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Comparative metagenomics and functional profiling of crude oil-polluted soils in Bodo West Community, Ogoni, with other sites of varying pollution history

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Abstract

The impact of long-term crude oil pollution on soil microbial community structure in Bodo West Community, Ogoniland, Nigeria, was investigated to determine the amenability of the soil to microbial mediated remediation. Crude oil-polluted and pristine soil samples were collected approximately from 0 to 30 cm depth for both chemical and microbiological analyses. Total petroleum hydrocarbons (TPH) and polycyclic aromatic hydrocarbons (PAH) were determined using gas chromatograph–mass spectrophotometer (GC-MS). The soil microbiome was determined using the Illumina MiSeq platform. Results from this study were then compared with publicly available data from other oil-polluted sites. Taxonomic biomarkers and pathways associated with oil-polluted soils were detected using bioinformatics pipelines. TPH in the polluted and pristine soils were 7591 mg/kg and 199.70 mg/kg respectively, while the values of PAHs were significantly higher (p < 0.05) in the oil-polluted soil. Predictive functional and biomarker analysis demonstrated that microbes detected in the oil-polluted environment were involved in different metabolic pathways for degradation of a broad set of xenobiotic aromatic compounds. Established hydrocarbon degraders belonging to the families Alcanivoracaceae and Oceanospirillaceae were mostly detected in the oil-polluted soils. Sneathiella, Parvibaculum, Sphingobium, and Oceanicaulis were among biomarker taxa. The bacterial families Acidithiobacillaceae and Desulfobacteraceae were differentially more abundant in Bodo West spill site than any other site used for comparison. Furthermore, differentially represented species in our study site and other oil-polluted sites ranged from 21 to 42 bacterial families. The findings from this study revealed the bacterial community had a strong dependence on hydrocarbons and that acid-tolerant bacterial families can as well contribute significantly to biodegradation in the site and other polluted sites in Ogoniland usually known to have an acidic pH. Further research on Bodo West spill site will reveal the novel enzymes and pathways for enhanced microbial mediated eco-restoration.

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Acknowledgements

The authors would like to thank the Centre for High Performance Computing (CHPC) facility, South Africa, for providing computational support for sequence data analysis.

Data accessibility statement

Sequence reads for Bodo West, Ogoniland, samples were deposited in GenBank (Sequence Reads Archive) under the SRA accession number SRP133543.

Funding

This study was self-funded by the authors.

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Authors and Affiliations

  1. Department of Microbiology, University of Port Harcourt, East-West Road, Choba. P.M.B. 5323, Port Harcourt, Nigeria

    Chioma Blaise Chikere & Ijeoma Jessie Mordi

  2. Environmental Studies Unit, Shell Petroleum Development Company (SPDC) Port Harcourt, P. O. Box 263, Rumuobiakani, Port Harcourt, Nigeria

    Blaise Ositadinma Chikere

  3. Department of Plant Sciences, University of the Free State, Qwaqwa Campus, Phuthaditjhaba, South Africa

    Ramganesh Selvarajan & Tom Omotayo Ashafa

  4. Africa Centre of Excellence in Oilfield Chemicals Research, University of Port Harcourt, East-West Road, Choba. P.M.B. 2, Port Harcourt, Nigeria

    Chinedu Christopher Obieze

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  1. Chioma Blaise Chikere
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Appendix

Appendix

Fig. 7
figure 7

Abundance and distribution of the five most abundant phyla across the samples. *USA (Pensacola beach oil-polluted and pristine soils). India (oil-polluted soils from Noonmati and Barhola oil refineries India). Bodo West (oil-polluted soils, Bodo West, Ogoniland, Nigeria)

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Fig. 8
figure 8

Comparison of microbial community structure and its abundance in the crude oil-polluted and the pristine soil samples obtained from Bodo West, Ogoniland, Nigeria. *IES (polluted soil). *ICES (pristine soil)

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Table 4 Summary information on datasets used for this study
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Table 5 PERMANOVA analysis for bacterial diversity using Bray–Curtis
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Table 6 PERMANOVA analysis for gene abundance using Bray–Curtis
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Chikere, C.B., Mordi, I.J., Chikere, B.O. et al. Comparative metagenomics and functional profiling of crude oil-polluted soils in Bodo West Community, Ogoni, with other sites of varying pollution history. Ann Microbiol 69, 495–513 (2019). https://doi.org/10.1007/s13213-019-1438-3

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