Integrated Multi-Omics Analysis Provides Insights into the Rhizosphere Microbial Dynamics in Soybean–Fusarium virguliforme Interaction

Sudden death syndrome (SDS) is a major disease that affects soybean (Glycine max) production, primarily caused by the soilborne fungus Fusarium virguliforme in North America. Understanding the interactions among soybeans, F. virguliforme, and microorganisms in the soil near the vicinity of roots can provide microbial candidates for SDS management. The objective of this study was to elucidate the role of rhizosphere microbial composition and activity, both in the presence and absence of F. virguliforme, across two commercial soybean cultivars with differing susceptibility to SDS. Bacterial and fungal community dynamics were assessed using full-length 16S rRNA and internal transcribed spacer 1 (ITS1) sequencing, respectively. Microbial activity was further evaluated with an optimized metatranscriptome workflow. Our analysis revealed that SDS-tolerant soybeans recruit microbes with growth-promoting and biocontrol potential, such as members of the genera Bacillus, Pseudomonas, Trichoderma, Mortierella, and Talaromyces, when exposed to F. virguliforme. This distinct microbial recruitment strategy in response to F. virguliforme could provide the ability for soybeans to survive under pathogen stress. In contrast, pathogen inoculation reduced the abundance and activity of the nitrogen-fixing Bradyrhizobium spp. These findings suggest that selective recruitment of beneficial microbes likely contributes to SDS tolerance, whereas pathogen pressure compromises symbiotic nitrogen fixation. The results highlight candidate taxa and interactions for developing synthetic microbial communities to support SDS management. The information generated from this study will be useful for assembling a combined synthetic microbial community and testing. [Figure: see text] Copyright © 2026 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.