Reducing Soil Moisture Fluctuations Significantly Improves Crop Yield and Quality: Insight into Multiomics in Soil–Plant Systems

Agricultural water scarcity is increasingly conflicting with demands for both crop yield and crop nutritional quality, yet current irrigation strategies are failing to achieve synergistic improvements. This study explores how reducing soil moisture fluctuations (SMFs) affects crop yield and quality, using tomato plants under three irrigation treatments: fast wetting (FW), medium wetting (MW), and slow wetting (SW). We analyzed soil moisture dynamics, yield, fruit quality, soil bacteria, and plant molecular responses. Slowing the wetting process significantly improved tomato yield by 10%–20% and increased vitamin C and lycopene content by 10%–17% and 7%–29%, respectively, while reducing the irrigation quota by 30%–35%. The results showed a significant increase in the relative abundance of Myxococcota and Chloroflexi, while the relative abundance of Actinobacteria significantly decreased. Functional prediction showed that the abundance of aerobic chemotrophic heterotrophy was suppressed, whereas nitrate reduction was promoted. Based on a joint analysis of transcriptomics and metabolomics, several genes encoding key enzymes ( GME , DHAR , IDH1 , crtB , and crtH ) in the pathways of ascorbic acid, lycopene, and organic acid cycles were significantly affected. Structural equation modeling (SEM) revealed that the stabilized soil moisture directly increased microbial community diversity and soil fertility, which subsequently activated transcriptional pathways associated with nutrient assimilation and antioxidant biosynthesis. This cascade of biological responses ultimately mediated improvements in crop productivity and quality. These findings challenge the conventional understanding of wet-dry cycles in irrigation. Reducing SMFs offers a practical approach to simultaneously improving water-use efficiency, crop yield, and fruit quality, with potential applications in sustainable agriculture.