Petroleum contamination significantly changes soil microbial communities in three oilfield locations in Delta State, Nigeria

Abstract

Soil microbial community structure is altered by petroleum contamination in response to compound toxicity and degradation. Understanding the relation between petroleum contamination and soil microbial community structure is crucial to determine the amenability of contaminated soils to bacterial- and fungal-aided remediation. To understand how petroleum contamination and soil physicochemical properties jointly shaped the microbial structure of soils from different oilfields, high-throughput sequencing of 16S and ITS amplicons were used to evaluate the shifts of microbial communities in the petroleum-contaminated soils in Ughelli East (UE), Utorogu (UT), and Ughelli West (UW) oilfields located in Delta State, Nigeria. The results showed 1515 bacteria and 919 fungal average OTU number, and community richness and diversity, trending as AL > UT > UW > UE and AL > UW > UT > UE for bacteria, and AL > UW > UT > UE and UW > UT > AL > UE for fungi, respectively. The bacterial taxa KCM-B-112, unclassified Saccharibacteria, unclassified Rhizobiales, Desulfurellaceae, and Acidobacteriaceae and fungal Trichocomaceae, unclassified Ascomycota, unclassified Sporidiobolales, and unclassified Fungi were found to be the dominant families in petroleum-contaminated soils. Redundancy analysis (RDA) and Spearman’s correlation analysis revealed that total carbon (TC), electric conductivity (EC), pH, and moisture content (MO) were the major drivers of bacterial and fungal communities, respectively. Gas chromatography-mass spectrophotometer (GC-MS) analysis exhibited that the differences in C7–C10, C11–C16, and C12–C29 compounds in the crude oil composition and soil MO content jointly constituted the microbial community variance among the contaminated soils. This study revealed the bacterial and fungal communities responsible for the biodegradation of petroleum contamination from these oilfields, which could serve as biomarkers to monitor oil spill site restoration within these areas. Further studies on these contaminated sites could offer useful insights into other contributing factors such as heavy metals.

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Data availability

The datasets used and/or analyzed during the current study are available from the corresponding authors on reasonable request.

References

  1. Abdul-hafeez EY, Mahmoud A, Ibrahim O (2016) Antibacterial activities and phytochemical screening of Alhagi pseudalhagi. Assiut J Agric Sci 46:33–47. https://doi.org/10.21608/ajas.2016.530

    Article  Google Scholar 

  2. Abia ALK, Alisoltani A, Keshri J, Ubomba-Jaswa E (2018) Metagenomic analysis of the bacterial communities and their functional profiles in water and sediments of the Apies River, South Africa, as a function of land use. Sci Total Environ 616–617:326–334. https://doi.org/10.1016/j.scitotenv.2017.10.322

    CAS  Article  Google Scholar 

  3. Adesipo AA, Freese D, Nwadinigwe AO (2020) Prospects of in-situ remediation of crude oil contaminated lands in Nigeria. Sci African 8:e00403. https://doi.org/10.1016/j.sciaf.2020.e00403

    Article  Google Scholar 

  4. Adserias-Garriga J, Hernández M, Quijada NM, Rodríguez Lázaro D, Steadman D, Garcia-Gil J (2017) Daily thanatomicrobiome changes in soil as an approach of postmortem interval estimation: an ecological perspective. Forensic Sci Int 278:388–395. https://doi.org/10.1016/j.forsciint.2017.07.017

    Article  Google Scholar 

  5. Adzitey F, Huda N, Ali GRR (2013) Molecular techniques for detecting and typing of bacteria, advantages and application to foodborne pathogens isolated from ducks. 3 Biotech 3:97–107. https://doi.org/10.1007/s13205-012-0074-4

    Article  Google Scholar 

  6. Akinola JO, Olawusi-Peters OO, Akpambang VOE (2019) Ecological hazards of total petroleum hydrocarbon in brackish water white shrimp Nematopalaemon hastatus (Aurivillus 1898). Egypt J Aquat Res 45:205–210. https://doi.org/10.1016/j.ejar.2019.07.004

    Article  Google Scholar 

  7. Albert ON, Amaratunga D, Haigh RP (2018) Evaluation of the impacts of oil spill disaster on communities and its influence on restiveness in Niger Delta, Nigeria. Procedia Eng 212:1054–1061. https://doi.org/10.1016/J.PROENG.2018.01.136

