Cross-scale modeling of bacteria-contaminant spatiotemporal dynamics in 3D bioprinted hydrogel for dye biodegradation

Three-dimensional (3D) bioprinting enables precise construction of functional biohydrogels, yet effective simulation bacterial dynamics within these structures remains challenging. Here, we developed a novel gelatin/cellulose/sodium alginate (GCSA) biohydrogel incorporating Shewanella oneidensis MR-1 with superior mechanical properties and biocompatibility. Using Direct Blue 71 (DB71) as a model contaminant, we demonstrated efficient bioremediation while elucidating protective mechanisms through comprehensive experimental characterization. We established a cross-scale "hydrogel-bacteria-digital model" framework integrating high-quality genome-scale metabolic model (GEM) with Computation Of Microbial Ecosystems in Time and Space (COMETS) simulation to bridge bacterial growth distribution and contaminant diffusion within biohydrogel microenvironments. This approach revealed fundamental mechanisms governing bacteria-pollutant interactions across multiple scales, validated optimal porous architecture for enhanced mass transfer, and demonstrated that biohydrogel encapsulation reduces bacterial oxidative stress while promoting metabolic activity. The framework exhibits flexibility and extensibility in addressing complex environmental challenges while advancing fundamental understanding of cross-scale interactions in engineered biological systems.