Search
Close this search box.

Impact of artisanal refining activities on bacterial diversity in a Niger Delta fallow land – Scientific Reports

  • Izah, S. Ecosystem of the Niger-Delta region of Nigeria: Potentials and threats. Biodivers. Int. J. 2, 338–345 (2018).

    Article 

    Google Scholar
     

  • Kadafa, A. A. Oil exploration and spillage in the Niger Delta of Nigeria. Civ. Environ. Res. 2, 38–51 (2012).


    Google Scholar
     

  • Enyoghasim, M. O. Oil exploration and exploitation in Nigeria and the challenge of sustainable development: An assessment of the Niger Delta. 670216917 (2019).

  • Nwozor, A., Audu, J. & Adama, I. J. The political economy of hydrocarbon pollution: Assessing socio-ecological sustainability of Nigeria’s Niger Delta region. Int. J. Energy Econ. Policy 9, 1–8 (2018).


    Google Scholar
     

  • Obida, C. B., Blackburn, G. A., Whyatt, J. D. & Semple, K. T. Quantifying the exposure of humans and the environment to oil pollution in the Niger Delta using advanced geostatistical techniques. Environ. Int. 111, 32–42 (2018).

    Article 
    PubMed 

    Google Scholar
     

  • Albert, O., Amaratunga, D. & Haigh, R. An investigation into root causes of sabotage and vandalism of pipes: A major environmental hazard in Niger Delta, Nigeria. in ASCENT Festival 2019: International Conference on Capacity Building for Research and Innovation in Disaster Resilience 22–37 (National Science Foundation of Sri Lanka, 2019).

  • Elum, Z. A., Mopipi, K. & Henri-Ukoha, A. Oil exploitation and its socioeconomic effects on the Niger Delta region of Nigeria. Environ. Sci. Pollut. Res. 23, 12880–12889 (2016).

    Article 
    CAS 

    Google Scholar
     

  • Osuji, L. Some environmental hazards of oil pollution in Niger Delta, Nigeria. Afr. J. Interdisc. Stud. 3, 11–17 (2002).


    Google Scholar
     

  • Ramírez, D. et al. Bacterial diversity in surface sediments from the continental shelf and slope of the North West gulf of Mexico and the presence of hydrocarbon degrading bacteria. Mar. Pollut. Bull. 150, 110590 (2020).

    Article 
    PubMed 

    Google Scholar
     

  • Cocârţă, D. M., Stoian, M. A. & Karademir, A. Crude oil contaminated sites: evaluation by using risk assessment approach. Sustainability 9, 1365 (2017).

    Article 

    Google Scholar
     

  • Neethu, C. S., Saravanakumar, C., Purvaja, R., Robin, R. S. & Ramesh, R. Oil-spill triggered shift in indigenous microbial structure and functional dynamics in different marine environmental matrices. Sci. Rep. 9, 1–13 (2019).

    Article 
    CAS 

    Google Scholar
     

  • Xu, X. et al. Petroleum hydrocarbon-degrading bacteria for the remediation of oil pollution under aerobic conditions: A perspective analysis. Front. Microbiol. 9, 2885 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Das, N. & Chandran, P. Microbial degradation of petroleum hydrocarbon contaminants: An overview. Biotechnol. Re. Int. 2011, 1–13 (2011).


    Google Scholar
     

  • Nzila, A. Current status of the degradation of aliphatic and aromatic petroleum hydrocarbons by thermophilic microbes and future perspectives. Int. J. Environ. Res. Public Health 15, 2782 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ali, S. S. et al. Recent advances in the life cycle assessment of biodiesel production linked to azo dye degradation using yeast symbionts of termite guts: A critical review. Energy Rep. 8, 7557–7581 (2022).

    Article 

    Google Scholar
     

  • Mironov, O. G. Black Sea microorganisms growing on hydrocarbons. Mikrobiologiia 38, 728–731 (1969).