    Article  Google Scholar 

  8. Asemoloye MD, Tosi S, Daccò C, Wang X, Xu S, Marchisio MA, Gao W, Jonathan SG, Pecoraro L (2020) Hydrocarbon degradation and enzyme activities of Aspergillus oryzae and Mucor irregularis isolated from nigerian crude oil-polluted sites. Microorganisms 8:1–19. https://doi.org/10.3390/microorganisms8121912

    Article  Google Scholar 

  9. Babatunde BB, Zabbey N, Vincent-Akpu IF, Mekuleyi GO (2018) Bunkering activities in Nigerian waters and their eco-economic consequences. Polit Ecol Oil Gas Act Niger Aquat Ecosyst:439–446. https://doi.org/10.1016/B978-0-12-809399-3.00026-4

  10. Bakke I, De Schryver P, Boon N, Vadstein O (2011) PCR-based community structure studies of bacteria associated with eukaryotic organisms: a simple PCR strategy to avoid co-amplification of eukaryotic DNA. J Microbiol Methods 84:349–351. https://doi.org/10.1016/j.mimet.2010.12.015

    CAS  Article  Google Scholar 

  11. Barnes NM, Khodse VB, Lotlikar NP, Meena RM, Damare SR (2018) Bioremediation potential of hydrocarbon-utilizing fungi from select marine niches of India. 3. Biotech 8:1–10. https://doi.org/10.1007/s13205-017-1043-8

    Article  Google Scholar 

  12. Bickel S, Or D (2020) Soil bacterial diversity mediated by microscale aqueous-phase processes across biomes. Nat Commun 11:1–9. https://doi.org/10.1038/s41467-019-13966-w

    CAS  Article  Google Scholar 

  13. Błońska E, Lasota J, Szuszkiewicz M, Łukasik A, Klamerus-Iwan A (2016) Assessment of forest soil contamination in Krakow surroundings in relation to the type of stand. Environ Earth Sci 75. https://doi.org/10.1007/s12665-016-6005-7

  14. Borem A, Fritsche-Neto R, Cruz CD et al (2014) Biometrics applied to molecular analysis in genetic diversity. Biotechnol Plant Breed. https://doi.org/10.1016/B978-0-12-418672-9.00003-9

  15. Borowik A, Wyszkowska J, Oszust K (2017) Functional diversity of fungal communities in soil contaminated with diesel oil. Front Microbiol 8:1–11. https://doi.org/10.3389/fmicb.2017.01862

    Article  Google Scholar 

  16. Brockett BFT, Prescott CE, Grayston SJ (2012) Soil moisture is the major factor influencing microbial community structure and enzyme activities across seven biogeoclimatic zones in western Canada. Soil Biol Biochem 44:9–20. https://doi.org/10.1016/J.SOILBIO.2011.09.003

    CAS  Article  Google Scholar 

  17. Bruederle A, Hodler R (2019) Effect of oil spills on infant mortality in Nigeria. Proc Natl Acad Sci U S A 116:5467–5471. https://doi.org/10.1073/pnas.1818303116

    CAS  Article  Google Scholar 

  18. Brzeszcz J, Kapusta P, Steliga T (2020) Hydrocarbon removal by two differently developed microbial inoculants and comparing their actions. Molecules 25:1–23. https://doi.org/10.3390/molecules25030661

    CAS  Article  Google Scholar 

  19. Chibuzo EB (2016) Alteration of organic matter by gas flaring activity: a case study of Utorogu Community in Niger-Delta , Nigeria. In: J. Environ. Earth Sci. Vol 6, No 9 https://www.iiste.org/Journals/index.php/JEES/article/view/32922. Accessed 17 Jan 2020

  20. Chikere CB, Mordi IJ, Chikere BO, Selvarajan R, Ashafa TO, Obieze CC (2019) 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. https://doi.org/10.1007/s13213-019-1438-3

    CAS  Article  Google Scholar 

  21. Chinedu E, Chukwuemeka CK (2018) Oil spillage and heavy metals toxicity risk in the Niger Delta, Nigeria. J Heal Pollut 8:180905. https://doi.org/10.5696/2156-9614-8.19.180905

    Article  Google Scholar 

  22. Clarke KR, Somerfield PJ, Chapman MG (2006) On resemblance measures for ecological studies, including taxonomic dissimilarities and a zero-adjusted Bray–Curtis coefficient for denuded assemblages. J Exp Mar Biol Ecol 330:55–80. https://doi.org/10.1016/J.JEMBE.2005.12.017

