Vol.:(0123456789) Folia Microbiologica https://doi.org/10.1007/s12223-024-01227-3 ORIGINAL ARTICLE Physicochemistry and comparative metagenomics of a tropical estuary persistently inundated with anthropogenic pollutants Lateef B. Salam 1  · Ebi‑Erefa Apollos 1  · Oluwafemi S. Obayori 2  · Gift Ihotu Michael 1 Received: 1 July 2024 / Accepted: 7 November 2024 © Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i. 2024 Abstract The physicochemistry, metabolic properties, and microbial community structure of a tropical estuary persistently inundated with anthropogenic pollutants were elucidated using diverse analytical tools and a shotgun metagenomics approach. The physicochemistry of the Awoye estuary surface water (AEW) and sediment (AES) revealed higher values in the sediment for most of the parameters analyzed, while aside from copper and zinc, the concentrations of the detected heavy metals (Cd, Cr, Pb, Fe, As, Ni, Hg, Mn, Se) in the water and sediment were higher than the acceptable thresholds. Hydrocarbon content analysis revealed increasingly high concentrations of high molecular weight polycyclic aromatic hydrocarbons (HMW PAHs) in the sediment. Structurally, the predominant taxa in the AEW metagenome are Proteobacteria (50.35%), Alphaproteobac- teria (43.31%), Brevundimonas (49.96%), and Leptolyngbya boryana (14.93%), while in the sediment (AES) metagenome, Proteobacteria (53.03%), Gammaproteobacteria (28.66%), Azospirillum (6.51%), and Acidihalobacter prosperus (7.56%) were preponderant. Statistical analysis of the two microbiomes (AEW, AES) revealed significant statistical differences (P < 0.05) at all the hierarchical levels. Functional characterization of the two metagenomes revealed extensive adaptations of the sediment microbiome to various environmental stressors as evident in the high numbers of putative genes involved in the degradation of diverse classes of aromatic hydrocarbons, efflux, detoxification, and transport of heavy metals, and metabolism of organic/inorganic nutrients. Findings from this study revealed that the estuary sediment is the sink for most of the anthropogenic pollutants and harbors the more adapted microbiome that could serve as a potential bioresource for the bioremediation of the perturbed estuary. Keywords Tropical estuary · Anthropogenic pollutants · Shotgun metagenomics · Hydrocarbons · Heavy metals Introduction Petroleum hydrocarbon pollution is inextricably linked to oil exploration, exploitation, transportation, and other upstream and downstream activities. Nigeria is a major oil producer and has had its share of environmental despoliation in almost 70 years of large-scale exploratory and production drilling (Ani et al. 2015; Babalola 2014). The Niger Delta region, spanning the inland and estuarine waters in the South-South and coastal reaches of the South-West remains the locale of most oil-related operations and consequences (Chijoke et al. 2018). Specifically, the anthropogenic activities of oil companies are a major contributor to the contamination of water and sediments with hydrocarbons and other toxic pollutants in the Niger Delta region, especially since some of these com- panies fail to comply with best practices (Ebong and John 2021). Spillages occur as a result of corrosion of pipes and equipment, sabotage, drilling and production operation, and loading and offloading of tankers and barges. In recent years, artisanal refiners’ bunkering activities have increased, which has made pollution worse (Howard et al. 2021). Estuaries present unique ecosystems characterized by rich and sometimes exotic aquaculture and do serve as focal points for spawning and nestling by diverse fauna and other biota. They also account for bounteous economic activities like fishing and tourism. Cravo-Laureau and Duran (2014) noted that the sediment ecology in coastal areas is very * Lateef B. Salam babssalaam@yahoo.com 1 Department of Biological Sciences, Microbiology Unit, Elizade University, Ondo State, Ilara-Mokin, Nigeria 2 Department of Microbiology, Lagos State University, Lagos, Ojo, Nigeria