Potato-onion intercropping enhances tomato yield and quality and modifies soil microbial diversity

Intercropping can promote sustainable agricultural development and increase economic benefits by enhancing ecosystem stability, soil health, and resource use efficiency. In this study, we analyzed the effects of tomato monoculture and tomato/potato-onion intercropping on tomato root distribution and bacterial and fungal communities in tomato rhizosphere by stratified subsection excavation method, quantitative PCR, and Illumina MiSeq sequencing. The results indicated that the root system of monoculture tomato farming did not exhibit significant displacement, whereas the tomato root system in intercropping exhibited spatial adjustments to avoid competition. Intercropping increased soil pH, nitrate nitrogen (NO₃^--N), available phosphorus (AP), and available potassium (AK), but decreased soil electrical conductivity (EC). Intercropping increased tomato biomass, yield, and quality, but reduced the number of diseased fruits caused by tomato blossom-end rot. Additionally, intercropping increased α-diversity and altered the composition and structure of bacterial and fungal communities, as well as the abundance of potentially beneficial bacteria (e.g., Bacillus spp. and Pseudomonas spp.). Redundancy analysis (RDA) based on the euclidean distance were used to evaluate the relationship between bacterial and fungal community structures and various factors. The results indicated that soil bacterial and fungal communities in tomato/potato-onion system were significantly positively correlated with AP, NO₃^--N, pH, and yield, while EC in monoculture system was significantly positively correlated with bacterial communities, but negatively correlated with fungal communities. Microbial co-occurrence network analysis showed that, compared with the monoculture tomato farming, the tomato rhizosphere bacterial community in the intercropping system exhibited significantly enhanced network connectivity. This was manifested by a substantial increase in degree and graph density, alongside reduced modularity. Conversely, the fungal community network connectivity in the intercropped tomato rhizosphere was significantly weakened, characterized by decreased degree and graph density, with a concurrent increase in modularity. Overall, our study demonstrated that intercropping with potato-onion changed tomato root distribution, increased soil microbial community diversity and changed community structure, and improved the soil environment, which may be the key factors to promote the growth of tomato and improve the yield and quality of tomato.