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
Volume 1, Issue 1, November 2016, Pages: 44-48
Received: Nov. 1, 2016; Accepted: Dec. 28, 2016; Published: Jan. 14, 2017
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Authors
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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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.
Keywords
Soil, Bacteria, Archaea, 16S rRNA, Real-Time PCR, Nigeria
To cite this article
Raji Habiba Mustapha, Ameh Joseph Baba, Ado Saleh Alhaji, Yakubu Sabo Ezemul, Webster Gordon, Weightman Andrew J., 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. Vol. 1, No. 1, 2016, pp. 44-48. doi: 10.11648/j.ijmb.20160101.17
Copyright
Copyright © 2016 Authors retain the copyright of this article.
This article is an open access article distributed under the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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