Microbiome responses to natural Fusarium infection in field-grown soybean plants

The rhizosphere microbiome plays a crucial role in plant health by mediating interactions between pathogens and beneficial microbes. Plants can recruit protective microbes in response to pathogen infection, but the extent and consistency of this process under field conditions remain unclear. In this study, we investigated the rhizosphere microbiome of field-grown soybean (Glycine max) naturally infected with root pathogens across three commercial fields in Kentucky (USA). Plants displaying foliar chlorosis, necrosis, and premature defoliation were sampled alongside symptomless plants to identify disease-associated microbial shifts. Amplicon sequencing revealed a diverse Fusarium community, with 54 distinct Fusarium amplicon sequence variants (ASVs). Among these, a single Fusarium solani ASV was consistently enriched in diseased plant rhizospheres across all fields, identifying it as the likely primary pathogen. While microbial community composition differed between diseased and symptomless plants, these differences were largely field-specific, reflecting the influence of local soil microbiomes on disease progression. Several ASVs representing fungal species with known plant-beneficial properties, including Clonostachys rosea, Penicillium, and Trichoderma, were more abundant in the rhizosphere of healthy plants, suggesting a potential role in disease suppression. Similarly, a Sphingomonas ASV, previously linked to plant disease suppression, was enriched in diseased plant rhizospheres in two fields, hinting at plant-driven recruitment to infection. In contrast, Macrophomina phaseolina, a generalist root pathogen, was also enriched in diseased plants, suggesting possible co-infection with F. solani. These findings highlight the complex interactions between soilborne pathogens and beneficial microbes in field conditions and underscore the need for field-specific microbiome research to inform sustainable disease management strategies.