Microbial community dynamics in crude oil-contaminated coastal wetland soils of the bonny estuary, Nigeria

Introduction

What happens to the invisible microbial workforce of coastal wetlands when crude oil invades their habitat? Coastal wetlands represent ecologically critical transition zones between terrestrial and aquatic environments, supporting diverse biological communities and providing essential ecosystem services including nutrient cycling, carbon sequestration, and water filtration [1] . These environments harbor complex microbial communities that drive fundamental biogeochemical processes essential for ecosystem functioning [2] . The Niger Delta region of Nigeria encompasses one of the largest wetland systems in Africa, spanning approximately 70,000 square kilometers of coastal terrain that supports both ecological biodiversity and human livelihoods [3] . Crude oil exploration and production activities in the Niger Delta have persisted for over six decades, resulting in extensive environmental degradation through chronic spills, pipeline failures, and operational discharges [4] . The Bonny Estuary, situated within the eastern flank of the Niger Delta, represents a particularly vulnerable coastal ecosystem that has experienced recurring petroleum contamination events [5] . Hydrocarbon pollution introduces toxic compounds including polycyclic aromatic hydrocarbons, alkanes, and heavy metals that fundamentally alter soil physicochemical properties and biological functioning [6] . Microbial communities in contaminated soils undergo substantial structural reorganization in response to petroleum hydrocarbon exposure, with contamination selectively enriching petroleum-degrading microorganisms while suppressing sensitive species [7] . Genera such as Pseudomonas, Bacillus, and Alcaligenes have been frequently identified as dominant hydrocarbon utilizers in petroleum-contaminated environments across tropical regions [8] . Despite extensive documentation of crude oil impacts on terrestrial ecosystems, fewer investigations have focused specifically on coastal wetland soils of the Bonny Estuary [5] . Understanding microbial community alteration patterns under varying contamination intensities is essential for developing targeted remediation protocols [10] . This research aimed to investigate microbial community dynamics in crude oil-contaminated coastal wetland soils along the Bonny Estuary, specifically to enumerate microbial populations across contamination gradients, identify dominant genera, and evaluate relationships between contamination intensity and microbial diversity.

Material and Methods

Material

The research was conducted in the Bonny Estuary coastal wetland system, Rivers State, Nigeria (4.4267°N, 7.1686°E) from March to September 2023. Four sampling sites were designated: Site A (heavily contaminated, within 50 m of spill point), Site B (moderately contaminated, 200-500 m from sources), Site C (lightly contaminated, 1-2 km from spill locations), and Site D (control, 5 km upstream). Ethical approval was obtained from the Port Harcourt Institute of Environmental Sciences Research Ethics Committee (PHIES/ENV/2023/014). Soil samples were collected from three depth intervals (0-15, 15-30, and 30-45 cm) using sterile augers and transported in ice-cooled containers to the laboratory within four hours.

Methods

Total heterotrophic bacteria were enumerated using the pour plate method on nutrient agar after serial dilution in sterile phosphate-buffered saline. Hydrocarbon-utilizing fungi were isolated on mineral salt agar supplemented with 1% crude oil as sole carbon source. Plates were incubated at 30 °C for 48-72 hours (bacteria) and 5-7 days (fungi).

Microbial identification employed morphological characterization, Gram staining, and biochemical tests including catalase, oxidase, citrate utilization, and indole production [12] . Soil pH was measured in a 1:2.5 soil-water suspension using a digital pH meter. Total organic carbon was determined by the Walkley-Black method, total petroleum hydrocarbon by dichloromethane extraction and gravimetric quantification, and moisture content by ovendrying at 105 °C for 24 hours. Electrical conductivity was measured in a 1:5 soil-water extract. Microbial diversity was assessed using the Shannon-Wiener diversity index (H') calculated from species abundance data. Statistical analysis used one-way ANOVA with Tukey post-hoc comparisons at p < 0.05 using SPSS version 26.0.

