The School of Molecular and Cellular Biology at the University of Illinois at Urbana-Champaign

Bacteria and Archaea represent the vast majority of biodiversity on Earth. In fact, the closer we look at microbial populations, the more diversity we see. For example, microbial environmental genomic, is uncovering patterns of sequence variation (microdiversity) within species that were once assumed to be homogeneous. Making sense of this diversity will require identifying the ways that dynamic ecological and evolutionary processes interact in the natural microbial world. Because microorganisms are integral parts of all ecosystems on earth, understanding these interactions will have great implications across basic and applied biological systems.

My lab focuses on the evolutionary ecology of microbial populations. We combine field sampling of natural populations with culture and non-culture based genetic and genomic analyses. Currently we are working on understanding how the interactions between basic population genetic parameters (mutation, selection, recombination and genetic exchange, neutral genetic drift, and biogeography) shape diversity, promote ecological differentiation, and lead to speciation in the microbial world. Ultimately we will develop a comparative approach, describing natural population dynamics of different species across spatial and temporal scales, with a particular interest in how population structures reflect the unique biology and ecology of organisms in the Archaeal domain.

        Typical Sulfolobus Habitat                          Sampling in Lassen National Park

Current Projects:

Population genomics of Sulfolobus islandicus.

We are investigating the tempo and mode of archaeal genome evolution through comparative genomics of 8 closely related Sulfolobus islandicus strains from biogeographically isolated geothermal environments. We are using this data to quantify the rate of horizontal gene transfer and other genome level dynamics over geologically-defined time scales. In addition, comparison of sequences derived from Sulfolobus strains from the same environment will allow us to quantify rates of recombination and identify genes under selection.

Coevolutionary interactions between Sulfolobus islandicus and its viruses.

We are investigating local adaptation in the coevolutionary interactions between Sulfolobus islandicus and mobile genetic elements such as plasmids, viruses and transposable elements. We are identifying to what extent the biogeographic distribution of mobile elements is determined by the biogeography of its hosts. We are investigating variation in the Sulfolobusimmune systems that may be responsible for defining the patterns of coevolutionary interactions.

Effects of disturbance on microbial populations.

Lake ecosystems are primary indicators of ecosystem health and response to climate change. We are investigating the population dynamics of bacterial and archaeal species in humic bogs in northern Wisconsin. We are using molecular tools to study how disturbances are introduced by seasonal mixing of the water column in fall and spring effect diversity within and between lake populations. We are investigating the balance between immigration and adaptation in microbial populations and how microbial population diversity relates to community diversity through a collaborative Microbial Observatory grant with other research labs at the University of Illinois and the University of Wisconsin.

North Sparkling Bog Minocqua, Wisconsin

Interested in joining the Whitaker lab?

I will be accepting graduate students in the fall of 2008