Year of Award


Document Type


Degree Type

Doctor of Philosophy (PhD)

Other Degree Name/Area of Focus

Microbiology and Biochemistry, Molecular Biology

Department or School/College

Division of Biological Sciences

Committee Co-chair

William Holben, Frank Rosenzweig

Commitee Members

Steve Lodmell, Scott Miller, Mark Pershouse


University of Montana


Intraspecific differences in genome composition and gene regulation are widespread in both natural and artificial prokaryotic systems. Understanding the molecular basis, population dynamics and fitness consequences of these differences can provide useful insight into many aspects of microbial ecology and evolution. The work presented here is a study of molecular variation in both natural and experimental populations of E. coli, conducted with the ultimate goal of gaining a better understanding of niche adaptation and the nature of molecular variation in microbes. In Chapter 2, the mechanistic basis of adaptation and diversification in a polymorphic experimental population of E. coli that spontaneously arose after -700 generations of glucose limitation in chemostats was explored. The results highlight the importance of mutations in both global and gene- specific regulators in maintaining the stable co-existence of clones, and the profound effect that founder genotype can have on evolutionary outcome. Chapter 3 examines the extant variation in genome composition at the gene level between natural isolates E. coli from different mammalian host species to address the basic question of how genetic measures of diversity are correlated with habitat variation. Our work shows that genome content is a more reliable indicator of host affiliation than a number of fingerprinting methods commonly used to distinguish host source, and that human-derived strains show patterns of gene presence/absence consistent with elevated genome recombination and convergence compared to isolates from other animals. The work in Chapter 4 extends these observations to include differences in gene transcription and suggests that mutations affecting the regulation of certain genes have occurred in parallel between unrelated isolates from the same host source. Finally, in Chapter 5, I describe a classroom inquiry developed during my year with the ECOS program at UM designed to introduce students to the nitrogen cycle from both a microbial and plant perspective. The broader significance and future directions of Chapters 2-5 are detailed in Chapter 6.



© Copyright 2009 Margaret Ann Kinnersley