Analysis of Bacterial and Archaeal 16S rRNA Gene in Soil Obtained from a Petroleum Refinery Effluent Site in Nigeria Using Real-Time PCR

Raji Habiba Mustapha; Ameh Joseph Baba; Ado Saleh Alhaji; Yakubu Sabo Ezemul; Webster Gordon; Weightman Andrew J.

doi:doi:10.11648/j.ijmb.20160101.17

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Analysis of Bacterial and Archaeal 16S rRNA Gene in Soil Obtained from a Petroleum Refinery Effluent Site in Nigeria Using Real-Time PCR

Raji Habiba Mustapha, Ameh Joseph Baba, Ado Saleh Alhaji, Yakubu Sabo Ezemul, Webster Gordon, Weightman Andrew J.

Published in International Journal of Microbiology and Biotechnology (Volume 1, Issue 1)

Received: 1 November 2016 Accepted: 28 December 2016 Published: 14 January 2017

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Abstract

The microbial community in environments exposed to effluents released from industrial processes such as petroleum refining are usually adapted to utilising and degrading these bye-products. Soil was sampled in an area adjacent to the water body containing refinery effluent released from the refinery in Nigerian National Petroleum Company (N. N. P. C), Kaduna. The samples were obtained at two depths, 17 – 20 cm and 37 – 40 cm respectively. Genomic DNA was extracted from these samples in triplicates and the 16S rRNA gene was amplified using the primers, 518F and 907R in 20µL reaction mixtures. The data obtained after the Q-PCR run was analysed using MxPro, Q-PCR software. The final number of target genes was an average of triplicate measurements from three independent DNA extractions from each soil sample. The average 16S gene copy number in the samples was in the range, 3.11E+07 – 1.23E+08 gene copies per gram of soil for bacteria and 8.13E+06 – 5.76E+07 gene copies per gram of soil, for archaea. Sampling depths of 17 – 20 cm had relatively higher gene copy number as opposed to depths of 37 - 40 cm. Soils closer to the surface are typically richer in nutrients and oxygen thus favouring bacterial growth. The 16S rRNA gene is highly conserved and very useful in phylogenetic studies of bacterial populations. However, in order to screen for specific activities such as degradation of toxic compounds by bacteria in soil, detection of functional genes is necessary.

Published in	International Journal of Microbiology and Biotechnology (Volume 1, Issue 1)
DOI	10.11648/j.ijmb.20160101.17
Page(s)	44-48
Creative Commons	This is an Open Access article, distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium or format, provided the original work is properly cited.
Copyright	Copyright © The Author(s), 2017. Published by Science Publishing Group

