Abstract

Soils and rocks host vast microbial communities that actively reshape
hydrologic processes occurring below the Earth’s surface. Through
motility, growth, and biofilm formation, microbes locally clog pores,
reorganize pore-network connectivity, and dynamically redistribute fluid
flow and solute transport in natural porous media. Beyond these physical
effects, microbes and their biofilm matrix modify pore-surface
reactivity and generate steep chemical gradients whose system-scale
consequences remain poorly quantified. This knowledge gap limits our
ability to predict microbially mediated processes central to timely
environmental applications like contaminant remediation, nutrient
cycling, and greenhouse gas emissions. In this talk, I present three
examples of living porous media in which pore-scale microbial processes
exert first-order control on macroscopic behavior.

We combine soil-on-a-chip microfluidic experiments of microbial growth with
pore-scale direct numerical simulations to resolve flow fields, solute
residence times, and mixing dynamics inaccessible to experiments alone.
First, we examine coupled biotic-abiotic controls on manganese
precipitation relevant to contaminant remediation efforts. Second, we
show how biofilm accumulation deforms solute mixing interfaces and
alters product formation in fast, mixing-limited reactions as a standard
toy case.

Finally, we investigate the physical and biological controls
governing redox heterogeneity in riverine sediments linked to greenhouse
gas production. Together, these insights reveal how microbial life
reshapes the physical and chemical fabric of the subsurface.