Is Early Tobacco–Rice Rotation Associated with Soil Nutrient Legacy and Shifts in Bacterial Ecological Potential in a Subtropical Paddy System?

In subtropical double-rice regions, replacing early-season rice with tobacco may alter the soil environment inherited by subsequent paddy cultivation. We conducted a one-year field experiment in 2023 to compare rice–rice (RR) and tobacco–rice (TR) pathways. Soils from the 0–10 and 10–20 cm layers were sampled during the early-season pathway-differentiation period and the late-season rice-growing period, and soil properties, bacterial 16S rRNA communities, predicted functional profiles, and rice agronomic traits were analyzed. Relative to RR, TR was associated with 4.12% lower grain yield but 5.10% higher 1000-grain weight and 23.74% higher aboveground dry matter, indicating altered yield formation rather than uniform growth suppression. TR was also associated with lower soil organic carbon (SOC), total nitrogen (TN), alkali-hydrolyzable nitrogen (AN), and available phosphorus (AP). Bacterial communities differed between pathways, with stronger Chloroflexi/Actinobacteriota and 16S-predicted aerobic, stress-tolerant, and chemoheterotrophic signals under TR. Together, these findings indicate that early TR was associated with lower measured C-, N-, and P-related soil pools, bacterial community reorganization, and altered late-season rice yield formation; therefore, nutrient and residue management should be planned across the tobacco–rice year rather than only during the rice season.