The interactions between plants and rhizosphere microbes mediated by plant root exudates are increasingly being investigated. The root-derived metabolites of medicinal plants are relatively diverse and have unique characteristics. However, whether medicinal plants influence their rhizosphere microbial community remains unknown. How medicinal plant species drive rhizosphere microbial community changes should be clarified. In this study involving high-throughput sequencing of rhizosphere microbes and an analysis of root exudates using a gas chromatograph coupled with a time-of-flight mass spectrometer, we revealed that the root exudate metabolites and microorganisms differed among the rhizosphere soils of five medicinal plants. Moreover, the results of a correlation analysis indicated that bacterial and fungal profiles in the rhizosphere soils of the five medicinal plants were extremely significantly or significantly affected by 10 root-associated metabolites. Furthermore, among the 10 root exudate metabolites, two (carvone and zymosterol) had opposite effects on rhizosphere bacteria and fungi. Our study findings suggest that plant-derived exudates modulate changes to rhizosphere microbial communities.

Amomum villosum, which is an important perennial medicinal plant, easily suffers from continuous cropping obstacles in the plantation. The aim of this study is to find an effective method to solve the problem of A. villosum continuous cropping. In this study, we analyzed four fields in which A. villosum was continuously cropped and a fallow field to reveal the effects of continuous cropping on the rhizosphere soil physicochemical properties, enzyme activities, and bacterial and fungal communities. Most of the soil nutrient contents gradually increased as the number of years of continuous cropping increased, whereas the soil pH decreased slightly. The soil urease and acid phosphatase activities tended to increase as the length of the continuous cropping period increased, which may have accelerated the conversion of soil substances. Furthermore, the alpha diversity of the bacterial and fungal communities decreased as the duration of the continuous cropping period increased. Additionally, the redundancy analysis revealed that bacterial and fungal community structures at the phylum level were the most correlated with pH value and catalase activity, respectively. This study may be useful for promoting the continuous cropping and sustainable development of A. villosum.

Coffee is one of the most valuable agricultural commodities worldwide, second only to oil in terms of international trade. Coffea arabica L. is a widely cultivated and economically important crop that is responsible for about 90% of the global production of coffee. In this study, we selected five C. arabica cultivation sites at different altitudes to clarify the effects of altitude on rhizospheric soil physical–chemical characteristics and microbial communities. The samples collected at low altitudes were more nutrient-deficient and acidic than the soil samples collected at medium–high altitudes. The Proteobacteria-to-Acidobacteria ratio increased from lower altitudes to medium–high altitudes. Additionally, although Ascomycota was the dominant fungal phylum, it was unaffected by the altitude. Furthermore, the alpha richness and diversity of the bacterial and fungal communities were higher at medium–high altitudes than at low altitudes. Moreover, the redundancy analysis indicated that microbial phyla were closely associated with pH. These findings suggest that C. arabica should be cultivated at medium–high altitudes, which is conducive to sustainable management and the production of high-quality C. arabica beans.

The forest–medicinal plant management system has benefited the commercial production of Amomum villosum. However, little is known about the influence of different forestlands on the cultivation of A. villosum. The present study investigated the potential differences in the A. villosum yield and quality parameters, rhizosphere soil properties, and rhizosphere soil microbiota between a rubber plantation (RP) and a natural secondary forest (NSF). No significant differences in yield or rhizosphere soil properties of A. villosum were observed between RP and NSF, although most of the A. villosum yield parameters, the rhizosphere soil physicochemical properties, and soil enzyme activities were higher in NSF than in RP. Furthermore, the 38 volatile components had significantly higher relative abundances in NSF than in RP. Furthermore, the alpha diversity indices for the microbiota communities in the A. villosum rhizosphere soil indicated that the richness of the bacterial and fungal communities was significantly higher in NSF than in RP. These findings suggest that NSF conditions may be more appropriate than RP conditions for growing A. villosum. The data generated in this study may be useful for increasing the production of high-quality A. villosum via the exploitation of natural environments.

This study investigates the interplay between volatile and non-volatile flavor metabolites and endophytic microbial communities during three developmental stages of Passiflora ligularis fruit juice. Using bioinformatics and metabolomics, we characterize microbial diversity and metabolic variations to understand flavor development. A total of 1490 bacterial and 1158 fungal operational taxonomic units (OTUs) were identified. Young fruits had higher microbial diversity, dominated by Proteobacteria and Firmicutes (bacteria) and Ascomycota and Basidiomycota (fungi). As the fruit matured, Proteobacteria increased while Firmicutes decreased, indicating that microbial succession is tied to development. Metabolomic profiling identified 87 volatile and 1002 non-volatile metabolites, with distinct chemical classes varying across stages. Saturated hydrocarbons and fatty alcohols were the main volatile metabolites, while organic acids and lipids among non-volatile metabolites showed stage-dependent changes, influencing flavor complexity. Correlation analysis showed microbial-flavor interactions: Proteobacteria negatively correlated with metabolites, while Firmicutes positively correlated with metabolites. Ascomycota positively correlated with volatile metabolites, whereas Basidiomycota showed an inverse relationship, highlighting their differential contributions to flavor biosynthesis. This study enhances understanding of microbial and metabolic factors shaping P. ligularis fruit flavor, highlighting the importance of microbial influence on fruit metabolomics. The findings suggest the potential for microbiome engineering to improve flavor quality, aiding postharvest management and industrial processing in the food and beverage industry.

Intercropping is widely promoted to sustain soil function, yet evidence for its application in rubber-based agroforestry, particularly with the shade-tolerant herb Amomum villosum , is limited. We evaluated whether A. villosum intercropping improves soil properties and reorganizes microbiomes across the vertical profile of mature rubber plantations. Soil samples were taken at 0–10, 10–20, and 20–30 cm depths in both intercropped and monoculture stands. Physical and chemical properties were quantified, and bacterial (16S rRNA V3–V4) and fungal (ITS2) communities were analyzed using high-throughput amplicon sequencing with depth-resolved data on diversity, composition, and functional inference (FAPROTAX, FUNGuild). Intercropping consistently improved soil structure and fertility, with the strongest effects at 0–10 cm. Total porosity (12%), organic matter (38.9%), alkali-hydrolyzable nitrogen (75.4%), and available phosphorus (131%) were markedly higher than in monoculture. Benefits extended to mid-depth with a 65.2% increase in alkali-hydrolyzable nitrogen. Microbial richness (bacteria and fungi) increased, and communities separated clearly by treatment and depth. Intercropped soils showed higher relative abundances of copiotrophic and particle-attached phyla (e.g., Proteobacteria, Planctomycetota), while Acidobacteriota and several Chloroflexi declined. Nitrospirota increased with depth. Fungal trophic structure shifted away from pathotrophs at 20–30 cm and toward symbiotrophs, particularly arbuscular mycorrhizal lineages, at subsurface layers. Functional predictions indicated greater potential for nitrogen transformations (e.g., nitrogen fixation, nitrification), greater C₁/hydrocarbon utilization, and a reduced bacterial plant-pathogen signal under intercropping. Collectively, A. villosum intercropping reorganizes the soil environment and microbiome in mutually reinforcing ways—improving physical structure, enlarging near-term nitrogen supply, and favoring beneficial fungal guilds. These depth-resolved effects help explain the agronomic appeal of rubber– A. villosum systems and support their wider deployment in rubber plantations.