(2ai) Engineering Biochemical Processes in Plant-Microbe Interactions for Sustainable Agriculture

Predictable manipulation of the biochemical processes governing beneficial and pathogenic plant-microbe interactions is essential to ensuring food security. There is a growing need to increase food production, improve agricultural system resiliency, and advance sustainable agricultural practices despite the pressures of climate change. Plant-microbe interactions are a key component of sustainable efforts to address these challenges. In natural systems, plants continuously interact with and regulate many thousands of microbes with their surrounding environment through biomolecular signals (proteins, peptides, and small metabolites). In contrast, conventional agricultural practices, which heavily rely on synthetic chemical fertilizers, tillage, and synthetic pesticides, disrupt these processes resulting in less mutualistic relationships and increased susceptibility to pathogens. My research program will leverage analytical biochemistry (MS, NMR, MD simulations, etc.) and chemical engineering principles (mass transport, kinetics, process systems, etc.) to elucidate how plants regulate beneficial and pathogenic microbes in their surrounding environment. Uncovering the rules of plant-microbe interactions will enable my research group to engineer these systems to enhance plant growth, resiliency against environmental stresses, and improve soil health.

Prior research experience:

My prior research has centered around understanding biological processes (peptide coassembly) and biological systems (corn-arbuscular mycorrhizal fungi) through analytical chemistry tools to develop design rules that allow the engineering and optimization of these processes and systems. My thesis research focused on deciphering the sequence-structure relationships that govern peptide coassembly into nanofibers. Peptide coassembly is an emerging horizon for the design of functional biomaterials with predictable and tunable properties for biomedical applications, such as drug delivery, tissue engineering, and vaccine platforms. My solid-state nuclear magnetic resonance (NMR) measurements and atomistic peptide nanofiber simulations revealed a significant amount of structural heterogeneity in many current coassembling designs. As a results, my collaborators and I developed a computational and experimental pipeline to screen new coassembling peptide sequence designs with specific supramolecular structures and macroscopic properties. These tools will help to advance the development and adoption of coassembling peptides as functional biomaterials.

My postdoctoral research focuses on advancing sustainable and regenerative agricultural practices by examining the role of microbes, such as arbuscular mycorrhizal fungi, in nutrient cycling. Mutualism between land plants and arbuscular mycorrhizal fungi (AMF) involves the exchange of plant-derived carbon for nitrogen and phosphorus forages by the AMF. This symbiosis can reduce chemical fertilizer use, increase soil carbon stocks, and improve plant resiliency against abiotic and biotic stresses. Current methods to quantify carbon allocation involve destructive sampling of plant and fungal biomass and is not spatially resolved. To address this technological gap, I have developed an experimental approach that combines carbon flow information from ¹¹C positron emission tomography (PET) with root structure information from x-ray computed tomography (CT) to spatially resolve the distribution of belowground carbon-containing photosynthates in situ. Preliminary results indicate that Rhizophagus irregularis, a common AMF species used in research, increases carbon allocation to maize roots by 11%. Some of this carbon is observed to increase lateral root growth, but the remaining carbon is exuded and exchanged with AMF for phosphorus and nitrogen. This experimental approach will allow researchers to evaluate the relative effects of fungal and plant genetics on plant-AMF symbiosis and facilitates the development of microbial consortia for improved plant growth and carbon sequestration.

Research Interests:

Plants interact with many thousands of microbes in their surrounding environment and regulate the relative abundance of beneficial and pathogenic microbes through biomolecules and metabolites. Decades of plant breeding under conventional agricultural practices have disincentivized mutualistic plant-microbe interactions and increased crop susceptibility to pathogens. My research program will focus on elucidating the biochemical rules governing these processes. Results from this research will enable my research group to engineer plant proteins, peptides, and small metabolites to enhance beneficial microbial interactions while reducing pathogenic microbe populations for improved food security.

