Chemical fertilizer reduction with organic material amendments alters co-occurrence network patterns of bacterium-fungus-nematode communities under the wheat–maize rotation regime

Purpose Deciphering the succession patterns of soil bacterium-fungus-nematode communities and functions in agroecosystems is one of the most important aspects of soil ecology research. However, how agricultural practices, especially the chemical fertilizer reduction and organic material application, influence soil bacterium-fungus-nematode networks remain unclear in wheat–maize rotation systems. Methods In the present study, a field experiment was established with five fertilization treatments, including chemical fertilizer with conventional application rate (F), chemical fertilizer reduction based on conventional fertilization (FR), chemical fertilizer reduction plus straw (FRS), chemical fertilizer reduction combined with organic fertilizer (FRO), and chemical fertilizer reduction combined with organic fertilizer and straw (FROS), under a wheat–maize rotation regime over a 4-year period. Co-occurrence network analysis was used to investigate the bacterium-fungus-nematode community relationships. Results The results showed that the kinless hubs assigned to Sordariomycetes, Agaricomycetes, and Dothideomycetes were of paramount significance to agricultural fertilization. Chemical fertilizer reduction combined with organic materials increased the total nodes, edges, and average degree (avgK), but decreased the average path distance (GD). The networks of bacterial metabolic pathway profile demonstrated that the edge numbers of FRS and FRO networks were obviously shorter than those of F and FR networks, but the GD showed an opposite phenomenon. In contrast, the FROS network had the highest edge number and shortest GD, producing a complicated co-occurrence network. Chemical fertilizer reduction with substitution by organic inputs significantly changed the fungal potential functions, and the genus Poaceascoma appeared to play a key part in shaping the fungal potential functions. Conclusion Overall, chemical fertilizer reduction and organic material application practices altered the responses of keystone taxa and topological features in the bacterium-fungus-nematode communities, such as increasing the scale of ecological network, complicating the relationship between species, and improving the efficiency of material, energy and information transfer between species. Furthermore, organic material substitution exhibited a greater influence on fungal functions, especially pathotrophic and saprotrophic fungi. The complicacy for the potential bacterial functions was we