This project will begin to answer the fundamental question of how bacteria survive long-term starvation. A great deal is known about the mechanics of how bacteria grow and multiply. By contrast, little is known about how bacteria survive long periods of nutrient starvation. This is a considerable knowledge gap given that natural environments tend to be nutrient-poor. As a consequence bacteria are forced to persist in a state of non-growth or very slow growth. How do bacteria survive long-term starvation? What is the genetic and physiological basis for this? When cells do die ? what are the most common causes of death? The proposed research will focus on a bacterium named Rhodopseudomonas palustris that has been identified as a good model for these studies. This bacterium stays alive for periods of weeks in a laboratory setting in a starved non-growing state. A comprehensive program of mutagenesis and high throughput DNA sequencing technology will define genes that contribute to starvation survival. These genes will be validated and their role in starvation survival defined in an iterative process of mutagenesis, laboratory studies and gene expression studies.
Broader impacts. The project will establish a user group in functional genomics of microbes. A group of eighteen investigators at the University of Washington who focus on microbial biology will form the core of this user group. The group will develop novel experimental and computational tools for data analysis that will be freely available to the scientific community. This will also serve as a focal point to train graduate students and undergraduates to apply global systems biology approaches to bacteria. The user group will seek to engage faculty and students from smaller schools in the area, including University of Puget Sound, Seattle Pacific University, Seattle University, Evergreen College, Bellevue Community College, and the Seattle Community Colleges. This project will also support a female postdoctoral fellow who will be trained to integrate data from bacterial genetics, physiology and computational analyses to answer questions about how cells function at the whole cell level. Finally, this research will lead to a better understanding of the role of non-growing microbes, which dominate in nature, and drive the global carbon and nitrogen cycles. It will also promote more efficient use of non-growing microbes as cell factories for production of value added products like biofuels.
In this project we conducted studies of a single-cell microbe that can convert energy from light to hydrogen gas. This is a form of bioenergy that can be used as a fuel. Our microbe produces higher amounts of hydrogen gas when it is not growing and in a resting state. This is probably because the cells are not diverting resources from hydrogen production to growth. Our microbe survives for months when it is not growing and it can produce hydrogen gas over this long time period. If we can understand what goes on inside the cell when it is in a non-growing state then this might be helpful for the design of strategies to sustain and improve microbial bioenergy production. We identified specific genes that are turned on when the microbe transitions to a non-growing state. We also identified genes that are essential for cells to survive when they are not growing, but that are dispensable when they are growing. Most of the essential genes were unexpected based on work done previously with other microbes. Some of the genes had been described as having a general function in other bacteria, but the precise function is not known. We also identified a significant number of genes essential for long term survival that are found in many other bacteria but have unknown functions. Our next step will be to determine exactly what the genes that we identified do to help cells have such good longevity.
