Metagenomic analysis of microbial physiological consortia in Iko River estuary impacted by petroleum products pollution

• Published in: Ecological genetics and genomics 2025-03, Vol.34, p.100323, Article 100323
• Main Authors: Unimke, Augustine A., Ibiene, Abiye A., Okerentugba, Phillip O.
• Format: Article
• Language: English
• Subjects: Bioremediation; Iko river estuary; Metagenomics; Molecular analysis; Petroleum hydrocarbons; Water
• ISSN: 2405-9854; 2405-9854
• DOI: 10.1016/j.egg.2025.100323

The application of genomics in microbial ecological research is of great importance especially in the marine environment with high anthropogenic impacts. Four functional analysis tools (NCBI CDD, PANNZER, and KEGG KOfamKOALA) were used to reveal the functional properties of each of the metagenome in relation to hydrocarbons biodegradation in Iko River estuary. From the 16S rRNA metagenomics result, in the phylum classification, the read counts obtained were; Proteobacteria 178.0, Actinobacteria 28.0, Firmicutes 8.0 and Bacteroidetes 3.0 at 82.03 %, 12.90 %, 3.69 %, and 1.38 % occurrence respectively. Various Classes to genera were all revealed. Nineteen top species were identified, these were Sphingomonas sp154.0 (70.97 %), Unknown1 23.0 (10.60 %), Unknown2 17.0 (7.83 %), Sphingomonas_asaccharolytica 5.0 (2.30 %), Mycobacterium sp 2.0 (0.92 %), Patulibacter sp 2.0 (0.92 %), Nocardioides_insulae 2.0 (0.92 %), Porphyromonas sp 1.0 (0.46 %), Knoellia_subterranea 1.0 (0.46 %), Hylemonella sp 1.0 (0.46 %), Tetrasphaera sp 1.0 (0.46 %), Sphingomonas_mali 1.0 (0.46 %), Robiginitalea sp 1.0 (0.46 %) and Prevotella_ruminicola 1.0 (0.46 %). Functional prediction showed the presence of genes and enzymes such as monooxygenase activity (GO:0004497), describing enzymes that incorporate one atom of oxygen into substrates, critical for the breakdown of hydrocarbons, dioxygenase activity (GO:0016706) describing enzymes that incorporate two atoms of oxygen, often involved in aromatic compound degradation, hydrolase activity (GO:0016787) describing enzymes that catalyze the hydrolysis of various bonds, playing a role in the breakdown of complex hydrocarbons as well as transferase activity (GO:0016740) describing enzymes that transfer functional groups from one substrate to another, relevant in modifying hydrocarbon compounds. This could help towards developing new bioremediation strategies in Iko River estuary. •The application of genomics in microbial ecological research is of great importance.•Presently, culture-dependent methods can only be used to cultivate less than 1% of microbial species.•The general understanding of biodegradation and bioremediation techniques has expanded as a result of metagenomics.•Iko River estuary is one of the most heavily anthropogenically impacted estuaries in the Niger Delta mangrove ecosystem.•The abundant enzymes and genes recorded signify the massive environmental processes in Iko River estuary.