Ecogenomics of Antibiotic-Degrading Microbial Communities in Pharmaceutical Wastewater Effluents Discharged into Nigerian Aquatic Ecosystems

Pharmaceutical manufacturing wastewater in Nigeria is discharged with limited treatment into freshwater ecosystems, yet the ecogenomics of antibiotic-degrading microbial communities selectively enriched in these effluent-impacted waters, and the resistance genes they accumulate, represent a critical and uninvestigated environmental health problem. This dissertation characterises the ecogenomics of antibiotic-degrading microbial communities in pharmaceutical wastewater effluents and receiving water bodies across pharmaceutical manufacturing corridors in Lagos (South West) and Ogun (South West) States. Effluent and river water samples were collected monthly for 12 months from five pharmaceutical effluent discharge points and downstream community water abstraction sites. Antibiotic concentrations were measured by LC-MS/MS. Metagenome-assembled genomes (MAGs) were reconstructed from shotgun metagenomic data to characterise antibiotic degradation gene content and community functional ecology. Resistome analysis quantified ARG abundance and diversity across sampling sites. Ciprofloxacin, tetracycline, and sulfamethoxazole were detected in all effluent samples, with concentrations exceeding minimum selection concentrations for resistance induction. Pharmaceutical effluent microbiomes were dominated by Proteobacteria with high frequencies of oqxAB, sul1, and tetX4 ARGs. Twelve MAGs encoding complete nitroreductase, monooxygenase, and hydrolase antibiotic degradation pathways were reconstructed, with six representing novel bacterial taxa. A significant downstream ARG gradient was confirmed, with community abstraction points showing 3.1-fold higher ARG richness than upstream controls. The dissertation provides the first ecogenomics dataset on pharmaceutical wastewater-antibiotic degrading communities in Nigeria. Keywords: ecogenomics, pharmaceutical wastewater, antibiotic degradation, resistome, Nigeria