Geomicrobial kinetics: a genome-scale metabolic modeling approach

University Of Oregon Eugene, Eugene OR

Investigators

Abstract

The investigator proposes to develop a new modeling method to address a compelling question in geobiology - how fast do microbial processes proceed in natural environments? Current methods predict microbial rates in the environment using Monod equation and other models of laboratory cultures. But unlike cultures grown in synthetic media, natural microbes face the challenge of limited and fluctuating availability of nutrients, and thus have to regulate biochemical pathways and to fine-tune the rate and efficiency of metabolism. To bring metabolic pathways and regulations into the prediction of microbial rates, the investigator will develop a new modeling method that explicitly links microbial genomics to geochemistry. This modeling approach would allow to answer the question - how fast do microbial processes proceed in natural environments? The project offers learning opportunities to high school students and supports one Ph.D. and two undergraduate students. The new method groups enzyme reactions within entire cells into two networks of catabolism and biosynthesis. It simulates the catabolic network using enzyme kinetics and biosynthesis network using flux balance analysis. The output of the simulation ranges from enzyme and metabolite concentrations at cellular level to microbial rates at organismal level. The investigator will apply the new method, coupled to biogeochemical reaction modeling, to simulate the metabolism of acetoclastic methanogens, a representative group of subsurface microbes, and to investigate the kinetics of methanogenesis in geological environments. The new method represents an important attempt to move beyond classical Monod equation-based models, toward an omics-enabled metabolism-based approach to the analysis and prediction of microbial processes in geological environments. Specifically, the new method predicts microbial kinetics and enzyme expression from genome and geochemistry of the environment, without the need of pure culture or laboratory experiment. This method therefore offers a new, and potentially powerful, method for studying microbial processes of geological environments, especially those cryptic processes that cannot be accurately analyzed in the field or faithfully reconstructed in the laboratory.