Location: Application Technology Research
Project Number: 5082-30500-001-085-S
Project Type: Non-Assistance Cooperative Agreement
Start Date: Sep 1, 2026
End Date: Aug 31, 2029
Objective:
The overall goal of this project is to improve soil health, broadly defined as the physical, chemical, and biological capacity of soils to sustain agricultural production, ecosystem function, crop and human health.
Specific objectives are:
(1) establish baseline soilborne disease management thresholds, (2) improve pathogen disease diagnostics, (3) measure crop responses to environmental stresses, (4) develop soil microbial community measures that capture both pathogenic and beneficial functions.
Approach:
To address the soil health problems in high tunnel systems and to help farmers make informed management decisions, it is critical to detect the microbial communities (microbiomes) that occur in the soil with a focus on soil pathogens and beneficials. We will also conduct experiments and efficacy trials for various cultural practices and measure the change in composition and function of soil microorganisms and plant stress response to disease to develop biotic soil health indicators. In order to conduct this research, we will use modern molecular diagnostic tools such as PCR and qPCR to target detection of soilborne plant pathogens (e.g., bacteria, fungi, nematodes) in both the soil and plants (e.g., roots). The communities of microorganisms will be detected and studied using various DNA sequencing tools to provide a list of microbes in the soil through amplicon-based sequencing, metagenomics to find specific microbes and functional genes important for disease, as well as metabolite detection tools and workflows (e.g., metabolomics) to measure crop stress under disease conditions.
This project is conducted through a multi-institutional collaboration. We will leverage existing high tunnel infrastructure to implement coordinated experiments designed to improve and maintain soil health such as developing soil disinfection approaches. A central focus is the need to quantify soilborne pathogen loads and link pathogen abundance to microbial community structure, soil conditions, and crop performance.
We will draw from our soilborne disease expertise and multi-omics genetic tools, to identify key pathogenic and beneficial taxa and to research how microbial communities influence crop stress responses for developing disease risk solutions for growers.
In Years 1 and 2, we will establish disease management thresholds, quantify pathogen loads, and measure crop responses to stress across sites. Crop-based indicators will be identified in Years 1 through 3 to create measures of soil health that reflect microbial activity and disease pressure. Soilborne disease diagnostic tools for high tunnel systems will be improved in specificity and sensitivity to key soilborne pathogens (e.g., fungi, bacteria, nematodes) during Years 2 and 3. From Year 1-3, microbial community surveys of pathogens and beneficials will be conducted in previously established in the cooperator’s high tunnel soils and data will be collected and analyzed by trained personnel. Ultimately, our project aims to increase farmer productivity, improve crop quality and yield, and reduce economic losses.