Predictive modeling of microbial biomineralization across scales

Atiyeh Ahmadi, Maria Dittrich

Microorganisms influence mineral formation and transformation in natural
and engineered environments, with consequences for element cycling, contaminant mobility, and mineral records. Predicting these processes remains difficult
because microbial activity, local aqueous chemistry, interfacial reactions, and
mineral formation operate across different spatial and temporal scales. Here, we
review molecular, geochemical, reaction–transport, biofilm- and cell-based, and
data-driven models, focusing on what each can predict and how those predictions
are tested experimentally. We explain the quantities that may connect models
across scales, including ion binding, microbial activity, local chemical conditions,
mineralization kinetics, and transport properties. Existing studies show stronger
predictive development in geochemical and reactive-transport approaches than in
connections between molecular interactions, microbial microenvironments, and
mineral formation. We identify unresolved cross-scale relationships and discuss
how spatially resolved measurements and independent experimental tests can
strengthen predictive modeling of microbial biomineralization across scales.