    CAS 
    PubMed 

    Google Scholar
     

  • Koshlaf, E. & Ball, A. S. Soil bioremediation approaches for petroleum hydrocarbon polluted environments. AIMS Microbiol. 3, 25 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Shen, Z. et al. Bacterial diversity in surface sediments of collapsed lakes in Huaibei, China. Sci. Rep. 12, 1–12 (2022).

    Article 

    Google Scholar
     

  • Obieze, C. C. et al. Field-scale biostimulation shifts microbial community composition and improves soil pollution recovery at an artisanal crude oil refining site. Int. J. Environ. Stud. 198, 1–20 (2022).

    Article 

    Google Scholar
     

  • Chikere, C. B., Azubuike, C. C. & Fubara, E. M. Shift in microbial group during remediation by enhanced natural attenuation (RENA) of a crude oil-impacted soil: a case study of Ikarama Community, Bayelsa, Nigeria. 3 Biotech 7, 1–11 (2017).


    Google Scholar
     

  • Krauss, M. et al. Atmospheric versus biological sources of polycyclic aromatic hydrocarbons (PAHs) in a tropical rain forest environment. Environ. Pollut. 135, 143–154 (2005).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Kuppusamy, S., Maddela, N. R., Megharaj, M. & Venkateswarlu, K. Impact of total petroleum hydrocarbons on human health. in Total Petroleum Hydrocarbons, 139–165 (Springer, 2020).

  • Gallegos Martínez, M. et al. Diagnostic and resulting approaches to restore petroleum-contaminated soil in a Mexican tropical swamp. Water Sci. Technol. 42, 377–384 (2000).

    Article 

    Google Scholar
     

  • Olawuyi, D. S. & Tubodenyefa, Z. Review of the Environmental Guidelines and Standards for the Petroleum Industry in Nigeria (EGASPIN). (OGEES Institute, 2018).

  • Onakpohor, A., Fakinle, B. S., Sonibare, J. A., Oke, M. A. & Akeredolu, F. A. Investigation of air emissions from artisanal petroleum refineries in the Niger-Delta Nigeria. Heliyon 6, 05608 (2020).

    Article 

    Google Scholar
     

  • Azuamah, K. O., Appiah-Effah, E. & Akodwaa-Boadi, K. Water quality index, ecotoxicology and human health risk modelling of surface and groundwater along illegal crude oil refining sites in a developing economy. Heliyon 9, 20631 (2023).

    Article 

    Google Scholar
     

  • Onuh, P. A. et al. Artisanal refining of crude oil in the Niger Delta: A challenge to clean-up and remediation in Ogoniland. Local Econ. 36, 468–486 (2021).

    Article 

    Google Scholar
     

  • Ite, A. E., Harry, T. A., Obadimu, C. O., Asuaiko, E. R. & Inim, I. J. Petroleum hydrocarbons contamination of surface water and groundwater in the Niger Delta region of Nigeria. J. Environ. Pollut. Hum. Health 6, 51–61 (2018).

    Article 
    CAS 

    Google Scholar
     

  • Xue, Y., Chu, J., Li, Y. & Kong, X. The influence of air pollution on respiratory microbiome: A link to respiratory disease. Toxicol. Lett. 334, 14–20 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Viegi, G., Maio, S., Pistelli, F., Baldacci, S. & Carrozzi, L. Epidemiology of chronic obstructive pulmonary disease: Health effects of air pollution. Respirology 11, 523–532 (2006).

    Article 
    PubMed 

    Google Scholar
     

  • Ko, F. W. S. & Hui, D. S. C. Air pollution and chronic obstructive pulmonary disease. Respirology 17, 395–401 (2012).

    Article 
    PubMed 

    Google Scholar
     

  • Duan, R.-R., Hao, K. & Yang, T. Air pollution and chronic obstructive pulmonary disease. Chronic Dis. Transl. Med. 6, 260–269 (2020).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Onyena, A. P. & Sam, K. A review of the threat of oil exploitation to mangrove ecosystem: Insights from Niger Delta, Nigeria. Glob. Ecol. Conserv. 22, e00961 (2020).


