Assessment of exudate-triggered responses driving Fusarium solani species complex dominance in the soybean spermosphere

Abstract

The soybean (Glycine max L. Merr.) spermosphere, the narrow soil zone influenced by a germinating seed, is a transient yet ecologically significant niche where early plant-microbe interactions are initiated. Fusarium has been reported as a dominant fungal genus in this zone, but the molecular basis of its success remains unclear. This thesis tested the hypothesis that Fusarium senses soybean seed exudates, which in turn trigger transcriptomic responses that activate genes supporting its ecological dominance. Two soybean-associated FSSC isolates, F. solani Cherokee5 and F. falciforme Progeny4, were characterized through virulence assays, genome sequencing, and comparative analyses to uncover genomic features linked to adaptation and competitiveness. Hybrid assemblies generated from Oxford Nanopore and Illumina reads were highly contiguous (58–62.6 Mb) and complete (>95% BUSCO). Comparative genomics revealed extensive repeat content and accessory regions enriched for genes related to secondary metabolism, transport, and host interaction. Functional annotation identified more than 700 CAZymes, over 40 biosynthetic gene clusters (BGCs), and numerous secreted or GPI-anchored proteins, suggesting a genome well adapted for interaction with plant-derived compounds and microbial competitors. To evaluate transcriptional responses to seed exudates, F. falciforme Progeny4 was exposed to soybean seed extract and analyzed by RNA sequencing. The fungus exhibited strong induction of genes encoding polyketide synthases (PKS) and non-ribosomal peptide synthetases (NRPS), including clusters for fusarubin, gibepyrone, cyclosporin, and sansalvamide biosynthesis. Many of these metabolites have putative antimicrobial or stress-adaptive functions. Upregulation of glycosyl hydrolases, oxidoreductases, GPI anchored proteins and antimicrobial peptide encoding genes further indicated an active adjustment to the nutrient- and signal-rich exudate environment. Overall, the results support the hypothesis that Fusarium can sense chemical cues released from soybean seed exudates. These cues trigger changes in gene expression that activate pathways involved in metabolism, stress response, and microbial competition. The fungus appears to use both secondary metabolites and protein-based mechanisms to strengthen its ability to survive and dominate in the spermosphere.