Long-term manure addition restores soil microbial network complexity disrupted by chemical fertilization across 3 m soil profiles

Fertilization with chemical fertilizers and manure compost plays a vital role in crop production and soil fertility, but also strongly influences soil microbial communities that underpin agroecosystem multifunctionality. However, most studies have focused on topsoil, and little is known about whether fertilization practices can penetrate deeper soil layers to shape subsoil microbial communities. Here, based on an 8-year field experiment, we explored how solely chemical fertilization (CF) and chemical fertilizer combined with manure compost (CFM) affect microbial diversity and co-occurrence networks across the 0–3 m soil profile, compared with no fertilizer application (CK). Our results showed that microbial alpha diversity was both affected by fertilization and soil depth, while beta diversity was primarily driven by depth. Compared with CK, both CF and CFM decreased bacterial alpha diversity in the topsoil but did not affect fungal and archaeal diversity. Bacterial and fungal alpha diversity declined with increasing soil depth. Soil organic carbon (SOC), total nitrogen (TN), pH, and moisture were the key drivers affecting microbial diversity and community structure. Fertilization substantially altered microbial co-occurrence networks in upper soil and subsoil. Both CF and CFM increased network modularity. Compared with CK, the network connectivity and positive associations were decreased by CF. However, such negative effects were restored by CFM. The abundance of network hubs was closely associated with soil properties, such as SOC, TN, C:N ratio, and pH. Overall, the results revealed the effects of fertilization and depth on soil microbial diversity and community composition and demonstrate that fertilization practice could extend effects to deep soil layers to affect subsoil microbial community interactions. Our study suggests that manure compost addition could benefit the rebuilding of healthy microbial association networks, and provides valuable insights into fertilization management towards building a healthy soil. • The effect of fertilization on microbial diversity and network penetrated 3 m of soil. • Depth showed greater effects than fertilization on soil microbial diversity. • Chemical fertilization reduced co-occurrence network connectivity and complexity. • Manure addition restored network connectivity and rebuilt positive associations.