Keywords

Soil, Bacteria, Archaea, 16S rRNA, Real-Time PCR, Nigeria

References

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[2]	Cébron, A., Arsène-Ploetze, F., Bauda, P., Bertin, P. N., Billard, P., Carapito, C. Devin, S., Goulhen-Chollet, F., Poirel, J. and Leyval, C. (2014). Rapid impact of phenanthrene and arsenic on bacterial community structure and activities in sand batches. Microbial Ecology, 67: 129-144. DOI 10.1007/s00248-013-0313-1.
[3]	Department for Petroleum Resources-Environmental Guidelines and Standards for the Petroleum Industry in Nigeria (DPR-EGASPIN) (2002). Department for Petroleum Resources (DPR), Lagos, Nigeria.
[4]	Ding, G. C., Heuer, H., Zuhlke, S., Spiteller, M., Pronk, G. J., Heister, K., Kogel-Knabner, I. and Smalla, K. (2010) Soil type-dependent responses to phenanthrene as revealed by determining the diversity and abundance of polycyclic aromatic hydrocarbon ring hydroxylating dioxygenase genes by using a novel PCR detection system. Applied and Environmental Microbiology, 76 (14): 4765-4771.
[5]	Kasai, Y., Takahata, Y., Hoaki, T. and Watanabe, K. (2005). Physiological and molecular characterization of a microbial community established in unsaturated petroleum contaminated soil. Environmental Microbiology, 7 (6): 806-818.
[6]	Korotkevych, O., Josefiova, J., Praveckova, M., Cajthaml, T., Stavelova, M. and Brennerova, M. V. (2011). Functional adaptation of microbial communities from jet fuel contaminated soil under bioremediation treatment: Simulation of pollutant rebound. FEMS Microbiology Ecology, 78: 137-149.
[7]	Muyzer, G., De Waal, E. C., Uitterlinden, A. G. (1993). Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Applied Environmental Microbiology, 59: 695-700.
[8]	Muyzer, G. and Smalla, K. (1998). Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology. Antonie van Leeuwenhoek, 73: 127-141.
[9]	Nakatsu, C. H., Torsvik, V. and Ovreas, L. (2000). Soil community analysis using DGGE of 16S rDNA Polymerase Chain Reaction products Soil Science Society of America Journal, 64: 1382-1388.
[10]	United States Environmental Protection Agency (USEPA) Report (1996). Recent developments for In Situ treatment of metals contaminated soils, USEPA, Office of Solid Waste and Emergency Response.
[11]	United States Environmental Protection Agency (USEPA) Report (1996). Recent developments for In Situ treatment of metals contaminated soils, USEPA, Office of Solid Waste and Emergency Response.
[12]	Vetriani, C., Jannasch, H. W., MacGregor, B. J., Stahl, D. A., Reysenbach, A. L. (1999). Population structure and phylogenetic characterization of marine benthic archaea in deep-sea sediments. Applied and Environmental Microbiology, 65 (10): 4375-4384.
[13]	Wilms, R., Sass, H., Kopke, B., Cypionka, H., Engelen, B. (2007). Methane and sulphate profiles within the subsurface of a tidal flat are reflected by the distribution of sulphate-reducing bacteria and methanogenic archaea FEMS Microbial Ecology, 59 (3): 611-621.
[14]	Zhang, S. Y., Wang, Q. F. and Xie, S. G. (2012). Molecular characterization of phenanthrenedegrading methanogenic communities in leachate-contaminated aquifer sediment International Journal of Environmental Science and Technology 9: 705-712.

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Raji Habiba Mustapha, Ameh Joseph Baba, Ado Saleh Alhaji, Yakubu Sabo Ezemul, Webster Gordon, et al. (2017). Analysis of Bacterial and Archaeal 16S rRNA Gene in Soil Obtained from a Petroleum Refinery Effluent Site in Nigeria Using Real-Time PCR. International Journal of Microbiology and Biotechnology, 1(1), 44-48. https://doi.org/10.11648/j.ijmb.20160101.17

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ACS Style

Raji Habiba Mustapha; Ameh Joseph Baba; Ado Saleh Alhaji; Yakubu Sabo Ezemul; Webster Gordon, et al. Analysis of Bacterial and Archaeal 16S rRNA Gene in Soil Obtained from a Petroleum Refinery Effluent Site in Nigeria Using Real-Time PCR. Int. J. Microbiol. Biotechnol. 2017, 1(1), 44-48. doi: 10.11648/j.ijmb.20160101.17

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AMA Style

Raji Habiba Mustapha, Ameh Joseph Baba, Ado Saleh Alhaji, Yakubu Sabo Ezemul, Webster Gordon, et al. Analysis of Bacterial and Archaeal 16S rRNA Gene in Soil Obtained from a Petroleum Refinery Effluent Site in Nigeria Using Real-Time PCR. Int J Microbiol Biotechnol. 2017;1(1):44-48. doi: 10.11648/j.ijmb.20160101.17

