Short-Term Continuous Cropping of Dioscorea polystachya Alters the Rhizosphere Soil Microbiome and Degrades Soil Fertility

Chinese yam (Dioscorea polystachya) serves as both a food crop and a traditional Chinese medicine herb, yet it suffers from severe continuous cropping obstacles, typically requiring a six-year fallow period before replanting. Long-term continuous cropping changes soil properties, including the concentration of N, P, and K, as well as bacterial composition, but the overall impact of short-term continuous cropping on important soil factors such as mineral elements, enzymes, and microbial composition still remains poorly understood. To elucidate how monoculture affects soil health, we collected rhizosphere soils from D. polystachya fields under one-, two-, and three-year continuous cropping in Chenji Town, and analyzed soil properties using general chemical methods, as well as microbial composition by Illuminar high-throughput sequencing of 16S rRNA and ITS1 regions. Furthermore, the correlation between soil properties and microbial communities was examined. The results showed that soil pH, cation exchange capacity, and organic matter content increased significantly in continuous cropping soil, whereas the concentrations of soil mineral elements (N, P, K, Ca, Mg, Na, Cu, Fe, Mn, Zn, S, and Si) decreased significantly, with the concentration of available P, K, Cu, and Zn decreased by 72.8%, 64.1%, 99.3%, and 79.4%, respectively, in 3-year continuously cropped soil. Enzyme activities, including sucrase, urease, and alkaline phosphatase, also showed a decrease of more than 81%. Fungal diversity and abundance were markedly reduced with cropping duration, whereas bacterial communities showed less response. Notably, pathogenic fungi such as Dactylonectria, Neocosmospora, and Ilyonectria, along with bacteria Streptomyces, became enriched. These microbial shifts were primarily associated with soil pH, available potassium, and alkaline phosphatase. Our study demonstrates that the decline in soil fertility coupled with pathogen buildup constitutes a major cause of the continuous cropping obstacle in Chinese yams. The results provide a scientific basis for developing targeted strategies to mitigate continuous cropping obstacles in Chinese yam production.