SAMPLING BACTERIAL BIODIVERSITY FROM A HIGHLY CONTAMINATED STREAM FLOWING THROUGH A DENSELY POPULATED URBAN AREA IN KARACHI
AbstractBackground: Few studies have attempted to understand the complexity of microbial populations inPakistan where infectious diseases are prevalent. This study was undertaken to assess bacterialbiodiversity in Nehr-e-Khayyam a heavily polluted stream connected to the Arabian Gulf, which runsthrough a densely populated urban area in Karachi, Pakistan. Methods: Employing a universal pair ofoligonucleotides capable of amplifying species-specific segments of 16S rRNA gene from allEubacteria, we generated a library of PCR products using total DNA purified from the collectedsample, cloned the amplifers into pGEM-T-Easy and sequenced each recombinant clone. The obtainedDNA sequences were subjected to bio-informatic analyses. Results: A total of 71 recombinant cloneswere obtained from the amplified 16S rDNA products and sequenced. Bioinformatics analyses revealedthat 54 (out of 71) were unique sequences from which 42 shared >97% and 12 shared <97% homologyto their database counterparts. One sequence originated from the plastid DNA of eukaryotePyramimonas disomata. From the remaining 53 sequences, 45 were Proteo-bacteria and 8 Fermicute inorigin. Among 71 sequences, Alpha-, Beta- and Gamma-proteobacteria species constituted ~86% ofProteo-bacteria identified in the sample while only ~13% were Fermicutes. Conclusions: Themicrobial niche in Nehr-e-Khayyam is occupied predominantly by heterotrophic Proteo-bacterial andFirmicute strains, some of which are known human pathogens.Keywords: Bacteria, biodiversity, 16S rDNA, Karachi
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