Consecutive monoculture of sweet potato reduces yield due to deteriorated soil health and disrupted nutrient cycling

Sweet potato (Ipomoea batatas L.) is a staple food with many promising health benefits. However, obstacles associated with continuous cropping are common in modern intensive sweet potato production, partially due to imbalances in the soil microbiome. This research investigates the succession of the soil microbiome and its impacts following 1, 3, and 5 years of consecutive sweet potato monoculture. The results showed significantly higher diversity and homogeneity in bacteria than in fungi. Although a large proportion of operational taxonomic units (OTUs) were shared, richness analysis indicated a significant decrease in the total number of OTUs for both bacteria and fungi, especially in the fifth year. At the phylum level, Firmicutes and Parcubacteria significantly decreased, while Cryptomycota significantly increased (p < 0.05). Further analysis of the prokaryotic community using BugBase and the Functional Annotation of Prokaryotic Taxa (FAPROTAX) database showed significant changes in many phenotypes and functions. In particular, alterations in human pathogens and Cyanobacteria, as well as differences in carbon metabolism and nitrogen conversion in soils, were revealed for the first time. It was also observed that the contents of soil organic matter (OM), total carbon (TC), and total nitrogen (TN) had a linear correlation with the abundance of Cyanobacteria. However, yield was positively correlated with soil pH but negatively correlated with disease incidence. Taken together, in addition to the distinct succession of the microbial community structure, the study indicates that consecutive monoculture of sweet potato has a significant impact on the health status of soil and nutrient cycling.