Molecular characterization of soil microorganisms: effect of industrial pollution on distribution and biodiversity

The present study aimed to investigate variations in the diversity of the indigenous bacterial and fungal populations in contaminated soil. Soil samples were collected from highly contaminated agricultural soil adjacent to an industrial drain in the Nile Delta named the “Defsho” drain, located at the city of Kafr El-Dawar, 20 km south of Alexandria (Longitude 30.12917 and Latitude 31.13972). PCR has become a popular tool for the retrieval of the natural environmental rRNA genes that represent native microbial species. Soil DNA was extracted and the 16S and 18S rRNA genes were amplified using polymerase chain reaction (PCR) and gene cloning. About 5,000 clones were obtained and genotyped using denaturing high performance liquid chromatography (DHPLC) to fingerprinting the biodiversity in the soil. Clones, which give different peaks with DHPLC, were then subjected to partial sequencing. Five prokaryotic and two eukaryotic out of 1,000 recombinant clones were randomly selected and further studied by DNA sequencing analysis. These clones were designated PT and ET for prokaryotes and eukaryotes, respectively. Results confirmed the hazardous effects of pollution on the distribution and biodiversity of soil microorganisms where most of the native beneficial microorganisms were disappeared or non-cultured under these stressed conditions compared to the normal non-polluted soils in the same governorate which is certainly affecting soil fertility and productivity. Five prokaryotic (PT) and two eukaryotic (ET) recombinant clones were randomly selected and further studied by DNA sequence analysis. DNA sequencing revealed that most of the identified bacteria are members of the class Proteobacteria; subdivision Gammaproteobacteria; order Enterobacteriales and family Enterobacteriaceae. Two PT clones (PT2 and PT4) were identified as Shigella flexneri 301-AF499895; members of PT1 and PT3 were related to Escherichia sp. and the uncultured bacterium S000009863 while PT5 was uncultured bacterium-S000331457 in addition to unclassified member of Desulfobacteriaceae, subdivision Deltaproteobacteria. ET1 was uncultured Trichocomaceae clone HC-B1/1-AF548306 and ET2 represents uncultured fungus clone SBS8w47f-AY681463, respectively. In conclusion, the significant decline in the genetic diversity in Defsho soil emphasized the hazardous effect of the industrial pollution on the biodiversity, stability and functioning of the native microbial population. Results also proved the efficiency of molecular characterization as precise and fast techniques for determining soil biodiversity compared to the traditional cultivation methods.