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

Soil management affects chemical and microbiological properties of soils in ways that impact plant growth. We examined effects of amendment treatments and contrasting management treatments on chemical and microbiological soil properties and on expression of selected defense genes in laboratory-grown tomatoes (Solanum lycopersicum). Treatments imposed on a conventionally managed Maury silt loam included: compost, manure, vetch (Vicia villosa), inorganic N, and non-treated control. Non-amended, organically managed Maury soil, collected from the same location was also studied. Compost, manure, and vetch increased total organic C (TOC) and permanganate oxidizable C (POXC) in soil. Organically managed soil also had greater TOC and POXC than the control treatment. Soil N was increased by compost, manure, vetch and inorganic N treatment. Microbial communities from compost, vetch and manure treatments differed from each other and from communities in the other treatments. Defense genes: ChiB (chitinase), Osm (osmotin), and GluA (β-1,3-glucanase) were generally expressed less in plants from manure treated soil and organically managed soil. The PR1b (pathogenesis-related protein PR1b) gene was expressed more in plants from compost, inorganic N, and vetch treatments. Defense gene expression was negatively related to Gram-negative bacterial biomarkers, which were greatest in manure treated soil and organically managed soil. These results suggest that increased relative abundance of Gram-negative members of soil microbial communities in manure treated or organically managed soils may indirectly reduce the steady state expression of defense genes in plants, allowing plants to shift resources from defense to other beneficial functions such as fruit or biomass production.