Characterization of Prokaryotic Community Dynamics and Functional Profiles in Soils Contaminated Long Term with Petroleum Hydrocarbons in Response to the Addition of Soil Bioremediation Nutrients

Deciphering microbial communities and functions is crucial to understanding ecosystem self-purification in response to contamination by petroleum hydrocarbons (PHCs). This study aimed to determine the dynamics of the prokaryotic community composition, ecological functions and functional genes using third-generation sequencing and quantitative PCR before and after the addition of soil bioremediation nutrients (SBN) to PHC-contaminated soils. Differential prokaryotic community compositions and ecological functions were observed in soils from 4 areas contaminated long-term with different levels and compositions of PHCs. Biostimulation by SBN and water with soil turning for Biopiles B and D led to obvious reconstruction of prokaryotic communities and functional profiles. The addition of SBN with soil turning which increased oxygen supply enhanced degradation of polycyclic aromatic hydrocarbons (PAHs) by increasing the abundance of the PAH-degrading Immundisolibacter cernigliae, Rugosibacter aromaticivorans and Sphingobium fuliginis. Tax4fun2 analysis revealed increases in xenobiotic biodegradation and metabolism/PHC-degraded enzymes after adding SBN which might promote the potential degradation of PHCs. Increases in the abundance of alkB, alkB1, XylE and PHE and in the expression of PHE after adding SBN reflected that the growth of bacteria with these genes was enhanced and considerable amounts of phenol induced the expression of PHE. The concentrations of PHCs and nutrients were primary factors affecting prokaryotic community compositions and functions. The study provides insights into the potential functions of the changes of prokaryotic communities regulating by the addition of SBN, to their efficiency to degrade PHCs. This information is the basic requirements for applying successful bioremediation strategies to remedy the PHC-contaminated soil.