Location: Citrus and Other Subtropical Products Research
2025 Annual Report
Objectives
1. Develop and improve non-fumigant crop production approaches to maximize efficacy and optimize crop productivity.
1a. Optimize anaerobic soil disinfestation (ASD) application for effectively managing soilborne pests and increasing plant health and yield.
1b. Combine ASD with novel crop production tools for increased value.
1c. Develop and implement adaptation of methyl bromide alternatives to soil fumigation, including non-fumigant approaches to management of nematodes and other pathogens in California carrot and strawberry production, such as anaerobic soil disinfestation.
2. Establish methods for improving soil health, plant nutrition, and pathogen management in greenhouse and other controlled environment production systems.
2a. Increase the environmental benefit of ASD through incorporation of reclaimed water for nursery production.
2b. Utilizing ASD to managing bacterial wilt in controlled environments.
2c. Ascertain methods to increase microgreen production and manage pathogens.
3. Characterize microbial communities and plant interactions that contribute to soil health and plant disease management.
3a. Identify abiotic and biotic factors that contribute to rootstock resistance breakdown.
3b. Characterize the relationship between the soil microbiome and plant health.
Approach
Soilborne plant pathogens, weeds, nematodes, and nutrient mismanagement cause considerable yield losses in vegetable and ornamental crops. In the Southeast, although methyl bromide was banned, soil fumigation remains a critical component in vegetables and fruits production. Alternative chemicals continue to be investigated, but only 1,3-dichloropropene, chloropicrin, an allyisothiocyanate biofumigant, and methyl isothiocyanate generators remain available. Dimethyl disulfide is registered, although there is currently no U.S. distributor. These materials, applied alone or in various combinations, do not provide the spectrum or level of control that resulted from the use of methyl bromide. Dependence on fumigation leaves growers vulnerable to regulatory and economic forces associated with pesticide use. Crop production systems, soil treatments, and nutrient management tools that control pests and maximize yield, while reducing negative environmental and human impacts, are the focus of the proposed research project on development and improvement of biological and cultural management strategies for pathogens and weeds impacting fruit, vegetable, and ornamental crop yields. These systems will be assessed holistically for their potential impact on the environment and product quality. An integrated approach of improving and understanding the role of the soil microbiome, soil quality, and plant nutrition in mitigating impacts of biotic and abiotic stressors will result in regenerative agricultural practices that increase crop productivity. While independent research will be conducted in laboratories, greenhouses, and in the field, ongoing and new collaborations with other ARS, university, and industry researchers will broaden the scope of the research. Continued stakeholder engagement is critical for effective technology transfer and for ensuring practical tool delivery. Mitigating the impact of soilborne pests impacting crop production while improving U.S. agroecology aligns with the USDA-ARS mission, “to sustain a competitive agricultural economy".
Progress Report
ARS scientists in Fort Pierce, Florida implemented anaerobic soil disinfestation (ASD) field trials to optimize the non-chemical microbially based technique to manage biological limiting factors that reduce plant health and yield. In accordance with Objective 1. scientists collaborated with farmers and producers and University of Florida researchers to optimize ASD for conventional and organic production systems. While inclement weather delayed the establishment of field trials and first planting, the team has collected sufficient data to develop recommendations for strawberry growers to utilize ASD based on plant health, yield, and economic data. To fulfill subobjectives 1a1 and 1a2 repeated field trials and biometric assessments of novel crops grown in ASD treated soils were conducted. Furthermore, to increase adoption of ASD, trials have been conducted with biodegradable mulch and slow release halosulfuron for weed control to fulfill subobjectives 1b1 and 1b2. Additionally, experiments focused on the management of root knot nematodes in carrots, including field experiments comparing carrots grown in ASD and non-ASD treated soil under various tarps during the treatment period. Greenhouse experiments evaluating biologically based agricultural inputs for nematode suppression in organic carrot production were initiated. The decomposition of biodegradable mulches was assumed to be microbial derived, while true for some of the biodegradable mulch other factors such as heat and moisture also affect the integrity of the biodegradable plastic. Multiple bacterial strains were isolated from degraded plastic, several of which were propagated on plastic-impregnated media, which will allow for the identification of strains that may be of industrial importance. The combination of halosulfuron applied to the soil and halosulfuron incorporated mulch with ASD appears to provide greater weed management than ASD alone.
