Strain-Specific Fungal–Bacterial Co-Inoculation Regulates Rhizosphere Microecology and Plant–Soil–Microbiome Responses in Conifer Seedlings

Beneficial fungal–bacterial interactions are important drivers of rhizosphere microecology and plant–soil functional coupling in conifer seedling systems, but their strain-combination-specific effects remain insufficiently understood. In this study, Pinus sylvestris var. mongolica seedlings were inoculated with three plant growth-promoting rhizobacteria (PGPR) strains, Serratia plymuthica A13, Acinetobacter lwoffii A07, and Pseudomonas koreensis A20, the ectomycorrhizal fungal strain Suillus luteus N94, and their corresponding co-inoculation combinations. Seedling growth, root architecture, plant nutrients, soil nutrients, soil enzyme activities, bacterial and fungal communities, differential taxa, network key taxa, and plant–soil functional indices were analyzed. Different inoculation treatments produced treatment- and trait-specific responses, with several N94–PGPR combinations showing advantages in particular growth, root, and soil functional traits, while some single-inoculation treatments also showed distinct positive effects. N94_A20 showed the greatest increases in seedling height, total dry weight, soil available phosphorus, and soil multifunctionality, whereas N94_A07 showed the strongest root architecture response and relative interaction index. Co-inoculation also reshaped rhizosphere bacterial and fungal communities and generated treatment-specific microbial enrichment patterns. Massilia, Ramlibacter, Holtermanniella, and Naganishia were positively associated with plant–soil functional indices. These results indicate that PGPR–N94 co-inoculation promotes conifer seedling growth through coordinated changes in root architecture, nutrient acquisition, soil biochemical function, and rhizosphere microbial community assembly.