Functional specialization and enzymatic mechanisms of poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) (PHBH) degradation in anaerobic digesters: Insights from shotgun metagenomics and molecular modeling

This study investigates the anaerobic degradation of poly(3-hydroxybutyrate- co -3-hydroxyhexanoate) (PHBH) using shotgun metagenomics and molecular docking to analyze temporal shifts in microbial communities and key enzymes under batch and semi-batch conditions. Comparative analysis of the microbial communities revealed a decline in generalist taxa and an increased contribution of Bacteroidota, Chloroflexota, and methanogenic Euryarchaeota. KEGG-annotations suggested that modules affiliated with depolymerases, esterases, β-oxidation and methanogenic pathways would be co-activated. Furthermore, PlasticDB-based computational analysis evidenced a stepwise enrichment of PHB- and PHA-related enzymes, which confirmed the substrate-mediated microbial specialization. A prominent metagenomic depolymerase (R1_379815) showed well-conserved catalytic residues (Ser134, His284, Asp211) and a substrate-binding affinity comparable to the native counterpart 9BYU, confirming its substrate preference and functional identity with previously reported PHB depolymerases. Collectively, this integrative metagenomic and computational approach provides mechanistic insights into PHBH biodegradation under anaerobic conditions, aiding in the identification of potential target enzymes for enhancing plastic degradability and methane recovery in anaerobic digestion systems. These findings contribute to the advancement of sustainable bioplastic waste management through process-level and enzymatic optimization. • Genome-centric analysis of PHBH degradation in anaerobic digesters • Microbial shifts diverge under batch vs semi-batch conditions • Substrate input drives enzyme-level community specialization • Semi-batch mode enriches syntrophic functional networks • PHB/PHA depolymerases enriched across all digestion phases