Reactive transport processes in a porous medium will often both cause changes to the pore structure, via precipitation and dissolution of biomass or minerals, and be affected by these changes, via changes to the material’s porosity and permeability. An understanding of the pore structure morphology and the changes to flow parameters during these processes is critical when modeling reactive transport. Commonly applied porosity–permeability relations in simulation models on the REV scale use a power-law relation, often with slight modifications, to describe such features; they are often used for modeling the effects of mineral precipitation and/or dissolution on permeability. To predict the reduction in permeability due to biomass growth, many different and often rather complex relations have been developed and published by a variety of authors. Some authors use exponential or simplified Kozeny–Carman relations. However, many of these relations do not lead to fundamentally different predictions of permeability alteration when compared to a simple power-law relation with a suitable exponent. Exceptions to this general trend are only few of the porosity–permeability relations developed for biomass clogging; these consider a residual permeability even when the pore space is completely filled with biomass. Other exceptions are relations that consider a critical porosity at which the porous medium becomes impermeable; this is often used when modeling the effect of mineral precipitation. This review first defines the scale on which porosity–permeability relations are typically used and aims at explaining why these relations are not unique. It shows the variety of existing approaches and concludes with their essential features.

The model for microbially induced calcite precipitation (MICP) published by Ebigbo et al. (2012) has been improved based on new insights obtained from experiments and model calibration. The challenge in constructing a predictive model for permeability reduction in the underground with MICP is the quantification of the complex interaction between flow, transport, biofilm growth, and reaction kinetics. New data from Lauchnor et al. (2015) on whole‐cell ureolysis kinetics from batch experiments were incorporated into the model, which has allowed for a more precise quantification of the relevant parameters as well as a simplification of the reaction kinetics in the equations of the model. Further, the model has been calibrated objectively by inverse modeling using quasi‐1D column experiments and a radial flow experiment. From the postprocessing of the inverse modeling, a comprehensive sensitivity analysis has been performed with focus on the model input parameters that were fitted in the course of the model calibration. It reveals that calcite precipitation and concentrations of <!--${MathJax: TeX-AMS-MML_HTMLorMML}--> ${\text{NH}}_4^{+}$ and <!--${MathJax: TeX-AMS-MML_HTMLorMML}--> ${\text{Ca}}^{2+}$ are particularly sensitive to parameters associated with the ureolysis rate and the attachment behavior of biomass. Based on the determined sensitivities and the ranges of values for the estimated parameters in the inversion, it is possible to identify focal areas where further research can have a high impact toward improving the understanding and engineering of MICP.

Enzymatically induced calcium carbonate precipitation (EICP) is an emerging engineered mineralization method similar to others such as microbially induced calcium carbonate precipitation (MICP). EICP is advantageous compared to MICP as the enzyme is still active at conditions where microbes, e.g., Sporosarcina pasteurii, commonly used for MICP, cannot grow. Especially, EICP expands the applicability of ureolysis-induced calcium carbonate mineral precipitation to higher temperatures, enabling its use in leakage mitigation deeper in the subsurface than previously thought to be possible with MICP. A new conceptual and numerical model for EICP is presented. The model was calibrated and validated using quasi-1D column experiments designed to provide the necessary data for model calibration and can now be used to assess the potential of EICP applications for leakage mitigation and other subsurface modifications.

Attachment of bacteria in porous media is a complex mixture of processes resulting in the transfer and immobilization of suspended cells onto a solid surface within the porous medium. Quantifying the rate of attachment is difficult due to the many simultaneous processes possibly involved in attachment, including straining, sorption, and sedimentation, and the difficulties in measuring metabolically active cells attached to porous media. Preliminary experiments confirmed the difficulty associated with measuring active Sporosarcina pasteurii cells attached to porous media. However, attachment is a key process in applications of biofilm-mediated reactions in the subsurface such as microbially induced calcite precipitation. Independent of the exact processes involved, attachment determines both the distribution and the initial amount of attached biomass and as such the initial reaction rate. As direct experimental investigations are difficult, this study is limited to a numerical investigation of the effect of various initial biomass distributions and initial amounts of attached biomass. This is performed for various injection strategies, changing the injection rate as well as alternating between continuous and pulsed injections. The results of this study indicate that, for the selected scenarios, both the initial amount and the distribution of attached biomass have minor influence on the Ca $$^{2+}$$ 2 + precipitation efficiency as well as the distribution of the precipitates compared to the influence of the injection strategy. The influence of the initial biomass distribution on the resulting final distribution of the precipitated calcite is limited, except for the continuous injection at intermediate injection rate. But even for this injection strategy, the Ca $$^{2+}$$ 2 + precipitation efficiency shows no significant dependence on the initial biomass distribution.

Enzymatically induced calcium carbonate precipitation is a promising geotechnique with the potential, for example, to seal leakage pathways in the subsurface or to stabilize soils. Precipitation of calcium carbonate in a porous medium reduces the porosity and, consequently, the permeability. With pseudo-2D microfluidic experiments, including pressure monitoring and, for visualization, optical microscopy and X-ray computed tomography, pore-space alterations were reliably related to corresponding hydraulic responses. The study comprises six experiments with two different pore structures, a simple, quasi-1D structure, and a 2D structure. Using a continuous injection strategy with either constant or step-wise reduced flow rates, we identified key mechanisms that significantly influence the relationship between porosity and permeability. In the quasi-1D structure, the location of precipitates is more relevant to the hydraulic response (pressure gradients) than the overall porosity change. In the quasi-2D structure, this is different, because flow can bypass locally clogged regions, thus leading to steadier porosity–permeability relationships. Moreover, in quasi-2D systems, during continuous injection, preferential flow paths can evolve and remain open. Classical porosity–permeability power-law relationships with constant exponents cannot adequately describe this phenomenon. We furthermore observed coexistence and transformation of different polymorphs of calcium carbonate, namely amorphous calcium carbonate, vaterite, and calcite and discuss their influence on the observed development of preferential flow paths. This has so far not been accounted for in the state-of-the-art approaches for porosity–permeability relationships during calcium carbonate precipitation in porous media.