    Article  Google Scholar 

  23. Climate-Data.org (2019) Warri Climate-Data. In: Climate-Data.org. https://en.climate-data.org/location/24741/. Accessed 19 Sep 2018

  24. Conradie T, Jacobs K (2020) Seasonal and agricultural response of Acidobacteria present in two fynbos rhizosphere soils. Diversity 12. https://doi.org/10.3390/d12070277

  25. Cui JQ, He QS, Liu MH, Chen H, Sun MB, Wen JP (2020) Comparative study on different remediation strategies applied in petroleum-contaminated soils. Int J Environ Res Public Health 17:1–17. https://doi.org/10.3390/ijerph17051606

    CAS  Article  Google Scholar 

  26. De Castro VHL, Schroeder LF, Quirino BF et al (2013) Acidobacteria from oligotrophic soil from the Cerrado can grow in a wide range of carbon source concentrations. Can J Microbiol 59:746–753. https://doi.org/10.1139/cjm-2013-0331

    CAS  Article  Google Scholar 

  27. Devatha CP, Vishnu Vishal A, Purna Chandra Rao J (2019) Investigation of physical and chemical characteristics on soil due to crude oil contamination and its remediation. Appl Water Sci 9:1–10. https://doi.org/10.1007/s13201-019-0970-4

    CAS  Article  Google Scholar 

  28. Erlandson SR, Savage JA, Cavender-Bares JM, Peay KG (2016) Soil moisture and chemistry influence diversity of ectomycorrhizal fungal communities associating with willow along an hydrologic gradient. FEMS Microbiol Ecol 92:1–9. https://doi.org/10.1093/femsec/fiv148

    CAS  Article  Google Scholar 

  29. Ezekoye C, Chikere G, Okpokwasili C (2018a) Field metagenomics of bacterial community involved in bioremediation of crude cil-polluted soil. J Bioremediat Biodegrad 09:09. https://doi.org/10.4172/2155-6199.1000449

    CAS  Article  Google Scholar 

  30. Ezekoye CC, Chikere CB, Okpokwasili GC (2018b) Fungal diversity associated with crude oil-impacted soil undergoing in-situ bioremediation. Sustain Chem Pharm 10:148–152. https://doi.org/10.1016/j.scp.2018.11.003

    Article  Google Scholar 

  31. Fan XY, Gao JF, Pan KL, Li DC, Dai HH, Li X (2018) Functional genera, potential pathogens and predicted antibiotic resistance genes in 16 full-scale wastewater treatment plants treating different types of wastewater. Bioresour Technol 268:97–106. https://doi.org/10.1016/j.biortech.2018.07.118

    CAS  Article  Google Scholar 

  32. Feng X, Liu Z, Jia X, Lu W (2020) Distribution of bacterial communities in petroleum-contaminated soils from the Dagang oilfield, China. Trans Tianjin Univ 26:22–32. https://doi.org/10.1007/s12209-019-00226-7

    CAS  Article  Google Scholar 

  33. Feyzi H, Chorom M, Bagheri G (2020) Urease activity and microbial biomass of carbon in hydrocarbon contaminated soils. A case study of cheshmeh-khosh oil field, Iran. Ecotoxicol Environ Saf 199:110664. https://doi.org/10.1016/j.ecoenv.2020.110664

    CAS  Article  Google Scholar 

  34. Fierascu I, Georgiev MI, Ortan A, Fierascu RC, Avramescu SM, Ionescu D, Sutan A, Brinzan A, Ditu LM (2017) Phyto-mediated metallic nano-architectures via Melissa officinalis L.: synthesis, characterization and biological properties. Sci Rep 7:1–3. https://doi.org/10.1038/s41598-017-12804-7

    CAS  Article  Google Scholar 

  35. Franco-Duarte R, Černáková L, Kadam S, S. Kaushik K, Salehi B, Bevilacqua A, Corbo MR, Antolak H, Dybka-Stępień K, Leszczewicz M, Relison Tintino S, Alexandrino de Souza VC, Sharifi-Rad J, Melo Coutinho HD, Martins N, Rodrigues CF (2019) Advances in chemical and biological methods to identify microorganisms—from past to present. Microorganisms 7:130. https://doi.org/10.3390/microorganisms7050130

