Scientists using new techniques based on DNA sequencing are now able to study how bacteria thrive in many different conditions. This is important because bacteria are much simpler and easier to study than other life forms such as plants and animals, and much of what is learned using bacteria can be applied to other types of organisms. However, most research involves studies of bacteria living in isolation in the laboratory. Very few organisms live in isolation in nature, and therefore it is important to develop research methods to study bacteria living in communities. The research will show how genes and other component parts of the bacteria work together in order to sustain life and especially how these interactions help bacteria survive in harsh and rapidly changing situations. The results of this research will help predict how organisms can adapt and survive when their surroundings change to less hospitable conditions. The project is anticipated to have applications in many different areas including the study of bacteria that live in and on the human body, the design and control of pollution clean-up systems, and acquisition of fundamental knowledge of how organisms in aquatic environments survive and thrive.This project will provide interdisciplinary training to students (undergraduate and graduate) and postdoctoral fellows in engineering, microbiology, biotechnology and computational biology, in the context of both academic research and industrial applications.
A primary goal of systems biology is to develop a quantitative understanding of how microorganisms respond to changing conditions. Therefore, it is important to understand the molecular and regulatory "wiring diagrams" that enable unculturable organisms to thrive in dynamic environments. One such group of unculturable organisms,the biotechnologically-relevant group of bacteria (Accumulibacter), combines metabolic and regulatory processes in different ways to yield novel phenotypes in response to environmental stimuli. Accumulibacter is a well-studied yet uncultivated microbe. It must constantly adapt its global physiological response to changing environmental stresses, namely biphasic cycles of anaerobic "feast" and aerobic "famine" conditions. These oscillating conditions select strongly for the Accumulibacter phenotype, which includes the ability to sequester massive amounts of carbon and phosphate intracellularly in different phases of the cycle. However, the regulatory and metabolic network dynamics that coordinate such precise transitions remain poorly understood. Employing a variety of -omics techniques and a systems biology framework within the context of a tractable and self-assembled microbial community, studies will: 1) identify the metabolic modules responsible for Accumulibacter's unique physiology via comparative genomics and transcriptomics; 2) map the regulons that coordinate Accumulibacter's storage response via ChIP-seq targeting candidate regulatory elements; and 3) identify environmental drivers of Accumulibacter's regulatory program.