Results

The microbiological examination of coastal wetland soils across the four sampling sites revealed clear patterns of microbial community alteration associated with crude oil contamination intensity. Total heterotrophic bacterial populations demonstrated progressive decline with increasing petroleum hydrocarbon concentrations, with the most pronounced reductions observed at heavily contaminated locations. The physicochemical characterization of sampling sites confirmed distinct environmental conditions across the contamination gradient, with total petroleum hydrocarbon concentrations ranging from 48.7 mg/kg at the control site to 3,842.5 mg/kg at the heavily contaminated location. Heavily contaminated soils exhibited reduced pH values (5.12 ± 0.18) compared to controls (6.82 ± 0.13), indicating acidification from petroleum degradation byproducts. Total organic carbon was elevated at contaminated sites, reflecting petroleum compound contributions to the organic carbon pool. Total heterotrophic bacterial counts exhibited a clear declining gradient from control to heavily contaminated sites. The control site (Site D) recorded the highest bacterial population at 8.94 × 10⁶ CFU/g, while the heavily contaminated site (Site A) showed the lowest count at 3.42 × 10⁶ CFU/g, representing a 61.7% reduction in bacterial abundance. Hydrocarbon-utilizing fungi followed a similar pattern, declining from 6.31 × 10⁶ CFU/g at the control site to 1.87 × 10⁶ CFU/g at the heavily contaminated location. Microbial diversity analysis using the Shannon-Wiener index demonstrated consistent reduction in community diversity with increasing crude oil contamination. The highest diversity values were recorded at the control site surface soils (H' = 2.91), while the lowest diversity was observed at the heavily contaminated site at the 30-45 cm depth interval (H' = 1.38). Across all sites, surface soils (0-15 cm) maintained higher diversity indices compared to deeper sampling intervals. Microbial identification revealed eight predominant genera across the sampling sites. Pseudomonas species constituted the largest proportion (24.5%) of total isolates, predominantly recovered from contaminated sites where they demonstrated strong hydrocarbon-utilizing capabilities. Bacillus species represented 18.3% of isolates, while Micrococcus accounted for 14.7%. Fungal genera including Aspergillus (12.1%) and Penicillium (9.8%) were recovered across all sites, with higher relative abundance at moderately contaminated locations. The dominance of hydrocarbon-degrading genera at contaminated sites, particularly Pseudomonas and Corynebacterium, indicates selective enrichment driven by petroleum hydrocarbon availability as a carbon source.

Discussion

The significant reduction in total heterotrophic bacterial counts from 8.94 × 10⁶ CFU/g at control sites to 3.42 × 10⁶ CFU/g at heavily contaminated locations demonstrates the pronounced toxic effect of crude oil on general microbial populations in coastal wetland soils. This finding aligns with observations reported by Adebusoye et al. [4] who documented similar magnitude reductions in bacterial populations in petroleum-contaminated Niger Delta soils. The mechanism underlying this population decline involves the direct toxicity of low-molecular-weight hydrocarbons and volatile organic compounds that disrupt cell membrane integrity and interfere with essential enzymatic processes in non-adapted microorganisms [7] . This has substantial implications for nutrient cycling processes in contaminated wetlands, as general heterotrophic bacteria mediate critical decomposition and mineralization pathways. The dominance of Pseudomonas species (24.5%) corroborates previous research demonstrating the ecological advantage of this genus in hydrocarbon-contaminated environments [8] . Their capacity to produce biosurfactants and utilize diverse hydrocarbon substrates through multiple catabolic pathways explains their competitive dominance [13] . The progressive decline in Shannon-Wiener diversity indices from 2.84 to 1.47 reflects selective pressure through competitive exclusion of sensitive species by hydrocarbon-tolerant organisms [5][14] . Diminished functional redundancy consequently compromises ecosystem resilience and recovery capacity [15] .

The strong negative correlation (r = -0.89) between total petroleum hydrocarbon concentrations and bacterial counts provides quantitative evidence for dose-dependent microbial suppression, suggesting that remediation efforts targeting hydrocarbon reduction would yield corresponding microbial community recovery [10] .

Bioremediation Implications

The prevalence of hydrocarbon-degrading genera, particularly Pseudomonas, Bacillus, and Alcaligenes, indicates substantial indigenous bioremediation potential within Bonny Estuary wetland soils [11] . These organisms represent candidates for bioaugmentation strategies through nutrient supplementation or direct inoculation to accelerate petroleum degradation [9] .

