Co-Inoculation of Rhizobia and a Multifunctional Microbial Consortium Is Associated with Improved Soybean Performance and Bacterial Community Reassembly in Soybean Fields

Rhizobial inoculation is an important strategy for improving nitrogen supply in soybean systems, but its field performance is often limited by soil constraints and interactions with indigenous microbiomes. Multifunctional microbial consortia may complement rhizobia by modifying rhizosphere soil conditions and nutrient availability. Here, we combined pot and one-season field experiments in a meadow albic black soil of the Sanjiang Plain, China, to evaluate the effects of rhizobia, a multifunctional bacterial consortium, and their co-inoculation (CRF) on soybean performance, soil properties, enzyme activities, and bacterial communities. CRF produced the highest soybean yield, reaching 2230 kg ha⁻¹, which was 6.74%, 1.54%, and 1.50% higher than conventional fertilization (F), single consortium inoculation (CF), and single rhizobial inoculation (RF), respectively. Compared with F, CRF showed higher values of selected short-term soil indicators at specific growth stages, including pH, soil organic matter, alkali-hydrolyzable nitrogen (+7.51–21.14%), and available phosphorus (+19.29–42.68%). At maturity, sucrase, urease, and acid phosphatase activities under CRF were 18.6%, 15.3%, and 22.4% higher than those under F, respectively. Bacterial OTU richness increased by 11.70% under CRF, whereas evenness-related indices decreased, suggesting treatment-associated bacterial community reassembly. Soil pH explained 11.63% and 13.24% of bacterial community variation at the phylum and genus levels, respectively. These findings suggest that rhizobia–consortium co-inoculation was associated with improved soybean yield, altered rhizosphere soil indicators, and bacterial community shifts during one soybean growing season. Longer-term field trials are needed to confirm the persistence and mechanisms of these effects.