Strategic intercropping with mulberry (Morus alba L.) predictably modulates rhizosphere microbiome assembly and enriches pathways for secondary metabolite production

Intercropping is a key strategy for sustainable agriculture, but its effects on the rhizosphere microbiome remain poorly understood. Here, we investigated how intercropping mulberry (Morus alba L.) with functionally distinct partners-a nitrogen-fixing legume (Pisum sativum), a saprotrophic fungus (Morchella esculenta), and a medicinal plant (Polygonatum sibiricum)-shapes its rhizosphere bacterial community. Compared to monoculture, all intercropping systems significantly increased bacterial diversity and established unique community structures and functional signatures. Legume intercropping specifically enriched nitrogen-cycling bacteria like Bradyrhizobium and enhanced nitrogen metabolism pathways, whereas fungal intercropping fostered anaerobic decomposers. Crucially, all systems enriched pathways for secondary metabolite biosynthesis, suggesting a potential to enhance mulberry's economic value. Our findings establish that strategic partner selection is a powerful microbiome design tool, enabling predictable modulation of rhizosphere function for sustainable mulberry cultivation.