Fusarium oxysporum-Induced Root Rot Severity Reshapes the Soybean Rhizosphere Microbiome and Affects Its Functional Potential

Soybean root rot caused by Fusarium oxysporum is an important soil-borne disease that affects soybean growth and disrupts rhizosphere microbial communities. However, how rhizosphere microbiomes respond to different levels of disease severity remains poorly understood. In this study, a five-level root rot severity gradient (F0–F4) was established using a carrier-matched inoculation design, and changes in soybean growth, rhizosphere soil properties, enzyme activities, microbial community composition, and functional potential were investigated using shotgun metagenomic sequencing. Increasing disease severity reduced soybean growth, with leaf area decreasing from 312.98 cm2 in F0 to 32.45 cm2 in F4. Root rot progression altered rhizosphere microbial communities, with fungal communities showing stronger responses than bacterial communities. The bacterial Chao1 richness index increased by 34.6% in F4 compared with F0, whereas fungal Shannon diversity decreased by 46.7%. Taxonomic analysis revealed clear shifts in microbial community composition, with Fusarium becoming strongly enriched under diseased conditions, increasing from 16.9% in F0 to maximum relative abundance of 68.8% in F2 and remaining highly abundant at 61.5% in F4, while Trichoderma decreased from 7.3% to 2.2% and Rhizophagus declined from 38.1% to nearly undetectable levels. Metagenomic functional profiling revealed disease-associated changes in microbial functional potential, particularly in pathways related to metabolism, membrane transport, signal transduction, and secondary metabolite biosynthesis. In addition, soil physicochemical properties and enzyme activities varied across the disease severity gradient, indicating changes in the rhizosphere environment during disease development. Overall, soybean root rot progression was associated with coordinated changes in plant performance, soil biochemical characteristics, microbial community structure, and functional potential, with fungal communities exhibiting stronger responses to disease-associated disturbance than bacterial communities.