To survive and proliferate, cells need to coordinate their metabolism, gene expression, and cell division. To understand this coordination and the consequences of its failure, we uncoupled biomass synthesis from nutrient signaling by growing, in chemostats, yeast auxotrophs for histidine, lysine, or uracil in excess of natural nutrients (i.e., sources of carbon, nitrogen, sulfur, and phosphorus...

While we have good understanding of bacterial metabolism at the population level, we know little about the metabolic behavior of individual cells: do single cells in clonal populations sometimes specialize on different metabolic pathways? Such metabolic specialization could be driven by stochastic gene expression and could provide individual cells with growth benefits of specialization. We meas...

Introduction We propose to develop novel, adaptively evolved, hybrid yeast strains having phenotypes that enhance the efficiency of industrial-scale biomass conversion. Specifically, we propose to develop heatand ethanol-tolerant yeast that convert both xylose and glucose to ethanol, studying key aspects of their functional and systems biology as they evolve. Initially, we will increase the amo...

Interactions between natural selection and environmental change are well recognized and sit at the core of ecology and evolutionary biology. Reciprocal interactions between ecology and evolution, eco-evolutionary feedbacks, are less well studied, even though they may be critical for understanding the evolution of biological diversity, the structure of communities and the function of ecosystems....

The recruitment of a gene to a foreign regulatory system is a major evolutionary event that can lead to novel phenotypes. However, the evolvability potential of cells depends on their ability to cope with challenges presented by gene recruitment. To study this ability, we combined synthetic gene recruitment with continuous culture and online measurements of the metabolic and regulatory dynamics...

Levels of mRNAs encoding metabolic enzymes and their cellular activities were measured on continuous culture samples of the parasitic protists Trypanosoma brucei and Trichomonas vaginalis. The organisms were grown in chemostats at varying growth rates under glucose limitation or in the presence of excess glucose (EG), resulting in extensive adaptation of the cellular activities of glycolytic en...

In aquatic ecosystems, species diversity is known to be higher in poor nutrient conditions. The enrichment of nutrition often induces the loss of biodiversity. This phenomenon is called the paradox of enrichment, since higher nutrient levels can support more species. Furthermore, the species diversity is usually high in most natural communities of phytoplankton. However, the niches of planktoni...

Complex dynamics, such as population cycles, can arise when the individual members of a population become synchronized. However, it is an open question how readily and through which mechanisms synchronization-driven cycles can occur in unstructured microbial populations. In experimental chemostats we studied large populations (>10(9) cells) of unicellular phytoplankton that displayed regular, i...

The methanogens catalyze a major component of the Earth’s H2 cycle. They are especially active in anaerobic environments where they are the primary consumers of fermentatively produced H2. These strictly anaerobic Archaea have evolved unique adaptations to H2 metabolism, many of which are poorly understood. Our research examines the enzymes and pathways in H2 metabolism in methanogens, especial...

The responses of Escherichia coli central carbon metabolism to knockout mutations in phosphoglucose isomerase and glucose-6-phosphate (G6P) dehydrogenase genes were investigated by using glucose- and ammonia-limited chemostats. The metabolic network structures and intracellular carbon fluxes in the wild type and in the knockout mutants were characterized by using the complementary methods of fl...