Polycyclic aromatic hydrocarbon substrate-driven divergence in predicted functional genomic architecture of enriched bacterial consortia

Polycyclic aromatic hydrocarbons (PAHs) function as ecological selective agents that impose differential pressures on microbial communities, driving divergent functional genomic profiles. This study investigated how pyrene, anthracene, and crude oil waste sludge, representing a gradient of hydrocarbon complexity, shape the functional genomic architecture of enriched bacterial consortia from a compost–COWS matrix following a 60-day serial sub-culture to establish stabilized endpoint communities. The V3–V4 16S rRNA gene region was sequenced using Illumina MiSeq (2 × 250 bp) and functional profiling performed using PICRUSt2 to infer metagenomic content. Community profiling revealed substrate-driven structuring of taxonomic and functional genomic composition, with dominance by Proteobacteria and Actinobacteria , with Pseudomonas , Sphingomonas , Microbacterium , Rhodococcus , and Burkholderia as the principal genera. Inter-consortium Bray-Curtis distances (0.45–0.61) indicated distinct taxonomic clustering across hydrocarbon regimes. PICRUSt2 predicted 2070 EC functions and 390 MetaCyc pathways, including 127 EC functions and 23 pathways consistent with predicted enrichment of ring-cleavage dioxygenases, ring-hydroxylating dioxygenases, and beta-ketoadipate pathway enzymes. Although overall predicted EC class architecture remained broadly conserved (transferases ~30–31%, oxidoreductases ~22%, hydrolases ~21%), substrate-specific functional signatures were evident at finer resolution. Vanillate monooxygenase (EC:1.14.13.82) was predicted to be selectively enriched in pyrene, indicating ecological selection for methoxylated intermediate metabolism during pyrene degradation. The salicylate degradation superpathway was proportionally enriched in crude oil waste sludge, suggesting adaptation to crude-oil-associated aromatic catabolism. Internal EC–MetaCyc concordance and low NSTI scores inference reliability. These findings demonstrate that PAH substrate chemistry shapes community functional genomic architecture and provide a predictive framework for bioremediation design.