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Reactive transport modeling of microbially mediated processes has contributed significantly to an improved understanding of elemental cycling in Earth’s near-surface environments. We describe key characteristics of microbial reactive transport models, recent advances in modeling approaches, and the application of such models to terrestrial and marine environmental problems. We introduce relevant case studies and discuss ways to integrate omics data (e.g., genomics, proteomics, metabolomics) that can inform and validate microbial reactive transport models, thereby improving our ability to address some of the grand challenges in a changing world.

Isotopes have a rich history as tracers of biogeochemical processes, but they are commonly interpreted using distillation models that lump multiple compounding effects, including advection, diffusion, and complex chemical transformations. Today, as our ability to measure small differences in relative mass continues to improve, a new generation of process-based models are being developed that explicitly track individual isotopes across an increasingly diverse range of environments. Advances in isotopic reactive transport models are now yielding new insight into fundamental questions across the Earth sciences, including the relationships between experiments and natural systems and the conditions under which isotopes record past environments.

Continental rocks chemically weather when surficial waters and gases interact with the minerals and organisms that inhabit Earth’s critical zone. To understand and quantify this process, researchers use reactive transport models to track the kinetics and thermodynamics of weathering reactions and the transport of products and reactants. These models are powerful tools to explore how weathering sculpts the Earth’s surface from the scale of mineral grains to watersheds, and across temporal scales from seconds to millions of years. Reactive transport model simulations are now a vital tool for elucidating the complex links between climate, rock ­weathering, and biota.

The disposal of spent nuclear fuel and high-level radioactive waste in the subsurface represents one of the greatest challenges for the geosciences. Most disposal strategies rely on a multiple barrier system, consisting of both natural and engineered materials, to prevent or delay the contact of groundwater with the waste and radionuclide release to the environment. Reactive transport models have been central to understanding and assessing how thermal, hydrological, and geochemical processes are coupled in these containment barriers, which are expected to experience a range of temperatures and geochemical conditions, yet, must maintain their integrity for millions of years.

The engineered storage of CO2 in Earth’s subsurface provides one of the most promising means of reducing net greenhouse gas emissions. Paramount to the success of this method is ensuring that CO2 injected into the subsurface is securely stored. Reactive transport models can be used to answer the key question regarding CO2 storage, “Will the injected CO2 be secure, and over what timescale?” Here, we explore examples of how reactive transport models have been used to simulate the range of geochemical and hydrologic processes that will take place over thousands of years and across many spatial scales to answer that key question.

The hydrochemical composition of most groundwater systems, whether pristine or affected by anthropogenic activities, evolves as a result of complex interactions between flow, solute transport and biogeochemical processes. An in-depth analysis of these processes and their interactions is essential for deciphering what controls groundwater quality. Reactive transport modeling has emerged as an invaluable tool for distilling complex systems into their salient components. Based on experimental data, reactive transport models have been successfully used in the rigorous, process-based quantification of coupled processes at bench and field scales. We illustrate how reactive transport modeling can aid in identifying and quantifying controls over groundwater quality.

Beneath our feet is a fascinating world of flowing water, cosmopolitan microbes, and complex mineral assemblages. Yet we see none of it from above. Our quest to investigate these complex subsurface interactions has led to the development of reactive transport models. These are computer algorithms that allow us to explore, in a virtual way, the natural dynamics of Earth’s systems and our anthropogenic impact on those systems. Here, we explain the concepts behind reactive transport models—which include the transport of aqueous species and the descriptions of biogeochemical reactions involving solutes, surfaces and microorganisms—and introduce to reactive transport applications in terrestrial and marine environments.