Short-term continuous cropping leads to a decline in rhizosphere soil fertility by modulating the perilla root exudates

Continuous cropping obstacles are a prevalent issue in agricultural production worldwide. However, the key factors leading to these obstacles differ among various crops. This study utilized high-throughput sequencing and metabolomics to assess the community structure of microbes and the types and abundance of metabolites in rhizosphere soil after different continuous cropping years of Perilla frutescens L. Britt. (perilla). The results indicate that differential metabolites in soils of varying continuous cropping years are primarily associated with pathways for cellular lipid formation, oxidative stress responses, and energy metabolism. These findings suggest that the changes in soil composition over time are linked to specific biological processes related to lipid formation, oxidative stress, and energy metabolism. The relative abundance of beneficial bacteria in the soil, such as Sphingomonas, Gemmatimonas, and Blastococcus, decreased significantly (p < 0.05), while harmful fungi, such as Neocosmospora and Didymella, increased in response to the increase in continuous cropping years (p < 0.05). The symbiotic network between bacteria and fungi has become less dense and stable after continuous cropping. Enzymatic activities in rhizosphere soil decreased significantly (p < 0.05). Soil organic matter, total nitrogen, total phosphorus, total potassium, available phosphorus, and available potassium declined significantly (p < 0.05). Pearson correlation analysis identified 10 differential secondary metabolites that were closely related to the relative abundance of key microorganisms. Among them, cinnamic acid and flavonoid compounds are key factors leading to changes in microbial diversity, and they can regulate the microorganisms-soil- plants interactions. In summary, this study provides a novel scientific explanation for how continuous cropping can reduce soil fertility and a theoretical basis for subsequent cultivation strategies of perilla.