Research

 

Our program advances discovery in soil microbial ecology while addressing real-world production challenges by integrating participatory, on‑farm research with mechanistic studies of plant–soil–microbiome assembly and function. Stakeholder engagement guides priority setting, and field experiments are paired with controlled greenhouse and laboratory studies that leverage multi‑omics approaches, hyperspectral sensing, and machine learning to resolve mechanisms underlying beneficial plant-soil-microbial interactions. Our studies pursue two complementary pathways: (i) identifying management practices that enrich soil microbial consortia driving key agroecosystem services, and (ii) characterizing plant genetic traits and molecular markers that regulate microbiome recruitment and function to enable microbiome‑assisted crop breeding. By linking field‑based inquiry with high‑resolution analytical tools, we build mechanistic insight and predictive capacity to design resilient agroecosystems that enhance sustainability, environmental stewardship, food quality, and the long‑term viability of diversified farming systems.

Controlling plant and food-borne pathogens using biological control strategies

Growers consistently identify plant disease management as a primary production constraint, particularly under warm, humid conditions that favor pathogen proliferation. Although host genetic resistance remains one of the most effective control strategies, pathogen populations rapidly evolve to overcome plant defenses, while repeated pesticide use can select for resistant strains and disrupt beneficial microbial communities. Concurrently, food safety risks posed by human enteric pathogens such as Escherichia coli and Salmonella enterica present an additional challenge, as these organisms can colonize edible tissues despite adherence to standard mitigation practices. Our research addresses these intersecting challenges by advancing an ecological understanding of plant and food-borne pathogens within specialty crop systems. We focus on leveraging soil and root-associated microbiomes to suppress pathogen survival and virulence through mechanisms that can include competitive exclusion, antimicrobial metabolite production, and induction of plant systemic defenses, thereby developing biologically based strategies that enhance both crop health and food safety.

 

Improving nitrogen-use efficiency in specialty crop production systems

Nitrogen (N) is typically the most limiting nutrient in crop production systems, leading growers to apply substantial fertilizer inputs to meet crop demand. However, plants often recover less than 50% of applied N, with the remainder lost through leaching and emissions of nitrous oxide (N₂O), a potent greenhouse gas with significant environmental consequences. Both over- and under-application further destabilize plant health by increasing susceptibility to pathogens and insect pests and reducing yield and product quality. While organic fertility sources such as leguminous cover crops and animal manures can mitigate N losses, synchronizing N availability with crop demand remains challenging because these inputs require microbially mediated mineralization. Our research addresses this constraint by investigating the ecological and biochemical controls over microbial communities that regulate soil N cycling. We also examine how plants actively shape rhizosphere and endosphere microbiomes through root exudation and signaling to influence N transformations, and how these plant–microbe interactions intersect with pathogen dynamics in specialty crop systems.

Increasing the nutritional quality of produce while preventing accumulation of toxic heavy metals

Fruits and vegetables are critical sources of vitamins and health-promoting phytochemicals, yet they can also accumulate toxic heavy metals such as cadmium, lead, and arsenic in edible tissues, posing risks to human health. Elevated soil metal concentrations further impose physiological stress on plants, increasing susceptibility to pathogens and insect pests while reducing yield and quality. Soil and plant microbiomes play a central role in mediating these outcomes by regulating metal speciation, mobility, and plant uptake, thereby influencing both the accumulation of toxic elements and the bioavailability of essential micronutrients such as iron and zinc. In addition, plant-associated microbes can modulate the synthesis of health-promoting compounds, including antioxidants, through effects on plant stress physiology. Our research seeks to enhance the productivity, quality, and safety of specialty crops by elucidating how soil, crop, and environmental factors shape these microbially mediated processes. In parallel, we identify practical strategies to stabilize and sequester toxic metals in soils, characterize crop genotypes that limit metal uptake while maintaining nutrient acquisition, and develop management practices that improve the nutritional quality of produce.

Developing new improved tomato and carrot varieties for low-input and organic farming systems

Demand for locally produced fruits and vegetables grown under environmentally sustainable management is increasing rapidly, yet many existing cultivars were bred for broad adaptability and long-distance supply chains, often prioritizing yield and post-harvest durability over flavor and ecological performance. In addition, most varieties have been developed under high-input conventional systems and may lack traits needed to perform optimally in low-input or organic production. Our research addresses these gaps by investigating the genetic basis of plant traits that regulate recruitment and function of beneficial soil microbiomes, including those that enhance nutrient acquisition and confer resistance to pests and pathogens. The long-term objective is to integrate selection for plant–microbe interactions into crop improvement programs, thereby enabling more effective use of endogenous soil microbial communities to support plant health and productivity. In parallel, we contribute to the development of improved carrot and tomato cultivars and identify varieties adapted to low-input and organic systems through coordinated research station and on-farm trials evaluating advanced breeding lines.