    CAS  Article  Google Scholar 

  36. Giwa SO, Nwaokocha CN, Kuye SI, Adama KO (2019) Gas flaring attendant impacts of criteria and particulate pollutants: a case of Niger Delta region of Nigeria. J King Saud Univ - Eng Sci 31:209–217. https://doi.org/10.1016/J.JKSUES.2017.04.003

    Article  Google Scholar 

  37. Gleason FH, Daynes CN, McGee PA (2010) Some zoosporic fungi can grow and survive within a wide pH range. Fungal Ecol 3:31–37. https://doi.org/10.1016/j.funeco.2009.05.004

    Article  Google Scholar 

  38. Hewelke E, Szatyłowicz J, Hewelke P, Gnatowski T, Aghalarov R (2018) The impact of diesel oil pollution on the hydrophobicity and CO2 efflux of forest soils. Water Air Soil Pollut 229. https://doi.org/10.1007/s11270-018-3720-6

  39. Hugerth LW, Andersson AF (2017) Analysing microbial community composition through amplicon sequencing: from sampling to hypothesis testing. Front Microbiol 8:1–22. https://doi.org/10.3389/fmicb.2017.01561

    Article  Google Scholar 

  40. International Agency for Research on Cancer (1989) International agency for research on cancer iarc monographs on the evaluation of carcinogenic risks to humans. Iarc Monogr Eval Carcinog Risks To Humansarc Monogr Eval Carcinog Risks To Humans 45:1–390. https://doi.org/10.1002/food.19940380335

    Article  Google Scholar 

  41. Iwegbue CMA, Bebenimibo E, Tesi GO, Egobueze FE, Martincigh BS (2020) Spatial characteristics and risk assessment of polychlorinated biphenyls in surficial sediments around crude oil production facilities in the Escravos River Basin, Niger Delta, Nigeria. Mar Pollut Bull 159:111462. https://doi.org/10.1016/j.marpolbul.2020.111462

    CAS  Article  Google Scholar 

  42. Jia J, Zong S, Hu L, Shi S, Zhai X, Wang B, Li G, Zhang D (2017) The dynamic change of microbial communities in crude oil-contaminated soils from oil fields in China. Soil Sediment Contam 26:171–183. https://doi.org/10.1080/15320383.2017.1264923

    CAS  Article  Google Scholar 

  43. Jiang B, Adebayo A, Jia J, Xing Y, Deng S, Guo L, Liang Y, Zhang D (2019) Impacts of heavy metals and soil properties at a Nigerian e-waste site on soil microbial community. J Hazard Mater 362:187–195. https://doi.org/10.1016/j.jhazmat.2018.08.060

    CAS  Article  Google Scholar 

  44. Kämpfer P (2010) Actinobacteria. Handb Hydrocarb Lipid Microbiol. https://doi.org/10.1007/978-3-540-77587-4

  45. Kang XH, Leng Y, Macdonald OM et al (2020) The seasonal changes of core bacterial community decide sewage purification in sub-plateau municipal sewage treatment plants. Bioprocess Biosyst Eng 43:1609–1617. https://doi.org/10.1007/s00449-020-02352-2

    CAS  Article  Google Scholar 

  46. Kaufmann K, Christophersen M, Buttler A, Harms H, Höhener P (2004) Microbial community response to petroleum hydrocarbon contamination in the unsaturated zone at the experimental field site Værløse, Denmark. FEMS Microbiol Ecol 48:387–399. https://doi.org/10.1016/j.femsec.2004.02.011

    CAS  Article  Google Scholar 

  47. Kivlin SN, Hawkes CV (2016) Temporal and spatial variation of soil bacteria richness, composition, and function in a neotropical rainforest. PLoS One 11:1–17. https://doi.org/10.1371/journal.pone.0159131

    CAS  Article  Google Scholar 

  48. Kurm V, Van Der Putten WH, Hol WHG (2019) Cultivation-success of rare soil bacteria is not influenced by incubation time and growth medium. PLoS One 14:1–14. https://doi.org/10.1371/journal.pone.0210073

    CAS  Article  Google Scholar 

  49. Liang Y, Zhang X, Wang J, Li G (2012) Spatial variations of hydrocarbon contamination and soil properties in oil exploring fields across China. J Hazard Mater 241–242:371–378. https://doi.org/10.1016/j.jhazmat.2012.09.055

