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The aquatic microbial communities are relatively complex with a high level of prokaryotic diversities. Standard and novel microbiological, analytical, and statistical techniques were employed in the collection, analysis, and comprehensive study of the samples. From the study, the mean values of total heterotrophic bacteria were determined to be 1.35 ± 0.18 (×107), 1.59 ± 0.64 (×107), and 1.56 ± 0.52 (×107) for upstream, midstream, and downstream, respectively, while the mean values for crude oil-utilizing bacteria were 1.08 ± 0.12 (×106), 1.28 ± 0.58 (×106), and 1.24 ± 0.44 (×106) for upstream, midstream, and downstream, respectively. The mean concentrations of physicochemical parameters and heavy metals obtained in the benthic sediment were significantly higher than the mean concentrations in the water samples (tidal and intertidal) (p < 0.02). The result of the component analysis of total petroleum hydrocarbons (including polycyclic aromatic hydrocarbon and benzene, toluene, ethylbenzene, and xylene) revealed significantly higher levels in the sediment than tidal and intertidal water. Structural metagenomics revealed seven top phyla, namely, Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes, Planctomycetes, Fusobacteria, and Chloroflexi. The significantly (p < 0.05) high levels of hydrocarbon-utilizing microorganisms in Iko River estuary can be taken as a sensitive index of environmental exposure to hydrocarbon pollutants in the estuary. This research revealed the response patterns of microorganisms to natural and anthropogenic gradients toward sustainability in Iko River estuary.

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  • Microbial community can be restored following a disturbance.

  • Industrial pollutants have tremendous impacts on the biogeochemistry of an environment.

  • An increase in biofilm biomass has been linked to an increase in nutrient (carbon and nitrogen) and metal (zinc) concentrations.

  • Artificial structures may also affect microbial communities.

  • Studies of the microbial community can lead to an anthropogenic response.

bioremediation, estuary, hydrocarbons, molecular analysis, physicochemical
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