Understanding the molecular basis of plant response to organic versus conventional fertilizer using a metatranscriptomic approach

This project addresses breeding, varietal selection, management practices, processing, or marketing practices to increase food quality, nutrition, safety or access. In a previous study, we demonstrated that tomato fruit grown under an organic fertilizer regime had higher phytonutrient content. Thereafter, using a comprehensive transcriptome analysis we tested the following hypotheses : 1. Growth under organic fertilizer regime will result in differential expression of the tomato genome and 2. Genes and pathways associated with phytonutrients that were observed to be significantly higher under organic fertilizer regime will demonstrate higher expression.  Both the hypotheses tested true, indicating an adjustment of the plants’ genomic activity in response to a different nitrogen regime. We have identified genes and associated pathways—among them, lycopene, ascorbate, soluble solids, and salvage pathways—which are expressed at higher levels under organic conditions.  Next, investigation of the genomic response of the roots immediately after exposure to organic vs conventional fertilizer will provide understanding of how the two different forms of nitrogen are metabolized. We propose to test the following hypotheses: 1. Different fertilizer regimes will elicit differential expression of nitrogen metabolism genes, and 2. A different microbiome will be fostered under organic nitrogen conditions. This investigation will entail a time course root and microbiome-targeted transcriptome analysis in which we will focus specifically on genes and pathways associated with nitrogen metabolism and on the microbial symbionts whose activity is favored under the different fertilizer conditions. The gene-based knowledge generated through our investigation will facilitate identification of genotypes that are able to utilize organic fertilizer efficiently.