2s, 3 RAVs, and 1 Soloist, based on their structural domains. These CcAP2/ERF genes were unevenly distributed across nine chromosomes. Analysis of gene duplication events identified 17 CcAP2/ERF gene pairs in the genome, with 7 involved in tandem duplication events and 10 involved in segmental duplicate events, indicating that both types of duplications contributed to the expansion of the AP2/ERF gene family. The Ka / Ks ratio analysis suggested that the CcAP2/ERF gene family underwent strong purifying selection. Two phytohormones, methyl jasmonate and abscisic acid, were identified as potential key inducers of BIAs biosynthesis due to the cis -acting element prediction. Analysis of the spatial transcriptomic data revealed that 28 differentially expressed AP2/ERF genes had the highest or relatively higher expression levels in the rhizome, 17 of which positively correlated with the tissue-specific accumulation of BIAs. Further real-time PCR verification and protein-protein interaction analysis indicated that DREB1B might be one of the central regulators in a highly complex BIAs biosynthesis network. Conclusion These findings provide significant insight into the function of AP2/ERF genes in C. chinensis , particularly in the regulatory network of BIAs biosynthesis in C. chinensis . This study also identifies candidate genes for metabolic engineering to increase BIAs content in C. chinensis .

Conventional antibiotic treatments for infected wounds often inadequately regulate the complex inflammatory cascade and fail to sufficiently promote tissue regeneration, leading to delayed healing and potential secondary tissue damage. Consequently, designing multifunctional biomaterials capable that can simultaneously exert antibacterial, anti-inflammatory, and pro-regenerative actions remains a critical challenge in wound management. In this study, we developed a soluble microneedle (MN) array loaded with nanovesicles derived from Coptis chinensis (CDVs), which serves as an integrated tri-functional platform to synergistically accelerate healing of infected wounds. The CDVs were effectively encapsulated within sodium alginate-based microneedles, with calcium ions introduced to reinforce structural crosslinking. Upon penetration into the wound bed, the MNs facilitated deep tissue delivery and sustained release of CDVs, which triggered a ROS burst inside bacteria, resulting in membrane disruption and bacterial eradication. Both in vitro and in vivo evaluations confirmed that the released CDVs promoted macrophage polarization toward the M2 phenotype and enhanced glucose uptake via the AMPK/mTOR pathway, thereby remodeling the inflammatory microenvironment and stimulating angiogenesis and tissue regeneration. Notably, in vivo wound healing assays demonstrated that the MN-mediated delivery of CDVs significantly enhanced repair outcomes compared to free vesicle treatment. This study highlights the rational integration of multifunctional plant-derived nanovesicles with a microneedle platform as a promising and translatable strategy for developing safe and effective therapeutics for infected wound healing. Graphical Abstract Graphical Abstract

Background The present study intends to optimize the processing technology for the wine-processing of Rhizoma Coptidis, using alkaloids as indicators. Method In the present study, the Box–Behnken design method was adopted to optimize the processing technology for Rhizoma Coptidis, using the alkaloid component quantities as the index. 100 g of Rhizoma Coptidis slices and 12.5 g of Rhizoma Coptidis wine were used. After full mixing, box-Behnken design method was used to optimize the processing time, processing temperature and processing time of coptis chinensis by taking alkaloid content as index. After mixing well, these components were fried in a container at 125 °C for 6 min and exhibited good parallelism. Results The content of alkaloids in coptis chinensis was the highest after roasting at 125 °C for 6 min. The characteristic components were berberine hydrochloride, and the relative content was about 15.96%. And showed good parallelism. The effective components of Rhizoma Coptidis were primarily alkaloids. Conclusion The optimized processing technology for Rhizoma Coptidis is good.

Background Biofilm formation is a key virulence factor in Staphylococcus epidermidis . Rhizoma Coptidis , the medicinal root of Coptis chinensis , has been traditionally used in Chinese medicine for its broad-spectrum antimicrobial properties. Results This study investigated the antibacterial and anti-biofilm effects of Rhizoma Coptidis extract against S. epidermidis ATCC 35984. UPLC-MS/MS analysis revealed the chemical composition of the extract. The extract significantly reduced ATPase and succinate dehydrogenase activities, decreased membrane potential, and disrupted cell wall and membrane integrity. These effects led to increased extracellular alkaline phosphatase activity and leakage of proteins and nucleic acids. Anti-biofilm activity was further confirmed using scanning electron microscopy and confocal laser scanning microscopy. Transcriptomic and metabolomic analyses identified significant changes in 366 genes and 286 metabolites after treatment. Integrated omics analysis suggested that the extract impaired cell membrane and wall integrity, disrupted amino acid and nucleic acid metabolism, inhibited the TCA cycle, reduced nitrate reductase activity, suppressed efflux systems, and hindered biofilm formation. Conclusions The study provides new insights into the antibacterial and anti-biofilm mechanisms of Rhizoma Coptidis extract against S. epidermidis , highlighting its potential as a therapeutic agent for combating biofilm-associated infections.