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@article{10.11648/j.ijmb.20160101.17,
  author = {Raji Habiba Mustapha and Ameh Joseph Baba and Ado Saleh Alhaji and Yakubu Sabo Ezemul and Webster Gordon and Weightman Andrew J.},
  title = {Analysis of Bacterial and Archaeal 16S rRNA Gene in Soil Obtained from a Petroleum Refinery Effluent Site in Nigeria Using Real-Time PCR},
  journal = {International Journal of Microbiology and Biotechnology},
  volume = {1},
  number = {1},
  pages = {44-48},
  doi = {10.11648/j.ijmb.20160101.17},
  url = {https://doi.org/10.11648/j.ijmb.20160101.17},
  eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.ijmb.20160101.17},
  abstract = {The microbial community in environments exposed to effluents released from industrial processes such as petroleum refining are usually adapted to utilising and degrading these bye-products. Soil was sampled in an area adjacent to the water body containing refinery effluent released from the refinery in Nigerian National Petroleum Company (N. N. P. C), Kaduna. The samples were obtained at two depths, 17 – 20 cm and 37 – 40 cm respectively. Genomic DNA was extracted from these samples in triplicates and the 16S rRNA gene was amplified using the primers, 518F and 907R in 20µL reaction mixtures. The data obtained after the Q-PCR run was analysed using MxPro, Q-PCR software. The final number of target genes was an average of triplicate measurements from three independent DNA extractions from each soil sample. The average 16S gene copy number in the samples was in the range, 3.11E+07 – 1.23E+08 gene copies per gram of soil for bacteria and 8.13E+06 – 5.76E+07 gene copies per gram of soil, for archaea. Sampling depths of 17 – 20 cm had relatively higher gene copy number as opposed to depths of 37 - 40 cm. Soils closer to the surface are typically richer in nutrients and oxygen thus favouring bacterial growth. The 16S rRNA gene is highly conserved and very useful in phylogenetic studies of bacterial populations. However, in order to screen for specific activities such as degradation of toxic compounds by bacteria in soil, detection of functional genes is necessary.},
 year = {2017}
}

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TY - JOUR
T1 - Analysis of Bacterial and Archaeal 16S rRNA Gene in Soil Obtained from a Petroleum Refinery Effluent Site in Nigeria Using Real-Time PCR
AU - Raji Habiba Mustapha
AU - Ameh Joseph Baba
AU - Ado Saleh Alhaji
AU - Yakubu Sabo Ezemul
AU - Webster Gordon
AU - Weightman Andrew J.
Y1 - 2017/01/14
PY - 2017
N1 - https://doi.org/10.11648/j.ijmb.20160101.17
DO - 10.11648/j.ijmb.20160101.17
T2 - International Journal of Microbiology and Biotechnology
JF - International Journal of Microbiology and Biotechnology
JO - International Journal of Microbiology and Biotechnology
SP - 44
EP - 48
PB - Science Publishing Group
SN - 2578-9686
UR - https://doi.org/10.11648/j.ijmb.20160101.17
AB - The microbial community in environments exposed to effluents released from industrial processes such as petroleum refining are usually adapted to utilising and degrading these bye-products. Soil was sampled in an area adjacent to the water body containing refinery effluent released from the refinery in Nigerian National Petroleum Company (N. N. P. C), Kaduna. The samples were obtained at two depths, 17 – 20 cm and 37 – 40 cm respectively. Genomic DNA was extracted from these samples in triplicates and the 16S rRNA gene was amplified using the primers, 518F and 907R in 20µL reaction mixtures. The data obtained after the Q-PCR run was analysed using MxPro, Q-PCR software. The final number of target genes was an average of triplicate measurements from three independent DNA extractions from each soil sample. The average 16S gene copy number in the samples was in the range, 3.11E+07 – 1.23E+08 gene copies per gram of soil for bacteria and 8.13E+06 – 5.76E+07 gene copies per gram of soil, for archaea. Sampling depths of 17 – 20 cm had relatively higher gene copy number as opposed to depths of 37 - 40 cm. Soils closer to the surface are typically richer in nutrients and oxygen thus favouring bacterial growth. The 16S rRNA gene is highly conserved and very useful in phylogenetic studies of bacterial populations. However, in order to screen for specific activities such as degradation of toxic compounds by bacteria in soil, detection of functional genes is necessary.
VL - 1
IS - 1
ER -

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Author Information

Raji Habiba Mustapha

Dept. of Microbiology, Ahmadu Bello University, Zaria, Nigeria
Ameh Joseph Baba

Dept. of Microbiology, Ahmadu Bello University, Zaria, Nigeria
Ado Saleh Alhaji

Dept. of Microbiology, Ahmadu Bello University, Zaria, Nigeria
Yakubu Sabo Ezemul

Dept. of Microbiology, Ahmadu Bello University, Zaria, Nigeria
Webster Gordon

School of Biosciences, Cardiff University, Cardiff, Wales, United Kingdom
Weightman Andrew J.

