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

Sudden death syndrome (SDS) is a major disease that affects soybean (<i>Glycine max</i>) production, primarily caused by the soil-borne fungus, <i>Fusarium virguliforme</i> in North America. Understanding the interactions among soybeans, <i>F. virguliforme</i>, 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 <i>F. virguliforme</i>, 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. The analysis revealed that SDS-tolerant soybeans recruit microbes with growth-promoting and biocontrol potential, such as members of the genera <i>Bacillus, Pseudomonas, Trichoderma, Mortierella,</i> and <i>Talaromyces</i>, when exposed to <i>F. virguliforme</i>. This distinct microbial recruitment strategy in response to <i>F. virguliforme</i> could provide the ability for soybeans to survive under pathogen stress. In contrast, pathogen inoculation reduced the abundance and activity of the nitrogen-fixing <i>Bradyrhizobium</i> spp. These findings suggest that selective recruitment of beneficial microbes likely contributes to SDS tolerance, while 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 is useful for assembling a combined synthetic microbial community and testing.