SAMPLING BACTERIAL BIODIVERSITY FROM A HIGHLY CONTAMINATED STREAM FLOWING THROUGH A DENSELY POPULATED URBAN AREA IN KARACHI

Authors

  • Syed Faaiz Enam
  • Humaira Qureshi
  • Sohail A. Qureshi

Abstract

Background: 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

References

DeSantis TZ, Brodie EL, Moberg JP, Zubieta IX, Piceno YM,

Andersen GL.. High-density universal 16S rRNA microarray

analysis reveals broader diversity than typical clone library when

sampling the environment. Microb Ecol 2007;53:371–83.

Humblot C, Guyot JP. Pyrosequencing of tagged 16S rRNA gene

amplicons for rapid deciphering of the microbiomes of fermented

foods such as pearl millet slurries. Appl Environ Microbiol

;75:4354–61.

Leclerc M, Delgenes JP, Godon JJ. Diversity of the archaeal

community in 44 anaerobic digesters as determined by single

strand conformation polymorphism analysis and 16S rDNA

sequencing. Environ Microbiol 2004;6:809–19

Thies FL, Konig W, Konig B. Rapid characterization of the

normal and disturbed vaginal microbiota by application of 16S

rRNA gene terminal RFLP fingerprinting. J Med Microbiol

;56:755–61.

Tzeneva VA, Heilig HG, van Vliet WA, Akkermans AD, de Vos

WM, Smidt H. 16S rRNA targeted DGGE fingerprinting of

microbial communities. Methods Mol Biol 2008;410:335–49.

Huang WM. Bacterial diversity based on type II DNA

topoisomerase genes. Annu Rev Genet 1996;30:79–107.

Meyer B, Kuever J. Phylogenetic diversity and spatial

distribution of the microbial community associated with the

Caribbean deep-water sponge Polymastia cf. corticata by 16S

rRNA, aprA, and amoA gene analysis. Microb Ecol

;56:306–21.

Santillana N, Ramirez-Bahena MH, Garcia-Fraile P, Velazquez

E, Zuniga D. Phylogenetic diversity based on rrs, atpD, recA

genes and 16S-23S intergenic sequence analyses of rhizobial

strains isolated from Vicia faba and Pisum sativum in Peru. Arch

Microbiol 2008;189:239–47.

Yin H, Cao L, Qiu G, Wang D, Kellogg L, Zhou J, et al.

Molecular diversity of 16S rRNA and gyrB genes in copper

mines. Arch Microbiol 2008;189:101–10.

Tringe SG, Hugenholtz P. A renaissance for the pioneering 16S

rRNA gene. Curr Opin Microbiol 2008;11:442–6.

Kim TK, Thomas SM, Ho M, Sharma S, Reich CI, Frank JA, et

al. Heterogeneity of vaginal microbial communities within

individuals. J Clin Microbiol 2009;47:1181–9.

Ventura M, Turroni F, Canchaya C, Vaughan EE, O'Toole PW,

van Sinderen D.. Microbial diversity in the human intestine and

novel insights from metagenomics. Front Biosci 2009;14:3214–21.

Ghauri MA, Khalid AM, Grant S, Grant WD, Heaphy S.

Phylogenetic analysis of bacterial isolates from man-made highpH, high-salt environments and identification of gene-cassetteassociated open reading frames. Curr Microbiol 2006;52:487–92

Ghauri MA, Khalid AM, Grant S, Heaphy S, Grant WD.

Phylogenetic analysis of different isolates of Sulfobacillus spp.

isolated from uranium-rich environments and recovery of genes

using integron-specific primers. Extremophiles 2003;7:341–5

Maukonen J, Saarela M. Microbial communities in industrial

environment. Curr Opin Microbiol 2009;12:238–43.

Downloads

Published

2011-06-01

Issue

Vol. 23 No. 2 (2011): JOURNAL OF AYUB MEDICAL COLLEGE, ABBOTTABAD

Section

ORIGINAL ARTICLE

License

Journal of Ayub Medical College, Abbottabad is an OPEN ACCESS JOURNAL which means that all content is FREELY available without charge to all users whether registered with the journal or not. The work published by J Ayub Med Coll Abbottabad is licensed and distributed under the creative commons License  CC BY ND Attribution-NoDerivs. Material printed in this journal is OPEN to access, and are FREE for use in academic and research work with proper citation. J Ayub Med Coll Abbottabad accepts only original material for publication with the understanding that except for abstracts, no part of the data has been published or will be submitted for publication elsewhere before appearing in J Ayub Med Coll Abbottabad. The Editorial Board of J Ayub Med Coll Abbottabad makes every effort to ensure the accuracy and authenticity of material printed in J Ayub Med Coll Abbottabad. However, conclusions and statements expressed are views of the authors and do not reflect the opinion/policy of J Ayub Med Coll Abbottabad or the Editorial Board.

USERS are allowed to read, download, copy, distribute, print, search, or link to the full texts of the articles, or use them for any other lawful purpose, without asking prior permission from the publisher or the author. This is in accordance with the BOAI definition of open access.

AUTHORS retain the rights of free downloading/unlimited e-print of full text and sharing/disseminating the article without any restriction, by any means including twitter, scholarly collaboration networks such as ResearchGate, Academia.eu, and social media sites such as Twitter, LinkedIn, Google Scholar and any other professional or academic networking site.