Making Waves: A layered bioenergetic partitioning framework for the per-cell yield gap in ureolytic microbially...

Microbially induced carbonate precipitation (MICP) is a candidate technology for groundwater contaminant immobilisation, aquifer permeability reduction, and CO₂ trapping. Field-scale per-cell CaCO₃ yields sit approximately two orders of magnitude below the laboratory kinetic ceiling, and treatment-protocol optimisation has produced incremental gains. We ask: is the field-scale yield gap in ureolytic MICP a fundamental kinetic constraint, or a structured loss profile with mechanism identifiable in each layer? We propose a Layered Bioenergetic Partitioning (LBP) framework decomposing the gap into in-vivo enzymatic overhead, maintenance and Jahns-mechanism diversion, Ca²⁺/CaCO₃-induced inactivation (mechanistically integrated over contact time), post-treatment encapsulation, and delivery. Log-uniform sampling over bracket-valued factors gives 0.042 [0.015, 0.116] ng cell^-1d^-1 for short treatments, reproducing observed yields across four datasets without parameter fitting. The framework contains single-factor limiting-step models as special cases and yields a falsifiable intervention-layer map that reorders MICP design priorities toward layer-targeted mitigations.