Comparative Study of Metagenomic Profile of Bacteria Strains Present in an Abandoned Artisanal Refinery Site, in Obi-Ayagha Community, Delta State, Nigeria
Tudararo-Aherobo, Laurelta Esivweneta *
Department of Environmental Management and Toxicology, Federal University of Petroleum Resources, P.M.B. 1221, Effurun, Delta State, Nigeria.
Okorhi, Beatrice Folawe
Department of Environmental Management and Toxicology, Federal University of Petroleum Resources, P.M.B. 1221, Effurun, Delta State, Nigeria.
*Author to whom correspondence should be addressed.
Abstract
Aim: The aim of the study is to identify and compare the bacteria strains present in the control and Hydrocarbon impacted soil samples in the abandoned artisanal refinery site located in Obi-Ayagha community, Delta State, using high-throughput sequencing of the 16S rRNA gene.
Place and Duration of Study: The Hydrocarbon impacted soil was collected from the abandoned artisanal refinery site located in Obi-Ayagha community and analysed in the advanced research laboratory of the Department of Environmental Management and Toxicology, Federal University of Petroleum Resources, Effurun between 2022 and 2023.
Methodology: In the present study, soil samples were collected from five points to cover the expanse of the site, from depths of 0–15 cm of the abandoned artisanal site and composited. The bacterial community profile was analyzed using high-throughput sequencing of the 16S rRNA gene and the bacteria species were identified from Kingdom to species level.
Results: Taxonomical classification of bacteria, revealed the most abundant organisms present in each kingdom, phyla, class, in the contaminated and uncontaminated (control) samples. The dominant species at phylum-level microbial diversity identified in the petroleum-contaminated and uncontaminated site, is depicted by the dominant groups and were found to be the Actinobacteriota (21.94%) for the control in comparison the Firmicutes dominated the phylum with percentage occurrence of (99.86%) for the test samples. At the class level, the dominant group was Alphaproteobacteria (16.48%) for the control, while Bacilli dominated the class showing (99.76%) for the test samples.
Conclusion: Metagenomic profiling helps to predict the presence and relative abundances of microbes in a sample, which is a critical step in microbiome analysis.
Keywords: Metagenomic sequence, 16S rRNA gene, bacteria
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Lelario F, Scrano L, De Franchi S, Bonomo MG, Salzano G, Milan S, Bufo SA Identification and antimicrobial activity of most representative secondary metabolites from different plant species. Chemical and Biological Technologiesin Agriculture. 2018;5(1):1-12.
Sofo A, Zanella A, Ponge JF. Soil quality and fertility in sustainable agriculture with a contribuction to the biological classification of agricultural soils; 2022.
Kachienga L, Jitendra K Momba M. Metagenomic profiling for assessing microbial diversity and microbial adaptation to degradation of hydrocarbons in two South African petroleum-contaminated water aquifers. Scientific Report. 2018;8(1). DOI: 10.111038/541598-018-25961-0
Jiao S, Chen W, Wang J, Zhang L. Plant growth and oil contamination alter the diversity and composition of bacterial communities in agricultural soils across China. Land Degradation and Development. 2018;29(6). DOI. 10.1002/1dr 2932
Haritash AK, Kaushik CP. Biodegradation aspects of polycyclic aromatic hydrocarbons (PAHs): A review. J. Haz. Mater. 2009;169(13):1–15. DOI: 10.1016/j.jhazmat.2009.03.137
Patowary K, Patowary R, Kalita MC. Characterization of biosurfactant produced during degradation of hydrocarbons using crude oil as sole source of carbon. Frontiers in Microbiology. 2017;8;279. DOI: 10.3389/fmicb.2017.00279
Pacwa- Plociniczak M, Biniecka P, Bondarczuk K, Piotrowska- Seget Z. Metagenomic functional profiling reveals differences in bacterial composition and function during bioaugmentation of aged petroleum-contaminated soil. 2020;11:2106. DOI: 10.3389/fmicb.2020.02106
Pandey S, Pathak H, Dave S. Microbial ecology of hydrocarbon degradation in the soil: A review. Research Journal on Environmental Toxicology. 2016;10(1):1-15. DOI: 10.3923/rjet.2016.1.15
Jones AM, James II, Akpan PS, Eka II, Oruk AE, Ibuot AA. Characterization of Hydrocarbon Utilizing Bacteria in waste engine oil impacted sites; 2021. Available:https://doi.org/10/1101/2020.03.21.998872 DOI: 10.36462/h biosci.2021B
Kaushik S, Alatawi A, Djiwanti R, Pande A. Potential of extremophiles for Bioremediayion. Springer; 2021. DOI: 10.1007/978-981-15-7447-4_12
Ahmad Z, Gao B, Mosa A, Yu H, Yin X, Bashir A. Removal of CU (II), Cd (II) and Pb (II) ions from aqueous solutions by Biochars derived from potassium- rich biomass. Elsevier. 2018;159:74-82 DOI: 10.1016/J.CLAY.2017.12.050
Peng T, Zhang J, Tsang DC, Alessi DS, Shen Z, Hou D. Biochar application for the remediation of heavy metals polluted land: a review of in-situ field trials. Science of the Total Environment. 2018;819:816-826.
Gong JS. Metagenomic technology and genome mining: emerging areas for exploring novel nitrilases. Appl. Microbiol. Biotechnol. 2013;97:6603–6611. DOI: 10.1007/s00253-013-4932-8
Galazka A, Gizadziel J, Galazka R, Ukalska-Januga A, Strzelecka J, Smreczak B. Genetic and functional diversity of bacterial microbiome in soils with long termimpacts of petroleum hydrocarbons. Frontiers in Microbiology. 2018;9:1923.
Malla MA, Dubey A, Yeadav S, Kumar A, Hashem A, Abd Allah EF. Understanding nd designing te strategies for the microbe mediated remediation of environmental contaminants using omics approaches. Frontiers in Microbiology. 2018;9:1132.
Jin HM, Kim JM, Lee HJ, Madsen EL, Jeon CO. Alteromonas as a key agent of polycyclic aromatic hydrocarbon biodegradation in crude oil-contaminated coastal sediment. J. Env. Sci. Technol. 2012;46:7731–7740. DOI: 10.1021/es3018545.
Abbasian F, Lockington R, Mallavarapu M, Naidu R. The integration of sequencing and bioinformatics in metagenomics. Rev. Env. Sci. Biotechnol. 2015;14:357–383. DOI: 10.1007/s11157-015-9365-7
Dombrowski N, Donaho JA, Gutierrez T, Seitz KW, Teske AP, Baker BJ. Reconstructing metabolic pathways of hydrocarbon-degrading bacteria from the Deep water Horizon oil spill. Nat. Microbiol. 2016;1:16057. DOI: 10.1038/nmicrobiol.2016.57
Atlas RM. Microbial-degradation of petroleum-hydrocarbons – An environmental perspective. Microb. Rev. 1981;45:180–209.
Al-Kindi S, Abed RM. Comparing oil degradation efficiency and bacterial communities in contaminated. soils subjected to biostimulation using different organic wastes. Water Air Soil Pollut. 2016;227:36.
Tremblay J, Yergeau E, Fortin N, Cobanli S, Elias M, King TL, et al. Chemical dispersants enhance the activity of oil-and gas condensate-degrading marine bacteria. ISMEJ. 2017;11:2793–2808. DOI: 10.1038/ismej.2017.129