Bacterial Community Profiling and Predictive Functional Gene Analysis during Petroleum Biodegradation

Abstract Bacterial functional diversity in crude oil-polluted site undergoing remediation by enhanced natural attenuation (RENA) was monitored over an 8-week period. Soil samples were collected from the polluted site (>5,000mg/kg of TPH) at various phases of bioremediation while the control (unpolluted soil) was taken 80 meters away from the polluted site. Next generation sequencing on Illumina MiSeq platform was used to characterize the bacterial community composition. Functions of different operational taxonomic units (OTUs) and proportions of functional bacterial groups involved in each step of biodegradation were predicted using Kyoto encyclopaedia of genes and genomes (KEGG) and phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt). Principal component analysis (PCoA) of the functional genes was also carried out for statistical inferences. The predicted functional genes indicated the presence of genes responsible for benzoate, DDT, dioxin, fluorobenzoate, naphthalene, nitrotoluene, polyaromatic hydrocarbons, styrene, toluene and xylene degradation. Sample obtained post-bioremediation showed significant (P ≤ 0.05) differences in functional genes responsible for benzoate, xylene, ethyl benzene, valine, leucine and isoleucine, nitrotoluene, aminobenzoate and DDT degradation when compared with baseline (pre-remediation), polluted soil (PS) during remediation on days 0, 9, and 29. PCoA revealed that PS on days 0, 9, and baseline had similar functional genes spread while functional genes in PS days 29, 36 and 56 increased progressively with time. The top five known petroleum degrading bacterial phyla identified included Proteobacteria, Actinobacteria, Acidobacteria, Cyanobacteria and Firmicutes. The study area harboured a variety of bacteria with metabolic capacities for pollutant degradation. Functional genes related to petroleum degradation were widely distributed and found to be abundant especially in zones with higher pollution levels. Moreover, the study provided insights into in situ bacterial functional structures in crude oil-impacted site and unraveled the linkages between bacterial communities and environmental variables which are important in the application of bioremediation.