Research

To make new discoveries in soil microbial ecology while addressing real-world problems, our lab combines applied studies aimed at addressing specific crop production challenges with fundamental research investigating how soil and plant microbiomes evolve and functionally interact with plants to mediate critical agroecosystem services. We use formal and informal stakeholder surveys to identify the most problematic production challenges facing growers and many of our studies are conducted on-farm using a participatory research approach to ensure results will be practical and to aid in the adoption of improved practices. At the same time we conduct controlled studies in the greenhouse and growth chamber to verify specific mechanisms mediating beneficial plant-soil-microbial relationships. We use a combination of traditional microbiological approaches such as plate counts and enzyme assays as well as newer -omics based tools in the laboratory to answer our research questions. Specific aims of our on-going studies include:

Controlling plant and food-borne pathogens using biological control strategies

Phytophthora capsici causing damage in a melon field in southern Indiana (Photo: N. Shoaf)

Growers often report that controlling diseases caused by plant pathogens are one of their biggest production challenges, especially in warm and humid climates. While planting varieties with genetic resistance is one of the most effective strategies to control diseases caused by plant pathogens, these organisms are constantly evolving to overcome existing plant defense strategies. At the same time, many pesticides are also becoming increasingly ineffective as plant pathogens develop resistance to these products. Moreover, some pesticides can negatively affect beneficial microbes and other organisms as well as pathogens. Another challenge facing growers are human enteric pathogens such as Escherichia coli and Salmonella enterica that can attach to edible plant tissues and make people sick when they are consumed. Following food safety guidelines can help protect crops from food-borne enteric pathogens, but growers need additional strategies to ensure the safety of their crops. Our lab aims to address these challenges by learning more about the ecology of plant and food-borne pathogens in specialty crop production system. We are also investigating ways to actively suppress the survival and virulence of these pathogens by increasing populations of soil beneficial microbes that can outcompete these pathogens for resources, produce antibiotic compounds that directly suppress them, and/or induce systemic defense responses in plants that prevent colonization and proliferation.

Improving nitrogen-use efficiency in specialty crop production systems

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)

Nitrogen (N) is generally the most limiting nutrient in most crop production systems so growers supply substantial amounts of N fertilizers to meet crop needs. However, less than 50% of the N in these fertilizers is generally acquired by most crop plants and the rest is subject to loss via leaching and evolution of nitrous oxide (N2O), a potent greenhouse gas, which negatively impacts the health of the environment. Both over- and under-application of N fertilizers can also make crops more susceptible to pathogens and insect pests, and reduce the yield and quality of produce. Relying on organic fertility sources such as leguminous cover crops and animal waste products can help reduce N loss to the environment, however, timing nutrient availability with crop nutrient needs is difficult because these sources must mineralize via microbial mediated processes before they are available for plant uptake. Our lab aims to address this challenge by learning more about factors regulating the composition and activity of microbes that regulate the soil N cycle. We are also investigating how plants can influence soil N cycling by signaling and supporting specific microbial in their rhizospheres and endospheres, and how these processes interact with other microbes to influence pathogen dynamics in specialty crop production systems. 

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

Greenhouse trial investigating how quinoa genetics and seedborne endophytes interact to influence cadmium accumulation in grain

Fruits and vegetables provide significant sources of many vitamins and other health promoting compounds for the human diet, but these plants they can accumulate toxic heavy metals such as cadmium, lead and arsenic in their edible plant tissues which negatively affects human health. Elevated concentrations of heavy metals in soil can also stress plants making them more susceptible to pathogens and insect pests, and reduce the yield and quality of produce. Soil and plant microbiomes can mediate these plant stress responses and directly influence the amount and composition of health-promoting micronutrients in produce like iron and zinc as well as toxic heavy metals, by regulating the cycling of these elements in soil and influencing the translocation of these elements within plant organs. Many plant-associated microbes can also directly influence the concentrations of other health promoting plant compounds in produce such as antioxidants by altering plant physiological processes associated with biotic and abiotic stress tolerance. Our lab aims to increase the productivity, quality and safety of specialty crops by learning more about how soil, crop and environmental factors influence these microbial mediated processes. At the same time, we are conducting studies aimed at identifying: practical approaches to stabilize and sequester toxic heavy metals in soil, crop genotypes that exclude uptake of toxic heavy metals while maintaining or increasing uptake of beneficial micronutrients, and management practices that  can increase the nutritional quality of produce. 

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

TOMI and CIOA breeding nurseries behind the sunflowers at Purdue’s student farm in West Lafayette, IN.

Demand for fruits and vegetables grown locally using environmentally sustainable production practices is growing rapidly. Most crop varieties have been selected for broad adaptability across a range of diverse environments and in some cases, for harvest of immature fruit that can be shipped long distances which reduces flavor. Moreover, most crop varieties have been bred under conventional farming practices, so they may not have traits needed to optimize productivity in low-input and organic farming systems. Our lab aims to help address these challenges by investigating genetic factors influencing how different crop genotypes can signal and support beneficial soil microbes that help plants acquire nutrients and withstand attack by pests. The long-term goal of these studies is to identify practical approaches to integrate selection for beneficial plant-microbial relationships into crop breeding programs and as a result, better leverage beneficial soil microbial communities to increase the health and productivity of plants. At the same time, we are participating in the development of new improved carrot and tomato varieties and identifying varieties optimally adapted to Indiana by screening and selecting from advanced accessions in local research station and on-farm trials.