    CAS  Article  Google Scholar 

  50. Liu Y, Ding A, Sun Y, Xia X, Zhang D (2018) Impacts of n-alkane concentration on soil bacterial community structure and alkane monooxygenase genes abundance during bioremediation processes. Front Environ Sci Eng 12:1–13. https://doi.org/10.1007/s11783-018-1064-5

    CAS  Article  Google Scholar 

  51. Liu Q, Tang J, Liu X, Song B, Zhen M, Ashbolt NJ (2019) Vertical response of microbial community and degrading genes to petroleum hydrocarbon contamination in saline alkaline soil. J Environ Sci (China) 81:80–92. https://doi.org/10.1016/j.jes.2019.02.001

    Article  Google Scholar 

  52. Liu H, Gao H, Wu M, Ma C, Wu J, Ye X (2020) Distribution characteristics of bacterial communities and hydrocarbon degradation dynamics during the remediation of petroleum-contaminated soil by enhancing moisture content. Microb Ecol 80:202–211. https://doi.org/10.1007/s00248-019-01476-7

    CAS  Article  Google Scholar 

  53. Mafiana MO, Bashiru MD, Erhunmwunsee F, Dirisu CG, Li SW (2020) An insight into the current oil spills and on-site bioremediation approaches to contaminated sites in Nigeria. Environ Sci Pollut Res 28:4073–4094. https://doi.org/10.1007/s11356-020-11533-1

    Article  Google Scholar 

  54. Maron PA, Sarr A, Kaisermann A, Lévêque J, Mathieu O, Guigue J, Karimi B, Bernard L, Dequiedt S, Terrat S, Chabbi A, Ranjard L (2018) High microbial diversity promotes soil ecosystem functioning. Appl Environ Microbiol 84:1–13. https://doi.org/10.1128/AEM.02738-17

    Article  Google Scholar 

  55. Mills MA, McDonald TJ, Bonner JS et al (1999) Method for quantifying the fate of petroleum in the environment. Chemosphere 39:2563–2582. https://doi.org/10.1016/S0045-6535(99)00163-0

    CAS  Article  Google Scholar 

  56. Mukherjee A, Chettri B, Langpoklakpam JS, Basak P, Prasad A, Mukherjee AK, Bhattacharyya M, Singh AK, Chattopadhyay D (2017) Bioinformatic approaches including predictive metagenomic profiling reveal characteristics of bacterial response to petroleum hydrocarbon contamination in diverse environments. Sci Rep 7:1108. https://doi.org/10.1038/s41598-017-01126-3

    CAS  Article  Google Scholar 

  57. Nye TMW, Liò P, Gilks WR (2006) A novel algorithm and web-based tool for comparing two alternative phylogenetic trees. Bioinformatics 22:117–119. https://doi.org/10.1093/bioinformatics/bti720

    CAS  Article  Google Scholar 

  58. O’Brien FJM, Almaraz M, Foster MA, Hill AF, Huber DP, King EK, Langford H, Lowe MA, Mickan BS, Miller VS, Moore OW, Mathes F, Gleeson D, Leopold M (2019) Soil salinity and pH drive soil bacterial community composition and diversity along a lateritic slope in the Avon river critical zone observatory, Western Australia. Front Microbiol 10:1486. https://doi.org/10.3389/fmicb.2019.01486

    Article  Google Scholar 

  59. Obi CC, Adebusoye SA, Ugoji EO, Ilori MO, Amund OO, Hickey WJ (2016) Microbial communities in sediments of Lagos Lagoon, Nigeria: elucidation of community structure and potential impacts of contamination by municipal and industrial wastes. Front Microbiol 7:1213. https://doi.org/10.3389/fmicb.2016.01213

    Article  Google Scholar 

  60. Obiefuna JN, Nwilo PC, Atagbaza AO, Okolie CJ (2013) Spatial changes in the wetlands of Lagos/Lekki Lagoons of Lagos, Nigeria. J Sustain Dev 6. https://doi.org/10.5539/jsd.v6n7p123

  61. Obieze CC, Chikere CB, Adeleke R, Akaranta O (2019a) Formulation and evaluation of slow-release fertilizer from agricultural and industrial wastes for remediation of crude oil-polluted soils. Soc Pet Eng - SPE Niger Annu Int Conf Exhib 2019, NAIC 2019. https://doi.org/10.2118/198815-MS

