Soil treatment-induced differential gene expression in tomato: Relationships between defense gene expression and soil microbial community composition

•We compared effects of 5 treatments on soil microbes and tomato defense genes.•Effects were studied in a 28 day laboratory experiment.•Organic management and manure amendment reduced expression of defense genes.•Defense gene expression was negatively related to Gram-negative biomarker levels.•Organic management and manure amendment increased Gram-negative biomarker levels.