Regulation of nutrient assimilation in streamlined oligotrophic microorganisms

Oregon State University, Corvallis OR

Investigators

Abstract

This project concerns cells that compose the "dark matter" of microbial diversity. Many of these organisms are adapted to life in Earth's oceans, where much of carbon flux takes place at very low nutrient concentrations. Some microbes that grow at these low nutrient concentrations' oligotrophs - do not regulate biochemical pathways for nutrient assimilation involving carbon oxidation. In contrast, among the more commonly studied copiotrophs - cells that grow rapidly at high nutrient concentrations - regulation of nutrient assimilation is ubiquitous. An example of a cell that has reduced regulation is Pelagibacter, the most abundant organism in the oceans. At present there exists no explanation for the lack of regulatory systems for nutrient uptake in cells that live in low nutrient ecosystems. In this study, a combination of laboratory experiments, mathematical modeling and genome analysis will be used to examine hypotheses about the costs and benefits of regulating nutrient assimilation. Studying the costs and benefits of different strategies for nutrient assimilation in microbes will aid in the prediction of behavior of nutrient cycles and will lead to a better understanding of aquatic ecosystems. This research may also help scientists understand why so many common microbial cell types have been challenging to grow and study in scientific laboratories. The educational component of this project will involve training a graduate student and a postdoctoral scholar. A workshop on carbon cycling by microorganisms will be presented to teachers and high school students. In this project, the investigators will test the hypotheses that nutrient uptake systems may evolve to be unregulated due to (A) cost/benefit of regulation at different frequencies and magnitudes of nutrient pulses, (B) molecular biological constraints that prevent effective operation of a regulatory system at very low nutrient levels (excessive stochastic noise in the regulatory system), or (C) synergy with chemotaxis, which is typically not done by oligotrophs, so they experience nutrient patches at lower concentrations and for shorter times, or some combination of these mechanisms. A model will be developed to explicitly resolve the assimilation systems and their regulation at the gene level, accounting for the dynamics and metabolic costs of protein synthesis and function (Hypothesis A). An agent-based (aka individual-based) modeling approach will be used to explicitly resolve population heterogeneity (Hypothesis B) and individual transport by chemotaxis and diffusion (Hypothesis C). The investigators will also perform nutrient upshift experiments with a number of oligotrophs, copiotrophs and nutrients, to characterize the response times and induction concentration thresholds by measuring transcript abundance and uptake of radiolabeled nutrients. A subset of experiments will additionally include measurements of nutrient and cell concentrations, proteins and metabolites, nutrient uptake and oxidation rates, and growth rates. The data obtained from these experiments model will be used to calibrate and fine tune the model. The synergy between regulation and uptake (Hypothesis C) will also be tested by comparing genomes of oligotrophs and copiotrophs. A postdoctoral scholar and graduate student will be involved in the research and outreach will be performed to high school teachers and students. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.