Research
Our research connects fundamental microbial ecology with challenges facing specialty crop production. We seek to understand how plant genetics, soil conditions, and agricultural management shape the assembly and function of plant and soil microbiomes, and how these interactions influence plant health and resilience. We combine mechanistic laboratory and greenhouse studies with field and participatory on-farm research to identify microbial functions, plant traits, and soil processes that can be leveraged to improve crop health, resource-use efficiency, and resilience. Across this work, we are particularly interested in translating new understanding of plant-soil-microbe interactions into strategies for specialty crop improvement and management.
Harnessing microbiomes for plant health and disease suppression
Phytophthora capsici causing damage in a melon field in southern Indiana (Photo: N. Shoaf)
Plant and food-borne pathogens remain important constraints to specialty crop production and food safety. Our research seeks to understand how soil and plant-associated microbiomes influence pathogen establishment, survival, and disease development, and how these microbial communities can be leveraged to improve plant health. We investigate mechanisms of microbiome-mediated disease suppression, including microbial competition, antimicrobial activity, and plant-mediated defenses, and examine how these interactions are shaped by plant genetics, soil conditions, and crop management. Ultimately, we aim to translate this ecological understanding into biologically based strategies that improve specialty crop health, resilience, and food safety.
Improving nitrogen-use efficiency through plant-soil-microbial interactions
Research trial investigating how different types of fertility amendments altered soil N cycles and pepper health and productivity in high tunnel and open field production systems (Photo: M. Rudisill)
Our research examines how microbial processes and plant-microbe interactions regulate nutrient cycling and plant nutrition. We are particularly interested in how plants shape rhizosphere microbial communities and functions that influence nutrient availability and acquisition, and how these relationships vary with plant genetics, soil conditions, and management. Nitrogen cycling is an important focus of this work, providing a model for understanding how microbial functions can be leveraged to improve crop nutrition, plant health, and resource-use efficiency in specialty crop systems.
Understanding microbiome-mediated responses to metals and environmental stress
Greenhouse trial investigating how quinoa genetics and seedborne endophytes interact to influence cadmium accumulation in grain
Our research investigates how plant-soil-microbe interactions shape crop responses to environmental stress, including metals and emerging contaminants. We seek to understand how microbial processes influence contaminant fate and plant uptake, nutrient availability, and plant stress responses, and how these interactions vary among crop genotypes and environmental conditions. This work provides a mechanistic foundation for identifying plant traits, microbial functions, and management practices that improve crop resilience, quality, and food safety.
Leveraging plant genetics and microbiomes for specialty crop improvement
TOMI and CIOA breeding nurseries behind the sunflowers at Purdue’s student farm in West Lafayette, IN.
Plant genotypes differ in their ability to recruit and interact with beneficial microorganisms that contribute to nutrient acquisition, disease resistance, and resilience. Our research seeks to understand the genetic basis of these plant-microbiome interactions and how they can be leveraged for specialty crop improvement. We use genetic mapping to identify plant genomic regions and molecular markers associated with microbiome recruitment and function, with the long-term goal of incorporating beneficial plant-microbe interactions into crop breeding. Working primarily with tomato and carrot, we connect this mechanistic and genetic research with breeding nurseries, research-station experiments, and on-farm trials to develop and identify cultivars that perform well across diverse production environments, including low-input and organic systems.