Rotation system reshapes soil profile environmental gradients to reorganize bacterial communities and decouple potential nitrogen cycling functions

Cropping systems reshape soil profile environmental gradients, thereby driving the vertical reorganization of bacterial communities and regulating the coupling between microbial communities and predicted nitrogen-cycling (N-cycling) potential.

This study integrated soil chemical analyses, 16S rRNA gene sequencing, co-occurrence network analysis, PICRUSt2-based functional prediction, and structural equation modeling (SEM) across three long-term cropping systems: unclaimed land (U), tobacco-maize rotation (R), and continuous tobacco cropping (C), sampled at three soil depths (0-20, 20-40, and 40-60 cm; n = 3).

Environmental drivers exhibited distinct vertical shifts, with readily available nutrients (AN, AK, and AP) dominating surface soils (0-20 cm), microbial biomass (MBC and MBN) governing subsurface soils (20-40 cm), and total nutrient pools (OM, TN, and TP) becoming increasingly important in deeper soils (40-60 cm). Rotation buffered vertical environmental changes, increased bacterial richness in the 0-40 cm profile, enriched nitrifying and nitrogen-fixing taxa (e.g., Nitrospira, Sphingomonas, and MND1), and maintained higher predicted N-cycling potential throughout the soil profile, accompanied by enhanced network modularity and robustness. In contrast, continuous cropping reduced surface soil pH, OM, MBC, and MBN (with MBN declining by>60%), promoted stress-associated taxa (e.g., Bacillus and Lactobacillus), and weakened network connectivity and robustness, particularly at 20-40 cm where network fragmentation was most evident. SEM revealed a stronger statistical coupling among soil environment, bacterial communities, microbial networks, and predicted N-cycling potential under rotation (GOF > 0.7), whereas continuous cropping showed weakened associations among these components.

Collectively, these findings demonstrate that crop rotation promotes the stability of soil microbial ecological functions by preserving environmental gradient continuity and enhancing network resilience, whereas continuous cropping disrupts microbial network organization and weakens the linkage between resource availability and predicted functional potential. This study highlights the importance of maintaining multiscale environmental and microbial connectivity for improving the sustainability of agricultural soil ecosystems.