Ecological perspective on bacterial physiology

Studies of microbial physiology in model systems such as E. coli have historically focused on a set of environmental conditions defined more by convenience of laboratory growth and preconceived notions of nutrition and stress, rather than ecologically relevant environments and transitions.  These laboratory conditions and the corresponding behavioral responses likely under-estimate the complexity of bacterial behavior in their ecologically appropriate niche.  We are interested in the physiological responses of E. coli to perturbations that better represent the variation they see in their natural habitats.  Using microarray measurements of gene expression dynamics across these perturbations, we are gaining insights into the sensory integration and computations performed by signaling and transcriptional networks.  We have developed extensive experimental and computational machinery to identify the components of signaling pathways involved and to follow the path of the information all the way down to the level of transcription factor-binding site interactions on DNA. Our long-term aim is to relate these internal dynamics to the spatio-temporal structure of the habitats that have shaped them.

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