Metagenomic Characterisation of Hydrocarbon-Degrading Microbial Communities in Chronically Polluted Mangrove Sediments of the Western Niger Delta

Hydrocarbon-degrading microbial communities in chronically oil-polluted mangrove sediments represent both a critical component of natural attenuation capacity and an underexplored reservoir of bioprospecting potential, yet their community architecture and functional genomics are largely unknown in the Nigerian context. This research characterises the metagenomic diversity, functional gene repertoire, and hydrocarbon degradation potential of microbial communities in chronically polluted mangrove sediments across a contamination gradient in Western Niger Delta, Bayelsa and Delta States. Sediment metagenomes were generated using Illumina NovaSeq short-read and Oxford Nanopore long-read hybrid sequencing. Assembly, binning, and annotation were performed using MEGAHIT, MetaBAT2, and KEGG databases. Reconstruction of metagenome-assembled genomes enabled functional characterisation of dominant degraders. Enrichment culture experiments with crude oil as sole carbon source provided functional validation. A total of 847 non-redundant metagenome-assembled genomes were reconstructed from 18 sediment metagenomes. Gamma-proteobacteria of the genera Marinobacter, Cycloclasticus, and Alcanivorax dominated the hydrocarbon-enriched functional guild. Novel alkane monooxygenase gene families were identified in 14 MAGs representing previously undescribed lineages. Community assembly null model analysis demonstrated that deterministic selection driven by hydrocarbon substrate type was the dominant community structuring mechanism. Functional redundancy analysis revealed high redundancy for alkane degradation but low redundancy for polycyclic aromatic hydrocarbon ring cleavage pathways, identifying a metabolic vulnerability. Three novel biosurfactant gene clusters with potential biotechnological application were annotated. This research establishes the first comprehensive metagenomic baseline for Niger Delta mangrove degraders and provides targets for bioremediation augmentation strategies. Keywords: metagenomics, hydrocarbon degradation, mangrove sediments, Niger Delta, bioremediation.