Metagenomic and Molecular Simulation Insights into Plastic Degradation: Microenvironmental Matching and the Key Role of Residue Phe392

Abstract

Due to their chemical inertness, polyethylene (PE) and polystyrene (PS) persistently accumulate in the environment. This study integrates metagenomics, degradation profiling, and molecular simulations to elucidate their divergent microbial degradation pathways. PE degradation was dominated by Burkholderia (97%), with selective C–C bond cleavage causing a 29.8% reduction in weight-average molecular weight (Mw) and a 35.46% degradation rate. PS degradation relied on multispecies cooperation, primarily involving Acinetobacter (52%), Bacillus (21%), and Achromobacter (17%), resulting in random main-chain cleavage, a 9.0% reduction in number-average molecular weight (Mn), and an 18.63% degradation rate. Molecular docking and dynamics simulations showed that PS-degrading enzymes exhibit higher binding affinity (–8.0 kcal/mol) via π–π stacking and cation–π interactions, outperforming the hydrophobic interaction-dominated PE-degrading enzymes (–5.4 kcal/mol). Residue Phe392 exhibited dual functionality in PS degradation for the first time. These findings reveal a divergence in microbial strategies: single-species dominance in PE degradation versus functional consortia for PS. The underlying mechanism is the structural compatibility between polymer substrates and enzyme active sites. This work provides a mechanistic framework for understanding microbial plastic degradation and offers insights for engineering microbial consortia and enzymes for efficient bioremediation of mixed plastic pollution.