Designing primer for rapid detection of polluted river water

Abstract

Metagenomic now has been introduced as one of the new approaches to study the community of uncultured bacteria. Furthermore, the findings of previous studies can be stipulated to assess river water quality. Designing primer is the main focus in this experiment to detect whether the water samples are polluted or unpolluted. The 16S rRNA gene sequences of bacteria from previous studies have been used in the primer designed. Previous findings show that two groups of bacteria have being classed to polluted and unpolluted group of water samples. In this study, four water samples have been collected from UTM Lake, Sg. Melana, Sg. Skudai and Sg. Kempas. The unexpected findings show that primer sequences from unpolluted water samples has the potential to prime coliform bacteria compared to primer sequences from polluted water samples. The primers also being tested with wild types bacteria of E.coli, S.aureus, Enterobacter sp. and also B.licherformis. The results also shown that primers designed from unpolluted group can prime the sequences of the coliform wild type bacteria. Many factors can contribute to the present results but the most common reason is DNA extraction of the metagenome as previously being discussed by other researchers. This is because most common bacteria in the freshwater are Gram positive bacteria and always being underrepresented in the PCR library. Besides, different effluent or pollutants compared to previous studies can have major effects to the genomic DNA extracted. Further studies should be done to firmly state that the water is polluted or not only by using specifically designed primer that can broadly prime bacteria in polluted water area and also another specific primer sequences for unpolluted water.