Contrasting Effects of Beneficial and Pathogenic Fungal Inoculation on Rhizosphere Microbial Community Assembly, Network Properties, and Functional Contributions of Keystone Taxa in Cucumber Soil

Beneficial and pathogenic fungal inoculation can substantially influence plant growth by reshaping rhizosphere microbial communities. However, how different fungal inoculants differentially affect microbial community assembly processes, co-occurrence network stability, keystone taxa distribution, and their potential associations with plant growth remains poorly understood. Cucumber was used as the model plant, and Fusarium oxysporum (pathogenic, Foc) and Trichoderma guizhouense (beneficial, Tri) were selected as inoculants. 16S rRNA and ITS2 amplicon sequencing were used to investigate the diversity, composition, assembly processes, and co-occurrence network structure of rhizosphere bacterial and fungal communities, respectively. In addition, we used Zi–Pi topological role analysis, functional prediction, Mantel tests and random forest to characterize keystone taxa and link microbial assembly, network stability to plant nutrient and biomass traits. Foc decreased bacterial diversity while Tri increased it. Tri was associated with greater microbial network connectivity and complexity, as well as network characteristics consistent with higher inferred stability, with more connector keystone taxa enriched in glycan and terpenoid metabolic functions; by contrast, Foc simplified network structure and enriched saprotrophic fungal keystones. Bacterial assembly shifted toward deterministic processes under Foc, whereas stochastic processes remained predominant in Tri and control treatments. Random forest further confirmed divergent drivers: bacterial assembly depended mostly on community composition, while fungal assembly was regulated by plant nutrients and fungal diversity. All microbial properties were tightly linked to plant biomass and nutrient accumulation. Collectively, beneficial and pathogenic fungi exert opposing influences on rhizosphere microbial organization: Tri was associated with more connected microbial communities and a greater diversity of predicted functional traits, whereas Foc strengthened environmental filtering and simplified community structure, with plant–microbe–nutrient feedbacks likely contributing to rhizosphere assembly and ecosystem functionality.