Intercropping Amomum villosum enhances soil stratification, nutrient complementarity, and microbial communities in rubber plantations

Intercropping is widely promoted to sustain soil function, yet evidence for its application in rubber-based agroforestry, particularly with the shade-tolerant herb <i>Amomum villosum</i>, is limited. We evaluated whether <i>A. villosum</i> 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, <i>A. villosum</i> 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-<i>A. villosum</i> systems and support their wider deployment in rubber plantations.