Increased soil multifunctionality is determined by altered bacterial–fungal–protistan compositions and co‐occurrence network complexity during vegetation restoration in a Karst region, southwest China

Abstract Vegetation restoration is essential to manage rocky desertification and restore ecological functions in the karst region of southwest China. However, the contributions of soil multitrophic microbial diversity and network complexity for the multifunctionality of karst ecosystem during vegetation restoration remain poorly explored, despite the established significance of soil microbial communities in regulating various ecosystem functions. This study aimed to investigate the diversity of bacterial, fungal and protistan communities and their hierarchical co‐occurrence networks, as well as their relationships with soil ecosystem multifunctionality (SMF), in two different vegetation restoration modes: natural forest (NF) and artificial forest (AF), with cropland (CL) controls. The restoration of the karst vegetation significantly increased the carbon and nitrogen cycling indexes, the capacity of soil water regulation and SMF ( p < 0.05). The SMF exhibited positive correlations with the composition of the bacterial, fungal and protistan communities, as well as their hierarchical β‐diversity and the complexity of the network (e.g. degree and average path length). Notably, alterations in the abundance of sensitive amplicon sequence variants (sASVs) within Module 4 positively affected SMF, while the abundance of sASVs within Module 2 demonstrated a negative correlation with SMF under different modes of restoration of karst vegetation. Furthermore, bacterial keystone taxa, rather than fungal and protistan, were negatively associated with the SMF. Random forest (RF) modelling further identified Nitrospira , Halomonas , Immundissolibacter , Rhodoferax , Alicycliphilus and Castellaniella at the bacterial genus level as critical for maintaining the SMF. Additionally, carbon and nitrogen sources, minor elements (e.g. exchangeable Mg, exchangeable Ca, Cu, Zn, Fe and Mn) and soil water content were determined to be pivotal driving factors of SMF. Synthesis and applications . These findings provide a valuable insights into the influence of vegetation restoration on soil microbial hierarchical interactions and ecosystem functions in karst areas.