African Journal of
Microbiology Research

  • Abbreviation: Afr. J. Microbiol. Res.
  • Language: English
  • ISSN: 1996-0808
  • DOI: 10.5897/AJMR
  • Start Year: 2007
  • Published Articles: 5211

Full Length Research Paper

Random amplified polymorphic DNA (RAPD) analysis of microbial community diversity in soil affected by industrial pollutants: Reference to Mandideep industrial area

Anita Tilwari*, Deepak Chouhan and Rajesh Sharma    
Centre of Excellence in Biotechnology, M.P. Council of Science and Technology, Vigyan Bhawan, Science Hills, Nehru Nagar, Bhopal, Madhya Pradesh-462003, India.
Email: [email protected], [email protected]

  •  Accepted: 22 July 2013
  •  Published: 26 July 2013


The present study was aimed to investigate microbial diversity of industrially contaminated and uncontaminated agriculture field soil using random amplified polymorphic DNA (RAPD) analysis. Soil samples were collected from highly contaminated (industrial pollution) and uncontaminated agriculture fields away from polluted area. RAPD analysis was carried out using four ten-mer primers namely RBa-3, 4, 5 and 6 to find out the effect of industrial contamination on microbial community diversity. In total, 56 DNA fragments were generated using 4 deca-mer random primers with good reproducibility, 55 of them were polymorphic (99%) and 1 bands (loci) was monomorphic (1%). The average Jaccard’s similarity coefficient based on 4 primers ranged from 0.163 (cultivated soil) to 0.462 (industrially polluted soil) in all the accessions studied, which indicates that cultivated soil supports more diverse microbes than the polluted soil. Cluster analysis was performed based on the Jaccard’s similarity coefficient matrices, calculated from RAPD data. Different clustering methods including unweighed pair group method for arithmetic average (UPGMA), NJ and Bayesian tree almost produced similar results with good bootstrap and clade credibility values. In all accessions, three different clusters were obtained. These three clusters were further divided into subclusters. Samples from the agricultural field show high genetic affinity and are placed in a single cluster or clade.Results confirmed the effects of pollution on the distribution and biodiversity of soil microorganisms where most of the native beneficial microorganisms were disappeared or not cultured under these stress conditions as compared to the normal agricultural field soils, which is certainly affecting soil fertility and productivity.


Key words: Effluent contaminated soil, polymerase chain reaction-random amplified polymorphic DNA (PCR-RAPD), microbial community, lyzozyme, bacterial diversity.