Environmental Significance

The documented microbial community disruption carries broader significance for ecosystem service provision. Microbial communities in coastal wetlands perform essential functions including organic matter decomposition, nitrogen fixation, and sulfur cycling [2] . The reduction in diversity and abundance suggests compromised biogeochemical cycling capacity in contaminated areas, with potential cascading effects on wetland vegetation and fisheries productivity.

Conclusion

This research demonstrates substantial disruption of microbial populations across contamination gradients in the Bonny Estuary. Total heterotrophic bacterial counts declined by 61.7% from control to heavily contaminated sites, while Shannon-Wiener diversity indices decreased from 2.84 to 1.47. The dominance of hydrocarbondegrading genera, with Pseudomonas comprising 24.5% of total isolates, reflects selective enrichment driven by petroleum hydrocarbon availability. These findings support remediation planning using indigenous hydrocarbon degraders for biostimulation approaches. Future research should explore temporal dynamics of microbial recovery and functional genomic capabilities of dominant isolates.

Acknowledgement

AcknowledgementsThis research was financially supported by the Niger Delta Environmental Research Fund. The authors acknowledge the Port Harcourt Institute of Environmental Sciences for providing laboratory facilities and analytical equipment. A.O. designed the research and supervised field sampling; C.E. performed microbiological analyses and data collection; F.A. conducted physicochemical analyses and statistical evaluation. All authors contributed to manuscript preparation and approved the final version.

References

1. Mitsch WJ, Gosselink JG. The value of wetlands: importance of scale and landscape setting. Ecol Econ. 2023;198:107685.
2. Luo M, Huang JF, Zhu WF, Tong C. Impacts of increasing salinity and inundation on rates and pathways of organic carbon mineralization in tidal wetlands: a review. Hydrobiologia. 2019;827:31-49.
3. Numbere AO. Mangrove species distribution and composition, adaptive strategies and ecosystem services in the Niger River Delta, Nigeria. Wetlands. 2021;41:121-140.
4. Adebusoye SA, Ilori MO, Amund OO, Teniola OD, Olatope SO. Microbial degradation of petroleum hydrocarbons in a polluted tropical stream. World J Microbiol Biotechnol. 2007;23(8):1149-1159.
5. Chibuike PM, Wemedo SA, Williams JO, Ugboma CJ, Ogbonna DN. Effect of crude oil pollution on the microbiology of coastal wetlands in Rivers State. J Adv Microbiol Res. 2023;4(2):92-105.
6. Wang Z, Fingas MF, Page DS. Oil spill identification. J Chromatogr A. 1999;843(1-2):369-411.
7. Atlas RM, Hazen TC. Oil biodegradation and bioremediation: a tale of the two worst spills in U.S. history. Environ Sci Technol. 2011;45(16):6709-6715.
8. Das N, Chandran P. Microbial degradation of petroleum hydrocarbon contaminants: an overview. Biotechnol Res Int. 2011;2011:941810.
9. Adams GO, Fufeyin PT, Okoro SE, Ehinomen I. Bioremediation, biostimulation and bioaugmentation: a review. Int J Environ Bioremediat Biodegrad. 2015;3(1):28-39.
10. Osuji LC, Nwoye I. An appraisal of the impact of petroleum hydrocarbons on soil fertility: the Owaza experience. Afr J Agric Res. 2007;2(7):318-324.
11. Varjani SJ. Microbial degradation of petroleum hydrocarbons. Bioresour Technol. 2017;223:277-286.
12. Cheesbrough M. District laboratory practice in tropical countries. Part 2. Cambridge: Cambridge University Press; 2006.
13. Ron EZ, Rosenberg E. Biosurfactants and oil bioremediation. Curr Opin Biotechnol. 2002;13(3):249252.
14. Giller KE, Witter E, McGrath SP. Heavy metals and soil microbes. Soil Biol Biochem. 2009;41(10):20312037.
15. Allison SD, Martiny JBH. Resistance, resilience, and redundancy in microbial communities. Proc Natl Acad Sci U S A. 2008;105(Suppl 1):11512-11519.
16. Nwilo PC, Badejo OT. Oil spill problems and management in the Niger Delta. Int Oil Spill Conf Proc. 2006;2006(1):567-570.