Objective 2 was designed to conduct greenhouse experiments prior to large-scale or field application. Subobjective 2a1, focused on the potential use of reclaimed water for ASD establishment identified heavy metals as an impediment to the use of this resource. Water treatment facilities test for coliform bacteria and not for heavy metals, pharmaceuticals, or other potential toxins. Under subobjective 2b, greenhouse blueberry trials on ASD impacts on the important emerging disease, blueberry bacterial wilt, is on-going and data from replicated, repeated trials are currently being analyzed. Results obtained from several experiments conducted under subobjective 2c have been published and are reported below.
Objective 3 consists of experiments that result in a better understanding of variables that influence plant health and management of plant pathogens and phytoparasitic nematodes. In accordance with subobjective 3a, experiments were repeated in which the evaluation of temperature, tomato genetics, and nematode population compositions were tested for their impact on the field-observed loss of resistance of tomato to root-knot nematode. While temperature had an impact on the Mi gene, as previously reported, this was not true for all nematode species. In two locations in which the breakdown of resistance occurred have been identified as having Meloidogyne enterolobii, contrary to that history of those fields being reported as having only M. incognita, which could contribute to the lack of field performance of Mi-gene containing tomatoes. Addressing subobjective 3b, field soil from multiple farm sites was collected and prepared for experiments by autoclaving to remove field microbial populations or retained for planting with the native microbiome. The first round of greenhouse experiments is underway to determine the effects of the existing soil microbiome on tomato plant health and if the components of ASD contribute bacterial communities to the treated soil or only enhance existing bacterial communities.
Accomplishments
1. Soilborne pathogens, phytonematodes, and weeds reduce strawberry yield, plant health, and can contribute to major crop loss. ARS researchers from Fort Pierce, Florida believe growers typically use soil disinfestation chemicals to manage these limiting factors, however, due to state and federal restrictions, urbanization, and reduced supply of soil fumigants, Florida strawberry growers have limited preplant tools to manage these soilborne pests. Anaerobic soil disinfestation (ASD) offers a biologically based technique to manage these limiting factors. ASD optimized for Florida strawberry growers allows for treatment of buffer zones in which fumigant use is restricted and provides a growing organic strawberry sector with a preplant soil pest control option. In previous studies using ASD optimized for vegetable production, strawberries became overly vegetative, and fruit production was reduced. ARS scientists from Fort Pierce, Florida conducted field experiments with collaborators at the University of Florida to determine the optimal ratio of ASD soil amendments for Florida strawberry production. Repeated field experiments were conducted at two different organic field sites in Florida using two previously identified rates of soil amendments compared to an organic standard grower practice. Plants grown using both ASD treatments produced significantly greater yield than those produced using the standard practices. Additionally, six different strawberry cultivars were grown, and it was documented that there was a cultivar by treatment interaction. Farmer-driven on-farm demonstration trials were repeated in five locations and the application of ASD on flat ground using clear totally impermeable film resulted in the greatest reduction in nutsedge at three locations when compared to the grower standard or solarization applied alone.
2. Bacterial wilt caused by Ralstonia presents a relatively new significant threat to the Florida blueberry industry. ARS researchers from Fort Pierce, Florida believe Ralstonia solanacearum is a soilborne bacterium that can kill more than a hundred crops, including important members of the Solanaceae and Cucurbitaceae. It is very difficult to manage R. solanacearum and growers will often have to move from an infested field. ARS scientists from Fort Pierce, Florida conducted a greenhouse study to determine if blueberry bushes could grow in ASD treated soil/pine bark mixture, a common substrate for blueberry bushes. After a two-year study, no disease was observed, thus 224 blueberry bushes were split between ASD treated and non-treated soil at USDA ARS research farm where R. solanacearum was detected in soil, irrigation canals, and tomato plants. Four different blueberry cultivars were planted with varying susceptibility to bacterial wilt. This is the first blueberry preplant treatment for managing soilborne pathogens and pests.
