476183 Engineering the Plant Microbiome to Complement Host Phenotype

Sunday, November 13, 2016
Continental 4 & 5 (Hilton San Francisco Union Square)
Collin M. Timm, Biological and Nanoscale Systems Group, Oak Ridge National Laboratory, Oak Ridge, TN

Engineering the plant microbiome to complement host phenotype

Plant roots are a rich source of carbon in an otherwise nutrient starved soil environment, and as a result, a diverse community of microbes is attracted to the plant. The complex network of beneficial and antagonistic interactions of community members, with each other and with the host, forms a microbiome that is generally a beneficial extension of the host plant. The plant microbiome can increase nutrient acquisition rates, increase resistance to pathogens, and alleviate environmental stresses such as drought. Understanding how the microbiome functions and interfaces with the host has applications in food and bioenergy agriculture, production of secondary metabolites from plants for commodity chemicals and pharmaceuticals, and will improve our general understanding of the host-microbiome relationship. My research goal is to engineer the microbiome to optimize plant growth for sustainable agriculture and biochemical production.

Research Interests:

My current research is focused on the bacterial microbiome of Populus, a genera of fast-growing trees cultivated as a second-generation biofuel feedstock. Using metabolic models, comparative genomics, and phenotype screening we showed that the extreme diversity within 19 Pseudomonas fluorescens strains isolated from Populus was driven by the metabolite profile of the host and correlated with spatial organization of the microbiome. To gain further insight into spatial aspects of cooperation and inhibition, we designed a novel patterning approach to study distance dependent interactions between bacterial strains. We are also studying the molecular mechanisms that lead to phenotypic changes in the host when colonized by individual bacteria or mixtures using phenotype measures, metabolomics, and transcriptomics. The results show that bacteria can behave synergistically to help optimize and modify plant growth phenotypes. To study community behavior, we measured microbiome response to host stresses using 16S sequencing and identified candidate bacterial taxa that may help alleviate host response to drought, light limitation, and toxin stresses.

My research group will build on the results described by studying how constructed communities of bacteria respond to the host and environmental stresses. Specifically, we will design communities of genome-sequenced bacterial isolates using individual phenotypes, phylogenetic relationships, and predicted genomic content and test the ability of the community to mimic the natural microbiome response to stress. Our approach will include quantitative analysis of bacterial strains and their interactions, and characterization of community response to host stress. Models of bacterial kinetics, metabolism, and interactions in culture conditions will be used to predict behavior on the host plant. Integrating quantitative experimental data with predictive models will help us understand how the microbiome assembles in nature, ultimately leading to the ability to engineer constructed communities of bacteria with specific and predictable functions.

Postdoctoral Project: Interactions between Populus and cultured representatives of its bacterial microbiome

Mentors: Dale A Pelletier and David J Weston, Oak Ridge National Laboratory, Biosciences Division

PhD Dissertation: Kinetics of vesicular stomatitis virus mRNA and genomes during infection

Mentor:John Yin, University of Wisconsin-Madison, Department of Chemical and Biological Engineering

Research Career

My research career began as an undergraduate where I studied gas hydrate formation at the Colorado School of Mines. I helped develop software for predicting hydrate formation in gas pipelines and tested predictions using a novel reactor in the laboratory. This valuable experience familiarized me with quantitative experiments and laboratory techniques, but more importantly convinced me to go to graduate school to continue my academic career. In graduate school I changed my focus to biological engineering, where I learned how to design experiments and control biological systems to make quantitative measurements of viral replication. I used the data I collected to build kinetic models of viral infection, and showed that viral mRNA production is independent from host environment and only depends on viral genome number. This suggests that transcription is robust and insensitive and helps to identify targets for anti-viral strategies for RNA viruses. While studying interactions between two organisms (viruses and cells), I became interested in complex ecological systems with multi-member interactions. I was fortunate to find a post-doctoral position as a part of the Plant-Microbe Interfaces project at Oak Ridge National Laboratory studying the microbiome of Populus trees. I have focused specifically on understanding bacterial genetic and phenotypic diversity in the system to help determine how interactions between microbiome members and the host lead to overall system function. In my next step I will study how multi-member systems can be engineered to perform specific functions.

Teaching Interests:

As I have moved through my academic career I have become more active in my role as a teacher and mentor. During my undergraduate studies I worked closely with many of my peers, and began to appreciate the different learning and teaching styles present in the group. I had the opportunity to informally tutor younger students in heat and mass transfer classes; in both cases their grades improved after we began working together. In graduate school I got my first opportunity to formally teach classes to students. As a teaching assistant for the introductory transport course, I enjoyed spending time developing lectures and example problems for students, and focused on how I could engage the entire class in a single topic. I also worked as a TA for the process control laboratory where I helped students run experiments and taught them to present their results in concise reports. As a post-doc I have worked with undergraduate summer students and new graduate students from chemistry, biochemistry, biological systems engineering and chemical engineering. Their unique backgrounds have helped me generalize my teaching methods. I have helped them learn how to work in the laboratory, analyze data, and present results. The students helped identify metabolic pathways, isolated bacteria that grow on Populus metabolites, identified genes that affect plant growth, and developed methods for studying root growth in microfluidic devices. Watching students succeed with my input has been extremely important to my development and has helped me appreciate the commitment of my teachers and mentors throughout my academic career.

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