Localized co-inoculation of compatible Bacillus subtilis and Trichoderma afroharzianum is associated with shifts in the root microbiome and improves plant performance in sorghum.

Although bacterial-fungal consortia have been investigated for plant growth promotion, their effects on sorghum performance and associated root microbial taxa remain less characterized. Here, we investigated how individual and combined inoculation with Bacillus subtilis and Trichoderma afroharzianum influenced sorghum performance and root microbiome assembly. The in vitro co-culture assay demonstrated the compatibility of B. subtilis and T. afroharzianum as a microbial consortium. The B. subtilis-T. afroharzianum consortium demonstrated the highest CPPI (composite plant performance index) and shoot fresh weight in sorghum, while all inoculation treatments improved multiple growth and physiological traits. Split-root analysis showed that bilateral root co-inoculation generally produced the greatest whole-plant growth response. Also, B. subtilis-T. afroharzianum co-inoculation increased carbon levels in both roots and leaves, accompanied by enhanced rhizosphere siderophore production consistent with improved nutrient status. In microbial community analysis, neither bacterial nor fungal alpha or beta diversity differed significantly among treatments, although exploratory taxon-level analyses identified selective treatment-associated shifts in microbial taxa. The B. subtilis-T. afroharzianum consortium showed significant enrichment in plant growth-promoting Actinoplanes, siderophore-producing Enterobacter, and the plant-beneficial fungal genus Podospora. Interestingly, neither inoculant significantly improved sorghum growth in sterile soil, suggesting their potential dependence on the enriched microbes. Co-occurrence network analysis identified Rhodoplanes, Serendipita, and Zopfiella among hub taxa associated with B. subtilis-T. afroharzianum co-inoculation, suggesting potential roles in microbial community connectivity and organization. Furthermore, the persistence of Streptomyces and Serendipita, particularly the latter, suggests the presence of a beneficial microbial core that may contribute to sustained rhizosphere functioning. In addition, Bacillus and Serendipita were identified as indicator taxa associated with the inoculated treatment combinations. Devosia was associated with chlorophyll content, siderophore production, and shoot height, whereas Serendipita correlated with shoot biomass under the B. subtilis-T. afroharzianum co-inoculation. Taken together, these findings demonstrate improved sorghum performance following B. subtilis-T. afroharzianum co-inoculation and identify associated microbial taxa that warrant further functional validation in the field settings.