Genomic Assessment of Phenotypic Plasticity in an Aquatic Bacterium: Water Quality and Microhabitat Effects

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PI: Taylor Proposal: 0120677 The project by Ronald Taylor, Dartmouth College is supported by the program Biocomplexity in the Environment, subprogram Genomic-Enabled Environmental Science and Engineering (BE GEN-EN). Heterotrophic bacteria play a key role in pelagic nutrient cycling because they remineralize organic matter before it sinks out of the system. Two key bacterial behaviors that may influence remineralization rates are dormancy and attachment to plankton. Both of these behaviors are phenotypically plastic, allowing bacteria to respond to changes in their environment. For example, a high dormancy rate (30-95%) suggests that the bacterial community has a tremendous capability to respond rapidly to changes in environmental conditions that trigger the transition back to a metabolically active state. In contrast, little is known about the potential impact of bacteria living on planktonic substrates on ecosystem processes.The goal of this research project is to study the interaction between dormancy and attachment behaviors using whole-genome expression profiles for a focal species (Vibrio cholerae) under contrasting environmental conditions in both the field and laboratory. We are particularly interested in determining (1) the extent to which dormancy and attachment may be co-regulated under realistic environmental conditions and (2) how these behaviors might be altered by anthropogenic activities such as land use change or organic pollution. We will conduct three interrelated studies, each using microarrays, that will make major contributions to our understanding of the genetic processes that instigate transitions between active and dormant states and between unattached and attached states.Aim 1 contrasts the temporal dynamics of gene expression in unattached and attached bacteria under favorable vs. unfavorable environmental conditions over a two-week period. This will be the first comprehensive analysis of genetic co-regulation of dormancy and SRBs. Aim 2 will determine the direct effects and interactions of four key environmental parameters (temperature, salinity, pH, and nutrients) on gene expression in bacteria exposed to three different microhabitats (unattached, attached to zooplankton, attached to phytoplankton). This will be one of the first multi-factor experiments with microarrays, and will require introduction of new methods for analyzing microarray data. Aim 3 will quantify gene expression under seasonally varying field conditions using in situ incubations of bacteria in Bangladeshi ponds with contrasting anthropogenic impacts. As such, this will be one of the first projects to use microarrays to evaluate gene expression in a natural system rather than under laboratory conditions.The focal species, V. cholerae, is ideal for investigating these questions: it is found in plankton communities worldwide, is representative of a large family of bacteria (the Vibrionaceae), and has a fully sequenced and well-studied genome which enables the use of microarray technology. V. cholerae is also of considerable medical importance as the etiological agent of cholera. This research will be accomplished by an interdisciplinary and international team of researchers who specialize in ecology, microbiology, genetics and statistics. We plan to make all microarray results publicly available, and to educate the scientific community and the public about our results through a website, talks at scientific meetings, and our undergraduate and graduate courses.