    Google Scholar
     

  • Das, S. Ecological restoration and livelihood: Contribution of planted mangroves as nursery and habitat for artisanal and commercial fishery. World Dev. 94, 492–502 (2017).

    Article 

    Google Scholar
     

  • D’Costa, A., Shyama, S. K. & Kumar, M. P. Bioaccumulation of trace metals and total petroleum and genotoxicity responses in an edible fish population as indicators of marine pollution. Ecotoxicol. Environ. Saf. 142, 22–28 (2017).

    Article 
    PubMed 

    Google Scholar
     

  • Akinsanya, B., Adebusoye, S. A., Alinson, T. & Ukwa, U. D. Bioaccumulation of polycyclic aromatic hydrocarbons, histopathological alterations and parasito-fauna in bentho-pelagic host from Snake Island, Lagos, Nigeria. JoBAZ 79, 40 (2018).

    Article 

    Google Scholar
     

  • Kim, D., Choi, K. Y., Yoo, M., Zylstra, G. J. & Kim, E. Biotechnological Potential of Rhodococcus Biodegradative Pathways. (2018).

  • Zhou, Z., Tran, P. Q., Kieft, K. & Anantharaman, K. Genome diversification in globally distributed novel marine Proteobacteria is linked to environmental adaptation. ISME J. 14, 2060–2077 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Dube, J. P., Valverde, A., Steyn, J. M., Cowan, D. A. & Van der Waals, J. E. Differences in bacterial diversity, composition and function due to long-term agriculture in soils in the eastern free State of South Africa. Diversity 11, 61 (2019).

    Article 
    CAS 

    Google Scholar
     

  • Saadouli, I. et al. Diversity and adaptation properties of actinobacteria associated with Tunisian stone ruins. Front. Microbiol. 13, 7832 (2022).

    Article 

    Google Scholar
     

  • Baoune, H. et al. Petroleum degradation by endophytic Streptomyces spp. isolated from plants grown in contaminated soil of southern Algeria. Ecotoxicol. Environ. Saf. 147, 602–609 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Sun, S., Ma, B., Wang, G. & Tan, X. Linking microbial biogeochemical cycling genes to the rhizosphere of pioneering plants in a glacier foreland. Sci. Total Environ. 872, 161944 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Cockell, C. S., Kelly, L. C. & Marteinsson, V. Actinobacteria: An ancient phylum active in volcanic rock weathering. Geomicrobiol. J. 30, 706–720 (2013).

    Article 
    CAS 

    Google Scholar
     

  • Behera, S. & Das, S. Potential and prospects of Actinobacteria in the bioremediation of environmental pollutants: Cellular mechanisms and genetic regulations. Microbiol. Res. 273, 127399 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Farda, B., Djebaili, R., Vaccarelli, I., Del Gallo, M. & Pellegrini, M. Actinomycetes from caves: An overview of their diversity, biotechnological properties, and insights for their use in soil environments. Microorganisms 10, 453 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Alvarez, A. et al. Actinobacteria: Current research and perspectives for bioremediation of pesticides and heavy metals. Chemosphere 166, 41–62 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • El-Naggar, N. E.-A. Streptomyces-based cell factories for production of biomolecules and bioactive metabolites. in Microbial Cell Factories Engineering for Production of Biomolecules, 183–234 (Elsevier, 2021).

  • Sayed, A. M. et al. Extreme environments: Microbiology leading to specialized metabolites. J. Appl. Microbiol. 128, 630–657 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Shivlata, L. & Satyanarayana, T. Thermophilic and alkaliphilic Actinobacteria: Biology and potential applications. Front. Microbiol. 6, 1014 (2015).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Guesmi, S. et al. Roots of the xerophyte Panicum turgidum host a cohort of ionizing-radiation-resistant biotechnologically-valuable bacteria. Saudi J. Biol. Sci. 29, 1260–1268 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Bidja Abena, M. T. et al. Microbial diversity changes and enrichment of potential petroleum hydrocarbon degraders in crude oil-, diesel-, and gasoline-contaminated soil. 3 Biotech 10, 1–15 (2020).

