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.

Grant Information

  • Project ID: 144
  • Project Status: Complete



Sharpe RM, Gustafson L, Hewitt S, Kilian B, Crabb J, Hendrickson C, et al. (2020) Concomitant phytonutrient and transcriptome analysis of mature fruit and leaf tissues of tomato (Solanum lycopersicum L. cv. Oregon Spring) grown using organic and conventional fertilizer. PLoS ONE 15(1): e0227429. https://doi.org/10.1371/journal.pone.0227429

Additional Funds Leveraged

  • W-SARE Grant awarded to Seanna Hewitt in 2017
  • Support for a MS graduate student secured from WSU Graduate School.
  • Obtained funding from the Cowles Company, Stump Farmer Farm, and Cool Planet Inc. to evaluate the impact of organic fertilizer in conjunction with biochar.
  • USDA OREI grant in progress for submission in 2018 based on the results obtained from this and additional complementary projects. Awaiting publication of the first research article prior to grant submission.
  • I plan to apply to the NSF Integrated Ecological Physiology panel in 2018


  • Short-Term: The project will increase our knowledge of the relationship between observed phytonutrient changes and underlying gene expression changes in plants when grown under organic soil fertility management in a model crop plant (tomato). Such an interdisciplinary and comprehensive analysis remains to be done in the field of crop production. The results of this study will be used to apply for grant funding in USDA’s AFRI program in order to conduct a more comprehensive study, which includes field research.
  • Intermediate-Term: The knowledge generated from this BioAg and subsequent federal projects will assist organic and sustainable producers to develop management plans for soil fertility and pest control that help them optimize the nutritional quality and yields of their products. The understanding of gene function and of markers associated with those genes will help plant breeders in the breeding and selection of more efficient crop cultivars that optimize both nutritional quality and yields of crops grown using more sustainable farming practices.
  • Long-Term: Increased consumption of foods with better nutritional quality should contribute to the health of American children and adults and reduce health care costs. Using more sustainable farming practices, especially of soil fertility and pest management, will enhance the quality of U.S. agroecosystems. Besides improving agricultural sustainability and public health, this project could also contribute to the long-term economic viability of American farmers.