Pore‐scale modeling of microbial activity: What we have and what we need

Abstract

Under water-unsaturated conditions, environmental factors (e.g., substrate, nutrients, O 2 , water activity, and porous structure) controlling microbial activity are highly variable in space and time. The physical structure of porous media (pore size distribution and pore arrangements) has been considered to have a significant role in nutrient (either substrate and/or its reaction partners like O 2) fluxes. Understanding what eventually controls microbial activity thus requires a sound description of the physical and chemical conditions in the pore space down to the microscale, as well as knowledge on how microorganisms respond to the energy and matter fluxes in their microscale environment. Microscale modeling has the advantage to resolve the processes down to their fundamental level. In recent years, microscale models describing the physical setting in unsaturated porous media such as soils, as well as growth and functional performance of microorganisms, have become increasingly established and are supported by new experimental techniques resolving the distribution of solid, liquid, and gaseous phases at microscale resolution. Still, integration of these components for simulation of microbial activities in a soil system at the microscale is scarce. This mini-review highlights the available approaches for porescale modeling of flow and transport processes in both saturated and unsaturated porous media, and for modeling the dynamics of microbial activity constrained by different soil boundary conditions. Further, it is discussed what is required in terms of model development and improved modeling concepts to achieve a holistic reactive transport modeling approach describing microbial activity at the pore scale. 1 INTRODUCTION Soil systems and, in general, porous media are interesting domains for many engineering and scientific disciplines (e.g.

Soil carbon sequestration for climate change mitigation: Mineralization kinetics of organic inputs as an overlooked limitation

“…The geometry of the pore space in many soils may be so convoluted as to preclude microorganisms, and even their exoenzymes, access to potential substrates. These insights are increasingly reflected by a new generation of mathematical models that take the microscale heterogeneity of soils explicitly into account when describing the fate of organic matter (e.g., Falconer et al, 2015;Golparvar et al, 2021;König et al, 2020;Pot et al, 2022;Vogel et al, 2015).…”

A perspective on applied geochemistry in porous media: Reactive transport modeling of geochemical dynamics and the interplay with flow phenomena and physical alteration

“…Unsaturated reactive transport in porous media has been the holy grail of groundwater studies where the redox processes play a deterministic role in the fate of nutrients (Golparvar, Kästner, and Thullner 2021;Pot et al 2022). Oxygen as the main oxidant for the aerobic organisms diffuses from the gaseous phase into the aqueous phase.…”

“…Most of the studies in this field use macroscopic unsaturated solute transport models that solve Richard's equation (Richards 1931;van Genuchten 1980) at continuum scale, such as HYDRUS-PHREEQC (Jacques et al 2018) and MIN3P (Mayer, Frind, and Blowes 2002;Sihota and Ulrich Mayer 2012). Therefore, lack of a sophisticated unsaturated reactive pore-network model has been noted in which the redox processes are linked to the variability of water saturation in pores, and the reduction-oxidation reactions are mainly regulated by soil water content, next to other soil properties (Golparvar, Kästner, and Thullner 2021).…”

Accounting for soil architecture and microbial dynamics in microscale models: Current practices in soil science and the path ahead

“…To avoid this lumping together a new generation of SOM decomposition models has been developed, accounting for the three-dimensional architecture of soil and the heterogeneity of the distributions of microorganisms, water, air, SOM and reactive surfaces at the level of microbial habitats (Baveye et al, 2018). In two recent mini-reviews, König, Vogel, Harms, and Worrich (2020) reported on microscale models with a special focus on spatiotemporal dynamics of bacteria and bacterial functions in soil microhabitats, and Golparvar, Kästner, and Thullner (2021) reported on microscale models of reactive transport modelling in porous media.…”