Soil Type, Tomato Genotype, and Pathogen Stress Shape the Tomato Rhizobacterial Community

Although the effects of soil type, plant genotype, and pathogen invasion on plant rhizosphere microbiomes have been preliminarily explored, their relative contributions and interactive influences on rhizobacterial community assembly remain unclear. In this study, we used tomato as a model to evaluate the individual and combined impacts of these three factors on rhizosphere bacterial community structure and function within a unified experimental framework. Microbiome-based analyses revealed that soil type was the predominant driver, explaining 53.1% of structural and 49.6% of functional variation, followed by tomato genotype (15.6% and 36.1%, respectively) and Fusarium oxysporum f. sp. lycopersici (Fol) inoculation (2.1% and 0.9%). Notably, the interaction between soil type and tomato genotype exerted a stronger influence than any other factor combination. Total nitrogen emerged as the key abiotic factor shaping the taxonomic composition of rhizobacterial communities, whereas soil pH played a dominant role in determining their functional profiles. Distinct tomato genotypes harbored rhizobacterial communities with divergent taxonomic and functional compositions. Although pathogen inoculation triggered the recruitment of beneficial microbes by the host plants, its impact on rhizobacterial community assembly was considerably weaker compared with the effects of soil type and tomato genotype. These findings provide a framework for understanding how soil, host, and pathogen collectively shape rhizobacterial communities and offer insights for optimizing microbiome management in crop production.