Herbaceous intercropping reshapes soil microbial communities and induces transcriptomic responses in Morchella

Morchella cultivation faces challenges from continuous cropping obstacles, which are often linked to soil degradation and microbial community shifts. Intercropping has emerged as a potential strategy to mitigate these constraints, yet the ecological mechanisms underlying herbaceous companion plant effects on Morchella remain poorly understood. This study investigated how intercropping with two functionally distinct herbaceous species—Poa pratensis and Vicia sativa—affects Morchella growth, soil microbial assembly, and Morchella transcriptional responses. Three cultivation treatments were established: Morchella monoculture (CK), intercropping with P. pratensis (B), and intercropping with V. sativa (P). Soil physicochemical properties, microbial community composition (16 S rRNA and ITS amplicon sequencing), and Morchella fruiting body transcriptomes (RNA-seq) were analyzed. Intercropping reduced Morchella yield by 23.7% (P treatment) to 36.9% (B treatment) compared with monoculture, yet significantly increased soil available potassium and promoted companion plant growth. Microbial community analysis revealed that intercropping decreased the relative abundance of Ascomycota, particularly Morchella itself (reduced to approximately one-quarter of control levels), while increasing fungal α-diversity and enriching taxa such as Mortierella and Rhizopus. Bacterial communities also shifted, with Pseudomonas abundance increasing 3.3-fold (B) and 3.8-fold (P). Transcriptomic analysis identified 572 upregulated DEGs in the B treatment and 1,090 in the P treatment. Commonly upregulated DEGs were enriched in GO terms related to monocarboxylic acid metabolism, iron ion transport, and carbohydrate binding, and in KEGG pathways including fructose and mannose metabolism and nitrogen metabolism. Treatment-specific responses included enrichment of oxidation-reduction processes in B and symbiont attachment and biofilm formation in P. Continuously upregulated DEGs across the CK-B-P gradient were associated with chromatin assembly and metabolic pathway activation. Herbaceous intercropping reconfigures the Morchella cultivation system by altering soil nutrient availability, reshaping microbial community structure, and inducing adaptive transcriptional responses in the fungus. Although intercropping enhanced soil ecological conditions and microbial functional diversity, it did not translate into yield improvement, suggesting ecological trade-offs between resource competition and environmental optimization. These findings provide a foundation for understanding host–microbe–plant interactions in fungal cultivation systems and highlight the need to balance ecological benefits with productivity outcomes. Morchella–herbaceous intercropping reduced Morchella yield but increased soil organic matter and available potassium. Intercropping promoted the growth of Poa pratensis and Vicia sativa. Intercropping reshaped the soil microbiota by reducing Morchella abundance and increasing Pseudomonas abundance and fungal alpha diversity. Morchella enhanced competitiveness by upregulating monocarboxylic acid, iron transport, and carbohydrate metabolism.