Molecular Characterization of Environmental Metagenomic DNA from Aquatic Sediments in the Kaduna River: Biodiversity and Pollutant Exposure Implications

Metagenomic analysis of environmental DNA from aquatic sediments provides a comprehensive view of microbial community biodiversity and can reveal the presence of pollution-responsive and antibiotic resistance gene signatures linked to human industrial activity. This study characterized metagenomic DNA from sediment samples collected from three sites along the Kaduna River, Northwest Nigeria, representing an upstream reference site, an urban industrial discharge zone, and a downstream agricultural area. Sediment cores were processed for total microbial community DNA extraction. Shotgun metagenomic sequencing was performed on an Illumina NextSeq platform, and sequence data were processed using MetaPhlAn4 and HUMAnN3 pipelines. The CARD database was queried for antibiotic resistance gene (ARG) annotation. Significant shifts in microbial community composition were detected at the industrial discharge site, with elevated Proteobacteria and reduced methanogenic archaea abundance relative to the reference site. ARGs including sul1, blaTEM, and tetM were detected at 3.2-fold higher abundance at the industrial site compared to the upstream reference. Functional pathway analysis identified enrichment of xenobiotic degradation pathways at the industrial site. These metagenomic findings provide a molecular fingerprint of pollution-driven microbiome disruption in the Kaduna River and support metagenomics as a tool for environmental health monitoring. Keywords: metagenomics, Kaduna River, antibiotic resistance genes, sediment microbiome, environmental monitoring.