Progress 09/01/24 to 08/31/25
Outputs
Target Audience:During this reporting period, our extension activities primarily targeted certified organic tomato producers across multiple states. In Connecticut, the team engaged directly with organic farmers through outreach and educational efforts. At UC Davis, we collaborated with five certified organic growers, two in the San Joaquin Valley and three in the Sacramento Valley. In Florida we visited fields in a certified organic growers. The growers expressed interest in our project and allowed us to collect samples from their tomato fields. All five were invited to attend our annual project-sponsored webinar hosted by Penn State, with at least one confirmed participant. The Penn State team also focused their outreach on organic growers, using the webinar and other extension efforts to support sustainable disease management and soil health practices. Changes/Problems:We have encountered some challenges during this reporting period, such as finding certified tomato growers in Florida and it took a little longer to hire a postdoc. Some of our lab are still working on obtaining permits to work on the objective 2. What opportunities for training and professional development has the project provided?During this reporting period, the project provided significant professional development opportunities for early-career researchers across multiple institutions. At Penn State, postdoctoral researcher Dr. Melanie Lopez-Medina, led grower recruitment efforts, organized and delivered the first "office hour" presentation to growers, and developed experimental methods. Additionally, they gained experience in preparing the Institutional Review Board (IRB) protocol for exempt research. At UC Davis, postdoctoral scientist Dr. Hannah Goemann participated in several professional development workshops, including the Scientific Leadership and Management Skills course hosted by the Gladstone Institute, UC Davis, UC Berkeley, and the Lawrence Berkeley National Lab. She also engaged in informal bioinformatics training through the Emerson Lab and the UC Davis Grad Pathways Institute. Furthermore, Dr. Goemann attended the Ecological Society of America annual meeting in Baltimore, MD, from August 10-15, 2025, where she presented related agricultural viromics work and promoted the citizen science project proposed in Objective 3. At the University of Florida, postdoctoral researcher Dr. Vanessa Thomas gained valuable outreach experience by engaging directly with growers across Florida. She also contributed to the design of an infographic fact sheet aimed at helping growers understand soil amplicon sequencing and its relevance to soil health. How have the results been disseminated to communities of interest?Soil chemistry results for each participating farm in California has received the data from the early-season sample collection and will receive the fall sampling data as soon as it is processed. What do you plan to do during the next reporting period to accomplish the goals?In the upcoming reporting period, the Penn State team plans to collect and process soil samples from organic farms for the second timepoint, performing DNA extraction and microbiome analyses on all collected samples. At UC Davis, efforts will focus on completing sample collection and viromics processing for Objective 1, with samples submitted for sequencing and metabolomics analyses. Data analysis for viromes and metabolomes is expected to be well underway by the end of the period, pending availability of metabolomic data. The University of Florida (UF) plans to complete soil sample collection from organic tomato fields at or near planting and at the end of the growing season. These samples will be sent to collaborators for microbial and metabolomic analyses, and soil chemical analyses will be performed on samples from both time points, with results shared with growers. The Penn State team aims to evaluate the survival of micropredators in soil influenced by different organic amendments and anticipate publishing their first paper on predation in microcosms. At UF, the focus will be on evaluating the survival of plant pathogens in soil and assessing how their presence and abundance are influenced by various organic amendments. This work will include optimizing qPCR protocols and specific primers, with findings to be presented at conferences and prepared for potential publications. UF plans to conduct greenhouse experiments for objective 3 to test whether combining predator bioinoculants with organic matter (OM) amendments enhances plant growth and health, particularly for organic pathogen control. Three promising predator-amendment combinations will be selected based on prior correlations with pathogen suppression and micropredator diversity. These combinations, along with controls, will be applied to soil inoculated with pathogens and planted with tomato seedlings. Plant growth, disease symptoms, and pathogen levels will be monitored over 45 days. The best-performing combination will be validated in a second experiment with detailed physiological measurements and advanced microbial and viral community analyses, including metagenomics and functional assays, to uncover mechanisms driving plant health benefits. Results will be presented at conferences, and data will be used for potential publications. At Penn State, efforts will continue to coordinate and deliver office hours for growers, along with the development of one fact sheet. To increase registration and attendance of these sessions, the team will work on expanding their contact list to reach a wider audience of organic growers. Additionally, they are developing a microbiome testing kit to send to growers to gather information about the differences in microbes across different farms.
Impacts
What was accomplished under these goals?
During this reporting period, our teams made strong progress under Objective?1, focusing on collaborative soil sampling and analysis. In Pennsylvania, our group established relationships with farmers across four organic tomato farms and collected 54 soil samples that were sent to the University of Florida/IFAS Analytical Services for physicochemical analysis. We also secured an IRB determination of exempt status to gather detailed farm management histories from participants. In California, UC Davis hired a postdoctoral scientist, Hannah Goemann, who initiated the "predatorome" and soil health surveys in the San Joaquin and Sacramento Valleys. Early?season soil was collected from five certified organic tomato farms (from one to three fields per farm) and aliquoted for a comprehensive set of analyses: soil chemistry, metabarcoding, metabolomics, nematode assays, and viromics. DNA for viromics extractions succeeded for all samples, and the soil chemistry results have been shared with the growers. Fall sampling is currently underway and expected to finish by late September 2025. In Connecticut, the team collected soil from four certified organic farms and submitted them for testing, while the USDA?ARS Beltsville Nematology Lab began preliminary nematode analyses on nineteen pre-plant soil samples from our collaborators in California and Connecticut. In Florida one certified organic tomato grower was identified and a postdoc were recently hired. In support of Objective?2, the Penn State group conducted two microcosm experiments as preliminary trials to validate protocols for future work. These experiments assessed the survival of three bacterial plant pathogens in organic farm soil versus autoclaved soil. Two of the three pathogens remained viable in autoclaved soil for 15 days, whereas their populations declined precipitously in untreated soil within just three days. Recognizing the limitations of culture-dependent methods, the team is simultaneously developing a qPCR-based, culture-independent approach to increase throughput and sensitivity in future experiments. In Florida we have ordered an qPCR machine and developing qPCR protocols. As part of our outreach efforts aligned with Objective?4, Penn State hosted the inaugural "office hours" session for organic growers, introducing them to our project and the concept of soil micropredators in promoting disease resistance and soil health. During the session, presenters shared project insights, answered questions, and committed to follow-up communication. Fourteen growers registered, and six attended the live event. This activity marks the beginning of ongoing interactions and support between researchers and the organic farming community.
Publications
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