Metagenomic Insights Into Biopile Remediation of Petroleum-Contaminated Soil Using Chicken Droppings in Rivers State, Nigeria

Petroleum hydrocarbon pollution is an escalating global issue, particularly in developing countries, where it has attracted significant attention from researchers focusing on bioremediation, monitoring and sustainability. This study utilised metagenomics to investigate the bacterial community's response in polluted soil undergoing field-scale biopile treatment, with chicken droppings as a nutrient source. Hydrocarbon concentrations were monitored over a 90-day remediation period using the Fourier transform infrared (FTIR) spectrometry technique. Molecular and bioinformatic analyses were conducted to track the dynamics of bacterial species, their abundance and functional roles during the bioremediation process. The initial total petroleum hydrocarbon (TPH) concentration of 446 945 ppm was first reduced to 80 332 ppm through dilution. Following a 90-day bioremediation process using poultry waste, the level further decreased to 5326 ppm, representing a 93.37% reduction. In the metagenomic analysis, a total of 26 736 reads were obtained, averaging 6684 counts per sample. In addition, the study identified diverse bacterial metagenomes, including well-established hydrocarbon-degrading bacteria from Proteobacteria, Firmicutes, Acidobacteria and Actinobacteria phyla, and species previously not reported as hydrocarbon-degrading. Biomarkers associated with hydrocarbon metabolisms, such as aromatic dioxygenases, alkane-1-monooxygenase and methanol oxidation pathways, were identified. A significant decrease in the relative abundance of bacterial genera in heavily polluted soil was observed, alongside an increased presence of <i>Caballeronia</i>, <i>Paraburkholderia</i> and <i>Fontibacillus</i> genera. These findings indicate that chicken droppings contribute 0.30% to the reduction of TPH in the biopiling remediation technique used for treating heavily contaminated soil. A comparative assessment of hydrocarbon attenuation in nutrient-amended vs unamended soils indicates that a 3-month remediation timeframe is insufficient to achieve optimal bioremediation outcomes. However, the TPH reduction in unamended treatment highlights the intrinsic natural attenuation capacity of the impacted soil matrix, attributable to indigenous microbial consortia and prevailing environmental conditions.