Conserved Hydrocarbon Degradation Architectures in Petroleum-Associated Microbiomes Revealed by Genome-Resolved Analysis Using the Petroleum-Associated Genome Database (PaGeD)

Microbial communities play key roles across the oil supply chain, driving both detrimental processes such as corrosion and souring and beneficial applications including bioremediation. However, genomic and functional information on these microorganisms remains fragmented, limiting integrative analyses. Here, we perform a global genome-resolved analysis of petroleum-associated microbiomes based on a curated collection of 3334 prokaryotic genomes from reservoirs, produced waters, hydrocarbon-polluted sites and related environments worldwide, integrated within the Petroleum-Associated Genome Database (PaGeD). These genomes cluster into 2522 species-level units, more than half representing previously undescribed taxa, revealing extensive hidden microbial diversity in petroleum systems. Functional profiling using 144 KEGG ortholog groups linked to hydrocarbon degradation uncovers a modular organization in which central catabolic pathways are widely conserved across habitats and phylogenetic groups, whereas substrate-specific pathways are restricted to fewer taxa. Gene–genome network analysis further reveals a gradient of functional richness, from generalist genomes occupying central positions to specialized degraders at the periphery. Despite pronounced geographic and ecological heterogeneity, degradation profiles are largely conserved, indicating convergent functional adaptation to hydrocarbon exposure. This work provides a genome-resolved framework for understanding the ecological organization and biotechnological potential of petroleum-associated microbiomes.