  62. Obieze CC, Chikere CB, Adeleke R, Akaranta O (2019b) Formulation and evaluation of slow-release fertilizer from agricultural and industrial wastes for remediation of crude oil-polluted soils. In: Society of Petroleum Engineers - SPE Nigeria Annual International Conference and Exhibition 2019, NAIC 2019. OnePetro

  63. Okafor CP, Udemang NL, Chikere CB, Akaranta O, Ntushelo K (2021) Indigenous microbial strains as bioresource for remediation of chronically polluted Niger Delta soils. Sci African 11:e00682. https://doi.org/10.1016/j.sciaf.2020.e00682

    Article  Google Scholar 

  64. Osuji LC, Egbuson EJ, Ojinnaka CM (2006) Assessment and treatment of hydrocarbon inundated soils using inorganic nutrient (N-P-K) supplements: II. A case study of Eneka oil spillage in Niger Delta, Nigeria. Environ Monit Assess 115:265–278. https://doi.org/10.1007/s10661-006-6552-6

    CAS  Article  Google Scholar 

  65. Oyetibo GO, Miyauchi K, Huang Y, Chien MF, Ilori MO, Amund OO, Endo G (2017) Biotechnological remedies for the estuarine environment polluted with heavy metals and persistent organic pollutants. Int Biodeterior Biodegradation 119:614–625. https://doi.org/10.1016/J.IBIOD.2016.10.005

    CAS  Article  Google Scholar 

  66. Padmavathi J, Uma Devi K, Uma Maheswara Rao C (2003) The optimum and tolerance pH range is correlated to colonial morphology in isolates of the entomopathogenic fungus Beauveria bassiana—a potential biopesticide. World J Microbiol Biotechnol 19:469–477. https://doi.org/10.1023/A:1025151000398

    Article  Google Scholar 

  67. Pankratov TA, Kirsanova LA, Kaparullina EN, Kevbrin VV, Dedysh SN (2012) Telmatobacter bradus gen. nov., sp. nov., a cellulolytic facultative anaerobe from subdivision 1 of the Acidobacteria, and emended description of Acidobacterium capsulatum Kishimoto et al. 1991. Int J Syst Evol Microbiol 62:430–437. https://doi.org/10.1099/ijs.0.029629-0

    Article  Google Scholar 

  68. Peng M, Zi X, Wang Q (2015) Bacterial community diversity of oil-contaminated soils assessed by high throughput sequencing of 16S rRNA genes. Int J Environ Res Public Health 12:12002–12015. https://doi.org/10.3390/ijerph121012002

    CAS  Article  Google Scholar 

  69. Prince RC, Amande TJ, McGenity TJ (2018) Prokaryotic hydrocarbon degraders. Taxon Genomics Ecophysiol Hydrocarb Microbes 1–41. https://doi.org/10.1007/978-3-319-60053-6_15-1

  70. PubChem US National Library of Medicine. In: Natl. Cent. Biotechnol. Inf. https://pubchem.ncbi.nlm.nih.gov/. Accessed 14 Sep 2020

  71. Ramamurthy T, Ghosh A, Pazhani GP, Shinoda S (2014) Current perspectives on viable but non-culturable (VBNC) pathogenic bacteria. Front Public Health 2:1–9. https://doi.org/10.3389/fpubh.2014.00103

    Article  Google Scholar 

  72. Rodríguez-Rodríguez N, Rivera-Cruz MC, Trujillo-Narcía A, Almaráz-Suárez JJ, Salgado-García S (2016) Spatial distribution of oil and biostimulation through the rhizosphere of Leersia hexandra in degraded soil. Water Air Soil Pollut 227:227. https://doi.org/10.1007/s11270-016-3030-9

    CAS  Article  Google Scholar 

  73. Roesch LFW, Fulthorpe RR, Riva A, Casella G, Hadwin AKM, Kent AD, Daroub SH, Camargo FAO, Farmerie WG, Triplett EW (2007) Pyrosequencing enumerates and contrasts soil microbial diversity. Int Soc Microb Ecol 1:283–290. https://doi.org/10.1038/ismej.2007.53

    CAS  Article  Google Scholar 

  74. Rousk J, Bååth E, Brookes PC, Lauber CL, Lozupone C, Caporaso JG, Knight R, Fierer N (2010) Soil bacterial and fungal communities across a pH gradient in an arable soil. ISME J 4:1340–1351. https://doi.org/10.1038/ismej.2010.58

