Abstract

Microorganisms play a central role in various biogeochemical processes in Earth’s near-surface environments. These microbial activities are not only controlled by the surrounding environmental conditions but also have a significant impact on the characteristics of their environments. Therefore, it is essential to quantitatively understand the interactions between microbial processes and their immediate surroundings at the pore scale for accurately estimating and predicting the fate of chemicals in subsurface environments. This study aims to provide a comprehensive review of previous mathematical modeling studies that focus on microbial activities at the pore-scale in subsurface environments. First, the fundamentals of three major pore scale reactive transport models are summarized: direct numerical simulation, lattice Boltzmann method, and pore network model. Then, we delve into the traditional modeling approach for microbe-mediated biochemical reactions and more rigorous mathematical models for biofilm development. Lastly, we explore recent advances in genome-scale metabolic models in the context of reactive transport modeling. By analyzing and synthesizing the previous studies, this study provides valuable insights into the intricate relationship between microbial processes and their immediate environments, contributing to a better understanding of biogeochemical dynamics in subsurface environments.

Keywords biofilm, reactive transport, pore-scale, bioclogging, metabolic model