3. Nutrient deficiencies are problematic for Americans, especially for women and children. Microgreens, a newly emerging group of nutrient dense vegetables, are relatively easy to grow and are an excellent target for biofortification. ARS scientists from Fort Pierce, Florida conducted greenhouse studies to determine if alternating light or adding trace minerals to fertilizer could increase the microgreen growth and nutrient content and reduce the incident of pathogens previously observed in microgreen production. It was established that higher light intensities stimulated flavonoid, phenolic acid, and vitamin C biosynthesis, likely due to oxidative stress and photoinhibition. Zinc enrichment increased the accumulation of sulfur-containing and branched-chain amino acids, along with oxalic acid, which may contribute to metal detoxification. Overall, light intensity emerged as the primary driver of metabolic shifts across various metabolite classes, exerting a more pronounced influence than Zn application. These findings establish guidelines for enhancing the nutritional and functional quality of microgreens which contributes to sustainable and nutritious food production.
Review Publications
Ozbudak, E., Carrillo-Tarazona, Y., A. Diaz, E., Tabay Zambon, F., Rossi, L., Peres, N., Raffaele, S., M. Cano, L. 2025. Transcriptome analysis of Colletotrichum nymphaeae-Strawberry interaction reveals in planta expressed genes associated with virulence. Frontiers in Plant Science. 15:1390926. https://doi.org/10.3389/fpls.2024.1390926.
Trandel-Hayse, M., Bai, J., Jeffries, K.A., Poole, G., Hensley, M.E., Schonborn, W.A., Digioia, F., Rosskopf, E.N. Light source and spectra influence the phytochemical profile of amaranth microgreens. Food Bioscience. 64:105839. 2025. https://doi.org/10.1016/j.fbio.2025.105839.
Ono-Raphel, J., Custer, G., Arrington, K., Morrison, B., Kaye, J., Rosskopf, E.N., Din-Andreote, F., Di Gioia, F. Effects of carbon sources on soil bacterial community dynamics during anaerobic soil disinfestation in an organic tomato production system. Agriculture Ecosystems and the Environment. 381:109448. 2024. https://doi.org/10.1016/j.agee.2024.109448.
Poudel, P., Jeffries, K.A., Bai, J., Dorado, C., Rosskopf, E.N., Di Gioia, F. Radish microgreen metabolomic profile in response to zinc biofortification and light intensity. Journal of Agricultural and Food Chemistry. 2025. https://doi.org/10.1021/acs.jafc.5c03574.
Poudel, P., Jeffries, K.A., Bai, J., Dorado, C., Rosskopf, E.N., Di Gioia, F. Light intensity and zinc biofortification differentially impact the metabolomic profile of pea microgreens. Food Chemistry. 490:145146. 2025. https://doi.org/10.1016/j.foodchem.2025.145146.
Di Gioia, F., Hong, J.C., Zhao, X., Xu, N., Ono-Raphel, J., Morrison, B., Balaguer, R., Romano, C., Arrington, K., Moreira Calix, D., Desaeger, J., Dini-Andreote, F., Schmidt, C., Gao, Z., Chalam, R., Fronk, L., Ford, T., Elkner, T., Goodiel, Y., Demchak, K., Formiga, A., Gugino, B., Kaye, J., Rosskopf, E.N. Advancing organic amendment-based soil management approaches: a paradigm shift from soil disinfestation to nourishing soil health. Acta horticulturae. 1410:1-8. 2024. https://doi.org/10.17660/ActaHortic.2024.1410.1.
Di Gioia, F., Balaguer, R., Fritzner, P., Morrison, B., Ono-Raphel, J., Passerini, L., Vecchia, L., Demchak, K., Roman, C., Schmidt, C., Gugino, B., Elkner, T., Hong, J.C., Dini-Andreote, F., Rosskopf, E.N. Optimizing anaerobic soil disinfestation for high tunnel specialty crop production systems in the U.S. Mid-Atlantic region. Acta horticulturae. 1410:133-142. 2024. https://doi.org/10.17660/ActaHortic.2024.1410.19.