    Article  Google Scholar 

  75. Sam K, Zabbey N (2018) Contaminated land and wetland remediation in Nigeria: opportunities for sustainable livelihood creation. Sci Total Environ 639:1560–1573. https://doi.org/10.1016/j.scitotenv.2018.05.266

    CAS  Article  Google Scholar 

  76. Shen C, Shi Y, Fan K, He JS, Adams JM, Ge Y, Chu H (2019) Soil pH dominates elevational diversity pattern for bacteria in high elevation alkaline soils on the Tibetan Plateau. FEMS Microbiol Ecol 95:1–9. https://doi.org/10.1093/femsec/fiz003

    CAS  Article  Google Scholar 

  77. Sheng Y, Liu Y, Yang J, Dong H, Liu B, Zhang H, Li A, Wei Y, Li G, Zhang D (2021) History of petroleum disturbance triggering the depth-resolved assembly process of microbial communities in the vadose zone. J Hazard Mater 402:124060. https://doi.org/10.1016/j.jhazmat.2020.124060

    CAS  Article  Google Scholar 

  78. Siles JA, Margesin R (2018) Insights into microbial communities mediating the bioremediation of hydrocarbon-contaminated soil from an Alpine former military site. Appl Microbiol Biotechnol 102:4409–4421. https://doi.org/10.1007/s00253-018-8932-6

    CAS  Article  Google Scholar 

  79. Spini G, Spina F, Poli A, Blieux AL, Regnier T, Gramellini C, Varese GC, Puglisi E (2018) Molecular and microbiological insights on the enrichment procedures for the isolation of petroleum degrading bacteria and fungi. Front Microbiol 9:2543. https://doi.org/10.3389/fmicb.2018.02543

    Article  Google Scholar 

  80. Staley C, Breuillin-Sessoms F, Wang P, Kaiser T, Venterea RT, Sadowsky MJ (2018) Urea amendment decreases microbial diversity and selects for specific nitrifying strains in eight contrasting agricultural soils. Front Microbiol 9:1–13. https://doi.org/10.3389/fmicb.2018.00634

    Article  Google Scholar 

  81. Trejos-Delgado C, Cadavid-Restrepo GE, Hormaza-Anaguano A et al (2020) Oil bioremediation in a tropical contaminated soil using a reactor. An Acad Bras Cienc 92:e20181396. https://doi.org/10.1590/0001-3765202020181396

    CAS  Article  Google Scholar 

  82. UNEP (2011) Environmental assessment of Ogoniland site-specific fact sheets. In: United Nations Environ. Prot. Agency. https://wedocs.unep.org/handle/20.500.11822/23016. Accessed 16 Sep 2020

  83. Usman N, Atta HI, Tijjani MB (2020a) Biodegradation studies of benzene, toluene, ethylbenzene and xylene ( BTEX ) compounds by Gliocladium sp. and Aspergillus terreus. J Appl Sci Environ Manag 24:1063–1069. https://doi.org/10.4314/jasem.v24i6.19

    Article  Google Scholar 

  84. Usman N, Tijjani MB, Atta HI (2020b) Isolation and identification of BTEX-utilizing Fungi from soil polluted with petroleum hydrocarbons. In: Biosci. Res. J. http://ojs.klobexjournals.com/index.php/brj/article/view/458. Accessed 14 Sep 2020

  85. Ventorino V, Pascale A, Adamo P, Rocco C, Fiorentino N, Mori M, Faraco V, Pepe O, Fagnano M (2018) Comparative assessment of autochthonous bacterial and fungal communities and microbial biomarkers of polluted agricultural soils of the Terra dei Fuochi. Sci Rep 8:1–13. https://doi.org/10.1038/s41598-018-32688-5

    CAS  Article  Google Scholar 

  86. Viñas M, Sabaté J, Espuny MJ, Solanas AM (2005) Bacterial community dynamics and polycyclic aromatic hydrocarbon degradation during bioremediation of heavily creosote-contaminated soil. Appl Environ Microbiol 71:7008–7018. https://doi.org/10.1128/AEM.71.11.7008-7018.2005

    CAS  Article  Google Scholar 

  87. Wang X, Guan X, Zhang X, Xiang S, Zhang R, Liu M (2020) Microbial communities in petroleum-contaminated seasonally frozen soil and their response to temperature changes. Chemosphere 258:127375. https://doi.org/10.1016/j.chemosphere.2020.127375

