Transcriptome of Tomato (Solanum lycopersicum L.) Reveals Impacts of Rhizosphere Microbiomes on Host Interactions

Abstract The gut microbiome of worms from composting facilities potentially harbors organisms that are beneficial to plant growth and development. We transferred microbiomes from worm castings (i.e. vermicompost) into tomato (Solanum lycopersicum L.) rhizospheres to examine their impacts on plant growth and physiology. We hypothesized that tomatoes grown with living vermicompost microbiomes in their rhizospheres would display transcriptome changes in key nutrient pathways compared to sterilized vermicompost and control (no compost) inoculant treatments. Vermicompost microbiome treatment significantly impacted bacterial communities in tomato rhizospheres, but showed high fungal variability between treatments. Plants treated with vermicompost or sterile vermicompost exhibited increased productivity and foliar δ¹⁵N values at harvest, along with decreased fruit phytoene content at the red ripe stage, compared to the control. RNA sequencing revealed distinct gene expression changes in the vermicompost treatment, including upregulation of nutrient transporter genes. Despite phenotypic similarities between vermicompost and sterile vermicompost treatments, plant transcriptome analyses suggest that rhizosphere microbiomes derived from vermicompost can influence tomato gene expression and growth-related regulatory pathways. These findings highlight the potential of rhizosphere microbiomes to influence crops at the molecular level and the value of RNA sequencing in uncovering molecular responses in plant microbiome studies.