Natural Attenuation of Petroleum Hydrocarbons: Distinct Microbial Mechanisms in Soil Versus Groundwater

Natural attenuation is a potential way to reduce total petroleum hydrocarbons (TPH) contamination, but the microbial mechanisms that explain differences in attenuation performance between soil and groundwater remain unclear. In this study, field investigation and metagenomic analysis were conducted at a decommissioned refinery site with more than 20 years of operation. Over a four-year period, the average TPH degradation rate in the soil attenuation zone reached 307.7 ± 135.2 mg kg−1 year−1, whereas the groundwater attenuation group showed an average degradation rate of 5.2 ± 3.6 mg L−1 year−1. Metagenomic results showed that TPH attenuation in soil and groundwater was associated with two different microbial consortia adapted to local conditions. In soil, the attenuation zone was characterized by a possibly sessile and cooperative consortium dominated by Pseudomonadota and Actinomycetota, with Sphingomonas and Nocardioides as representative genera. The consortium showed broader amino acid metabolic potential (e.g., ko00250, ko00260, and ko00310) and a higher abundance of functions related to biofilm formation and quorum sensing, which may promote stable and surface-attached growth. In groundwater, the attenuation zone was characterized by a possibly motile and more specialized consortium dominated by Pseudomonadota, including Novosphingobium, Sphingorhabdus, and Tabrizicola. The consortium possessed a less complex catabolic network for TPHs and intermediates (e.g., ko01220/ko00621/ko00624; nahAc/catE/fadA/pcaD/atoB), coupled with stronger potential for motility and secretion. In both soil and groundwater, attenuation was associated with lower eukaryotic activity and enrichment of prokaryotic functions related to oxidative stress defenses and high-yield respiration. These results showed that natural attenuation of TPHs in soil and groundwater involved different microbial features, which could improve the evaluation of natural attenuation in heterogeneous environments.