Volume 117, Issue 6, November 2025, 111129Author links open overlay panel, , , , , , , , Highlights•

Mulberry intercropping enhances rhizosphere diversity.

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Legume partner enriches Bradyrhizobium and N-cycling.

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Fungal intercropping selects anaerobic decomposers.

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Predictive biomarkers enable microbiome-informed design.

Abstract

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.

Keywords

Mulberry cultivation

Intercropping systems

Rhizosphere microbiome

Bacterial community structure

Biomarker identification

Data availabilityThe datasets generated for this study, including key files from the analysis pipeline (ASV representative sequences ASV_reps.fasta, ASV_reps.qza; ASV abundance table ASV_table.xls; and the BIOM file asv_taxon.biom), can be found in the Zenodo repository and are publicly available at DOI: https://doi.org/10.5281/zenodo.15700142.

© 2025 The Authors. Published by Elsevier Inc.