Theme 1. Engineering nutrient transporters at mutualistic plant-microbe interfaces

Plants form specialized organs with certain mycorrhizal fungi and rhizobacteria during symbiosis, which facilitate the exchange of plant-derived carbon for essential nutrients (phosphorus and nitrogen). Conventional methods for plant breeding to identify advantageous mutations requires the screening of hundreds of genotypes and iterative selection over several years. This approach is made even more difficult by the lack of quantifiable plant-microbe traits. Thus, there is a fundamental need for technologies that accelerate the discovery of beneficial gene mutations that enhance plant-microbe mutualisms. Advances in computational biology methods and synthetic biology approaches are well-poised to rapidly decrease plant breeding timelines through predictions of genotype-phenotype relationships. My research group will leverage advances in protein structure prediction and protein-ligand simulations to computationally identify advantageous mutations that can be translated into plants through CRISPR-CAS genome editing. This computational and experimental pipeline will facilitate the discovery of advantageous genes for enhancing beneficial plant-microbe interactions in a predictive manner and can be applied to other protein targets, such as pattern recognition receptors and leucine-rich repeat receptors found in the plant immune system.

Theme 2. Design of de novo antimicrobial peptides as pesticides and therapeutics

The most common and prominent chemical defenses against pathogens in plants are antimicrobial peptides, e.g. defensins, thionins, and knottin-type peptides. Some antimicrobial peptides (AMP) in both plant and animal systems have been observed to form higher-order structures (oligomers and nanofibrils) which may be implicated in their mode of action. However, few antimicrobial peptide structures have been resolved which presents a knowledge gap in the sequence-structure-function relationships of AMPs. My group will employ solution and solid-state NMR methods commonly used in amyloid research to resolve the supramolecular structure of AMPs. Through the creation of a large library of AMP structures, researchers will be better able to resolve the mode of action of different classes of AMPs and develop sequence-structure-function relationships that underpin their antimicrobial activity and specificity towards particular pathogens. My research group will design de novo antimicrobial peptides that target emerging bacterial and fungal threats as novel pesticides and therapeutics for fungal infections, which are often difficult to clear with current medicines.

Theme 3. Manipulating plant-microbe chemical feedback processes to curate microbial communities

Plants continuously exude metabolites through their root system, and these root exudates curate the thousands of microbes in the soil close to the root known as the rhizosphere. In addition, microbes process root exudates and also excrete metabolites which results in positive and negative feedback processes between plants and microorganisms. While next-generation sequencing has rapidly accelerated our ability to identify microbial species within soils, the function of each species remains unknown and is dependent on the encompassing microbial community. To identify microbial functions, high-resolution experimental approaches are needed to reconstruct metabolic networks within these microbial communities. My research group will leverage analytical chemistry tools, such as mass spectrometry (MS), Fourier-transform infrared spectroscopy (FTIR), and NMR, to identify shifts in chemical signatures that correlate with shifts in microbial community composition within native and synthetic microbial communities. Stable isotope probing with ¹³C and ¹⁵N labelled metabolites will be used to trace metabolic pathways and test hypotheses of microbial function. A deepened knowledge of how metabolites drive changes in microbial community composition will enable the development of improved microbial inoculation strategies for enhancing plant growth and promoting soil health. These approaches and knowledge can also provide insights into the metabolic processes in the gut microbiome.

Teaching Interests:

I have broad interests in teaching core chemical engineering courses, especially transport, fluids, thermodynamics, and numerical methods, which are fundamental concepts in my past and future research. I am also excited to develop a graduate course on bioengineering in plant and microbial systems. My teaching experience includes serving as a teaching assistant in chemical engineering courses (unit operations, separations, and numerical methods in chemical engineering) as well as beginner and intermediate French. I have led an 8-week extended orientation graduate-level course focused on topics such as building community, mentor/advising relationships, professional development, stress/time management, resilience, diversity and inclusion, and leadership development. I have also been a guest lecturer for Washington University in St. Louis’s TRIO scholars program, which supports first generation, low income, and/or students with disabilities. The 45-minute lectures focused on types of research, career paths within research, and advice on finding undergraduate research positions. My teaching philosophy focuses on deep learning and leverages multimedia and computational resources to engage students at multiple levels and different learning styles. Critical thinking and creative problem solving are essential skills of successful engineers, and I plan to draw from my experiences as a process engineer and researcher to help develop these skills with real-world examples.

I have also mentored 13 students ranging from high school to undergraduate and graduate levels. Two of my undergraduate mentees have won undergraduate research awards ($1000) and are currently pursuing PhDs. One graduate student mentee was recently awarded a mini-grant (~$2500) to further develop our research examining changes in root exudation chemistry in intercropped systems. My mentoring philosophy centers around empowering mentees to achieve coaligned research and career goals as co-workers in a supportive and inclusive environment.