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

Aims: The rhizosphere microbiome influences plant health, for example, by mediating plant-pathogen interactions. Plants can recruit protective microbes in response to disease, but the consistency of this process in field conditions is unclear. We aimed to identify candidate beneficial microbes enriched during pathogen infection across multiple fields, offering potential to support crop resilience against disease. Methods: DNA amplicon sequencing was employed to examine the rhizosphere microbiome of field-grown soybean (Glycine max L.) naturally infected with root pathogens across three commercial fields in Kentucky, USA. Symptomatic and asymptomatic plants were sampled to assess disease-associated shifts in the bacterial and fungal rhizosphere microbiome. Results: We identified a diverse Fusarium community, with one Fusarium solani amplicon sequence variant (ASV) consistently enriched in diseased plants, identifying it as the likely pathogen. While microbial communities differed between diseased and healthy plants, these shifts were largely field-specific. Several fungal ASVs with known biocontrol potential (Clonostachys rosea, Penicillium, and Trichoderma) were enriched in healthy plants, implying a role in disease suppression. A Sphingomonas ASV, representing a genus previously linked to plant protection, was more abundant in diseased plant rhizospheres in two fields, suggesting pathogen-triggered recruitment. Conversely, Macrophomina phaseolina, a generalist root pathogen, was enriched in the rhizosphere of diseased plants in all fields, indicating possible co-infection with F. solani. Conclusions: These findings reveal complex pathogen-associated patterns in the rhizosphere microbiome of field-grown plants and emphasize the need for field-specific microbiome research to inform sustainable disease management strategies. Supplementary Information: The online version contains supplementary material available at 10.1007/s11104-025-07798-5.