    CAS  Article  Google Scholar 

  88. Wang Y, Feng J, Lin Q, Lyu X, Wang X, Wang G (2013) Effects of crude oil contamination on soil physical and chemical properties in momoge wetland of China. Chin Geogr Sci 23:708–715. https://doi.org/10.1007/s11769-013-0641-6

    Article  Google Scholar 

  89. Wang C, Liu D, Bai E (2018) Decreasing soil microbial diversity is associated with decreasing microbial biomass under nitrogen addition. Soil Biol Biochem 120:126–133. https://doi.org/10.1016/j.soilbio.2018.02.003

    CAS  Article  Google Scholar 

  90. Zegeye EK, Brislawn CJ, Farris Y, Fansler SJ, Hofmockel KS, Jansson JK, Wright AT, Graham EB, Naylor D, McClure RS, Bernstein HC (2019) Selection, succession, and stabilization of soil microbial consortia. Am Soc Microbiol 4:1–13. https://doi.org/10.1128/msystems.00055-19

    CAS  Article  Google Scholar 

  91. White TJ, Bruns TD, Lee S, Taylor J (1990) Amplification and direct sequencing of fungal ribosomal genes form phylogenetics. In: PCR Protoc. A Guid. to methods Appl. https://nature.berkeley.edu/brunslab/papers/white1990.pdfAccessed 16 Oct 2020

  92. Yamada-Onodera K, Mukumoto H, Katsuyama Y, Tani Y (2002) Degradation of long-chain alkanes by a polyethylene-degrading fungus, Penicillium simplicissimum YK. Enzym Microb Technol 30:828–831. https://doi.org/10.1016/S0141-0229(02)00065-0

    CAS  Article  Google Scholar 

  93. Yang R, Liu G, Chen T, Li S, An L, Zhang G, Li G, Chang S, Zhang W, Chen X, Wu X, Zhang B (2019) Characterization of the genome of a Nocardia strain isolated from soils in the Qinghai-Tibetan Plateau that specifically degrades crude oil and of this biodegradation. Genomics 111:356–366. https://doi.org/10.1016/j.ygeno.2018.02.010

    CAS  Article  Google Scholar 

  94. Zhao C, Long J, Liao H, Zheng C, Li J, Liu L, Zhang M (2019) Dynamics of soil microbial communities following vegetation succession in a karst mountain ecosystem, Southwest China. Sci Rep 9:1–10. https://doi.org/10.1038/s41598-018-36886-z

    CAS  Article  Google Scholar 

  95. Zeng XY, Li SW, Leng Y, Kang XH (2020) Structural and functional responses of bacterial and fungal communities to multiple heavy metal exposure in arid loess. Sci Total Environ 723:138081. https://doi.org/10.1016/j.scitotenv.2020.138081

    CAS  Article  Google Scholar 

  96. Zhalnina K, Dias R, de Quadros PD, Davis-Richardson A, Camargo FAO, Clark IM, McGrath SP, Hirsch PR, Triplett EW (2014) Soil pH determines microbial diversity and composition in the park grass experiment. Microb Ecol 69:395–406. https://doi.org/10.1007/s00248-014-0530-2

    CAS  Article  Google Scholar 

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Acknowledgements

The authors are thankful to the Chinese Scholarship Council (CSC) of China and the School of International Studies, Lanzhou Jiaotong University: The Nigerian Petroleum Development Corporation (NPDC) OML 34 team of sample collection assistance.

Funding

This work was supported through funding from the National Natural Science Foundation of China (31760110 and 31560121).

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MOM: conceived and designed the analysis; collecting of the data and analysis tools; experimental procedure; writing of the paper; XHK: collecting the data and analysis tools; analysis of data; YL: experimental procedure; LFH: experimental procedure; SWL: supervision, conceptualization, revision of manuscript

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Correspondence to Macdonald Ogorm Mafiana or Shi-Weng Li.

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Mafiana, M.O., Kang, XH., Leng, Y. et al. Petroleum contamination significantly changes soil microbial communities in three oilfield locations in Delta State, Nigeria. Environ Sci Pollut Res (2021). https://doi.org/10.1007/s11356-021-12955-1

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Keywords

  • Oil-contaminated soil
  • Microbial characterization
  • Species richness and diversity
  • Bioremediation