Microbial community dynamics and protein-level adaptation to petrochemical pollution in river systems on the northern margin of the Yellow River Delta, Shandong, China.

Petrochemical contamination poses significant ecological risks to aquatic ecosystems, and the molecular mechanisms contributing to microbial resilience are not yet fully characterised. In this study, high-throughput 16S rRNA sequencing was combined with protein molecular docking and molecular dynamics simulations to investigate microbial community dynamics and protein-level responses along a contamination gradient in Shandong, China. Contaminated sites displayed higher microbial diversity and evenness, suggesting adaptive plasticity. Genera such as hgcI clade, CL500-29 marine group, Mycobacterium, and Limnohabitans exhibited niche specialisation under petrochemical exposure. Functional annotation has indicated that TRP, DndB, and TTL are involved in amino acid biosynthesis, DNA modification, and cytoskeletal stabilization, respectively. Docking analyses demonstrated the occurrence of pollutant-specific binding, with strong affinities observed for DndB-2,2-dimethyldecane, TRP-eicosane, and TTL-1-methyl-2-pyrrolidinone (NMP). Molecular dynamics simulations supported the stability of these complexes, with van der Waals interactions predominating in TRP-hydrocarbon binding and electrostatic forces contributing to TTL-NMP stabilization. The results of this study provide a valuable insight into the structural features associated with protein functional stability under petrochemical stress, thereby expanding our understanding of microbial adaptation mechanisms in contaminated aquatic environments.