    Article 

    Google Scholar
     

  • Sethunathan, N. & Yoshida, T. Degradation of chlorinated hydrocarbons by Clostridium sp. isolated from lindane-amended, flooded soil. Plant Soil 38, 663–666 (1973).

    Article 
    CAS 

    Google Scholar
     

  • Tan, B. et al. Comparative analysis of metagenomes from three methanogenic hydrocarbon-degrading enrichment cultures with 41 environmental samples. ISME J. 9, 2028–2045 (2015).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Carrié, M., Gabelle, J.-C., Lopes-Ferreira, N. & Velly, H. Enzymatic breakdown of biofilm matrix to allow flow cytometry viability analysis of Clostridium beijerinckii cells. J. Appl. Microbiol. 134, 062 (2023).

    Article 

    Google Scholar
     

  • Fenibo, E. O., Selvarajan, R., Wang, H., Wang, Y. & Abia, A. L. K. Untapped talents: Insight into the ecological significance of methanotrophs and its prospects. Sci. Total Environ. 903, 166145 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Arinageswaran, S., Balaji, E., Srimuthu, G. & Uma, S. Methanotrophs and its metabolic cascade of biotransformation of methane into valuable products. Agric. Allied Sci. (2023).

  • Lee, S.-W., Keeney, D. R., Lim, D.-H., Dispirito, A. A. & Semrau, J. D. Mixed pollutant degradation by Methylosinus trichosporium OB3b expressing either soluble or particulate methane monooxygenase: Can the tortoise beat the hare?. Appl. Environ. Microbiol. 72, 7503–7509 (2006).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Elumalai, P. et al. Characterization of crude oil degrading bacterial communities and their impact on biofilm formation. Environ. Pollut. 286, 117556 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Saeed, M. et al. Biodegradation of PAHs by Bacillus marsiflavi, genome analysis and its plant growth promoting potential. Environ. Pollut. 292, 118343 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Thirumurugan, D. et al. Impact of biosurfactant produced by Bacillus spp. on biodegradation efficiency of crude oil and anthracene. Chemosphere 344, 140340 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Wu, Y. et al. The metagenomics of soil bacteria and fungi and the release of mechanical dormancy in hard seeds. Front. Plant Sci. 14, 1187416 (2023).


    Google Scholar
     

  • Zeng, J., Zhu, Q., Wu, Y. & Lin, X. Oxidation of polycyclic aromatic hydrocarbons using Bacillus subtilis CotA with high laccase activity and copper independence. Chemosphere 148, 1–7 (2016).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Das, S., Das, N., Choure, K. & Pandey, P. Biodegradation of asphaltene by lipopeptide-biosurfactant producing hydrocarbonoclastic, crude oil degrading Bacillus spp. Bioresour. Technol. 382, 129198 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Xia, Z. et al. Nitrogen removal pathway and dynamics of microbial community with the increase of salinity in simultaneous nitrification and denitrification process. Sci. Total Environ. 697, 134047 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Kawasaki, A., Watson, E. R. & Kertesz, M. A. Indirect effects of polycyclic aromatic hydrocarbon contamination on microbial communities in legume and grass rhizospheres. Plant Soil 358, 169–182 (2012).

    Article 
    CAS 

    Google Scholar
     

  • Tirandaz, H. et al. Pseudorhodoplanes sinuspersici gen. nov., sp. nov., isolated from oil-contaminated soil. Int. J. Syst. Evol. Microbiol. 65, 4743–4748 (2015).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Xu, S. et al. Total petroleum hydrocarbons and influencing factors in co-composting of rural sewage sludge and organic solid wastes. Environ. Pollut. 319, 120911 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Ulrich, N. et al. Response of aquatic bacterial communities to hydraulic fracturing in northwestern Pennsylvania: A five-year study. Sci. Rep. 8, 5683 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Al-Kindi, S. & Abed, R. M. M. Effect of biostimulation using sewage sludge, soybean meal, and wheat straw on oil degradation and bacterial community composition in a contaminated desert soil. Front. Microbiol. 7, 240 (2016).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Construction of a hydrocarbon-degrading consortium and characterization of two new lipopeptides biosurfactants. ScienceDirect. https://www.sciencedirect.com/science/article/abs/pii/S004896971936396X.

