Undergraduate Research in Microbial Characterization

Searching the deep sea for clues to enhance agricultural carbon fixation: An undergraduate research program to isolate, characterize, and sequence the genomes of novel autotrophs

In collaboration with Professor Shari Freyermuth at the University of Missouri, Columbia, and Professor Kathleen Scott at the University of South Florida, we are developing tools for undergraduates to isolate and characterize novel autotrophs (organisms that form the foundation of the food chain and the energy chain) collected from deep-sea vents. The curricular tools we are implementing and refining will enable students to develop an integrated understanding across several subdisciplines in biology: gene evolution, protein structure and function, metabolic pathways, and ecological adaptation. At the same time, students will discover how genomic knowledge is created and contextualized by participating in the process of converting sequence data into new knowledge.

The student research experience spans the entire process from novel microorganism isolation and molecular and biochemical characterization to genome sequencing and annotation. By participating in this process, students will gain an understanding of how biological knowledge is created, beginning with organism isolation and sequence data. Furthermore, they will experience the importance of bioinformatic tools in guiding and interpreting their wet-lab experiments. Focusing on real data, with all of its imperfections, will necessitate that students learn to use algorithms with discernment. Finally, the curricula developed here will emphasize contextualization of the results—in terms of cellular metabolism, organismal fitness, and evolution. This will allow an interdisciplinary synthesis of the observations and inferences drawn from our genomic data.

These projects can be incorporated into laboratory courses for life science majors at all levels. These modules will be shared with faculty at diverse types of undergraduate institutions through a workshop in the summer of 2010.

This work is supported by the USDA Higher Education Challenge Grant Program