February 28, 2018

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Thermodynamic Links Between Substrate, Enzyme, and Microbial Dynamics

A research team from LBNL present a mechanistic approach to link temperature dependencies of microbial reactions important in soil biogeochemistry.

The Science

The team introduced a simple but comprehensive mechanistic approach that uses thermodynamics and biochemical kinetics to link reaction rates, Michaelis-Menten constants, biomass yields, mortality rates, and temperature for soil microbes.

The Impact

Accurate prediction of microbially mediated reaction rates is critical for soil biogeochemical models. The team’s approach uses thermodynamics and biochemical kinetics to link the dominant controlling factors on these rates, including their temperature dependencies.

Summary

A research team from LBNL introduced a simple but comprehensive mechanistic approach that uses thermodynamics and biochemical kinetics to describe and link microbial reaction rates, Michaelis-Menten constants, biomass yields, mortality rates, and temperature. The temperature control is exerted by catabolic enthalpy at low temperatures and catabolic entropy at high temperatures, whereas changes in cell and enzyme–substrate heat capacity shift the anabolic electron use efficiency and the maximum reaction velocity. The researchers show that cells have optimal growth when the catabolic (differential) free energy of activation decreases the cell free energy harvest required to duplicate their internal structures as long as electrons for anabolism are available. With the described approach, the team accurately predicted observed glucose fermentation and ammonium nitrification dynamics across a wide temperature range with a minimal number of thermodynamics parameters, and the scientists highlight how kinetic parameters are linked to each other using first principles. These results can inform new microbe-explicit biogeochemistry models, such as those they are developing in E3SM.

Principal Investigator

William Riley
Lawrence Berkeley National Laboratory
wjriley@lbl.gov

Program Manager

Daniel Stover
U.S. Department of Energy, Biological and Environmental Research (SC-33)
Environmental System Science
daniel.stover@science.doe.gov

Funding

This research was supported by the Office of Biological and Environmental Research, within the U.S. Department of Energy Office of Science, under contract no. DE-AC02- 05CH11231 as part of the Lawrence Berkeley National Laboratory’s Terrestrial Ecosystem Science Scientific Focus Area (SFA) project.

References

Maggi, F. M., F. H. M. Tang, and W. J. Riley. "The thermokinetic link between substrate, enzyme and microbial dynamics in Michaeli-Menten-Monod kinetics". International Journal of Chemical Kinetics 50 (5), 343–356  (2018). https://doi.org/10.1002/kin.21163.