  • pahE, a functional marker gene for polycyclic aromatic hydrocarbon-degrading bacteria. Appl. Environ. Microbiol. https://doi.org/10.1128/aem.02399-18.

  • Al-Thukair, A. A., Malik, K. & Nzila, A. Biodegradation of selected hydrocarbons by novel bacterial strains isolated from contaminated Arabian Gulf sediment. Sci. Rep. 10, 21846 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Shibulal, B. et al. The potential of indigenous Paenibacillus ehimensis BHP for recovering heavy crude oil by biotransformation to light fractions. PLoS ONE 12, e0171432 (2017).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kanwal, M. et al. Biodegradation of petroleum hydrocarbons and the factors effecting rate of biodegradation. Am. J. Biomed. Sci. Res 16, 6 (2022).

    Article 

    Google Scholar
     

  • Mesbaiah, F. Z. et al. Preliminary characterization of biosurfactant produced by a PAH-degrading Paenibacillus sp. under thermophilic conditions. Environ. Sci. Pollut. Res. 23, 14221–14230 (2016).

    Article 
    CAS 

    Google Scholar
     

  • Dashti, N. et al. Most hydrocarbonoclastic bacteria in the total environment are diazotrophic, which highlights their value in the bioremediation of hydrocarbon contaminants. Microb. Environ. 30, 70–75 (2015).

    Article 

    Google Scholar
     

  • Langendries, S. & Goormachtig, S. Paenibacillus polymyxa, a Jack of all trades. Environ. Microbiol. 23, 5659–5669 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Timmusk, S., Teder, T. & Behers, L. Paenibacillus polymyxa A26 and its surfactant-deficient mutant degradation of polycyclic aromatic hydrocarbons. Stresses 1, 266–276 (2021).

    Article 

    Google Scholar
     

  • Zhang, X. et al. Study on the simultaneous degradation of five pesticides by Paenibacillus polymyxa from Panax ginseng and the characteristics of their products. Ecotoxicol. Environ. Saf. 168, 415–422 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Li, Y., Li, Y., Zhang, H., Wang, M. & Chen, S. Diazotrophic Paenibacillus beijingensis BJ-18 provides nitrogen for plant and promotes plant growth, nitrogen uptake and metabolism. Front. Microbiol. 10, 1119 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Tang, Q., Puri, A., Padda, K. P. & Chanway, C. P. Biological nitrogen fixation and plant growth promotion of lodgepole pine by an endophytic diazotroph Paenibacillus polymyxa and its GFP-tagged derivative. Botany 95, 611–619 (2017).

    Article 
    CAS 

    Google Scholar
     

  • Beneduzi, A. et al. Genome sequence of the diazotrophic gram-positive rhizobacterium Paenibacillus riograndensis SBR5 T. J. Bacteriol. 193, 6391–6392 (2011).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lee, Y., Lee, Y. & Jeon, C. O. Biodegradation of naphthalene, BTEX, and aliphatic hydrocarbons by Paraburkholderia aromaticivorans BN5 isolated from petroleum-contaminated soil. Sci. Rep. 9, 860 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Margesin, R., Volgger, G., Wagner, A. O., Zhang, D. & Poyntner, C. Biodegradation of lignin monomers and bioconversion of ferulic acid to vanillic acid by Paraburkholderia aromaticivorans AR20-38 isolated from Alpine forest soil. Appl. Microbiol. Biotechnol. 105, 2967–2977 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hwangbo, M., Shao, Y., Hatzinger, P. B. & Chu, K. Acidophilic methanotrophs: Occurrence, diversity, and possible bioremediation applications. Environ. Microbiol. Rep. 15, 265–281 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Sahoo, K. K., Goswami, G. & Das, D. Biotransformation of methane and carbon dioxide into high-value products by methanotrophs: Current state of art and future prospects. Front. Microbiol. 12, 636486 (2021).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Minamisawa, K. Mitigation of greenhouse gas emission by nitrogen-fixing bacteria. Biosci. Biotechnol. Biochem. 87, 7–12 (2023).

