Research Article

Molecular Characterization of Bacteria Associated with a Dumpsite Soil in University of Port Harcourt, Rivers State, Nigeria

Iyanyi, N. G.1*, Ataga, A. E.1, Soala, M.2, Jumbo, J.1
1 Department of Plant Science and Biotechnology, University of Port Harcourt, Port Harcourt, Nigeria
2 Regional Center for Biotechnology and Bioresources Research, University of Port Harcourt, Port Harcourt, Nigeria.
* Corresponding author: nkechi.iyanyi@gmail.com
Published: Dec, 2020
DOI: 10.67614/njm.2020.iau31dcd
Pages: 5294-5302

Abstract

This study identified the bacterial species associated with dumpsite soil using both cultural and molecular techniques. Soil samples were obtained from the University of Port Harcourt, Rivers State. Bacteria associated with dumpsite soil were isolated using both Nutrient agar and serial dilution method. Deoxyribonucleic acid (DNA) was extracted from pure cultures of bacterial isolates using Quick-DNA Fungal/Bacterial MiniPrepTM Kit and the concentration determined using Nanadrop 2000c Spectrophotometer. Polymerase chain reaction (PCR) amplification of I6S rRNA gene of the extracted DNA was carried out using bacteria universal primer pair; 16SF and 16SR. Sequencing was performed in an ABI3500 Genetic analyzer. The sequences were aligned and compared with some sequences on the National Centre for Biotechnology Information (NCBI) database for species identification and evolutionary trend. Four bacterial species were obtained. The result of the nucleotide sequence analysis revealed that isolate 1 with 1129bp had a 100% similarity to Enterobacter ludwigii; isolate 2 with 1235bp had a 91% similarity to Acinetobacter baumannii; isolate 3 having 1033bp had a 98% similarity to Lysinibacillus fusiformis; while isolate 4 with 1129bp had a 95% similarity to Burkholderia latens. The accession numbers MN310508, MK719842, MN396184 and MN207011 were assigned to isolates 1 to 4 respectively. This study provided more information on the bacteria species associated with dumpsite soils.

