Crop diversification alters soil microbial community structure without changing microbial diversity

Crop diversification is broadly adopted to enhance agricultural sustainability, yet its global effects on soil microbial communities remain insufficiently understood. A systematic analysis of 102 peer-reviewed publications was conducted to quantify the effects of crop diversification on soil microbial communities, yielding a dataset of 288 paired observations. The results indicated that crop diversification primarily altered soil microbial community structure rather than microbial diversity, and these responses varied with cropping systems, experiment duration, climatic variables, and soil properties. Specifically, (1) crop diversification had no significant effects on soil microbial α- and β-diversity, but significantly altered bacterial (106.33%) and fungal (41.69%) community structures; (2) crop rotation produced stronger structural shifts in bacterial (156.15%) and fungal (46.67%) communities, whereas intercropping increased fungal richness (12.75%) but did not alter bacterial or fungal community structure; (3) long-term experiments (>3 years) showed stronger effects on microbial community structure than short-term experiments (≤3 years), with larger effect sizes for bacterial (189.33% vs. 70.11%) and fungal (78.09% vs. 27.78%) structural shifts; (4) legume-inclusion systems showed stronger fungal structural shifts (58.11%) than non-legume systems (33.86%), whereas bacterial responses were comparable in both systems (108.59%); (5) crop diversification significantly increased soil total phosphorus (10.72%) and total potassium (4.18%); (6) structural equation modeling indicated that clay content was directly associated with bacterial and fungal community structures (β = 0.22 and β = −0.36, respectively), while the aridity index showed a direct association with fungal community structure (β = 0.93) and was positively associated with clay content (β = 0.70); (7) Spearman’s correlation analysis revealed that shifts in microbial community structure were significantly associated with soil pH ( ρ = −0.30) and available nitrogen ( ρ = 0.25). This study provides insights into optimizing context-specific crop diversification strategies for sustainable agricultural production.