    Article 

    Google Scholar
     

  • Chicca, I., Becarelli, S. & Di Gregorio, S. Microbial involvement in the bioremediation of total petroleum hydrocarbon polluted soils: Challenges and perspectives. Environments 9, 52 (2022).

    Article 

    Google Scholar
     

  • Shibulal, B. et al. Heavy crude oil biodegradation: Catechol dioxygenase gene copy number variation determination by droplet digital polymerase chain reaction. Geomicrobiol. J. 40, 295–306 (2023).

    Article 
    CAS 

    Google Scholar
     

  • Iturbe-Espinoza, P. et al. Microbial communities associated with landfarming amendments during bioremediation of crude oil in Niger Delta soils. Appl. Soil Ecol. 191, 105058 (2023).

    Article 

    Google Scholar
     

  • Remarkable impact of PAHs and TPHs on the richness. Google Scholar. https://scholar.google.com/scholar?hl=en&as_sdt=0%2C5&q=Remarkable+impact+of+PAHs+and+TPHs+on+the+richness+and+diversity+of+bacterial+species+in+surface+soils+exposed+to+long-term+hydrocarbon+pollution&btnG=.

  • Edet, U. O. & Antai, S. P. Correlation and distribution of xenobiotics genes and metabolic activities with level of total petroleum hydrocarbon in soil, sediment and estuary water in the Niger Delta Region of Nigeria. Asian J. Biotechnol. Genet. Eng. 1, 1–11 (2018).


    Google Scholar
     

  • Lee, E.-H., Lee, S. H. & Cho, K.-S. Bacterial diversity dynamics in a long-term petroleum-contaminated soil. J. Environ. Sci. Health A 46, 281–290 (2011).

    Article 
    CAS 

    Google Scholar
     

  • Mukherjee, S. et al. Spatial patterns of microbial diversity and activity in an aged creosote-contaminated site. ISME J. 8, 2131–2142 (2014).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Yerulker, G. et al. Comparative assessment of soil microbial community in crude oil contaminated sites. Environ. Pollut. 328, 121578 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Ramirez, D., Shaw, L. J. & Collins, C. D. Ecotoxicity of oil sludges and residuals from their washing with surfactants: Soil dehydrogenase and ryegrass germination tests. Environ. Sci. Pollut. Res. 28, 13312–13322 (2021).

    Article 
    CAS 

    Google Scholar
     

  • Guérin, J. & Buchanan, S. K. Protein import and export across the bacterial outer membrane. Curr. Opin. Struct. Biol. 69, 55–62 (2021).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Molan, K. & Žgur Bertok, D. Small prokaryotic DNA-binding proteins protect genome integrity throughout the life cycle. Int. J. Mol. Sci. 23, 4008 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Durak, A., Buyukguner, E. & Dogan, H. M. Determination of physical and chemical properties of the soils under different land managements. Asian J. Chem. 22, 6375–6386 (2010).

    CAS 

    Google Scholar
     

  • Babalola, E., Asad, M. H. & Bais, A. Soil surface texture classification using RGB images acquired under uncontrolled field conditions. IEEE Access 11, 67140 (2023).

    Article 

    Google Scholar
     

  • Adekiya, A. O. Different organic manure sources and NPK fertilizer on soil chemical properties, growth, yield and quality of okra. Sci. Rep. 4, 208 (2020).