Keywords

Dumpsite sequencing phylogeny bacteria

References

  1. Afon, A. (2012). A Survey of Operational Characteristics, Socio-economic and Health Effect of Scavenging Activity in Lagos Nigeria. Waste Management and Research, 30(7): 664-671.
  2. Alexander, Y. B. (2016). Determination of Active Travel Speed of Minimum Air Pollution Inhalation. International Journal of Sustainable Transportation, 10: 271-273.
  3. Alivisatos, A. P., Blaser, M. J., Brodie, E. L., Chun, M., Dangl, J. L., Donohue, T. J., Dorrestein, P. C., Gilbert, J. A., Green, J. L., Jansson, J. K., Knight, R., Maxon, M. E., McFall-Ngai, M. J., Miller, J. F., Pollard, K. S., Ruby, E. G. and Taha, S. A. (2015). A Unified Initiative to Harness Earth's Microbiomes. Science, 350(6260): 507-508.
  4. Cerqueira, G. M. and Peleg, A. Y. (2011). Insights into Acinetobacter baumannii Pathogenecity. IUBMB Life, 63:1055-1060.
  5. Elenya, U. E., Oyegue, T. O., Rwang, P. G., Ozuode, T. O. and Okey-Ndeche, N. F. (2017). Microbiological Analysis of Dumpsites in Bwari, Federal Capital Territory, Nigeria. Microbiology Research International, 22(3): 1-6.
  6. Enry, D. and Prinz, M. (2017). Microbiology Gut Microbes Augment Neurodegeneration. Nature, 544: 304-305.
  7. Fishbian, J and Peleg, A. Y. (2010). Treatment of Acinetobacter Infections. Clinical Infection Diseases, 51: 79-84.
  8. Fischer, M. A., Gullert, S., Neulinger, S. C., Streit, W. R. and Schmitz, R. A. (2016). Evaluation of 16S rRNA Gene Primer Pairs for Monitoring Microbial Community Structures Showed High Reproducibility within and Low Comparability between Datasets Generated with Multiple Archaeal and Bacterial Primer Pairs. Frontiers in Microbiology, 7:1297.
  9. Flemming, H. C., Wingender, J., Szewzyk, U., Steinberg, P., Rice, S. A. and Kjelleberg, S. (2016). Biofilms: An Emergent Form of Bacterial Life. Natural Research Microbiology, 14: 563-575.
  10. Gupta, R. S. (2016). Impact of Genomics on the Understanding of Microbial Evolution and Classification: The Importance of Darwin's on Classification. Microbiology Reviews, 40(40): 520-553.
  11. Hartman, D. (2011). Perfecting your Spread Plate Technique. Journal Microbiology and Biology Education, 12(2): 204-205.
  12. He, M., Li, X., Liu, H., Miller, S., Wang, G. and Rensing, C. (2010). Characterization and Genomic analysis of a Highly Chromate Resistant and Reducing Bacterial Strain Lysinibacillus fusiformis ZC1. Journal of Hazardous Materials, 185(2-3): 682-688.
  13. Hooper, L. V., Littman, D. R. and MacPherson, A. J. (2012). Interaction between the Microbiota and the Immune System. Science, 336: 1268-1273.
  14. Iyanyi, N. U., Ataga, A. E. and Nwachukwu, E. O. (2019). Biochemical and Molecular Characterization of Bacteria Associated With Cnidoscolus aconitifolius (Mill.) I. M. Johnston. IOSR Journal of Pharmacy and Biological Sciences, 14(4):78-85.
  15. Karen, A., Paula, M. C, Ai, L. T, Robert, J. M, Rebecca, C. H, Sheila, J. B, Emma S. G, Sherry N, Allan M. S, Johnny W, Shaillay D, Graham, C. B, Cyrus, C., Hazel, M, I, Catharine, R. G, Peter, D. G, Nicholas, C. H, Yap-Seng, C, Fabian, Y, Michael, J. M, Anne, R. G, Joanna, D. H, and Keith, M. G. (2015). Association between Perinatal Methylation of the Neuronal Differentiation Regulator and Childhood Neurocognitive Function and Behaviour. International Journal of Epidemiology, 44(4): 1263.
  16. Kumar, S., Stecher, G. and Tamura, K. (2016) MEGA 7; Molecular Evolutionary Genetics Analysis. Version 7.0 for Bigger Data Sets. Molecular Biology and Evolution, 33: 1870-1874.
  17. Kumar, S., Stecher, G., Li, M., Knyaz, C. and Tamura, K. (2018) MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. Molecular Biology and Evolution, 35:1547-1549.
  18. Oren, A. and Garrity, G. M. (2015). List of New Names and New Combination. Journal Systematic Evolution Microbiology, 65(7): 2017-2025.
  19. Osazee, O. J, Obayagbona, O. N, Daniel, E. O. (2013). Microbiological and Physiochemical Analyses of Top Soils obtained from Four Municipal Waste Dumpsites in Benin City, Nigeria. International Journal of Microbiology and Mycology, 1(1): 23-30.
  20. Pong, J. F. (2015). The Soil as an Ecosystem. Biology and Fertility of Soil, 51(6): 645-648.
  21. Roh, S. W., Abell, G. C. J., Kim, K. H., Nam, Y. D and Bae, J. W. (2010). Comparing Microarrays and Next-generation Sequencing Technologies for Microbial Ecology Research. Trends in Biotechnology, 28(6):291-299.
  22. Vimercah, L., Baldassare, A. and Gatti, M. F. (2016). Respiratory Health in Waste Collection and Disposal Workers. International Journal of Environmental Research Public Health, 13: 63-65.
  23. Wang, J., Yanhui, F. and Zhigang, Y. (2010). Isolation of a Lysinibacillus fusiformis Strain with Tetradoxin-producing Ability from Puffer Fish (Fugu Obscurus) and the Characterization of the Strain. Journal of Toxicum, 56(4): 640-643.
  24. Yousuf, S., Afzal, M., Reichenauer, T. G., Brady, C. L. and Sessitch, A. (2011). Hydrocarbon Degradation, Plant Colonization and Gene Expression of Alkane Degradation Gene by Endophytic Enerobacter ludwigii Strains. Journal of Environmental Pollution, 159(10): 2675-2683.
  25. Yu, C., Kamboj, S. Wang, C. and Jing-Jy, J. (2015). Data Collection Handbook to Support Modelling Impacts of Radioactive Material in Soil and Building Structures. Agronne National Laboratory, 14(3): 13-21.
  26. Zhou, H, Meng, A., Long, Y., Li, Q. and Zhang, Y. (2014). An Overview of Characteristics of Municipal Solid Waste Fuel in China: Physical, Chemical Composition and Heating Value. Renewable and Sustainable Energy Reviews, 36:107-122.
  27. Zhou, J. Z, He, Z, Yang, Y, Deng, Y., Tringe, S. G. and Alvarez-Cohen, L. (2015). High-throughput Metagenomic Technologies for Complex Microbial Community Analysis: Open and Closed Formats. mBio, 6(1): 1-17.
How to Cite

G., I. N., E., A. A., M., S., & J., J. (2020). Molecular Characterization of Bacteria Associated with a Dumpsite Soil in University of Port Harcourt, Rivers State, Nigeria. Nigerian Journal of Microbiology, 34(2), 5294-5302. https://doi.org/10.67614/njm.2020.iau31dcd

I. N. G., A. A. E., S. M., and J. J., "Molecular Characterization of Bacteria Associated with a Dumpsite Soil in University of Port Harcourt, Rivers State, Nigeria," Nigerian Journal of Microbiology, vol. 34, no. 2, pp. 5294-5302, December 2020. doi: 10.67614/njm.2020.iau31dcd

Share this article:
Facebook X / Twitter LinkedIn
Download PDF View Full Text (PDF) Back to Articles