Competitor and substrate sizes and diffusion together define enzymatic depolymerization and microbial substrate uptake rates


Diffusion limitations of extracellular enzymes and soluble monomers have been recognized as important mechanisms controlling soil organic matter (SOM) dynamics. Here we combine diffusion limitation with the geometric sizes of extracellular enzymes, polymer particles, monomers, and bacterial cells to derive testable relationships of SOM kinetic parameters, including (1) maximum reaction rates and (2) binding half saturation constants (also known as substrate affinity parameters). We integrate the relevant mechanisms with the Equilibrium Chemistry Approximation (ECA) kinetics, which has been shown to reasonably represent these complex competitive interactions in soils, and then evaluate the reverse and forward Michaelis-Menten kinetics approximations under different conditions. We found: (1) due to the size contrast between larger organic polymer particles and smaller enzyme molecules, depolymerization is limited by the abundance of enzyme binding sites supplied by polymer particles, making the reverse Michaelis-Menten kinetics a better approximation to the ECA kinetics for depolymerization, and (2) due to the size contrast between larger microbial cells and smaller monomer molecules, monomer uptake is limited by accessible microbial cell transporters, making the forward Michaelis-Menten kinetics a better approximation to ECA kinetics for microbial monomer substrate uptake. These results may explain conflicting applications in the literature associated with using reverse and forward Michaelis-Menten kinetics to represent SOM dynamics. Further, the size contrast between litter particles and extracellular enzymes suggests that litter fragmentation by soil fauna and fungi is an important process to be included in models of organic matter decomposition and challenges soil enzyme assays to accurately measure enzyme abundances in order to properly derive the kinetic parameters.

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Soil Biology and Biochemistry
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