    Google Scholar
     

  • Oyem, H. H., Oyem, I. M. & Ezeweali, D. Temperature, pH, electrical conductivity, total dissolved solids and chemical oxygen demand of groundwater in Boji-BojiAgbor/Owa area and immediate suburbs. Res. J. Environ. Sci. 8, 444 (2014).

    Article 

    Google Scholar
     

  • Mrayyan, B. & Battikhi, M. N. Biodegradation of total organic carbons (TOC) in Jordanian petroleum sludge. J. Hazard. Mater. 120, 127–134 (2005).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • De Varennes, A., Torres, M. O., Cunha-Queda, C., Goss, M. J. & Carranca, C. Nitrogen conservation in soil and crop residues as affected by crop rotation and soil disturbance under Mediterranean conditions. Biol. Fertil. Soils 44, 49–58 (2007).

    Article 

    Google Scholar
     

  • Minai-Tehrani, D. & Herfatmanesh, A. Biodegradation of aliphatic and aromatic fractions of heavy crude oil–contaminated soil: A pilot study. Bioremed. J. 11, 71–76 (2007).

    Article 
    CAS 

    Google Scholar
     

  • Sari, G. L., Trihadiningrum, Y., Suci, F. C. & FashanahHadining, A. Identification of total petroleum hydrocarbon and heavy metals levels in crude oil contaminated soil at Wonocolo public mining. Environ. Asia 11, 109–117 (2018).


    Google Scholar
     

  • dos Reis, C. B. L. et al. First report of the production of a potent biosurfactant with α, β-trehalose by Fusarium fujikuroi under optimized conditions of submerged fermentation. Braz. J. Microbiol. 49, 185–192 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Caporaso, J. G. et al. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 6, 1621–1624 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Uyaguari-Diaz, M. I. et al. A comprehensive method for amplicon-based and metagenomic characterization of viruses, bacteria, and eukaryotes in freshwater samples. Microbiome 4, 1–19 (2016).

    Article 

    Google Scholar
     

  • Gao, J. et al. Metagenome analysis of bacterial diversity in Tibetan kefir grains. Eur. Food Res. Technol. 236, 549–556 (2013).

    Article 
    CAS 

    Google Scholar
     

  • Hemmat-Jou, M. H., Safari-Sinegani, A. A., Mirzaie-Asl, A. & Tahmourespour, A. Analysis of microbial communities in heavy metals-contaminated soils using the metagenomic approach. Ecotoxicology 27, 1281–1291 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Qiu, Z. et al. Characterization of microbial community structure and metabolic potential using Illumina MiSeq platform during the black garlic processing. Food Res. Int. 106, 428–438 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Tawfik, S. A., Azab, M. M., Ahmed, A. A. A. & Fayyad, D. M. Illumina MiSeq sequencing for preliminary analysis of microbiome causing primary endodontic infections in Egypt. Int. J. Microbiol. 2018, 1–15 (2018).

    Article 

    Google Scholar
     

  • Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Bolyen, E. et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat. Biotechnol. 37, 852–857 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Callahan, B. J. et al. DADA2: High-resolution sample inference from Illumina amplicon data. Nat. Methods 13, 581–583 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Rognes, T., Flouri, T., Nichols, B., Quince, C. & Mahé, F. VSEARCH: A versatile open source tool for metagenomics. PeerJ 4, e2584 (2016).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wang, Q., Garrity, G. M., Tiedje, J. M. & Cole, J. R. Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 73, 5261–5267 (2007).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Douglas, G. M. et al. PICRUSt2 for prediction of metagenome functions. Nat. Biotechnol. 38, 685–688 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Dhariwal, A. et al. MicrobiomeAnalyst: A web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data. Nucleic Acids Res. 45, W180–W188 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kandlikar, G. S. et al. ranacapa: An R package and Shiny web app to explore environmental DNA data with exploratory statistics and interactive visualizations. F1000 Res. 7, 1734 (2018).

    Article 

    Google Scholar