Study on the Divergence Patterns of Soil Physicochemical Properties, Microbial Target Gene Copies and Enzyme Activities Under Different Continuous Cropping Years

Continuous cropping obstacles constrain the sustainability of intensive agricultural production, and investigating the dynamics of soil properties across different continuous cropping durations is important for the prevention and control of this problem. This study focused on field-grown Chrysanthemum morifolium and collected soil samples from plots with continuous cropping durations of 1 year (CR1), 3 years (CR3), 5 years (CR5), and 10 years (CR10) with three independent replicate plots per treatment, to analyze the changes and interrelationships among key soil physicochemical and microbial properties. The results showed that different soil properties exhibited distinct divergence patterns with different inflection points. The activities of fluorescein diacetate (FDA) hydrolase and chitinase decreased significantly during the first 1–3 years of continuous cropping and recovered continuously from years 5 to 10, representing the earliest responses. The target gene copies of Fusarium oxysporum f. sp. chrysanthemi (Foc) increased rapidly to a peak at CR5 and declined significantly at CR10; fungal target gene copies showed a similar pattern, peaking at 14.6 × 107 copies·g−1 in CR5. In contrast, bacterial target gene copies remained stable during years 1–5 but increased significantly by CR10. Meanwhile, fungal target gene copies (F), pH, and electrical conductivity (EC) all reached peaks or troughs between years 1 and 5, with significant rebound by year 10. Soil pH and EC dropped to their lowest levels in CR5 (pH 5.1, EC 85 μS·cm−1) and recovered markedly by CR10 (pH 6.5, EC 150 μS·cm−1). Soil organic matter, available phosphorus, and nitrate nitrogen increased continuously, with the highest values recorded in CR10, whereas ammonium nitrogen declined sharply to 0.52 mg·kg−1 in CR5. Correlation analysis and random forest modeling indicated that bacterial target gene copies, FDA hydrolase, chitinase, nitrate (NO3−), and pH were the most important predictors of Foc target gene copies, with fungal target gene copies ranking highest in predictive importance (%IncMSE = 26%), followed by bacterial target gene copies; the latter exhibited a significant negative association with Foc target gene copies. The proportion of antagonistic bacteria declined continuously from 6.0% to 1.0% during years 1–5 and recovered to 5.0% during years 5–10, exhibiting a trade-off pattern with Foc target gene copies. This study shows that different soil properties exhibit clear temporal divergence under continuous cropping, with microbial factors emerging as the dominant predictors of variation in pathogen target gene copies.