School of Biosciences, Cardiff University, Cardiff, Wales, United Kingdom

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APA Style

Raji Habiba Mustapha, Ameh Joseph Baba, Ado Saleh Alhaji, Yakubu Sabo Ezemul, Webster Gordon, et al. (2017). Analysis of Bacterial and Archaeal 16S rRNA Gene in Soil Obtained from a Petroleum Refinery Effluent Site in Nigeria Using Real-Time PCR. International Journal of Microbiology and Biotechnology, 1(1), 44-48. https://doi.org/10.11648/j.ijmb.20160101.17

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ACS Style

Raji Habiba Mustapha; Ameh Joseph Baba; Ado Saleh Alhaji; Yakubu Sabo Ezemul; Webster Gordon, et al. Analysis of Bacterial and Archaeal 16S rRNA Gene in Soil Obtained from a Petroleum Refinery Effluent Site in Nigeria Using Real-Time PCR. Int. J. Microbiol. Biotechnol. 2017, 1(1), 44-48. doi: 10.11648/j.ijmb.20160101.17

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AMA Style

Raji Habiba Mustapha, Ameh Joseph Baba, Ado Saleh Alhaji, Yakubu Sabo Ezemul, Webster Gordon, et al. Analysis of Bacterial and Archaeal 16S rRNA Gene in Soil Obtained from a Petroleum Refinery Effluent Site in Nigeria Using Real-Time PCR. Int J Microbiol Biotechnol. 2017;1(1):44-48. doi: 10.11648/j.ijmb.20160101.17

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@article{10.11648/j.ijmb.20160101.17,
  author = {Raji Habiba Mustapha and Ameh Joseph Baba and Ado Saleh Alhaji and Yakubu Sabo Ezemul and Webster Gordon and Weightman Andrew J.},
  title = {Analysis of Bacterial and Archaeal 16S rRNA Gene in Soil Obtained from a Petroleum Refinery Effluent Site in Nigeria Using Real-Time PCR},
  journal = {International Journal of Microbiology and Biotechnology},
  volume = {1},
  number = {1},
  pages = {44-48},
  doi = {10.11648/j.ijmb.20160101.17},
  url = {https://doi.org/10.11648/j.ijmb.20160101.17},
  eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.ijmb.20160101.17},
  abstract = {The microbial community in environments exposed to effluents released from industrial processes such as petroleum refining are usually adapted to utilising and degrading these bye-products. Soil was sampled in an area adjacent to the water body containing refinery effluent released from the refinery in Nigerian National Petroleum Company (N. N. P. C), Kaduna. The samples were obtained at two depths, 17 – 20 cm and 37 – 40 cm respectively. Genomic DNA was extracted from these samples in triplicates and the 16S rRNA gene was amplified using the primers, 518F and 907R in 20µL reaction mixtures. The data obtained after the Q-PCR run was analysed using MxPro, Q-PCR software. The final number of target genes was an average of triplicate measurements from three independent DNA extractions from each soil sample. The average 16S gene copy number in the samples was in the range, 3.11E+07 – 1.23E+08 gene copies per gram of soil for bacteria and 8.13E+06 – 5.76E+07 gene copies per gram of soil, for archaea. Sampling depths of 17 – 20 cm had relatively higher gene copy number as opposed to depths of 37 - 40 cm. Soils closer to the surface are typically richer in nutrients and oxygen thus favouring bacterial growth. The 16S rRNA gene is highly conserved and very useful in phylogenetic studies of bacterial populations. However, in order to screen for specific activities such as degradation of toxic compounds by bacteria in soil, detection of functional genes is necessary.},
 year = {2017}
}

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