Understanding the Molecular Basis of Plant Response to Organic Versus Conventional Fertilizer Using A Metatranscriptomic Approach

Project Overview

Project Type: Graduate Student
Funds awarded in 2018: $25,000.00
Projected End Date: 07/31/2020
Grant Recipient: Washington State University
Region: Western
State: Washington
Graduate Student:
Major Professor:
Amit Dhingra
Washington State University


Not commodity specific


  • Crop Production: crop improvement and selection, fertilizers, nutrient cycling
  • Education and Training: mentoring


    The goal of this project is to determine the physiological and genetic basis underlying the potential production of more nutrient dense crops in farming systems. This will enable farmers of crops produced in amended soils to integrate systems that favor more sustainable production. Previously, we demonstrated that tomato fruit grown under an organic fertilizer regime had elevated phytonutrient content compared to tomato fruit grown under a conventional fertilizer regime. 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 hypotheses tested true, indicating an adjustment of the plants’ genomic activity in response to a different nitrogen regime. We identified genes and associated pathways –among them, lycopene, ascorbate, soluble solids, and salvage pathways –which are expressed at higher levels under organic conditions (Sharpe et al. 2020).

    Building upon previous work, we aimed to examine the effects an organic fertilizer regime on soil microbial communities. In addition to using organic fertilizer, we used organic-certified biochar as a soil amendment as it is known to foster microbial growth. Utilization of biochar has arisen as a promising strategy for both enhancement of soil fertility and long-term sequestration of carbon. During the course of this work, we tested the hypothesis that the genomic responses of tomato roots, and microbial community profiles, will change over time following plant growth in control and soil amended with biochar under an organic fertilizer regime. We utilized a metatranscriptomic approach to evaluate this question. Taxonomic classification of microbial transcripts allowed us to characterize the spectrum of microbes present in the soil at each stage of development and under each biochar regime. Metatranscriptomic analysis is ongoing and is expected to reveal genes that are differentially expressed within the tomato roots, as well as within the various bacteria and fungi present in the soil, over time in each biochar treatment. Together, the results lend further insight into the precise impacts of biochar-based soil amendment for organic tomato growth and will inform new strategies for enhancement of soil fertility.

    Project objectives:

    Short-term: We aimed to increase knowledge of the relationship between phytonutrient content and underlying gene expression changes in plants when grown under different soil fertility management systems in a model crop plant (tomato). We hope to provide a basis for understanding of rhizosphere gene expression changes and metabolic profile shifts, which may in turn result in nutritional differences, following organic biochar amendment of soil. We aim to develop a model for comprehensive analysis of crop production in the field. We seek to use our study results to apply for grant funding in the USDA’s AFRI program in order to conduct a more comprehensive study, which will include field research.

    Intermediate-term: Knowledge generated from the project, particularly regarding effects on plant growth, alteration of the root/soil microbiome, and carbon sequestration, as well as corresponding phytonutrient profiles in the different regimes, will assist sustainable producers to develop management plans for soil fertility. Understanding of gene function and of markers associated with genes expressed differentially under different soil amendment regimes will help plant breeders in the crossing and selection of more efficient crop cultivars that optimize both nutritional quality and yields of crops grown using more sustainable farming practices.

    Long-term: Increase consumption of foods with improved nutritional quality, thereby contributing to the health of American children and adults and reducing health care costs. Implement more sustainable farming practices, particularly related to soil fertility and pest management, will enhance the quality of U.S. agro-ecosystems. Contribute to the long-term economic viability of American farmers.

    Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the view of the U.S. Department of Agriculture or SARE.