Assessment of Microbial Diversity and Functional Potential in Soils of the Niger Delta Oil Contamination Zone Using Metagenomic Analysis

Petroleum hydrocarbon contamination of soils in the Niger Delta has profoundly disrupted indigenous microbial communities, yet metagenomic characterisation of surviving and adaptive microbial populations in these soils offers both ecological understanding and bioremediation insight. This study assesses microbial diversity and functional potential in heavily oil-contaminated and adjacent uncontaminated soils in Rivers State, South South Nigeria, using whole metagenome shotgun sequencing. Soil samples were collected from three crude oil spill sites of varying contamination age (recent, 5-year, and 10-year) and paired control plots in Ogoni communities. DNA extraction, library preparation, and Illumina NovaSeq sequencing were performed on pooled triplicate samples from each site. Taxonomic profiling used Kraken2 and functional annotation used HUMAnN3 against UniRef90. Hydrocarbon contamination significantly reduced bacterial alpha diversity, with Shannon index dropping from 4.8 in controls to 2.9 in heavily contaminated soils. Gammaproteobacteria, particularly Alcanivorax and Marinobacter genera, were selectively enriched in contaminated soils. Functional annotation showed enrichment of alkane degradation and sulfur cycling pathways in contaminated metagenomes. The 10-year contamination sites showed partial diversity recovery. The study provides the first shotgun metagenome dataset from Ogoni oil-contaminated soils and identifies enriched hydrocarbon degraders suitable for bioaugmentation-based remediation strategies. Keywords: metagenomics, oil contamination, Niger Delta, microbial diversity, bioremediation